(function (global, factory) { typeof exports === 'object' && typeof module !== 'undefined' ? module.exports = factory() : typeof define === 'function' && define.amd ? define(factory) : (global = typeof globalThis !== 'undefined' ? globalThis : global || self, global.igv = factory()); }(this, (function () { 'use strict'; /*! * jQuery JavaScript Library v3.3.1 -ajax,-ajax/jsonp,-ajax/load,-ajax/parseXML,-ajax/script,-ajax/var/location,-ajax/var/nonce,-ajax/var/rquery,-ajax/xhr,-manipulation/_evalUrl,-event/ajax,-effects,-effects/Tween,-effects/animatedSelector * https://jquery.com/ * * Includes Sizzle.js * https://sizzlejs.com/ * * Copyright JS Foundation and other contributors * Released under the MIT license * https://jquery.org/license * * Date: 2018-01-20T17:24Z */ var arr = []; var document$2 = window.document; var getProto = Object.getPrototypeOf; var slice = arr.slice; var concat = arr.concat; var push = arr.push; var indexOf$1 = arr.indexOf; var class2type = {}; var toString$1 = class2type.toString; var hasOwn = class2type.hasOwnProperty; var fnToString = hasOwn.toString; var ObjectFunctionString = fnToString.call(Object); var support = {}; var isFunction = function isFunction(obj) { // Support: Chrome <=57, Firefox <=52 // In some browsers, typeof returns "function" for HTML elements // (i.e., `typeof document.createElement( "object" ) === "function"`). // We don't want to classify *any* DOM node as a function. return typeof obj === "function" && typeof obj.nodeType !== "number"; }; var isWindow = function isWindow(obj) { return obj != null && obj === obj.window; }; var preservedScriptAttributes = { type: true, src: true, noModule: true }; function DOMEval(code, doc, node) { doc = doc || document$2; var i, script = doc.createElement("script"); script.text = code; if (node) { for (i in preservedScriptAttributes) { if (node[i]) { script[i] = node[i]; } } } doc.head.appendChild(script).parentNode.removeChild(script); } function toType(obj) { if (obj == null) { return obj + ""; } // Support: Android <=2.3 only (functionish RegExp) return typeof obj === "object" || typeof obj === "function" ? class2type[toString$1.call(obj)] || "object" : typeof obj; } // global Symbol // Defining this global in .eslintrc.json would create a danger of using the global // unguarded in another place, it seems safer to define global only for this module var version$2 = "3.3.1 -ajax,-ajax/jsonp,-ajax/load,-ajax/parseXML,-ajax/script,-ajax/var/location,-ajax/var/nonce,-ajax/var/rquery,-ajax/xhr,-manipulation/_evalUrl,-event/ajax,-effects,-effects/Tween,-effects/animatedSelector", // Define a local copy of jQuery jQuery = function (selector, context) { // The jQuery object is actually just the init constructor 'enhanced' // Need init if jQuery is called (just allow error to be thrown if not included) return new jQuery.fn.init(selector, context); }, // Support: Android <=4.0 only // Make sure we trim BOM and NBSP rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g; jQuery.fn = jQuery.prototype = { // The current version of jQuery being used jquery: version$2, constructor: jQuery, // The default length of a jQuery object is 0 length: 0, toArray: function () { return slice.call(this); }, // Get the Nth element in the matched element set OR // Get the whole matched element set as a clean array get: function (num) { // Return all the elements in a clean array if (num == null) { return slice.call(this); } // Return just the one element from the set return num < 0 ? this[num + this.length] : this[num]; }, // Take an array of elements and push it onto the stack // (returning the new matched element set) pushStack: function (elems) { // Build a new jQuery matched element set var ret = jQuery.merge(this.constructor(), elems); // Add the old object onto the stack (as a reference) ret.prevObject = this; // Return the newly-formed element set return ret; }, // Execute a callback for every element in the matched set. each: function (callback) { return jQuery.each(this, callback); }, map: function (callback) { return this.pushStack(jQuery.map(this, function (elem, i) { return callback.call(elem, i, elem); })); }, slice: function () { return this.pushStack(slice.apply(this, arguments)); }, first: function () { return this.eq(0); }, last: function () { return this.eq(-1); }, eq: function (i) { var len = this.length, j = +i + (i < 0 ? len : 0); return this.pushStack(j >= 0 && j < len ? [this[j]] : []); }, end: function () { return this.prevObject || this.constructor(); }, // For internal use only. // Behaves like an Array's method, not like a jQuery method. push: push, sort: arr.sort, splice: arr.splice }; jQuery.extend = jQuery.fn.extend = function () { var options, name, src, copy, copyIsArray, clone, target = arguments[0] || {}, i = 1, length = arguments.length, deep = false; // Handle a deep copy situation if (typeof target === "boolean") { deep = target; // Skip the boolean and the target target = arguments[i] || {}; i++; } // Handle case when target is a string or something (possible in deep copy) if (typeof target !== "object" && !isFunction(target)) { target = {}; } // Extend jQuery itself if only one argument is passed if (i === length) { target = this; i--; } for (; i < length; i++) { // Only deal with non-null/undefined values if ((options = arguments[i]) != null) { // Extend the base object for (name in options) { src = target[name]; copy = options[name]; // Prevent never-ending loop if (target === copy) { continue; } // Recurse if we're merging plain objects or arrays if (deep && copy && (jQuery.isPlainObject(copy) || (copyIsArray = Array.isArray(copy)))) { if (copyIsArray) { copyIsArray = false; clone = src && Array.isArray(src) ? src : []; } else { clone = src && jQuery.isPlainObject(src) ? src : {}; } // Never move original objects, clone them target[name] = jQuery.extend(deep, clone, copy); // Don't bring in undefined values } else if (copy !== undefined) { target[name] = copy; } } } } // Return the modified object return target; }; jQuery.extend({ // Unique for each copy of jQuery on the page expando: "jQuery" + (version$2 + Math.random()).replace(/\D/g, ""), // Assume jQuery is ready without the ready module isReady: true, error: function (msg) { throw new Error(msg); }, noop: function () {}, isPlainObject: function (obj) { var proto, Ctor; // Detect obvious negatives // Use toString instead of jQuery.type to catch host objects if (!obj || toString$1.call(obj) !== "[object Object]") { return false; } proto = getProto(obj); // Objects with no prototype (e.g., `Object.create( null )`) are plain if (!proto) { return true; } // Objects with prototype are plain iff they were constructed by a global Object function Ctor = hasOwn.call(proto, "constructor") && proto.constructor; return typeof Ctor === "function" && fnToString.call(Ctor) === ObjectFunctionString; }, isEmptyObject: function (obj) { /* eslint-disable no-unused-vars */ // See https://github.com/eslint/eslint/issues/6125 var name; for (name in obj) { return false; } return true; }, // Evaluates a script in a global context globalEval: function (code) { DOMEval(code); }, each: function (obj, callback) { var length, i = 0; if (isArrayLike(obj)) { length = obj.length; for (; i < length; i++) { if (callback.call(obj[i], i, obj[i]) === false) { break; } } } else { for (i in obj) { if (callback.call(obj[i], i, obj[i]) === false) { break; } } } return obj; }, // Support: Android <=4.0 only trim: function (text) { return text == null ? "" : (text + "").replace(rtrim, ""); }, // results is for internal usage only makeArray: function (arr, results) { var ret = results || []; if (arr != null) { if (isArrayLike(Object(arr))) { jQuery.merge(ret, typeof arr === "string" ? [arr] : arr); } else { push.call(ret, arr); } } return ret; }, inArray: function (elem, arr, i) { return arr == null ? -1 : indexOf$1.call(arr, elem, i); }, // Support: Android <=4.0 only, PhantomJS 1 only // push.apply(_, arraylike) throws on ancient WebKit merge: function (first, second) { var len = +second.length, j = 0, i = first.length; for (; j < len; j++) { first[i++] = second[j]; } first.length = i; return first; }, grep: function (elems, callback, invert) { var callbackInverse, matches = [], i = 0, length = elems.length, callbackExpect = !invert; // Go through the array, only saving the items // that pass the validator function for (; i < length; i++) { callbackInverse = !callback(elems[i], i); if (callbackInverse !== callbackExpect) { matches.push(elems[i]); } } return matches; }, // arg is for internal usage only map: function (elems, callback, arg) { var length, value, i = 0, ret = []; // Go through the array, translating each of the items to their new values if (isArrayLike(elems)) { length = elems.length; for (; i < length; i++) { value = callback(elems[i], i, arg); if (value != null) { ret.push(value); } } // Go through every key on the object, } else { for (i in elems) { value = callback(elems[i], i, arg); if (value != null) { ret.push(value); } } } // Flatten any nested arrays return concat.apply([], ret); }, // A global GUID counter for objects guid: 1, // jQuery.support is not used in Core but other projects attach their // properties to it so it needs to exist. support: support }); if (typeof Symbol === "function") { jQuery.fn[Symbol.iterator] = arr[Symbol.iterator]; } // Populate the class2type map jQuery.each("Boolean Number String Function Array Date RegExp Object Error Symbol".split(" "), function (i, name) { class2type["[object " + name + "]"] = name.toLowerCase(); }); function isArrayLike(obj) { // Support: real iOS 8.2 only (not reproducible in simulator) // `in` check used to prevent JIT error (gh-2145) // hasOwn isn't used here due to false negatives // regarding Nodelist length in IE var length = !!obj && "length" in obj && obj.length, type = toType(obj); if (isFunction(obj) || isWindow(obj)) { return false; } return type === "array" || length === 0 || typeof length === "number" && length > 0 && length - 1 in obj; } var Sizzle = /*! * Sizzle CSS Selector Engine v2.3.3 * https://sizzlejs.com/ * * Copyright jQuery Foundation and other contributors * Released under the MIT license * http://jquery.org/license * * Date: 2016-08-08 */ function (window) { var i, support, Expr, getText, isXML, tokenize, compile, select, outermostContext, sortInput, hasDuplicate, // Local document vars setDocument, document, docElem, documentIsHTML, rbuggyQSA, rbuggyMatches, matches, contains, // Instance-specific data expando = "sizzle" + 1 * new Date(), preferredDoc = window.document, dirruns = 0, done = 0, classCache = createCache(), tokenCache = createCache(), compilerCache = createCache(), sortOrder = function (a, b) { if (a === b) { hasDuplicate = true; } return 0; }, // Instance methods hasOwn = {}.hasOwnProperty, arr = [], pop = arr.pop, push_native = arr.push, push = arr.push, slice = arr.slice, // Use a stripped-down indexOf as it's faster than native // https://jsperf.com/thor-indexof-vs-for/5 indexOf = function (list, elem) { var i = 0, len = list.length; for (; i < len; i++) { if (list[i] === elem) { return i; } } return -1; }, booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped", // Regular expressions // http://www.w3.org/TR/css3-selectors/#whitespace whitespace = "[\\x20\\t\\r\\n\\f]", // http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier identifier = "(?:\\\\.|[\\w-]|[^\0-\\xa0])+", // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace + // Operator (capture 2) "*([*^$|!~]?=)" + whitespace + // "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]" "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace + "*\\]", pseudos = ":(" + identifier + ")(?:\\((" + // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments: // 1. quoted (capture 3; capture 4 or capture 5) "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" + // 2. simple (capture 6) "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" + // 3. anything else (capture 2) ".*" + ")\\)|)", // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter rwhitespace = new RegExp(whitespace + "+", "g"), rtrim = new RegExp("^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g"), rcomma = new RegExp("^" + whitespace + "*," + whitespace + "*"), rcombinators = new RegExp("^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*"), rattributeQuotes = new RegExp("=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g"), rpseudo = new RegExp(pseudos), ridentifier = new RegExp("^" + identifier + "$"), matchExpr = { "ID": new RegExp("^#(" + identifier + ")"), "CLASS": new RegExp("^\\.(" + identifier + ")"), "TAG": new RegExp("^(" + identifier + "|[*])"), "ATTR": new RegExp("^" + attributes), "PSEUDO": new RegExp("^" + pseudos), "CHILD": new RegExp("^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace + "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace + "*(\\d+)|))" + whitespace + "*\\)|)", "i"), "bool": new RegExp("^(?:" + booleans + ")$", "i"), // For use in libraries implementing .is() // We use this for POS matching in `select` "needsContext": new RegExp("^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i") }, rinputs = /^(?:input|select|textarea|button)$/i, rheader = /^h\d$/i, rnative = /^[^{]+\{\s*\[native \w/, // Easily-parseable/retrievable ID or TAG or CLASS selectors rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/, rsibling = /[+~]/, // CSS escapes // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters runescape = new RegExp("\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig"), funescape = function (_, escaped, escapedWhitespace) { var high = "0x" + escaped - 0x10000; // NaN means non-codepoint // Support: Firefox<24 // Workaround erroneous numeric interpretation of +"0x" return high !== high || escapedWhitespace ? escaped : high < 0 ? // BMP codepoint String.fromCharCode(high + 0x10000) : // Supplemental Plane codepoint (surrogate pair) String.fromCharCode(high >> 10 | 0xD800, high & 0x3FF | 0xDC00); }, // CSS string/identifier serialization // https://drafts.csswg.org/cssom/#common-serializing-idioms // eslint-disable-next-line no-control-regex rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g, fcssescape = function (ch, asCodePoint) { if (asCodePoint) { // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER if (ch === "\0") { return "\uFFFD"; } // Control characters and (dependent upon position) numbers get escaped as code points return ch.slice(0, -1) + "\\" + ch.charCodeAt(ch.length - 1).toString(16) + " "; } // Other potentially-special ASCII characters get backslash-escaped return "\\" + ch; }, // Used for iframes // See setDocument() // Removing the function wrapper causes a "Permission Denied" // error in IE unloadHandler = function () { setDocument(); }, disabledAncestor = addCombinator(function (elem) { return elem.disabled === true && ("form" in elem || "label" in elem); }, { dir: "parentNode", next: "legend" }); // Optimize for push.apply( _, NodeList ) try { push.apply(arr = slice.call(preferredDoc.childNodes), preferredDoc.childNodes); // Support: Android<4.0 // Detect silently failing push.apply arr[preferredDoc.childNodes.length].nodeType; } catch (e) { push = { apply: arr.length ? // Leverage slice if possible function (target, els) { push_native.apply(target, slice.call(els)); } : // Support: IE<9 // Otherwise append directly function (target, els) { var j = target.length, i = 0; // Can't trust NodeList.length while (target[j++] = els[i++]) {} target.length = j - 1; } }; } function Sizzle(selector, context, results, seed) { var m, i, elem, nid, match, groups, newSelector, newContext = context && context.ownerDocument, // nodeType defaults to 9, since context defaults to document nodeType = context ? context.nodeType : 9; results = results || []; // Return early from calls with invalid selector or context if (typeof selector !== "string" || !selector || nodeType !== 1 && nodeType !== 9 && nodeType !== 11) { return results; } // Try to shortcut find operations (as opposed to filters) in HTML documents if (!seed) { if ((context ? context.ownerDocument || context : preferredDoc) !== document) { setDocument(context); } context = context || document; if (documentIsHTML) { // If the selector is sufficiently simple, try using a "get*By*" DOM method // (excepting DocumentFragment context, where the methods don't exist) if (nodeType !== 11 && (match = rquickExpr.exec(selector))) { // ID selector if (m = match[1]) { // Document context if (nodeType === 9) { if (elem = context.getElementById(m)) { // Support: IE, Opera, Webkit // TODO: identify versions // getElementById can match elements by name instead of ID if (elem.id === m) { results.push(elem); return results; } } else { return results; } // Element context } else { // Support: IE, Opera, Webkit // TODO: identify versions // getElementById can match elements by name instead of ID if (newContext && (elem = newContext.getElementById(m)) && contains(context, elem) && elem.id === m) { results.push(elem); return results; } } // Type selector } else if (match[2]) { push.apply(results, context.getElementsByTagName(selector)); return results; // Class selector } else if ((m = match[3]) && support.getElementsByClassName && context.getElementsByClassName) { push.apply(results, context.getElementsByClassName(m)); return results; } } // Take advantage of querySelectorAll if (support.qsa && !compilerCache[selector + " "] && (!rbuggyQSA || !rbuggyQSA.test(selector))) { if (nodeType !== 1) { newContext = context; newSelector = selector; // qSA looks outside Element context, which is not what we want // Thanks to Andrew Dupont for this workaround technique // Support: IE <=8 // Exclude object elements } else if (context.nodeName.toLowerCase() !== "object") { // Capture the context ID, setting it first if necessary if (nid = context.getAttribute("id")) { nid = nid.replace(rcssescape, fcssescape); } else { context.setAttribute("id", nid = expando); } // Prefix every selector in the list groups = tokenize(selector); i = groups.length; while (i--) { groups[i] = "#" + nid + " " + toSelector(groups[i]); } newSelector = groups.join(","); // Expand context for sibling selectors newContext = rsibling.test(selector) && testContext(context.parentNode) || context; } if (newSelector) { try { push.apply(results, newContext.querySelectorAll(newSelector)); return results; } catch (qsaError) {} finally { if (nid === expando) { context.removeAttribute("id"); } } } } } } // All others return select(selector.replace(rtrim, "$1"), context, results, seed); } /** * Create key-value caches of limited size * @returns {function(string, object)} Returns the Object data after storing it on itself with * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength) * deleting the oldest entry */ function createCache() { var keys = []; function cache(key, value) { // Use (key + " ") to avoid collision with native prototype properties (see Issue #157) if (keys.push(key + " ") > Expr.cacheLength) { // Only keep the most recent entries delete cache[keys.shift()]; } return cache[key + " "] = value; } return cache; } /** * Mark a function for special use by Sizzle * @param {Function} fn The function to mark */ function markFunction(fn) { fn[expando] = true; return fn; } /** * Support testing using an element * @param {Function} fn Passed the created element and returns a boolean result */ function assert(fn) { var el = document.createElement("fieldset"); try { return !!fn(el); } catch (e) { return false; } finally { // Remove from its parent by default if (el.parentNode) { el.parentNode.removeChild(el); } // release memory in IE el = null; } } /** * Checks document order of two siblings * @param {Element} a * @param {Element} b * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b */ function siblingCheck(a, b) { var cur = b && a, diff = cur && a.nodeType === 1 && b.nodeType === 1 && a.sourceIndex - b.sourceIndex; // Use IE sourceIndex if available on both nodes if (diff) { return diff; } // Check if b follows a if (cur) { while (cur = cur.nextSibling) { if (cur === b) { return -1; } } } return a ? 1 : -1; } /** * Returns a function to use in pseudos for input types * @param {String} type */ function createInputPseudo(type) { return function (elem) { var name = elem.nodeName.toLowerCase(); return name === "input" && elem.type === type; }; } /** * Returns a function to use in pseudos for buttons * @param {String} type */ function createButtonPseudo(type) { return function (elem) { var name = elem.nodeName.toLowerCase(); return (name === "input" || name === "button") && elem.type === type; }; } /** * Returns a function to use in pseudos for :enabled/:disabled * @param {Boolean} disabled true for :disabled; false for :enabled */ function createDisabledPseudo(disabled) { // Known :disabled false positives: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable return function (elem) { // Only certain elements can match :enabled or :disabled // https://html.spec.whatwg.org/multipage/scripting.html#selector-enabled // https://html.spec.whatwg.org/multipage/scripting.html#selector-disabled if ("form" in elem) { // Check for inherited disabledness on relevant non-disabled elements: // * listed form-associated elements in a disabled fieldset // https://html.spec.whatwg.org/multipage/forms.html#category-listed // https://html.spec.whatwg.org/multipage/forms.html#concept-fe-disabled // * option elements in a disabled optgroup // https://html.spec.whatwg.org/multipage/forms.html#concept-option-disabled // All such elements have a "form" property. if (elem.parentNode && elem.disabled === false) { // Option elements defer to a parent optgroup if present if ("label" in elem) { if ("label" in elem.parentNode) { return elem.parentNode.disabled === disabled; } else { return elem.disabled === disabled; } } // Support: IE 6 - 11 // Use the isDisabled shortcut property to check for disabled fieldset ancestors return elem.isDisabled === disabled || // Where there is no isDisabled, check manually /* jshint -W018 */ elem.isDisabled !== !disabled && disabledAncestor(elem) === disabled; } return elem.disabled === disabled; // Try to winnow out elements that can't be disabled before trusting the disabled property. // Some victims get caught in our net (label, legend, menu, track), but it shouldn't // even exist on them, let alone have a boolean value. } else if ("label" in elem) { return elem.disabled === disabled; } // Remaining elements are neither :enabled nor :disabled return false; }; } /** * Returns a function to use in pseudos for positionals * @param {Function} fn */ function createPositionalPseudo(fn) { return markFunction(function (argument) { argument = +argument; return markFunction(function (seed, matches) { var j, matchIndexes = fn([], seed.length, argument), i = matchIndexes.length; // Match elements found at the specified indexes while (i--) { if (seed[j = matchIndexes[i]]) { seed[j] = !(matches[j] = seed[j]); } } }); }); } /** * Checks a node for validity as a Sizzle context * @param {Element|Object=} context * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value */ function testContext(context) { return context && typeof context.getElementsByTagName !== "undefined" && context; } // Expose support vars for convenience support = Sizzle.support = {}; /** * Detects XML nodes * @param {Element|Object} elem An element or a document * @returns {Boolean} True iff elem is a non-HTML XML node */ isXML = Sizzle.isXML = function (elem) { // documentElement is verified for cases where it doesn't yet exist // (such as loading iframes in IE - #4833) var documentElement = elem && (elem.ownerDocument || elem).documentElement; return documentElement ? documentElement.nodeName !== "HTML" : false; }; /** * Sets document-related variables once based on the current document * @param {Element|Object} [doc] An element or document object to use to set the document * @returns {Object} Returns the current document */ setDocument = Sizzle.setDocument = function (node) { var hasCompare, subWindow, doc = node ? node.ownerDocument || node : preferredDoc; // Return early if doc is invalid or already selected if (doc === document || doc.nodeType !== 9 || !doc.documentElement) { return document; } // Update global variables document = doc; docElem = document.documentElement; documentIsHTML = !isXML(document); // Support: IE 9-11, Edge // Accessing iframe documents after unload throws "permission denied" errors (jQuery #13936) if (preferredDoc !== document && (subWindow = document.defaultView) && subWindow.top !== subWindow) { // Support: IE 11, Edge if (subWindow.addEventListener) { subWindow.addEventListener("unload", unloadHandler, false); // Support: IE 9 - 10 only } else if (subWindow.attachEvent) { subWindow.attachEvent("onunload", unloadHandler); } } /* Attributes ---------------------------------------------------------------------- */ // Support: IE<8 // Verify that getAttribute really returns attributes and not properties // (excepting IE8 booleans) support.attributes = assert(function (el) { el.className = "i"; return !el.getAttribute("className"); }); /* getElement(s)By* ---------------------------------------------------------------------- */ // Check if getElementsByTagName("*") returns only elements support.getElementsByTagName = assert(function (el) { el.appendChild(document.createComment("")); return !el.getElementsByTagName("*").length; }); // Support: IE<9 support.getElementsByClassName = rnative.test(document.getElementsByClassName); // Support: IE<10 // Check if getElementById returns elements by name // The broken getElementById methods don't pick up programmatically-set names, // so use a roundabout getElementsByName test support.getById = assert(function (el) { docElem.appendChild(el).id = expando; return !document.getElementsByName || !document.getElementsByName(expando).length; }); // ID filter and find if (support.getById) { Expr.filter["ID"] = function (id) { var attrId = id.replace(runescape, funescape); return function (elem) { return elem.getAttribute("id") === attrId; }; }; Expr.find["ID"] = function (id, context) { if (typeof context.getElementById !== "undefined" && documentIsHTML) { var elem = context.getElementById(id); return elem ? [elem] : []; } }; } else { Expr.filter["ID"] = function (id) { var attrId = id.replace(runescape, funescape); return function (elem) { var node = typeof elem.getAttributeNode !== "undefined" && elem.getAttributeNode("id"); return node && node.value === attrId; }; }; // Support: IE 6 - 7 only // getElementById is not reliable as a find shortcut Expr.find["ID"] = function (id, context) { if (typeof context.getElementById !== "undefined" && documentIsHTML) { var node, i, elems, elem = context.getElementById(id); if (elem) { // Verify the id attribute node = elem.getAttributeNode("id"); if (node && node.value === id) { return [elem]; } // Fall back on getElementsByName elems = context.getElementsByName(id); i = 0; while (elem = elems[i++]) { node = elem.getAttributeNode("id"); if (node && node.value === id) { return [elem]; } } } return []; } }; } // Tag Expr.find["TAG"] = support.getElementsByTagName ? function (tag, context) { if (typeof context.getElementsByTagName !== "undefined") { return context.getElementsByTagName(tag); // DocumentFragment nodes don't have gEBTN } else if (support.qsa) { return context.querySelectorAll(tag); } } : function (tag, context) { var elem, tmp = [], i = 0, // By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too results = context.getElementsByTagName(tag); // Filter out possible comments if (tag === "*") { while (elem = results[i++]) { if (elem.nodeType === 1) { tmp.push(elem); } } return tmp; } return results; }; // Class Expr.find["CLASS"] = support.getElementsByClassName && function (className, context) { if (typeof context.getElementsByClassName !== "undefined" && documentIsHTML) { return context.getElementsByClassName(className); } }; /* QSA/matchesSelector ---------------------------------------------------------------------- */ // QSA and matchesSelector support // matchesSelector(:active) reports false when true (IE9/Opera 11.5) rbuggyMatches = []; // qSa(:focus) reports false when true (Chrome 21) // We allow this because of a bug in IE8/9 that throws an error // whenever `document.activeElement` is accessed on an iframe // So, we allow :focus to pass through QSA all the time to avoid the IE error // See https://bugs.jquery.com/ticket/13378 rbuggyQSA = []; if (support.qsa = rnative.test(document.querySelectorAll)) { // Build QSA regex // Regex strategy adopted from Diego Perini assert(function (el) { // Select is set to empty string on purpose // This is to test IE's treatment of not explicitly // setting a boolean content attribute, // since its presence should be enough // https://bugs.jquery.com/ticket/12359 docElem.appendChild(el).innerHTML = "" + ""; // Support: IE8, Opera 11-12.16 // Nothing should be selected when empty strings follow ^= or $= or *= // The test attribute must be unknown in Opera but "safe" for WinRT // https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section if (el.querySelectorAll("[msallowcapture^='']").length) { rbuggyQSA.push("[*^$]=" + whitespace + "*(?:''|\"\")"); } // Support: IE8 // Boolean attributes and "value" are not treated correctly if (!el.querySelectorAll("[selected]").length) { rbuggyQSA.push("\\[" + whitespace + "*(?:value|" + booleans + ")"); } // Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+ if (!el.querySelectorAll("[id~=" + expando + "-]").length) { rbuggyQSA.push("~="); } // Webkit/Opera - :checked should return selected option elements // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked // IE8 throws error here and will not see later tests if (!el.querySelectorAll(":checked").length) { rbuggyQSA.push(":checked"); } // Support: Safari 8+, iOS 8+ // https://bugs.webkit.org/show_bug.cgi?id=136851 // In-page `selector#id sibling-combinator selector` fails if (!el.querySelectorAll("a#" + expando + "+*").length) { rbuggyQSA.push(".#.+[+~]"); } }); assert(function (el) { el.innerHTML = "" + ""; // Support: Windows 8 Native Apps // The type and name attributes are restricted during .innerHTML assignment var input = document.createElement("input"); input.setAttribute("type", "hidden"); el.appendChild(input).setAttribute("name", "D"); // Support: IE8 // Enforce case-sensitivity of name attribute if (el.querySelectorAll("[name=d]").length) { rbuggyQSA.push("name" + whitespace + "*[*^$|!~]?="); } // FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled) // IE8 throws error here and will not see later tests if (el.querySelectorAll(":enabled").length !== 2) { rbuggyQSA.push(":enabled", ":disabled"); } // Support: IE9-11+ // IE's :disabled selector does not pick up the children of disabled fieldsets docElem.appendChild(el).disabled = true; if (el.querySelectorAll(":disabled").length !== 2) { rbuggyQSA.push(":enabled", ":disabled"); } // Opera 10-11 does not throw on post-comma invalid pseudos el.querySelectorAll("*,:x"); rbuggyQSA.push(",.*:"); }); } if (support.matchesSelector = rnative.test(matches = docElem.matches || docElem.webkitMatchesSelector || docElem.mozMatchesSelector || docElem.oMatchesSelector || docElem.msMatchesSelector)) { assert(function (el) { // Check to see if it's possible to do matchesSelector // on a disconnected node (IE 9) support.disconnectedMatch = matches.call(el, "*"); // This should fail with an exception // Gecko does not error, returns false instead matches.call(el, "[s!='']:x"); rbuggyMatches.push("!=", pseudos); }); } rbuggyQSA = rbuggyQSA.length && new RegExp(rbuggyQSA.join("|")); rbuggyMatches = rbuggyMatches.length && new RegExp(rbuggyMatches.join("|")); /* Contains ---------------------------------------------------------------------- */ hasCompare = rnative.test(docElem.compareDocumentPosition); // Element contains another // Purposefully self-exclusive // As in, an element does not contain itself contains = hasCompare || rnative.test(docElem.contains) ? function (a, b) { var adown = a.nodeType === 9 ? a.documentElement : a, bup = b && b.parentNode; return a === bup || !!(bup && bup.nodeType === 1 && (adown.contains ? adown.contains(bup) : a.compareDocumentPosition && a.compareDocumentPosition(bup) & 16)); } : function (a, b) { if (b) { while (b = b.parentNode) { if (b === a) { return true; } } } return false; }; /* Sorting ---------------------------------------------------------------------- */ // Document order sorting sortOrder = hasCompare ? function (a, b) { // Flag for duplicate removal if (a === b) { hasDuplicate = true; return 0; } // Sort on method existence if only one input has compareDocumentPosition var compare = !a.compareDocumentPosition - !b.compareDocumentPosition; if (compare) { return compare; } // Calculate position if both inputs belong to the same document compare = (a.ownerDocument || a) === (b.ownerDocument || b) ? a.compareDocumentPosition(b) : // Otherwise we know they are disconnected 1; // Disconnected nodes if (compare & 1 || !support.sortDetached && b.compareDocumentPosition(a) === compare) { // Choose the first element that is related to our preferred document if (a === document || a.ownerDocument === preferredDoc && contains(preferredDoc, a)) { return -1; } if (b === document || b.ownerDocument === preferredDoc && contains(preferredDoc, b)) { return 1; } // Maintain original order return sortInput ? indexOf(sortInput, a) - indexOf(sortInput, b) : 0; } return compare & 4 ? -1 : 1; } : function (a, b) { // Exit early if the nodes are identical if (a === b) { hasDuplicate = true; return 0; } var cur, i = 0, aup = a.parentNode, bup = b.parentNode, ap = [a], bp = [b]; // Parentless nodes are either documents or disconnected if (!aup || !bup) { return a === document ? -1 : b === document ? 1 : aup ? -1 : bup ? 1 : sortInput ? indexOf(sortInput, a) - indexOf(sortInput, b) : 0; // If the nodes are siblings, we can do a quick check } else if (aup === bup) { return siblingCheck(a, b); } // Otherwise we need full lists of their ancestors for comparison cur = a; while (cur = cur.parentNode) { ap.unshift(cur); } cur = b; while (cur = cur.parentNode) { bp.unshift(cur); } // Walk down the tree looking for a discrepancy while (ap[i] === bp[i]) { i++; } return i ? // Do a sibling check if the nodes have a common ancestor siblingCheck(ap[i], bp[i]) : // Otherwise nodes in our document sort first ap[i] === preferredDoc ? -1 : bp[i] === preferredDoc ? 1 : 0; }; return document; }; Sizzle.matches = function (expr, elements) { return Sizzle(expr, null, null, elements); }; Sizzle.matchesSelector = function (elem, expr) { // Set document vars if needed if ((elem.ownerDocument || elem) !== document) { setDocument(elem); } // Make sure that attribute selectors are quoted expr = expr.replace(rattributeQuotes, "='$1']"); if (support.matchesSelector && documentIsHTML && !compilerCache[expr + " "] && (!rbuggyMatches || !rbuggyMatches.test(expr)) && (!rbuggyQSA || !rbuggyQSA.test(expr))) { try { var ret = matches.call(elem, expr); // IE 9's matchesSelector returns false on disconnected nodes if (ret || support.disconnectedMatch || // As well, disconnected nodes are said to be in a document // fragment in IE 9 elem.document && elem.document.nodeType !== 11) { return ret; } } catch (e) {} } return Sizzle(expr, document, null, [elem]).length > 0; }; Sizzle.contains = function (context, elem) { // Set document vars if needed if ((context.ownerDocument || context) !== document) { setDocument(context); } return contains(context, elem); }; Sizzle.attr = function (elem, name) { // Set document vars if needed if ((elem.ownerDocument || elem) !== document) { setDocument(elem); } var fn = Expr.attrHandle[name.toLowerCase()], // Don't get fooled by Object.prototype properties (jQuery #13807) val = fn && hasOwn.call(Expr.attrHandle, name.toLowerCase()) ? fn(elem, name, !documentIsHTML) : undefined; return val !== undefined ? val : support.attributes || !documentIsHTML ? elem.getAttribute(name) : (val = elem.getAttributeNode(name)) && val.specified ? val.value : null; }; Sizzle.escape = function (sel) { return (sel + "").replace(rcssescape, fcssescape); }; Sizzle.error = function (msg) { throw new Error("Syntax error, unrecognized expression: " + msg); }; /** * Document sorting and removing duplicates * @param {ArrayLike} results */ Sizzle.uniqueSort = function (results) { var elem, duplicates = [], j = 0, i = 0; // Unless we *know* we can detect duplicates, assume their presence hasDuplicate = !support.detectDuplicates; sortInput = !support.sortStable && results.slice(0); results.sort(sortOrder); if (hasDuplicate) { while (elem = results[i++]) { if (elem === results[i]) { j = duplicates.push(i); } } while (j--) { results.splice(duplicates[j], 1); } } // Clear input after sorting to release objects // See https://github.com/jquery/sizzle/pull/225 sortInput = null; return results; }; /** * Utility function for retrieving the text value of an array of DOM nodes * @param {Array|Element} elem */ getText = Sizzle.getText = function (elem) { var node, ret = "", i = 0, nodeType = elem.nodeType; if (!nodeType) { // If no nodeType, this is expected to be an array while (node = elem[i++]) { // Do not traverse comment nodes ret += getText(node); } } else if (nodeType === 1 || nodeType === 9 || nodeType === 11) { // Use textContent for elements // innerText usage removed for consistency of new lines (jQuery #11153) if (typeof elem.textContent === "string") { return elem.textContent; } else { // Traverse its children for (elem = elem.firstChild; elem; elem = elem.nextSibling) { ret += getText(elem); } } } else if (nodeType === 3 || nodeType === 4) { return elem.nodeValue; } // Do not include comment or processing instruction nodes return ret; }; Expr = Sizzle.selectors = { // Can be adjusted by the user cacheLength: 50, createPseudo: markFunction, match: matchExpr, attrHandle: {}, find: {}, relative: { ">": { dir: "parentNode", first: true }, " ": { dir: "parentNode" }, "+": { dir: "previousSibling", first: true }, "~": { dir: "previousSibling" } }, preFilter: { "ATTR": function (match) { match[1] = match[1].replace(runescape, funescape); // Move the given value to match[3] whether quoted or unquoted match[3] = (match[3] || match[4] || match[5] || "").replace(runescape, funescape); if (match[2] === "~=") { match[3] = " " + match[3] + " "; } return match.slice(0, 4); }, "CHILD": function (match) { /* matches from matchExpr["CHILD"] 1 type (only|nth|...) 2 what (child|of-type) 3 argument (even|odd|\d*|\d*n([+-]\d+)?|...) 4 xn-component of xn+y argument ([+-]?\d*n|) 5 sign of xn-component 6 x of xn-component 7 sign of y-component 8 y of y-component */ match[1] = match[1].toLowerCase(); if (match[1].slice(0, 3) === "nth") { // nth-* requires argument if (!match[3]) { Sizzle.error(match[0]); } // numeric x and y parameters for Expr.filter.CHILD // remember that false/true cast respectively to 0/1 match[4] = +(match[4] ? match[5] + (match[6] || 1) : 2 * (match[3] === "even" || match[3] === "odd")); match[5] = +(match[7] + match[8] || match[3] === "odd"); // other types prohibit arguments } else if (match[3]) { Sizzle.error(match[0]); } return match; }, "PSEUDO": function (match) { var excess, unquoted = !match[6] && match[2]; if (matchExpr["CHILD"].test(match[0])) { return null; } // Accept quoted arguments as-is if (match[3]) { match[2] = match[4] || match[5] || ""; // Strip excess characters from unquoted arguments } else if (unquoted && rpseudo.test(unquoted) && (excess = tokenize(unquoted, true)) && (excess = unquoted.indexOf(")", unquoted.length - excess) - unquoted.length)) { // excess is a negative index match[0] = match[0].slice(0, excess); match[2] = unquoted.slice(0, excess); } // Return only captures needed by the pseudo filter method (type and argument) return match.slice(0, 3); } }, filter: { "TAG": function (nodeNameSelector) { var nodeName = nodeNameSelector.replace(runescape, funescape).toLowerCase(); return nodeNameSelector === "*" ? function () { return true; } : function (elem) { return elem.nodeName && elem.nodeName.toLowerCase() === nodeName; }; }, "CLASS": function (className) { var pattern = classCache[className + " "]; return pattern || (pattern = new RegExp("(^|" + whitespace + ")" + className + "(" + whitespace + "|$)")) && classCache(className, function (elem) { return pattern.test(typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== "undefined" && elem.getAttribute("class") || ""); }); }, "ATTR": function (name, operator, check) { return function (elem) { var result = Sizzle.attr(elem, name); if (result == null) { return operator === "!="; } if (!operator) { return true; } result += ""; return operator === "=" ? result === check : operator === "!=" ? result !== check : operator === "^=" ? check && result.indexOf(check) === 0 : operator === "*=" ? check && result.indexOf(check) > -1 : operator === "$=" ? check && result.slice(-check.length) === check : operator === "~=" ? (" " + result.replace(rwhitespace, " ") + " ").indexOf(check) > -1 : operator === "|=" ? result === check || result.slice(0, check.length + 1) === check + "-" : false; }; }, "CHILD": function (type, what, argument, first, last) { var simple = type.slice(0, 3) !== "nth", forward = type.slice(-4) !== "last", ofType = what === "of-type"; return first === 1 && last === 0 ? // Shortcut for :nth-*(n) function (elem) { return !!elem.parentNode; } : function (elem, context, xml) { var cache, uniqueCache, outerCache, node, nodeIndex, start, dir = simple !== forward ? "nextSibling" : "previousSibling", parent = elem.parentNode, name = ofType && elem.nodeName.toLowerCase(), useCache = !xml && !ofType, diff = false; if (parent) { // :(first|last|only)-(child|of-type) if (simple) { while (dir) { node = elem; while (node = node[dir]) { if (ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1) { return false; } } // Reverse direction for :only-* (if we haven't yet done so) start = dir = type === "only" && !start && "nextSibling"; } return true; } start = [forward ? parent.firstChild : parent.lastChild]; // non-xml :nth-child(...) stores cache data on `parent` if (forward && useCache) { // Seek `elem` from a previously-cached index // ...in a gzip-friendly way node = parent; outerCache = node[expando] || (node[expando] = {}); // Support: IE <9 only // Defend against cloned attroperties (jQuery gh-1709) uniqueCache = outerCache[node.uniqueID] || (outerCache[node.uniqueID] = {}); cache = uniqueCache[type] || []; nodeIndex = cache[0] === dirruns && cache[1]; diff = nodeIndex && cache[2]; node = nodeIndex && parent.childNodes[nodeIndex]; while (node = ++nodeIndex && node && node[dir] || (diff = nodeIndex = 0) || start.pop()) { // When found, cache indexes on `parent` and break if (node.nodeType === 1 && ++diff && node === elem) { uniqueCache[type] = [dirruns, nodeIndex, diff]; break; } } } else { // Use previously-cached element index if available if (useCache) { // ...in a gzip-friendly way node = elem; outerCache = node[expando] || (node[expando] = {}); // Support: IE <9 only // Defend against cloned attroperties (jQuery gh-1709) uniqueCache = outerCache[node.uniqueID] || (outerCache[node.uniqueID] = {}); cache = uniqueCache[type] || []; nodeIndex = cache[0] === dirruns && cache[1]; diff = nodeIndex; } // xml :nth-child(...) // or :nth-last-child(...) or :nth(-last)?-of-type(...) if (diff === false) { // Use the same loop as above to seek `elem` from the start while (node = ++nodeIndex && node && node[dir] || (diff = nodeIndex = 0) || start.pop()) { if ((ofType ? node.nodeName.toLowerCase() === name : node.nodeType === 1) && ++diff) { // Cache the index of each encountered element if (useCache) { outerCache = node[expando] || (node[expando] = {}); // Support: IE <9 only // Defend against cloned attroperties (jQuery gh-1709) uniqueCache = outerCache[node.uniqueID] || (outerCache[node.uniqueID] = {}); uniqueCache[type] = [dirruns, diff]; } if (node === elem) { break; } } } } } // Incorporate the offset, then check against cycle size diff -= last; return diff === first || diff % first === 0 && diff / first >= 0; } }; }, "PSEUDO": function (pseudo, argument) { // pseudo-class names are case-insensitive // http://www.w3.org/TR/selectors/#pseudo-classes // Prioritize by case sensitivity in case custom pseudos are added with uppercase letters // Remember that setFilters inherits from pseudos var args, fn = Expr.pseudos[pseudo] || Expr.setFilters[pseudo.toLowerCase()] || Sizzle.error("unsupported pseudo: " + pseudo); // The user may use createPseudo to indicate that // arguments are needed to create the filter function // just as Sizzle does if (fn[expando]) { return fn(argument); } // But maintain support for old signatures if (fn.length > 1) { args = [pseudo, pseudo, "", argument]; return Expr.setFilters.hasOwnProperty(pseudo.toLowerCase()) ? markFunction(function (seed, matches) { var idx, matched = fn(seed, argument), i = matched.length; while (i--) { idx = indexOf(seed, matched[i]); seed[idx] = !(matches[idx] = matched[i]); } }) : function (elem) { return fn(elem, 0, args); }; } return fn; } }, pseudos: { // Potentially complex pseudos "not": markFunction(function (selector) { // Trim the selector passed to compile // to avoid treating leading and trailing // spaces as combinators var input = [], results = [], matcher = compile(selector.replace(rtrim, "$1")); return matcher[expando] ? markFunction(function (seed, matches, context, xml) { var elem, unmatched = matcher(seed, null, xml, []), i = seed.length; // Match elements unmatched by `matcher` while (i--) { if (elem = unmatched[i]) { seed[i] = !(matches[i] = elem); } } }) : function (elem, context, xml) { input[0] = elem; matcher(input, null, xml, results); // Don't keep the element (issue #299) input[0] = null; return !results.pop(); }; }), "has": markFunction(function (selector) { return function (elem) { return Sizzle(selector, elem).length > 0; }; }), "contains": markFunction(function (text) { text = text.replace(runescape, funescape); return function (elem) { return (elem.textContent || elem.innerText || getText(elem)).indexOf(text) > -1; }; }), // "Whether an element is represented by a :lang() selector // is based solely on the element's language value // being equal to the identifier C, // or beginning with the identifier C immediately followed by "-". // The matching of C against the element's language value is performed case-insensitively. // The identifier C does not have to be a valid language name." // http://www.w3.org/TR/selectors/#lang-pseudo "lang": markFunction(function (lang) { // lang value must be a valid identifier if (!ridentifier.test(lang || "")) { Sizzle.error("unsupported lang: " + lang); } lang = lang.replace(runescape, funescape).toLowerCase(); return function (elem) { var elemLang; do { if (elemLang = documentIsHTML ? elem.lang : elem.getAttribute("xml:lang") || elem.getAttribute("lang")) { elemLang = elemLang.toLowerCase(); return elemLang === lang || elemLang.indexOf(lang + "-") === 0; } } while ((elem = elem.parentNode) && elem.nodeType === 1); return false; }; }), // Miscellaneous "target": function (elem) { var hash = window.location && window.location.hash; return hash && hash.slice(1) === elem.id; }, "root": function (elem) { return elem === docElem; }, "focus": function (elem) { return elem === document.activeElement && (!document.hasFocus || document.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex); }, // Boolean properties "enabled": createDisabledPseudo(false), "disabled": createDisabledPseudo(true), "checked": function (elem) { // In CSS3, :checked should return both checked and selected elements // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked var nodeName = elem.nodeName.toLowerCase(); return nodeName === "input" && !!elem.checked || nodeName === "option" && !!elem.selected; }, "selected": function (elem) { // Accessing this property makes selected-by-default // options in Safari work properly if (elem.parentNode) { elem.parentNode.selectedIndex; } return elem.selected === true; }, // Contents "empty": function (elem) { // http://www.w3.org/TR/selectors/#empty-pseudo // :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5), // but not by others (comment: 8; processing instruction: 7; etc.) // nodeType < 6 works because attributes (2) do not appear as children for (elem = elem.firstChild; elem; elem = elem.nextSibling) { if (elem.nodeType < 6) { return false; } } return true; }, "parent": function (elem) { return !Expr.pseudos["empty"](elem); }, // Element/input types "header": function (elem) { return rheader.test(elem.nodeName); }, "input": function (elem) { return rinputs.test(elem.nodeName); }, "button": function (elem) { var name = elem.nodeName.toLowerCase(); return name === "input" && elem.type === "button" || name === "button"; }, "text": function (elem) { var attr; return elem.nodeName.toLowerCase() === "input" && elem.type === "text" && ((attr = elem.getAttribute("type")) == null || attr.toLowerCase() === "text"); }, // Position-in-collection "first": createPositionalPseudo(function () { return [0]; }), "last": createPositionalPseudo(function (matchIndexes, length) { return [length - 1]; }), "eq": createPositionalPseudo(function (matchIndexes, length, argument) { return [argument < 0 ? argument + length : argument]; }), "even": createPositionalPseudo(function (matchIndexes, length) { var i = 0; for (; i < length; i += 2) { matchIndexes.push(i); } return matchIndexes; }), "odd": createPositionalPseudo(function (matchIndexes, length) { var i = 1; for (; i < length; i += 2) { matchIndexes.push(i); } return matchIndexes; }), "lt": createPositionalPseudo(function (matchIndexes, length, argument) { var i = argument < 0 ? argument + length : argument; for (; --i >= 0;) { matchIndexes.push(i); } return matchIndexes; }), "gt": createPositionalPseudo(function (matchIndexes, length, argument) { var i = argument < 0 ? argument + length : argument; for (; ++i < length;) { matchIndexes.push(i); } return matchIndexes; }) } }; Expr.pseudos["nth"] = Expr.pseudos["eq"]; // Add button/input type pseudos for (i in { radio: true, checkbox: true, file: true, password: true, image: true }) { Expr.pseudos[i] = createInputPseudo(i); } for (i in { submit: true, reset: true }) { Expr.pseudos[i] = createButtonPseudo(i); } // Easy API for creating new setFilters function setFilters() {} setFilters.prototype = Expr.filters = Expr.pseudos; Expr.setFilters = new setFilters(); tokenize = Sizzle.tokenize = function (selector, parseOnly) { var matched, match, tokens, type, soFar, groups, preFilters, cached = tokenCache[selector + " "]; if (cached) { return parseOnly ? 0 : cached.slice(0); } soFar = selector; groups = []; preFilters = Expr.preFilter; while (soFar) { // Comma and first run if (!matched || (match = rcomma.exec(soFar))) { if (match) { // Don't consume trailing commas as valid soFar = soFar.slice(match[0].length) || soFar; } groups.push(tokens = []); } matched = false; // Combinators if (match = rcombinators.exec(soFar)) { matched = match.shift(); tokens.push({ value: matched, // Cast descendant combinators to space type: match[0].replace(rtrim, " ") }); soFar = soFar.slice(matched.length); } // Filters for (type in Expr.filter) { if ((match = matchExpr[type].exec(soFar)) && (!preFilters[type] || (match = preFilters[type](match)))) { matched = match.shift(); tokens.push({ value: matched, type: type, matches: match }); soFar = soFar.slice(matched.length); } } if (!matched) { break; } } // Return the length of the invalid excess // if we're just parsing // Otherwise, throw an error or return tokens return parseOnly ? soFar.length : soFar ? Sizzle.error(selector) : // Cache the tokens tokenCache(selector, groups).slice(0); }; function toSelector(tokens) { var i = 0, len = tokens.length, selector = ""; for (; i < len; i++) { selector += tokens[i].value; } return selector; } function addCombinator(matcher, combinator, base) { var dir = combinator.dir, skip = combinator.next, key = skip || dir, checkNonElements = base && key === "parentNode", doneName = done++; return combinator.first ? // Check against closest ancestor/preceding element function (elem, context, xml) { while (elem = elem[dir]) { if (elem.nodeType === 1 || checkNonElements) { return matcher(elem, context, xml); } } return false; } : // Check against all ancestor/preceding elements function (elem, context, xml) { var oldCache, uniqueCache, outerCache, newCache = [dirruns, doneName]; // We can't set arbitrary data on XML nodes, so they don't benefit from combinator caching if (xml) { while (elem = elem[dir]) { if (elem.nodeType === 1 || checkNonElements) { if (matcher(elem, context, xml)) { return true; } } } } else { while (elem = elem[dir]) { if (elem.nodeType === 1 || checkNonElements) { outerCache = elem[expando] || (elem[expando] = {}); // Support: IE <9 only // Defend against cloned attroperties (jQuery gh-1709) uniqueCache = outerCache[elem.uniqueID] || (outerCache[elem.uniqueID] = {}); if (skip && skip === elem.nodeName.toLowerCase()) { elem = elem[dir] || elem; } else if ((oldCache = uniqueCache[key]) && oldCache[0] === dirruns && oldCache[1] === doneName) { // Assign to newCache so results back-propagate to previous elements return newCache[2] = oldCache[2]; } else { // Reuse newcache so results back-propagate to previous elements uniqueCache[key] = newCache; // A match means we're done; a fail means we have to keep checking if (newCache[2] = matcher(elem, context, xml)) { return true; } } } } } return false; }; } function elementMatcher(matchers) { return matchers.length > 1 ? function (elem, context, xml) { var i = matchers.length; while (i--) { if (!matchers[i](elem, context, xml)) { return false; } } return true; } : matchers[0]; } function multipleContexts(selector, contexts, results) { var i = 0, len = contexts.length; for (; i < len; i++) { Sizzle(selector, contexts[i], results); } return results; } function condense(unmatched, map, filter, context, xml) { var elem, newUnmatched = [], i = 0, len = unmatched.length, mapped = map != null; for (; i < len; i++) { if (elem = unmatched[i]) { if (!filter || filter(elem, context, xml)) { newUnmatched.push(elem); if (mapped) { map.push(i); } } } } return newUnmatched; } function setMatcher(preFilter, selector, matcher, postFilter, postFinder, postSelector) { if (postFilter && !postFilter[expando]) { postFilter = setMatcher(postFilter); } if (postFinder && !postFinder[expando]) { postFinder = setMatcher(postFinder, postSelector); } return markFunction(function (seed, results, context, xml) { var temp, i, elem, preMap = [], postMap = [], preexisting = results.length, // Get initial elements from seed or context elems = seed || multipleContexts(selector || "*", context.nodeType ? [context] : context, []), // Prefilter to get matcher input, preserving a map for seed-results synchronization matcherIn = preFilter && (seed || !selector) ? condense(elems, preMap, preFilter, context, xml) : elems, matcherOut = matcher ? // If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results, postFinder || (seed ? preFilter : preexisting || postFilter) ? // ...intermediate processing is necessary [] : // ...otherwise use results directly results : matcherIn; // Find primary matches if (matcher) { matcher(matcherIn, matcherOut, context, xml); } // Apply postFilter if (postFilter) { temp = condense(matcherOut, postMap); postFilter(temp, [], context, xml); // Un-match failing elements by moving them back to matcherIn i = temp.length; while (i--) { if (elem = temp[i]) { matcherOut[postMap[i]] = !(matcherIn[postMap[i]] = elem); } } } if (seed) { if (postFinder || preFilter) { if (postFinder) { // Get the final matcherOut by condensing this intermediate into postFinder contexts temp = []; i = matcherOut.length; while (i--) { if (elem = matcherOut[i]) { // Restore matcherIn since elem is not yet a final match temp.push(matcherIn[i] = elem); } } postFinder(null, matcherOut = [], temp, xml); } // Move matched elements from seed to results to keep them synchronized i = matcherOut.length; while (i--) { if ((elem = matcherOut[i]) && (temp = postFinder ? indexOf(seed, elem) : preMap[i]) > -1) { seed[temp] = !(results[temp] = elem); } } } // Add elements to results, through postFinder if defined } else { matcherOut = condense(matcherOut === results ? matcherOut.splice(preexisting, matcherOut.length) : matcherOut); if (postFinder) { postFinder(null, results, matcherOut, xml); } else { push.apply(results, matcherOut); } } }); } function matcherFromTokens(tokens) { var checkContext, matcher, j, len = tokens.length, leadingRelative = Expr.relative[tokens[0].type], implicitRelative = leadingRelative || Expr.relative[" "], i = leadingRelative ? 1 : 0, // The foundational matcher ensures that elements are reachable from top-level context(s) matchContext = addCombinator(function (elem) { return elem === checkContext; }, implicitRelative, true), matchAnyContext = addCombinator(function (elem) { return indexOf(checkContext, elem) > -1; }, implicitRelative, true), matchers = [function (elem, context, xml) { var ret = !leadingRelative && (xml || context !== outermostContext) || ((checkContext = context).nodeType ? matchContext(elem, context, xml) : matchAnyContext(elem, context, xml)); // Avoid hanging onto element (issue #299) checkContext = null; return ret; }]; for (; i < len; i++) { if (matcher = Expr.relative[tokens[i].type]) { matchers = [addCombinator(elementMatcher(matchers), matcher)]; } else { matcher = Expr.filter[tokens[i].type].apply(null, tokens[i].matches); // Return special upon seeing a positional matcher if (matcher[expando]) { // Find the next relative operator (if any) for proper handling j = ++i; for (; j < len; j++) { if (Expr.relative[tokens[j].type]) { break; } } return setMatcher(i > 1 && elementMatcher(matchers), i > 1 && toSelector( // If the preceding token was a descendant combinator, insert an implicit any-element `*` tokens.slice(0, i - 1).concat({ value: tokens[i - 2].type === " " ? "*" : "" })).replace(rtrim, "$1"), matcher, i < j && matcherFromTokens(tokens.slice(i, j)), j < len && matcherFromTokens(tokens = tokens.slice(j)), j < len && toSelector(tokens)); } matchers.push(matcher); } } return elementMatcher(matchers); } function matcherFromGroupMatchers(elementMatchers, setMatchers) { var bySet = setMatchers.length > 0, byElement = elementMatchers.length > 0, superMatcher = function (seed, context, xml, results, outermost) { var elem, j, matcher, matchedCount = 0, i = "0", unmatched = seed && [], setMatched = [], contextBackup = outermostContext, // We must always have either seed elements or outermost context elems = seed || byElement && Expr.find["TAG"]("*", outermost), // Use integer dirruns iff this is the outermost matcher dirrunsUnique = dirruns += contextBackup == null ? 1 : Math.random() || 0.1, len = elems.length; if (outermost) { outermostContext = context === document || context || outermost; } // Add elements passing elementMatchers directly to results // Support: IE<9, Safari // Tolerate NodeList properties (IE: "length"; Safari: ) matching elements by id for (; i !== len && (elem = elems[i]) != null; i++) { if (byElement && elem) { j = 0; if (!context && elem.ownerDocument !== document) { setDocument(elem); xml = !documentIsHTML; } while (matcher = elementMatchers[j++]) { if (matcher(elem, context || document, xml)) { results.push(elem); break; } } if (outermost) { dirruns = dirrunsUnique; } } // Track unmatched elements for set filters if (bySet) { // They will have gone through all possible matchers if (elem = !matcher && elem) { matchedCount--; } // Lengthen the array for every element, matched or not if (seed) { unmatched.push(elem); } } } // `i` is now the count of elements visited above, and adding it to `matchedCount` // makes the latter nonnegative. matchedCount += i; // Apply set filters to unmatched elements // NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount` // equals `i`), unless we didn't visit _any_ elements in the above loop because we have // no element matchers and no seed. // Incrementing an initially-string "0" `i` allows `i` to remain a string only in that // case, which will result in a "00" `matchedCount` that differs from `i` but is also // numerically zero. if (bySet && i !== matchedCount) { j = 0; while (matcher = setMatchers[j++]) { matcher(unmatched, setMatched, context, xml); } if (seed) { // Reintegrate element matches to eliminate the need for sorting if (matchedCount > 0) { while (i--) { if (!(unmatched[i] || setMatched[i])) { setMatched[i] = pop.call(results); } } } // Discard index placeholder values to get only actual matches setMatched = condense(setMatched); } // Add matches to results push.apply(results, setMatched); // Seedless set matches succeeding multiple successful matchers stipulate sorting if (outermost && !seed && setMatched.length > 0 && matchedCount + setMatchers.length > 1) { Sizzle.uniqueSort(results); } } // Override manipulation of globals by nested matchers if (outermost) { dirruns = dirrunsUnique; outermostContext = contextBackup; } return unmatched; }; return bySet ? markFunction(superMatcher) : superMatcher; } compile = Sizzle.compile = function (selector, match /* Internal Use Only */ ) { var i, setMatchers = [], elementMatchers = [], cached = compilerCache[selector + " "]; if (!cached) { // Generate a function of recursive functions that can be used to check each element if (!match) { match = tokenize(selector); } i = match.length; while (i--) { cached = matcherFromTokens(match[i]); if (cached[expando]) { setMatchers.push(cached); } else { elementMatchers.push(cached); } } // Cache the compiled function cached = compilerCache(selector, matcherFromGroupMatchers(elementMatchers, setMatchers)); // Save selector and tokenization cached.selector = selector; } return cached; }; /** * A low-level selection function that works with Sizzle's compiled * selector functions * @param {String|Function} selector A selector or a pre-compiled * selector function built with Sizzle.compile * @param {Element} context * @param {Array} [results] * @param {Array} [seed] A set of elements to match against */ select = Sizzle.select = function (selector, context, results, seed) { var i, tokens, token, type, find, compiled = typeof selector === "function" && selector, match = !seed && tokenize(selector = compiled.selector || selector); results = results || []; // Try to minimize operations if there is only one selector in the list and no seed // (the latter of which guarantees us context) if (match.length === 1) { // Reduce context if the leading compound selector is an ID tokens = match[0] = match[0].slice(0); if (tokens.length > 2 && (token = tokens[0]).type === "ID" && context.nodeType === 9 && documentIsHTML && Expr.relative[tokens[1].type]) { context = (Expr.find["ID"](token.matches[0].replace(runescape, funescape), context) || [])[0]; if (!context) { return results; // Precompiled matchers will still verify ancestry, so step up a level } else if (compiled) { context = context.parentNode; } selector = selector.slice(tokens.shift().value.length); } // Fetch a seed set for right-to-left matching i = matchExpr["needsContext"].test(selector) ? 0 : tokens.length; while (i--) { token = tokens[i]; // Abort if we hit a combinator if (Expr.relative[type = token.type]) { break; } if (find = Expr.find[type]) { // Search, expanding context for leading sibling combinators if (seed = find(token.matches[0].replace(runescape, funescape), rsibling.test(tokens[0].type) && testContext(context.parentNode) || context)) { // If seed is empty or no tokens remain, we can return early tokens.splice(i, 1); selector = seed.length && toSelector(tokens); if (!selector) { push.apply(results, seed); return results; } break; } } } } // Compile and execute a filtering function if one is not provided // Provide `match` to avoid retokenization if we modified the selector above (compiled || compile(selector, match))(seed, context, !documentIsHTML, results, !context || rsibling.test(selector) && testContext(context.parentNode) || context); return results; }; // One-time assignments // Sort stability support.sortStable = expando.split("").sort(sortOrder).join("") === expando; // Support: Chrome 14-35+ // Always assume duplicates if they aren't passed to the comparison function support.detectDuplicates = !!hasDuplicate; // Initialize against the default document setDocument(); return Sizzle; }(window); jQuery.find = Sizzle; jQuery.expr = Sizzle.selectors; // Deprecated jQuery.expr[":"] = jQuery.expr.pseudos; jQuery.uniqueSort = jQuery.unique = Sizzle.uniqueSort; jQuery.text = Sizzle.getText; jQuery.isXMLDoc = Sizzle.isXML; jQuery.contains = Sizzle.contains; jQuery.escapeSelector = Sizzle.escape; var dir = function (elem, dir, until) { var matched = [], truncate = until !== undefined; while ((elem = elem[dir]) && elem.nodeType !== 9) { if (elem.nodeType === 1) { if (truncate && jQuery(elem).is(until)) { break; } matched.push(elem); } } return matched; }; var siblings = function (n, elem) { var matched = []; for (; n; n = n.nextSibling) { if (n.nodeType === 1 && n !== elem) { matched.push(n); } } return matched; }; var rneedsContext = jQuery.expr.match.needsContext; function nodeName(elem, name) { return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase(); } var rsingleTag = /^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i; // Implement the identical functionality for filter and not function winnow(elements, qualifier, not) { if (isFunction(qualifier)) { return jQuery.grep(elements, function (elem, i) { return !!qualifier.call(elem, i, elem) !== not; }); } // Single element if (qualifier.nodeType) { return jQuery.grep(elements, function (elem) { return elem === qualifier !== not; }); } // Arraylike of elements (jQuery, arguments, Array) if (typeof qualifier !== "string") { return jQuery.grep(elements, function (elem) { return indexOf$1.call(qualifier, elem) > -1 !== not; }); } // Filtered directly for both simple and complex selectors return jQuery.filter(qualifier, elements, not); } jQuery.filter = function (expr, elems, not) { var elem = elems[0]; if (not) { expr = ":not(" + expr + ")"; } if (elems.length === 1 && elem.nodeType === 1) { return jQuery.find.matchesSelector(elem, expr) ? [elem] : []; } return jQuery.find.matches(expr, jQuery.grep(elems, function (elem) { return elem.nodeType === 1; })); }; jQuery.fn.extend({ find: function (selector) { var i, ret, len = this.length, self = this; if (typeof selector !== "string") { return this.pushStack(jQuery(selector).filter(function () { for (i = 0; i < len; i++) { if (jQuery.contains(self[i], this)) { return true; } } })); } ret = this.pushStack([]); for (i = 0; i < len; i++) { jQuery.find(selector, self[i], ret); } return len > 1 ? jQuery.uniqueSort(ret) : ret; }, filter: function (selector) { return this.pushStack(winnow(this, selector || [], false)); }, not: function (selector) { return this.pushStack(winnow(this, selector || [], true)); }, is: function (selector) { return !!winnow(this, // If this is a positional/relative selector, check membership in the returned set // so $("p:first").is("p:last") won't return true for a doc with two "p". typeof selector === "string" && rneedsContext.test(selector) ? jQuery(selector) : selector || [], false).length; } }); // Initialize a jQuery object // A central reference to the root jQuery(document) var rootjQuery, // A simple way to check for HTML strings // Prioritize #id over to avoid XSS via location.hash (#9521) // Strict HTML recognition (#11290: must start with <) // Shortcut simple #id case for speed rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/, init$2 = jQuery.fn.init = function (selector, context, root) { var match, elem; // HANDLE: $(""), $(null), $(undefined), $(false) if (!selector) { return this; } // Method init() accepts an alternate rootjQuery // so migrate can support jQuery.sub (gh-2101) root = root || rootjQuery; // Handle HTML strings if (typeof selector === "string") { if (selector[0] === "<" && selector[selector.length - 1] === ">" && selector.length >= 3) { // Assume that strings that start and end with <> are HTML and skip the regex check match = [null, selector, null]; } else { match = rquickExpr.exec(selector); } // Match html or make sure no context is specified for #id if (match && (match[1] || !context)) { // HANDLE: $(html) -> $(array) if (match[1]) { context = context instanceof jQuery ? context[0] : context; // Option to run scripts is true for back-compat // Intentionally let the error be thrown if parseHTML is not present jQuery.merge(this, jQuery.parseHTML(match[1], context && context.nodeType ? context.ownerDocument || context : document$2, true)); // HANDLE: $(html, props) if (rsingleTag.test(match[1]) && jQuery.isPlainObject(context)) { for (match in context) { // Properties of context are called as methods if possible if (isFunction(this[match])) { this[match](context[match]); // ...and otherwise set as attributes } else { this.attr(match, context[match]); } } } return this; // HANDLE: $(#id) } else { elem = document$2.getElementById(match[2]); if (elem) { // Inject the element directly into the jQuery object this[0] = elem; this.length = 1; } return this; } // HANDLE: $(expr, $(...)) } else if (!context || context.jquery) { return (context || root).find(selector); // HANDLE: $(expr, context) // (which is just equivalent to: $(context).find(expr) } else { return this.constructor(context).find(selector); } // HANDLE: $(DOMElement) } else if (selector.nodeType) { this[0] = selector; this.length = 1; return this; // HANDLE: $(function) // Shortcut for document ready } else if (isFunction(selector)) { return root.ready !== undefined ? root.ready(selector) : // Execute immediately if ready is not present selector(jQuery); } return jQuery.makeArray(selector, this); }; // Give the init function the jQuery prototype for later instantiation init$2.prototype = jQuery.fn; // Initialize central reference rootjQuery = jQuery(document$2); var rparentsprev = /^(?:parents|prev(?:Until|All))/, // Methods guaranteed to produce a unique set when starting from a unique set guaranteedUnique = { children: true, contents: true, next: true, prev: true }; jQuery.fn.extend({ has: function (target) { var targets = jQuery(target, this), l = targets.length; return this.filter(function () { var i = 0; for (; i < l; i++) { if (jQuery.contains(this, targets[i])) { return true; } } }); }, closest: function (selectors, context) { var cur, i = 0, l = this.length, matched = [], targets = typeof selectors !== "string" && jQuery(selectors); // Positional selectors never match, since there's no _selection_ context if (!rneedsContext.test(selectors)) { for (; i < l; i++) { for (cur = this[i]; cur && cur !== context; cur = cur.parentNode) { // Always skip document fragments if (cur.nodeType < 11 && (targets ? targets.index(cur) > -1 : // Don't pass non-elements to Sizzle cur.nodeType === 1 && jQuery.find.matchesSelector(cur, selectors))) { matched.push(cur); break; } } } } return this.pushStack(matched.length > 1 ? jQuery.uniqueSort(matched) : matched); }, // Determine the position of an element within the set index: function (elem) { // No argument, return index in parent if (!elem) { return this[0] && this[0].parentNode ? this.first().prevAll().length : -1; } // Index in selector if (typeof elem === "string") { return indexOf$1.call(jQuery(elem), this[0]); } // Locate the position of the desired element return indexOf$1.call(this, // If it receives a jQuery object, the first element is used elem.jquery ? elem[0] : elem); }, add: function (selector, context) { return this.pushStack(jQuery.uniqueSort(jQuery.merge(this.get(), jQuery(selector, context)))); }, addBack: function (selector) { return this.add(selector == null ? this.prevObject : this.prevObject.filter(selector)); } }); function sibling(cur, dir) { while ((cur = cur[dir]) && cur.nodeType !== 1) {} return cur; } jQuery.each({ parent: function (elem) { var parent = elem.parentNode; return parent && parent.nodeType !== 11 ? parent : null; }, parents: function (elem) { return dir(elem, "parentNode"); }, parentsUntil: function (elem, i, until) { return dir(elem, "parentNode", until); }, next: function (elem) { return sibling(elem, "nextSibling"); }, prev: function (elem) { return sibling(elem, "previousSibling"); }, nextAll: function (elem) { return dir(elem, "nextSibling"); }, prevAll: function (elem) { return dir(elem, "previousSibling"); }, nextUntil: function (elem, i, until) { return dir(elem, "nextSibling", until); }, prevUntil: function (elem, i, until) { return dir(elem, "previousSibling", until); }, siblings: function (elem) { return siblings((elem.parentNode || {}).firstChild, elem); }, children: function (elem) { return siblings(elem.firstChild); }, contents: function (elem) { if (nodeName(elem, "iframe")) { return elem.contentDocument; } // Support: IE 9 - 11 only, iOS 7 only, Android Browser <=4.3 only // Treat the template element as a regular one in browsers that // don't support it. if (nodeName(elem, "template")) { elem = elem.content || elem; } return jQuery.merge([], elem.childNodes); } }, function (name, fn) { jQuery.fn[name] = function (until, selector) { var matched = jQuery.map(this, fn, until); if (name.slice(-5) !== "Until") { selector = until; } if (selector && typeof selector === "string") { matched = jQuery.filter(selector, matched); } if (this.length > 1) { // Remove duplicates if (!guaranteedUnique[name]) { jQuery.uniqueSort(matched); } // Reverse order for parents* and prev-derivatives if (rparentsprev.test(name)) { matched.reverse(); } } return this.pushStack(matched); }; }); var rnothtmlwhite = /[^\x20\t\r\n\f]+/g; // Convert String-formatted options into Object-formatted ones function createOptions(options) { var object = {}; jQuery.each(options.match(rnothtmlwhite) || [], function (_, flag) { object[flag] = true; }); return object; } /* * Create a callback list using the following parameters: * * options: an optional list of space-separated options that will change how * the callback list behaves or a more traditional option object * * By default a callback list will act like an event callback list and can be * "fired" multiple times. * * Possible options: * * once: will ensure the callback list can only be fired once (like a Deferred) * * memory: will keep track of previous values and will call any callback added * after the list has been fired right away with the latest "memorized" * values (like a Deferred) * * unique: will ensure a callback can only be added once (no duplicate in the list) * * stopOnFalse: interrupt callings when a callback returns false * */ jQuery.Callbacks = function (options) { // Convert options from String-formatted to Object-formatted if needed // (we check in cache first) options = typeof options === "string" ? createOptions(options) : jQuery.extend({}, options); var // Flag to know if list is currently firing firing, // Last fire value for non-forgettable lists memory, // Flag to know if list was already fired fired, // Flag to prevent firing locked, // Actual callback list list = [], // Queue of execution data for repeatable lists queue = [], // Index of currently firing callback (modified by add/remove as needed) firingIndex = -1, // Fire callbacks fire = function () { // Enforce single-firing locked = locked || options.once; // Execute callbacks for all pending executions, // respecting firingIndex overrides and runtime changes fired = firing = true; for (; queue.length; firingIndex = -1) { memory = queue.shift(); while (++firingIndex < list.length) { // Run callback and check for early termination if (list[firingIndex].apply(memory[0], memory[1]) === false && options.stopOnFalse) { // Jump to end and forget the data so .add doesn't re-fire firingIndex = list.length; memory = false; } } } // Forget the data if we're done with it if (!options.memory) { memory = false; } firing = false; // Clean up if we're done firing for good if (locked) { // Keep an empty list if we have data for future add calls if (memory) { list = []; // Otherwise, this object is spent } else { list = ""; } } }, // Actual Callbacks object self = { // Add a callback or a collection of callbacks to the list add: function () { if (list) { // If we have memory from a past run, we should fire after adding if (memory && !firing) { firingIndex = list.length - 1; queue.push(memory); } (function add(args) { jQuery.each(args, function (_, arg) { if (isFunction(arg)) { if (!options.unique || !self.has(arg)) { list.push(arg); } } else if (arg && arg.length && toType(arg) !== "string") { // Inspect recursively add(arg); } }); })(arguments); if (memory && !firing) { fire(); } } return this; }, // Remove a callback from the list remove: function () { jQuery.each(arguments, function (_, arg) { var index; while ((index = jQuery.inArray(arg, list, index)) > -1) { list.splice(index, 1); // Handle firing indexes if (index <= firingIndex) { firingIndex--; } } }); return this; }, // Check if a given callback is in the list. // If no argument is given, return whether or not list has callbacks attached. has: function (fn) { return fn ? jQuery.inArray(fn, list) > -1 : list.length > 0; }, // Remove all callbacks from the list empty: function () { if (list) { list = []; } return this; }, // Disable .fire and .add // Abort any current/pending executions // Clear all callbacks and values disable: function () { locked = queue = []; list = memory = ""; return this; }, disabled: function () { return !list; }, // Disable .fire // Also disable .add unless we have memory (since it would have no effect) // Abort any pending executions lock: function () { locked = queue = []; if (!memory && !firing) { list = memory = ""; } return this; }, locked: function () { return !!locked; }, // Call all callbacks with the given context and arguments fireWith: function (context, args) { if (!locked) { args = args || []; args = [context, args.slice ? args.slice() : args]; queue.push(args); if (!firing) { fire(); } } return this; }, // Call all the callbacks with the given arguments fire: function () { self.fireWith(this, arguments); return this; }, // To know if the callbacks have already been called at least once fired: function () { return !!fired; } }; return self; }; function Identity(v) { return v; } function Thrower(ex) { throw ex; } function adoptValue(value, resolve, reject, noValue) { var method; try { // Check for promise aspect first to privilege synchronous behavior if (value && isFunction(method = value.promise)) { method.call(value).done(resolve).fail(reject); // Other thenables } else if (value && isFunction(method = value.then)) { method.call(value, resolve, reject); // Other non-thenables } else { // Control `resolve` arguments by letting Array#slice cast boolean `noValue` to integer: // * false: [ value ].slice( 0 ) => resolve( value ) // * true: [ value ].slice( 1 ) => resolve() resolve.apply(undefined, [value].slice(noValue)); } // For Promises/A+, convert exceptions into rejections // Since jQuery.when doesn't unwrap thenables, we can skip the extra checks appearing in // Deferred#then to conditionally suppress rejection. } catch (value) { // Support: Android 4.0 only // Strict mode functions invoked without .call/.apply get global-object context reject.apply(undefined, [value]); } } jQuery.extend({ Deferred: function (func) { var tuples = [// action, add listener, callbacks, // ... .then handlers, argument index, [final state] ["notify", "progress", jQuery.Callbacks("memory"), jQuery.Callbacks("memory"), 2], ["resolve", "done", jQuery.Callbacks("once memory"), jQuery.Callbacks("once memory"), 0, "resolved"], ["reject", "fail", jQuery.Callbacks("once memory"), jQuery.Callbacks("once memory"), 1, "rejected"]], state = "pending", promise = { state: function () { return state; }, always: function () { deferred.done(arguments).fail(arguments); return this; }, "catch": function (fn) { return promise.then(null, fn); }, // Keep pipe for back-compat pipe: function () { var fns = arguments; return jQuery.Deferred(function (newDefer) { jQuery.each(tuples, function (i, tuple) { // Map tuples (progress, done, fail) to arguments (done, fail, progress) var fn = isFunction(fns[tuple[4]]) && fns[tuple[4]]; // deferred.progress(function() { bind to newDefer or newDefer.notify }) // deferred.done(function() { bind to newDefer or newDefer.resolve }) // deferred.fail(function() { bind to newDefer or newDefer.reject }) deferred[tuple[1]](function () { var returned = fn && fn.apply(this, arguments); if (returned && isFunction(returned.promise)) { returned.promise().progress(newDefer.notify).done(newDefer.resolve).fail(newDefer.reject); } else { newDefer[tuple[0] + "With"](this, fn ? [returned] : arguments); } }); }); fns = null; }).promise(); }, then: function (onFulfilled, onRejected, onProgress) { var maxDepth = 0; function resolve(depth, deferred, handler, special) { return function () { var that = this, args = arguments, mightThrow = function () { var returned, then; // Support: Promises/A+ section 2.3.3.3.3 // https://promisesaplus.com/#point-59 // Ignore double-resolution attempts if (depth < maxDepth) { return; } returned = handler.apply(that, args); // Support: Promises/A+ section 2.3.1 // https://promisesaplus.com/#point-48 if (returned === deferred.promise()) { throw new TypeError("Thenable self-resolution"); } // Support: Promises/A+ sections 2.3.3.1, 3.5 // https://promisesaplus.com/#point-54 // https://promisesaplus.com/#point-75 // Retrieve `then` only once then = returned && (typeof returned === "object" || typeof returned === "function") && returned.then; // Handle a returned thenable if (isFunction(then)) { // Special processors (notify) just wait for resolution if (special) { then.call(returned, resolve(maxDepth, deferred, Identity, special), resolve(maxDepth, deferred, Thrower, special)); // Normal processors (resolve) also hook into progress } else { // ...and disregard older resolution values maxDepth++; then.call(returned, resolve(maxDepth, deferred, Identity, special), resolve(maxDepth, deferred, Thrower, special), resolve(maxDepth, deferred, Identity, deferred.notifyWith)); } // Handle all other returned values } else { // Only substitute handlers pass on context // and multiple values (non-spec behavior) if (handler !== Identity) { that = undefined; args = [returned]; } // Process the value(s) // Default process is resolve (special || deferred.resolveWith)(that, args); } }, // Only normal processors (resolve) catch and reject exceptions process = special ? mightThrow : function () { try { mightThrow(); } catch (e) { if (jQuery.Deferred.exceptionHook) { jQuery.Deferred.exceptionHook(e, process.stackTrace); } // Support: Promises/A+ section 2.3.3.3.4.1 // https://promisesaplus.com/#point-61 // Ignore post-resolution exceptions if (depth + 1 >= maxDepth) { // Only substitute handlers pass on context // and multiple values (non-spec behavior) if (handler !== Thrower) { that = undefined; args = [e]; } deferred.rejectWith(that, args); } } }; // Support: Promises/A+ section 2.3.3.3.1 // https://promisesaplus.com/#point-57 // Re-resolve promises immediately to dodge false rejection from // subsequent errors if (depth) { process(); } else { // Call an optional hook to record the stack, in case of exception // since it's otherwise lost when execution goes async if (jQuery.Deferred.getStackHook) { process.stackTrace = jQuery.Deferred.getStackHook(); } window.setTimeout(process); } }; } return jQuery.Deferred(function (newDefer) { // progress_handlers.add( ... ) tuples[0][3].add(resolve(0, newDefer, isFunction(onProgress) ? onProgress : Identity, newDefer.notifyWith)); // fulfilled_handlers.add( ... ) tuples[1][3].add(resolve(0, newDefer, isFunction(onFulfilled) ? onFulfilled : Identity)); // rejected_handlers.add( ... ) tuples[2][3].add(resolve(0, newDefer, isFunction(onRejected) ? onRejected : Thrower)); }).promise(); }, // Get a promise for this deferred // If obj is provided, the promise aspect is added to the object promise: function (obj) { return obj != null ? jQuery.extend(obj, promise) : promise; } }, deferred = {}; // Add list-specific methods jQuery.each(tuples, function (i, tuple) { var list = tuple[2], stateString = tuple[5]; // promise.progress = list.add // promise.done = list.add // promise.fail = list.add promise[tuple[1]] = list.add; // Handle state if (stateString) { list.add(function () { // state = "resolved" (i.e., fulfilled) // state = "rejected" state = stateString; }, // rejected_callbacks.disable // fulfilled_callbacks.disable tuples[3 - i][2].disable, // rejected_handlers.disable // fulfilled_handlers.disable tuples[3 - i][3].disable, // progress_callbacks.lock tuples[0][2].lock, // progress_handlers.lock tuples[0][3].lock); } // progress_handlers.fire // fulfilled_handlers.fire // rejected_handlers.fire list.add(tuple[3].fire); // deferred.notify = function() { deferred.notifyWith(...) } // deferred.resolve = function() { deferred.resolveWith(...) } // deferred.reject = function() { deferred.rejectWith(...) } deferred[tuple[0]] = function () { deferred[tuple[0] + "With"](this === deferred ? undefined : this, arguments); return this; }; // deferred.notifyWith = list.fireWith // deferred.resolveWith = list.fireWith // deferred.rejectWith = list.fireWith deferred[tuple[0] + "With"] = list.fireWith; }); // Make the deferred a promise promise.promise(deferred); // Call given func if any if (func) { func.call(deferred, deferred); } // All done! return deferred; }, // Deferred helper when: function (singleValue) { var // count of uncompleted subordinates remaining = arguments.length, // count of unprocessed arguments i = remaining, // subordinate fulfillment data resolveContexts = Array(i), resolveValues = slice.call(arguments), // the master Deferred master = jQuery.Deferred(), // subordinate callback factory updateFunc = function (i) { return function (value) { resolveContexts[i] = this; resolveValues[i] = arguments.length > 1 ? slice.call(arguments) : value; if (! --remaining) { master.resolveWith(resolveContexts, resolveValues); } }; }; // Single- and empty arguments are adopted like Promise.resolve if (remaining <= 1) { adoptValue(singleValue, master.done(updateFunc(i)).resolve, master.reject, !remaining); // Use .then() to unwrap secondary thenables (cf. gh-3000) if (master.state() === "pending" || isFunction(resolveValues[i] && resolveValues[i].then)) { return master.then(); } } // Multiple arguments are aggregated like Promise.all array elements while (i--) { adoptValue(resolveValues[i], updateFunc(i), master.reject); } return master.promise(); } }); // These usually indicate a programmer mistake during development, // warn about them ASAP rather than swallowing them by default. var rerrorNames = /^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/; jQuery.Deferred.exceptionHook = function (error, stack) { // Support: IE 8 - 9 only // Console exists when dev tools are open, which can happen at any time if (window.console && window.console.warn && error && rerrorNames.test(error.name)) { window.console.warn("jQuery.Deferred exception: " + error.message, error.stack, stack); } }; jQuery.readyException = function (error) { window.setTimeout(function () { throw error; }); }; // The deferred used on DOM ready var readyList = jQuery.Deferred(); jQuery.fn.ready = function (fn) { readyList.then(fn) // Wrap jQuery.readyException in a function so that the lookup // happens at the time of error handling instead of callback // registration. .catch(function (error) { jQuery.readyException(error); }); return this; }; jQuery.extend({ // Is the DOM ready to be used? Set to true once it occurs. isReady: false, // A counter to track how many items to wait for before // the ready event fires. See #6781 readyWait: 1, // Handle when the DOM is ready ready: function (wait) { // Abort if there are pending holds or we're already ready if (wait === true ? --jQuery.readyWait : jQuery.isReady) { return; } // Remember that the DOM is ready jQuery.isReady = true; // If a normal DOM Ready event fired, decrement, and wait if need be if (wait !== true && --jQuery.readyWait > 0) { return; } // If there are functions bound, to execute readyList.resolveWith(document$2, [jQuery]); } }); jQuery.ready.then = readyList.then; // The ready event handler and self cleanup method function completed() { document$2.removeEventListener("DOMContentLoaded", completed); window.removeEventListener("load", completed); jQuery.ready(); } // Catch cases where $(document).ready() is called // after the browser event has already occurred. // Support: IE <=9 - 10 only // Older IE sometimes signals "interactive" too soon if (document$2.readyState === "complete" || document$2.readyState !== "loading" && !document$2.documentElement.doScroll) { // Handle it asynchronously to allow scripts the opportunity to delay ready window.setTimeout(jQuery.ready); } else { // Use the handy event callback document$2.addEventListener("DOMContentLoaded", completed); // A fallback to window.onload, that will always work window.addEventListener("load", completed); } // Multifunctional method to get and set values of a collection // The value/s can optionally be executed if it's a function var access = function (elems, fn, key, value, chainable, emptyGet, raw) { var i = 0, len = elems.length, bulk = key == null; // Sets many values if (toType(key) === "object") { chainable = true; for (i in key) { access(elems, fn, i, key[i], true, emptyGet, raw); } // Sets one value } else if (value !== undefined) { chainable = true; if (!isFunction(value)) { raw = true; } if (bulk) { // Bulk operations run against the entire set if (raw) { fn.call(elems, value); fn = null; // ...except when executing function values } else { bulk = fn; fn = function (elem, key, value) { return bulk.call(jQuery(elem), value); }; } } if (fn) { for (; i < len; i++) { fn(elems[i], key, raw ? value : value.call(elems[i], i, fn(elems[i], key))); } } } if (chainable) { return elems; } // Gets if (bulk) { return fn.call(elems); } return len ? fn(elems[0], key) : emptyGet; }; // Matches dashed string for camelizing var rmsPrefix = /^-ms-/, rdashAlpha = /-([a-z])/g; // Used by camelCase as callback to replace() function fcamelCase(all, letter) { return letter.toUpperCase(); } // Convert dashed to camelCase; used by the css and data modules // Support: IE <=9 - 11, Edge 12 - 15 // Microsoft forgot to hump their vendor prefix (#9572) function camelCase(string) { return string.replace(rmsPrefix, "ms-").replace(rdashAlpha, fcamelCase); } var acceptData = function (owner) { // Accepts only: // - Node // - Node.ELEMENT_NODE // - Node.DOCUMENT_NODE // - Object // - Any return owner.nodeType === 1 || owner.nodeType === 9 || !+owner.nodeType; }; function Data() { this.expando = jQuery.expando + Data.uid++; } Data.uid = 1; Data.prototype = { cache: function (owner) { // Check if the owner object already has a cache var value = owner[this.expando]; // If not, create one if (!value) { value = {}; // We can accept data for non-element nodes in modern browsers, // but we should not, see #8335. // Always return an empty object. if (acceptData(owner)) { // If it is a node unlikely to be stringify-ed or looped over // use plain assignment if (owner.nodeType) { owner[this.expando] = value; // Otherwise secure it in a non-enumerable property // configurable must be true to allow the property to be // deleted when data is removed } else { Object.defineProperty(owner, this.expando, { value: value, configurable: true }); } } } return value; }, set: function (owner, data, value) { var prop, cache = this.cache(owner); // Handle: [ owner, key, value ] args // Always use camelCase key (gh-2257) if (typeof data === "string") { cache[camelCase(data)] = value; // Handle: [ owner, { properties } ] args } else { // Copy the properties one-by-one to the cache object for (prop in data) { cache[camelCase(prop)] = data[prop]; } } return cache; }, get: function (owner, key) { return key === undefined ? this.cache(owner) : // Always use camelCase key (gh-2257) owner[this.expando] && owner[this.expando][camelCase(key)]; }, access: function (owner, key, value) { // In cases where either: // // 1. No key was specified // 2. A string key was specified, but no value provided // // Take the "read" path and allow the get method to determine // which value to return, respectively either: // // 1. The entire cache object // 2. The data stored at the key // if (key === undefined || key && typeof key === "string" && value === undefined) { return this.get(owner, key); } // When the key is not a string, or both a key and value // are specified, set or extend (existing objects) with either: // // 1. An object of properties // 2. A key and value // this.set(owner, key, value); // Since the "set" path can have two possible entry points // return the expected data based on which path was taken[*] return value !== undefined ? value : key; }, remove: function (owner, key) { var i, cache = owner[this.expando]; if (cache === undefined) { return; } if (key !== undefined) { // Support array or space separated string of keys if (Array.isArray(key)) { // If key is an array of keys... // We always set camelCase keys, so remove that. key = key.map(camelCase); } else { key = camelCase(key); // If a key with the spaces exists, use it. // Otherwise, create an array by matching non-whitespace key = key in cache ? [key] : key.match(rnothtmlwhite) || []; } i = key.length; while (i--) { delete cache[key[i]]; } } // Remove the expando if there's no more data if (key === undefined || jQuery.isEmptyObject(cache)) { // Support: Chrome <=35 - 45 // Webkit & Blink performance suffers when deleting properties // from DOM nodes, so set to undefined instead // https://bugs.chromium.org/p/chromium/issues/detail?id=378607 (bug restricted) if (owner.nodeType) { owner[this.expando] = undefined; } else { delete owner[this.expando]; } } }, hasData: function (owner) { var cache = owner[this.expando]; return cache !== undefined && !jQuery.isEmptyObject(cache); } }; var dataPriv = new Data(); var dataUser = new Data(); // Implementation Summary // // 1. Enforce API surface and semantic compatibility with 1.9.x branch // 2. Improve the module's maintainability by reducing the storage // paths to a single mechanism. // 3. Use the same single mechanism to support "private" and "user" data. // 4. _Never_ expose "private" data to user code (TODO: Drop _data, _removeData) // 5. Avoid exposing implementation details on user objects (eg. expando properties) // 6. Provide a clear path for implementation upgrade to WeakMap in 2014 var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/, rmultiDash = /[A-Z]/g; function getData(data) { if (data === "true") { return true; } if (data === "false") { return false; } if (data === "null") { return null; } // Only convert to a number if it doesn't change the string if (data === +data + "") { return +data; } if (rbrace.test(data)) { return JSON.parse(data); } return data; } function dataAttr(elem, key, data) { var name; // If nothing was found internally, try to fetch any // data from the HTML5 data-* attribute if (data === undefined && elem.nodeType === 1) { name = "data-" + key.replace(rmultiDash, "-$&").toLowerCase(); data = elem.getAttribute(name); if (typeof data === "string") { try { data = getData(data); } catch (e) {} // Make sure we set the data so it isn't changed later dataUser.set(elem, key, data); } else { data = undefined; } } return data; } jQuery.extend({ hasData: function (elem) { return dataUser.hasData(elem) || dataPriv.hasData(elem); }, data: function (elem, name, data) { return dataUser.access(elem, name, data); }, removeData: function (elem, name) { dataUser.remove(elem, name); }, // TODO: Now that all calls to _data and _removeData have been replaced // with direct calls to dataPriv methods, these can be deprecated. _data: function (elem, name, data) { return dataPriv.access(elem, name, data); }, _removeData: function (elem, name) { dataPriv.remove(elem, name); } }); jQuery.fn.extend({ data: function (key, value) { var i, name, data, elem = this[0], attrs = elem && elem.attributes; // Gets all values if (key === undefined) { if (this.length) { data = dataUser.get(elem); if (elem.nodeType === 1 && !dataPriv.get(elem, "hasDataAttrs")) { i = attrs.length; while (i--) { // Support: IE 11 only // The attrs elements can be null (#14894) if (attrs[i]) { name = attrs[i].name; if (name.indexOf("data-") === 0) { name = camelCase(name.slice(5)); dataAttr(elem, name, data[name]); } } } dataPriv.set(elem, "hasDataAttrs", true); } } return data; } // Sets multiple values if (typeof key === "object") { return this.each(function () { dataUser.set(this, key); }); } return access(this, function (value) { var data; // The calling jQuery object (element matches) is not empty // (and therefore has an element appears at this[ 0 ]) and the // `value` parameter was not undefined. An empty jQuery object // will result in `undefined` for elem = this[ 0 ] which will // throw an exception if an attempt to read a data cache is made. if (elem && value === undefined) { // Attempt to get data from the cache // The key will always be camelCased in Data data = dataUser.get(elem, key); if (data !== undefined) { return data; } // Attempt to "discover" the data in // HTML5 custom data-* attrs data = dataAttr(elem, key); if (data !== undefined) { return data; } // We tried really hard, but the data doesn't exist. return; } // Set the data... this.each(function () { // We always store the camelCased key dataUser.set(this, key, value); }); }, null, value, arguments.length > 1, null, true); }, removeData: function (key) { return this.each(function () { dataUser.remove(this, key); }); } }); jQuery.extend({ queue: function (elem, type, data) { var queue; if (elem) { type = (type || "fx") + "queue"; queue = dataPriv.get(elem, type); // Speed up dequeue by getting out quickly if this is just a lookup if (data) { if (!queue || Array.isArray(data)) { queue = dataPriv.access(elem, type, jQuery.makeArray(data)); } else { queue.push(data); } } return queue || []; } }, dequeue: function (elem, type) { type = type || "fx"; var queue = jQuery.queue(elem, type), startLength = queue.length, fn = queue.shift(), hooks = jQuery._queueHooks(elem, type), next = function () { jQuery.dequeue(elem, type); }; // If the fx queue is dequeued, always remove the progress sentinel if (fn === "inprogress") { fn = queue.shift(); startLength--; } if (fn) { // Add a progress sentinel to prevent the fx queue from being // automatically dequeued if (type === "fx") { queue.unshift("inprogress"); } // Clear up the last queue stop function delete hooks.stop; fn.call(elem, next, hooks); } if (!startLength && hooks) { hooks.empty.fire(); } }, // Not public - generate a queueHooks object, or return the current one _queueHooks: function (elem, type) { var key = type + "queueHooks"; return dataPriv.get(elem, key) || dataPriv.access(elem, key, { empty: jQuery.Callbacks("once memory").add(function () { dataPriv.remove(elem, [type + "queue", key]); }) }); } }); jQuery.fn.extend({ queue: function (type, data) { var setter = 2; if (typeof type !== "string") { data = type; type = "fx"; setter--; } if (arguments.length < setter) { return jQuery.queue(this[0], type); } return data === undefined ? this : this.each(function () { var queue = jQuery.queue(this, type, data); // Ensure a hooks for this queue jQuery._queueHooks(this, type); if (type === "fx" && queue[0] !== "inprogress") { jQuery.dequeue(this, type); } }); }, dequeue: function (type) { return this.each(function () { jQuery.dequeue(this, type); }); }, clearQueue: function (type) { return this.queue(type || "fx", []); }, // Get a promise resolved when queues of a certain type // are emptied (fx is the type by default) promise: function (type, obj) { var tmp, count = 1, defer = jQuery.Deferred(), elements = this, i = this.length, resolve = function () { if (! --count) { defer.resolveWith(elements, [elements]); } }; if (typeof type !== "string") { obj = type; type = undefined; } type = type || "fx"; while (i--) { tmp = dataPriv.get(elements[i], type + "queueHooks"); if (tmp && tmp.empty) { count++; tmp.empty.add(resolve); } } resolve(); return defer.promise(obj); } }); var pnum = /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/.source; var rcssNum = new RegExp("^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i"); var cssExpand = ["Top", "Right", "Bottom", "Left"]; var isHiddenWithinTree = function (elem, el) { // isHiddenWithinTree might be called from jQuery#filter function; // in that case, element will be second argument elem = el || elem; // Inline style trumps all return elem.style.display === "none" || elem.style.display === "" && // Otherwise, check computed style // Support: Firefox <=43 - 45 // Disconnected elements can have computed display: none, so first confirm that elem is // in the document. jQuery.contains(elem.ownerDocument, elem) && jQuery.css(elem, "display") === "none"; }; var swap = function (elem, options, callback, args) { var ret, name, old = {}; // Remember the old values, and insert the new ones for (name in options) { old[name] = elem.style[name]; elem.style[name] = options[name]; } ret = callback.apply(elem, args || []); // Revert the old values for (name in options) { elem.style[name] = old[name]; } return ret; }; function adjustCSS(elem, prop, valueParts, tween) { var adjusted, scale, maxIterations = 20, currentValue = tween ? function () { return tween.cur(); } : function () { return jQuery.css(elem, prop, ""); }, initial = currentValue(), unit = valueParts && valueParts[3] || (jQuery.cssNumber[prop] ? "" : "px"), // Starting value computation is required for potential unit mismatches initialInUnit = (jQuery.cssNumber[prop] || unit !== "px" && +initial) && rcssNum.exec(jQuery.css(elem, prop)); if (initialInUnit && initialInUnit[3] !== unit) { // Support: Firefox <=54 // Halve the iteration target value to prevent interference from CSS upper bounds (gh-2144) initial = initial / 2; // Trust units reported by jQuery.css unit = unit || initialInUnit[3]; // Iteratively approximate from a nonzero starting point initialInUnit = +initial || 1; while (maxIterations--) { // Evaluate and update our best guess (doubling guesses that zero out). // Finish if the scale equals or crosses 1 (making the old*new product non-positive). jQuery.style(elem, prop, initialInUnit + unit); if ((1 - scale) * (1 - (scale = currentValue() / initial || 0.5)) <= 0) { maxIterations = 0; } initialInUnit = initialInUnit / scale; } initialInUnit = initialInUnit * 2; jQuery.style(elem, prop, initialInUnit + unit); // Make sure we update the tween properties later on valueParts = valueParts || []; } if (valueParts) { initialInUnit = +initialInUnit || +initial || 0; // Apply relative offset (+=/-=) if specified adjusted = valueParts[1] ? initialInUnit + (valueParts[1] + 1) * valueParts[2] : +valueParts[2]; if (tween) { tween.unit = unit; tween.start = initialInUnit; tween.end = adjusted; } } return adjusted; } var defaultDisplayMap = {}; function getDefaultDisplay(elem) { var temp, doc = elem.ownerDocument, nodeName = elem.nodeName, display = defaultDisplayMap[nodeName]; if (display) { return display; } temp = doc.body.appendChild(doc.createElement(nodeName)); display = jQuery.css(temp, "display"); temp.parentNode.removeChild(temp); if (display === "none") { display = "block"; } defaultDisplayMap[nodeName] = display; return display; } function showHide(elements, show) { var display, elem, values = [], index = 0, length = elements.length; // Determine new display value for elements that need to change for (; index < length; index++) { elem = elements[index]; if (!elem.style) { continue; } display = elem.style.display; if (show) { // Since we force visibility upon cascade-hidden elements, an immediate (and slow) // check is required in this first loop unless we have a nonempty display value (either // inline or about-to-be-restored) if (display === "none") { values[index] = dataPriv.get(elem, "display") || null; if (!values[index]) { elem.style.display = ""; } } if (elem.style.display === "" && isHiddenWithinTree(elem)) { values[index] = getDefaultDisplay(elem); } } else { if (display !== "none") { values[index] = "none"; // Remember what we're overwriting dataPriv.set(elem, "display", display); } } } // Set the display of the elements in a second loop to avoid constant reflow for (index = 0; index < length; index++) { if (values[index] != null) { elements[index].style.display = values[index]; } } return elements; } jQuery.fn.extend({ show: function () { return showHide(this, true); }, hide: function () { return showHide(this); }, toggle: function (state) { if (typeof state === "boolean") { return state ? this.show() : this.hide(); } return this.each(function () { if (isHiddenWithinTree(this)) { jQuery(this).show(); } else { jQuery(this).hide(); } }); } }); var rcheckableType = /^(?:checkbox|radio)$/i; var rtagName = /<([a-z][^\/\0>\x20\t\r\n\f]+)/i; var rscriptType = /^$|^module$|\/(?:java|ecma)script/i; // We have to close these tags to support XHTML (#13200) var wrapMap = { // Support: IE <=9 only option: [1, ""], // XHTML parsers do not magically insert elements in the // same way that tag soup parsers do. So we cannot shorten // this by omitting or other required elements. thead: [1, "", "
"], col: [2, "", "
"], tr: [2, "", "
"], td: [3, "", "
"], _default: [0, "", ""] }; // Support: IE <=9 only wrapMap.optgroup = wrapMap.option; wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead; wrapMap.th = wrapMap.td; function getAll(context, tag) { // Support: IE <=9 - 11 only // Use typeof to avoid zero-argument method invocation on host objects (#15151) var ret; if (typeof context.getElementsByTagName !== "undefined") { ret = context.getElementsByTagName(tag || "*"); } else if (typeof context.querySelectorAll !== "undefined") { ret = context.querySelectorAll(tag || "*"); } else { ret = []; } if (tag === undefined || tag && nodeName(context, tag)) { return jQuery.merge([context], ret); } return ret; } // Mark scripts as having already been evaluated function setGlobalEval(elems, refElements) { var i = 0, l = elems.length; for (; i < l; i++) { dataPriv.set(elems[i], "globalEval", !refElements || dataPriv.get(refElements[i], "globalEval")); } } var rhtml = /<|&#?\w+;/; function buildFragment(elems, context, scripts, selection, ignored) { var elem, tmp, tag, wrap, contains, j, fragment = context.createDocumentFragment(), nodes = [], i = 0, l = elems.length; for (; i < l; i++) { elem = elems[i]; if (elem || elem === 0) { // Add nodes directly if (toType(elem) === "object") { // Support: Android <=4.0 only, PhantomJS 1 only // push.apply(_, arraylike) throws on ancient WebKit jQuery.merge(nodes, elem.nodeType ? [elem] : elem); // Convert non-html into a text node } else if (!rhtml.test(elem)) { nodes.push(context.createTextNode(elem)); // Convert html into DOM nodes } else { tmp = tmp || fragment.appendChild(context.createElement("div")); // Deserialize a standard representation tag = (rtagName.exec(elem) || ["", ""])[1].toLowerCase(); wrap = wrapMap[tag] || wrapMap._default; tmp.innerHTML = wrap[1] + jQuery.htmlPrefilter(elem) + wrap[2]; // Descend through wrappers to the right content j = wrap[0]; while (j--) { tmp = tmp.lastChild; } // Support: Android <=4.0 only, PhantomJS 1 only // push.apply(_, arraylike) throws on ancient WebKit jQuery.merge(nodes, tmp.childNodes); // Remember the top-level container tmp = fragment.firstChild; // Ensure the created nodes are orphaned (#12392) tmp.textContent = ""; } } } // Remove wrapper from fragment fragment.textContent = ""; i = 0; while (elem = nodes[i++]) { // Skip elements already in the context collection (trac-4087) if (selection && jQuery.inArray(elem, selection) > -1) { if (ignored) { ignored.push(elem); } continue; } contains = jQuery.contains(elem.ownerDocument, elem); // Append to fragment tmp = getAll(fragment.appendChild(elem), "script"); // Preserve script evaluation history if (contains) { setGlobalEval(tmp); } // Capture executables if (scripts) { j = 0; while (elem = tmp[j++]) { if (rscriptType.test(elem.type || "")) { scripts.push(elem); } } } } return fragment; } (function () { var fragment = document$2.createDocumentFragment(), div = fragment.appendChild(document$2.createElement("div")), input = document$2.createElement("input"); // Support: Android 4.0 - 4.3 only // Check state lost if the name is set (#11217) // Support: Windows Web Apps (WWA) // `name` and `type` must use .setAttribute for WWA (#14901) input.setAttribute("type", "radio"); input.setAttribute("checked", "checked"); input.setAttribute("name", "t"); div.appendChild(input); // Support: Android <=4.1 only // Older WebKit doesn't clone checked state correctly in fragments support.checkClone = div.cloneNode(true).cloneNode(true).lastChild.checked; // Support: IE <=11 only // Make sure textarea (and checkbox) defaultValue is properly cloned div.innerHTML = ""; support.noCloneChecked = !!div.cloneNode(true).lastChild.defaultValue; })(); var documentElement = document$2.documentElement; var rkeyEvent = /^key/, rmouseEvent = /^(?:mouse|pointer|contextmenu|drag|drop)|click/, rtypenamespace = /^([^.]*)(?:\.(.+)|)/; function returnTrue() { return true; } function returnFalse() { return false; } // Support: IE <=9 only // See #13393 for more info function safeActiveElement() { try { return document$2.activeElement; } catch (err) {} } function on(elem, types, selector, data, fn, one) { var origFn, type; // Types can be a map of types/handlers if (typeof types === "object") { // ( types-Object, selector, data ) if (typeof selector !== "string") { // ( types-Object, data ) data = data || selector; selector = undefined; } for (type in types) { on(elem, type, selector, data, types[type], one); } return elem; } if (data == null && fn == null) { // ( types, fn ) fn = selector; data = selector = undefined; } else if (fn == null) { if (typeof selector === "string") { // ( types, selector, fn ) fn = data; data = undefined; } else { // ( types, data, fn ) fn = data; data = selector; selector = undefined; } } if (fn === false) { fn = returnFalse; } else if (!fn) { return elem; } if (one === 1) { origFn = fn; fn = function (event) { // Can use an empty set, since event contains the info jQuery().off(event); return origFn.apply(this, arguments); }; // Use same guid so caller can remove using origFn fn.guid = origFn.guid || (origFn.guid = jQuery.guid++); } return elem.each(function () { jQuery.event.add(this, types, fn, data, selector); }); } /* * Helper functions for managing events -- not part of the public interface. * Props to Dean Edwards' addEvent library for many of the ideas. */ jQuery.event = { global: {}, add: function (elem, types, handler, data, selector) { var handleObjIn, eventHandle, tmp, events, t, handleObj, special, handlers, type, namespaces, origType, elemData = dataPriv.get(elem); // Don't attach events to noData or text/comment nodes (but allow plain objects) if (!elemData) { return; } // Caller can pass in an object of custom data in lieu of the handler if (handler.handler) { handleObjIn = handler; handler = handleObjIn.handler; selector = handleObjIn.selector; } // Ensure that invalid selectors throw exceptions at attach time // Evaluate against documentElement in case elem is a non-element node (e.g., document) if (selector) { jQuery.find.matchesSelector(documentElement, selector); } // Make sure that the handler has a unique ID, used to find/remove it later if (!handler.guid) { handler.guid = jQuery.guid++; } // Init the element's event structure and main handler, if this is the first if (!(events = elemData.events)) { events = elemData.events = {}; } if (!(eventHandle = elemData.handle)) { eventHandle = elemData.handle = function (e) { // Discard the second event of a jQuery.event.trigger() and // when an event is called after a page has unloaded return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ? jQuery.event.dispatch.apply(elem, arguments) : undefined; }; } // Handle multiple events separated by a space types = (types || "").match(rnothtmlwhite) || [""]; t = types.length; while (t--) { tmp = rtypenamespace.exec(types[t]) || []; type = origType = tmp[1]; namespaces = (tmp[2] || "").split(".").sort(); // There *must* be a type, no attaching namespace-only handlers if (!type) { continue; } // If event changes its type, use the special event handlers for the changed type special = jQuery.event.special[type] || {}; // If selector defined, determine special event api type, otherwise given type type = (selector ? special.delegateType : special.bindType) || type; // Update special based on newly reset type special = jQuery.event.special[type] || {}; // handleObj is passed to all event handlers handleObj = jQuery.extend({ type: type, origType: origType, data: data, handler: handler, guid: handler.guid, selector: selector, needsContext: selector && jQuery.expr.match.needsContext.test(selector), namespace: namespaces.join(".") }, handleObjIn); // Init the event handler queue if we're the first if (!(handlers = events[type])) { handlers = events[type] = []; handlers.delegateCount = 0; // Only use addEventListener if the special events handler returns false if (!special.setup || special.setup.call(elem, data, namespaces, eventHandle) === false) { if (elem.addEventListener) { elem.addEventListener(type, eventHandle); } } } if (special.add) { special.add.call(elem, handleObj); if (!handleObj.handler.guid) { handleObj.handler.guid = handler.guid; } } // Add to the element's handler list, delegates in front if (selector) { handlers.splice(handlers.delegateCount++, 0, handleObj); } else { handlers.push(handleObj); } // Keep track of which events have ever been used, for event optimization jQuery.event.global[type] = true; } }, // Detach an event or set of events from an element remove: function (elem, types, handler, selector, mappedTypes) { var j, origCount, tmp, events, t, handleObj, special, handlers, type, namespaces, origType, elemData = dataPriv.hasData(elem) && dataPriv.get(elem); if (!elemData || !(events = elemData.events)) { return; } // Once for each type.namespace in types; type may be omitted types = (types || "").match(rnothtmlwhite) || [""]; t = types.length; while (t--) { tmp = rtypenamespace.exec(types[t]) || []; type = origType = tmp[1]; namespaces = (tmp[2] || "").split(".").sort(); // Unbind all events (on this namespace, if provided) for the element if (!type) { for (type in events) { jQuery.event.remove(elem, type + types[t], handler, selector, true); } continue; } special = jQuery.event.special[type] || {}; type = (selector ? special.delegateType : special.bindType) || type; handlers = events[type] || []; tmp = tmp[2] && new RegExp("(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)"); // Remove matching events origCount = j = handlers.length; while (j--) { handleObj = handlers[j]; if ((mappedTypes || origType === handleObj.origType) && (!handler || handler.guid === handleObj.guid) && (!tmp || tmp.test(handleObj.namespace)) && (!selector || selector === handleObj.selector || selector === "**" && handleObj.selector)) { handlers.splice(j, 1); if (handleObj.selector) { handlers.delegateCount--; } if (special.remove) { special.remove.call(elem, handleObj); } } } // Remove generic event handler if we removed something and no more handlers exist // (avoids potential for endless recursion during removal of special event handlers) if (origCount && !handlers.length) { if (!special.teardown || special.teardown.call(elem, namespaces, elemData.handle) === false) { jQuery.removeEvent(elem, type, elemData.handle); } delete events[type]; } } // Remove data and the expando if it's no longer used if (jQuery.isEmptyObject(events)) { dataPriv.remove(elem, "handle events"); } }, dispatch: function (nativeEvent) { // Make a writable jQuery.Event from the native event object var event = jQuery.event.fix(nativeEvent); var i, j, ret, matched, handleObj, handlerQueue, args = new Array(arguments.length), handlers = (dataPriv.get(this, "events") || {})[event.type] || [], special = jQuery.event.special[event.type] || {}; // Use the fix-ed jQuery.Event rather than the (read-only) native event args[0] = event; for (i = 1; i < arguments.length; i++) { args[i] = arguments[i]; } event.delegateTarget = this; // Call the preDispatch hook for the mapped type, and let it bail if desired if (special.preDispatch && special.preDispatch.call(this, event) === false) { return; } // Determine handlers handlerQueue = jQuery.event.handlers.call(this, event, handlers); // Run delegates first; they may want to stop propagation beneath us i = 0; while ((matched = handlerQueue[i++]) && !event.isPropagationStopped()) { event.currentTarget = matched.elem; j = 0; while ((handleObj = matched.handlers[j++]) && !event.isImmediatePropagationStopped()) { // Triggered event must either 1) have no namespace, or 2) have namespace(s) // a subset or equal to those in the bound event (both can have no namespace). if (!event.rnamespace || event.rnamespace.test(handleObj.namespace)) { event.handleObj = handleObj; event.data = handleObj.data; ret = ((jQuery.event.special[handleObj.origType] || {}).handle || handleObj.handler).apply(matched.elem, args); if (ret !== undefined) { if ((event.result = ret) === false) { event.preventDefault(); event.stopPropagation(); } } } } } // Call the postDispatch hook for the mapped type if (special.postDispatch) { special.postDispatch.call(this, event); } return event.result; }, handlers: function (event, handlers) { var i, handleObj, sel, matchedHandlers, matchedSelectors, handlerQueue = [], delegateCount = handlers.delegateCount, cur = event.target; // Find delegate handlers if (delegateCount && // Support: IE <=9 // Black-hole SVG instance trees (trac-13180) cur.nodeType && // Support: Firefox <=42 // Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861) // https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click // Support: IE 11 only // ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343) !(event.type === "click" && event.button >= 1)) { for (; cur !== this; cur = cur.parentNode || this) { // Don't check non-elements (#13208) // Don't process clicks on disabled elements (#6911, #8165, #11382, #11764) if (cur.nodeType === 1 && !(event.type === "click" && cur.disabled === true)) { matchedHandlers = []; matchedSelectors = {}; for (i = 0; i < delegateCount; i++) { handleObj = handlers[i]; // Don't conflict with Object.prototype properties (#13203) sel = handleObj.selector + " "; if (matchedSelectors[sel] === undefined) { matchedSelectors[sel] = handleObj.needsContext ? jQuery(sel, this).index(cur) > -1 : jQuery.find(sel, this, null, [cur]).length; } if (matchedSelectors[sel]) { matchedHandlers.push(handleObj); } } if (matchedHandlers.length) { handlerQueue.push({ elem: cur, handlers: matchedHandlers }); } } } } // Add the remaining (directly-bound) handlers cur = this; if (delegateCount < handlers.length) { handlerQueue.push({ elem: cur, handlers: handlers.slice(delegateCount) }); } return handlerQueue; }, addProp: function (name, hook) { Object.defineProperty(jQuery.Event.prototype, name, { enumerable: true, configurable: true, get: isFunction(hook) ? function () { if (this.originalEvent) { return hook(this.originalEvent); } } : function () { if (this.originalEvent) { return this.originalEvent[name]; } }, set: function (value) { Object.defineProperty(this, name, { enumerable: true, configurable: true, writable: true, value: value }); } }); }, fix: function (originalEvent) { return originalEvent[jQuery.expando] ? originalEvent : new jQuery.Event(originalEvent); }, special: { load: { // Prevent triggered image.load events from bubbling to window.load noBubble: true }, focus: { // Fire native event if possible so blur/focus sequence is correct trigger: function () { if (this !== safeActiveElement() && this.focus) { this.focus(); return false; } }, delegateType: "focusin" }, blur: { trigger: function () { if (this === safeActiveElement() && this.blur) { this.blur(); return false; } }, delegateType: "focusout" }, click: { // For checkbox, fire native event so checked state will be right trigger: function () { if (this.type === "checkbox" && this.click && nodeName(this, "input")) { this.click(); return false; } }, // For cross-browser consistency, don't fire native .click() on links _default: function (event) { return nodeName(event.target, "a"); } }, beforeunload: { postDispatch: function (event) { // Support: Firefox 20+ // Firefox doesn't alert if the returnValue field is not set. if (event.result !== undefined && event.originalEvent) { event.originalEvent.returnValue = event.result; } } } } }; jQuery.removeEvent = function (elem, type, handle) { // This "if" is needed for plain objects if (elem.removeEventListener) { elem.removeEventListener(type, handle); } }; jQuery.Event = function (src, props) { // Allow instantiation without the 'new' keyword if (!(this instanceof jQuery.Event)) { return new jQuery.Event(src, props); } // Event object if (src && src.type) { this.originalEvent = src; this.type = src.type; // Events bubbling up the document may have been marked as prevented // by a handler lower down the tree; reflect the correct value. this.isDefaultPrevented = src.defaultPrevented || src.defaultPrevented === undefined && // Support: Android <=2.3 only src.returnValue === false ? returnTrue : returnFalse; // Create target properties // Support: Safari <=6 - 7 only // Target should not be a text node (#504, #13143) this.target = src.target && src.target.nodeType === 3 ? src.target.parentNode : src.target; this.currentTarget = src.currentTarget; this.relatedTarget = src.relatedTarget; // Event type } else { this.type = src; } // Put explicitly provided properties onto the event object if (props) { jQuery.extend(this, props); } // Create a timestamp if incoming event doesn't have one this.timeStamp = src && src.timeStamp || Date.now(); // Mark it as fixed this[jQuery.expando] = true; }; // jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding // https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html jQuery.Event.prototype = { constructor: jQuery.Event, isDefaultPrevented: returnFalse, isPropagationStopped: returnFalse, isImmediatePropagationStopped: returnFalse, isSimulated: false, preventDefault: function () { var e = this.originalEvent; this.isDefaultPrevented = returnTrue; if (e && !this.isSimulated) { e.preventDefault(); } }, stopPropagation: function () { var e = this.originalEvent; this.isPropagationStopped = returnTrue; if (e && !this.isSimulated) { e.stopPropagation(); } }, stopImmediatePropagation: function () { var e = this.originalEvent; this.isImmediatePropagationStopped = returnTrue; if (e && !this.isSimulated) { e.stopImmediatePropagation(); } this.stopPropagation(); } }; // Includes all common event props including KeyEvent and MouseEvent specific props jQuery.each({ altKey: true, bubbles: true, cancelable: true, changedTouches: true, ctrlKey: true, detail: true, eventPhase: true, metaKey: true, pageX: true, pageY: true, shiftKey: true, view: true, "char": true, charCode: true, key: true, keyCode: true, button: true, buttons: true, clientX: true, clientY: true, offsetX: true, offsetY: true, pointerId: true, pointerType: true, screenX: true, screenY: true, targetTouches: true, toElement: true, touches: true, which: function (event) { var button = event.button; // Add which for key events if (event.which == null && rkeyEvent.test(event.type)) { return event.charCode != null ? event.charCode : event.keyCode; } // Add which for click: 1 === left; 2 === middle; 3 === right if (!event.which && button !== undefined && rmouseEvent.test(event.type)) { if (button & 1) { return 1; } if (button & 2) { return 3; } if (button & 4) { return 2; } return 0; } return event.which; } }, jQuery.event.addProp); // Create mouseenter/leave events using mouseover/out and event-time checks // so that event delegation works in jQuery. // Do the same for pointerenter/pointerleave and pointerover/pointerout // // Support: Safari 7 only // Safari sends mouseenter too often; see: // https://bugs.chromium.org/p/chromium/issues/detail?id=470258 // for the description of the bug (it existed in older Chrome versions as well). jQuery.each({ mouseenter: "mouseover", mouseleave: "mouseout", pointerenter: "pointerover", pointerleave: "pointerout" }, function (orig, fix) { jQuery.event.special[orig] = { delegateType: fix, bindType: fix, handle: function (event) { var ret, target = this, related = event.relatedTarget, handleObj = event.handleObj; // For mouseenter/leave call the handler if related is outside the target. // NB: No relatedTarget if the mouse left/entered the browser window if (!related || related !== target && !jQuery.contains(target, related)) { event.type = handleObj.origType; ret = handleObj.handler.apply(this, arguments); event.type = fix; } return ret; } }; }); jQuery.fn.extend({ on: function (types, selector, data, fn) { return on(this, types, selector, data, fn); }, one: function (types, selector, data, fn) { return on(this, types, selector, data, fn, 1); }, off: function (types, selector, fn) { var handleObj, type; if (types && types.preventDefault && types.handleObj) { // ( event ) dispatched jQuery.Event handleObj = types.handleObj; jQuery(types.delegateTarget).off(handleObj.namespace ? handleObj.origType + "." + handleObj.namespace : handleObj.origType, handleObj.selector, handleObj.handler); return this; } if (typeof types === "object") { // ( types-object [, selector] ) for (type in types) { this.off(type, selector, types[type]); } return this; } if (selector === false || typeof selector === "function") { // ( types [, fn] ) fn = selector; selector = undefined; } if (fn === false) { fn = returnFalse; } return this.each(function () { jQuery.event.remove(this, types, fn, selector); }); } }); var /* eslint-disable max-len */ // See https://github.com/eslint/eslint/issues/3229 rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([a-z][^\/\0>\x20\t\r\n\f]*)[^>]*)\/>/gi, /* eslint-enable */ // Support: IE <=10 - 11, Edge 12 - 13 only // In IE/Edge using regex groups here causes severe slowdowns. // See https://connect.microsoft.com/IE/feedback/details/1736512/ rnoInnerhtml = /\s*$/g; // Prefer a tbody over its parent table for containing new rows function manipulationTarget(elem, content) { if (nodeName(elem, "table") && nodeName(content.nodeType !== 11 ? content : content.firstChild, "tr")) { return jQuery(elem).children("tbody")[0] || elem; } return elem; } // Replace/restore the type attribute of script elements for safe DOM manipulation function disableScript(elem) { elem.type = (elem.getAttribute("type") !== null) + "/" + elem.type; return elem; } function restoreScript(elem) { if ((elem.type || "").slice(0, 5) === "true/") { elem.type = elem.type.slice(5); } else { elem.removeAttribute("type"); } return elem; } function cloneCopyEvent(src, dest) { var i, l, type, pdataOld, pdataCur, udataOld, udataCur, events; if (dest.nodeType !== 1) { return; } // 1. Copy private data: events, handlers, etc. if (dataPriv.hasData(src)) { pdataOld = dataPriv.access(src); pdataCur = dataPriv.set(dest, pdataOld); events = pdataOld.events; if (events) { delete pdataCur.handle; pdataCur.events = {}; for (type in events) { for (i = 0, l = events[type].length; i < l; i++) { jQuery.event.add(dest, type, events[type][i]); } } } } // 2. Copy user data if (dataUser.hasData(src)) { udataOld = dataUser.access(src); udataCur = jQuery.extend({}, udataOld); dataUser.set(dest, udataCur); } } // Fix IE bugs, see support tests function fixInput(src, dest) { var nodeName = dest.nodeName.toLowerCase(); // Fails to persist the checked state of a cloned checkbox or radio button. if (nodeName === "input" && rcheckableType.test(src.type)) { dest.checked = src.checked; // Fails to return the selected option to the default selected state when cloning options } else if (nodeName === "input" || nodeName === "textarea") { dest.defaultValue = src.defaultValue; } } function domManip(collection, args, callback, ignored) { // Flatten any nested arrays args = concat.apply([], args); var fragment, first, scripts, hasScripts, node, doc, i = 0, l = collection.length, iNoClone = l - 1, value = args[0], valueIsFunction = isFunction(value); // We can't cloneNode fragments that contain checked, in WebKit if (valueIsFunction || l > 1 && typeof value === "string" && !support.checkClone && rchecked.test(value)) { return collection.each(function (index) { var self = collection.eq(index); if (valueIsFunction) { args[0] = value.call(this, index, self.html()); } domManip(self, args, callback, ignored); }); } if (l) { fragment = buildFragment(args, collection[0].ownerDocument, false, collection, ignored); first = fragment.firstChild; if (fragment.childNodes.length === 1) { fragment = first; } // Require either new content or an interest in ignored elements to invoke the callback if (first || ignored) { scripts = jQuery.map(getAll(fragment, "script"), disableScript); hasScripts = scripts.length; // Use the original fragment for the last item // instead of the first because it can end up // being emptied incorrectly in certain situations (#8070). for (; i < l; i++) { node = fragment; if (i !== iNoClone) { node = jQuery.clone(node, true, true); // Keep references to cloned scripts for later restoration if (hasScripts) { // Support: Android <=4.0 only, PhantomJS 1 only // push.apply(_, arraylike) throws on ancient WebKit jQuery.merge(scripts, getAll(node, "script")); } } callback.call(collection[i], node, i); } if (hasScripts) { doc = scripts[scripts.length - 1].ownerDocument; // Reenable scripts jQuery.map(scripts, restoreScript); // Evaluate executable scripts on first document insertion for (i = 0; i < hasScripts; i++) { node = scripts[i]; if (rscriptType.test(node.type || "") && !dataPriv.access(node, "globalEval") && jQuery.contains(doc, node)) { if (node.src && (node.type || "").toLowerCase() !== "module") { // Optional AJAX dependency, but won't run scripts if not present if (jQuery._evalUrl) { jQuery._evalUrl(node.src); } } else { DOMEval(node.textContent.replace(rcleanScript, ""), doc, node); } } } } } } return collection; } function remove(elem, selector, keepData) { var node, nodes = selector ? jQuery.filter(selector, elem) : elem, i = 0; for (; (node = nodes[i]) != null; i++) { if (!keepData && node.nodeType === 1) { jQuery.cleanData(getAll(node)); } if (node.parentNode) { if (keepData && jQuery.contains(node.ownerDocument, node)) { setGlobalEval(getAll(node, "script")); } node.parentNode.removeChild(node); } } return elem; } jQuery.extend({ htmlPrefilter: function (html) { return html.replace(rxhtmlTag, "<$1>"); }, clone: function (elem, dataAndEvents, deepDataAndEvents) { var i, l, srcElements, destElements, clone = elem.cloneNode(true), inPage = jQuery.contains(elem.ownerDocument, elem); // Fix IE cloning issues if (!support.noCloneChecked && (elem.nodeType === 1 || elem.nodeType === 11) && !jQuery.isXMLDoc(elem)) { // We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2 destElements = getAll(clone); srcElements = getAll(elem); for (i = 0, l = srcElements.length; i < l; i++) { fixInput(srcElements[i], destElements[i]); } } // Copy the events from the original to the clone if (dataAndEvents) { if (deepDataAndEvents) { srcElements = srcElements || getAll(elem); destElements = destElements || getAll(clone); for (i = 0, l = srcElements.length; i < l; i++) { cloneCopyEvent(srcElements[i], destElements[i]); } } else { cloneCopyEvent(elem, clone); } } // Preserve script evaluation history destElements = getAll(clone, "script"); if (destElements.length > 0) { setGlobalEval(destElements, !inPage && getAll(elem, "script")); } // Return the cloned set return clone; }, cleanData: function (elems) { var data, elem, type, special = jQuery.event.special, i = 0; for (; (elem = elems[i]) !== undefined; i++) { if (acceptData(elem)) { if (data = elem[dataPriv.expando]) { if (data.events) { for (type in data.events) { if (special[type]) { jQuery.event.remove(elem, type); // This is a shortcut to avoid jQuery.event.remove's overhead } else { jQuery.removeEvent(elem, type, data.handle); } } } // Support: Chrome <=35 - 45+ // Assign undefined instead of using delete, see Data#remove elem[dataPriv.expando] = undefined; } if (elem[dataUser.expando]) { // Support: Chrome <=35 - 45+ // Assign undefined instead of using delete, see Data#remove elem[dataUser.expando] = undefined; } } } } }); jQuery.fn.extend({ detach: function (selector) { return remove(this, selector, true); }, remove: function (selector) { return remove(this, selector); }, text: function (value) { return access(this, function (value) { return value === undefined ? jQuery.text(this) : this.empty().each(function () { if (this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9) { this.textContent = value; } }); }, null, value, arguments.length); }, append: function () { return domManip(this, arguments, function (elem) { if (this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9) { var target = manipulationTarget(this, elem); target.appendChild(elem); } }); }, prepend: function () { return domManip(this, arguments, function (elem) { if (this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9) { var target = manipulationTarget(this, elem); target.insertBefore(elem, target.firstChild); } }); }, before: function () { return domManip(this, arguments, function (elem) { if (this.parentNode) { this.parentNode.insertBefore(elem, this); } }); }, after: function () { return domManip(this, arguments, function (elem) { if (this.parentNode) { this.parentNode.insertBefore(elem, this.nextSibling); } }); }, empty: function () { var elem, i = 0; for (; (elem = this[i]) != null; i++) { if (elem.nodeType === 1) { // Prevent memory leaks jQuery.cleanData(getAll(elem, false)); // Remove any remaining nodes elem.textContent = ""; } } return this; }, clone: function (dataAndEvents, deepDataAndEvents) { dataAndEvents = dataAndEvents == null ? false : dataAndEvents; deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents; return this.map(function () { return jQuery.clone(this, dataAndEvents, deepDataAndEvents); }); }, html: function (value) { return access(this, function (value) { var elem = this[0] || {}, i = 0, l = this.length; if (value === undefined && elem.nodeType === 1) { return elem.innerHTML; } // See if we can take a shortcut and just use innerHTML if (typeof value === "string" && !rnoInnerhtml.test(value) && !wrapMap[(rtagName.exec(value) || ["", ""])[1].toLowerCase()]) { value = jQuery.htmlPrefilter(value); try { for (; i < l; i++) { elem = this[i] || {}; // Remove element nodes and prevent memory leaks if (elem.nodeType === 1) { jQuery.cleanData(getAll(elem, false)); elem.innerHTML = value; } } elem = 0; // If using innerHTML throws an exception, use the fallback method } catch (e) {} } if (elem) { this.empty().append(value); } }, null, value, arguments.length); }, replaceWith: function () { var ignored = []; // Make the changes, replacing each non-ignored context element with the new content return domManip(this, arguments, function (elem) { var parent = this.parentNode; if (jQuery.inArray(this, ignored) < 0) { jQuery.cleanData(getAll(this)); if (parent) { parent.replaceChild(elem, this); } } // Force callback invocation }, ignored); } }); jQuery.each({ appendTo: "append", prependTo: "prepend", insertBefore: "before", insertAfter: "after", replaceAll: "replaceWith" }, function (name, original) { jQuery.fn[name] = function (selector) { var elems, ret = [], insert = jQuery(selector), last = insert.length - 1, i = 0; for (; i <= last; i++) { elems = i === last ? this : this.clone(true); jQuery(insert[i])[original](elems); // Support: Android <=4.0 only, PhantomJS 1 only // .get() because push.apply(_, arraylike) throws on ancient WebKit push.apply(ret, elems.get()); } return this.pushStack(ret); }; }); var rnumnonpx = new RegExp("^(" + pnum + ")(?!px)[a-z%]+$", "i"); var getStyles = function (elem) { // Support: IE <=11 only, Firefox <=30 (#15098, #14150) // IE throws on elements created in popups // FF meanwhile throws on frame elements through "defaultView.getComputedStyle" var view = elem.ownerDocument.defaultView; if (!view || !view.opener) { view = window; } return view.getComputedStyle(elem); }; var rboxStyle = new RegExp(cssExpand.join("|"), "i"); (function () { // Executing both pixelPosition & boxSizingReliable tests require only one layout // so they're executed at the same time to save the second computation. function computeStyleTests() { // This is a singleton, we need to execute it only once if (!div) { return; } container.style.cssText = "position:absolute;left:-11111px;width:60px;" + "margin-top:1px;padding:0;border:0"; div.style.cssText = "position:relative;display:block;box-sizing:border-box;overflow:scroll;" + "margin:auto;border:1px;padding:1px;" + "width:60%;top:1%"; documentElement.appendChild(container).appendChild(div); var divStyle = window.getComputedStyle(div); pixelPositionVal = divStyle.top !== "1%"; // Support: Android 4.0 - 4.3 only, Firefox <=3 - 44 reliableMarginLeftVal = roundPixelMeasures(divStyle.marginLeft) === 12; // Support: Android 4.0 - 4.3 only, Safari <=9.1 - 10.1, iOS <=7.0 - 9.3 // Some styles come back with percentage values, even though they shouldn't div.style.right = "60%"; pixelBoxStylesVal = roundPixelMeasures(divStyle.right) === 36; // Support: IE 9 - 11 only // Detect misreporting of content dimensions for box-sizing:border-box elements boxSizingReliableVal = roundPixelMeasures(divStyle.width) === 36; // Support: IE 9 only // Detect overflow:scroll screwiness (gh-3699) div.style.position = "absolute"; scrollboxSizeVal = div.offsetWidth === 36 || "absolute"; documentElement.removeChild(container); // Nullify the div so it wouldn't be stored in the memory and // it will also be a sign that checks already performed div = null; } function roundPixelMeasures(measure) { return Math.round(parseFloat(measure)); } var pixelPositionVal, boxSizingReliableVal, scrollboxSizeVal, pixelBoxStylesVal, reliableMarginLeftVal, container = document$2.createElement("div"), div = document$2.createElement("div"); // Finish early in limited (non-browser) environments if (!div.style) { return; } // Support: IE <=9 - 11 only // Style of cloned element affects source element cloned (#8908) div.style.backgroundClip = "content-box"; div.cloneNode(true).style.backgroundClip = ""; support.clearCloneStyle = div.style.backgroundClip === "content-box"; jQuery.extend(support, { boxSizingReliable: function () { computeStyleTests(); return boxSizingReliableVal; }, pixelBoxStyles: function () { computeStyleTests(); return pixelBoxStylesVal; }, pixelPosition: function () { computeStyleTests(); return pixelPositionVal; }, reliableMarginLeft: function () { computeStyleTests(); return reliableMarginLeftVal; }, scrollboxSize: function () { computeStyleTests(); return scrollboxSizeVal; } }); })(); function curCSS(elem, name, computed) { var width, minWidth, maxWidth, ret, // Support: Firefox 51+ // Retrieving style before computed somehow // fixes an issue with getting wrong values // on detached elements style = elem.style; computed = computed || getStyles(elem); // getPropertyValue is needed for: // .css('filter') (IE 9 only, #12537) // .css('--customProperty) (#3144) if (computed) { ret = computed.getPropertyValue(name) || computed[name]; if (ret === "" && !jQuery.contains(elem.ownerDocument, elem)) { ret = jQuery.style(elem, name); } // A tribute to the "awesome hack by Dean Edwards" // Android Browser returns percentage for some values, // but width seems to be reliably pixels. // This is against the CSSOM draft spec: // https://drafts.csswg.org/cssom/#resolved-values if (!support.pixelBoxStyles() && rnumnonpx.test(ret) && rboxStyle.test(name)) { // Remember the original values width = style.width; minWidth = style.minWidth; maxWidth = style.maxWidth; // Put in the new values to get a computed value out style.minWidth = style.maxWidth = style.width = ret; ret = computed.width; // Revert the changed values style.width = width; style.minWidth = minWidth; style.maxWidth = maxWidth; } } return ret !== undefined ? // Support: IE <=9 - 11 only // IE returns zIndex value as an integer. ret + "" : ret; } function addGetHookIf(conditionFn, hookFn) { // Define the hook, we'll check on the first run if it's really needed. return { get: function () { if (conditionFn()) { // Hook not needed (or it's not possible to use it due // to missing dependency), remove it. delete this.get; return; } // Hook needed; redefine it so that the support test is not executed again. return (this.get = hookFn).apply(this, arguments); } }; } var // Swappable if display is none or starts with table // except "table", "table-cell", or "table-caption" // See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display rdisplayswap = /^(none|table(?!-c[ea]).+)/, rcustomProp = /^--/, cssShow = { position: "absolute", visibility: "hidden", display: "block" }, cssNormalTransform = { letterSpacing: "0", fontWeight: "400" }, cssPrefixes = ["Webkit", "Moz", "ms"], emptyStyle = document$2.createElement("div").style; // Return a css property mapped to a potentially vendor prefixed property function vendorPropName(name) { // Shortcut for names that are not vendor prefixed if (name in emptyStyle) { return name; } // Check for vendor prefixed names var capName = name[0].toUpperCase() + name.slice(1), i = cssPrefixes.length; while (i--) { name = cssPrefixes[i] + capName; if (name in emptyStyle) { return name; } } } // Return a property mapped along what jQuery.cssProps suggests or to // a vendor prefixed property. function finalPropName(name) { var ret = jQuery.cssProps[name]; if (!ret) { ret = jQuery.cssProps[name] = vendorPropName(name) || name; } return ret; } function setPositiveNumber(elem, value, subtract) { // Any relative (+/-) values have already been // normalized at this point var matches = rcssNum.exec(value); return matches ? // Guard against undefined "subtract", e.g., when used as in cssHooks Math.max(0, matches[2] - (subtract || 0)) + (matches[3] || "px") : value; } function boxModelAdjustment(elem, dimension, box, isBorderBox, styles, computedVal) { var i = dimension === "width" ? 1 : 0, extra = 0, delta = 0; // Adjustment may not be necessary if (box === (isBorderBox ? "border" : "content")) { return 0; } for (; i < 4; i += 2) { // Both box models exclude margin if (box === "margin") { delta += jQuery.css(elem, box + cssExpand[i], true, styles); } // If we get here with a content-box, we're seeking "padding" or "border" or "margin" if (!isBorderBox) { // Add padding delta += jQuery.css(elem, "padding" + cssExpand[i], true, styles); // For "border" or "margin", add border if (box !== "padding") { delta += jQuery.css(elem, "border" + cssExpand[i] + "Width", true, styles); // But still keep track of it otherwise } else { extra += jQuery.css(elem, "border" + cssExpand[i] + "Width", true, styles); } // If we get here with a border-box (content + padding + border), we're seeking "content" or // "padding" or "margin" } else { // For "content", subtract padding if (box === "content") { delta -= jQuery.css(elem, "padding" + cssExpand[i], true, styles); } // For "content" or "padding", subtract border if (box !== "margin") { delta -= jQuery.css(elem, "border" + cssExpand[i] + "Width", true, styles); } } } // Account for positive content-box scroll gutter when requested by providing computedVal if (!isBorderBox && computedVal >= 0) { // offsetWidth/offsetHeight is a rounded sum of content, padding, scroll gutter, and border // Assuming integer scroll gutter, subtract the rest and round down delta += Math.max(0, Math.ceil(elem["offset" + dimension[0].toUpperCase() + dimension.slice(1)] - computedVal - delta - extra - 0.5)); } return delta; } function getWidthOrHeight(elem, dimension, extra) { // Start with computed style var styles = getStyles(elem), val = curCSS(elem, dimension, styles), isBorderBox = jQuery.css(elem, "boxSizing", false, styles) === "border-box", valueIsBorderBox = isBorderBox; // Support: Firefox <=54 // Return a confounding non-pixel value or feign ignorance, as appropriate. if (rnumnonpx.test(val)) { if (!extra) { return val; } val = "auto"; } // Check for style in case a browser which returns unreliable values // for getComputedStyle silently falls back to the reliable elem.style valueIsBorderBox = valueIsBorderBox && (support.boxSizingReliable() || val === elem.style[dimension]); // Fall back to offsetWidth/offsetHeight when value is "auto" // This happens for inline elements with no explicit setting (gh-3571) // Support: Android <=4.1 - 4.3 only // Also use offsetWidth/offsetHeight for misreported inline dimensions (gh-3602) if (val === "auto" || !parseFloat(val) && jQuery.css(elem, "display", false, styles) === "inline") { val = elem["offset" + dimension[0].toUpperCase() + dimension.slice(1)]; // offsetWidth/offsetHeight provide border-box values valueIsBorderBox = true; } // Normalize "" and auto val = parseFloat(val) || 0; // Adjust for the element's box model return val + boxModelAdjustment(elem, dimension, extra || (isBorderBox ? "border" : "content"), valueIsBorderBox, styles, // Provide the current computed size to request scroll gutter calculation (gh-3589) val) + "px"; } jQuery.extend({ // Add in style property hooks for overriding the default // behavior of getting and setting a style property cssHooks: { opacity: { get: function (elem, computed) { if (computed) { // We should always get a number back from opacity var ret = curCSS(elem, "opacity"); return ret === "" ? "1" : ret; } } } }, // Don't automatically add "px" to these possibly-unitless properties cssNumber: { "animationIterationCount": true, "columnCount": true, "fillOpacity": true, "flexGrow": true, "flexShrink": true, "fontWeight": true, "lineHeight": true, "opacity": true, "order": true, "orphans": true, "widows": true, "zIndex": true, "zoom": true }, // Add in properties whose names you wish to fix before // setting or getting the value cssProps: {}, // Get and set the style property on a DOM Node style: function (elem, name, value, extra) { // Don't set styles on text and comment nodes if (!elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style) { return; } // Make sure that we're working with the right name var ret, type, hooks, origName = camelCase(name), isCustomProp = rcustomProp.test(name), style = elem.style; // Make sure that we're working with the right name. We don't // want to query the value if it is a CSS custom property // since they are user-defined. if (!isCustomProp) { name = finalPropName(origName); } // Gets hook for the prefixed version, then unprefixed version hooks = jQuery.cssHooks[name] || jQuery.cssHooks[origName]; // Check if we're setting a value if (value !== undefined) { type = typeof value; // Convert "+=" or "-=" to relative numbers (#7345) if (type === "string" && (ret = rcssNum.exec(value)) && ret[1]) { value = adjustCSS(elem, name, ret); // Fixes bug #9237 type = "number"; } // Make sure that null and NaN values aren't set (#7116) if (value == null || value !== value) { return; } // If a number was passed in, add the unit (except for certain CSS properties) if (type === "number") { value += ret && ret[3] || (jQuery.cssNumber[origName] ? "" : "px"); } // background-* props affect original clone's values if (!support.clearCloneStyle && value === "" && name.indexOf("background") === 0) { style[name] = "inherit"; } // If a hook was provided, use that value, otherwise just set the specified value if (!hooks || !("set" in hooks) || (value = hooks.set(elem, value, extra)) !== undefined) { if (isCustomProp) { style.setProperty(name, value); } else { style[name] = value; } } } else { // If a hook was provided get the non-computed value from there if (hooks && "get" in hooks && (ret = hooks.get(elem, false, extra)) !== undefined) { return ret; } // Otherwise just get the value from the style object return style[name]; } }, css: function (elem, name, extra, styles) { var val, num, hooks, origName = camelCase(name), isCustomProp = rcustomProp.test(name); // Make sure that we're working with the right name. We don't // want to modify the value if it is a CSS custom property // since they are user-defined. if (!isCustomProp) { name = finalPropName(origName); } // Try prefixed name followed by the unprefixed name hooks = jQuery.cssHooks[name] || jQuery.cssHooks[origName]; // If a hook was provided get the computed value from there if (hooks && "get" in hooks) { val = hooks.get(elem, true, extra); } // Otherwise, if a way to get the computed value exists, use that if (val === undefined) { val = curCSS(elem, name, styles); } // Convert "normal" to computed value if (val === "normal" && name in cssNormalTransform) { val = cssNormalTransform[name]; } // Make numeric if forced or a qualifier was provided and val looks numeric if (extra === "" || extra) { num = parseFloat(val); return extra === true || isFinite(num) ? num || 0 : val; } return val; } }); jQuery.each(["height", "width"], function (i, dimension) { jQuery.cssHooks[dimension] = { get: function (elem, computed, extra) { if (computed) { // Certain elements can have dimension info if we invisibly show them // but it must have a current display style that would benefit return rdisplayswap.test(jQuery.css(elem, "display")) && (!elem.getClientRects().length || !elem.getBoundingClientRect().width) ? swap(elem, cssShow, function () { return getWidthOrHeight(elem, dimension, extra); }) : getWidthOrHeight(elem, dimension, extra); } }, set: function (elem, value, extra) { var matches, styles = getStyles(elem), isBorderBox = jQuery.css(elem, "boxSizing", false, styles) === "border-box", subtract = extra && boxModelAdjustment(elem, dimension, extra, isBorderBox, styles); // Account for unreliable border-box dimensions by comparing offset* to computed and // faking a content-box to get border and padding (gh-3699) if (isBorderBox && support.scrollboxSize() === styles.position) { subtract -= Math.ceil(elem["offset" + dimension[0].toUpperCase() + dimension.slice(1)] - parseFloat(styles[dimension]) - boxModelAdjustment(elem, dimension, "border", false, styles) - 0.5); } // Convert to pixels if value adjustment is needed if (subtract && (matches = rcssNum.exec(value)) && (matches[3] || "px") !== "px") { elem.style[dimension] = value; value = jQuery.css(elem, dimension); } return setPositiveNumber(elem, value, subtract); } }; }); jQuery.cssHooks.marginLeft = addGetHookIf(support.reliableMarginLeft, function (elem, computed) { if (computed) { return (parseFloat(curCSS(elem, "marginLeft")) || elem.getBoundingClientRect().left - swap(elem, { marginLeft: 0 }, function () { return elem.getBoundingClientRect().left; })) + "px"; } }); // These hooks are used by animate to expand properties jQuery.each({ margin: "", padding: "", border: "Width" }, function (prefix, suffix) { jQuery.cssHooks[prefix + suffix] = { expand: function (value) { var i = 0, expanded = {}, // Assumes a single number if not a string parts = typeof value === "string" ? value.split(" ") : [value]; for (; i < 4; i++) { expanded[prefix + cssExpand[i] + suffix] = parts[i] || parts[i - 2] || parts[0]; } return expanded; } }; if (prefix !== "margin") { jQuery.cssHooks[prefix + suffix].set = setPositiveNumber; } }); jQuery.fn.extend({ css: function (name, value) { return access(this, function (elem, name, value) { var styles, len, map = {}, i = 0; if (Array.isArray(name)) { styles = getStyles(elem); len = name.length; for (; i < len; i++) { map[name[i]] = jQuery.css(elem, name[i], false, styles); } return map; } return value !== undefined ? jQuery.style(elem, name, value) : jQuery.css(elem, name); }, name, value, arguments.length > 1); } }); // Based off of the plugin by Clint Helfers, with permission. // https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/ jQuery.fn.delay = function (time, type) { time = jQuery.fx ? jQuery.fx.speeds[time] || time : time; type = type || "fx"; return this.queue(type, function (next, hooks) { var timeout = window.setTimeout(next, time); hooks.stop = function () { window.clearTimeout(timeout); }; }); }; (function () { var input = document$2.createElement("input"), select = document$2.createElement("select"), opt = select.appendChild(document$2.createElement("option")); input.type = "checkbox"; // Support: Android <=4.3 only // Default value for a checkbox should be "on" support.checkOn = input.value !== ""; // Support: IE <=11 only // Must access selectedIndex to make default options select support.optSelected = opt.selected; // Support: IE <=11 only // An input loses its value after becoming a radio input = document$2.createElement("input"); input.value = "t"; input.type = "radio"; support.radioValue = input.value === "t"; })(); var boolHook, attrHandle = jQuery.expr.attrHandle; jQuery.fn.extend({ attr: function (name, value) { return access(this, jQuery.attr, name, value, arguments.length > 1); }, removeAttr: function (name) { return this.each(function () { jQuery.removeAttr(this, name); }); } }); jQuery.extend({ attr: function (elem, name, value) { var ret, hooks, nType = elem.nodeType; // Don't get/set attributes on text, comment and attribute nodes if (nType === 3 || nType === 8 || nType === 2) { return; } // Fallback to prop when attributes are not supported if (typeof elem.getAttribute === "undefined") { return jQuery.prop(elem, name, value); } // Attribute hooks are determined by the lowercase version // Grab necessary hook if one is defined if (nType !== 1 || !jQuery.isXMLDoc(elem)) { hooks = jQuery.attrHooks[name.toLowerCase()] || (jQuery.expr.match.bool.test(name) ? boolHook : undefined); } if (value !== undefined) { if (value === null) { jQuery.removeAttr(elem, name); return; } if (hooks && "set" in hooks && (ret = hooks.set(elem, value, name)) !== undefined) { return ret; } elem.setAttribute(name, value + ""); return value; } if (hooks && "get" in hooks && (ret = hooks.get(elem, name)) !== null) { return ret; } ret = jQuery.find.attr(elem, name); // Non-existent attributes return null, we normalize to undefined return ret == null ? undefined : ret; }, attrHooks: { type: { set: function (elem, value) { if (!support.radioValue && value === "radio" && nodeName(elem, "input")) { var val = elem.value; elem.setAttribute("type", value); if (val) { elem.value = val; } return value; } } } }, removeAttr: function (elem, value) { var name, i = 0, // Attribute names can contain non-HTML whitespace characters // https://html.spec.whatwg.org/multipage/syntax.html#attributes-2 attrNames = value && value.match(rnothtmlwhite); if (attrNames && elem.nodeType === 1) { while (name = attrNames[i++]) { elem.removeAttribute(name); } } } }); // Hooks for boolean attributes boolHook = { set: function (elem, value, name) { if (value === false) { // Remove boolean attributes when set to false jQuery.removeAttr(elem, name); } else { elem.setAttribute(name, name); } return name; } }; jQuery.each(jQuery.expr.match.bool.source.match(/\w+/g), function (i, name) { var getter = attrHandle[name] || jQuery.find.attr; attrHandle[name] = function (elem, name, isXML) { var ret, handle, lowercaseName = name.toLowerCase(); if (!isXML) { // Avoid an infinite loop by temporarily removing this function from the getter handle = attrHandle[lowercaseName]; attrHandle[lowercaseName] = ret; ret = getter(elem, name, isXML) != null ? lowercaseName : null; attrHandle[lowercaseName] = handle; } return ret; }; }); var rfocusable = /^(?:input|select|textarea|button)$/i, rclickable = /^(?:a|area)$/i; jQuery.fn.extend({ prop: function (name, value) { return access(this, jQuery.prop, name, value, arguments.length > 1); }, removeProp: function (name) { return this.each(function () { delete this[jQuery.propFix[name] || name]; }); } }); jQuery.extend({ prop: function (elem, name, value) { var ret, hooks, nType = elem.nodeType; // Don't get/set properties on text, comment and attribute nodes if (nType === 3 || nType === 8 || nType === 2) { return; } if (nType !== 1 || !jQuery.isXMLDoc(elem)) { // Fix name and attach hooks name = jQuery.propFix[name] || name; hooks = jQuery.propHooks[name]; } if (value !== undefined) { if (hooks && "set" in hooks && (ret = hooks.set(elem, value, name)) !== undefined) { return ret; } return elem[name] = value; } if (hooks && "get" in hooks && (ret = hooks.get(elem, name)) !== null) { return ret; } return elem[name]; }, propHooks: { tabIndex: { get: function (elem) { // Support: IE <=9 - 11 only // elem.tabIndex doesn't always return the // correct value when it hasn't been explicitly set // https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/ // Use proper attribute retrieval(#12072) var tabindex = jQuery.find.attr(elem, "tabindex"); if (tabindex) { return parseInt(tabindex, 10); } if (rfocusable.test(elem.nodeName) || rclickable.test(elem.nodeName) && elem.href) { return 0; } return -1; } } }, propFix: { "for": "htmlFor", "class": "className" } }); // Support: IE <=11 only // Accessing the selectedIndex property // forces the browser to respect setting selected // on the option // The getter ensures a default option is selected // when in an optgroup // eslint rule "no-unused-expressions" is disabled for this code // since it considers such accessions noop if (!support.optSelected) { jQuery.propHooks.selected = { get: function (elem) { /* eslint no-unused-expressions: "off" */ var parent = elem.parentNode; if (parent && parent.parentNode) { parent.parentNode.selectedIndex; } return null; }, set: function (elem) { /* eslint no-unused-expressions: "off" */ var parent = elem.parentNode; if (parent) { parent.selectedIndex; if (parent.parentNode) { parent.parentNode.selectedIndex; } } } }; } jQuery.each(["tabIndex", "readOnly", "maxLength", "cellSpacing", "cellPadding", "rowSpan", "colSpan", "useMap", "frameBorder", "contentEditable"], function () { jQuery.propFix[this.toLowerCase()] = this; }); // Strip and collapse whitespace according to HTML spec // https://infra.spec.whatwg.org/#strip-and-collapse-ascii-whitespace function stripAndCollapse(value) { var tokens = value.match(rnothtmlwhite) || []; return tokens.join(" "); } function getClass(elem) { return elem.getAttribute && elem.getAttribute("class") || ""; } function classesToArray(value) { if (Array.isArray(value)) { return value; } if (typeof value === "string") { return value.match(rnothtmlwhite) || []; } return []; } jQuery.fn.extend({ addClass: function (value) { var classes, elem, cur, curValue, clazz, j, finalValue, i = 0; if (isFunction(value)) { return this.each(function (j) { jQuery(this).addClass(value.call(this, j, getClass(this))); }); } classes = classesToArray(value); if (classes.length) { while (elem = this[i++]) { curValue = getClass(elem); cur = elem.nodeType === 1 && " " + stripAndCollapse(curValue) + " "; if (cur) { j = 0; while (clazz = classes[j++]) { if (cur.indexOf(" " + clazz + " ") < 0) { cur += clazz + " "; } } // Only assign if different to avoid unneeded rendering. finalValue = stripAndCollapse(cur); if (curValue !== finalValue) { elem.setAttribute("class", finalValue); } } } } return this; }, removeClass: function (value) { var classes, elem, cur, curValue, clazz, j, finalValue, i = 0; if (isFunction(value)) { return this.each(function (j) { jQuery(this).removeClass(value.call(this, j, getClass(this))); }); } if (!arguments.length) { return this.attr("class", ""); } classes = classesToArray(value); if (classes.length) { while (elem = this[i++]) { curValue = getClass(elem); // This expression is here for better compressibility (see addClass) cur = elem.nodeType === 1 && " " + stripAndCollapse(curValue) + " "; if (cur) { j = 0; while (clazz = classes[j++]) { // Remove *all* instances while (cur.indexOf(" " + clazz + " ") > -1) { cur = cur.replace(" " + clazz + " ", " "); } } // Only assign if different to avoid unneeded rendering. finalValue = stripAndCollapse(cur); if (curValue !== finalValue) { elem.setAttribute("class", finalValue); } } } } return this; }, toggleClass: function (value, stateVal) { var type = typeof value, isValidValue = type === "string" || Array.isArray(value); if (typeof stateVal === "boolean" && isValidValue) { return stateVal ? this.addClass(value) : this.removeClass(value); } if (isFunction(value)) { return this.each(function (i) { jQuery(this).toggleClass(value.call(this, i, getClass(this), stateVal), stateVal); }); } return this.each(function () { var className, i, self, classNames; if (isValidValue) { // Toggle individual class names i = 0; self = jQuery(this); classNames = classesToArray(value); while (className = classNames[i++]) { // Check each className given, space separated list if (self.hasClass(className)) { self.removeClass(className); } else { self.addClass(className); } } // Toggle whole class name } else if (value === undefined || type === "boolean") { className = getClass(this); if (className) { // Store className if set dataPriv.set(this, "__className__", className); } // If the element has a class name or if we're passed `false`, // then remove the whole classname (if there was one, the above saved it). // Otherwise bring back whatever was previously saved (if anything), // falling back to the empty string if nothing was stored. if (this.setAttribute) { this.setAttribute("class", className || value === false ? "" : dataPriv.get(this, "__className__") || ""); } } }); }, hasClass: function (selector) { var className, elem, i = 0; className = " " + selector + " "; while (elem = this[i++]) { if (elem.nodeType === 1 && (" " + stripAndCollapse(getClass(elem)) + " ").indexOf(className) > -1) { return true; } } return false; } }); var rreturn = /\r/g; jQuery.fn.extend({ val: function (value) { var hooks, ret, valueIsFunction, elem = this[0]; if (!arguments.length) { if (elem) { hooks = jQuery.valHooks[elem.type] || jQuery.valHooks[elem.nodeName.toLowerCase()]; if (hooks && "get" in hooks && (ret = hooks.get(elem, "value")) !== undefined) { return ret; } ret = elem.value; // Handle most common string cases if (typeof ret === "string") { return ret.replace(rreturn, ""); } // Handle cases where value is null/undef or number return ret == null ? "" : ret; } return; } valueIsFunction = isFunction(value); return this.each(function (i) { var val; if (this.nodeType !== 1) { return; } if (valueIsFunction) { val = value.call(this, i, jQuery(this).val()); } else { val = value; } // Treat null/undefined as ""; convert numbers to string if (val == null) { val = ""; } else if (typeof val === "number") { val += ""; } else if (Array.isArray(val)) { val = jQuery.map(val, function (value) { return value == null ? "" : value + ""; }); } hooks = jQuery.valHooks[this.type] || jQuery.valHooks[this.nodeName.toLowerCase()]; // If set returns undefined, fall back to normal setting if (!hooks || !("set" in hooks) || hooks.set(this, val, "value") === undefined) { this.value = val; } }); } }); jQuery.extend({ valHooks: { option: { get: function (elem) { var val = jQuery.find.attr(elem, "value"); return val != null ? val : // Support: IE <=10 - 11 only // option.text throws exceptions (#14686, #14858) // Strip and collapse whitespace // https://html.spec.whatwg.org/#strip-and-collapse-whitespace stripAndCollapse(jQuery.text(elem)); } }, select: { get: function (elem) { var value, option, i, options = elem.options, index = elem.selectedIndex, one = elem.type === "select-one", values = one ? null : [], max = one ? index + 1 : options.length; if (index < 0) { i = max; } else { i = one ? index : 0; } // Loop through all the selected options for (; i < max; i++) { option = options[i]; // Support: IE <=9 only // IE8-9 doesn't update selected after form reset (#2551) if ((option.selected || i === index) && // Don't return options that are disabled or in a disabled optgroup !option.disabled && (!option.parentNode.disabled || !nodeName(option.parentNode, "optgroup"))) { // Get the specific value for the option value = jQuery(option).val(); // We don't need an array for one selects if (one) { return value; } // Multi-Selects return an array values.push(value); } } return values; }, set: function (elem, value) { var optionSet, option, options = elem.options, values = jQuery.makeArray(value), i = options.length; while (i--) { option = options[i]; /* eslint-disable no-cond-assign */ if (option.selected = jQuery.inArray(jQuery.valHooks.option.get(option), values) > -1) { optionSet = true; } /* eslint-enable no-cond-assign */ } // Force browsers to behave consistently when non-matching value is set if (!optionSet) { elem.selectedIndex = -1; } return values; } } } }); // Radios and checkboxes getter/setter jQuery.each(["radio", "checkbox"], function () { jQuery.valHooks[this] = { set: function (elem, value) { if (Array.isArray(value)) { return elem.checked = jQuery.inArray(jQuery(elem).val(), value) > -1; } } }; if (!support.checkOn) { jQuery.valHooks[this].get = function (elem) { return elem.getAttribute("value") === null ? "on" : elem.value; }; } }); // Return jQuery for attributes-only inclusion support.focusin = "onfocusin" in window; var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/, stopPropagationCallback = function (e) { e.stopPropagation(); }; jQuery.extend(jQuery.event, { trigger: function (event, data, elem, onlyHandlers) { var i, cur, tmp, bubbleType, ontype, handle, special, lastElement, eventPath = [elem || document$2], type = hasOwn.call(event, "type") ? event.type : event, namespaces = hasOwn.call(event, "namespace") ? event.namespace.split(".") : []; cur = lastElement = tmp = elem = elem || document$2; // Don't do events on text and comment nodes if (elem.nodeType === 3 || elem.nodeType === 8) { return; } // focus/blur morphs to focusin/out; ensure we're not firing them right now if (rfocusMorph.test(type + jQuery.event.triggered)) { return; } if (type.indexOf(".") > -1) { // Namespaced trigger; create a regexp to match event type in handle() namespaces = type.split("."); type = namespaces.shift(); namespaces.sort(); } ontype = type.indexOf(":") < 0 && "on" + type; // Caller can pass in a jQuery.Event object, Object, or just an event type string event = event[jQuery.expando] ? event : new jQuery.Event(type, typeof event === "object" && event); // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true) event.isTrigger = onlyHandlers ? 2 : 3; event.namespace = namespaces.join("."); event.rnamespace = event.namespace ? new RegExp("(^|\\.)" + namespaces.join("\\.(?:.*\\.|)") + "(\\.|$)") : null; // Clean up the event in case it is being reused event.result = undefined; if (!event.target) { event.target = elem; } // Clone any incoming data and prepend the event, creating the handler arg list data = data == null ? [event] : jQuery.makeArray(data, [event]); // Allow special events to draw outside the lines special = jQuery.event.special[type] || {}; if (!onlyHandlers && special.trigger && special.trigger.apply(elem, data) === false) { return; } // Determine event propagation path in advance, per W3C events spec (#9951) // Bubble up to document, then to window; watch for a global ownerDocument var (#9724) if (!onlyHandlers && !special.noBubble && !isWindow(elem)) { bubbleType = special.delegateType || type; if (!rfocusMorph.test(bubbleType + type)) { cur = cur.parentNode; } for (; cur; cur = cur.parentNode) { eventPath.push(cur); tmp = cur; } // Only add window if we got to document (e.g., not plain obj or detached DOM) if (tmp === (elem.ownerDocument || document$2)) { eventPath.push(tmp.defaultView || tmp.parentWindow || window); } } // Fire handlers on the event path i = 0; while ((cur = eventPath[i++]) && !event.isPropagationStopped()) { lastElement = cur; event.type = i > 1 ? bubbleType : special.bindType || type; // jQuery handler handle = (dataPriv.get(cur, "events") || {})[event.type] && dataPriv.get(cur, "handle"); if (handle) { handle.apply(cur, data); } // Native handler handle = ontype && cur[ontype]; if (handle && handle.apply && acceptData(cur)) { event.result = handle.apply(cur, data); if (event.result === false) { event.preventDefault(); } } } event.type = type; // If nobody prevented the default action, do it now if (!onlyHandlers && !event.isDefaultPrevented()) { if ((!special._default || special._default.apply(eventPath.pop(), data) === false) && acceptData(elem)) { // Call a native DOM method on the target with the same name as the event. // Don't do default actions on window, that's where global variables be (#6170) if (ontype && isFunction(elem[type]) && !isWindow(elem)) { // Don't re-trigger an onFOO event when we call its FOO() method tmp = elem[ontype]; if (tmp) { elem[ontype] = null; } // Prevent re-triggering of the same event, since we already bubbled it above jQuery.event.triggered = type; if (event.isPropagationStopped()) { lastElement.addEventListener(type, stopPropagationCallback); } elem[type](); if (event.isPropagationStopped()) { lastElement.removeEventListener(type, stopPropagationCallback); } jQuery.event.triggered = undefined; if (tmp) { elem[ontype] = tmp; } } } } return event.result; }, // Piggyback on a donor event to simulate a different one // Used only for `focus(in | out)` events simulate: function (type, elem, event) { var e = jQuery.extend(new jQuery.Event(), event, { type: type, isSimulated: true }); jQuery.event.trigger(e, null, elem); } }); jQuery.fn.extend({ trigger: function (type, data) { return this.each(function () { jQuery.event.trigger(type, data, this); }); }, triggerHandler: function (type, data) { var elem = this[0]; if (elem) { return jQuery.event.trigger(type, data, elem, true); } } }); // Support: Firefox <=44 // Firefox doesn't have focus(in | out) events // Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787 // // Support: Chrome <=48 - 49, Safari <=9.0 - 9.1 // focus(in | out) events fire after focus & blur events, // which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order // Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857 if (!support.focusin) { jQuery.each({ focus: "focusin", blur: "focusout" }, function (orig, fix) { // Attach a single capturing handler on the document while someone wants focusin/focusout var handler = function (event) { jQuery.event.simulate(fix, event.target, jQuery.event.fix(event)); }; jQuery.event.special[fix] = { setup: function () { var doc = this.ownerDocument || this, attaches = dataPriv.access(doc, fix); if (!attaches) { doc.addEventListener(orig, handler, true); } dataPriv.access(doc, fix, (attaches || 0) + 1); }, teardown: function () { var doc = this.ownerDocument || this, attaches = dataPriv.access(doc, fix) - 1; if (!attaches) { doc.removeEventListener(orig, handler, true); dataPriv.remove(doc, fix); } else { dataPriv.access(doc, fix, attaches); } } }; }); } var rbracket = /\[\]$/, rCRLF = /\r?\n/g, rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i, rsubmittable = /^(?:input|select|textarea|keygen)/i; function buildParams(prefix, obj, traditional, add) { var name; if (Array.isArray(obj)) { // Serialize array item. jQuery.each(obj, function (i, v) { if (traditional || rbracket.test(prefix)) { // Treat each array item as a scalar. add(prefix, v); } else { // Item is non-scalar (array or object), encode its numeric index. buildParams(prefix + "[" + (typeof v === "object" && v != null ? i : "") + "]", v, traditional, add); } }); } else if (!traditional && toType(obj) === "object") { // Serialize object item. for (name in obj) { buildParams(prefix + "[" + name + "]", obj[name], traditional, add); } } else { // Serialize scalar item. add(prefix, obj); } } // Serialize an array of form elements or a set of // key/values into a query string jQuery.param = function (a, traditional) { var prefix, s = [], add = function (key, valueOrFunction) { // If value is a function, invoke it and use its return value var value = isFunction(valueOrFunction) ? valueOrFunction() : valueOrFunction; s[s.length] = encodeURIComponent(key) + "=" + encodeURIComponent(value == null ? "" : value); }; // If an array was passed in, assume that it is an array of form elements. if (Array.isArray(a) || a.jquery && !jQuery.isPlainObject(a)) { // Serialize the form elements jQuery.each(a, function () { add(this.name, this.value); }); } else { // If traditional, encode the "old" way (the way 1.3.2 or older // did it), otherwise encode params recursively. for (prefix in a) { buildParams(prefix, a[prefix], traditional, add); } } // Return the resulting serialization return s.join("&"); }; jQuery.fn.extend({ serialize: function () { return jQuery.param(this.serializeArray()); }, serializeArray: function () { return this.map(function () { // Can add propHook for "elements" to filter or add form elements var elements = jQuery.prop(this, "elements"); return elements ? jQuery.makeArray(elements) : this; }).filter(function () { var type = this.type; // Use .is( ":disabled" ) so that fieldset[disabled] works return this.name && !jQuery(this).is(":disabled") && rsubmittable.test(this.nodeName) && !rsubmitterTypes.test(type) && (this.checked || !rcheckableType.test(type)); }).map(function (i, elem) { var val = jQuery(this).val(); if (val == null) { return null; } if (Array.isArray(val)) { return jQuery.map(val, function (val) { return { name: elem.name, value: val.replace(rCRLF, "\r\n") }; }); } return { name: elem.name, value: val.replace(rCRLF, "\r\n") }; }).get(); } }); jQuery.fn.extend({ wrapAll: function (html) { var wrap; if (this[0]) { if (isFunction(html)) { html = html.call(this[0]); } // The elements to wrap the target around wrap = jQuery(html, this[0].ownerDocument).eq(0).clone(true); if (this[0].parentNode) { wrap.insertBefore(this[0]); } wrap.map(function () { var elem = this; while (elem.firstElementChild) { elem = elem.firstElementChild; } return elem; }).append(this); } return this; }, wrapInner: function (html) { if (isFunction(html)) { return this.each(function (i) { jQuery(this).wrapInner(html.call(this, i)); }); } return this.each(function () { var self = jQuery(this), contents = self.contents(); if (contents.length) { contents.wrapAll(html); } else { self.append(html); } }); }, wrap: function (html) { var htmlIsFunction = isFunction(html); return this.each(function (i) { jQuery(this).wrapAll(htmlIsFunction ? html.call(this, i) : html); }); }, unwrap: function (selector) { this.parent(selector).not("body").each(function () { jQuery(this).replaceWith(this.childNodes); }); return this; } }); jQuery.expr.pseudos.hidden = function (elem) { return !jQuery.expr.pseudos.visible(elem); }; jQuery.expr.pseudos.visible = function (elem) { return !!(elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length); }; // Support: Safari 8 only // In Safari 8 documents created via document.implementation.createHTMLDocument // collapse sibling forms: the second one becomes a child of the first one. // Because of that, this security measure has to be disabled in Safari 8. // https://bugs.webkit.org/show_bug.cgi?id=137337 support.createHTMLDocument = function () { var body = document$2.implementation.createHTMLDocument("").body; body.innerHTML = "
"; return body.childNodes.length === 2; }(); // Argument "data" should be string of html // context (optional): If specified, the fragment will be created in this context, // defaults to document // keepScripts (optional): If true, will include scripts passed in the html string jQuery.parseHTML = function (data, context, keepScripts) { if (typeof data !== "string") { return []; } if (typeof context === "boolean") { keepScripts = context; context = false; } var base, parsed, scripts; if (!context) { // Stop scripts or inline event handlers from being executed immediately // by using document.implementation if (support.createHTMLDocument) { context = document$2.implementation.createHTMLDocument(""); // Set the base href for the created document // so any parsed elements with URLs // are based on the document's URL (gh-2965) base = context.createElement("base"); base.href = document$2.location.href; context.head.appendChild(base); } else { context = document$2; } } parsed = rsingleTag.exec(data); scripts = !keepScripts && []; // Single tag if (parsed) { return [context.createElement(parsed[1])]; } parsed = buildFragment([data], context, scripts); if (scripts && scripts.length) { jQuery(scripts).remove(); } return jQuery.merge([], parsed.childNodes); }; jQuery.offset = { setOffset: function (elem, options, i) { var curPosition, curLeft, curCSSTop, curTop, curOffset, curCSSLeft, calculatePosition, position = jQuery.css(elem, "position"), curElem = jQuery(elem), props = {}; // Set position first, in-case top/left are set even on static elem if (position === "static") { elem.style.position = "relative"; } curOffset = curElem.offset(); curCSSTop = jQuery.css(elem, "top"); curCSSLeft = jQuery.css(elem, "left"); calculatePosition = (position === "absolute" || position === "fixed") && (curCSSTop + curCSSLeft).indexOf("auto") > -1; // Need to be able to calculate position if either // top or left is auto and position is either absolute or fixed if (calculatePosition) { curPosition = curElem.position(); curTop = curPosition.top; curLeft = curPosition.left; } else { curTop = parseFloat(curCSSTop) || 0; curLeft = parseFloat(curCSSLeft) || 0; } if (isFunction(options)) { // Use jQuery.extend here to allow modification of coordinates argument (gh-1848) options = options.call(elem, i, jQuery.extend({}, curOffset)); } if (options.top != null) { props.top = options.top - curOffset.top + curTop; } if (options.left != null) { props.left = options.left - curOffset.left + curLeft; } if ("using" in options) { options.using.call(elem, props); } else { curElem.css(props); } } }; jQuery.fn.extend({ // offset() relates an element's border box to the document origin offset: function (options) { // Preserve chaining for setter if (arguments.length) { return options === undefined ? this : this.each(function (i) { jQuery.offset.setOffset(this, options, i); }); } var rect, win, elem = this[0]; if (!elem) { return; } // Return zeros for disconnected and hidden (display: none) elements (gh-2310) // Support: IE <=11 only // Running getBoundingClientRect on a // disconnected node in IE throws an error if (!elem.getClientRects().length) { return { top: 0, left: 0 }; } // Get document-relative position by adding viewport scroll to viewport-relative gBCR rect = elem.getBoundingClientRect(); win = elem.ownerDocument.defaultView; return { top: rect.top + win.pageYOffset, left: rect.left + win.pageXOffset }; }, // position() relates an element's margin box to its offset parent's padding box // This corresponds to the behavior of CSS absolute positioning position: function () { if (!this[0]) { return; } var offsetParent, offset, doc, elem = this[0], parentOffset = { top: 0, left: 0 }; // position:fixed elements are offset from the viewport, which itself always has zero offset if (jQuery.css(elem, "position") === "fixed") { // Assume position:fixed implies availability of getBoundingClientRect offset = elem.getBoundingClientRect(); } else { offset = this.offset(); // Account for the *real* offset parent, which can be the document or its root element // when a statically positioned element is identified doc = elem.ownerDocument; offsetParent = elem.offsetParent || doc.documentElement; while (offsetParent && (offsetParent === doc.body || offsetParent === doc.documentElement) && jQuery.css(offsetParent, "position") === "static") { offsetParent = offsetParent.parentNode; } if (offsetParent && offsetParent !== elem && offsetParent.nodeType === 1) { // Incorporate borders into its offset, since they are outside its content origin parentOffset = jQuery(offsetParent).offset(); parentOffset.top += jQuery.css(offsetParent, "borderTopWidth", true); parentOffset.left += jQuery.css(offsetParent, "borderLeftWidth", true); } } // Subtract parent offsets and element margins return { top: offset.top - parentOffset.top - jQuery.css(elem, "marginTop", true), left: offset.left - parentOffset.left - jQuery.css(elem, "marginLeft", true) }; }, // This method will return documentElement in the following cases: // 1) For the element inside the iframe without offsetParent, this method will return // documentElement of the parent window // 2) For the hidden or detached element // 3) For body or html element, i.e. in case of the html node - it will return itself // // but those exceptions were never presented as a real life use-cases // and might be considered as more preferable results. // // This logic, however, is not guaranteed and can change at any point in the future offsetParent: function () { return this.map(function () { var offsetParent = this.offsetParent; while (offsetParent && jQuery.css(offsetParent, "position") === "static") { offsetParent = offsetParent.offsetParent; } return offsetParent || documentElement; }); } }); // Create scrollLeft and scrollTop methods jQuery.each({ scrollLeft: "pageXOffset", scrollTop: "pageYOffset" }, function (method, prop) { var top = "pageYOffset" === prop; jQuery.fn[method] = function (val) { return access(this, function (elem, method, val) { // Coalesce documents and windows var win; if (isWindow(elem)) { win = elem; } else if (elem.nodeType === 9) { win = elem.defaultView; } if (val === undefined) { return win ? win[prop] : elem[method]; } if (win) { win.scrollTo(!top ? val : win.pageXOffset, top ? val : win.pageYOffset); } else { elem[method] = val; } }, method, val, arguments.length); }; }); // Support: Safari <=7 - 9.1, Chrome <=37 - 49 // Add the top/left cssHooks using jQuery.fn.position // Webkit bug: https://bugs.webkit.org/show_bug.cgi?id=29084 // Blink bug: https://bugs.chromium.org/p/chromium/issues/detail?id=589347 // getComputedStyle returns percent when specified for top/left/bottom/right; // rather than make the css module depend on the offset module, just check for it here jQuery.each(["top", "left"], function (i, prop) { jQuery.cssHooks[prop] = addGetHookIf(support.pixelPosition, function (elem, computed) { if (computed) { computed = curCSS(elem, prop); // If curCSS returns percentage, fallback to offset return rnumnonpx.test(computed) ? jQuery(elem).position()[prop] + "px" : computed; } }); }); // Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods jQuery.each({ Height: "height", Width: "width" }, function (name, type) { jQuery.each({ padding: "inner" + name, content: type, "": "outer" + name }, function (defaultExtra, funcName) { // Margin is only for outerHeight, outerWidth jQuery.fn[funcName] = function (margin, value) { var chainable = arguments.length && (defaultExtra || typeof margin !== "boolean"), extra = defaultExtra || (margin === true || value === true ? "margin" : "border"); return access(this, function (elem, type, value) { var doc; if (isWindow(elem)) { // $( window ).outerWidth/Height return w/h including scrollbars (gh-1729) return funcName.indexOf("outer") === 0 ? elem["inner" + name] : elem.document.documentElement["client" + name]; } // Get document width or height if (elem.nodeType === 9) { doc = elem.documentElement; // Either scroll[Width/Height] or offset[Width/Height] or client[Width/Height], // whichever is greatest return Math.max(elem.body["scroll" + name], doc["scroll" + name], elem.body["offset" + name], doc["offset" + name], doc["client" + name]); } return value === undefined ? // Get width or height on the element, requesting but not forcing parseFloat jQuery.css(elem, type, extra) : // Set width or height on the element jQuery.style(elem, type, value, extra); }, type, chainable ? margin : undefined, chainable); }; }); }); jQuery.each(("blur focus focusin focusout resize scroll click dblclick " + "mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " + "change select submit keydown keypress keyup contextmenu").split(" "), function (i, name) { // Handle event binding jQuery.fn[name] = function (data, fn) { return arguments.length > 0 ? this.on(name, null, data, fn) : this.trigger(name); }; }); jQuery.fn.extend({ hover: function (fnOver, fnOut) { return this.mouseenter(fnOver).mouseleave(fnOut || fnOver); } }); jQuery.fn.extend({ bind: function (types, data, fn) { return this.on(types, null, data, fn); }, unbind: function (types, fn) { return this.off(types, null, fn); }, delegate: function (selector, types, data, fn) { return this.on(types, selector, data, fn); }, undelegate: function (selector, types, fn) { // ( namespace ) or ( selector, types [, fn] ) return arguments.length === 1 ? this.off(selector, "**") : this.off(types, selector || "**", fn); } }); // Bind a function to a context, optionally partially applying any // arguments. // jQuery.proxy is deprecated to promote standards (specifically Function#bind) // However, it is not slated for removal any time soon jQuery.proxy = function (fn, context) { var tmp, args, proxy; if (typeof context === "string") { tmp = fn[context]; context = fn; fn = tmp; } // Quick check to determine if target is callable, in the spec // this throws a TypeError, but we will just return undefined. if (!isFunction(fn)) { return undefined; } // Simulated bind args = slice.call(arguments, 2); proxy = function () { return fn.apply(context || this, args.concat(slice.call(arguments))); }; // Set the guid of unique handler to the same of original handler, so it can be removed proxy.guid = fn.guid = fn.guid || jQuery.guid++; return proxy; }; jQuery.holdReady = function (hold) { if (hold) { jQuery.readyWait++; } else { jQuery.ready(true); } }; jQuery.isArray = Array.isArray; jQuery.parseJSON = JSON.parse; jQuery.nodeName = nodeName; jQuery.isFunction = isFunction; jQuery.isWindow = isWindow; jQuery.camelCase = camelCase; jQuery.type = toType; jQuery.now = Date.now; jQuery.isNumeric = function (obj) { // As of jQuery 3.0, isNumeric is limited to // strings and numbers (primitives or objects) // that can be coerced to finite numbers (gh-2662) var type = jQuery.type(obj); return (type === "number" || type === "string") && // parseFloat NaNs numeric-cast false positives ("") // ...but misinterprets leading-number strings, particularly hex literals ("0x...") // subtraction forces infinities to NaN !isNaN(obj - parseFloat(obj)); }; const $ = jQuery; function div$1(options) { return create$1("div", options); } function create$1(tag, options) { const elem = document.createElement(tag); if (options) { if (options.class) { elem.classList.add(options.class); } if (options.id) { elem.id = options.id; } if (options.style) { applyStyle$1(elem, options.style); } } return elem; } function hide$1(elem) { const cssStyle = getComputedStyle(elem); if (cssStyle.display !== "none") { elem._initialDisplay = cssStyle.display; } elem.style.display = "none"; } function offset$1(elem) { // Return zeros for disconnected and hidden (display: none) elements (gh-2310) // Support: IE <=11 only // Running getBoundingClientRect on a // disconnected node in IE throws an error if (!elem.getClientRects().length) { return { top: 0, left: 0 }; } // Get document-relative position by adding viewport scroll to viewport-relative gBCR const rect = elem.getBoundingClientRect(); const win = elem.ownerDocument.defaultView; return { top: rect.top + win.pageYOffset, left: rect.left + win.pageXOffset }; } function pageCoordinates$1(e) { if (e.type.startsWith("touch")) { const touch = e.touches[0]; return { x: touch.pageX, y: touch.pageY }; } else { return { x: e.pageX, y: e.pageY }; } } const relativeDOMBBox = (parentElement, childElement) => { const { x: x_p, y: y_p, width: width_p, height: height_p } = parentElement.getBoundingClientRect(); const { x: x_c, y: y_c, width: width_c, height: height_c } = 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document.createElement("div"); parent.appendChild(container); container.appendChild(createIcon$2("times")); container.addEventListener('click', function (e) { e.preventDefault(); e.stopPropagation(); closeHandler(); }); } /** * @fileoverview Zlib namespace. Zlib ã®ä»•æ§˜ã«æº–æ‹ ã—ãŸåœ§ç¸®ã¯ Zlib.Deflate で実装 * されている. これは Inflate との共存を考慮している為. */ const ZLIB_STREAM_RAW_INFLATE_BUFFER_SIZE$1 = 65000; var Zlib$1 = { Huffman: {}, Util: {}, CRC32: {} }; /** * Compression Method * @enum {number} */ Zlib$1.CompressionMethod = { DEFLATE: 8, RESERVED: 15 }; /** * @param {Object=} opt_params options. * @constructor */ Zlib$1.Zip = function (opt_params) { opt_params = opt_params || {}; /** @type {Array.<{ * buffer: !(Array.|Uint8Array), * option: Object, * compressed: boolean, * encrypted: boolean, * size: number, * crc32: number * }>} */ this.files = []; /** @type {(Array.|Uint8Array)} */ this.comment = opt_params['comment']; /** @type {(Array.|Uint8Array)} */ this.password; }; /** * @enum {number} */ Zlib$1.Zip.CompressionMethod = { STORE: 0, DEFLATE: 8 }; /** * @enum {number} */ Zlib$1.Zip.OperatingSystem = { MSDOS: 0, UNIX: 3, MACINTOSH: 7 }; /** * @enum {number} */ Zlib$1.Zip.Flags = { ENCRYPT: 0x0001, DESCRIPTOR: 0x0008, UTF8: 0x0800 }; /** * @type {Array.} * @const */ Zlib$1.Zip.FileHeaderSignature = [0x50, 0x4b, 0x01, 0x02]; /** * @type {Array.} * @const */ Zlib$1.Zip.LocalFileHeaderSignature = [0x50, 0x4b, 0x03, 0x04]; /** * @type {Array.} * @const */ Zlib$1.Zip.CentralDirectorySignature = [0x50, 0x4b, 0x05, 0x06]; /** * @param {Array.|Uint8Array} input * @param {Object=} opt_params options. */ Zlib$1.Zip.prototype.addFile = function (input, opt_params) { opt_params = opt_params || {}; /** @type {string} */ opt_params['filename']; /** @type {boolean} */ var compressed; /** @type {number} */ var size = input.length; /** @type {number} */ var crc32 = 0; if (input instanceof Array) { input = new Uint8Array(input); } // default if (typeof opt_params['compressionMethod'] !== 'number') { opt_params['compressionMethod'] = Zlib$1.Zip.CompressionMethod.DEFLATE; } // ãã®å ´ã§åœ§ç¸®ã™ã‚‹å ´åˆ if (opt_params['compress']) { switch (opt_params['compressionMethod']) { case Zlib$1.Zip.CompressionMethod.STORE: break; case Zlib$1.Zip.CompressionMethod.DEFLATE: crc32 = Zlib$1.CRC32.calc(input); input = this.deflateWithOption(input, opt_params); compressed = true; break; default: throw new Error('unknown compression method:' + opt_params['compressionMethod']); } } this.files.push({ buffer: input, option: opt_params, compressed: compressed, encrypted: false, size: size, crc32: crc32 }); }; /** * @param {(Array.|Uint8Array)} password */ Zlib$1.Zip.prototype.setPassword = function (password) { this.password = password; }; Zlib$1.Zip.prototype.compress = function () { /** @type {Array.<{ * buffer: !(Array.|Uint8Array), * option: Object, * compressed: boolean, * encrypted: boolean, * size: number, * crc32: number * }>} */ var files = this.files; /** @type {{ * buffer: !(Array.|Uint8Array), * option: Object, * compressed: boolean, * encrypted: boolean, * size: number, * crc32: number * }} */ var file; /** @type {!(Array.|Uint8Array)} */ var output; /** @type {number} */ var op1; /** @type {number} */ var op2; /** @type {number} */ var op3; /** @type {number} */ var localFileSize = 0; /** @type {number} */ var centralDirectorySize = 0; /** @type {number} */ var endOfCentralDirectorySize; /** @type {number} */ var offset; /** @type {number} */ var needVersion; /** @type {number} */ var flags; /** @type {Zlib.Zip.CompressionMethod} */ var compressionMethod; /** @type {Date} */ var date; /** @type {number} */ var crc32; /** @type {number} */ var size; /** @type {number} */ var plainSize; /** @type {number} */ var filenameLength; /** @type {number} */ var extraFieldLength; /** @type {number} */ var commentLength; /** @type {(Array.|Uint8Array)} */ var filename; /** @type {(Array.|Uint8Array)} */ var extraField; /** @type {(Array.|Uint8Array)} */ var comment; /** @type {(Array.|Uint8Array)} */ var buffer; /** @type {*} */ var tmp; /** @type {Array.|Uint32Array|Object} */ var key; /** @type {number} */ var i; /** @type {number} */ var il; /** @type {number} */ var j; /** @type {number} */ var jl; // ファイルの圧縮 for (i = 0, il = files.length; i < il; ++i) { file = files[i]; filenameLength = file.option['filename'] ? file.option['filename'].length : 0; extraFieldLength = file.option['extraField'] ? file.option['extraField'].length : 0; commentLength = file.option['comment'] ? file.option['comment'].length : 0; // 圧縮されていなかったら圧縮 if (!file.compressed) { // 圧縮前に CRC32 の計算をしておく file.crc32 = Zlib$1.CRC32.calc(file.buffer); switch (file.option['compressionMethod']) { case Zlib$1.Zip.CompressionMethod.STORE: break; case Zlib$1.Zip.CompressionMethod.DEFLATE: file.buffer = this.deflateWithOption(file.buffer, file.option); file.compressed = true; break; default: throw new Error('unknown compression method:' + file.option['compressionMethod']); } } // encryption if (file.option['password'] !== void 0 || this.password !== void 0) { // init encryption key = this.createEncryptionKey(file.option['password'] || this.password); // add header buffer = file.buffer; { tmp = new Uint8Array(buffer.length + 12); tmp.set(buffer, 12); buffer = tmp; } for (j = 0; j < 12; ++j) { buffer[j] = this.encode(key, i === 11 ? file.crc32 & 0xff : Math.random() * 256 | 0); } // data encryption for (jl = buffer.length; j < jl; ++j) { buffer[j] = this.encode(key, buffer[j]); } file.buffer = buffer; } // 必要バッファサイズの計算 localFileSize += // local file header 30 + filenameLength + // file data file.buffer.length; centralDirectorySize += // file header 46 + filenameLength + commentLength; } // end of central directory endOfCentralDirectorySize = 22 + (this.comment ? this.comment.length : 0); output = new (Uint8Array )(localFileSize + centralDirectorySize + endOfCentralDirectorySize); op1 = 0; op2 = localFileSize; op3 = op2 + centralDirectorySize; // ファイルの圧縮 for (i = 0, il = files.length; i < il; ++i) { file = files[i]; filenameLength = file.option['filename'] ? file.option['filename'].length : 0; extraFieldLength = 0; // TODO commentLength = file.option['comment'] ? file.option['comment'].length : 0; //------------------------------------------------------------------------- // local file header & file header //------------------------------------------------------------------------- offset = op1; // signature // local file header output[op1++] = Zlib$1.Zip.LocalFileHeaderSignature[0]; output[op1++] = Zlib$1.Zip.LocalFileHeaderSignature[1]; output[op1++] = Zlib$1.Zip.LocalFileHeaderSignature[2]; output[op1++] = Zlib$1.Zip.LocalFileHeaderSignature[3]; // file header output[op2++] = Zlib$1.Zip.FileHeaderSignature[0]; output[op2++] = Zlib$1.Zip.FileHeaderSignature[1]; output[op2++] = Zlib$1.Zip.FileHeaderSignature[2]; output[op2++] = Zlib$1.Zip.FileHeaderSignature[3]; // compressor info needVersion = 20; output[op2++] = needVersion & 0xff; output[op2++] = /** @type {Zlib.Zip.OperatingSystem} */ file.option['os'] || Zlib$1.Zip.OperatingSystem.MSDOS; // need version output[op1++] = output[op2++] = needVersion & 0xff; output[op1++] = output[op2++] = needVersion >> 8 & 0xff; // general purpose bit flag flags = 0; if (file.option['password'] || this.password) { flags |= Zlib$1.Zip.Flags.ENCRYPT; } output[op1++] = output[op2++] = flags & 0xff; output[op1++] = output[op2++] = flags >> 8 & 0xff; // compression method compressionMethod = file.option['compressionMethod']; output[op1++] = output[op2++] = compressionMethod & 0xff; output[op1++] = output[op2++] = compressionMethod >> 8 & 0xff; // date date = /** @type {(Date|undefined)} */ file.option['date'] || new Date(); output[op1++] = output[op2++] = (date.getMinutes() & 0x7) << 5 | (date.getSeconds() / 2 | 0); output[op1++] = output[op2++] = date.getHours() << 3 | date.getMinutes() >> 3; // output[op1++] = output[op2++] = (date.getMonth() + 1 & 0x7) << 5 | date.getDate(); output[op1++] = output[op2++] = (date.getFullYear() - 1980 & 0x7f) << 1 | date.getMonth() + 1 >> 3; // CRC-32 crc32 = file.crc32; output[op1++] = output[op2++] = crc32 & 0xff; output[op1++] = output[op2++] = crc32 >> 8 & 0xff; output[op1++] = output[op2++] = crc32 >> 16 & 0xff; output[op1++] = output[op2++] = crc32 >> 24 & 0xff; // compressed size size = file.buffer.length; output[op1++] = output[op2++] = size & 0xff; output[op1++] = output[op2++] = size >> 8 & 0xff; output[op1++] = output[op2++] = size >> 16 & 0xff; output[op1++] = output[op2++] = size >> 24 & 0xff; // uncompressed size plainSize = file.size; output[op1++] = output[op2++] = plainSize & 0xff; output[op1++] = output[op2++] = plainSize >> 8 & 0xff; output[op1++] = output[op2++] = plainSize >> 16 & 0xff; output[op1++] = output[op2++] = plainSize >> 24 & 0xff; // filename length output[op1++] = output[op2++] = filenameLength & 0xff; output[op1++] = output[op2++] = filenameLength >> 8 & 0xff; // extra field length output[op1++] = output[op2++] = extraFieldLength & 0xff; output[op1++] = output[op2++] = extraFieldLength >> 8 & 0xff; // file comment length output[op2++] = commentLength & 0xff; output[op2++] = commentLength >> 8 & 0xff; // disk number start output[op2++] = 0; output[op2++] = 0; // internal file attributes output[op2++] = 0; output[op2++] = 0; // external file attributes output[op2++] = 0; output[op2++] = 0; output[op2++] = 0; output[op2++] = 0; // relative offset of local header output[op2++] = offset & 0xff; output[op2++] = offset >> 8 & 0xff; output[op2++] = offset >> 16 & 0xff; output[op2++] = offset >> 24 & 0xff; // filename filename = file.option['filename']; if (filename) { { output.set(filename, op1); output.set(filename, op2); op1 += filenameLength; op2 += filenameLength; } } // extra field extraField = file.option['extraField']; if (extraField) { { output.set(extraField, op1); output.set(extraField, op2); op1 += extraFieldLength; op2 += extraFieldLength; } } // comment comment = file.option['comment']; if (comment) { { output.set(comment, op2); op2 += commentLength; } } //------------------------------------------------------------------------- // file data //------------------------------------------------------------------------- { output.set(file.buffer, op1); op1 += file.buffer.length; } } //------------------------------------------------------------------------- // end of central directory //------------------------------------------------------------------------- // signature output[op3++] = Zlib$1.Zip.CentralDirectorySignature[0]; output[op3++] = Zlib$1.Zip.CentralDirectorySignature[1]; output[op3++] = Zlib$1.Zip.CentralDirectorySignature[2]; output[op3++] = Zlib$1.Zip.CentralDirectorySignature[3]; // number of this disk output[op3++] = 0; output[op3++] = 0; // number of the disk with the start of the central directory output[op3++] = 0; output[op3++] = 0; // total number of entries in the central directory on this disk output[op3++] = il & 0xff; output[op3++] = il >> 8 & 0xff; // total number of entries in the central directory output[op3++] = il & 0xff; output[op3++] = il >> 8 & 0xff; // size of the central directory output[op3++] = centralDirectorySize & 0xff; output[op3++] = centralDirectorySize >> 8 & 0xff; output[op3++] = centralDirectorySize >> 16 & 0xff; output[op3++] = centralDirectorySize >> 24 & 0xff; // offset of start of central directory with respect to the starting disk number output[op3++] = localFileSize & 0xff; output[op3++] = localFileSize >> 8 & 0xff; output[op3++] = localFileSize >> 16 & 0xff; output[op3++] = localFileSize >> 24 & 0xff; // .ZIP file comment length commentLength = this.comment ? this.comment.length : 0; output[op3++] = commentLength & 0xff; output[op3++] = commentLength >> 8 & 0xff; // .ZIP file comment if (this.comment) { { output.set(this.comment, op3); op3 += commentLength; } } return output; }; /** * @param {!(Array.|Uint8Array)} input * @param {Object=} opt_params options. * @return {!(Array.|Uint8Array)} */ Zlib$1.Zip.prototype.deflateWithOption = function (input, opt_params) { /** @type {Zlib.RawDeflate} */ var deflator = new Zlib$1.RawDeflate(input, opt_params['deflateOption']); return deflator.compress(); }; /** * @param {(Array.|Uint32Array)} key * @return {number} */ Zlib$1.Zip.prototype.getByte = function (key) { /** @type {number} */ var tmp = key[2] & 0xffff | 2; return tmp * (tmp ^ 1) >> 8 & 0xff; }; /** * @param {(Array.|Uint32Array|Object)} key * @param {number} n * @return {number} */ Zlib$1.Zip.prototype.encode = function (key, n) { /** @type {number} */ var tmp = this.getByte(key); this.updateKeys(key, n); return tmp ^ n; }; /** * @param {(Array.|Uint32Array)} key * @param {number} n */ Zlib$1.Zip.prototype.updateKeys = function (key, n) { key[0] = Zlib$1.CRC32.single(key[0], n); key[1] = (((key[1] + (key[0] & 0xff)) * 20173 >>> 0) * 6681 >>> 0) + 1 >>> 0; key[2] = Zlib$1.CRC32.single(key[2], key[1] >>> 24); }; /** * @param {(Array.|Uint8Array)} password * @return {!(Array.|Uint32Array|Object)} */ Zlib$1.Zip.prototype.createEncryptionKey = function (password) { /** @type {!(Array.|Uint32Array)} */ var key = [305419896, 591751049, 878082192]; /** @type {number} */ var i; /** @type {number} */ var il; { key = new Uint32Array(key); } for (i = 0, il = password.length; i < il; ++i) { this.updateKeys(key, password[i] & 0xff); } return key; }; /** * build huffman table from length list. * @param {!(Array.|Uint8Array)} lengths length list. * @return {!Array} huffman table. */ Zlib$1.Huffman.buildHuffmanTable = function (lengths) { /** @type {number} length list size. */ var listSize = lengths.length; /** @type {number} max code length for table size. */ var maxCodeLength = 0; /** @type {number} min code length for table size. */ var minCodeLength = Number.POSITIVE_INFINITY; /** @type {number} table size. */ var size; /** @type {!(Array|Uint8Array)} huffman code table. */ var table; /** @type {number} bit length. */ var bitLength; /** @type {number} huffman code. */ var code; /** * サイズが 2^maxlength 個のテーブルを埋めるためのスキップ長. * @type {number} skip length for table filling. */ var skip; /** @type {number} reversed code. */ var reversed; /** @type {number} reverse temp. */ var rtemp; /** @type {number} loop counter. */ var i; /** @type {number} loop limit. */ var il; /** @type {number} loop counter. */ var j; /** @type {number} table value. */ var value; // Math.max は遅いので最長の値は for-loop で取得する for (i = 0, il = listSize; i < il; ++i) { if (lengths[i] > maxCodeLength) { maxCodeLength = lengths[i]; } if (lengths[i] < minCodeLength) { minCodeLength = lengths[i]; } } size = 1 << maxCodeLength; table = new (Uint32Array )(size); // ãƒ“ãƒƒãƒˆé•·ã®çŸ­ã„é †ã‹ã‚‰ãƒãƒ•ãƒžãƒ³ç¬¦å·ã‚’å‰²ã‚Šå½“ã¦ã‚‹ for (bitLength = 1, code = 0, skip = 2; bitLength <= maxCodeLength;) { for (i = 0; i < listSize; ++i) { if (lengths[i] === bitLength) { // ビットオーダーが逆になるためビット長分並びを反転する for (reversed = 0, rtemp = code, j = 0; j < bitLength; ++j) { reversed = reversed << 1 | rtemp & 1; rtemp >>= 1; } // 最大ビット長をもとにテーブルを作るため、 // 最大ビット長以外では 0 / 1 どちらでも良い箇所ができる // ãã®ã©ã¡ã‚‰ã§ã‚‚è‰¯ã„å ´æ‰€ã¯åŒã˜å€¤ã§åŸ‹ã‚ã‚‹ã“ã¨ã§ // 本来のビット長以上のビット数取得しても問題が起こらないようにする value = bitLength << 16 | i; for (j = reversed; j < size; j += skip) { table[j] = value; } ++code; } } // 次のビット長へ ++bitLength; code <<= 1; skip <<= 1; } return [table, maxCodeLength, minCodeLength]; }; //----------------------------------------------------------------------------- /** @define {number} buffer block size. */ var ZLIB_RAW_INFLATE_BUFFER_SIZE$1 = 0x8000; // [ 0x8000 >= ZLIB_BUFFER_BLOCK_SIZE ] //----------------------------------------------------------------------------- var buildHuffmanTable$1 = Zlib$1.Huffman.buildHuffmanTable; /** * @constructor * @param {!(Uint8Array|Array.)} input input buffer. * @param {Object} opt_params option parameter. * * opt_params は以下のプロパティを指定する事ができます。 * - index: input buffer の deflate コンテナの開始位置. * - blockSize: バッファのブロックサイズ. * - bufferType: Zlib.RawInflate.BufferType の値によってバッファの管理方法を指定する. * - resize: ç¢ºä¿ã—ãŸãƒãƒƒãƒ•ã‚¡ãŒå®Ÿéš›ã®å¤§ãã•ã‚ˆã‚Šå¤§ãã‹ã£ãŸå ´åˆã«åˆ‡ã‚Šè©°ã‚ã‚‹. */ Zlib$1.RawInflate = function (input, opt_params) { /** @type {!(Array.|Uint8Array)} inflated buffer */ this.buffer; /** @type {!Array.<(Array.|Uint8Array)>} */ this.blocks = []; /** @type {number} block size. */ this.bufferSize = ZLIB_RAW_INFLATE_BUFFER_SIZE$1; /** @type {!number} total output buffer pointer. */ this.totalpos = 0; /** @type {!number} input buffer pointer. */ this.ip = 0; /** @type {!number} bit stream reader buffer. */ this.bitsbuf = 0; /** @type {!number} bit stream reader buffer size. */ this.bitsbuflen = 0; /** @type {!(Array.|Uint8Array)} input buffer. */ this.input = new Uint8Array(input) ; /** @type {!(Uint8Array|Array.)} output buffer. */ this.output; /** @type {!number} output buffer pointer. */ this.op; /** @type {boolean} is final block flag. */ this.bfinal = false; /** @type {Zlib.RawInflate.BufferType} buffer management. */ this.bufferType = Zlib$1.RawInflate.BufferType.ADAPTIVE; /** @type {boolean} resize flag for memory size optimization. */ this.resize = false; // option parameters if (opt_params || !(opt_params = {})) { if (opt_params['index']) { this.ip = opt_params['index']; } if (opt_params['bufferSize']) { this.bufferSize = opt_params['bufferSize']; } if (opt_params['bufferType']) { this.bufferType = opt_params['bufferType']; } if (opt_params['resize']) { this.resize = opt_params['resize']; } } // initialize switch (this.bufferType) { case Zlib$1.RawInflate.BufferType.BLOCK: this.op = Zlib$1.RawInflate.MaxBackwardLength; this.output = new (Uint8Array )(Zlib$1.RawInflate.MaxBackwardLength + this.bufferSize + Zlib$1.RawInflate.MaxCopyLength); break; case Zlib$1.RawInflate.BufferType.ADAPTIVE: this.op = 0; this.output = new (Uint8Array )(this.bufferSize); break; default: throw new Error('invalid inflate mode'); } }; /** * @enum {number} */ Zlib$1.RawInflate.BufferType = { BLOCK: 0, ADAPTIVE: 1 }; /** * decompress. * @return {!(Uint8Array|Array.)} inflated buffer. */ Zlib$1.RawInflate.prototype.decompress = function () { while (!this.bfinal) { this.parseBlock(); } switch (this.bufferType) { case Zlib$1.RawInflate.BufferType.BLOCK: return this.concatBufferBlock(); case Zlib$1.RawInflate.BufferType.ADAPTIVE: return this.concatBufferDynamic(); default: throw new Error('invalid inflate mode'); } }; /** * @const * @type {number} max backward length for LZ77. */ Zlib$1.RawInflate.MaxBackwardLength = 32768; /** * @const * @type {number} max copy length for LZ77. */ Zlib$1.RawInflate.MaxCopyLength = 258; /** * huffman order * @const * @type {!(Array.|Uint8Array)} */ Zlib$1.RawInflate.Order = function (table) { return new Uint16Array(table) ; }([16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15]); /** * huffman length code table. * @const * @type {!(Array.|Uint16Array)} */ Zlib$1.RawInflate.LengthCodeTable = function (table) { return new Uint16Array(table) ; }([0x0003, 0x0004, 0x0005, 0x0006, 0x0007, 0x0008, 0x0009, 0x000a, 0x000b, 0x000d, 0x000f, 0x0011, 0x0013, 0x0017, 0x001b, 0x001f, 0x0023, 0x002b, 0x0033, 0x003b, 0x0043, 0x0053, 0x0063, 0x0073, 0x0083, 0x00a3, 0x00c3, 0x00e3, 0x0102, 0x0102, 0x0102]); /** * huffman length extra-bits table. * @const * @type {!(Array.|Uint8Array)} */ Zlib$1.RawInflate.LengthExtraTable = function (table) { return new Uint8Array(table) ; }([0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 0, 0, 0]); /** * huffman dist code table. * @const * @type {!(Array.|Uint16Array)} */ Zlib$1.RawInflate.DistCodeTable = function (table) { return new Uint16Array(table) ; }([0x0001, 0x0002, 0x0003, 0x0004, 0x0005, 0x0007, 0x0009, 0x000d, 0x0011, 0x0019, 0x0021, 0x0031, 0x0041, 0x0061, 0x0081, 0x00c1, 0x0101, 0x0181, 0x0201, 0x0301, 0x0401, 0x0601, 0x0801, 0x0c01, 0x1001, 0x1801, 0x2001, 0x3001, 0x4001, 0x6001]); /** * huffman dist extra-bits table. * @const * @type {!(Array.|Uint8Array)} */ Zlib$1.RawInflate.DistExtraTable = function (table) { return new Uint8Array(table) ; }([0, 0, 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 13, 13]); /** * fixed huffman length code table * @const * @type {!Array} */ Zlib$1.RawInflate.FixedLiteralLengthTable = function (table) { return table; }(function () { var lengths = new (Uint8Array )(288); var i, il; for (i = 0, il = lengths.length; i < il; ++i) { lengths[i] = i <= 143 ? 8 : i <= 255 ? 9 : i <= 279 ? 7 : 8; } return buildHuffmanTable$1(lengths); }()); /** * fixed huffman distance code table * @const * @type {!Array} */ Zlib$1.RawInflate.FixedDistanceTable = function (table) { return table; }(function () { var lengths = new (Uint8Array )(30); var i, il; for (i = 0, il = lengths.length; i < il; ++i) { lengths[i] = 5; } return buildHuffmanTable$1(lengths); }()); /** * parse deflated block. */ Zlib$1.RawInflate.prototype.parseBlock = function () { /** @type {number} header */ var hdr = this.readBits(3); // BFINAL if (hdr & 0x1) { this.bfinal = true; } // BTYPE hdr >>>= 1; switch (hdr) { // uncompressed case 0: this.parseUncompressedBlock(); break; // fixed huffman case 1: this.parseFixedHuffmanBlock(); break; // dynamic huffman case 2: this.parseDynamicHuffmanBlock(); break; // reserved or other default: throw new Error('unknown BTYPE: ' + hdr); } }; /** * read inflate bits * @param {number} length bits length. * @return {number} read bits. */ Zlib$1.RawInflate.prototype.readBits = function (length) { var bitsbuf = this.bitsbuf; var bitsbuflen = this.bitsbuflen; var input = this.input; var ip = this.ip; /** @type {number} */ var inputLength = input.length; /** @type {number} input and output byte. */ var octet; // input byte if (ip + (length - bitsbuflen + 7 >> 3) >= inputLength) { throw new Error('input buffer is broken'); } // not enough buffer while (bitsbuflen < length) { bitsbuf |= input[ip++] << bitsbuflen; bitsbuflen += 8; } // output byte octet = bitsbuf & (1 << length) - 1; bitsbuf >>>= length; bitsbuflen -= length; this.bitsbuf = bitsbuf; this.bitsbuflen = bitsbuflen; this.ip = ip; return octet; }; /** * read huffman code using table * @param {!(Array.|Uint8Array|Uint16Array)} table huffman code table. * @return {number} huffman code. */ Zlib$1.RawInflate.prototype.readCodeByTable = function (table) { var bitsbuf = this.bitsbuf; var bitsbuflen = this.bitsbuflen; var input = this.input; var ip = this.ip; /** @type {number} */ var inputLength = input.length; /** @type {!(Array.|Uint8Array)} huffman code table */ var codeTable = table[0]; /** @type {number} */ var maxCodeLength = table[1]; /** @type {number} code length & code (16bit, 16bit) */ var codeWithLength; /** @type {number} code bits length */ var codeLength; // not enough buffer while (bitsbuflen < maxCodeLength) { if (ip >= inputLength) { break; } bitsbuf |= input[ip++] << bitsbuflen; bitsbuflen += 8; } // read max length codeWithLength = codeTable[bitsbuf & (1 << maxCodeLength) - 1]; codeLength = codeWithLength >>> 16; if (codeLength > bitsbuflen) { throw new Error('invalid code length: ' + codeLength); } this.bitsbuf = bitsbuf >> codeLength; this.bitsbuflen = bitsbuflen - codeLength; this.ip = ip; return codeWithLength & 0xffff; }; /** * parse uncompressed block. */ Zlib$1.RawInflate.prototype.parseUncompressedBlock = function () { var input = this.input; var ip = this.ip; var output = this.output; var op = this.op; /** @type {number} */ var inputLength = input.length; /** @type {number} block length */ var len; /** @type {number} number for check block length */ var nlen; /** @type {number} output buffer length */ var olength = output.length; /** @type {number} copy counter */ var preCopy; // skip buffered header bits this.bitsbuf = 0; this.bitsbuflen = 0; // len if (ip + 1 >= inputLength) { throw new Error('invalid uncompressed block header: LEN'); } len = input[ip++] | input[ip++] << 8; // nlen if (ip + 1 >= inputLength) { throw new Error('invalid uncompressed block header: NLEN'); } nlen = input[ip++] | input[ip++] << 8; // check len & nlen if (len === ~nlen) { throw new Error('invalid uncompressed block header: length verify'); } // check size if (ip + len > input.length) { throw new Error('input buffer is broken'); } // expand buffer switch (this.bufferType) { case Zlib$1.RawInflate.BufferType.BLOCK: // pre copy while (op + len > output.length) { preCopy = olength - op; len -= preCopy; { output.set(input.subarray(ip, ip + preCopy), op); op += preCopy; ip += preCopy; } this.op = op; output = this.expandBufferBlock(); op = this.op; } break; case Zlib$1.RawInflate.BufferType.ADAPTIVE: while (op + len > output.length) { output = this.expandBufferAdaptive({ fixRatio: 2 }); } break; default: throw new Error('invalid inflate mode'); } // copy { output.set(input.subarray(ip, ip + len), op); op += len; ip += len; } this.ip = ip; this.op = op; this.output = output; }; /** * parse fixed huffman block. */ Zlib$1.RawInflate.prototype.parseFixedHuffmanBlock = function () { switch (this.bufferType) { case Zlib$1.RawInflate.BufferType.ADAPTIVE: this.decodeHuffmanAdaptive(Zlib$1.RawInflate.FixedLiteralLengthTable, Zlib$1.RawInflate.FixedDistanceTable); break; case Zlib$1.RawInflate.BufferType.BLOCK: this.decodeHuffmanBlock(Zlib$1.RawInflate.FixedLiteralLengthTable, Zlib$1.RawInflate.FixedDistanceTable); break; default: throw new Error('invalid inflate mode'); } }; /** * parse dynamic huffman block. */ Zlib$1.RawInflate.prototype.parseDynamicHuffmanBlock = function () { /** @type {number} number of literal and length codes. */ var hlit = this.readBits(5) + 257; /** @type {number} number of distance codes. */ var hdist = this.readBits(5) + 1; /** @type {number} number of code lengths. */ var hclen = this.readBits(4) + 4; /** @type {!(Uint8Array|Array.)} code lengths. */ var codeLengths = new (Uint8Array )(Zlib$1.RawInflate.Order.length); /** @type {!Array} code lengths table. */ var codeLengthsTable; /** @type {!(Uint8Array|Array.)} literal and length code table. */ var litlenTable; /** @type {!(Uint8Array|Array.)} distance code table. */ var distTable; /** @type {!(Uint8Array|Array.)} code length table. */ var lengthTable; /** @type {number} */ var code; /** @type {number} */ var prev; /** @type {number} */ var repeat; /** @type {number} loop counter. */ var i; /** @type {number} loop limit. */ var il; // decode code lengths for (i = 0; i < hclen; ++i) { codeLengths[Zlib$1.RawInflate.Order[i]] = this.readBits(3); } codeLengthsTable = buildHuffmanTable$1(codeLengths); lengthTable = new (Uint8Array )(hlit + hdist); for (i = 0, il = hlit + hdist; i < il;) { code = this.readCodeByTable(codeLengthsTable); switch (code) { case 16: repeat = 3 + this.readBits(2); while (repeat--) { lengthTable[i++] = prev; } break; case 17: repeat = 3 + this.readBits(3); while (repeat--) { lengthTable[i++] = 0; } prev = 0; break; case 18: repeat = 11 + this.readBits(7); while (repeat--) { lengthTable[i++] = 0; } prev = 0; break; default: lengthTable[i++] = code; prev = code; break; } } litlenTable = buildHuffmanTable$1(lengthTable.subarray(0, hlit)) ; distTable = buildHuffmanTable$1(lengthTable.subarray(hlit)) ; switch (this.bufferType) { case Zlib$1.RawInflate.BufferType.ADAPTIVE: this.decodeHuffmanAdaptive(litlenTable, distTable); break; case Zlib$1.RawInflate.BufferType.BLOCK: this.decodeHuffmanBlock(litlenTable, distTable); break; default: throw new Error('invalid inflate mode'); } }; /** * decode huffman code * @param {!(Array.|Uint16Array)} litlen literal and length code table. * @param {!(Array.|Uint8Array)} dist distination code table. */ Zlib$1.RawInflate.prototype.decodeHuffmanBlock = function (litlen, dist) { var output = this.output; var op = this.op; this.currentLitlenTable = litlen; /** @type {number} output position limit. */ var olength = output.length - Zlib$1.RawInflate.MaxCopyLength; /** @type {number} huffman code. */ var code; /** @type {number} table index. */ var ti; /** @type {number} huffman code distination. */ var codeDist; /** @type {number} huffman code length. */ var codeLength; var lengthCodeTable = Zlib$1.RawInflate.LengthCodeTable; var lengthExtraTable = Zlib$1.RawInflate.LengthExtraTable; var distCodeTable = Zlib$1.RawInflate.DistCodeTable; var distExtraTable = Zlib$1.RawInflate.DistExtraTable; while ((code = this.readCodeByTable(litlen)) !== 256) { // literal if (code < 256) { if (op >= olength) { this.op = op; output = this.expandBufferBlock(); op = this.op; } output[op++] = code; continue; } // length code ti = code - 257; codeLength = lengthCodeTable[ti]; if (lengthExtraTable[ti] > 0) { codeLength += this.readBits(lengthExtraTable[ti]); } // dist code code = this.readCodeByTable(dist); codeDist = distCodeTable[code]; if (distExtraTable[code] > 0) { codeDist += this.readBits(distExtraTable[code]); } // lz77 decode if (op >= olength) { this.op = op; output = this.expandBufferBlock(); op = this.op; } while (codeLength--) { output[op] = output[op++ - codeDist]; } } while (this.bitsbuflen >= 8) { this.bitsbuflen -= 8; this.ip--; } this.op = op; }; /** * decode huffman code (adaptive) * @param {!(Array.|Uint16Array)} litlen literal and length code table. * @param {!(Array.|Uint8Array)} dist distination code table. */ Zlib$1.RawInflate.prototype.decodeHuffmanAdaptive = function (litlen, dist) { var output = this.output; var op = this.op; this.currentLitlenTable = litlen; /** @type {number} output position limit. */ var olength = output.length; /** @type {number} huffman code. */ var code; /** @type {number} table index. */ var ti; /** @type {number} huffman code distination. */ var codeDist; /** @type {number} huffman code length. */ var codeLength; var lengthCodeTable = Zlib$1.RawInflate.LengthCodeTable; var lengthExtraTable = Zlib$1.RawInflate.LengthExtraTable; var distCodeTable = Zlib$1.RawInflate.DistCodeTable; var distExtraTable = Zlib$1.RawInflate.DistExtraTable; while ((code = this.readCodeByTable(litlen)) !== 256) { // literal if (code < 256) { if (op >= olength) { output = this.expandBufferAdaptive(); olength = output.length; } output[op++] = code; continue; } // length code ti = code - 257; codeLength = lengthCodeTable[ti]; if (lengthExtraTable[ti] > 0) { codeLength += this.readBits(lengthExtraTable[ti]); } // dist code code = this.readCodeByTable(dist); codeDist = distCodeTable[code]; if (distExtraTable[code] > 0) { codeDist += this.readBits(distExtraTable[code]); } // lz77 decode if (op + codeLength > olength) { output = this.expandBufferAdaptive(); olength = output.length; } while (codeLength--) { output[op] = output[op++ - codeDist]; } } while (this.bitsbuflen >= 8) { this.bitsbuflen -= 8; this.ip--; } this.op = op; }; /** * expand output buffer. * @param {Object=} opt_param option parameters. * @return {!(Array.|Uint8Array)} output buffer. */ Zlib$1.RawInflate.prototype.expandBufferBlock = function (opt_param) { /** @type {!(Array.|Uint8Array)} store buffer. */ var buffer = new (Uint8Array )(this.op - Zlib$1.RawInflate.MaxBackwardLength); /** @type {number} backward base point */ var backward = this.op - Zlib$1.RawInflate.MaxBackwardLength; var output = this.output; // copy to output buffer { buffer.set(output.subarray(Zlib$1.RawInflate.MaxBackwardLength, buffer.length)); } this.blocks.push(buffer); this.totalpos += buffer.length; // copy to backward buffer { output.set(output.subarray(backward, backward + Zlib$1.RawInflate.MaxBackwardLength)); } this.op = Zlib$1.RawInflate.MaxBackwardLength; return output; }; /** * expand output buffer. (adaptive) * @param {Object=} opt_param option parameters. * @return {!(Array.|Uint8Array)} output buffer pointer. */ Zlib$1.RawInflate.prototype.expandBufferAdaptive = function (opt_param) { /** @type {!(Array.|Uint8Array)} store buffer. */ var buffer; /** @type {number} expantion ratio. */ var ratio = this.input.length / this.ip + 1 | 0; /** @type {number} maximum number of huffman code. */ var maxHuffCode; /** @type {number} new output buffer size. */ var newSize; /** @type {number} max inflate size. */ var maxInflateSize; var input = this.input; var output = this.output; if (opt_param) { if (typeof opt_param.fixRatio === 'number') { ratio = opt_param.fixRatio; } if (typeof opt_param.addRatio === 'number') { ratio += opt_param.addRatio; } } // calculate new buffer size if (ratio < 2) { maxHuffCode = (input.length - this.ip) / this.currentLitlenTable[2]; maxInflateSize = maxHuffCode / 2 * 258 | 0; newSize = maxInflateSize < output.length ? output.length + maxInflateSize : output.length << 1; } else { newSize = output.length * ratio; } // buffer expantion { buffer = new Uint8Array(newSize); buffer.set(output); } this.output = buffer; return this.output; }; /** * concat output buffer. * @return {!(Array.|Uint8Array)} output buffer. */ Zlib$1.RawInflate.prototype.concatBufferBlock = function () { /** @type {number} buffer pointer. */ var pos = 0; /** @type {number} buffer pointer. */ var limit = this.totalpos + (this.op - Zlib$1.RawInflate.MaxBackwardLength); /** @type {!(Array.|Uint8Array)} output block array. */ var output = this.output; /** @type {!Array} blocks array. */ var blocks = this.blocks; /** @type {!(Array.|Uint8Array)} output block array. */ var block; /** @type {!(Array.|Uint8Array)} output buffer. */ var buffer = new (Uint8Array )(limit); /** @type {number} loop counter. */ var i; /** @type {number} loop limiter. */ var il; /** @type {number} loop counter. */ var j; /** @type {number} loop limiter. */ var jl; // single buffer if (blocks.length === 0) { return this.output.subarray(Zlib$1.RawInflate.MaxBackwardLength, this.op) ; } // copy to buffer for (i = 0, il = blocks.length; i < il; ++i) { block = blocks[i]; for (j = 0, jl = block.length; j < jl; ++j) { buffer[pos++] = block[j]; } } // current buffer for (i = Zlib$1.RawInflate.MaxBackwardLength, il = this.op; i < il; ++i) { buffer[pos++] = output[i]; } this.blocks = []; this.buffer = buffer; return this.buffer; }; /** * concat output buffer. (dynamic) * @return {!(Array.|Uint8Array)} output buffer. */ Zlib$1.RawInflate.prototype.concatBufferDynamic = function () { /** @type {Array.|Uint8Array} output buffer. */ var buffer; var op = this.op; { if (this.resize) { buffer = new Uint8Array(op); buffer.set(this.output.subarray(0, op)); } else { buffer = this.output.subarray(0, op); } } this.buffer = buffer; return this.buffer; }; var buildHuffmanTable$1 = Zlib$1.Huffman.buildHuffmanTable; /** * @param {!(Uint8Array|Array.)} input input buffer. * @param {number} ip input buffer pointer. * @param {number=} opt_buffersize buffer block size. * @constructor */ Zlib$1.RawInflateStream = function (input, ip, opt_buffersize) { /** @type {!Array.<(Array|Uint8Array)>} */ this.blocks = []; /** @type {number} block size. */ this.bufferSize = opt_buffersize ? opt_buffersize : ZLIB_STREAM_RAW_INFLATE_BUFFER_SIZE$1; /** @type {!number} total output buffer pointer. */ this.totalpos = 0; /** @type {!number} input buffer pointer. */ this.ip = ip === void 0 ? 0 : ip; /** @type {!number} bit stream reader buffer. */ this.bitsbuf = 0; /** @type {!number} bit stream reader buffer size. */ this.bitsbuflen = 0; /** @type {!(Array|Uint8Array)} input buffer. */ this.input = new Uint8Array(input) ; /** @type {!(Uint8Array|Array)} output buffer. */ this.output = new (Uint8Array )(this.bufferSize); /** @type {!number} output buffer pointer. */ this.op = 0; /** @type {boolean} is final block flag. */ this.bfinal = false; /** @type {number} uncompressed block length. */ this.blockLength; /** @type {boolean} resize flag for memory size optimization. */ this.resize = false; /** @type {Array} */ this.litlenTable; /** @type {Array} */ this.distTable; /** @type {number} */ this.sp = 0; // stream pointer /** @type {Zlib.RawInflateStream.Status} */ this.status = Zlib$1.RawInflateStream.Status.INITIALIZED; // // backup // /** @type {!number} */ this.ip_; /** @type {!number} */ this.bitsbuflen_; /** @type {!number} */ this.bitsbuf_; }; /** * @enum {number} */ Zlib$1.RawInflateStream.BlockType = { UNCOMPRESSED: 0, FIXED: 1, DYNAMIC: 2 }; /** * @enum {number} */ Zlib$1.RawInflateStream.Status = { INITIALIZED: 0, BLOCK_HEADER_START: 1, BLOCK_HEADER_END: 2, BLOCK_BODY_START: 3, BLOCK_BODY_END: 4, DECODE_BLOCK_START: 5, DECODE_BLOCK_END: 6 }; /** * decompress. * @return {!(Uint8Array|Array)} inflated buffer. */ Zlib$1.RawInflateStream.prototype.decompress = function (newInput, ip) { /** @type {boolean} */ var stop = false; if (newInput !== void 0) { this.input = newInput; } if (ip !== void 0) { this.ip = ip; } // decompress while (!stop) { switch (this.status) { // block header case Zlib$1.RawInflateStream.Status.INITIALIZED: case Zlib$1.RawInflateStream.Status.BLOCK_HEADER_START: if (this.readBlockHeader() < 0) { stop = true; } break; // block body case Zlib$1.RawInflateStream.Status.BLOCK_HEADER_END: /* FALLTHROUGH */ case Zlib$1.RawInflateStream.Status.BLOCK_BODY_START: switch (this.currentBlockType) { case Zlib$1.RawInflateStream.BlockType.UNCOMPRESSED: if (this.readUncompressedBlockHeader() < 0) { stop = true; } break; case Zlib$1.RawInflateStream.BlockType.FIXED: if (this.parseFixedHuffmanBlock() < 0) { stop = true; } break; case Zlib$1.RawInflateStream.BlockType.DYNAMIC: if (this.parseDynamicHuffmanBlock() < 0) { stop = true; } break; } break; // decode data case Zlib$1.RawInflateStream.Status.BLOCK_BODY_END: case Zlib$1.RawInflateStream.Status.DECODE_BLOCK_START: switch (this.currentBlockType) { case Zlib$1.RawInflateStream.BlockType.UNCOMPRESSED: if (this.parseUncompressedBlock() < 0) { stop = true; } break; case Zlib$1.RawInflateStream.BlockType.FIXED: /* FALLTHROUGH */ case Zlib$1.RawInflateStream.BlockType.DYNAMIC: if (this.decodeHuffman() < 0) { stop = true; } break; } break; case Zlib$1.RawInflateStream.Status.DECODE_BLOCK_END: if (this.bfinal) { stop = true; } else { this.status = Zlib$1.RawInflateStream.Status.INITIALIZED; } break; } } return this.concatBuffer(); }; /** * @const * @type {number} max backward length for LZ77. */ Zlib$1.RawInflateStream.MaxBackwardLength = 32768; /** * @const * @type {number} max copy length for LZ77. */ Zlib$1.RawInflateStream.MaxCopyLength = 258; /** * huffman order * @const * @type {!(Array.|Uint8Array)} */ Zlib$1.RawInflateStream.Order = function (table) { return new Uint16Array(table) ; }([16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15]); /** * huffman length code table. * @const * @type {!(Array.|Uint16Array)} */ Zlib$1.RawInflateStream.LengthCodeTable = function (table) { return new Uint16Array(table) ; }([0x0003, 0x0004, 0x0005, 0x0006, 0x0007, 0x0008, 0x0009, 0x000a, 0x000b, 0x000d, 0x000f, 0x0011, 0x0013, 0x0017, 0x001b, 0x001f, 0x0023, 0x002b, 0x0033, 0x003b, 0x0043, 0x0053, 0x0063, 0x0073, 0x0083, 0x00a3, 0x00c3, 0x00e3, 0x0102, 0x0102, 0x0102]); /** * huffman length extra-bits table. * @const * @type {!(Array.|Uint8Array)} */ Zlib$1.RawInflateStream.LengthExtraTable = function (table) { return new Uint8Array(table) ; }([0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 0, 0, 0]); /** * huffman dist code table. * @const * @type {!(Array.|Uint16Array)} */ Zlib$1.RawInflateStream.DistCodeTable = function (table) { return new Uint16Array(table) ; }([0x0001, 0x0002, 0x0003, 0x0004, 0x0005, 0x0007, 0x0009, 0x000d, 0x0011, 0x0019, 0x0021, 0x0031, 0x0041, 0x0061, 0x0081, 0x00c1, 0x0101, 0x0181, 0x0201, 0x0301, 0x0401, 0x0601, 0x0801, 0x0c01, 0x1001, 0x1801, 0x2001, 0x3001, 0x4001, 0x6001]); /** * huffman dist extra-bits table. * @const * @type {!(Array.|Uint8Array)} */ Zlib$1.RawInflateStream.DistExtraTable = function (table) { return new Uint8Array(table) ; }([0, 0, 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 13, 13]); /** * fixed huffman length code table * @const * @type {!Array} */ Zlib$1.RawInflateStream.FixedLiteralLengthTable = function (table) { return table; }(function () { var lengths = new (Uint8Array )(288); var i, il; for (i = 0, il = lengths.length; i < il; ++i) { lengths[i] = i <= 143 ? 8 : i <= 255 ? 9 : i <= 279 ? 7 : 8; } return buildHuffmanTable$1(lengths); }()); /** * fixed huffman distance code table * @const * @type {!Array} */ Zlib$1.RawInflateStream.FixedDistanceTable = function (table) { return table; }(function () { var lengths = new (Uint8Array )(30); var i, il; for (i = 0, il = lengths.length; i < il; ++i) { lengths[i] = 5; } return buildHuffmanTable$1(lengths); }()); /** * parse deflated block. */ Zlib$1.RawInflateStream.prototype.readBlockHeader = function () { /** @type {number} header */ var hdr; this.status = Zlib$1.RawInflateStream.Status.BLOCK_HEADER_START; this.save_(); if ((hdr = this.readBits(3)) < 0) { this.restore_(); return -1; } // BFINAL if (hdr & 0x1) { this.bfinal = true; } // BTYPE hdr >>>= 1; switch (hdr) { case 0: // uncompressed this.currentBlockType = Zlib$1.RawInflateStream.BlockType.UNCOMPRESSED; break; case 1: // fixed huffman this.currentBlockType = Zlib$1.RawInflateStream.BlockType.FIXED; break; case 2: // dynamic huffman this.currentBlockType = Zlib$1.RawInflateStream.BlockType.DYNAMIC; break; default: // reserved or other throw new Error('unknown BTYPE: ' + hdr); } this.status = Zlib$1.RawInflateStream.Status.BLOCK_HEADER_END; }; /** * read inflate bits * @param {number} length bits length. * @return {number} read bits. */ Zlib$1.RawInflateStream.prototype.readBits = function (length) { var bitsbuf = this.bitsbuf; var bitsbuflen = this.bitsbuflen; var input = this.input; var ip = this.ip; /** @type {number} input and output byte. */ var octet; // not enough buffer while (bitsbuflen < length) { // input byte if (input.length <= ip) { return -1; } octet = input[ip++]; // concat octet bitsbuf |= octet << bitsbuflen; bitsbuflen += 8; } // output byte octet = bitsbuf & (1 << length) - 1; bitsbuf >>>= length; bitsbuflen -= length; this.bitsbuf = bitsbuf; this.bitsbuflen = bitsbuflen; this.ip = ip; return octet; }; /** * read huffman code using table * @param {Array} table huffman code table. * @return {number} huffman code. */ Zlib$1.RawInflateStream.prototype.readCodeByTable = function (table) { var bitsbuf = this.bitsbuf; var bitsbuflen = this.bitsbuflen; var input = this.input; var ip = this.ip; /** @type {!(Array|Uint8Array)} huffman code table */ var codeTable = table[0]; /** @type {number} */ var maxCodeLength = table[1]; /** @type {number} input byte */ var octet; /** @type {number} code length & code (16bit, 16bit) */ var codeWithLength; /** @type {number} code bits length */ var codeLength; // not enough buffer while (bitsbuflen < maxCodeLength) { if (input.length <= ip) { return -1; } octet = input[ip++]; bitsbuf |= octet << bitsbuflen; bitsbuflen += 8; } // read max length codeWithLength = codeTable[bitsbuf & (1 << maxCodeLength) - 1]; codeLength = codeWithLength >>> 16; if (codeLength > bitsbuflen) { throw new Error('invalid code length: ' + codeLength); } this.bitsbuf = bitsbuf >> codeLength; this.bitsbuflen = bitsbuflen - codeLength; this.ip = ip; return codeWithLength & 0xffff; }; /** * read uncompressed block header */ Zlib$1.RawInflateStream.prototype.readUncompressedBlockHeader = function () { /** @type {number} block length */ var len; /** @type {number} number for check block length */ var nlen; var input = this.input; var ip = this.ip; this.status = Zlib$1.RawInflateStream.Status.BLOCK_BODY_START; if (ip + 4 >= input.length) { return -1; } len = input[ip++] | input[ip++] << 8; nlen = input[ip++] | input[ip++] << 8; // check len & nlen if (len === ~nlen) { throw new Error('invalid uncompressed block header: length verify'); } // skip buffered header bits this.bitsbuf = 0; this.bitsbuflen = 0; this.ip = ip; this.blockLength = len; this.status = Zlib$1.RawInflateStream.Status.BLOCK_BODY_END; }; /** * parse uncompressed block. */ Zlib$1.RawInflateStream.prototype.parseUncompressedBlock = function () { var input = this.input; var ip = this.ip; var output = this.output; var op = this.op; var len = this.blockLength; this.status = Zlib$1.RawInflateStream.Status.DECODE_BLOCK_START; // copy // XXX: ã¨ã‚Šã‚ãˆãšç´ ç›´ã«ã‚³ãƒ”ãƒ¼ while (len--) { if (op === output.length) { output = this.expandBuffer({ fixRatio: 2 }); } // not enough input buffer if (ip >= input.length) { this.ip = ip; this.op = op; this.blockLength = len + 1; // コピーしてないので戻す return -1; } output[op++] = input[ip++]; } if (len < 0) { this.status = Zlib$1.RawInflateStream.Status.DECODE_BLOCK_END; } this.ip = ip; this.op = op; return 0; }; /** * parse fixed huffman block. */ Zlib$1.RawInflateStream.prototype.parseFixedHuffmanBlock = function () { this.status = Zlib$1.RawInflateStream.Status.BLOCK_BODY_START; this.litlenTable = Zlib$1.RawInflateStream.FixedLiteralLengthTable; this.distTable = Zlib$1.RawInflateStream.FixedDistanceTable; this.status = Zlib$1.RawInflateStream.Status.BLOCK_BODY_END; return 0; }; /** * オブジェクトのコンテキストを別のプロパティに退避する. * @private */ Zlib$1.RawInflateStream.prototype.save_ = function () { this.ip_ = this.ip; this.bitsbuflen_ = this.bitsbuflen; this.bitsbuf_ = this.bitsbuf; }; /** * 別のプロパティに退避したコンテキストを復元する. * @private */ Zlib$1.RawInflateStream.prototype.restore_ = function () { this.ip = this.ip_; this.bitsbuflen = this.bitsbuflen_; this.bitsbuf = this.bitsbuf_; }; /** * parse dynamic huffman block. */ Zlib$1.RawInflateStream.prototype.parseDynamicHuffmanBlock = function () { /** @type {number} number of literal and length codes. */ var hlit; /** @type {number} number of distance codes. */ var hdist; /** @type {number} number of code lengths. */ var hclen; /** @type {!(Uint8Array|Array)} code lengths. */ var codeLengths = new (Uint8Array )(Zlib$1.RawInflateStream.Order.length); /** @type {!Array} code lengths table. */ var codeLengthsTable; this.status = Zlib$1.RawInflateStream.Status.BLOCK_BODY_START; this.save_(); hlit = this.readBits(5) + 257; hdist = this.readBits(5) + 1; hclen = this.readBits(4) + 4; if (hlit < 0 || hdist < 0 || hclen < 0) { this.restore_(); return -1; } try { parseDynamicHuffmanBlockImpl.call(this); } catch (e) { this.restore_(); return -1; } function parseDynamicHuffmanBlockImpl() { /** @type {number} */ var bits; var code; var prev = 0; var repeat; /** @type {!(Uint8Array|Array.)} code length table. */ var lengthTable; /** @type {number} loop counter. */ var i; /** @type {number} loop limit. */ var il; // decode code lengths for (i = 0; i < hclen; ++i) { if ((bits = this.readBits(3)) < 0) { throw new Error('not enough input'); } codeLengths[Zlib$1.RawInflateStream.Order[i]] = bits; } // decode length table codeLengthsTable = buildHuffmanTable$1(codeLengths); lengthTable = new (Uint8Array )(hlit + hdist); for (i = 0, il = hlit + hdist; i < il;) { code = this.readCodeByTable(codeLengthsTable); if (code < 0) { throw new Error('not enough input'); } switch (code) { case 16: if ((bits = this.readBits(2)) < 0) { throw new Error('not enough input'); } repeat = 3 + bits; while (repeat--) { lengthTable[i++] = prev; } break; case 17: if ((bits = this.readBits(3)) < 0) { throw new Error('not enough input'); } repeat = 3 + bits; while (repeat--) { lengthTable[i++] = 0; } prev = 0; break; case 18: if ((bits = this.readBits(7)) < 0) { throw new Error('not enough input'); } repeat = 11 + bits; while (repeat--) { lengthTable[i++] = 0; } prev = 0; break; default: lengthTable[i++] = code; prev = code; break; } } // literal and length code this.litlenTable = buildHuffmanTable$1(lengthTable.subarray(0, hlit)) ; this.distTable = buildHuffmanTable$1(lengthTable.subarray(hlit)) ; } this.status = Zlib$1.RawInflateStream.Status.BLOCK_BODY_END; return 0; }; /** * decode huffman code (dynamic) * @return {(number|undefined)} -1 is error. */ Zlib$1.RawInflateStream.prototype.decodeHuffman = function () { var output = this.output; var op = this.op; /** @type {number} huffman code. */ var code; /** @type {number} table index. */ var ti; /** @type {number} huffman code distination. */ var codeDist; /** @type {number} huffman code length. */ var codeLength; var litlen = this.litlenTable; var dist = this.distTable; var olength = output.length; var bits; this.status = Zlib$1.RawInflateStream.Status.DECODE_BLOCK_START; while (true) { this.save_(); code = this.readCodeByTable(litlen); if (code < 0) { this.op = op; this.restore_(); return -1; } if (code === 256) { break; } // literal if (code < 256) { if (op === olength) { output = this.expandBuffer(); olength = output.length; } output[op++] = code; continue; } // length code ti = code - 257; codeLength = Zlib$1.RawInflateStream.LengthCodeTable[ti]; if (Zlib$1.RawInflateStream.LengthExtraTable[ti] > 0) { bits = this.readBits(Zlib$1.RawInflateStream.LengthExtraTable[ti]); if (bits < 0) { this.op = op; this.restore_(); return -1; } codeLength += bits; } // dist code code = this.readCodeByTable(dist); if (code < 0) { this.op = op; this.restore_(); return -1; } codeDist = Zlib$1.RawInflateStream.DistCodeTable[code]; if (Zlib$1.RawInflateStream.DistExtraTable[code] > 0) { bits = this.readBits(Zlib$1.RawInflateStream.DistExtraTable[code]); if (bits < 0) { this.op = op; this.restore_(); return -1; } codeDist += bits; } // lz77 decode if (op + codeLength >= olength) { output = this.expandBuffer(); olength = output.length; } while (codeLength--) { output[op] = output[op++ - codeDist]; } // break if (this.ip === this.input.length) { this.op = op; return -1; } } while (this.bitsbuflen >= 8) { this.bitsbuflen -= 8; this.ip--; } this.op = op; this.status = Zlib$1.RawInflateStream.Status.DECODE_BLOCK_END; }; /** * expand output buffer. (dynamic) * @param {Object=} opt_param option parameters. * @return {!(Array|Uint8Array)} output buffer pointer. */ Zlib$1.RawInflateStream.prototype.expandBuffer = function (opt_param) { /** @type {!(Array|Uint8Array)} store buffer. */ var buffer; /** @type {number} expantion ratio. */ var ratio = this.input.length / this.ip + 1 | 0; /** @type {number} maximum number of huffman code. */ var maxHuffCode; /** @type {number} new output buffer size. */ var newSize; /** @type {number} max inflate size. */ var maxInflateSize; var input = this.input; var output = this.output; if (opt_param) { if (typeof opt_param.fixRatio === 'number') { ratio = opt_param.fixRatio; } if (typeof opt_param.addRatio === 'number') { ratio += opt_param.addRatio; } } // calculate new buffer size if (ratio < 2) { maxHuffCode = (input.length - this.ip) / this.litlenTable[2]; maxInflateSize = maxHuffCode / 2 * 258 | 0; newSize = maxInflateSize < output.length ? output.length + maxInflateSize : output.length << 1; } else { newSize = output.length * ratio; } // buffer expantion { buffer = new Uint8Array(newSize); buffer.set(output); } this.output = buffer; return this.output; }; /** * concat output buffer. (dynamic) * @return {!(Array|Uint8Array)} output buffer. */ Zlib$1.RawInflateStream.prototype.concatBuffer = function () { /** @type {!(Array|Uint8Array)} output buffer. */ var buffer; /** @type {number} */ var op = this.op; /** @type {Uint8Array} */ var tmp; if (this.resize) { { buffer = new Uint8Array(this.output.subarray(this.sp, op)); } } else { buffer = this.output.subarray(this.sp, op) ; } this.sp = op; // compaction if (op > Zlib$1.RawInflateStream.MaxBackwardLength + this.bufferSize) { this.op = this.sp = Zlib$1.RawInflateStream.MaxBackwardLength; { tmp = this.output; this.output = new Uint8Array(this.bufferSize + Zlib$1.RawInflateStream.MaxBackwardLength); this.output.set(tmp.subarray(op - Zlib$1.RawInflateStream.MaxBackwardLength, op)); } } return buffer; }; /** * @constructor * @param {!(Uint8Array|Array)} input deflated buffer. * @param {Object=} opt_params option parameters. * * opt_params は以下のプロパティを指定する事ができます。 * - index: input buffer の deflate コンテナの開始位置. * - blockSize: バッファのブロックサイズ. * - verify: 伸張が終わった後 adler-32 checksum の検証を行うか. * - bufferType: Zlib.Inflate.BufferType の値によってバッファの管理方法を指定する. * Zlib.Inflate.BufferType は Zlib.RawInflate.BufferType のエイリアス. */ Zlib$1.Inflate = function (input, opt_params) { /** @type {number} */ var cmf; /** @type {number} */ var flg; /** @type {!(Uint8Array|Array)} */ this.input = input; /** @type {number} */ this.ip = 0; /** @type {Zlib.RawInflate} */ this.rawinflate; /** @type {(boolean|undefined)} verify flag. */ this.verify; // option parameters if (opt_params || !(opt_params = {})) { if (opt_params['index']) { this.ip = opt_params['index']; } if (opt_params['verify']) { this.verify = opt_params['verify']; } } // Compression Method and Flags cmf = input[this.ip++]; flg = input[this.ip++]; // compression method switch (cmf & 0x0f) { case Zlib$1.CompressionMethod.DEFLATE: this.method = Zlib$1.CompressionMethod.DEFLATE; break; default: throw new Error('unsupported compression method'); } // fcheck if (((cmf << 8) + flg) % 31 !== 0) { throw new Error('invalid fcheck flag:' + ((cmf << 8) + flg) % 31); } // fdict (not supported) if (flg & 0x20) { throw new Error('fdict flag is not supported'); } // RawInflate this.rawinflate = new Zlib$1.RawInflate(input, { 'index': this.ip, 'bufferSize': opt_params['bufferSize'], 'bufferType': opt_params['bufferType'], 'resize': opt_params['resize'] }); }; /** * @enum {number} */ Zlib$1.Inflate.BufferType = Zlib$1.RawInflate.BufferType; /** * decompress. * @return {!(Uint8Array|Array)} inflated buffer. */ Zlib$1.Inflate.prototype.decompress = function () { /** @type {!(Array|Uint8Array)} input buffer. */ var input = this.input; /** @type {!(Uint8Array|Array)} inflated buffer. */ var buffer; /** @type {number} adler-32 checksum */ var adler32; buffer = this.rawinflate.decompress(); this.ip = this.rawinflate.ip; // verify adler-32 if (this.verify) { adler32 = (input[this.ip++] << 24 | input[this.ip++] << 16 | input[this.ip++] << 8 | input[this.ip++]) >>> 0; if (adler32 !== Zlib$1.Adler32(buffer)) { throw new Error('invalid adler-32 checksum'); } } return buffer; }; /* vim:set expandtab ts=2 sw=2 tw=80: */ /** * @param {!(Uint8Array|Array)} input deflated buffer. * @constructor */ Zlib$1.InflateStream = function (input) { /** @type {!(Uint8Array|Array)} */ this.input = input === void 0 ? new (Uint8Array )() : input; /** @type {number} */ this.ip = 0; /** @type {Zlib.RawInflateStream} */ this.rawinflate = new Zlib$1.RawInflateStream(this.input, this.ip); /** @type {Zlib.CompressionMethod} */ this.method; /** @type {!(Array|Uint8Array)} */ this.output = this.rawinflate.output; }; /** * decompress. * @return {!(Uint8Array|Array)} inflated buffer. */ Zlib$1.InflateStream.prototype.decompress = function (input) { /** @type {!(Uint8Array|Array)} inflated buffer. */ var buffer; // XXX Array, Uint8Array のチェックを行うか確認する if (input !== void 0) { { var tmp = new Uint8Array(this.input.length + input.length); tmp.set(this.input, 0); tmp.set(input, this.input.length); this.input = tmp; } } if (this.method === void 0) { if (this.readHeader() < 0) { return new (Uint8Array )(); } } buffer = this.rawinflate.decompress(this.input, this.ip); if (this.rawinflate.ip !== 0) { this.input = this.input.subarray(this.rawinflate.ip) ; this.ip = 0; } // verify adler-32 /* if (this.verify) { adler32 = input[this.ip++] << 24 | input[this.ip++] << 16 | input[this.ip++] << 8 | input[this.ip++]; if (adler32 !== Zlib.Adler32(buffer)) { throw new Error('invalid adler-32 checksum'); } } */ return buffer; }; Zlib$1.InflateStream.prototype.readHeader = function () { var ip = this.ip; var input = this.input; // Compression Method and Flags var cmf = input[ip++]; var flg = input[ip++]; if (cmf === void 0 || flg === void 0) { return -1; } // compression method switch (cmf & 0x0f) { case Zlib$1.CompressionMethod.DEFLATE: this.method = Zlib$1.CompressionMethod.DEFLATE; break; default: throw new Error('unsupported compression method'); } // fcheck if (((cmf << 8) + flg) % 31 !== 0) { throw new Error('invalid fcheck flag:' + ((cmf << 8) + flg) % 31); } // fdict (not supported) if (flg & 0x20) { throw new Error('fdict flag is not supported'); } this.ip = ip; }; /** * @fileoverview GZIP (RFC1952) 展開コンテナ実装. */ /** * @constructor * @param {!(Array|Uint8Array)} input input buffer. * @param {Object=} opt_params option parameters. */ Zlib$1.Gunzip = function (input, opt_params) { /** @type {!(Array.|Uint8Array)} input buffer. */ this.input = input; /** @type {number} input buffer pointer. */ this.ip = 0; /** @type {Array.} */ this.member = []; /** @type {boolean} */ this.decompressed = false; }; /** * @return {Array.} */ Zlib$1.Gunzip.prototype.getMembers = function () { if (!this.decompressed) { this.decompress(); } return this.member.slice(); }; /** * inflate gzip data. * @return {!(Array.|Uint8Array)} inflated buffer. */ Zlib$1.Gunzip.prototype.decompress = function () { /** @type {number} input length. */ var il = this.input.length; while (this.ip < il) { this.decodeMember(); } this.decompressed = true; return this.concatMember(); }; /** * decode gzip member. */ Zlib$1.Gunzip.prototype.decodeMember = function () { /** @type {Zlib.GunzipMember} */ var member = new Zlib$1.GunzipMember(); /** @type {number} */ var isize; /** @type {Zlib.RawInflate} RawInflate implementation. */ var rawinflate; /** @type {!(Array.|Uint8Array)} inflated data. */ var inflated; /** @type {number} inflate size */ var inflen; /** @type {number} character code */ var c; /** @type {number} character index in string. */ var ci; /** @type {Array.} character array. */ var str; /** @type {number} modification time. */ var mtime; /** @type {number} */ var crc32; var input = this.input; var ip = this.ip; member.id1 = input[ip++]; member.id2 = input[ip++]; // check signature if (member.id1 !== 0x1f || member.id2 !== 0x8b) { throw new Error('invalid file signature:' + member.id1 + ',' + member.id2); } // check compression method member.cm = input[ip++]; switch (member.cm) { case 8: /* XXX: use Zlib const */ break; default: throw new Error('unknown compression method: ' + member.cm); } // flags member.flg = input[ip++]; // modification time mtime = input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24; member.mtime = new Date(mtime * 1000); // extra flags member.xfl = input[ip++]; // operating system member.os = input[ip++]; // extra if ((member.flg & Zlib$1.Gzip.FlagsMask.FEXTRA) > 0) { member.xlen = input[ip++] | input[ip++] << 8; ip = this.decodeSubField(ip, member.xlen); } // fname if ((member.flg & Zlib$1.Gzip.FlagsMask.FNAME) > 0) { for (str = [], ci = 0; (c = input[ip++]) > 0;) { str[ci++] = String.fromCharCode(c); } member.name = str.join(''); } // fcomment if ((member.flg & Zlib$1.Gzip.FlagsMask.FCOMMENT) > 0) { for (str = [], ci = 0; (c = input[ip++]) > 0;) { str[ci++] = String.fromCharCode(c); } member.comment = str.join(''); } // fhcrc if ((member.flg & Zlib$1.Gzip.FlagsMask.FHCRC) > 0) { member.crc16 = Zlib$1.CRC32.calc(input, 0, ip) & 0xffff; if (member.crc16 !== (input[ip++] | input[ip++] << 8)) { throw new Error('invalid header crc16'); } } // isize を事前に取得すると展開後のサイズが分かるため、 // inflate処理のバッファサイズが事前に分かり、高速になる isize = input[input.length - 4] | input[input.length - 3] << 8 | input[input.length - 2] << 16 | input[input.length - 1] << 24; // isize の妥当性チェック // ハフマン符号では最小 2-bit のため、最大で 1/4 になる // LZ77 符号では 長さと距離 2-Byte で最大 258-Byte を表現できるため、 // 1/128 になるとする // ここから入力バッファの残りが isize の 512 倍以上だったら // サイズ指定のバッファ確保は行わない事とする if (input.length - ip - /* CRC-32 */ 4 - /* ISIZE */ 4 < isize * 512) { inflen = isize; } // compressed block rawinflate = new Zlib$1.RawInflate(input, { 'index': ip, 'bufferSize': inflen }); member.data = inflated = rawinflate.decompress(); ip = rawinflate.ip; // crc32 member.crc32 = crc32 = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; if (Zlib$1.CRC32.calc(inflated) !== crc32) { throw new Error('invalid CRC-32 checksum: 0x' + Zlib$1.CRC32.calc(inflated).toString(16) + ' / 0x' + crc32.toString(16)); } // input size member.isize = isize = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; if ((inflated.length & 0xffffffff) !== isize) { throw new Error('invalid input size: ' + (inflated.length & 0xffffffff) + ' / ' + isize); } this.member.push(member); this.ip = ip; }; /** * サブフィールドのデコード * XXX: 現在は何もせずスキップする */ Zlib$1.Gunzip.prototype.decodeSubField = function (ip, length) { return ip + length; }; /** * @return {!(Array.|Uint8Array)} */ Zlib$1.Gunzip.prototype.concatMember = function () { /** @type {Array.} */ var member = this.member; /** @type {number} */ var i; /** @type {number} */ var il; /** @type {number} */ var p = 0; /** @type {number} */ var size = 0; /** @type {!(Array.|Uint8Array)} */ var buffer; for (i = 0, il = member.length; i < il; ++i) { size += member[i].data.length; } { buffer = new Uint8Array(size); for (i = 0; i < il; ++i) { buffer.set(member[i].data, p); p += member[i].data.length; } } return buffer; }; /** * @constructor */ Zlib$1.GunzipMember = function () { /** @type {number} signature first byte. */ this.id1; /** @type {number} signature second byte. */ this.id2; /** @type {number} compression method. */ this.cm; /** @type {number} flags. */ this.flg; /** @type {Date} modification time. */ this.mtime; /** @type {number} extra flags. */ this.xfl; /** @type {number} operating system number. */ this.os; /** @type {number} CRC-16 value for FHCRC flag. */ this.crc16; /** @type {number} extra length. */ this.xlen; /** @type {number} CRC-32 value for verification. */ this.crc32; /** @type {number} input size modulo 32 value. */ this.isize; /** @type {string} filename. */ this.name; /** @type {string} comment. */ this.comment; /** @type {!(Uint8Array|Array.)} */ this.data; }; Zlib$1.GunzipMember.prototype.getName = function () { return this.name; }; Zlib$1.GunzipMember.prototype.getData = function () { return this.data; }; Zlib$1.GunzipMember.prototype.getMtime = function () { return this.mtime; }; /** * @fileoverview GZIP (RFC1952) 実装. */ /** * @constructor * @param {!(Array|Uint8Array)} input input buffer. * @param {Object=} opt_params option parameters. */ Zlib$1.Gzip = function (input, opt_params) { /** @type {!(Array.|Uint8Array)} input buffer. */ this.input = input; /** @type {number} input buffer pointer. */ this.ip = 0; /** @type {!(Array.|Uint8Array)} output buffer. */ this.output; /** @type {number} output buffer. */ this.op = 0; /** @type {!Object} flags option flags. */ this.flags = {}; /** @type {!string} filename. */ this.filename; /** @type {!string} comment. */ this.comment; /** @type {!Object} deflate options. */ this.deflateOptions; // option parameters if (opt_params) { if (opt_params['flags']) { this.flags = opt_params['flags']; } if (typeof opt_params['filename'] === 'string') { this.filename = opt_params['filename']; } if (typeof opt_params['comment'] === 'string') { this.comment = opt_params['comment']; } if (opt_params['deflateOptions']) { this.deflateOptions = opt_params['deflateOptions']; } } if (!this.deflateOptions) { this.deflateOptions = {}; } }; /** * @type {number} * @const */ Zlib$1.Gzip.DefaultBufferSize = 0x8000; /** * encode gzip members. * @return {!(Array|Uint8Array)} gzip binary array. */ Zlib$1.Gzip.prototype.compress = function () { /** @type {number} flags. */ var flg; /** @type {number} modification time. */ var mtime; /** @type {number} CRC-16 value for FHCRC flag. */ var crc16; /** @type {number} CRC-32 value for verification. */ var crc32; /** @type {!Zlib.RawDeflate} raw deflate object. */ var rawdeflate; /** @type {number} character code */ var c; /** @type {number} loop counter. */ var i; /** @type {number} loop limiter. */ var il; /** @type {!(Array|Uint8Array)} output buffer. */ var output = new (Uint8Array )(Zlib$1.Gzip.DefaultBufferSize); /** @type {number} output buffer pointer. */ var op = 0; var input = this.input; var ip = this.ip; var filename = this.filename; var comment = this.comment; // check signature output[op++] = 0x1f; output[op++] = 0x8b; // check compression method output[op++] = 8; /* XXX: use Zlib const */ // flags flg = 0; if (this.flags['fname']) flg |= Zlib$1.Gzip.FlagsMask.FNAME; if (this.flags['fcomment']) flg |= Zlib$1.Gzip.FlagsMask.FCOMMENT; if (this.flags['fhcrc']) flg |= Zlib$1.Gzip.FlagsMask.FHCRC; // XXX: FTEXT // XXX: FEXTRA output[op++] = flg; // modification time mtime = (Date.now ? Date.now() : +new Date()) / 1000 | 0; output[op++] = mtime & 0xff; output[op++] = mtime >>> 8 & 0xff; output[op++] = mtime >>> 16 & 0xff; output[op++] = mtime >>> 24 & 0xff; // extra flags output[op++] = 0; // operating system output[op++] = Zlib$1.Gzip.OperatingSystem.UNKNOWN; // extra /* NOP */ // fname if (this.flags['fname'] !== void 0) { for (i = 0, il = filename.length; i < il; ++i) { c = filename.charCodeAt(i); if (c > 0xff) { output[op++] = c >>> 8 & 0xff; } output[op++] = c & 0xff; } output[op++] = 0; // null termination } // fcomment if (this.flags['comment']) { for (i = 0, il = comment.length; i < il; ++i) { c = comment.charCodeAt(i); if (c > 0xff) { output[op++] = c >>> 8 & 0xff; } output[op++] = c & 0xff; } output[op++] = 0; // null termination } // fhcrc if (this.flags['fhcrc']) { crc16 = Zlib$1.CRC32.calc(output, 0, op) & 0xffff; output[op++] = crc16 & 0xff; output[op++] = crc16 >>> 8 & 0xff; } // add compress option this.deflateOptions['outputBuffer'] = output; this.deflateOptions['outputIndex'] = op; // compress rawdeflate = new Zlib$1.RawDeflate(input, this.deflateOptions); output = rawdeflate.compress(); op = rawdeflate.op; // expand buffer { if (op + 8 > output.buffer.byteLength) { this.output = new Uint8Array(op + 8); this.output.set(new Uint8Array(output.buffer)); output = this.output; } else { output = new Uint8Array(output.buffer); } } // crc32 crc32 = Zlib$1.CRC32.calc(input); output[op++] = crc32 & 0xff; output[op++] = crc32 >>> 8 & 0xff; output[op++] = crc32 >>> 16 & 0xff; output[op++] = crc32 >>> 24 & 0xff; // input size il = input.length; output[op++] = il & 0xff; output[op++] = il >>> 8 & 0xff; output[op++] = il >>> 16 & 0xff; output[op++] = il >>> 24 & 0xff; this.ip = ip; if (op < output.length) { this.output = output = output.subarray(0, op); } return output; }; /** @enum {number} */ Zlib$1.Gzip.OperatingSystem = { FAT: 0, AMIGA: 1, VMS: 2, UNIX: 3, VM_CMS: 4, ATARI_TOS: 5, HPFS: 6, MACINTOSH: 7, Z_SYSTEM: 8, CP_M: 9, TOPS_20: 10, NTFS: 11, QDOS: 12, ACORN_RISCOS: 13, UNKNOWN: 255 }; /** @enum {number} */ Zlib$1.Gzip.FlagsMask = { FTEXT: 0x01, FHCRC: 0x02, FEXTRA: 0x04, FNAME: 0x08, FCOMMENT: 0x10 }; /** * @fileoverview Heap Sort 実装. ハフマン符号化で使用する. */ /** * カスタムハフマン符号で使用するヒープ実装 * @param {number} length ヒープサイズ. * @constructor */ Zlib$1.Heap = function (length) { this.buffer = new (Uint16Array )(length * 2); this.length = 0; }; /** * 親ノードの index 取得 * @param {number} index 子ノードの index. * @return {number} 親ノードの index. * */ Zlib$1.Heap.prototype.getParent = function (index) { return ((index - 2) / 4 | 0) * 2; }; /** * 子ノードの index 取得 * @param {number} index 親ノードの index. * @return {number} 子ノードの index. */ Zlib$1.Heap.prototype.getChild = function (index) { return 2 * index + 2; }; /** * Heap ã«å€¤ã‚’è¿½åŠ ã™ã‚‹ * @param {number} index キー index. * @param {number} value 値. * @return {number} 現在のヒープ長. */ Zlib$1.Heap.prototype.push = function (index, value) { var current, parent, heap = this.buffer, swap; current = this.length; heap[this.length++] = value; heap[this.length++] = index; // ルートノードにたどり着くまで入れ替えを試みる while (current > 0) { parent = this.getParent(current); // 親ノードと比較して親の方が小さければ入れ替える if (heap[current] > heap[parent]) { swap = heap[current]; heap[current] = heap[parent]; heap[parent] = swap; swap = heap[current + 1]; heap[current + 1] = heap[parent + 1]; heap[parent + 1] = swap; current = parent; // 入れ替えが必要なくなったらそこで抜ける } else { break; } } return this.length; }; /** * Heapから一番大きい値を返す * @return {{index: number, value: number, length: number}} {index: キーindex, * value: 値, length: ヒープ長} の Object. */ Zlib$1.Heap.prototype.pop = function () { var index, value, heap = this.buffer, swap, current, parent; value = heap[0]; index = heap[1]; // 後ろから値を取る this.length -= 2; heap[0] = heap[this.length]; heap[1] = heap[this.length + 1]; parent = 0; // ルートノードから下がっていく while (true) { current = this.getChild(parent); // 範囲チェック if (current >= this.length) { break; } // 隣のノードと比較して、隣の方が値が大きければ隣を現在ノードとして選択 if (current + 2 < this.length && heap[current + 2] > heap[current]) { current += 2; } // è¦ªãƒŽãƒ¼ãƒ‰ã¨æ¯”è¼ƒã—ã¦è¦ªã®æ–¹ãŒå°ã•ã„å ´åˆã¯å…¥ã‚Œæ›¿ãˆã‚‹ if (heap[current] > heap[parent]) { swap = heap[parent]; heap[parent] = heap[current]; heap[current] = swap; swap = heap[parent + 1]; heap[parent + 1] = heap[current + 1]; heap[current + 1] = swap; } else { break; } parent = current; } return { index: index, value: value, length: this.length }; }; /* vim:set expandtab ts=2 sw=2 tw=80: */ /** * @fileoverview Deflate (RFC1951) 符号化アルゴリズム実装. */ /** * Raw Deflate 実装 * * @constructor * @param {!(Array.|Uint8Array)} input 符号化する対象のバッファ. * @param {Object=} opt_params option parameters. * * typed array が使用可能なとき、outputBuffer が Array は自動的に Uint8Array に * 変換されます. * 別のオブジェクトになるため出力バッファを参照している変数などは * 更新する必要があります. */ Zlib$1.RawDeflate = function (input, opt_params) { /** @type {Zlib.RawDeflate.CompressionType} */ this.compressionType = Zlib$1.RawDeflate.CompressionType.DYNAMIC; /** @type {number} */ this.lazy = 0; /** @type {!(Array.|Uint32Array)} */ this.freqsLitLen; /** @type {!(Array.|Uint32Array)} */ this.freqsDist; /** @type {!(Array.|Uint8Array)} */ this.input = input instanceof Array ? new Uint8Array(input) : input; /** @type {!(Array.|Uint8Array)} output output buffer. */ this.output; /** @type {number} pos output buffer position. */ this.op = 0; // option parameters if (opt_params) { if (opt_params['lazy']) { this.lazy = opt_params['lazy']; } if (typeof opt_params['compressionType'] === 'number') { this.compressionType = opt_params['compressionType']; } if (opt_params['outputBuffer']) { this.output = opt_params['outputBuffer'] instanceof Array ? new Uint8Array(opt_params['outputBuffer']) : opt_params['outputBuffer']; } if (typeof opt_params['outputIndex'] === 'number') { this.op = opt_params['outputIndex']; } } if (!this.output) { this.output = new (Uint8Array )(0x8000); } }; /** * @enum {number} */ Zlib$1.RawDeflate.CompressionType = { NONE: 0, FIXED: 1, DYNAMIC: 2, RESERVED: 3 }; /** * LZ77 の最小マッチ長 * @const * @type {number} */ Zlib$1.RawDeflate.Lz77MinLength = 3; /** * LZ77 の最大マッチ長 * @const * @type {number} */ Zlib$1.RawDeflate.Lz77MaxLength = 258; /** * LZ77 のウィンドウサイズ * @const * @type {number} */ Zlib$1.RawDeflate.WindowSize = 0x8000; /** * 最長の符号長 * @const * @type {number} */ Zlib$1.RawDeflate.MaxCodeLength = 16; /** * ハフマン符号の最大数値 * @const * @type {number} */ Zlib$1.RawDeflate.HUFMAX = 286; /** * 固定ハフマン符号の符号化テーブル * @const * @type {Array.>} */ Zlib$1.RawDeflate.FixedHuffmanTable = function () { var table = [], i; for (i = 0; i < 288; i++) { switch (true) { case i <= 143: table.push([i + 0x030, 8]); break; case i <= 255: table.push([i - 144 + 0x190, 9]); break; case i <= 279: table.push([i - 256 + 0x000, 7]); break; case i <= 287: table.push([i - 280 + 0x0C0, 8]); break; default: throw 'invalid literal: ' + i; } } return table; }(); /** * DEFLATE ブロックの作成 * @return {!(Array.|Uint8Array)} 圧縮済み byte array. */ Zlib$1.RawDeflate.prototype.compress = function () { /** @type {!(Array.|Uint8Array)} */ var blockArray; /** @type {number} */ var position; /** @type {number} */ var length; var input = this.input; // compression switch (this.compressionType) { case Zlib$1.RawDeflate.CompressionType.NONE: // each 65535-Byte (length header: 16-bit) for (position = 0, length = input.length; position < length;) { blockArray = input.subarray(position, position + 0xffff) ; position += blockArray.length; this.makeNocompressBlock(blockArray, position === length); } break; case Zlib$1.RawDeflate.CompressionType.FIXED: this.output = this.makeFixedHuffmanBlock(input, true); this.op = this.output.length; break; case Zlib$1.RawDeflate.CompressionType.DYNAMIC: this.output = this.makeDynamicHuffmanBlock(input, true); this.op = this.output.length; break; default: throw 'invalid compression type'; } return this.output; }; /** * 非圧縮ブロックの作成 * @param {!(Array.|Uint8Array)} blockArray ブロックデータ byte array. * @param {!boolean} isFinalBlock 最後のブロックならばtrue. * @return {!(Array.|Uint8Array)} 非圧縮ブロック byte array. */ Zlib$1.RawDeflate.prototype.makeNocompressBlock = function (blockArray, isFinalBlock) { /** @type {number} */ var bfinal; /** @type {Zlib.RawDeflate.CompressionType} */ var btype; /** @type {number} */ var len; /** @type {number} */ var nlen; var output = this.output; var op = this.op; // expand buffer { output = new Uint8Array(this.output.buffer); while (output.length <= op + blockArray.length + 5) { output = new Uint8Array(output.length << 1); } output.set(this.output); } // header bfinal = isFinalBlock ? 1 : 0; btype = Zlib$1.RawDeflate.CompressionType.NONE; output[op++] = bfinal | btype << 1; // length len = blockArray.length; nlen = ~len + 0x10000 & 0xffff; output[op++] = len & 0xff; output[op++] = len >>> 8 & 0xff; output[op++] = nlen & 0xff; output[op++] = nlen >>> 8 & 0xff; // copy buffer { output.set(blockArray, op); op += blockArray.length; output = output.subarray(0, op); } this.op = op; this.output = output; return output; }; /** * 固定ハフマンブロックの作成 * @param {!(Array.|Uint8Array)} blockArray ブロックデータ byte array. * @param {!boolean} isFinalBlock 最後のブロックならばtrue. * @return {!(Array.|Uint8Array)} 固定ハフマン符号化ブロック byte array. */ Zlib$1.RawDeflate.prototype.makeFixedHuffmanBlock = function (blockArray, isFinalBlock) { /** @type {Zlib.BitStream} */ var stream = new Zlib$1.BitStream(new Uint8Array(this.output.buffer) , this.op); /** @type {number} */ var bfinal; /** @type {Zlib.RawDeflate.CompressionType} */ var btype; /** @type {!(Array.|Uint16Array)} */ var data; // header bfinal = isFinalBlock ? 1 : 0; btype = Zlib$1.RawDeflate.CompressionType.FIXED; stream.writeBits(bfinal, 1, true); stream.writeBits(btype, 2, true); data = this.lz77(blockArray); this.fixedHuffman(data, stream); return stream.finish(); }; /** * 動的ハフマンブロックの作成 * @param {!(Array.|Uint8Array)} blockArray ブロックデータ byte array. * @param {!boolean} isFinalBlock 最後のブロックならばtrue. * @return {!(Array.|Uint8Array)} 動的ハフマン符号ブロック byte array. */ Zlib$1.RawDeflate.prototype.makeDynamicHuffmanBlock = function (blockArray, isFinalBlock) { /** @type {Zlib.BitStream} */ var stream = new Zlib$1.BitStream(new Uint8Array(this.output.buffer) , this.op); /** @type {number} */ var bfinal; /** @type {Zlib.RawDeflate.CompressionType} */ var btype; /** @type {!(Array.|Uint16Array)} */ var data; /** @type {number} */ var hlit; /** @type {number} */ var hdist; /** @type {number} */ var hclen; /** @const @type {Array.} */ var hclenOrder = [16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15]; /** @type {!(Array.|Uint8Array)} */ var litLenLengths; /** @type {!(Array.|Uint16Array)} */ var litLenCodes; /** @type {!(Array.|Uint8Array)} */ var distLengths; /** @type {!(Array.|Uint16Array)} */ var distCodes; /** @type {{ * codes: !(Array.|Uint32Array), * freqs: !(Array.|Uint8Array) * }} */ var treeSymbols; /** @type {!(Array.|Uint8Array)} */ var treeLengths; /** @type {Array} */ var transLengths = new Array(19); /** @type {!(Array.|Uint16Array)} */ var treeCodes; /** @type {number} */ var code; /** @type {number} */ var bitlen; /** @type {number} */ var i; /** @type {number} */ var il; // header bfinal = isFinalBlock ? 1 : 0; btype = Zlib$1.RawDeflate.CompressionType.DYNAMIC; stream.writeBits(bfinal, 1, true); stream.writeBits(btype, 2, true); data = this.lz77(blockArray); // リテラル・長さ, 距離のハフマン符号と符号長の算出 litLenLengths = this.getLengths_(this.freqsLitLen, 15); litLenCodes = this.getCodesFromLengths_(litLenLengths); distLengths = this.getLengths_(this.freqsDist, 7); distCodes = this.getCodesFromLengths_(distLengths); // HLIT, HDIST の決定 for (hlit = 286; hlit > 257 && litLenLengths[hlit - 1] === 0; hlit--) {} for (hdist = 30; hdist > 1 && distLengths[hdist - 1] === 0; hdist--) {} // HCLEN treeSymbols = this.getTreeSymbols_(hlit, litLenLengths, hdist, distLengths); treeLengths = this.getLengths_(treeSymbols.freqs, 7); for (i = 0; i < 19; i++) { transLengths[i] = treeLengths[hclenOrder[i]]; } for (hclen = 19; hclen > 4 && transLengths[hclen - 1] === 0; hclen--) {} treeCodes = this.getCodesFromLengths_(treeLengths); // 出力 stream.writeBits(hlit - 257, 5, true); stream.writeBits(hdist - 1, 5, true); stream.writeBits(hclen - 4, 4, true); for (i = 0; i < hclen; i++) { stream.writeBits(transLengths[i], 3, true); } // ツリーの出力 for (i = 0, il = treeSymbols.codes.length; i < il; i++) { code = treeSymbols.codes[i]; stream.writeBits(treeCodes[code], treeLengths[code], true); // extra bits if (code >= 16) { i++; switch (code) { case 16: bitlen = 2; break; case 17: bitlen = 3; break; case 18: bitlen = 7; break; default: throw 'invalid code: ' + code; } stream.writeBits(treeSymbols.codes[i], bitlen, true); } } this.dynamicHuffman(data, [litLenCodes, litLenLengths], [distCodes, distLengths], stream); return stream.finish(); }; /** * 動的ハフマン符号化(カスタムハフマンテーブル) * @param {!(Array.|Uint16Array)} dataArray LZ77 符号化済み byte array. * @param {!Zlib.BitStream} stream 書き込み用ビットストリーム. * @return {!Zlib.BitStream} ハフマン符号化済みビットストリームオブジェクト. */ Zlib$1.RawDeflate.prototype.dynamicHuffman = function (dataArray, litLen, dist, stream) { /** @type {number} */ var index; /** @type {number} */ var length; /** @type {number} */ var literal; /** @type {number} */ var code; /** @type {number} */ var litLenCodes; /** @type {number} */ var litLenLengths; /** @type {number} */ var distCodes; /** @type {number} */ var distLengths; litLenCodes = litLen[0]; litLenLengths = litLen[1]; distCodes = dist[0]; distLengths = dist[1]; // 符号を BitStream に書き込んでいく for (index = 0, length = dataArray.length; index < length; ++index) { literal = dataArray[index]; // literal or length stream.writeBits(litLenCodes[literal], litLenLengths[literal], true); // 長さ・距離符号 if (literal > 256) { // length extra stream.writeBits(dataArray[++index], dataArray[++index], true); // distance code = dataArray[++index]; stream.writeBits(distCodes[code], distLengths[code], true); // distance extra stream.writeBits(dataArray[++index], dataArray[++index], true); // 終端 } else if (literal === 256) { break; } } return stream; }; /** * 固定ハフマン符号化 * @param {!(Array.|Uint16Array)} dataArray LZ77 符号化済み byte array. * @param {!Zlib.BitStream} stream 書き込み用ビットストリーム. * @return {!Zlib.BitStream} ハフマン符号化済みビットストリームオブジェクト. */ Zlib$1.RawDeflate.prototype.fixedHuffman = function (dataArray, stream) { /** @type {number} */ var index; /** @type {number} */ var length; /** @type {number} */ var literal; // 符号を BitStream に書き込んでいく for (index = 0, length = dataArray.length; index < length; index++) { literal = dataArray[index]; // 符号の書き込み Zlib$1.BitStream.prototype.writeBits.apply(stream, Zlib$1.RawDeflate.FixedHuffmanTable[literal]); // 長さ・距離符号 if (literal > 0x100) { // length extra stream.writeBits(dataArray[++index], dataArray[++index], true); // distance stream.writeBits(dataArray[++index], 5); // distance extra stream.writeBits(dataArray[++index], dataArray[++index], true); // 終端 } else if (literal === 0x100) { break; } } return stream; }; /** * ãƒžãƒƒãƒæƒ…å ± * @param {!number} length マッチした長さ. * @param {!number} backwardDistance マッチ位置との距離. * @constructor */ Zlib$1.RawDeflate.Lz77Match = function (length, backwardDistance) { /** @type {number} match length. */ this.length = length; /** @type {number} backward distance. */ this.backwardDistance = backwardDistance; }; /** * 長さ符号テーブル. * [コード, 拡張ビット, 拡張ビット長] の配列となっている. * @const * @type {!(Array.|Uint32Array)} */ Zlib$1.RawDeflate.Lz77Match.LengthCodeTable = function (table) { return new Uint32Array(table) ; }(function () { /** @type {!Array} */ var table = []; /** @type {number} */ var i; /** @type {!Array.} */ var c; for (i = 3; i <= 258; i++) { c = code(i); table[i] = c[2] << 24 | c[1] << 16 | c[0]; } /** * @param {number} length lz77 length. * @return {!Array.} lz77 codes. */ function code(length) { switch (true) { case length === 3: return [257, length - 3, 0]; case length === 4: return [258, length - 4, 0]; case length === 5: return [259, length - 5, 0]; case length === 6: return [260, length - 6, 0]; case length === 7: return [261, length - 7, 0]; case length === 8: return [262, length - 8, 0]; case length === 9: return [263, length - 9, 0]; case length === 10: return [264, length - 10, 0]; case length <= 12: return [265, length - 11, 1]; case length <= 14: return [266, length - 13, 1]; case length <= 16: return [267, length - 15, 1]; case length <= 18: return [268, length - 17, 1]; case length <= 22: return [269, length - 19, 2]; case length <= 26: return [270, length - 23, 2]; case length <= 30: return [271, length - 27, 2]; case length <= 34: return [272, length - 31, 2]; case length <= 42: return [273, length - 35, 3]; case length <= 50: return [274, length - 43, 3]; case length <= 58: return [275, length - 51, 3]; case length <= 66: return [276, length - 59, 3]; case length <= 82: return [277, length - 67, 4]; case length <= 98: return [278, length - 83, 4]; case length <= 114: return [279, length - 99, 4]; case length <= 130: return [280, length - 115, 4]; case length <= 162: return [281, length - 131, 5]; case length <= 194: return [282, length - 163, 5]; case length <= 226: return [283, length - 195, 5]; case length <= 257: return [284, length - 227, 5]; case length === 258: return [285, length - 258, 0]; default: throw 'invalid length: ' + length; } } return table; }()); /** * 距離符号テーブル * @param {!number} dist 距離. * @return {!Array.} コード、拡張ビット、拡張ビット長の配列. * @private */ Zlib$1.RawDeflate.Lz77Match.prototype.getDistanceCode_ = function (dist) { /** @type {!Array.} distance code table. */ var r; switch (true) { case dist === 1: r = [0, dist - 1, 0]; break; case dist === 2: r = [1, dist - 2, 0]; break; case dist === 3: r = [2, dist - 3, 0]; break; case dist === 4: r = [3, dist - 4, 0]; break; case dist <= 6: r = [4, dist - 5, 1]; break; case dist <= 8: r = [5, dist - 7, 1]; break; case dist <= 12: r = [6, dist - 9, 2]; break; case dist <= 16: r = [7, dist - 13, 2]; break; case dist <= 24: r = [8, dist - 17, 3]; break; case dist <= 32: r = [9, dist - 25, 3]; break; case dist <= 48: r = [10, dist - 33, 4]; break; case dist <= 64: r = [11, dist - 49, 4]; break; case dist <= 96: r = [12, dist - 65, 5]; break; case dist <= 128: r = [13, dist - 97, 5]; break; case dist <= 192: r = [14, dist - 129, 6]; break; case dist <= 256: r = [15, dist - 193, 6]; break; case dist <= 384: r = [16, dist - 257, 7]; break; case dist <= 512: r = [17, dist - 385, 7]; break; case dist <= 768: r = [18, dist - 513, 8]; break; case dist <= 1024: r = [19, dist - 769, 8]; break; case dist <= 1536: r = [20, dist - 1025, 9]; break; case dist <= 2048: r = [21, dist - 1537, 9]; break; case dist <= 3072: r = [22, dist - 2049, 10]; break; case dist <= 4096: r = [23, dist - 3073, 10]; break; case dist <= 6144: r = [24, dist - 4097, 11]; break; case dist <= 8192: r = [25, dist - 6145, 11]; break; case dist <= 12288: r = [26, dist - 8193, 12]; break; case dist <= 16384: r = [27, dist - 12289, 12]; break; case dist <= 24576: r = [28, dist - 16385, 13]; break; case dist <= 32768: r = [29, dist - 24577, 13]; break; default: throw 'invalid distance'; } return r; }; /** * ãƒžãƒƒãƒæƒ…å ±ã‚’ LZ77 符号化配列で返す. * なお、ここでは以下の内部仕様で符号化している * [ CODE, EXTRA-BIT-LEN, EXTRA, CODE, EXTRA-BIT-LEN, EXTRA ] * @return {!Array.} LZ77 符号化 byte array. */ Zlib$1.RawDeflate.Lz77Match.prototype.toLz77Array = function () { /** @type {number} */ var length = this.length; /** @type {number} */ var dist = this.backwardDistance; /** @type {Array} */ var codeArray = []; /** @type {number} */ var pos = 0; /** @type {!Array.} */ var code; // length code = Zlib$1.RawDeflate.Lz77Match.LengthCodeTable[length]; codeArray[pos++] = code & 0xffff; codeArray[pos++] = code >> 16 & 0xff; codeArray[pos++] = code >> 24; // distance code = this.getDistanceCode_(dist); codeArray[pos++] = code[0]; codeArray[pos++] = code[1]; codeArray[pos++] = code[2]; return codeArray; }; /** * LZ77 実装 * @param {!(Array.|Uint8Array)} dataArray LZ77 符号化するバイト配列. * @return {!(Array.|Uint16Array)} LZ77 符号化した配列. */ Zlib$1.RawDeflate.prototype.lz77 = function (dataArray) { /** @type {number} input position */ var position; /** @type {number} input length */ var length; /** @type {number} loop counter */ var i; /** @type {number} loop limiter */ var il; /** @type {number} chained-hash-table key */ var matchKey; /** @type {Object.>} chained-hash-table */ var table = {}; /** @const @type {number} */ var windowSize = Zlib$1.RawDeflate.WindowSize; /** @type {Array.} match list */ var matchList; /** @type {Zlib.RawDeflate.Lz77Match} longest match */ var longestMatch; /** @type {Zlib.RawDeflate.Lz77Match} previous longest match */ var prevMatch; /** @type {!(Array.|Uint16Array)} lz77 buffer */ var lz77buf = new Uint16Array(dataArray.length * 2) ; /** @type {number} lz77 output buffer pointer */ var pos = 0; /** @type {number} lz77 skip length */ var skipLength = 0; /** @type {!(Array.|Uint32Array)} */ var freqsLitLen = new (Uint32Array )(286); /** @type {!(Array.|Uint32Array)} */ var freqsDist = new (Uint32Array )(30); /** @type {number} */ var lazy = this.lazy; /** @type {*} temporary variable */ var tmp; // 初期化 freqsLitLen[256] = 1; // EOB の最低出現回数は 1 /** * マッチデータの書き込み * @param {Zlib.RawDeflate.Lz77Match} match LZ77 Match data. * @param {!number} offset スキップ開始位置(相対指定). * @private */ function writeMatch(match, offset) { /** @type {Array.} */ var lz77Array = match.toLz77Array(); /** @type {number} */ var i; /** @type {number} */ var il; for (i = 0, il = lz77Array.length; i < il; ++i) { lz77buf[pos++] = lz77Array[i]; } freqsLitLen[lz77Array[0]]++; freqsDist[lz77Array[3]]++; skipLength = match.length + offset - 1; prevMatch = null; } // LZ77 符号化 for (position = 0, length = dataArray.length; position < length; ++position) { // ハッシュキーの作成 for (matchKey = 0, i = 0, il = Zlib$1.RawDeflate.Lz77MinLength; i < il; ++i) { if (position + i === length) { break; } matchKey = matchKey << 8 | dataArray[position + i]; } // テーブルが未定義だったら作成する if (table[matchKey] === void 0) { table[matchKey] = []; } matchList = table[matchKey]; // skip if (skipLength-- > 0) { matchList.push(position); continue; } // マッチテーブルの更新 (最大戻り距離を超えているものを削除する) while (matchList.length > 0 && position - matchList[0] > windowSize) { matchList.shift(); } // ãƒ‡ãƒ¼ã‚¿æœ«å°¾ã§ãƒžãƒƒãƒã—ã‚ˆã†ãŒãªã„å ´åˆã¯ãã®ã¾ã¾æµã—ã“ã‚€ if (position + Zlib$1.RawDeflate.Lz77MinLength >= length) { if (prevMatch) { writeMatch(prevMatch, -1); } for (i = 0, il = length - position; i < il; ++i) { tmp = dataArray[position + i]; lz77buf[pos++] = tmp; ++freqsLitLen[tmp]; } break; } // マッチ候補から最長のものを探す if (matchList.length > 0) { longestMatch = this.searchLongestMatch_(dataArray, position, matchList); if (prevMatch) { // 現在のマッチの方が前回のマッチよりも長い if (prevMatch.length < longestMatch.length) { // write previous literal tmp = dataArray[position - 1]; lz77buf[pos++] = tmp; ++freqsLitLen[tmp]; // write current match writeMatch(longestMatch, 0); } else { // write previous match writeMatch(prevMatch, -1); } } else if (longestMatch.length < lazy) { prevMatch = longestMatch; } else { writeMatch(longestMatch, 0); } // 前回マッチしていて今回マッチがなかったら前回のを採用 } else if (prevMatch) { writeMatch(prevMatch, -1); } else { tmp = dataArray[position]; lz77buf[pos++] = tmp; ++freqsLitLen[tmp]; } matchList.push(position); // マッチテーブルに現在の位置を保存 } // 終端処理 lz77buf[pos++] = 256; freqsLitLen[256]++; this.freqsLitLen = freqsLitLen; this.freqsDist = freqsDist; return lz77buf.subarray(0, pos) ; }; /** * マッチした候補の中から最長一致を探す * @param {!Object} data plain data byte array. * @param {!number} position plain data byte array position. * @param {!Array.} matchList 候補となる位置の配列. * @return {!Zlib.RawDeflate.Lz77Match} 最長かつ最短距離のマッチオブジェクト. * @private */ Zlib$1.RawDeflate.prototype.searchLongestMatch_ = function (data, position, matchList) { var match, currentMatch, matchMax = 0, matchLength, i, j, l, dl = data.length; // 候補を後ろから 1 つずつ絞り込んでゆく permatch: for (i = 0, l = matchList.length; i < l; i++) { match = matchList[l - i - 1]; matchLength = Zlib$1.RawDeflate.Lz77MinLength; // 前回までの最長一致を末尾から一致検索する if (matchMax > Zlib$1.RawDeflate.Lz77MinLength) { for (j = matchMax; j > Zlib$1.RawDeflate.Lz77MinLength; j--) { if (data[match + j - 1] !== data[position + j - 1]) { continue permatch; } } matchLength = matchMax; } // 最長一致探索 while (matchLength < Zlib$1.RawDeflate.Lz77MaxLength && position + matchLength < dl && data[match + matchLength] === data[position + matchLength]) { ++matchLength; } // ãƒžãƒƒãƒé•·ãŒåŒã˜å ´åˆã¯å¾Œæ–¹ã‚’å„ªå…ˆ if (matchLength > matchMax) { currentMatch = match; matchMax = matchLength; } // 最長が確定したら後の処理は省略 if (matchLength === Zlib$1.RawDeflate.Lz77MaxLength) { break; } } return new Zlib$1.RawDeflate.Lz77Match(matchMax, position - currentMatch); }; /** * Tree-Transmit Symbols の算出 * reference: PuTTY Deflate implementation * @param {number} hlit HLIT. * @param {!(Array.|Uint8Array)} litlenLengths リテラルと長さ符号の符号長配列. * @param {number} hdist HDIST. * @param {!(Array.|Uint8Array)} distLengths 距離符号の符号長配列. * @return {{ * codes: !(Array.|Uint32Array), * freqs: !(Array.|Uint8Array) * }} Tree-Transmit Symbols. */ Zlib$1.RawDeflate.prototype.getTreeSymbols_ = function (hlit, litlenLengths, hdist, distLengths) { var src = new (Uint32Array )(hlit + hdist), i, j, runLength, l, result = new (Uint32Array )(286 + 30), nResult, rpt, freqs = new (Uint8Array )(19); j = 0; for (i = 0; i < hlit; i++) { src[j++] = litlenLengths[i]; } for (i = 0; i < hdist; i++) { src[j++] = distLengths[i]; } // 初期化 nResult = 0; for (i = 0, l = src.length; i < l; i += j) { // Run Length Encoding for (j = 1; i + j < l && src[i + j] === src[i]; ++j) {} runLength = j; if (src[i] === 0) { // 0 の繰り返しが 3 回未満ならばそのまま if (runLength < 3) { while (runLength-- > 0) { result[nResult++] = 0; freqs[0]++; } } else { while (runLength > 0) { // 繰り返しは最大 138 までなので切り詰める rpt = runLength < 138 ? runLength : 138; if (rpt > runLength - 3 && rpt < runLength) { rpt = runLength - 3; } // 3-10 回 -> 17 if (rpt <= 10) { result[nResult++] = 17; result[nResult++] = rpt - 3; freqs[17]++; // 11-138 回 -> 18 } else { result[nResult++] = 18; result[nResult++] = rpt - 11; freqs[18]++; } runLength -= rpt; } } } else { result[nResult++] = src[i]; freqs[src[i]]++; runLength--; // 繰り返し回数が3回未満ならばランレングス符号は要らない if (runLength < 3) { while (runLength-- > 0) { result[nResult++] = src[i]; freqs[src[i]]++; } // 3 回以上ならばランレングス符号化 } else { while (runLength > 0) { // runLengthã‚’ 3-6 で分割 rpt = runLength < 6 ? runLength : 6; if (rpt > runLength - 3 && rpt < runLength) { rpt = runLength - 3; } result[nResult++] = 16; result[nResult++] = rpt - 3; freqs[16]++; runLength -= rpt; } } } } return { codes: result.subarray(0, nResult) , freqs: freqs }; }; /** * ハフマン符号の長さを取得する * @param {!(Array.|Uint8Array|Uint32Array)} freqs 出現カウント. * @param {number} limit 符号長の制限. * @return {!(Array.|Uint8Array)} 符号長配列. * @private */ Zlib$1.RawDeflate.prototype.getLengths_ = function (freqs, limit) { /** @type {number} */ var nSymbols = freqs.length; /** @type {Zlib.Heap} */ var heap = new Zlib$1.Heap(2 * Zlib$1.RawDeflate.HUFMAX); /** @type {!(Array.|Uint8Array)} */ var length = new (Uint8Array )(nSymbols); /** @type {Array} */ var nodes; /** @type {!(Array.|Uint32Array)} */ var values; /** @type {!(Array.|Uint8Array)} */ var codeLength; /** @type {number} */ var i; /** @type {number} */ var il; // 配列の初期化 for (i = 0; i < nSymbols; ++i) { if (freqs[i] > 0) { heap.push(i, freqs[i]); } } nodes = new Array(heap.length / 2); values = new (Uint32Array )(heap.length / 2); // 非 0 ã®è¦ç´ ãŒä¸€ã¤ã ã‘ã ã£ãŸå ´åˆã¯ã€ãã®ã‚·ãƒ³ãƒœãƒ«ã«ç¬¦å·é•· 1 を割り当てて終了 if (nodes.length === 1) { length[heap.pop().index] = 1; return length; } // Reverse Package Merge Algorithm による Canonical Huffman Code の符号長決定 for (i = 0, il = heap.length / 2; i < il; ++i) { nodes[i] = heap.pop(); values[i] = nodes[i].value; } codeLength = this.reversePackageMerge_(values, values.length, limit); for (i = 0, il = nodes.length; i < il; ++i) { length[nodes[i].index] = codeLength[i]; } return length; }; /** * Reverse Package Merge Algorithm. * @param {!(Array.|Uint32Array)} freqs sorted probability. * @param {number} symbols number of symbols. * @param {number} limit code length limit. * @return {!(Array.|Uint8Array)} code lengths. */ Zlib$1.RawDeflate.prototype.reversePackageMerge_ = function (freqs, symbols, limit) { /** @type {!(Array.|Uint16Array)} */ var minimumCost = new (Uint16Array )(limit); /** @type {!(Array.|Uint8Array)} */ var flag = new (Uint8Array )(limit); /** @type {!(Array.|Uint8Array)} */ var codeLength = new (Uint8Array )(symbols); /** @type {Array} */ var value = new Array(limit); /** @type {Array} */ var type = new Array(limit); /** @type {Array.} */ var currentPosition = new Array(limit); /** @type {number} */ var excess = (1 << limit) - symbols; /** @type {number} */ var half = 1 << limit - 1; /** @type {number} */ var i; /** @type {number} */ var j; /** @type {number} */ var t; /** @type {number} */ var weight; /** @type {number} */ var next; /** * @param {number} j */ function takePackage(j) { /** @type {number} */ var x = type[j][currentPosition[j]]; if (x === symbols) { takePackage(j + 1); takePackage(j + 1); } else { --codeLength[x]; } ++currentPosition[j]; } minimumCost[limit - 1] = symbols; for (j = 0; j < limit; ++j) { if (excess < half) { flag[j] = 0; } else { flag[j] = 1; excess -= half; } excess <<= 1; minimumCost[limit - 2 - j] = (minimumCost[limit - 1 - j] / 2 | 0) + symbols; } minimumCost[0] = flag[0]; value[0] = new Array(minimumCost[0]); type[0] = new Array(minimumCost[0]); for (j = 1; j < limit; ++j) { if (minimumCost[j] > 2 * minimumCost[j - 1] + flag[j]) { minimumCost[j] = 2 * minimumCost[j - 1] + flag[j]; } value[j] = new Array(minimumCost[j]); type[j] = new Array(minimumCost[j]); } for (i = 0; i < symbols; ++i) { codeLength[i] = limit; } for (t = 0; t < minimumCost[limit - 1]; ++t) { value[limit - 1][t] = freqs[t]; type[limit - 1][t] = t; } for (i = 0; i < limit; ++i) { currentPosition[i] = 0; } if (flag[limit - 1] === 1) { --codeLength[0]; ++currentPosition[limit - 1]; } for (j = limit - 2; j >= 0; --j) { i = 0; weight = 0; next = currentPosition[j + 1]; for (t = 0; t < minimumCost[j]; t++) { weight = value[j + 1][next] + value[j + 1][next + 1]; if (weight > freqs[i]) { value[j][t] = weight; type[j][t] = symbols; next += 2; } else { value[j][t] = freqs[i]; type[j][t] = i; ++i; } } currentPosition[j] = 0; if (flag[j] === 1) { takePackage(j); } } return codeLength; }; /** * 符号長配列からハフマン符号を取得する * reference: PuTTY Deflate implementation * @param {!(Array.|Uint8Array)} lengths 符号長配列. * @return {!(Array.|Uint16Array)} ハフマン符号配列. * @private */ Zlib$1.RawDeflate.prototype.getCodesFromLengths_ = function (lengths) { var codes = new (Uint16Array )(lengths.length), count = [], startCode = [], code = 0, i, il, j, m; // Count the codes of each length. for (i = 0, il = lengths.length; i < il; i++) { count[lengths[i]] = (count[lengths[i]] | 0) + 1; } // Determine the starting code for each length block. for (i = 1, il = Zlib$1.RawDeflate.MaxCodeLength; i <= il; i++) { startCode[i] = code; code += count[i] | 0; code <<= 1; } // Determine the code for each symbol. Mirrored, of course. for (i = 0, il = lengths.length; i < il; i++) { code = startCode[lengths[i]]; startCode[lengths[i]] += 1; codes[i] = 0; for (j = 0, m = lengths[i]; j < m; j++) { codes[i] = codes[i] << 1 | code & 1; code >>>= 1; } } return codes; }; /** * @param {!(Array.|Uint8Array)} input input buffer. * @param {Object=} opt_params options. * @constructor */ Zlib$1.Unzip = function (input, opt_params) { opt_params = opt_params || {}; /** @type {!(Array.|Uint8Array)} */ this.input = input instanceof Array ? new Uint8Array(input) : input; /** @type {number} */ this.ip = 0; /** @type {number} */ this.eocdrOffset; /** @type {number} */ this.numberOfThisDisk; /** @type {number} */ this.startDisk; /** @type {number} */ this.totalEntriesThisDisk; /** @type {number} */ this.totalEntries; /** @type {number} */ this.centralDirectorySize; /** @type {number} */ this.centralDirectoryOffset; /** @type {number} */ this.commentLength; /** @type {(Array.|Uint8Array)} */ this.comment; /** @type {Array.} */ this.fileHeaderList; /** @type {Object.} */ this.filenameToIndex; /** @type {boolean} */ this.verify = opt_params['verify'] || false; /** @type {(Array.|Uint8Array)} */ this.password = opt_params['password']; }; Zlib$1.Unzip.CompressionMethod = Zlib$1.Zip.CompressionMethod; /** * @type {Array.} * @const */ Zlib$1.Unzip.FileHeaderSignature = Zlib$1.Zip.FileHeaderSignature; /** * @type {Array.} * @const */ Zlib$1.Unzip.LocalFileHeaderSignature = Zlib$1.Zip.LocalFileHeaderSignature; /** * @type {Array.} * @const */ Zlib$1.Unzip.CentralDirectorySignature = Zlib$1.Zip.CentralDirectorySignature; /** * @param {!(Array.|Uint8Array)} input input buffer. * @param {number} ip input position. * @constructor */ Zlib$1.Unzip.FileHeader = function (input, ip) { /** @type {!(Array.|Uint8Array)} */ this.input = input; /** @type {number} */ this.offset = ip; /** @type {number} */ this.length; /** @type {number} */ this.version; /** @type {number} */ this.os; /** @type {number} */ this.needVersion; /** @type {number} */ this.flags; /** @type {number} */ this.compression; /** @type {number} */ this.time; /** @type {number} */ this.date; /** @type {number} */ this.crc32; /** @type {number} */ this.compressedSize; /** @type {number} */ this.plainSize; /** @type {number} */ this.fileNameLength; /** @type {number} */ this.extraFieldLength; /** @type {number} */ this.fileCommentLength; /** @type {number} */ this.diskNumberStart; /** @type {number} */ this.internalFileAttributes; /** @type {number} */ this.externalFileAttributes; /** @type {number} */ this.relativeOffset; /** @type {string} */ this.filename; /** @type {!(Array.|Uint8Array)} */ this.extraField; /** @type {!(Array.|Uint8Array)} */ this.comment; }; Zlib$1.Unzip.FileHeader.prototype.parse = function () { /** @type {!(Array.|Uint8Array)} */ var input = this.input; /** @type {number} */ var ip = this.offset; // central file header signature if (input[ip++] !== Zlib$1.Unzip.FileHeaderSignature[0] || input[ip++] !== Zlib$1.Unzip.FileHeaderSignature[1] || input[ip++] !== Zlib$1.Unzip.FileHeaderSignature[2] || input[ip++] !== Zlib$1.Unzip.FileHeaderSignature[3]) { throw new Error('invalid file header signature'); } // version made by this.version = input[ip++]; this.os = input[ip++]; // version needed to extract this.needVersion = input[ip++] | input[ip++] << 8; // general purpose bit flag this.flags = input[ip++] | input[ip++] << 8; // compression method this.compression = input[ip++] | input[ip++] << 8; // last mod file time this.time = input[ip++] | input[ip++] << 8; //last mod file date this.date = input[ip++] | input[ip++] << 8; // crc-32 this.crc32 = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // compressed size this.compressedSize = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // uncompressed size this.plainSize = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // file name length this.fileNameLength = input[ip++] | input[ip++] << 8; // extra field length this.extraFieldLength = input[ip++] | input[ip++] << 8; // file comment length this.fileCommentLength = input[ip++] | input[ip++] << 8; // disk number start this.diskNumberStart = input[ip++] | input[ip++] << 8; // internal file attributes this.internalFileAttributes = input[ip++] | input[ip++] << 8; // external file attributes this.externalFileAttributes = input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24; // relative offset of local header this.relativeOffset = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // file name this.filename = String.fromCharCode.apply(null, input.subarray(ip, ip += this.fileNameLength) ); // extra field this.extraField = input.subarray(ip, ip += this.extraFieldLength) ; // file comment this.comment = input.subarray(ip, ip + this.fileCommentLength) ; this.length = ip - this.offset; }; /** * @param {!(Array.|Uint8Array)} input input buffer. * @param {number} ip input position. * @constructor */ Zlib$1.Unzip.LocalFileHeader = function (input, ip) { /** @type {!(Array.|Uint8Array)} */ this.input = input; /** @type {number} */ this.offset = ip; /** @type {number} */ this.length; /** @type {number} */ this.needVersion; /** @type {number} */ this.flags; /** @type {number} */ this.compression; /** @type {number} */ this.time; /** @type {number} */ this.date; /** @type {number} */ this.crc32; /** @type {number} */ this.compressedSize; /** @type {number} */ this.plainSize; /** @type {number} */ this.fileNameLength; /** @type {number} */ this.extraFieldLength; /** @type {string} */ this.filename; /** @type {!(Array.|Uint8Array)} */ this.extraField; }; Zlib$1.Unzip.LocalFileHeader.Flags = Zlib$1.Zip.Flags; Zlib$1.Unzip.LocalFileHeader.prototype.parse = function () { /** @type {!(Array.|Uint8Array)} */ var input = this.input; /** @type {number} */ var ip = this.offset; // local file header signature if (input[ip++] !== Zlib$1.Unzip.LocalFileHeaderSignature[0] || input[ip++] !== Zlib$1.Unzip.LocalFileHeaderSignature[1] || input[ip++] !== Zlib$1.Unzip.LocalFileHeaderSignature[2] || input[ip++] !== Zlib$1.Unzip.LocalFileHeaderSignature[3]) { throw new Error('invalid local file header signature'); } // version needed to extract this.needVersion = input[ip++] | input[ip++] << 8; // general purpose bit flag this.flags = input[ip++] | input[ip++] << 8; // compression method this.compression = input[ip++] | input[ip++] << 8; // last mod file time this.time = input[ip++] | input[ip++] << 8; //last mod file date this.date = input[ip++] | input[ip++] << 8; // crc-32 this.crc32 = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // compressed size this.compressedSize = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // uncompressed size this.plainSize = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // file name length this.fileNameLength = input[ip++] | input[ip++] << 8; // extra field length this.extraFieldLength = input[ip++] | input[ip++] << 8; // file name this.filename = String.fromCharCode.apply(null, input.subarray(ip, ip += this.fileNameLength) ); // extra field this.extraField = input.subarray(ip, ip += this.extraFieldLength) ; this.length = ip - this.offset; }; Zlib$1.Unzip.prototype.searchEndOfCentralDirectoryRecord = function () { /** @type {!(Array.|Uint8Array)} */ var input = this.input; /** @type {number} */ var ip; for (ip = input.length - 12; ip > 0; --ip) { if (input[ip] === Zlib$1.Unzip.CentralDirectorySignature[0] && input[ip + 1] === Zlib$1.Unzip.CentralDirectorySignature[1] && input[ip + 2] === Zlib$1.Unzip.CentralDirectorySignature[2] && input[ip + 3] === Zlib$1.Unzip.CentralDirectorySignature[3]) { this.eocdrOffset = ip; return; } } throw new Error('End of Central Directory Record not found'); }; Zlib$1.Unzip.prototype.parseEndOfCentralDirectoryRecord = function () { /** @type {!(Array.|Uint8Array)} */ var input = this.input; /** @type {number} */ var ip; if (!this.eocdrOffset) { this.searchEndOfCentralDirectoryRecord(); } ip = this.eocdrOffset; // signature if (input[ip++] !== Zlib$1.Unzip.CentralDirectorySignature[0] || input[ip++] !== Zlib$1.Unzip.CentralDirectorySignature[1] || input[ip++] !== Zlib$1.Unzip.CentralDirectorySignature[2] || input[ip++] !== Zlib$1.Unzip.CentralDirectorySignature[3]) { throw new Error('invalid signature'); } // number of this disk this.numberOfThisDisk = input[ip++] | input[ip++] << 8; // number of the disk with the start of the central directory this.startDisk = input[ip++] | input[ip++] << 8; // total number of entries in the central directory on this disk this.totalEntriesThisDisk = input[ip++] | input[ip++] << 8; // total number of entries in the central directory this.totalEntries = input[ip++] | input[ip++] << 8; // size of the central directory this.centralDirectorySize = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // offset of start of central directory with respect to the starting disk number this.centralDirectoryOffset = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // .ZIP file comment length this.commentLength = input[ip++] | input[ip++] << 8; // .ZIP file comment this.comment = input.subarray(ip, ip + this.commentLength) ; }; Zlib$1.Unzip.prototype.parseFileHeader = function () { /** @type {Array.} */ var filelist = []; /** @type {Object.} */ var filetable = {}; /** @type {number} */ var ip; /** @type {Zlib.Unzip.FileHeader} */ var fileHeader; /*: @type {number} */ var i; /*: @type {number} */ var il; if (this.fileHeaderList) { return; } if (this.centralDirectoryOffset === void 0) { this.parseEndOfCentralDirectoryRecord(); } ip = this.centralDirectoryOffset; for (i = 0, il = this.totalEntries; i < il; ++i) { fileHeader = new Zlib$1.Unzip.FileHeader(this.input, ip); fileHeader.parse(); ip += fileHeader.length; filelist[i] = fileHeader; filetable[fileHeader.filename] = i; } if (this.centralDirectorySize < ip - this.centralDirectoryOffset) { throw new Error('invalid file header size'); } this.fileHeaderList = filelist; this.filenameToIndex = filetable; }; /** * @param {number} index file header index. * @param {Object=} opt_params * @return {!(Array.|Uint8Array)} file data. */ Zlib$1.Unzip.prototype.getFileData = function (index, opt_params) { opt_params = opt_params || {}; /** @type {!(Array.|Uint8Array)} */ var input = this.input; /** @type {Array.} */ var fileHeaderList = this.fileHeaderList; /** @type {Zlib.Unzip.LocalFileHeader} */ var localFileHeader; /** @type {number} */ var offset; /** @type {number} */ var length; /** @type {!(Array.|Uint8Array)} */ var buffer; /** @type {number} */ var crc32; /** @type {Array.|Uint32Array|Object} */ var key; /** @type {number} */ var i; /** @type {number} */ var il; if (!fileHeaderList) { this.parseFileHeader(); } if (fileHeaderList[index] === void 0) { throw new Error('wrong index'); } offset = fileHeaderList[index].relativeOffset; localFileHeader = new Zlib$1.Unzip.LocalFileHeader(this.input, offset); localFileHeader.parse(); offset += localFileHeader.length; length = localFileHeader.compressedSize; // decryption if ((localFileHeader.flags & Zlib$1.Unzip.LocalFileHeader.Flags.ENCRYPT) !== 0) { if (!(opt_params['password'] || this.password)) { throw new Error('please set password'); } key = this.createDecryptionKey(opt_params['password'] || this.password); // encryption header for (i = offset, il = offset + 12; i < il; ++i) { this.decode(key, input[i]); } offset += 12; length -= 12; // decryption for (i = offset, il = offset + length; i < il; ++i) { input[i] = this.decode(key, input[i]); } } switch (localFileHeader.compression) { case Zlib$1.Unzip.CompressionMethod.STORE: buffer = this.input.subarray(offset, offset + length) ; break; case Zlib$1.Unzip.CompressionMethod.DEFLATE: buffer = new Zlib$1.RawInflate(this.input, { 'index': offset, 'bufferSize': localFileHeader.plainSize }).decompress(); break; default: throw new Error('unknown compression type'); } if (this.verify) { crc32 = Zlib$1.CRC32.calc(buffer); if (localFileHeader.crc32 !== crc32) { throw new Error('wrong crc: file=0x' + localFileHeader.crc32.toString(16) + ', data=0x' + crc32.toString(16)); } } return buffer; }; /** * @return {Array.} */ Zlib$1.Unzip.prototype.getFilenames = function () { /** @type {Array.} */ var filenameList = []; /** @type {number} */ var i; /** @type {number} */ var il; /** @type {Array.} */ var fileHeaderList; if (!this.fileHeaderList) { this.parseFileHeader(); } fileHeaderList = this.fileHeaderList; for (i = 0, il = fileHeaderList.length; i < il; ++i) { filenameList[i] = fileHeaderList[i].filename; } return filenameList; }; /** * @param {string} filename extract filename. * @param {Object=} opt_params * @return {!(Array.|Uint8Array)} decompressed data. */ Zlib$1.Unzip.prototype.decompress = function (filename, opt_params) { /** @type {number} */ var index; if (!this.filenameToIndex) { this.parseFileHeader(); } index = this.filenameToIndex[filename]; if (index === void 0) { throw new Error(filename + ' not found'); } return this.getFileData(index, opt_params); }; /** * @param {(Array.|Uint8Array)} password */ Zlib$1.Unzip.prototype.setPassword = function (password) { this.password = password; }; /** * @param {(Array.|Uint32Array|Object)} key * @param {number} n * @return {number} */ Zlib$1.Unzip.prototype.decode = function (key, n) { n ^= this.getByte(key); this.updateKeys(key, n); return n; }; // common method Zlib$1.Unzip.prototype.updateKeys = Zlib$1.Zip.prototype.updateKeys; Zlib$1.Unzip.prototype.createDecryptionKey = Zlib$1.Zip.prototype.createEncryptionKey; Zlib$1.Unzip.prototype.getByte = Zlib$1.Zip.prototype.getByte; /** * @fileoverview 雑多な関数群をまとめたモジュール実装. */ /** * Byte String から Byte Array に変換. * @param {!string} str byte string. * @return {!Array.} byte array. */ Zlib$1.Util.stringToByteArray = function (str) { /** @type {!Array.<(string|number)>} */ var tmp = str.split(''); /** @type {number} */ var i; /** @type {number} */ var il; for (i = 0, il = tmp.length; i < il; i++) { tmp[i] = (tmp[i].charCodeAt(0) & 0xff) >>> 0; } return tmp; }; /** * @fileoverview Adler32 checksum 実装. */ /** * Adler32 ハッシュ値の作成 * @param {!(Array|Uint8Array|string)} array 算出に使用する byte array. * @return {number} Adler32 ハッシュ値. */ Zlib$1.Adler32 = function (array) { if (typeof array === 'string') { array = Zlib$1.Util.stringToByteArray(array); } return Zlib$1.Adler32.update(1, array); }; /** * Adler32 ハッシュ値の更新 * @param {number} adler 現在のハッシュ値. * @param {!(Array|Uint8Array)} array 更新に使用する byte array. * @return {number} Adler32 ハッシュ値. */ Zlib$1.Adler32.update = function (adler, array) { /** @type {number} */ var s1 = adler & 0xffff; /** @type {number} */ var s2 = adler >>> 16 & 0xffff; /** @type {number} array length */ var len = array.length; /** @type {number} loop length (don't overflow) */ var tlen; /** @type {number} array index */ var i = 0; while (len > 0) { tlen = len > Zlib$1.Adler32.OptimizationParameter ? Zlib$1.Adler32.OptimizationParameter : len; len -= tlen; do { s1 += array[i++]; s2 += s1; } while (--tlen); s1 %= 65521; s2 %= 65521; } return (s2 << 16 | s1) >>> 0; }; /** * Adler32 最適化パラメータ * 現状では 1024 程度が最適. * @see http://jsperf.com/adler-32-simple-vs-optimized/3 * @define {number} */ Zlib$1.Adler32.OptimizationParameter = 1024; /** * ビットストリーム* @constructor * @param {!(Array|Uint8Array)=} buffer output buffer. * @param {number=} bufferPosition start buffer pointer. */ Zlib$1.BitStream = function (buffer, bufferPosition) { /** @type {number} buffer index. */ this.index = typeof bufferPosition === 'number' ? bufferPosition : 0; /** @type {number} bit index. */ this.bitindex = 0; /** @type {!(Array|Uint8Array)} bit-stream output buffer. */ this.buffer = buffer instanceof (Uint8Array ) ? buffer : new (Uint8Array )(Zlib$1.BitStream.DefaultBlockSize); // 入力された index が足りなかったら拡張するが、倍にしてもダメなら不正とする if (this.buffer.length * 2 <= this.index) { throw new Error("invalid index"); } else if (this.buffer.length <= this.index) { this.expandBuffer(); } }; /** * デフォルトブロックサイズ. * @const * @type {number} */ Zlib$1.BitStream.DefaultBlockSize = 0x8000; /** * expand buffer. * @return {!(Array|Uint8Array)} new buffer. */ Zlib$1.BitStream.prototype.expandBuffer = function () { /** @type {!(Array|Uint8Array)} old buffer. */ var oldbuf = this.buffer; /** @type {number} loop limiter. */ var il = oldbuf.length; /** @type {!(Array|Uint8Array)} new buffer. */ var buffer = new (Uint8Array )(il << 1); // copy buffer { buffer.set(oldbuf); } return this.buffer = buffer; }; /** * 数値をビットで指定した数だけ書き込む. * @param {number} number 書き込む数値. * @param {number} n 書き込むビット数. * @param {boolean=} reverse é€†é †ã«æ›¸ãè¾¼ã‚€ãªã‚‰ã° true. */ Zlib$1.BitStream.prototype.writeBits = function (number, n, reverse) { var buffer = this.buffer; var index = this.index; var bitindex = this.bitindex; /** @type {number} current octet. */ var current = buffer[index]; /** @type {number} loop counter. */ var i; /** * 32-bit æ•´æ•°ã®ãƒ“ãƒƒãƒˆé †ã‚’é€†ã«ã™ã‚‹ * @param {number} n 32-bit integer. * @return {number} reversed 32-bit integer. * @private */ function rev32_(n) { return Zlib$1.BitStream.ReverseTable[n & 0xFF] << 24 | Zlib$1.BitStream.ReverseTable[n >>> 8 & 0xFF] << 16 | Zlib$1.BitStream.ReverseTable[n >>> 16 & 0xFF] << 8 | Zlib$1.BitStream.ReverseTable[n >>> 24 & 0xFF]; } if (reverse && n > 1) { number = n > 8 ? rev32_(number) >> 32 - n : Zlib$1.BitStream.ReverseTable[number] >> 8 - n; } // Byte 境界を超えないとき if (n + bitindex < 8) { current = current << n | number; bitindex += n; // Byte 境界を超えるとき } else { for (i = 0; i < n; ++i) { current = current << 1 | number >> n - i - 1 & 1; // next byte if (++bitindex === 8) { bitindex = 0; buffer[index++] = Zlib$1.BitStream.ReverseTable[current]; current = 0; // expand if (index === buffer.length) { buffer = this.expandBuffer(); } } } } buffer[index] = current; this.buffer = buffer; this.bitindex = bitindex; this.index = index; }; /** * ストリームの終端処理を行う * @return {!(Array|Uint8Array)} 終端処理後のバッファを byte array で返す. */ Zlib$1.BitStream.prototype.finish = function () { var buffer = this.buffer; var index = this.index; /** @type {!(Array|Uint8Array)} output buffer. */ var output; // bitindex が 0 の時は余分に index が進んでいる状態 if (this.bitindex > 0) { buffer[index] <<= 8 - this.bitindex; buffer[index] = Zlib$1.BitStream.ReverseTable[buffer[index]]; index++; } // array truncation { output = buffer.subarray(0, index); } return output; }; /** * 0-255 ã®ãƒ“ãƒƒãƒˆé †ã‚’åè»¢ã—ãŸãƒ†ãƒ¼ãƒ–ãƒ« * @const * @type {!(Uint8Array|Array.)} */ Zlib$1.BitStream.ReverseTable = function (table) { return table; }(function () { /** @type {!(Array|Uint8Array)} reverse table. */ var table = new (Uint8Array )(256); /** @type {number} loop counter. */ var i; // generate for (i = 0; i < 256; ++i) { table[i] = function (n) { var r = n; var s = 7; for (n >>>= 1; n; n >>>= 1) { r <<= 1; r |= n & 1; --s; } return (r << s & 0xff) >>> 0; }(i); } return table; }()); /** * CRC32 ハッシュ値を取得 * @param {!(Array.|Uint8Array)} data data byte array. * @param {number=} pos data position. * @param {number=} length data length. * @return {number} CRC32. */ Zlib$1.CRC32.calc = function (data, pos, length) { return Zlib$1.CRC32.update(data, 0, pos, length); }; /** * CRC32ハッシュ値を更新 * @param {!(Array.|Uint8Array)} data data byte array. * @param {number} crc CRC32. * @param {number=} pos data position. * @param {number=} length data length. * @return {number} CRC32. */ Zlib$1.CRC32.update = function (data, crc, pos, length) { var table = Zlib$1.CRC32.Table; var i = typeof pos === 'number' ? pos : pos = 0; var il = typeof length === 'number' ? length : data.length; crc ^= 0xffffffff; // loop unrolling for performance for (i = il & 7; i--; ++pos) { crc = crc >>> 8 ^ table[(crc ^ data[pos]) & 0xff]; } for (i = il >> 3; i--; pos += 8) { crc = crc >>> 8 ^ table[(crc ^ data[pos]) & 0xff]; crc = crc >>> 8 ^ table[(crc ^ data[pos + 1]) & 0xff]; crc = crc >>> 8 ^ table[(crc ^ data[pos + 2]) & 0xff]; crc = crc >>> 8 ^ table[(crc ^ data[pos + 3]) & 0xff]; crc = crc >>> 8 ^ table[(crc ^ data[pos + 4]) & 0xff]; crc = crc >>> 8 ^ table[(crc ^ data[pos + 5]) & 0xff]; crc = crc >>> 8 ^ table[(crc ^ data[pos + 6]) & 0xff]; crc = crc >>> 8 ^ table[(crc ^ data[pos + 7]) & 0xff]; } return (crc ^ 0xffffffff) >>> 0; }; /** * @param {number} num * @param {number} crc * @returns {number} */ Zlib$1.CRC32.single = function (num, crc) { return (Zlib$1.CRC32.Table[(num ^ crc) & 0xff] ^ num >>> 8) >>> 0; }; /** * @type {Array.} * @const * @private */ Zlib$1.CRC32.Table_ = [0x00000000, 0x77073096, 0xee0e612c, 0x990951ba, 0x076dc419, 0x706af48f, 0xe963a535, 0x9e6495a3, 0x0edb8832, 0x79dcb8a4, 0xe0d5e91e, 0x97d2d988, 0x09b64c2b, 0x7eb17cbd, 0xe7b82d07, 0x90bf1d91, 0x1db71064, 0x6ab020f2, 0xf3b97148, 0x84be41de, 0x1adad47d, 0x6ddde4eb, 0xf4d4b551, 0x83d385c7, 0x136c9856, 0x646ba8c0, 0xfd62f97a, 0x8a65c9ec, 0x14015c4f, 0x63066cd9, 0xfa0f3d63, 0x8d080df5, 0x3b6e20c8, 0x4c69105e, 0xd56041e4, 0xa2677172, 0x3c03e4d1, 0x4b04d447, 0xd20d85fd, 0xa50ab56b, 0x35b5a8fa, 0x42b2986c, 0xdbbbc9d6, 0xacbcf940, 0x32d86ce3, 0x45df5c75, 0xdcd60dcf, 0xabd13d59, 0x26d930ac, 0x51de003a, 0xc8d75180, 0xbfd06116, 0x21b4f4b5, 0x56b3c423, 0xcfba9599, 0xb8bda50f, 0x2802b89e, 0x5f058808, 0xc60cd9b2, 0xb10be924, 0x2f6f7c87, 0x58684c11, 0xc1611dab, 0xb6662d3d, 0x76dc4190, 0x01db7106, 0x98d220bc, 0xefd5102a, 0x71b18589, 0x06b6b51f, 0x9fbfe4a5, 0xe8b8d433, 0x7807c9a2, 0x0f00f934, 0x9609a88e, 0xe10e9818, 0x7f6a0dbb, 0x086d3d2d, 0x91646c97, 0xe6635c01, 0x6b6b51f4, 0x1c6c6162, 0x856530d8, 0xf262004e, 0x6c0695ed, 0x1b01a57b, 0x8208f4c1, 0xf50fc457, 0x65b0d9c6, 0x12b7e950, 0x8bbeb8ea, 0xfcb9887c, 0x62dd1ddf, 0x15da2d49, 0x8cd37cf3, 0xfbd44c65, 0x4db26158, 0x3ab551ce, 0xa3bc0074, 0xd4bb30e2, 0x4adfa541, 0x3dd895d7, 0xa4d1c46d, 0xd3d6f4fb, 0x4369e96a, 0x346ed9fc, 0xad678846, 0xda60b8d0, 0x44042d73, 0x33031de5, 0xaa0a4c5f, 0xdd0d7cc9, 0x5005713c, 0x270241aa, 0xbe0b1010, 0xc90c2086, 0x5768b525, 0x206f85b3, 0xb966d409, 0xce61e49f, 0x5edef90e, 0x29d9c998, 0xb0d09822, 0xc7d7a8b4, 0x59b33d17, 0x2eb40d81, 0xb7bd5c3b, 0xc0ba6cad, 0xedb88320, 0x9abfb3b6, 0x03b6e20c, 0x74b1d29a, 0xead54739, 0x9dd277af, 0x04db2615, 0x73dc1683, 0xe3630b12, 0x94643b84, 0x0d6d6a3e, 0x7a6a5aa8, 0xe40ecf0b, 0x9309ff9d, 0x0a00ae27, 0x7d079eb1, 0xf00f9344, 0x8708a3d2, 0x1e01f268, 0x6906c2fe, 0xf762575d, 0x806567cb, 0x196c3671, 0x6e6b06e7, 0xfed41b76, 0x89d32be0, 0x10da7a5a, 0x67dd4acc, 0xf9b9df6f, 0x8ebeeff9, 0x17b7be43, 0x60b08ed5, 0xd6d6a3e8, 0xa1d1937e, 0x38d8c2c4, 0x4fdff252, 0xd1bb67f1, 0xa6bc5767, 0x3fb506dd, 0x48b2364b, 0xd80d2bda, 0xaf0a1b4c, 0x36034af6, 0x41047a60, 0xdf60efc3, 0xa867df55, 0x316e8eef, 0x4669be79, 0xcb61b38c, 0xbc66831a, 0x256fd2a0, 0x5268e236, 0xcc0c7795, 0xbb0b4703, 0x220216b9, 0x5505262f, 0xc5ba3bbe, 0xb2bd0b28, 0x2bb45a92, 0x5cb36a04, 0xc2d7ffa7, 0xb5d0cf31, 0x2cd99e8b, 0x5bdeae1d, 0x9b64c2b0, 0xec63f226, 0x756aa39c, 0x026d930a, 0x9c0906a9, 0xeb0e363f, 0x72076785, 0x05005713, 0x95bf4a82, 0xe2b87a14, 0x7bb12bae, 0x0cb61b38, 0x92d28e9b, 0xe5d5be0d, 0x7cdcefb7, 0x0bdbdf21, 0x86d3d2d4, 0xf1d4e242, 0x68ddb3f8, 0x1fda836e, 0x81be16cd, 0xf6b9265b, 0x6fb077e1, 0x18b74777, 0x88085ae6, 0xff0f6a70, 0x66063bca, 0x11010b5c, 0x8f659eff, 0xf862ae69, 0x616bffd3, 0x166ccf45, 0xa00ae278, 0xd70dd2ee, 0x4e048354, 0x3903b3c2, 0xa7672661, 0xd06016f7, 0x4969474d, 0x3e6e77db, 0xaed16a4a, 0xd9d65adc, 0x40df0b66, 0x37d83bf0, 0xa9bcae53, 0xdebb9ec5, 0x47b2cf7f, 0x30b5ffe9, 0xbdbdf21c, 0xcabac28a, 0x53b39330, 0x24b4a3a6, 0xbad03605, 0xcdd70693, 0x54de5729, 0x23d967bf, 0xb3667a2e, 0xc4614ab8, 0x5d681b02, 0x2a6f2b94, 0xb40bbe37, 0xc30c8ea1, 0x5a05df1b, 0x2d02ef8d]; /** * @type {!(Array.|Uint32Array)} CRC-32 Table. * @const */ Zlib$1.CRC32.Table = new Uint32Array(Zlib$1.CRC32.Table_) ; /** * @fileoverview Deflate (RFC1951) 実装. * Deflateアルゴリズム本体は Zlib.RawDeflate で実装されている. */ /** * Zlib Deflate * @constructor * @param {!(Array|Uint8Array)} input 符号化する対象の byte array. * @param {Object=} opt_params option parameters. */ Zlib$1.Deflate = function (input, opt_params) { /** @type {!(Array|Uint8Array)} */ this.input = input; /** @type {!(Array|Uint8Array)} */ this.output = new (Uint8Array )(Zlib$1.Deflate.DefaultBufferSize); /** @type {Zlib.Deflate.CompressionType} */ this.compressionType = Zlib$1.Deflate.CompressionType.DYNAMIC; /** @type {Zlib.RawDeflate} */ this.rawDeflate; /** @type {Object} */ var rawDeflateOption = {}; /** @type {string} */ var prop; // option parameters if (opt_params || !(opt_params = {})) { if (typeof opt_params['compressionType'] === 'number') { this.compressionType = opt_params['compressionType']; } } // copy options for (prop in opt_params) { rawDeflateOption[prop] = opt_params[prop]; } // set raw-deflate output buffer rawDeflateOption['outputBuffer'] = this.output; this.rawDeflate = new Zlib$1.RawDeflate(this.input, rawDeflateOption); }; /** * @const * @type {number} デフォルトバッファサイズ. */ Zlib$1.Deflate.DefaultBufferSize = 0x8000; /** * @enum {number} */ Zlib$1.Deflate.CompressionType = Zlib$1.RawDeflate.CompressionType; /** * 直接圧縮に掛ける. * @param {!(Array|Uint8Array)} input target buffer. * @param {Object=} opt_params option parameters. * @return {!(Array|Uint8Array)} compressed data byte array. */ Zlib$1.Deflate.compress = function (input, opt_params) { return new Zlib$1.Deflate(input, opt_params).compress(); }; /** * Deflate Compression. * @return {!(Array|Uint8Array)} compressed data byte array. */ Zlib$1.Deflate.prototype.compress = function () { /** @type {Zlib.CompressionMethod} */ var cm; /** @type {number} */ var cinfo; /** @type {number} */ var cmf; /** @type {number} */ var flg; /** @type {number} */ var fcheck; /** @type {number} */ var fdict; /** @type {number} */ var flevel; /** @type {number} */ var adler; /** @type {!(Array|Uint8Array)} */ var output; /** @type {number} */ var pos = 0; output = this.output; // Compression Method and Flags cm = Zlib$1.CompressionMethod.DEFLATE; switch (cm) { case Zlib$1.CompressionMethod.DEFLATE: cinfo = Math.LOG2E * Math.log(Zlib$1.RawDeflate.WindowSize) - 8; break; default: throw new Error('invalid compression method'); } cmf = cinfo << 4 | cm; output[pos++] = cmf; // Flags fdict = 0; switch (cm) { case Zlib$1.CompressionMethod.DEFLATE: switch (this.compressionType) { case Zlib$1.Deflate.CompressionType.NONE: flevel = 0; break; case Zlib$1.Deflate.CompressionType.FIXED: flevel = 1; break; case Zlib$1.Deflate.CompressionType.DYNAMIC: flevel = 2; break; default: throw new Error('unsupported compression type'); } break; default: throw new Error('invalid compression method'); } flg = flevel << 6 | fdict << 5; fcheck = 31 - (cmf * 256 + flg) % 31; flg |= fcheck; output[pos++] = flg; // Adler-32 checksum adler = Zlib$1.Adler32(this.input); this.rawDeflate.op = pos; output = this.rawDeflate.compress(); pos = output.length; { // subarray 分を元にもどす output = new Uint8Array(output.buffer); // expand buffer if (output.length <= pos + 4) { this.output = new Uint8Array(output.length + 4); this.output.set(output); output = this.output; } output = output.subarray(0, pos + 4); } // adler32 output[pos++] = adler >> 24 & 0xff; output[pos++] = adler >> 16 & 0xff; output[pos++] = adler >> 8 & 0xff; output[pos++] = adler & 0xff; return output; }; /** * Covers string literals and String objects * @param x * @returns {boolean} */ function isString$6(x) { return typeof x === "string" || x instanceof String; } // StackOverflow: http://stackoverflow.com/a/10810674/116169 function numberFormatter$1(rawNumber) { var dec = String(rawNumber).split(/[.,]/), sep = ',', decsep = '.'; return dec[0].split('').reverse().reduce(function (prev, now, i) { return i % 3 === 0 ? prev + sep + now : prev + now; }).split('').reverse().join('') + (dec[1] ? decsep + dec[1] : ''); } const splitLines$3 = function (string) { return string.split(/\n|\r\n|\r/g); }; function splitStringRespectingQuotes(string, delim) { var tokens = [], len = string.length, i, n = 0, quote = false, c; if (len > 0) { tokens[n] = string.charAt(0); for (i = 1; i < len; i++) { c = string.charAt(i); if (c === '"') { quote = !quote; } else if (!quote && c === delim) { n++; tokens[n] = ""; } else { tokens[n] += c; } } } return tokens; } function stripQuotes(str) { if (str === undefined) { return str; } if (str.startsWith("'") || str.startsWith('"')) { str = str.substring(1); } if (str.endsWith("'") || str.endsWith('"')) { str = str.substring(0, str.length - 1); } return str; } function hashCode$1(s) { return s.split("").reduce(function (a, b) { a = (a << 5) - a + b.charCodeAt(0); return a & a; }, 0); } /** * Compress string and encode in a url safe form * @param s */ function compressString(str) { const bytes = []; for (var i = 0; i < str.length; i++) { bytes.push(str.charCodeAt(i)); } const compressedBytes = new Zlib$1.RawDeflate(bytes).compress(); // UInt8Arry const compressedString = String.fromCharCode.apply(null, compressedBytes); // Convert to string let enc = btoa(compressedString); return enc.replace(/\+/g, '.').replace(/\//g, '_').replace(/=/g, '-'); // URL safe } /** * Uncompress the url-safe encoded compressed string, presumably created by compressString above * * @param enc * @returns {string} */ function uncompressString(enc) { enc = enc.replace(/\./g, '+').replace(/_/g, '/').replace(/-/g, '='); const compressedString = atob(enc); const compressedBytes = []; for (let i = 0; i < compressedString.length; i++) { compressedBytes.push(compressedString.charCodeAt(i)); } const bytes = new Zlib$1.RawInflate(compressedBytes).decompress(); let str = ''; for (let b of bytes) { str += String.fromCharCode(b); } return str; } function capitalize(str) { return str.length > 0 ? str.charAt(0).toUpperCase() + str.slice(1) : str; } /** * Parse a locus string and return a range object. Locus string is of the form chr:start-end. End is optional * */ function parseLocusString$1(string) { const t1 = string.split(":"); const t2 = t1[1].split("-"); const range = { chr: t1[0], start: Number.parseInt(t2[0].replace(/,/g, '')) - 1 }; if (t2.length > 1) { range.end = Number.parseInt(t2[1].replace(/,/g, '')); } else { range.end = range.start + 1; } return range; } const FileFormats = { gwascatalog: { fields: ['bin', 'chr', 'start', 'end', 'name', 'pubMedID', 'author', 'pubDate', 'journal', 'title', 'trait', 'initSample', 'replSample', 'region', 'genes', 'riskAllele', 'riskAlFreq', 'pValue', 'pValueDesc', 'orOrBeta', 'ci95', 'platform', 'cnv'] }, wgrna: { fields: ['bin', 'chr', 'start', 'end', 'name', 'score', 'strand', 'thickStart', 'thickEnd', 'type'] }, cpgislandext: { fields: ['bin', 'chr', 'start', 'end', 'name', 'length', 'cpgNum', 'gcNum', 'perCpg', 'perGc', 'obsExp'] }, clinVarMain: { fields: ['chr1', 'start', 'end', 'name', 'score', 'strand', 'thickStart', 'thickEnd', 'reserved', 'blockCount', // Number of blocks 'blockSizes', // Comma separated list of block sizes 'chromStarts', // Start positions relative to chromStart 'origName', // NM_198053.2(CD247):c.462C>T (p.Asp154=) ClinVar Variation Report 'clinSign', // Likely benign Clinical significance 'reviewStatus', // based on: criteria provided,single submitter Review Status 'type', // single nucleotide variant Type of Variant 'geneId', // CD247 Gene Symbol 'snpId', // 181656780 dbSNP ID 'nsvId', // dbVar ID 'rcvAcc', // RCV000642347 ClinVar Allele Submission 'testedInGtr', // N Genetic Testing Registry 'phenotypeList', // Immunodeficiency due to defect in cd3-zeta Phenotypes 'phenotype', // MedGen:C1857798, OMIM:610163 Phenotype identifiers 'origin', // germline Data origin 'assembly', // GRCh37 Genome assembly 'cytogenetic', // 1q24.2 Cytogenetic status 'hgvsCod', // NM_198053.2:c.462C>T Nucleotide HGVS 'hgvsProt', // NP_932170.1:p.Asp154= Protein HGVS 'numSubmit', // 1 Number of submitters 'lastEval', // Dec 19,2017 Last evaluation 'guidelines', // Guidelines 'otherIds'] } }; /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const knownFileExtensions = new Set(["narrowpeak", "broadpeak", "regionpeak", "peaks", "bedgraph", "wig", "gff3", "gff", "gtf", "fusionjuncspan", "refflat", "seg", "aed", "bed", "vcf", "bb", "bigbed", "bw", "bigwig", "bam", "tdf", "refgene", "genepred", "genepredext", "bedpe", "bp", "snp", "rmsk", "cram", "gwas"]); /** * Return a custom format object with the given name. * @param name * @returns {*} */ function getFormat(name) { if (FileFormats && FileFormats[name]) { return expandFormat(FileFormats[name]); } else { return undefined; } function expandFormat(format) { const fields = format.fields; const keys = ['chr', 'start', 'end']; for (let i = 0; i < fields.length; i++) { for (let key of keys) { if (key === fields[i]) { format[key] = i; } } } return format; } } function inferFileFormat(fn) { var idx, ext; fn = fn.toLowerCase(); // Special case -- UCSC refgene files if (fn.endsWith("refgene.txt.gz") || fn.endsWith("refgene.txt.bgz") || fn.endsWith("refgene.txt") || fn.endsWith("refgene.sorted.txt.gz") || fn.endsWith("refgene.sorted.txt.bgz")) { return "refgene"; } //Strip parameters -- handle local files later idx = fn.indexOf("?"); if (idx > 0) { fn = fn.substr(0, idx); } //Strip aux extensions .gz, .tab, and .txt if (fn.endsWith(".gz")) { fn = fn.substr(0, fn.length - 3); } if (fn.endsWith(".txt") || fn.endsWith(".tab") || fn.endsWith(".bgz")) { fn = fn.substr(0, fn.length - 4); } idx = fn.lastIndexOf("."); ext = idx < 0 ? fn : fn.substr(idx + 1); switch (ext) { case "bw": return "bigwig"; case "bb": return "bigbed"; default: if (knownFileExtensions.has(ext)) { return ext; } else { return undefined; } } } function inferIndexPath(url, extension) { var idx; if (url instanceof File) { throw new Error("Cannot infer an index path for a local File. Please select explicitly"); } if (url.includes("?")) { idx = url.indexOf("?"); return url.substring(0, idx) + "." + extension + url.substring(idx); } else { return url + "." + extension; } } function isGoogleURL(url) { return url.includes("googleapis") && !url.includes("urlshortener") || isGoogleStorageURL(url) || isGoogleDriveURL(url); } function isGoogleStorageURL(url) { return url.startsWith("gs://") || url.startsWith("https://www.googleapis.com/storage") || url.startsWith("https://storage.cloud.google.com") || url.startsWith("https://storage.googleapis.com"); } function isGoogleDriveURL(url) { return url.indexOf("drive.google.com") >= 0 || url.indexOf("www.googleapis.com/drive") > 0; } /** * Translate gs:// urls to https * See https://cloud.google.com/storage/docs/json_api/v1 * @param gsUrl * @returns {string|*} */ function translateGoogleCloudURL(gsUrl) { let { bucket, object } = parseBucketName(gsUrl); object = encode(object); const qIdx = gsUrl.indexOf('?'); const paramString = qIdx > 0 ? gsUrl.substring(qIdx) + "&alt=media" : "?alt=media"; return `https://storage.googleapis.com/storage/v1/b/${bucket}/o/${object}${paramString}`; } /** * Parse a google bucket and object name from a google storage URL. Known forms include * * gs://BUCKET_NAME/OBJECT_NAME * https://storage.googleapis.com/BUCKET_NAME/OBJECT_NAME * https://storage.googleapis.com/storage/v1/b/BUCKET_NAME/o/OBJECT_NAME * https://www.googleapis.com/storage/v1/b/BUCKET_NAME/o/OBJECT_NAME" * https://storage.googleapis.com/download/storage/v1/b/BUCKET_NAME/o/OBJECT_NAME * * @param url */ function parseBucketName(url) { let bucket; let object; if (url.startsWith("gs://")) { const i = url.indexOf('/', 5); if (i >= 0) { bucket = url.substring(5, i); const qIdx = url.indexOf('?'); object = qIdx < 0 ? url.substring(i + 1) : url.substring(i + 1, qIdx); } } else if (url.startsWith("https://storage.googleapis.com") || url.startsWith("https://storage.cloud.google.com")) { const bucketIdx = url.indexOf("/v1/b/", 8); if (bucketIdx > 0) { const objIdx = url.indexOf("/o/", bucketIdx); if (objIdx > 0) { const queryIdx = url.indexOf("?", objIdx); bucket = url.substring(bucketIdx + 6, objIdx); object = queryIdx > 0 ? url.substring(objIdx + 3, queryIdx) : url.substring(objIdx + 3); } } else { const idx1 = url.indexOf("/", 8); const idx2 = url.indexOf("/", idx1 + 1); const idx3 = url.indexOf("?", idx2); if (idx2 > 0) { bucket = url.substring(idx1 + 1, idx2); object = idx3 < 0 ? url.substring(idx2 + 1) : url.substring(idx2 + 1, idx3); } } } else if (url.startsWith("https://www.googleapis.com/storage/v1/b")) { const bucketIdx = url.indexOf("/v1/b/", 8); const objIdx = url.indexOf("/o/", bucketIdx); if (objIdx > 0) { const queryIdx = url.indexOf("?", objIdx); bucket = url.substring(bucketIdx + 6, objIdx); object = queryIdx > 0 ? url.substring(objIdx + 3, queryIdx) : url.substring(objIdx + 3); } } if (bucket && object) { return { bucket, object }; } else { throw Error(`Unrecognized Google Storage URI: ${url}`); } } function driveDownloadURL(link) { // Return a google drive download url for the sharable link //https://drive.google.com/open?id=0B-lleX9c2pZFbDJ4VVRxakJzVGM //https://drive.google.com/file/d/1_FC4kCeO8E3V4dJ1yIW7A0sn1yURKIX-/view?usp=sharing var id = getGoogleDriveFileID(link); return id ? "https://www.googleapis.com/drive/v3/files/" + id + "?alt=media&supportsTeamDrives=true" : link; } function getGoogleDriveFileID(link) { //https://drive.google.com/file/d/1_FC4kCeO8E3V4dJ1yIW7A0sn1yURKIX-/view?usp=sharing //https://www.googleapis.com/drive/v3/files/1w-tvo6p1SH4p1OaQSVxpkV_EJgGIstWF?alt=media&supportsTeamDrives=true" if (link.includes("/open?id=")) { const i1 = link.indexOf("/open?id=") + 9; const i2 = link.indexOf("&"); if (i1 > 0 && i2 > i1) { return link.substring(i1, i2); } else if (i1 > 0) { return link.substring(i1); } } else if (link.includes("/file/d/")) { const i1 = link.indexOf("/file/d/") + 8; const i2 = link.lastIndexOf("/"); return link.substring(i1, i2); } else if (link.startsWith("https://www.googleapis.com/drive")) { let i1 = link.indexOf("/files/"); const i2 = link.indexOf("?"); if (i1 > 0) { i1 += 7; return i2 > 0 ? link.substring(i1, i2) : link.substring(i1); } } throw Error("Unknown Google Drive url format: " + link); } /** * Percent a GCS object name. See https://cloud.google.com/storage/docs/request-endpoints * Specific characters to encode: * !, #, $, &, ', (, ), *, +, ,, /, :, ;, =, ?, @, [, ], and space characters. * @param obj */ function encode(objectName) { let result = ''; objectName.split('').forEach(function (letter) { if (encodings$1.has(letter)) { result += encodings$1.get(letter); } else { result += letter; } }); return result; } // %23 %24 %25 %26 %27 %28 %29 %2A %2B %2C %2F %3A %3B %3D %3F %40 %5B %5D const encodings$1 = new Map(); encodings$1.set("!", "%21"); encodings$1.set("#", "%23"); encodings$1.set("$", "%24"); encodings$1.set("%", "%25"); encodings$1.set("&", "%26"); encodings$1.set("'", "%27"); encodings$1.set("(", "%28"); encodings$1.set(")", "%29"); encodings$1.set("*", "%2A"); encodings$1.set("+", "%2B"); encodings$1.set(",", "%2C"); encodings$1.set("/", "%2F"); encodings$1.set(":", "%3A"); encodings$1.set(";", "%3B"); encodings$1.set("=", "%3D"); encodings$1.set("?", "%3F"); encodings$1.set("@", "%40"); encodings$1.set("[", "%5B"); encodings$1.set("]", "%5D"); encodings$1.set(" ", "%20"); // For testing // Convenience functions for the gapi oAuth library. const FIVE_MINUTES = 5 * 60 * 1000; async function load$1(library) { return new Promise(function (resolve, reject) { gapi.load(library, { callback: resolve, onerror: reject }); }); } async function init$1(config) { if (isInitialized()) { console.warn("oAuth has already been initialized"); return; } gapi.apiKey = config.apiKey; // copy config, gapi will modify it const configCopy = Object.assign({}, config); if (!configCopy.scope) { configCopy.scope = 'profile'; } if (!config.client_id) { config.client_id = config.clientId; } await load$1("auth2"); return new Promise(function (resolve, reject) { gapi.auth2.init(configCopy).then(resolve, reject); }); } function isInitialized() { return typeof gapi !== "undefined" && gapi.auth2 && gapi.auth2.getAuthInstance(); } let inProgress = false; async function getAccessToken(scope) { if (typeof gapi === "undefined") { throw Error("Google authentication requires the 'gapi' library"); } if (!gapi.auth2) { throw Error("Google 'auth2' has not been initialized"); } if (inProgress) { return new Promise(function (resolve, reject) { let intervalID; const checkForToken = () => { // Wait for inProgress to equal "false" try { if (inProgress === false) { //console.log("Delayed resolution for " + scope); resolve(getAccessToken(scope)); clearInterval(intervalID); } } catch (e) { clearInterval(intervalID); reject(e); } }; intervalID = setInterval(checkForToken, 100); }); } else { inProgress = true; try { let currentUser = gapi.auth2.getAuthInstance().currentUser.get(); let token; if (currentUser.isSignedIn()) { if (!currentUser.hasGrantedScopes(scope)) { await currentUser.grant({ scope }); } const { access_token, expires_at } = currentUser.getAuthResponse(); if (Date.now() < expires_at - FIVE_MINUTES) { token = { access_token, expires_at }; } else { const { access_token, expires_at } = currentUser.reloadAuthResponse(); token = { access_token, expires_at }; } } else { currentUser = await signIn(scope); const { access_token, expires_at } = currentUser.getAuthResponse(); token = { access_token, expires_at }; } return token; } finally { inProgress = false; } } } /** * Return the current access token if the user is signed in, or undefined otherwise. This function does not * attempt a signIn or request any specfic scopes. * * @returns access_token || undefined */ function getCurrentAccessToken() { let currentUser = gapi.auth2.getAuthInstance().currentUser.get(); if (currentUser && currentUser.isSignedIn()) { const { access_token, expires_at } = currentUser.getAuthResponse(); return { access_token, expires_at }; } else { return undefined; } } async function signIn(scope) { const options = new gapi.auth2.SigninOptionsBuilder(); options.setPrompt('select_account'); options.setScope(scope); return gapi.auth2.getAuthInstance().signIn(options); } function getScopeForURL(url) { if (isGoogleDriveURL(url)) { return "https://www.googleapis.com/auth/drive.file"; } else if (isGoogleStorageURL(url)) { return "https://www.googleapis.com/auth/devstorage.read_only"; } else { return 'https://www.googleapis.com/auth/userinfo.profile'; } } function getApiKey() { return gapi.apiKey; } async function getDriveFileInfo(googleDriveURL) { const id = getGoogleDriveFileID(googleDriveURL); let endPoint = "https://www.googleapis.com/drive/v3/files/" + id + "?supportsTeamDrives=true"; const apiKey = getApiKey(); if (apiKey) { endPoint += "&key=" + apiKey; } const response = await fetch(endPoint); let json = await response.json(); if (json.error && json.error.code === 404) { const { access_token } = await getAccessToken("https://www.googleapis.com/auth/drive.readonly"); if (access_token) { const response = await fetch(endPoint, { headers: { 'Authorization': `Bearer ${access_token}` } }); json = await response.json(); if (json.error) { throw Error(json.error); } } else { throw Error(json.error); } } return json; } if (typeof process === 'object' && typeof window === 'undefined') { global.atob = function (str) { return Buffer.from(str, 'base64').toString('binary'); }; } /** * @param dataURI * @returns {Array|Uint8Array} */ function decodeDataURI$1(dataURI) { const split = dataURI.split(','); const info = split[0].split(':')[1]; let dataString = split[1]; if (info.indexOf('base64') >= 0) { dataString = atob(dataString); } else { dataString = decodeURI(dataString); // URL encoded string -- not currently used of tested } const bytes = new Uint8Array(dataString.length); for (let i = 0; i < dataString.length; i++) { bytes[i] = dataString.charCodeAt(i); } let plain; if (info.indexOf('gzip') > 0) { const inflate = new Zlib$1.Gunzip(bytes); plain = inflate.decompress(); } else { plain = bytes; } return plain; } function parseUri(str) { var o = options, m = o.parser["loose"].exec(str), uri = {}, i = 14; while (i--) uri[o.key[i]] = m[i] || ""; uri[o.q.name] = {}; uri[o.key[12]].replace(o.q.parser, function ($0, $1, $2) { if ($1) uri[o.q.name][$1] = $2; }); return uri; } const options = { strictMode: false, key: ["source", "protocol", "authority", "userInfo", "user", "password", "host", "port", "relative", "path", "directory", "file", "query", "anchor"], q: { name: "queryKey", parser: /(?:^|&)([^&=]*)=?([^&]*)/g }, parser: { strict: /^(?:([^:\/?#]+):)?(?:\/\/((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?))?((((?:[^?#\/]*\/)*)([^?#]*))(?:\?([^#]*))?(?:#(.*))?)/, loose: /^(?:(?![^:@]+:[^:@\/]*@)([^:\/?#.]+):)?(?:\/\/)?((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?)(((\/(?:[^?#](?![^?#\/]*\.[^?#\/.]+(?:[?#]|$)))*\/?)?([^?#\/]*))(?:\?([^#]*))?(?:#(.*))?)/ } }; /** * Resolve a url, which might be a string, function (that returns a string or Promse), or Promise (that resolves to a string) * * @param url * @returns {Promise<*>} */ async function resolveURL(url) { return typeof url === 'function' ? url() : url; } /** * Return the filename from the path. Example * https://foo.com/bar.bed?param=2 => bar.bed * @param urlOrFile */ function getFilename$2(urlOrFile) { if (urlOrFile instanceof File) { return urlOrFile.name; } else if (isString$6(urlOrFile)) { let index = urlOrFile.lastIndexOf("/"); let filename = index < 0 ? urlOrFile : urlOrFile.substr(index + 1); //Strip parameters -- handle local files later index = filename.indexOf("?"); if (index > 0) { filename = filename.substr(0, index); } return filename; } else { throw Error(`Expected File or string, got ${typeof urlOrFile}`); } } function isFilePath(path) { return path instanceof File; } function download(filename, data) { const element = document.createElement('a'); element.setAttribute('href', data); element.setAttribute('download', filename); element.style.display = 'none'; document.body.appendChild(element); element.click(); document.body.removeChild(element); } // Uncompress data, assumed to be series of bgzipped blocks function unbgzf(data, lim) { const oBlockList = []; let ptr = 0; let totalSize = 0; lim = lim || data.byteLength - 18; while (ptr < lim) { try { const ba = new Uint8Array(data, ptr, 18); const xlen = ba[11] << 8 | ba[10]; const si1 = ba[12]; const si2 = ba[13]; const slen = ba[15] << 8 | ba[14]; const bsize = (ba[17] << 8 | ba[16]) + 1; const start = 12 + xlen + ptr; // Start of CDATA const bytesLeft = data.byteLength - start; const cDataSize = bsize - xlen - 19; if (bytesLeft < cDataSize || cDataSize <= 0) break; const a = new Uint8Array(data, start, cDataSize); const inflate = new Zlib$1.RawInflate(a); const unc = inflate.decompress(); ptr += inflate.ip + 26; totalSize += unc.byteLength; oBlockList.push(unc); } catch (e) { console.error(e); break; } } // Concatenate decompressed blocks if (oBlockList.length === 1) { return oBlockList[0]; } else { const out = new Uint8Array(totalSize); let cursor = 0; for (let i = 0; i < oBlockList.length; ++i) { var b = new Uint8Array(oBlockList[i]); arrayCopy(b, 0, out, cursor, b.length); cursor += b.length; } return out; } } function bgzBlockSize(data) { const ba = new Uint8Array(data); const bsize = (ba[17] << 8 | ba[16]) + 1; return bsize; } // From Thomas Down's zlib implementation const testArray = new Uint8Array(1); const hasSubarray = typeof testArray.subarray === 'function'; /* (typeof testArray.slice === 'function'); */ // Chrome slice performance is so dire that we're currently not using it... function arrayCopy(src, srcOffset, dest, destOffset, count) { if (count === 0) { return; } if (!src) { throw "Undef src"; } else if (!dest) { throw "Undef dest"; } if (srcOffset === 0 && count === src.length) { arrayCopy_fast(src, dest, destOffset); } else if (hasSubarray) { arrayCopy_fast(src.subarray(srcOffset, srcOffset + count), dest, destOffset); } else if (src.BYTES_PER_ELEMENT === 1 && count > 100) { arrayCopy_fast(new Uint8Array(src.buffer, src.byteOffset + srcOffset, count), dest, destOffset); } else { arrayCopy_slow(src, srcOffset, dest, destOffset, count); } } function arrayCopy_slow(src, srcOffset, dest, destOffset, count) { for (let i = 0; i < count; ++i) { dest[destOffset + i] = src[srcOffset + i]; } } function arrayCopy_fast(src, dest, destOffset) { dest.set(src, destOffset); } /* * The MIT License (MIT) * * Copyright (c) 2016-2017 The Regents of the University of California * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const IGVMath = { lerp: (v0, v1, t) => { return (1 - t) * v0 + t * v1; }, mean: function (array) { var t = 0, n = 0, i; for (i = 0; i < array.length; i++) { if (!isNaN(array[i])) { t += array[i]; n++; } } return n > 0 ? t / n : 0; }, meanAndStdev: function (array) { var v, t = 0, t2 = 0, n = 0, i; for (i = 0; i < array.length; i++) { v = array[i]; if (!isNaN(v)) { t += v; t2 += v * v; n++; } } return n > 0 ? { mean: t / n, stdev: Math.sqrt(t2 - t * t / n) } : { mean: 0, stdev: 0 }; }, median: function (numbers) { // median of [3, 5, 4, 4, 1, 1, 2, 3] = 3 var median = 0, numsLen = numbers.length; numbers.sort(); if (numsLen % 2 === 0 // is even ) { // average of two middle numbers median = (numbers[numsLen / 2 - 1] + numbers[numsLen / 2]) / 2; } else { // is odd // middle number only median = numbers[(numsLen - 1) / 2]; } return median; }, // Fast percentile function for "p" near edges. This needs profiled for p in middle (e.g. median) percentile: function (array, p) { if (array.length === 0) return undefined; var k = Math.floor(array.length * ((100 - p) / 100)); if (k === 0) { array.sort(function (a, b) { return b - a; }); return array[k]; } else { return selectElement(array, k); } }, clamp: function (value, min, max) { return Math.min(Math.max(value, min), max); }, log2: function (x) { return Math.log(x) / Math.LN2; } }; function selectElement(array, k) { // Credit Steve Hanov http://stevehanov.ca/blog/index.php?id=122 var heap = new BinaryHeap(), i; for (i = 0; i < array.length; i++) { var item = array[i]; // If we have not yet found k items, or the current item is larger than // the smallest item on the heap, add current item if (heap.content.length < k || item > heap.content[0]) { // If the heap is full, remove the smallest element on the heap. if (heap.content.length === k) { heap.pop(); } heap.push(item); } } return heap.content[0]; } function BinaryHeap() { this.content = []; } BinaryHeap.prototype = { push: function (element) { // Add the new element to the end of the array. this.content.push(element); // Allow it to bubble up. this.bubbleUp(this.content.length - 1); }, pop: function () { // Store the first element so we can return it later. var result = this.content[0]; // Get the element at the end of the array. var end = this.content.pop(); // If there are any elements left, put the end element at the // start, and let it sink down. if (this.content.length > 0) { this.content[0] = end; this.sinkDown(0); } return result; }, remove: function (node) { var length = this.content.length; // To remove a value, we must search through the array to find // it. for (var i = 0; i < length; i++) { if (this.content[i] !== node) continue; // When it is found, the process seen in 'pop' is repeated // to fill up the hole. var end = this.content.pop(); // If the element we popped was the one we needed to remove, // we're done. if (i === length - 1) break; // Otherwise, we replace the removed element with the popped // one, and allow it to float up or sink down as appropriate. this.content[i] = end; this.bubbleUp(i); this.sinkDown(i); break; } }, size: function () { return this.content.length; }, bubbleUp: function (n) { // Fetch the element that has to be moved. var element = this.content[n], score = element; // When at 0, an element can not go up any further. while (n > 0) { // Compute the parent element's index, and fetch it. var parentN = Math.floor((n + 1) / 2) - 1, parent = this.content[parentN]; // If the parent has a lesser score, things are in order and we // are done. if (score >= parent) break; // Otherwise, swap the parent with the current element and // continue. this.content[parentN] = element; this.content[n] = parent; n = parentN; } }, sinkDown: function (n) { // Look up the target element and its score. var length = this.content.length, element = this.content[n], elemScore = element; while (true) { // Compute the indices of the child elements. var child2N = (n + 1) * 2, child1N = child2N - 1; // This is used to store the new position of the element, // if any. var swap = null; // If the first child exists (is inside the array)... if (child1N < length) { // Look it up and compute its score. var child1 = this.content[child1N], child1Score = child1; // If the score is less than our element's, we need to swap. if (child1Score < elemScore) swap = child1N; } // Do the same checks for the other child. if (child2N < length) { var child2 = this.content[child2N], child2Score = child2; if (child2Score < (swap == null ? elemScore : child1Score)) swap = child2N; } // No need to swap further, we are done. if (swap == null) break; // Otherwise, swap and continue. this.content[n] = this.content[swap]; this.content[swap] = element; n = swap; } } }; /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ function _random(min, max) { return Math.random() * (max - min) + min; } const IGVColor = { rgbListFromHSV: () => { let s = 1; let accumulation = []; for (let v = 1; v >= 0.5; v -= .1) { for (let h = 0; h < 1; h += 1 / 28) { const r = "rgb(" + IGVColor.hsvToRgb(h, s, v).join(",") + ")"; accumulation.push(r); } } // add black accumulation.pop(); accumulation.push(IGVColor.rgbColor(16, 16, 16)); return accumulation; }, rgbToHex: function (rgb) { rgb = rgb.match(/^rgba?[\s+]?\([\s+]?(\d+)[\s+]?,[\s+]?(\d+)[\s+]?,[\s+]?(\d+)[\s+]?/i); return rgb && rgb.length === 4 ? "#" + ("0" + parseInt(rgb[1], 10).toString(16)).slice(-2) + ("0" + parseInt(rgb[2], 10).toString(16)).slice(-2) + ("0" + parseInt(rgb[3], 10).toString(16)).slice(-2) : ''; }, hexToRgb: function (hex) { var cooked = /^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(hex); if (null === cooked) { return undefined; } return "rgb(" + parseInt(cooked[1], 16) + "," + parseInt(cooked[2], 16) + "," + parseInt(cooked[3], 16) + ")"; }, /** * Converts an HSV color value to RGB. Conversion formula * adapted from http://en.wikipedia.org/wiki/HSV_color_space. * Assumes h, s, and v are contained in the set [0, 1] and * returns r, g, and b in the set [0, 255]. * * Credit: https://gist.githubusercontent.com/mjackson/5311256 * * @param h The hue * @param s The saturation * @param v The value * @return Array The RGB representation */ hsvToRgb: function (h, s, v) { var r, g, b; var i = Math.floor(h * 6); var f = h * 6 - i; var p = v * (1 - s); var q = v * (1 - f * s); var t = v * (1 - (1 - f) * s); switch (i % 6) { case 0: r = v, g = t, b = p; break; case 1: r = q, g = v, b = p; break; case 2: r = p, g = v, b = t; break; case 3: r = p, g = q, b = v; break; case 4: r = t, g = p, b = v; break; case 5: r = v, g = p, b = q; break; } return [Math.floor(r * 255), Math.floor(g * 255), Math.floor(b * 255)]; }, /** * Converts an HSL color value to RGB. Conversion formula * adapted from http://en.wikipedia.org/wiki/HSL_color_space. * Assumes h, s, and l are contained in the set [0, 1] and * returns r, g, and b in the set [0, 255]. * * Credit: https://gist.githubusercontent.com/mjackson/5311256 * * @param h The hue * @param s The saturation * @param l The lightness * @return Array The RGB representation */ hslToRgb: function (h, s, l) { var r, g, b; if (s === 0) { r = g = b = l; // achromatic } else { var q = l < 0.5 ? l * (1 + s) : l + s - l * s; var p = 2 * l - q; r = IGVColor.hue2rgb(p, q, h + 1 / 3); g = IGVColor.hue2rgb(p, q, h); b = IGVColor.hue2rgb(p, q, h - 1 / 3); } return [r * 255, g * 255, b * 255]; }, hue2rgb: (p, q, t) => { if (t < 0) t += 1; if (t > 1) t -= 1; if (t < 1 / 6) return p + (q - p) * 6 * t; if (t < 1 / 2) return q; if (t < 2 / 3) return p + (q - p) * (2 / 3 - t) * 6; return p; }, rgbaColor: function (r, g, b, a) { r = IGVMath.clamp(r, 0, 255); g = IGVMath.clamp(g, 0, 255); b = IGVMath.clamp(b, 0, 255); a = IGVMath.clamp(a, 0.0, 1.0); return "rgba(" + r + "," + g + "," + b + "," + a + ")"; }, rgbColor: function (r, g, b) { r = IGVMath.clamp(r, 0, 255); g = IGVMath.clamp(g, 0, 255); b = IGVMath.clamp(b, 0, 255); return "rgb(" + r + "," + g + "," + b + ")"; }, greyScale: function (value) { var grey = IGVMath.clamp(value, 0, 255); return "rgb(" + grey + "," + grey + "," + grey + ")"; }, randomGrey: function (min, max) { min = IGVMath.clamp(min, 0, 255); max = IGVMath.clamp(max, 0, 255); var g = Math.round(_random(min, max)).toString(10); return "rgb(" + g + "," + g + "," + g + ")"; }, randomRGB: function (min, max) { min = IGVMath.clamp(min, 0, 255); max = IGVMath.clamp(max, 0, 255); var r = Math.round(_random(min, max)).toString(10); var g = Math.round(_random(min, max)).toString(10); var b = Math.round(_random(min, max)).toString(10); return "rgb(" + r + "," + g + "," + b + ")"; }, randomRGBConstantAlpha: function (min, max, alpha) { min = IGVMath.clamp(min, 0, 255); max = IGVMath.clamp(max, 0, 255); var r = Math.round(_random(min, max)).toString(10); var g = Math.round(_random(min, max)).toString(10); var b = Math.round(_random(min, max)).toString(10); return "rgba(" + r + "," + g + "," + b + "," + alpha + ")"; }, addAlpha: function (color, alpha) { if (color === "0" || color === ".") { color = "rgb(0,0,0)"; } else { const c = this.colorNameToHex(color); if (c) { color = c; } } var isHex = /(^#[0-9A-F]{6}$)|(^#[0-9A-F]{3}$)/i.test(color); if (color.startsWith("rgba")) { const idx = color.lastIndexOf(","); return color.substring(0, idx + 1) + alpha.toString() + ")"; } if (isHex) { color = IGVColor.hexToRgb(color); } if (color.startsWith("rgb")) { return color.replace("rgb", "rgba").replace(")", ", " + alpha + ")"); } else { return color; } }, rgbComponents: function (color) { if (color === "0" || color === ".") { return [0, 0, 0]; } const isHex = /(^#[0-9A-F]{6}$)|(^#[0-9A-F]{3}$)/i.test(color); if (isHex) { color = IGVColor.hexToRgb(color); } else { if (!color.startsWith("rgb")) { const hex = this.colorNameToHex(color); color = this.hexToRgb(hex); } } if (color.startsWith("rgb(")) { return color.substring(4, color.length - 1).split(",").map(s => Number.parseInt(s.trim())); } else if (color.startsWith("rgba(")) { return color.substring(5, color.length - 1).split(",").map((s, i) => { s = s.trim(); return i === 3 ? Number.parseFloat(s) : Number.parseInt(s); }); } else { throw Error("Unrecognized color string: color"); } }, /** * * @param dest RGB components as an array * @param src RGB components as an array * @param alpha alpha transparancy in the range 0-1 * @returns {} */ getCompositeColor: function (dest, src, alpha) { var r = Math.floor(alpha * src[0] + (1 - alpha) * dest[0]), g = Math.floor(alpha * src[1] + (1 - alpha) * dest[1]), b = Math.floor(alpha * src[2] + (1 - alpha) * dest[2]); return "rgb(" + r + "," + g + "," + b + ")"; }, createColorString: function (str) { // Excel will quote color strings, strip all quotes str = stripQuotes(str); if (str.includes(",")) { return str.startsWith("rgb") ? str : "rgb(" + str + ")"; } else { return str; } }, darkenLighten: function (color, amt) { let src; let hexColor = this.colorNameToHex(color); if (hexColor) { src = IGVColor.hexToRgb(hexColor); } else { src = color.startsWith('rgb(') ? color : IGVColor.hexToRgb(color); } const components = src.replace(")", "").substring(4).split(","); const r = Math.max(0, Math.min(255, Number.parseInt(components[0].trim()) + amt)); const g = Math.max(0, Math.min(255, Number.parseInt(components[1].trim()) + amt)); const b = Math.max(0, Math.min(255, Number.parseInt(components[2].trim()) + amt)); return 'rgb(' + r.toString() + ',' + g.toString() + ',' + b.toString() + ')'; }, /** * Convert html/css color name to hex value. Adapted from https://gist.github.com/mxfh/4719348 * @param colorName * @returns {*} */ colorNameToHex: function (colorName) { // color list from http://stackoverflow.com/q/1573053/731179 with added gray/gray const definedColorNames = { "aliceblue": "#f0f8ff", "antiquewhite": "#faebd7", "aqua": "#00ffff", "aquamarine": "#7fffd4", "azure": "#f0ffff", "beige": "#f5f5dc", "bisque": "#ffe4c4", "black": "#000000", "blanchedalmond": "#ffebcd", "blue": "#0000ff", "blueviolet": "#8a2be2", "brown": "#a52a2a", "burlywood": "#deb887", "cadetblue": "#5f9ea0", "chartreuse": "#7fff00", "chocolate": "#d2691e", "coral": "#ff7f50", "cornflowerblue": "#6495ed", "cornsilk": "#fff8dc", "crimson": "#dc143c", "cyan": "#00ffff", "darkblue": "#00008b", "darkcyan": "#008b8b", "darkgoldenrod": "#b8860b", "darkgray": "#a9a9a9", "darkgreen": "#006400", "darkkhaki": "#bdb76b", "darkmagenta": "#8b008b", "darkolivegreen": "#556b2f", "darkorange": "#ff8c00", "darkorchid": "#9932cc", "darkred": "#8b0000", "darksalmon": "#e9967a", "darkseagreen": "#8fbc8f", "darkslateblue": "#483d8b", "darkslategray": "#2f4f4f", "darkturquoise": "#00ced1", "darkviolet": "#9400d3", "deeppink": "#ff1493", "deepskyblue": "#00bfff", "dimgray": "#696969", "dodgerblue": "#1e90ff", "firebrick": "#b22222", "floralwhite": "#fffaf0", "forestgreen": "#228b22", "fuchsia": "#ff00ff", "gainsboro": "#dcdcdc", "ghostwhite": "#f8f8ff", "gold": "#ffd700", "goldenrod": "#daa520", "gray": "#808080", "green": "#008000", "greenyellow": "#adff2f", "honeydew": "#f0fff0", "hotpink": "#ff69b4", "indianred ": "#cd5c5c", "indigo ": "#4b0082", "ivory": "#fffff0", "khaki": "#f0e68c", "lavender": "#e6e6fa", "lavenderblush": "#fff0f5", "lawngreen": "#7cfc00", "lemonchiffon": "#fffacd", "lightblue": "#add8e6", "lightcoral": "#f08080", "lightcyan": "#e0ffff", "lightgoldenrodyellow": "#fafad2", "lightgrey": "#d3d3d3", "lightgreen": "#90ee90", "lightpink": "#ffb6c1", "lightsalmon": "#ffa07a", "lightseagreen": "#20b2aa", "lightskyblue": "#87cefa", "lightslategray": "#778899", "lightsteelblue": "#b0c4de", "lightyellow": "#ffffe0", "lime": "#00ff00", "limegreen": "#32cd32", "linen": "#faf0e6", "magenta": "#ff00ff", "maroon": "#800000", "mediumaquamarine": "#66cdaa", "mediumblue": "#0000cd", "mediumorchid": "#ba55d3", "mediumpurple": "#9370d8", "mediumseagreen": "#3cb371", "mediumslateblue": "#7b68ee", "mediumspringgreen": "#00fa9a", "mediumturquoise": "#48d1cc", "mediumvioletred": "#c71585", "midnightblue": "#191970", "mintcream": "#f5fffa", "mistyrose": "#ffe4e1", "moccasin": "#ffe4b5", "navajowhite": "#ffdead", "navy": "#000080", "oldlace": "#fdf5e6", "olive": "#808000", "olivedrab": "#6b8e23", "orange": "#ffa500", "orangered": "#ff4500", "orchid": "#da70d6", "palegoldenrod": "#eee8aa", "palegreen": "#98fb98", "paleturquoise": "#afeeee", "palevioletred": "#d87093", "papayawhip": "#ffefd5", "peachpuff": "#ffdab9", "peru": "#cd853f", "pink": "#ffc0cb", "plum": "#dda0dd", "powderblue": "#b0e0e6", "purple": "#800080", "red": "#ff0000", "rosybrown": "#bc8f8f", "royalblue": "#4169e1", "saddlebrown": "#8b4513", "salmon": "#fa8072", "sandybrown": "#f4a460", "seagreen": "#2e8b57", "seashell": "#fff5ee", "sienna": "#a0522d", "silver": "#c0c0c0", "skyblue": "#87ceeb", "slateblue": "#6a5acd", "slategray": "#708090", "snow": "#fffafa", "springgreen": "#00ff7f", "steelblue": "#4682b4", "tan": "#d2b48c", "teal": "#008080", "thistle": "#d8bfd8", "tomato": "#ff6347", "turquoise": "#40e0d0", "violet": "#ee82ee", "wheat": "#f5deb3", "white": "#ffffff", "whitesmoke": "#f5f5f5", "yellow": "#ffff00", "yellowgreen": "#9acd32", "darkgrey": "#a9a9a9", "darkslategrey": "#2f4f4f", "dimgrey": "#696969", "grey": "#808080", "lightgray": "#d3d3d3", "lightslategrey": "#778899", "slategrey": "#708090" }; return definedColorNames[colorName]; } }; /** * Make the target element movable by clicking and dragging on the handle. This is not a general purprose function, * it makes several options specific to igv dialogs, the primary one being that the * target is absolutely positioned in pixel coordinates */ let dragData$1; // Its assumed we are only dragging one element at a time. function makeDraggable$1(target, handle) { handle.addEventListener('mousedown', dragStart$1.bind(target)); } function dragStart$1(event) { event.stopPropagation(); event.preventDefault(); offset$1(this); const dragFunction = drag$1.bind(this); const dragEndFunction = dragEnd$1.bind(this); const computedStyle = getComputedStyle(this); const top = parseInt(computedStyle.top.replace("px", "")); const left = parseInt(computedStyle.left.replace("px", "")); dragData$1 = { dragFunction: dragFunction, dragEndFunction: dragEndFunction, screenX: event.screenX, screenY: event.screenY, top: top, left: left }; document.addEventListener('mousemove', dragFunction); document.addEventListener('mouseup', dragEndFunction); document.addEventListener('mouseleave', dragEndFunction); document.addEventListener('mouseexit', dragEndFunction); } function drag$1(event) { if (!dragData$1) { return; } event.stopPropagation(); event.preventDefault(); const dx = event.screenX - dragData$1.screenX; const dy = event.screenY - dragData$1.screenY; this.style.left = `${dragData$1.left + dx}px`; this.style.top = `${dragData$1.top + dy}px`; } function dragEnd$1(event) { if (!dragData$1) { return; } event.stopPropagation(); event.preventDefault(); const dragFunction = dragData$1.dragFunction; const dragEndFunction = dragData$1.dragEndFunction; document.removeEventListener('mousemove', dragFunction); document.removeEventListener('mouseup', dragEndFunction); document.removeEventListener('mouseleave', dragEndFunction); document.removeEventListener('mouseexit', dragEndFunction); dragData$1 = undefined; } // Support for oauth token based authorization // This class supports explicit setting of an oauth token either globally or for specific hosts. // // The variable oauth.google.access_token, which becomes igv.oauth.google.access_token on ES5 conversion is // supported for backward compatibility const DEFAULT_HOST = "googleapis"; const oauth = { oauthTokens: {}, setToken: function (token, host) { host = host || DEFAULT_HOST; this.oauthTokens[host] = token; if (host === DEFAULT_HOST) { this.google.access_token = token; // legacy support } }, getToken: function (host) { host = host || DEFAULT_HOST; let token; for (let key of Object.keys(this.oauthTokens)) { const regex = wildcardToRegExp(key); if (regex.test(host)) { token = this.oauthTokens[key]; break; } } return token; }, removeToken: function (host) { host = host || DEFAULT_HOST; for (let key of Object.keys(this.oauthTokens)) { const regex = wildcardToRegExp(key); if (regex.test(host)) { this.oauthTokens[key] = undefined; } } if (host === DEFAULT_HOST) { this.google.access_token = undefined; // legacy support } }, // Special object for google -- legacy support google: { setToken: function (token) { oauth.setToken(token); } } }; /** * Creates a RegExp from the given string, converting asterisks to .* expressions, * and escaping all other characters. * * credit https://gist.github.com/donmccurdy/6d073ce2c6f3951312dfa45da14a420f */ function wildcardToRegExp(s) { return new RegExp('^' + s.split(/\*+/).map(regExpEscape).join('.*') + '$'); } /** * RegExp-escapes all characters in the given string. * * credit https://gist.github.com/donmccurdy/6d073ce2c6f3951312dfa45da14a420f */ function regExpEscape(s) { return s.replace(/[|\\{}()[\]^$+*?.]/g, '\\$&'); } // The MIT License (MIT) /** * @constructor * @param {Object} options A set op options to pass to the throttle function * @param {number} requestsPerSecond The amount of requests per second * the library will limit to */ class Throttle$1 { constructor(options) { this.requestsPerSecond = options.requestsPerSecond || 10; this.lastStartTime = 0; this.queued = []; } /** * Adds a promise * @param {Function} async function to be executed * @param {Object} options A set of options. * @return {Promise} A promise */ add(asyncFunction, options) { var self = this; return new Promise(function (resolve, reject) { self.queued.push({ resolve: resolve, reject: reject, asyncFunction: asyncFunction }); self.dequeue(); }); } /** * Adds all the promises passed as parameters * @param {Function} promises An array of functions that return a promise * @param {Object} options A set of options. * @param {number} options.signal An AbortSignal object that can be used to abort the returned promise * @param {number} options.weight A "weight" of each operation resolving by array of promises * @return {Promise} A promise that succeeds when all the promises passed as options do */ addAll(promises, options) { var addedPromises = promises.map(function (promise) { return this.add(promise, options); }.bind(this)); return Promise.all(addedPromises); } /** * Dequeues a promise * @return {void} */ dequeue() { if (this.queued.length > 0) { var now = new Date(), inc = 1000 / this.requestsPerSecond + 1, elapsed = now - this.lastStartTime; if (elapsed >= inc) { this._execute(); } else { // we have reached the limit, schedule a dequeue operation setTimeout(function () { this.dequeue(); }.bind(this), inc - elapsed); } } } /** * Executes the promise * @private * @return {void} */ async _execute() { this.lastStartTime = new Date(); var candidate = this.queued.shift(); const f = candidate.asyncFunction; try { const r = await f(); candidate.resolve(r); } catch (e) { candidate.reject(e); } } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ var NONE = 0; var GZIP = 1; var BGZF = 2; var UNKNOWN = 3; let RANGE_WARNING_GIVEN = false; const googleThrottle = new Throttle$1({ requestsPerSecond: 8 }); const igvxhr = { apiKey: undefined, setApiKey: function (key) { this.apiKey = key; }, load: load, loadArrayBuffer: async function (url, options) { options = options || {}; if (!options.responseType) { options.responseType = "arraybuffer"; } if (url instanceof File) { return loadFileSlice(url, options); } else { return load(url, options); } }, loadJson: async function (url, options) { options = options || {}; const method = options.method || (options.sendData ? "POST" : "GET"); if (method === "POST") { options.contentType = "application/json"; } const result = await this.loadString(url, options); if (result) { return JSON.parse(result); } else { return result; } }, loadString: async function (path, options) { options = options || {}; if (path instanceof File) { return loadStringFromFile(path, options); } else { return loadStringFromUrl(path, options); } } }; async function load(url, options) { options = options || {}; const urlType = typeof url; // Resolve functions, promises, and functions that return promises url = await (typeof url === 'function' ? url() : url); if (url instanceof File) { return loadFileSlice(url, options); } else if (typeof url.startsWith === 'function') { // Test for string if (url.startsWith("data:")) { return decodeDataURI$1(url); } else { if (url.startsWith("https://drive.google.com")) { url = driveDownloadURL(url); } if (isGoogleDriveURL(url) || url.startsWith("https://www.dropbox.com")) { return googleThrottle.add(async function () { return loadURL(url, options); }); } else { return loadURL(url, options); } } } else { throw Error(`url must be either a 'File', 'string', 'function', or 'Promise'. Actual type: ${urlType}`); } } async function loadURL(url, options) { //console.log(`${Date.now()} ${url}`) url = mapUrl(url); options = options || {}; let oauthToken = options.oauthToken || getOauthToken(url); if (oauthToken) { oauthToken = await (typeof oauthToken === 'function' ? oauthToken() : oauthToken); } return new Promise(function (resolve, reject) { // Various Google tansformations if (isGoogleURL(url)) { if (isGoogleStorageURL(url)) { url = translateGoogleCloudURL(url); } url = addApiKey(url); if (isGoogleDriveURL(url)) { addTeamDrive(url); } // If we have an access token try it, but don't force a signIn or request for scopes yet if (!oauthToken) { oauthToken = getCurrentGoogleAccessToken(); } } const headers = options.headers || {}; if (oauthToken) { addOauthHeaders(headers, oauthToken); } const range = options.range; const isChrome = navigator.userAgent.indexOf('Chrome') > -1; navigator.vendor.indexOf("Apple") === 0 && /\sSafari\//.test(navigator.userAgent); if (range && isChrome && !isAmazonV4Signed(url)) { // Hack to prevent caching for byte-ranges. Attempt to fix net:err-cache errors in Chrome url += url.includes("?") ? "&" : "?"; url += "someRandomSeed=" + Math.random().toString(36); } const xhr = new XMLHttpRequest(); const sendData = options.sendData || options.body; const method = options.method || (sendData ? "POST" : "GET"); const responseType = options.responseType; const contentType = options.contentType; const mimeType = options.mimeType; xhr.open(method, url); if (options.timeout) { xhr.timeout = options.timeout; } if (range) { var rangeEnd = range.size ? range.start + range.size - 1 : ""; xhr.setRequestHeader("Range", "bytes=" + range.start + "-" + rangeEnd); // xhr.setRequestHeader("Cache-Control", "no-cache"); <= This can cause CORS issues, disabled for now } if (contentType) { xhr.setRequestHeader("Content-Type", contentType); } if (mimeType) { xhr.overrideMimeType(mimeType); } if (responseType) { xhr.responseType = responseType; } if (headers) { for (let key of Object.keys(headers)) { const value = headers[key]; xhr.setRequestHeader(key, value); } } // NOTE: using withCredentials with servers that return "*" for access-allowed-origin will fail if (options.withCredentials === true) { xhr.withCredentials = true; } xhr.onload = async function (event) { // when the url points to a local file, the status is 0 but that is not an error if (xhr.status === 0 || xhr.status >= 200 && xhr.status <= 300) { if (range && xhr.status !== 206 && range.start !== 0) { // For small files a range starting at 0 can return the whole file => 200 // Provide just the slice we asked for, throw out the rest quietly // If file is large warn user if (xhr.response.length > 100000 && !RANGE_WARNING_GIVEN) { alert(`Warning: Range header ignored for URL: ${url}. This can have performance impacts.`); } resolve(xhr.response.slice(range.start, range.start + range.size)); } else { resolve(xhr.response); } } else if (typeof gapi !== "undefined" && (xhr.status === 404 || xhr.status === 401 || xhr.status === 403) && isGoogleURL(url) && !options.retries) { tryGoogleAuth(); } else { if (xhr.status === 403) { handleError("Access forbidden: " + url); } else if (xhr.status === 416) { // Tried to read off the end of the file. This shouldn't happen, but if it does return an handleError("Unsatisfiable range"); } else { handleError(xhr.status); } } }; xhr.onerror = function (event) { if (isGoogleURL(url) && !options.retries) { tryGoogleAuth(); } handleError("Error accessing resource: " + url + " Status: " + xhr.status); }; xhr.ontimeout = function (event) { handleError("Timed out"); }; xhr.onabort = function (event) { reject(event); }; try { xhr.send(sendData); } catch (e) { reject(e); } function handleError(error) { if (reject) { reject(error); } else { throw error; } } async function tryGoogleAuth() { try { const accessToken = await fetchGoogleAccessToken(url); options.retries = 1; options.oauthToken = accessToken; const response = await load(url, options); resolve(response); } catch (e) { if (e.error) { const msg = e.error.startsWith("popup_blocked") ? "Google login popup blocked by browser." : e.error; alert(msg); } else { handleError(e); } } } }); } async function loadFileSlice(localfile, options) { let blob = options && options.range ? localfile.slice(options.range.start, options.range.start + options.range.size) : localfile; if ("arraybuffer" === options.responseType) { return blobToArrayBuffer(blob); } else { // binary string format, shouldn't be used anymore return new Promise(function (resolve, reject) { const fileReader = new FileReader(); fileReader.onload = function (e) { resolve(fileReader.result); }; fileReader.onerror = function (e) { console.error("reject uploading local file " + localfile.name); reject(null, fileReader); }; fileReader.readAsBinaryString(blob); console.warn("Deprecated method used: readAsBinaryString"); }); } } async function loadStringFromFile(localfile, options) { const blob = options.range ? localfile.slice(options.range.start, options.range.start + options.range.size) : localfile; let compression = NONE; if (options && options.bgz || localfile.name.endsWith(".bgz")) { compression = BGZF; } else if (localfile.name.endsWith(".gz")) { compression = GZIP; } if (compression === NONE) { return blobToText(blob); } else { const arrayBuffer = await blobToArrayBuffer(blob); return arrayBufferToString(arrayBuffer, compression); } } async function blobToArrayBuffer(blob) { if (typeof blob.arrayBuffer === 'function') { return blob.arrayBuffer(); } return new Promise(function (resolve, reject) { const fileReader = new FileReader(); fileReader.onload = function (e) { resolve(fileReader.result); }; fileReader.onerror = function (e) { console.error("reject uploading local file " + localfile.name); reject(null, fileReader); }; fileReader.readAsArrayBuffer(blob); }); } async function blobToText(blob) { if (typeof blob.text === 'function') { return blob.text(); } return new Promise(function (resolve, reject) { const fileReader = new FileReader(); fileReader.onload = function (e) { resolve(fileReader.result); }; fileReader.onerror = function (e) { console.error("reject uploading local file " + localfile.name); reject(null, fileReader); }; fileReader.readAsText(blob); }); } async function loadStringFromUrl(url, options) { options = options || {}; const fn = options.filename || (await getFilename$1(url)); let compression = UNKNOWN; if (options.bgz) { compression = BGZF; } else if (fn.endsWith(".gz")) { compression = GZIP; } options.responseType = "arraybuffer"; const data = await igvxhr.load(url, options); return arrayBufferToString(data, compression); } function isAmazonV4Signed(url) { return url.indexOf("X-Amz-Signature") > -1; } function getOauthToken(url) { // Google is the default provider, don't try to parse host for google URLs const host = isGoogleURL(url) ? undefined : parseUri(url).host; let token = oauth.getToken(host); if (token) { return token; } else if (host === undefined) { const googleToken = getCurrentGoogleAccessToken(); if (googleToken && googleToken.expires_at > Date.now()) { return googleToken.access_token; } } } /** * Return a Google oAuth token, triggering a sign in if required. This method should not be called until we know * a token is required, that is until we've tried the url and received a 401, 403, or 404. * * @param url * @returns the oauth token */ async function fetchGoogleAccessToken(url) { if (isInitialized()) { const scope = getScopeForURL(url); const googleToken = await getAccessToken(scope); return googleToken ? googleToken.access_token : undefined; } else { throw Error(`Authorization is required, but Google oAuth has not been initalized. Contact your site administrator for assistance.`); } } /** * Return the current google access token, if one exists. Do not triger signOn or request additional scopes. * @returns {undefined|access_token} */ function getCurrentGoogleAccessToken() { if (isInitialized()) { const googleToken = getCurrentAccessToken(); return googleToken ? googleToken.access_token : undefined; } else { return undefined; } } function addOauthHeaders(headers, acToken) { if (acToken) { headers["Cache-Control"] = "no-cache"; headers["Authorization"] = "Bearer " + acToken; } return headers; } function addApiKey(url) { let apiKey = igvxhr.apiKey; if (!apiKey && typeof gapi !== "undefined") { apiKey = gapi.apiKey; } if (apiKey !== undefined && !url.includes("key=")) { const paramSeparator = url.includes("?") ? "&" : "?"; url = url + paramSeparator + "key=" + apiKey; } return url; } function addTeamDrive(url) { if (url.includes("supportsTeamDrive")) { return url; } else { const paramSeparator = url.includes("?") ? "&" : "?"; url = url + paramSeparator + "supportsTeamDrive=true"; } } /** * Perform some well-known url mappings. * @param url */ function mapUrl(url) { if (url.includes("//www.dropbox.com")) { return url.replace("//www.dropbox.com", "//dl.dropboxusercontent.com"); } else if (url.includes("//drive.google.com")) { return driveDownloadURL(url); } else if (url.includes("//www.broadinstitute.org/igvdata")) { return url.replace("//www.broadinstitute.org/igvdata", "//data.broadinstitute.org/igvdata"); } else if (url.includes("//igvdata.broadinstitute.org")) { return url.replace("//igvdata.broadinstitute.org", "https://dn7ywbm9isq8j.cloudfront.net"); } else if (url.startsWith("ftp://ftp.ncbi.nlm.nih.gov/geo")) { return url.replace("ftp://", "https://"); } else { return url; } } function arrayBufferToString(arraybuffer, compression) { if (compression === UNKNOWN && arraybuffer.byteLength > 2) { const m = new Uint8Array(arraybuffer, 0, 2); if (m[0] === 31 && m[1] === 139) { compression = GZIP; } } let plain; if (compression === GZIP) { const inflate = new Zlib$1.Gunzip(new Uint8Array(arraybuffer)); plain = inflate.decompress(); } else if (compression === BGZF) { plain = unbgzf(arraybuffer); } else { plain = new Uint8Array(arraybuffer); } if ('TextDecoder' in getGlobalObject()) { return new TextDecoder().decode(plain); } else { return decodeUTF8(plain); } } /** * Use when TextDecoder is not available (primarily IE). * * From: https://gist.github.com/Yaffle/5458286 * * @param octets * @returns {string} */ function decodeUTF8(octets) { var string = ""; var i = 0; while (i < octets.length) { var octet = octets[i]; var bytesNeeded = 0; var codePoint = 0; if (octet <= 0x7F) { bytesNeeded = 0; codePoint = octet & 0xFF; } else if (octet <= 0xDF) { bytesNeeded = 1; codePoint = octet & 0x1F; } else if (octet <= 0xEF) { bytesNeeded = 2; codePoint = octet & 0x0F; } else if (octet <= 0xF4) { bytesNeeded = 3; codePoint = octet & 0x07; } if (octets.length - i - bytesNeeded > 0) { var k = 0; while (k < bytesNeeded) { octet = octets[i + k + 1]; codePoint = codePoint << 6 | octet & 0x3F; k += 1; } } else { codePoint = 0xFFFD; bytesNeeded = octets.length - i; } string += String.fromCodePoint(codePoint); i += bytesNeeded + 1; } return string; } function getGlobalObject() { if (typeof self !== 'undefined') { return self; } if (typeof global !== 'undefined') { return global; } else { return window; } } async function getFilename$1(url) { if (isString$6(url) && url.startsWith("https://drive.google.com")) { // This will fail if Google API key is not defined if (getApiKey() === undefined) { throw Error("Google drive is referenced, but API key is not defined. An API key is required for Google Drive access"); } const json = await getDriveFileInfo(url); return json.originalFileName || json.name; } else { return getFilename$2(url); } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ /** An implementation of an interval tree, following the explanation. * from CLR. * * Public interface: * Constructor IntervalTree * Insertion insert * Search findOverlapping */ var BLACK = 1; var RED = 2; var NIL = {}; NIL.color = BLACK; NIL.parent = NIL; NIL.left = NIL; NIL.right = NIL; class IntervalTree { constructor() { this.root = NIL; } insert(start, end, value) { var interval = new Interval(start, end, value); var x = new Node(interval); this.treeInsert(x); x.color = RED; while (x !== this.root && x.parent.color === RED) { if (x.parent === x.parent.parent.left) { let y = x.parent.parent.right; if (y.color === RED) { x.parent.color = BLACK; y.color = BLACK; x.parent.parent.color = RED; x = x.parent.parent; } else { if (x === x.parent.right) { x = x.parent; leftRotate.call(this, x); } x.parent.color = BLACK; x.parent.parent.color = RED; rightRotate.call(this, x.parent.parent); } } else { let y = x.parent.parent.left; if (y.color === RED) { x.parent.color = BLACK; y.color = BLACK; x.parent.parent.color = RED; x = x.parent.parent; } else { if (x === x.parent.left) { x = x.parent; rightRotate.call(this, x); } x.parent.color = BLACK; x.parent.parent.color = RED; leftRotate.call(this, x.parent.parent); } } } this.root.color = BLACK; } /** * * @param start - query interval * @param end - query interval * @returns Array of all intervals overlapping the query region */ findOverlapping(start, end) { var searchInterval = new Interval(start, end, 0); if (this.root === NIL) return []; var intervals = searchAll.call(this, searchInterval, this.root, []); if (intervals.length > 1) { intervals.sort(function (i1, i2) { return i1.low - i2.low; }); } return intervals; } /** * Dump info on intervals to console. For debugging. */ logIntervals() { logNode(this.root); function logNode(node, indent) { if (node.left !== NIL) logNode(node.left); if (node.right !== NIL) logNode(node.right); } } mapIntervals(func) { applyInterval(this.root); function applyInterval(node) { func(node.interval); if (node.left !== NIL) applyInterval(node.left); if (node.right !== NIL) applyInterval(node.right); } } /** * Note: Does not maintain RB constraints, this is done post insert * * @param x a Node */ treeInsert(x) { var node = this.root; var y = NIL; while (node !== NIL) { y = node; if (x.interval.low <= node.interval.low) { node = node.left; } else { node = node.right; } } x.parent = y; if (y === NIL) { this.root = x; x.left = x.right = NIL; } else { if (x.interval.low <= y.interval.low) { y.left = x; } else { y.right = x; } } applyUpdate.call(this, x); } } function searchAll(interval, node, results) { if (node.interval.overlaps(interval)) { results.push(node.interval); } if (node.left !== NIL && node.left.max >= interval.low) { searchAll.call(this, interval, node.left, results); } if (node.right !== NIL && node.right.min <= interval.high) { searchAll.call(this, interval, node.right, results); } return results; } function leftRotate(x) { var y = x.right; x.right = y.left; if (y.left !== NIL) { y.left.parent = x; } y.parent = x.parent; if (x.parent === NIL) { this.root = y; } else { if (x.parent.left === x) { x.parent.left = y; } else { x.parent.right = y; } } y.left = x; x.parent = y; applyUpdate.call(this, x); // no need to apply update on y, since it'll y is an ancestor // of x, and will be touched by applyUpdate(). } function rightRotate(x) { var y = x.left; x.left = y.right; if (y.right !== NIL) { y.right.parent = x; } y.parent = x.parent; if (x.parent === NIL) { this.root = y; } else { if (x.parent.right === x) { x.parent.right = y; } else { x.parent.left = y; } } y.right = x; x.parent = y; applyUpdate.call(this, x); // no need to apply update on y, since it'll y is an ancestor // of x, and will be touched by applyUpdate(). } // Applies the statistic update on the node and its ancestors. function applyUpdate(node) { while (node !== NIL) { var nodeMax = node.left.max > node.right.max ? node.left.max : node.right.max; var intervalHigh = node.interval.high; node.max = nodeMax > intervalHigh ? nodeMax : intervalHigh; var nodeMin = node.left.min < node.right.min ? node.left.min : node.right.min; var intervalLow = node.interval.low; node.min = nodeMin < intervalLow ? nodeMin : intervalLow; node = node.parent; } } class Interval { constructor(low, high, value) { this.low = low; this.high = high; this.value = value; } equals(other) { if (!other) { return false; } if (this === other) { return true; } return this.low === other.low && this.high === other.high; } compareTo(other) { if (this.low < other.low) return -1; if (this.low > other.low) return 1; if (this.high < other.high) return -1; if (this.high > other.high) return 1; return 0; } /** * Returns true if this interval overlaps the other. */ overlaps(other) { return this.low <= other.high && other.low <= this.high; } } function Node(interval) { this.parent = NIL; this.left = NIL; this.right = NIL; this.interval = interval; this.color = RED; } // /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ /** * Object for caching lists of features. Supports effecient queries for sub-range (chr, start, end) * * @param featureList * @param The genomic range spanned by featureList (optional) * @constructor */ class FeatureCache { constructor(featureList, genome, range) { featureList = featureList || []; this.treeMap = this.buildTreeMap(featureList, genome); this.range = range; this.count = featureList.length; } containsRange(genomicRange) { // No range means cache contains all features return this.range === undefined || this.range.contains(genomicRange.chr, genomicRange.start, genomicRange.end); } queryFeatures(chr, start, end) { const tree = this.treeMap[chr]; if (!tree) return []; const intervals = tree.findOverlapping(start, end); if (intervals.length === 0) { return []; } else { // Trim the list of features in the intervals to those // overlapping the requested range. // Assumption: features are sorted by start position const featureList = []; const all = this.allFeatures[chr]; if (all) { for (let interval of intervals) { const indexRange = interval.value; for (let i = indexRange.start; i < indexRange.end; i++) { let feature = all[i]; if (feature.start > end) break;else if (feature.end >= start) { featureList.push(feature); } } } featureList.sort(function (a, b) { return a.start - b.start; }); } return featureList; } } /** * Returns all features, unsorted. * * @returns {Array} */ getAllFeatures() { return this.allFeatures; } buildTreeMap(featureList, genome) { const treeMap = {}; const chromosomes = []; this.allFeatures = {}; if (featureList) { for (let feature of featureList) { let chr = feature.chr; // Translate to "official" name if (genome) { chr = genome.getChromosomeName(chr); } let geneList = this.allFeatures[chr]; if (!geneList) { chromosomes.push(chr); geneList = []; this.allFeatures[chr] = geneList; } geneList.push(feature); } // Now build interval tree for each chromosome for (let chr of chromosomes) { const chrFeatures = this.allFeatures[chr]; chrFeatures.sort(function (f1, f2) { return f1.start === f2.start ? 0 : f1.start > f2.start ? 1 : -1; }); treeMap[chr] = buildIntervalTree$1(chrFeatures); } } return treeMap; } } /** * Build an interval tree from the feature list for fast interval based queries. We lump features in groups * of 10, or total size / 100, to reduce size of the tree. * * @param featureList */ function buildIntervalTree$1(featureList) { const tree = new IntervalTree(); const len = featureList.length; const chunkSize = Math.max(10, Math.round(len / 10)); for (let i = 0; i < len; i += chunkSize) { const e = Math.min(len, i + chunkSize); const subArray = new IndexRange(i, e); //featureList.slice(i, e); const iStart = featureList[i].start; // let iEnd = iStart; for (let j = i; j < e; j++) { iEnd = Math.max(iEnd, featureList[j].end); } tree.insert(iStart, iEnd, subArray); } return tree; } class IndexRange { constructor(start, end) { this.start = start; this.end = end; } } /* * The MIT License (MIT) * * Copyright (c) 2016-2017 The Regents of the University of California * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const FeatureUtils = { packFeatures: function (features, maxRows, sorted) { var start; var end; if (!features) return; maxRows = maxRows || 10000; if (!sorted) { features.sort(function (a, b) { return a.start - b.start; }); } if (features.length === 0) { return []; } else { var bucketList = [], allocatedCount = 0, lastAllocatedCount = 0, nextStart, row, index, bucket, feature, gap = 2, bucketStart; start = features[0].start; end = features[features.length - 1].start; bucketStart = Math.max(start, features[0].start); nextStart = bucketStart; features.forEach(function (alignment) { var buckListIndex = Math.max(0, alignment.start - bucketStart); if (bucketList[buckListIndex] === undefined) { bucketList[buckListIndex] = []; } bucketList[buckListIndex].push(alignment); }); row = 0; while (allocatedCount < features.length && row <= maxRows) { while (nextStart <= end) { bucket = undefined; while (!bucket && nextStart <= end) { index = nextStart - bucketStart; if (bucketList[index] === undefined) { ++nextStart; // No buckets at this index } else { bucket = bucketList[index]; } } // while (bucket) if (!bucket) { break; } feature = bucket.pop(); if (0 === bucket.length) { bucketList[index] = undefined; } feature.row = row; nextStart = feature.end + gap; ++allocatedCount; } // while (nextStart) row++; nextStart = bucketStart; if (allocatedCount === lastAllocatedCount) break; // Protect from infinite loops lastAllocatedCount = allocatedCount; } // while (allocatedCount) } }, /** * Find features overlapping the given interval. It is assumed that all features share the same chromosome. * * TODO -- significant overlap with FeatureCache, refactor to combine * * @param featureList * @param start * @param end */ findOverlapping: function (featureList, start, end) { if (!featureList || featureList.length === 0) { return []; } else { const tree = buildIntervalTree(featureList); const intervals = tree.findOverlapping(start, end); if (intervals.length === 0) { return []; } else { // Trim the list of features in the intervals to those // overlapping the requested range. // Assumption: features are sorted by start position featureList = []; intervals.forEach(function (interval) { const intervalFeatures = interval.value; const len = intervalFeatures.length; for (let i = 0; i < len; i++) { const feature = intervalFeatures[i]; if (feature.start > end) break;else if (feature.end > start) { featureList.push(feature); } } }); featureList.sort(function (a, b) { return a.start - b.start; }); return featureList; } } } }; /** * Build an interval tree from the feature list for fast interval based queries. We lump features in groups * of 10, or total size / 100, to reduce size of the tree. * * @param featureList */ function buildIntervalTree(featureList) { const tree = new IntervalTree(); const len = featureList.length; const chunkSize = Math.max(10, Math.round(len / 100)); featureList.sort(function (f1, f2) { return f1.start === f2.start ? 0 : f1.start > f2.start ? 1 : -1; }); for (let i = 0; i < len; i += chunkSize) { const e = Math.min(len, i + chunkSize); const subArray = featureList.slice(i, e); const iStart = subArray[0].start; let iEnd = iStart; subArray.forEach(function (feature) { iEnd = Math.max(iEnd, feature.end); }); tree.insert(iStart, iEnd, subArray); } return tree; } function createCheckbox$1(name, initialState) { const $container = $('
', { class: 'igv-menu-popup-check-container' }); const $div = $('
'); $container.append($div); const svg = createIcon$2('check', true === initialState ? '#444' : 'transparent'); $div.append($(svg)); const $label = $('
' /*, { class: 'igv-some-label-class' }*/ ); $label.text(name); $container.append($label); return $container; } function createIcon$1(name, color) { return $(createIcon$2(name, color)); } /** * Configure item list for track "gear" menu. * @param trackView */ const MenuUtils = { trackMenuItemList: function (trackView) { const vizWindowTypes = new Set(['alignment', 'annotation', 'variant', 'eqtl', 'snp']); const hasVizWindow = trackView.track.config && trackView.track.config.visibilityWindow !== undefined; let menuItems = []; if (trackView.track.config.type !== 'sequence') { menuItems.push(trackRenameMenuItem(trackView)); menuItems.push(trackHeightMenuItem(trackView)); } if (this.showColorPicker(trackView.track)) { menuItems.push('
'); menuItems.push(colorPickerMenuItem({ trackView, label: "Set track color", option: "color" })); menuItems.push(unsetColorMenuItem({ trackView, label: "Unset track color" })); menuItems.push(colorPickerMenuItem({ trackView, label: "Set alt color", option: "altColor" })); } if (trackView.track.menuItemList) { menuItems = menuItems.concat(trackView.track.menuItemList()); } if (hasVizWindow || vizWindowTypes.has(trackView.track.type)) { menuItems.push('
'); menuItems.push(visibilityWindowMenuItem(trackView)); } if (trackView.track.removable !== false) { menuItems.push('
'); menuItems.push(trackRemovalMenuItem(trackView)); } return menuItems; }, numericDataMenuItems: function (trackView) { const menuItems = []; // Data range const $e = $('
'); $e.text('Set data range'); const clickHandler = function () { trackView.browser.dataRangeDialog.configure(trackView); trackView.browser.dataRangeDialog.present($(trackView.trackDiv)); }; menuItems.push({ object: $e, click: clickHandler }); if (trackView.track.logScale !== undefined) { menuItems.push({ object: createCheckbox$1("Log scale", trackView.track.logScale), click: () => { trackView.track.logScale = !trackView.track.logScale; trackView.repaintViews(); } }); } menuItems.push({ object: createCheckbox$1("Autoscale", trackView.track.autoscale), click: () => { trackView.track.autoscale = !trackView.track.autoscale; trackView.updateViews(); } }); return menuItems; }, trackMenuItemListHelper: function (itemList, $popover) { var list = []; if (itemList.length > 0) { list = itemList.map(function (item, i) { var $e; // name and object fields checked for backward compatibility if (item.name) { $e = $('
'); $e.text(item.name); } else if (item.object) { $e = item.object; } else if (typeof item.label === 'string') { $e = $('
'); $e.html(item.label); } else if (typeof item === 'string') { if (item.startsWith("<")) { $e = $(item); } else { $e = $("
" + item + "
"); } } if (0 === i) { $e.addClass('igv-track-menu-border-top'); } if (item.click) { $e.on('click', handleClick); $e.on('touchend', function (e) { handleClick(e); }); $e.on('mouseup', function (e) { e.preventDefault(); e.stopPropagation(); }); // eslint-disable-next-line no-inner-declarations function handleClick(e) { item.click(e); $popover.hide(); e.preventDefault(); e.stopPropagation(); } } return { object: $e, init: item.init || undefined }; }); } return list; }, showColorPicker(track) { return undefined === track.type || "bedtype" === track.type || "alignment" === track.type || "annotation" === track.type || "variant" === track.type || "wig" === track.type; } }; function visibilityWindowMenuItem(trackView) { const click = e => { const callback = () => { let value = trackView.browser.inputDialog.input.value; value = '' === value || undefined === value ? -1 : value.trim(); trackView.track.visibilityWindow = Number.parseInt(value); trackView.track.config.visibilityWindow = Number.parseInt(value); trackView.updateViews(); }; const config = { label: 'Visibility Window', value: trackView.track.visibilityWindow, callback }; trackView.browser.inputDialog.present(config, e); }; const object = $('
'); object.text('Set visibility window'); return { object, click }; } function trackRemovalMenuItem(trackView) { var $e, menuClickHandler; $e = $('
'); $e.text('Remove track'); menuClickHandler = function () { trackView.browser.removeTrack(trackView.track); }; return { object: $e, click: menuClickHandler }; } function colorPickerMenuItem({ trackView, label, option }) { const $e = $('
'); $e.text(label); return { object: $e, click: () => trackView.presentColorPicker(option) }; } function unsetColorMenuItem({ trackView, label }) { const $e = $('
'); $e.text(label); return { object: $e, click: () => { trackView.track.color = undefined; trackView.repaintViews(); } }; } function trackRenameMenuItem(trackView) { const click = e => { const callback = function () { let value = trackView.browser.inputDialog.input.value; value = '' === value || undefined === value ? 'untitled' : value.trim(); trackView.browser.setTrackLabelName(trackView, value); }; const config = { label: 'Track Name', value: getTrackLabelText(trackView.track) || 'unnamed', callback }; trackView.browser.inputDialog.present(config, e); }; const object = $('
'); object.text('Set track name'); return { object, click }; } function trackHeightMenuItem(trackView) { const click = e => { const callback = () => { const number = parseFloat(trackView.browser.inputDialog.input.value, 10); if (undefined !== number) { // If explicitly setting the height adust min or max, if neccessary. if (trackView.track.minHeight !== undefined && trackView.track.minHeight > number) { trackView.track.minHeight = number; } if (trackView.track.maxHeight !== undefined && trackView.track.maxHeight < number) { trackView.track.minHeight = number; } trackView.setTrackHeight(number, true); // Explicitly setting track height turns off autoHeight trackView.track.autoHeight = false; } }; const config = { label: 'Track Height', value: trackView.trackDiv.clientHeight, callback }; trackView.browser.inputDialog.present(config, e); }; const object = $('
'); object.text('Set track height'); return { object, click }; } function getTrackLabelText(track) { var vp, txt; vp = track.trackView.viewports[0]; txt = vp.$trackLabel.text(); return txt; } function div(options) { return create("div", options); } function create(tag, options) { const elem = document.createElement(tag); if (options) { if (options.class) { elem.classList.add(options.class); } if (options.id) { elem.id = options.id; } if (options.style) { applyStyle(elem, options.style); } } return elem; } function hide(elem) { const cssStyle = getComputedStyle(elem); if (cssStyle.display !== "none") { elem._initialDisplay = cssStyle.display; } elem.style.display = "none"; } function show(elem) { const currentDisplay = getComputedStyle(elem).display; if (currentDisplay === "none") { const d = elem._initialDisplay || "block"; elem.style.display = d; } } function offset(elem) { // Return zeros for disconnected and hidden (display: none) elements (gh-2310) // Support: IE <=11 only // Running getBoundingClientRect on a // disconnected node in IE throws an error if (!elem.getClientRects().length) { return { top: 0, left: 0 }; } // Get document-relative position by adding viewport scroll to viewport-relative gBCR const rect = elem.getBoundingClientRect(); const win = elem.ownerDocument.defaultView; return { top: rect.top + win.pageYOffset, left: rect.left + win.pageXOffset }; } function pageCoordinates(e) { if (e.type.startsWith("touch")) { const touch = e.touches[0]; return { x: touch.pageX, y: touch.pageY }; } else { return { x: e.pageX, y: e.pageY }; } } function applyStyle(elem, style) { for (let key of Object.keys(style)) { elem.style[key] = style[key]; } } let getMouseXY = (domElement, { clientX, clientY }) => { // DOMRect object with eight properties: left, top, right, bottom, x, y, width, height const { left, top, width, height } = domElement.getBoundingClientRect(); const x = clientX - left; const y = clientY - top; return { x, y, xNormalized: x / width, yNormalized: y / height, width, height }; }; /** * Translate the mouse coordinates for the event to the coordinates for the given target element * @param event * @param domElement * @returns {{x: number, y: number}} */ function translateMouseCoordinates(event, domElement) { const { clientX, clientY } = event; return getMouseXY(domElement, { clientX, clientY }); } function createCheckbox(name, initialState) { const container = div({ class: 'igv-ui-trackgear-popover-check-container' }); const svg = iconMarkup('check', true === initialState ? 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Zlib ã®ä»•æ§˜ã«æº–æ‹ ã—ãŸåœ§ç¸®ã¯ Zlib.Deflate で実装 * されている. これは Inflate との共存を考慮している為. */ const ZLIB_STREAM_RAW_INFLATE_BUFFER_SIZE = 65000; var Zlib = { Huffman: {}, Util: {}, CRC32: {} }; /** * Compression Method * @enum {number} */ Zlib.CompressionMethod = { DEFLATE: 8, RESERVED: 15 }; /** * @param {Object=} opt_params options. * @constructor */ Zlib.Zip = function (opt_params) { opt_params = opt_params || {}; /** @type {Array.<{ * buffer: !(Array.|Uint8Array), * option: Object, * compressed: boolean, * encrypted: boolean, * size: number, * crc32: number * }>} */ this.files = []; /** @type {(Array.|Uint8Array)} */ this.comment = opt_params['comment']; /** @type {(Array.|Uint8Array)} */ this.password; }; /** * @enum {number} */ Zlib.Zip.CompressionMethod = { STORE: 0, DEFLATE: 8 }; /** * @enum {number} */ Zlib.Zip.OperatingSystem = { MSDOS: 0, UNIX: 3, MACINTOSH: 7 }; /** * @enum {number} */ Zlib.Zip.Flags = { ENCRYPT: 0x0001, DESCRIPTOR: 0x0008, UTF8: 0x0800 }; /** * @type {Array.} * @const */ Zlib.Zip.FileHeaderSignature = [0x50, 0x4b, 0x01, 0x02]; /** * @type {Array.} * @const */ Zlib.Zip.LocalFileHeaderSignature = [0x50, 0x4b, 0x03, 0x04]; /** * @type {Array.} * @const */ Zlib.Zip.CentralDirectorySignature = [0x50, 0x4b, 0x05, 0x06]; /** * @param {Array.|Uint8Array} input * @param {Object=} opt_params options. */ Zlib.Zip.prototype.addFile = function (input, opt_params) { opt_params = opt_params || {}; /** @type {string} */ opt_params['filename']; /** @type {boolean} */ var compressed; /** @type {number} */ var size = input.length; /** @type {number} */ var crc32 = 0; if (input instanceof Array) { input = new Uint8Array(input); } // default if (typeof opt_params['compressionMethod'] !== 'number') { opt_params['compressionMethod'] = Zlib.Zip.CompressionMethod.DEFLATE; } // ãã®å ´ã§åœ§ç¸®ã™ã‚‹å ´åˆ if (opt_params['compress']) { switch (opt_params['compressionMethod']) { case Zlib.Zip.CompressionMethod.STORE: break; case Zlib.Zip.CompressionMethod.DEFLATE: crc32 = Zlib.CRC32.calc(input); input = this.deflateWithOption(input, opt_params); compressed = true; break; default: throw new Error('unknown compression method:' + opt_params['compressionMethod']); } } this.files.push({ buffer: input, option: opt_params, compressed: compressed, encrypted: false, size: size, crc32: crc32 }); }; /** * @param {(Array.|Uint8Array)} password */ Zlib.Zip.prototype.setPassword = function (password) { this.password = password; }; Zlib.Zip.prototype.compress = function () { /** @type {Array.<{ * buffer: !(Array.|Uint8Array), * option: Object, * compressed: boolean, * encrypted: boolean, * size: number, * crc32: number * }>} */ var files = this.files; /** @type {{ * buffer: !(Array.|Uint8Array), * option: Object, * compressed: boolean, * encrypted: boolean, * size: number, * crc32: number * }} */ var file; /** @type {!(Array.|Uint8Array)} */ var output; /** @type {number} */ var op1; /** @type {number} */ var op2; /** @type {number} */ var op3; /** @type {number} */ var localFileSize = 0; /** @type {number} */ var centralDirectorySize = 0; /** @type {number} */ var endOfCentralDirectorySize; /** @type {number} */ var offset; /** @type {number} */ var needVersion; /** @type {number} */ var flags; /** @type {Zlib.Zip.CompressionMethod} */ var compressionMethod; /** @type {Date} */ var date; /** @type {number} */ var crc32; /** @type {number} */ var size; /** @type {number} */ var plainSize; /** @type {number} */ var filenameLength; /** @type {number} */ var extraFieldLength; /** @type {number} */ var commentLength; /** @type {(Array.|Uint8Array)} */ var filename; /** @type {(Array.|Uint8Array)} */ var extraField; /** @type {(Array.|Uint8Array)} */ var comment; /** @type {(Array.|Uint8Array)} */ var buffer; /** @type {*} */ var tmp; /** @type {Array.|Uint32Array|Object} */ var key; /** @type {number} */ var i; /** @type {number} */ var il; /** @type {number} */ var j; /** @type {number} */ var jl; // ファイルの圧縮 for (i = 0, il = files.length; i < il; ++i) { file = files[i]; filenameLength = file.option['filename'] ? file.option['filename'].length : 0; extraFieldLength = file.option['extraField'] ? file.option['extraField'].length : 0; commentLength = file.option['comment'] ? file.option['comment'].length : 0; // 圧縮されていなかったら圧縮 if (!file.compressed) { // 圧縮前に CRC32 の計算をしておく file.crc32 = Zlib.CRC32.calc(file.buffer); switch (file.option['compressionMethod']) { case Zlib.Zip.CompressionMethod.STORE: break; case Zlib.Zip.CompressionMethod.DEFLATE: file.buffer = this.deflateWithOption(file.buffer, file.option); file.compressed = true; break; default: throw new Error('unknown compression method:' + file.option['compressionMethod']); } } // encryption if (file.option['password'] !== void 0 || this.password !== void 0) { // init encryption key = this.createEncryptionKey(file.option['password'] || this.password); // add header buffer = file.buffer; { tmp = new Uint8Array(buffer.length + 12); tmp.set(buffer, 12); buffer = tmp; } for (j = 0; j < 12; ++j) { buffer[j] = this.encode(key, i === 11 ? file.crc32 & 0xff : Math.random() * 256 | 0); } // data encryption for (jl = buffer.length; j < jl; ++j) { buffer[j] = this.encode(key, buffer[j]); } file.buffer = buffer; } // 必要バッファサイズの計算 localFileSize += // local file header 30 + filenameLength + // file data file.buffer.length; centralDirectorySize += // file header 46 + filenameLength + commentLength; } // end of central directory endOfCentralDirectorySize = 22 + (this.comment ? this.comment.length : 0); output = new Uint8Array(localFileSize + centralDirectorySize + endOfCentralDirectorySize); op1 = 0; op2 = localFileSize; op3 = op2 + centralDirectorySize; // ファイルの圧縮 for (i = 0, il = files.length; i < il; ++i) { file = files[i]; filenameLength = file.option['filename'] ? file.option['filename'].length : 0; extraFieldLength = 0; // TODO commentLength = file.option['comment'] ? file.option['comment'].length : 0; //------------------------------------------------------------------------- // local file header & file header //------------------------------------------------------------------------- offset = op1; // signature // local file header output[op1++] = Zlib.Zip.LocalFileHeaderSignature[0]; output[op1++] = Zlib.Zip.LocalFileHeaderSignature[1]; output[op1++] = Zlib.Zip.LocalFileHeaderSignature[2]; output[op1++] = Zlib.Zip.LocalFileHeaderSignature[3]; // file header output[op2++] = Zlib.Zip.FileHeaderSignature[0]; output[op2++] = Zlib.Zip.FileHeaderSignature[1]; output[op2++] = Zlib.Zip.FileHeaderSignature[2]; output[op2++] = Zlib.Zip.FileHeaderSignature[3]; // compressor info needVersion = 20; output[op2++] = needVersion & 0xff; output[op2++] = /** @type {Zlib.Zip.OperatingSystem} */ file.option['os'] || Zlib.Zip.OperatingSystem.MSDOS; // need version output[op1++] = output[op2++] = needVersion & 0xff; output[op1++] = output[op2++] = needVersion >> 8 & 0xff; // general purpose bit flag flags = 0; if (file.option['password'] || this.password) { flags |= Zlib.Zip.Flags.ENCRYPT; } output[op1++] = output[op2++] = flags & 0xff; output[op1++] = output[op2++] = flags >> 8 & 0xff; // compression method compressionMethod = file.option['compressionMethod']; output[op1++] = output[op2++] = compressionMethod & 0xff; output[op1++] = output[op2++] = compressionMethod >> 8 & 0xff; // date date = /** @type {(Date|undefined)} */ file.option['date'] || new Date(); output[op1++] = output[op2++] = (date.getMinutes() & 0x7) << 5 | (date.getSeconds() / 2 | 0); output[op1++] = output[op2++] = date.getHours() << 3 | date.getMinutes() >> 3; // output[op1++] = output[op2++] = (date.getMonth() + 1 & 0x7) << 5 | date.getDate(); output[op1++] = output[op2++] = (date.getFullYear() - 1980 & 0x7f) << 1 | date.getMonth() + 1 >> 3; // CRC-32 crc32 = file.crc32; output[op1++] = output[op2++] = crc32 & 0xff; output[op1++] = output[op2++] = crc32 >> 8 & 0xff; output[op1++] = output[op2++] = crc32 >> 16 & 0xff; output[op1++] = output[op2++] = crc32 >> 24 & 0xff; // compressed size size = file.buffer.length; output[op1++] = output[op2++] = size & 0xff; output[op1++] = output[op2++] = size >> 8 & 0xff; output[op1++] = output[op2++] = size >> 16 & 0xff; output[op1++] = output[op2++] = size >> 24 & 0xff; // uncompressed size plainSize = file.size; output[op1++] = output[op2++] = plainSize & 0xff; output[op1++] = output[op2++] = plainSize >> 8 & 0xff; output[op1++] = output[op2++] = plainSize >> 16 & 0xff; output[op1++] = output[op2++] = plainSize >> 24 & 0xff; // filename length output[op1++] = output[op2++] = filenameLength & 0xff; output[op1++] = output[op2++] = filenameLength >> 8 & 0xff; // extra field length output[op1++] = output[op2++] = extraFieldLength & 0xff; output[op1++] = output[op2++] = extraFieldLength >> 8 & 0xff; // file comment length output[op2++] = commentLength & 0xff; output[op2++] = commentLength >> 8 & 0xff; // disk number start output[op2++] = 0; output[op2++] = 0; // internal file attributes output[op2++] = 0; output[op2++] = 0; // external file attributes output[op2++] = 0; output[op2++] = 0; output[op2++] = 0; output[op2++] = 0; // relative offset of local header output[op2++] = offset & 0xff; output[op2++] = offset >> 8 & 0xff; output[op2++] = offset >> 16 & 0xff; output[op2++] = offset >> 24 & 0xff; // filename filename = file.option['filename']; if (filename) { { output.set(filename, op1); output.set(filename, op2); op1 += filenameLength; op2 += filenameLength; } } // extra field extraField = file.option['extraField']; if (extraField) { { output.set(extraField, op1); output.set(extraField, op2); op1 += extraFieldLength; op2 += extraFieldLength; } } // comment comment = file.option['comment']; if (comment) { { output.set(comment, op2); op2 += commentLength; } } //------------------------------------------------------------------------- // file data //------------------------------------------------------------------------- { output.set(file.buffer, op1); op1 += file.buffer.length; } } //------------------------------------------------------------------------- // end of central directory //------------------------------------------------------------------------- // signature output[op3++] = Zlib.Zip.CentralDirectorySignature[0]; output[op3++] = Zlib.Zip.CentralDirectorySignature[1]; output[op3++] = Zlib.Zip.CentralDirectorySignature[2]; output[op3++] = Zlib.Zip.CentralDirectorySignature[3]; // number of this disk output[op3++] = 0; output[op3++] = 0; // number of the disk with the start of the central directory output[op3++] = 0; output[op3++] = 0; // total number of entries in the central directory on this disk output[op3++] = il & 0xff; output[op3++] = il >> 8 & 0xff; // total number of entries in the central directory output[op3++] = il & 0xff; output[op3++] = il >> 8 & 0xff; // size of the central directory output[op3++] = centralDirectorySize & 0xff; output[op3++] = centralDirectorySize >> 8 & 0xff; output[op3++] = centralDirectorySize >> 16 & 0xff; output[op3++] = centralDirectorySize >> 24 & 0xff; // offset of start of central directory with respect to the starting disk number output[op3++] = localFileSize & 0xff; output[op3++] = localFileSize >> 8 & 0xff; output[op3++] = localFileSize >> 16 & 0xff; output[op3++] = localFileSize >> 24 & 0xff; // .ZIP file comment length commentLength = this.comment ? this.comment.length : 0; output[op3++] = commentLength & 0xff; output[op3++] = commentLength >> 8 & 0xff; // .ZIP file comment if (this.comment) { { output.set(this.comment, op3); op3 += commentLength; } } return output; }; /** * @param {!(Array.|Uint8Array)} input * @param {Object=} opt_params options. * @return {!(Array.|Uint8Array)} */ Zlib.Zip.prototype.deflateWithOption = function (input, opt_params) { /** @type {Zlib.RawDeflate} */ var deflator = new Zlib.RawDeflate(input, opt_params['deflateOption']); return deflator.compress(); }; /** * @param {(Array.|Uint32Array)} key * @return {number} */ Zlib.Zip.prototype.getByte = function (key) { /** @type {number} */ var tmp = key[2] & 0xffff | 2; return tmp * (tmp ^ 1) >> 8 & 0xff; }; /** * @param {(Array.|Uint32Array|Object)} key * @param {number} n * @return {number} */ Zlib.Zip.prototype.encode = function (key, n) { /** @type {number} */ var tmp = this.getByte(key); this.updateKeys(key, n); return tmp ^ n; }; /** * @param {(Array.|Uint32Array)} key * @param {number} n */ Zlib.Zip.prototype.updateKeys = function (key, n) { key[0] = Zlib.CRC32.single(key[0], n); key[1] = (((key[1] + (key[0] & 0xff)) * 20173 >>> 0) * 6681 >>> 0) + 1 >>> 0; key[2] = Zlib.CRC32.single(key[2], key[1] >>> 24); }; /** * @param {(Array.|Uint8Array)} password * @return {!(Array.|Uint32Array|Object)} */ Zlib.Zip.prototype.createEncryptionKey = function (password) { /** @type {!(Array.|Uint32Array)} */ var key = [305419896, 591751049, 878082192]; /** @type {number} */ var i; /** @type {number} */ var il; { key = new Uint32Array(key); } for (i = 0, il = password.length; i < il; ++i) { this.updateKeys(key, password[i] & 0xff); } return key; }; /** * build huffman table from length list. * @param {!(Array.|Uint8Array)} lengths length list. * @return {!Array} huffman table. */ Zlib.Huffman.buildHuffmanTable = function (lengths) { /** @type {number} length list size. */ var listSize = lengths.length; /** @type {number} max code length for table size. */ var maxCodeLength = 0; /** @type {number} min code length for table size. */ var minCodeLength = Number.POSITIVE_INFINITY; /** @type {number} table size. */ var size; /** @type {!(Array|Uint8Array)} huffman code table. */ var table; /** @type {number} bit length. */ var bitLength; /** @type {number} huffman code. */ var code; /** * サイズが 2^maxlength 個のテーブルを埋めるためのスキップ長. * @type {number} skip length for table filling. */ var skip; /** @type {number} reversed code. */ var reversed; /** @type {number} reverse temp. */ var rtemp; /** @type {number} loop counter. */ var i; /** @type {number} loop limit. */ var il; /** @type {number} loop counter. */ var j; /** @type {number} table value. */ var value; // Math.max は遅いので最長の値は for-loop で取得する for (i = 0, il = listSize; i < il; ++i) { if (lengths[i] > maxCodeLength) { maxCodeLength = lengths[i]; } if (lengths[i] < minCodeLength) { minCodeLength = lengths[i]; } } size = 1 << maxCodeLength; table = new Uint32Array(size); // ãƒ“ãƒƒãƒˆé•·ã®çŸ­ã„é †ã‹ã‚‰ãƒãƒ•ãƒžãƒ³ç¬¦å·ã‚’å‰²ã‚Šå½“ã¦ã‚‹ for (bitLength = 1, code = 0, skip = 2; bitLength <= maxCodeLength;) { for (i = 0; i < listSize; ++i) { if (lengths[i] === bitLength) { // ビットオーダーが逆になるためビット長分並びを反転する for (reversed = 0, rtemp = code, j = 0; j < bitLength; ++j) { reversed = reversed << 1 | rtemp & 1; rtemp >>= 1; } // 最大ビット長をもとにテーブルを作るため、 // 最大ビット長以外では 0 / 1 どちらでも良い箇所ができる // ãã®ã©ã¡ã‚‰ã§ã‚‚è‰¯ã„å ´æ‰€ã¯åŒã˜å€¤ã§åŸ‹ã‚ã‚‹ã“ã¨ã§ // 本来のビット長以上のビット数取得しても問題が起こらないようにする value = bitLength << 16 | i; for (j = reversed; j < size; j += skip) { table[j] = value; } ++code; } } // 次のビット長へ ++bitLength; code <<= 1; skip <<= 1; } return [table, maxCodeLength, minCodeLength]; }; //----------------------------------------------------------------------------- /** @define {number} buffer block size. */ var ZLIB_RAW_INFLATE_BUFFER_SIZE = 0x8000; // [ 0x8000 >= ZLIB_BUFFER_BLOCK_SIZE ] //----------------------------------------------------------------------------- var buildHuffmanTable = Zlib.Huffman.buildHuffmanTable; /** * @constructor * @param {!(Uint8Array|Array.)} input input buffer. * @param {Object} opt_params option parameter. * * opt_params は以下のプロパティを指定する事ができます。 * - index: input buffer の deflate コンテナの開始位置. * - blockSize: バッファのブロックサイズ. * - bufferType: Zlib.RawInflate.BufferType の値によってバッファの管理方法を指定する. * - resize: ç¢ºä¿ã—ãŸãƒãƒƒãƒ•ã‚¡ãŒå®Ÿéš›ã®å¤§ãã•ã‚ˆã‚Šå¤§ãã‹ã£ãŸå ´åˆã«åˆ‡ã‚Šè©°ã‚ã‚‹. */ Zlib.RawInflate = function (input, opt_params) { /** @type {!(Array.|Uint8Array)} inflated buffer */ this.buffer; /** @type {!Array.<(Array.|Uint8Array)>} */ this.blocks = []; /** @type {number} block size. */ this.bufferSize = ZLIB_RAW_INFLATE_BUFFER_SIZE; /** @type {!number} total output buffer pointer. */ this.totalpos = 0; /** @type {!number} input buffer pointer. */ this.ip = 0; /** @type {!number} bit stream reader buffer. */ this.bitsbuf = 0; /** @type {!number} bit stream reader buffer size. */ this.bitsbuflen = 0; /** @type {!(Array.|Uint8Array)} input buffer. */ this.input = new Uint8Array(input); /** @type {!(Uint8Array|Array.)} output buffer. */ this.output; /** @type {!number} output buffer pointer. */ this.op; /** @type {boolean} is final block flag. */ this.bfinal = false; /** @type {Zlib.RawInflate.BufferType} buffer management. */ this.bufferType = Zlib.RawInflate.BufferType.ADAPTIVE; /** @type {boolean} resize flag for memory size optimization. */ this.resize = false; // option parameters if (opt_params || !(opt_params = {})) { if (opt_params['index']) { this.ip = opt_params['index']; } if (opt_params['bufferSize']) { this.bufferSize = opt_params['bufferSize']; } if (opt_params['bufferType']) { this.bufferType = opt_params['bufferType']; } if (opt_params['resize']) { this.resize = opt_params['resize']; } } // initialize switch (this.bufferType) { case Zlib.RawInflate.BufferType.BLOCK: this.op = Zlib.RawInflate.MaxBackwardLength; this.output = new Uint8Array(Zlib.RawInflate.MaxBackwardLength + this.bufferSize + Zlib.RawInflate.MaxCopyLength); break; case Zlib.RawInflate.BufferType.ADAPTIVE: this.op = 0; this.output = new Uint8Array(this.bufferSize); break; default: throw new Error('invalid inflate mode'); } }; /** * @enum {number} */ Zlib.RawInflate.BufferType = { BLOCK: 0, ADAPTIVE: 1 }; /** * decompress. * @return {!(Uint8Array|Array.)} inflated buffer. */ Zlib.RawInflate.prototype.decompress = function () { while (!this.bfinal) { this.parseBlock(); } switch (this.bufferType) { case Zlib.RawInflate.BufferType.BLOCK: return this.concatBufferBlock(); case Zlib.RawInflate.BufferType.ADAPTIVE: return this.concatBufferDynamic(); default: throw new Error('invalid inflate mode'); } }; /** * @const * @type {number} max backward length for LZ77. */ Zlib.RawInflate.MaxBackwardLength = 32768; /** * @const * @type {number} max copy length for LZ77. */ Zlib.RawInflate.MaxCopyLength = 258; /** * huffman order * @const * @type {!(Array.|Uint8Array)} */ Zlib.RawInflate.Order = function (table) { return new Uint16Array(table); }([16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15]); /** * huffman length code table. * @const * @type {!(Array.|Uint16Array)} */ Zlib.RawInflate.LengthCodeTable = function (table) { return new Uint16Array(table); }([0x0003, 0x0004, 0x0005, 0x0006, 0x0007, 0x0008, 0x0009, 0x000a, 0x000b, 0x000d, 0x000f, 0x0011, 0x0013, 0x0017, 0x001b, 0x001f, 0x0023, 0x002b, 0x0033, 0x003b, 0x0043, 0x0053, 0x0063, 0x0073, 0x0083, 0x00a3, 0x00c3, 0x00e3, 0x0102, 0x0102, 0x0102]); /** * huffman length extra-bits table. * @const * @type {!(Array.|Uint8Array)} */ Zlib.RawInflate.LengthExtraTable = function (table) { return new Uint8Array(table); }([0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 0, 0, 0]); /** * huffman dist code table. * @const * @type {!(Array.|Uint16Array)} */ Zlib.RawInflate.DistCodeTable = function (table) { return new Uint16Array(table); }([0x0001, 0x0002, 0x0003, 0x0004, 0x0005, 0x0007, 0x0009, 0x000d, 0x0011, 0x0019, 0x0021, 0x0031, 0x0041, 0x0061, 0x0081, 0x00c1, 0x0101, 0x0181, 0x0201, 0x0301, 0x0401, 0x0601, 0x0801, 0x0c01, 0x1001, 0x1801, 0x2001, 0x3001, 0x4001, 0x6001]); /** * huffman dist extra-bits table. * @const * @type {!(Array.|Uint8Array)} */ Zlib.RawInflate.DistExtraTable = function (table) { return new Uint8Array(table); }([0, 0, 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 13, 13]); /** * fixed huffman length code table * @const * @type {!Array} */ Zlib.RawInflate.FixedLiteralLengthTable = function (table) { return table; }(function () { var lengths = new Uint8Array(288); var i, il; for (i = 0, il = lengths.length; i < il; ++i) { lengths[i] = i <= 143 ? 8 : i <= 255 ? 9 : i <= 279 ? 7 : 8; } return buildHuffmanTable(lengths); }()); /** * fixed huffman distance code table * @const * @type {!Array} */ Zlib.RawInflate.FixedDistanceTable = function (table) { return table; }(function () { var lengths = new Uint8Array(30); var i, il; for (i = 0, il = lengths.length; i < il; ++i) { lengths[i] = 5; } return buildHuffmanTable(lengths); }()); /** * parse deflated block. */ Zlib.RawInflate.prototype.parseBlock = function () { /** @type {number} header */ var hdr = this.readBits(3); // BFINAL if (hdr & 0x1) { this.bfinal = true; } // BTYPE hdr >>>= 1; switch (hdr) { // uncompressed case 0: this.parseUncompressedBlock(); break; // fixed huffman case 1: this.parseFixedHuffmanBlock(); break; // dynamic huffman case 2: this.parseDynamicHuffmanBlock(); break; // reserved or other default: throw new Error('unknown BTYPE: ' + hdr); } }; /** * read inflate bits * @param {number} length bits length. * @return {number} read bits. */ Zlib.RawInflate.prototype.readBits = function (length) { var bitsbuf = this.bitsbuf; var bitsbuflen = this.bitsbuflen; var input = this.input; var ip = this.ip; /** @type {number} */ var inputLength = input.length; /** @type {number} input and output byte. */ var octet; // input byte if (ip + (length - bitsbuflen + 7 >> 3) >= inputLength) { throw new Error('input buffer is broken'); } // not enough buffer while (bitsbuflen < length) { bitsbuf |= input[ip++] << bitsbuflen; bitsbuflen += 8; } // output byte octet = bitsbuf & (1 << length) - 1; bitsbuf >>>= length; bitsbuflen -= length; this.bitsbuf = bitsbuf; this.bitsbuflen = bitsbuflen; this.ip = ip; return octet; }; /** * read huffman code using table * @param {!(Array.|Uint8Array|Uint16Array)} table huffman code table. * @return {number} huffman code. */ Zlib.RawInflate.prototype.readCodeByTable = function (table) { var bitsbuf = this.bitsbuf; var bitsbuflen = this.bitsbuflen; var input = this.input; var ip = this.ip; /** @type {number} */ var inputLength = input.length; /** @type {!(Array.|Uint8Array)} huffman code table */ var codeTable = table[0]; /** @type {number} */ var maxCodeLength = table[1]; /** @type {number} code length & code (16bit, 16bit) */ var codeWithLength; /** @type {number} code bits length */ var codeLength; // not enough buffer while (bitsbuflen < maxCodeLength) { if (ip >= inputLength) { break; } bitsbuf |= input[ip++] << bitsbuflen; bitsbuflen += 8; } // read max length codeWithLength = codeTable[bitsbuf & (1 << maxCodeLength) - 1]; codeLength = codeWithLength >>> 16; if (codeLength > bitsbuflen) { throw new Error('invalid code length: ' + codeLength); } this.bitsbuf = bitsbuf >> codeLength; this.bitsbuflen = bitsbuflen - codeLength; this.ip = ip; return codeWithLength & 0xffff; }; /** * parse uncompressed block. */ Zlib.RawInflate.prototype.parseUncompressedBlock = function () { var input = this.input; var ip = this.ip; var output = this.output; var op = this.op; /** @type {number} */ var inputLength = input.length; /** @type {number} block length */ var len; /** @type {number} number for check block length */ var nlen; /** @type {number} output buffer length */ var olength = output.length; /** @type {number} copy counter */ var preCopy; // skip buffered header bits this.bitsbuf = 0; this.bitsbuflen = 0; // len if (ip + 1 >= inputLength) { throw new Error('invalid uncompressed block header: LEN'); } len = input[ip++] | input[ip++] << 8; // nlen if (ip + 1 >= inputLength) { throw new Error('invalid uncompressed block header: NLEN'); } nlen = input[ip++] | input[ip++] << 8; // check len & nlen if (len === ~nlen) { throw new Error('invalid uncompressed block header: length verify'); } // check size if (ip + len > input.length) { throw new Error('input buffer is broken'); } // expand buffer switch (this.bufferType) { case Zlib.RawInflate.BufferType.BLOCK: // pre copy while (op + len > output.length) { preCopy = olength - op; len -= preCopy; { output.set(input.subarray(ip, ip + preCopy), op); op += preCopy; ip += preCopy; } this.op = op; output = this.expandBufferBlock(); op = this.op; } break; case Zlib.RawInflate.BufferType.ADAPTIVE: while (op + len > output.length) { output = this.expandBufferAdaptive({ fixRatio: 2 }); } break; default: throw new Error('invalid inflate mode'); } // copy { output.set(input.subarray(ip, ip + len), op); op += len; ip += len; } this.ip = ip; this.op = op; this.output = output; }; /** * parse fixed huffman block. */ Zlib.RawInflate.prototype.parseFixedHuffmanBlock = function () { switch (this.bufferType) { case Zlib.RawInflate.BufferType.ADAPTIVE: this.decodeHuffmanAdaptive(Zlib.RawInflate.FixedLiteralLengthTable, Zlib.RawInflate.FixedDistanceTable); break; case Zlib.RawInflate.BufferType.BLOCK: this.decodeHuffmanBlock(Zlib.RawInflate.FixedLiteralLengthTable, Zlib.RawInflate.FixedDistanceTable); break; default: throw new Error('invalid inflate mode'); } }; /** * parse dynamic huffman block. */ Zlib.RawInflate.prototype.parseDynamicHuffmanBlock = function () { /** @type {number} number of literal and length codes. */ var hlit = this.readBits(5) + 257; /** @type {number} number of distance codes. */ var hdist = this.readBits(5) + 1; /** @type {number} number of code lengths. */ var hclen = this.readBits(4) + 4; /** @type {!(Uint8Array|Array.)} code lengths. */ var codeLengths = new Uint8Array(Zlib.RawInflate.Order.length); /** @type {!Array} code lengths table. */ var codeLengthsTable; /** @type {!(Uint8Array|Array.)} literal and length code table. */ var litlenTable; /** @type {!(Uint8Array|Array.)} distance code table. */ var distTable; /** @type {!(Uint8Array|Array.)} code length table. */ var lengthTable; /** @type {number} */ var code; /** @type {number} */ var prev; /** @type {number} */ var repeat; /** @type {number} loop counter. */ var i; /** @type {number} loop limit. */ var il; // decode code lengths for (i = 0; i < hclen; ++i) { codeLengths[Zlib.RawInflate.Order[i]] = this.readBits(3); } // decode length table codeLengthsTable = buildHuffmanTable(codeLengths); lengthTable = new Uint8Array(hlit + hdist); for (i = 0, il = hlit + hdist; i < il;) { code = this.readCodeByTable(codeLengthsTable); switch (code) { case 16: repeat = 3 + this.readBits(2); while (repeat--) { lengthTable[i++] = prev; } break; case 17: repeat = 3 + this.readBits(3); while (repeat--) { lengthTable[i++] = 0; } prev = 0; break; case 18: repeat = 11 + this.readBits(7); while (repeat--) { lengthTable[i++] = 0; } prev = 0; break; default: lengthTable[i++] = code; prev = code; break; } } litlenTable = buildHuffmanTable(lengthTable.subarray(0, hlit)); distTable = buildHuffmanTable(lengthTable.subarray(hlit)); switch (this.bufferType) { case Zlib.RawInflate.BufferType.ADAPTIVE: this.decodeHuffmanAdaptive(litlenTable, distTable); break; case Zlib.RawInflate.BufferType.BLOCK: this.decodeHuffmanBlock(litlenTable, distTable); break; default: throw new Error('invalid inflate mode'); } }; /** * decode huffman code * @param {!(Array.|Uint16Array)} litlen literal and length code table. * @param {!(Array.|Uint8Array)} dist distination code table. */ Zlib.RawInflate.prototype.decodeHuffmanBlock = function (litlen, dist) { var output = this.output; var op = this.op; this.currentLitlenTable = litlen; /** @type {number} output position limit. */ var olength = output.length - Zlib.RawInflate.MaxCopyLength; /** @type {number} huffman code. */ var code; /** @type {number} table index. */ var ti; /** @type {number} huffman code distination. */ var codeDist; /** @type {number} huffman code length. */ var codeLength; var lengthCodeTable = Zlib.RawInflate.LengthCodeTable; var lengthExtraTable = Zlib.RawInflate.LengthExtraTable; var distCodeTable = Zlib.RawInflate.DistCodeTable; var distExtraTable = Zlib.RawInflate.DistExtraTable; while ((code = this.readCodeByTable(litlen)) !== 256) { // literal if (code < 256) { if (op >= olength) { this.op = op; output = this.expandBufferBlock(); op = this.op; } output[op++] = code; continue; } // length code ti = code - 257; codeLength = lengthCodeTable[ti]; if (lengthExtraTable[ti] > 0) { codeLength += this.readBits(lengthExtraTable[ti]); } // dist code code = this.readCodeByTable(dist); codeDist = distCodeTable[code]; if (distExtraTable[code] > 0) { codeDist += this.readBits(distExtraTable[code]); } // lz77 decode if (op >= olength) { this.op = op; output = this.expandBufferBlock(); op = this.op; } while (codeLength--) { output[op] = output[op++ - codeDist]; } } while (this.bitsbuflen >= 8) { this.bitsbuflen -= 8; this.ip--; } this.op = op; }; /** * decode huffman code (adaptive) * @param {!(Array.|Uint16Array)} litlen literal and length code table. * @param {!(Array.|Uint8Array)} dist distination code table. */ Zlib.RawInflate.prototype.decodeHuffmanAdaptive = function (litlen, dist) { var output = this.output; var op = this.op; this.currentLitlenTable = litlen; /** @type {number} output position limit. */ var olength = output.length; /** @type {number} huffman code. */ var code; /** @type {number} table index. */ var ti; /** @type {number} huffman code distination. */ var codeDist; /** @type {number} huffman code length. */ var codeLength; var lengthCodeTable = Zlib.RawInflate.LengthCodeTable; var lengthExtraTable = Zlib.RawInflate.LengthExtraTable; var distCodeTable = Zlib.RawInflate.DistCodeTable; var distExtraTable = Zlib.RawInflate.DistExtraTable; while ((code = this.readCodeByTable(litlen)) !== 256) { // literal if (code < 256) { if (op >= olength) { output = this.expandBufferAdaptive(); olength = output.length; } output[op++] = code; continue; } // length code ti = code - 257; codeLength = lengthCodeTable[ti]; if (lengthExtraTable[ti] > 0) { codeLength += this.readBits(lengthExtraTable[ti]); } // dist code code = this.readCodeByTable(dist); codeDist = distCodeTable[code]; if (distExtraTable[code] > 0) { codeDist += this.readBits(distExtraTable[code]); } // lz77 decode if (op + codeLength > olength) { output = this.expandBufferAdaptive(); olength = output.length; } while (codeLength--) { output[op] = output[op++ - codeDist]; } } while (this.bitsbuflen >= 8) { this.bitsbuflen -= 8; this.ip--; } this.op = op; }; /** * expand output buffer. * @param {Object=} opt_param option parameters. * @return {!(Array.|Uint8Array)} output buffer. */ Zlib.RawInflate.prototype.expandBufferBlock = function (opt_param) { /** @type {!(Array.|Uint8Array)} store buffer. */ var buffer = new Uint8Array(this.op - Zlib.RawInflate.MaxBackwardLength); /** @type {number} backward base point */ var backward = this.op - Zlib.RawInflate.MaxBackwardLength; var output = this.output; // copy to output buffer { buffer.set(output.subarray(Zlib.RawInflate.MaxBackwardLength, buffer.length)); } this.blocks.push(buffer); this.totalpos += buffer.length; // copy to backward buffer { output.set(output.subarray(backward, backward + Zlib.RawInflate.MaxBackwardLength)); } this.op = Zlib.RawInflate.MaxBackwardLength; return output; }; /** * expand output buffer. (adaptive) * @param {Object=} opt_param option parameters. * @return {!(Array.|Uint8Array)} output buffer pointer. */ Zlib.RawInflate.prototype.expandBufferAdaptive = function (opt_param) { /** @type {!(Array.|Uint8Array)} store buffer. */ var buffer; /** @type {number} expantion ratio. */ var ratio = this.input.length / this.ip + 1 | 0; /** @type {number} maximum number of huffman code. */ var maxHuffCode; /** @type {number} new output buffer size. */ var newSize; /** @type {number} max inflate size. */ var maxInflateSize; var input = this.input; var output = this.output; if (opt_param) { if (typeof opt_param.fixRatio === 'number') { ratio = opt_param.fixRatio; } if (typeof opt_param.addRatio === 'number') { ratio += opt_param.addRatio; } } // calculate new buffer size if (ratio < 2) { maxHuffCode = (input.length - this.ip) / this.currentLitlenTable[2]; maxInflateSize = maxHuffCode / 2 * 258 | 0; newSize = maxInflateSize < output.length ? output.length + maxInflateSize : output.length << 1; } else { newSize = output.length * ratio; } // buffer expantion { buffer = new Uint8Array(newSize); buffer.set(output); } this.output = buffer; return this.output; }; /** * concat output buffer. * @return {!(Array.|Uint8Array)} output buffer. */ Zlib.RawInflate.prototype.concatBufferBlock = function () { /** @type {number} buffer pointer. */ var pos = 0; /** @type {number} buffer pointer. */ var limit = this.totalpos + (this.op - Zlib.RawInflate.MaxBackwardLength); /** @type {!(Array.|Uint8Array)} output block array. */ var output = this.output; /** @type {!Array} blocks array. */ var blocks = this.blocks; /** @type {!(Array.|Uint8Array)} output block array. */ var block; /** @type {!(Array.|Uint8Array)} output buffer. */ var buffer = new Uint8Array(limit); /** @type {number} loop counter. */ var i; /** @type {number} loop limiter. */ var il; /** @type {number} loop counter. */ var j; /** @type {number} loop limiter. */ var jl; // single buffer if (blocks.length === 0) { return this.output.subarray(Zlib.RawInflate.MaxBackwardLength, this.op); } // copy to buffer for (i = 0, il = blocks.length; i < il; ++i) { block = blocks[i]; for (j = 0, jl = block.length; j < jl; ++j) { buffer[pos++] = block[j]; } } // current buffer for (i = Zlib.RawInflate.MaxBackwardLength, il = this.op; i < il; ++i) { buffer[pos++] = output[i]; } this.blocks = []; this.buffer = buffer; return this.buffer; }; /** * concat output buffer. (dynamic) * @return {!(Array.|Uint8Array)} output buffer. */ Zlib.RawInflate.prototype.concatBufferDynamic = function () { /** @type {Array.|Uint8Array} output buffer. */ var buffer; var op = this.op; { if (this.resize) { buffer = new Uint8Array(op); buffer.set(this.output.subarray(0, op)); } else { buffer = this.output.subarray(0, op); } } this.buffer = buffer; return this.buffer; }; var buildHuffmanTable = Zlib.Huffman.buildHuffmanTable; /** * @param {!(Uint8Array|Array.)} input input buffer. * @param {number} ip input buffer pointer. * @param {number=} opt_buffersize buffer block size. * @constructor */ Zlib.RawInflateStream = function (input, ip, opt_buffersize) { /** @type {!Array.<(Array|Uint8Array)>} */ this.blocks = []; /** @type {number} block size. */ this.bufferSize = opt_buffersize ? opt_buffersize : ZLIB_STREAM_RAW_INFLATE_BUFFER_SIZE; /** @type {!number} total output buffer pointer. */ this.totalpos = 0; /** @type {!number} input buffer pointer. */ this.ip = ip === void 0 ? 0 : ip; /** @type {!number} bit stream reader buffer. */ this.bitsbuf = 0; /** @type {!number} bit stream reader buffer size. */ this.bitsbuflen = 0; /** @type {!(Array|Uint8Array)} input buffer. */ this.input = new Uint8Array(input); /** @type {!(Uint8Array|Array)} output buffer. */ this.output = new Uint8Array(this.bufferSize); /** @type {!number} output buffer pointer. */ this.op = 0; /** @type {boolean} is final block flag. */ this.bfinal = false; /** @type {number} uncompressed block length. */ this.blockLength; /** @type {boolean} resize flag for memory size optimization. */ this.resize = false; /** @type {Array} */ this.litlenTable; /** @type {Array} */ this.distTable; /** @type {number} */ this.sp = 0; // stream pointer /** @type {Zlib.RawInflateStream.Status} */ this.status = Zlib.RawInflateStream.Status.INITIALIZED; // // backup // /** @type {!number} */ this.ip_; /** @type {!number} */ this.bitsbuflen_; /** @type {!number} */ this.bitsbuf_; }; /** * @enum {number} */ Zlib.RawInflateStream.BlockType = { UNCOMPRESSED: 0, FIXED: 1, DYNAMIC: 2 }; /** * @enum {number} */ Zlib.RawInflateStream.Status = { INITIALIZED: 0, BLOCK_HEADER_START: 1, BLOCK_HEADER_END: 2, BLOCK_BODY_START: 3, BLOCK_BODY_END: 4, DECODE_BLOCK_START: 5, DECODE_BLOCK_END: 6 }; /** * decompress. * @return {!(Uint8Array|Array)} inflated buffer. */ Zlib.RawInflateStream.prototype.decompress = function (newInput, ip) { /** @type {boolean} */ var stop = false; if (newInput !== void 0) { this.input = newInput; } if (ip !== void 0) { this.ip = ip; } // decompress while (!stop) { switch (this.status) { // block header case Zlib.RawInflateStream.Status.INITIALIZED: case Zlib.RawInflateStream.Status.BLOCK_HEADER_START: if (this.readBlockHeader() < 0) { stop = true; } break; // block body case Zlib.RawInflateStream.Status.BLOCK_HEADER_END: /* FALLTHROUGH */ case Zlib.RawInflateStream.Status.BLOCK_BODY_START: switch (this.currentBlockType) { case Zlib.RawInflateStream.BlockType.UNCOMPRESSED: if (this.readUncompressedBlockHeader() < 0) { stop = true; } break; case Zlib.RawInflateStream.BlockType.FIXED: if (this.parseFixedHuffmanBlock() < 0) { stop = true; } break; case Zlib.RawInflateStream.BlockType.DYNAMIC: if (this.parseDynamicHuffmanBlock() < 0) { stop = true; } break; } break; // decode data case Zlib.RawInflateStream.Status.BLOCK_BODY_END: case Zlib.RawInflateStream.Status.DECODE_BLOCK_START: switch (this.currentBlockType) { case Zlib.RawInflateStream.BlockType.UNCOMPRESSED: if (this.parseUncompressedBlock() < 0) { stop = true; } break; case Zlib.RawInflateStream.BlockType.FIXED: /* FALLTHROUGH */ case Zlib.RawInflateStream.BlockType.DYNAMIC: if (this.decodeHuffman() < 0) { stop = true; } break; } break; case Zlib.RawInflateStream.Status.DECODE_BLOCK_END: if (this.bfinal) { stop = true; } else { this.status = Zlib.RawInflateStream.Status.INITIALIZED; } break; } } return this.concatBuffer(); }; /** * @const * @type {number} max backward length for LZ77. */ Zlib.RawInflateStream.MaxBackwardLength = 32768; /** * @const * @type {number} max copy length for LZ77. */ Zlib.RawInflateStream.MaxCopyLength = 258; /** * huffman order * @const * @type {!(Array.|Uint8Array)} */ Zlib.RawInflateStream.Order = function (table) { return new Uint16Array(table); }([16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15]); /** * huffman length code table. * @const * @type {!(Array.|Uint16Array)} */ Zlib.RawInflateStream.LengthCodeTable = function (table) { return new Uint16Array(table); }([0x0003, 0x0004, 0x0005, 0x0006, 0x0007, 0x0008, 0x0009, 0x000a, 0x000b, 0x000d, 0x000f, 0x0011, 0x0013, 0x0017, 0x001b, 0x001f, 0x0023, 0x002b, 0x0033, 0x003b, 0x0043, 0x0053, 0x0063, 0x0073, 0x0083, 0x00a3, 0x00c3, 0x00e3, 0x0102, 0x0102, 0x0102]); /** * huffman length extra-bits table. * @const * @type {!(Array.|Uint8Array)} */ Zlib.RawInflateStream.LengthExtraTable = function (table) { return new Uint8Array(table); }([0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 0, 0, 0]); /** * huffman dist code table. * @const * @type {!(Array.|Uint16Array)} */ Zlib.RawInflateStream.DistCodeTable = function (table) { return new Uint16Array(table); }([0x0001, 0x0002, 0x0003, 0x0004, 0x0005, 0x0007, 0x0009, 0x000d, 0x0011, 0x0019, 0x0021, 0x0031, 0x0041, 0x0061, 0x0081, 0x00c1, 0x0101, 0x0181, 0x0201, 0x0301, 0x0401, 0x0601, 0x0801, 0x0c01, 0x1001, 0x1801, 0x2001, 0x3001, 0x4001, 0x6001]); /** * huffman dist extra-bits table. * @const * @type {!(Array.|Uint8Array)} */ Zlib.RawInflateStream.DistExtraTable = function (table) { return new Uint8Array(table); }([0, 0, 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 13, 13]); /** * fixed huffman length code table * @const * @type {!Array} */ Zlib.RawInflateStream.FixedLiteralLengthTable = function (table) { return table; }(function () { var lengths = new Uint8Array(288); var i, il; for (i = 0, il = lengths.length; i < il; ++i) { lengths[i] = i <= 143 ? 8 : i <= 255 ? 9 : i <= 279 ? 7 : 8; } return buildHuffmanTable(lengths); }()); /** * fixed huffman distance code table * @const * @type {!Array} */ Zlib.RawInflateStream.FixedDistanceTable = function (table) { return table; }(function () { var lengths = new Uint8Array(30); var i, il; for (i = 0, il = lengths.length; i < il; ++i) { lengths[i] = 5; } return buildHuffmanTable(lengths); }()); /** * parse deflated block. */ Zlib.RawInflateStream.prototype.readBlockHeader = function () { /** @type {number} header */ var hdr; this.status = Zlib.RawInflateStream.Status.BLOCK_HEADER_START; this.save_(); if ((hdr = this.readBits(3)) < 0) { this.restore_(); return -1; } // BFINAL if (hdr & 0x1) { this.bfinal = true; } // BTYPE hdr >>>= 1; switch (hdr) { case 0: // uncompressed this.currentBlockType = Zlib.RawInflateStream.BlockType.UNCOMPRESSED; break; case 1: // fixed huffman this.currentBlockType = Zlib.RawInflateStream.BlockType.FIXED; break; case 2: // dynamic huffman this.currentBlockType = Zlib.RawInflateStream.BlockType.DYNAMIC; break; default: // reserved or other throw new Error('unknown BTYPE: ' + hdr); } this.status = Zlib.RawInflateStream.Status.BLOCK_HEADER_END; }; /** * read inflate bits * @param {number} length bits length. * @return {number} read bits. */ Zlib.RawInflateStream.prototype.readBits = function (length) { var bitsbuf = this.bitsbuf; var bitsbuflen = this.bitsbuflen; var input = this.input; var ip = this.ip; /** @type {number} input and output byte. */ var octet; // not enough buffer while (bitsbuflen < length) { // input byte if (input.length <= ip) { return -1; } octet = input[ip++]; // concat octet bitsbuf |= octet << bitsbuflen; bitsbuflen += 8; } // output byte octet = bitsbuf & (1 << length) - 1; bitsbuf >>>= length; bitsbuflen -= length; this.bitsbuf = bitsbuf; this.bitsbuflen = bitsbuflen; this.ip = ip; return octet; }; /** * read huffman code using table * @param {Array} table huffman code table. * @return {number} huffman code. */ Zlib.RawInflateStream.prototype.readCodeByTable = function (table) { var bitsbuf = this.bitsbuf; var bitsbuflen = this.bitsbuflen; var input = this.input; var ip = this.ip; /** @type {!(Array|Uint8Array)} huffman code table */ var codeTable = table[0]; /** @type {number} */ var maxCodeLength = table[1]; /** @type {number} input byte */ var octet; /** @type {number} code length & code (16bit, 16bit) */ var codeWithLength; /** @type {number} code bits length */ var codeLength; // not enough buffer while (bitsbuflen < maxCodeLength) { if (input.length <= ip) { return -1; } octet = input[ip++]; bitsbuf |= octet << bitsbuflen; bitsbuflen += 8; } // read max length codeWithLength = codeTable[bitsbuf & (1 << maxCodeLength) - 1]; codeLength = codeWithLength >>> 16; if (codeLength > bitsbuflen) { throw new Error('invalid code length: ' + codeLength); } this.bitsbuf = bitsbuf >> codeLength; this.bitsbuflen = bitsbuflen - codeLength; this.ip = ip; return codeWithLength & 0xffff; }; /** * read uncompressed block header */ Zlib.RawInflateStream.prototype.readUncompressedBlockHeader = function () { /** @type {number} block length */ var len; /** @type {number} number for check block length */ var nlen; var input = this.input; var ip = this.ip; this.status = Zlib.RawInflateStream.Status.BLOCK_BODY_START; if (ip + 4 >= input.length) { return -1; } len = input[ip++] | input[ip++] << 8; nlen = input[ip++] | input[ip++] << 8; // check len & nlen if (len === ~nlen) { throw new Error('invalid uncompressed block header: length verify'); } // skip buffered header bits this.bitsbuf = 0; this.bitsbuflen = 0; this.ip = ip; this.blockLength = len; this.status = Zlib.RawInflateStream.Status.BLOCK_BODY_END; }; /** * parse uncompressed block. */ Zlib.RawInflateStream.prototype.parseUncompressedBlock = function () { var input = this.input; var ip = this.ip; var output = this.output; var op = this.op; var len = this.blockLength; this.status = Zlib.RawInflateStream.Status.DECODE_BLOCK_START; // copy // XXX: ã¨ã‚Šã‚ãˆãšç´ ç›´ã«ã‚³ãƒ”ãƒ¼ while (len--) { if (op === output.length) { output = this.expandBuffer({ fixRatio: 2 }); } // not enough input buffer if (ip >= input.length) { this.ip = ip; this.op = op; this.blockLength = len + 1; // コピーしてないので戻す return -1; } output[op++] = input[ip++]; } if (len < 0) { this.status = Zlib.RawInflateStream.Status.DECODE_BLOCK_END; } this.ip = ip; this.op = op; return 0; }; /** * parse fixed huffman block. */ Zlib.RawInflateStream.prototype.parseFixedHuffmanBlock = function () { this.status = Zlib.RawInflateStream.Status.BLOCK_BODY_START; this.litlenTable = Zlib.RawInflateStream.FixedLiteralLengthTable; this.distTable = Zlib.RawInflateStream.FixedDistanceTable; this.status = Zlib.RawInflateStream.Status.BLOCK_BODY_END; return 0; }; /** * オブジェクトのコンテキストを別のプロパティに退避する. * @private */ Zlib.RawInflateStream.prototype.save_ = function () { this.ip_ = this.ip; this.bitsbuflen_ = this.bitsbuflen; this.bitsbuf_ = this.bitsbuf; }; /** * 別のプロパティに退避したコンテキストを復元する. * @private */ Zlib.RawInflateStream.prototype.restore_ = function () { this.ip = this.ip_; this.bitsbuflen = this.bitsbuflen_; this.bitsbuf = this.bitsbuf_; }; /** * parse dynamic huffman block. */ Zlib.RawInflateStream.prototype.parseDynamicHuffmanBlock = function () { /** @type {number} number of literal and length codes. */ var hlit; /** @type {number} number of distance codes. */ var hdist; /** @type {number} number of code lengths. */ var hclen; /** @type {!(Uint8Array|Array)} code lengths. */ var codeLengths = new Uint8Array(Zlib.RawInflateStream.Order.length); /** @type {!Array} code lengths table. */ var codeLengthsTable; this.status = Zlib.RawInflateStream.Status.BLOCK_BODY_START; this.save_(); hlit = this.readBits(5) + 257; hdist = this.readBits(5) + 1; hclen = this.readBits(4) + 4; if (hlit < 0 || hdist < 0 || hclen < 0) { this.restore_(); return -1; } try { parseDynamicHuffmanBlockImpl.call(this); } catch (e) { this.restore_(); return -1; } function parseDynamicHuffmanBlockImpl() { /** @type {number} */ var bits; var code; var prev = 0; var repeat; /** @type {!(Uint8Array|Array.)} code length table. */ var lengthTable; /** @type {number} loop counter. */ var i; /** @type {number} loop limit. */ var il; // decode code lengths for (i = 0; i < hclen; ++i) { if ((bits = this.readBits(3)) < 0) { throw new Error('not enough input'); } codeLengths[Zlib.RawInflateStream.Order[i]] = bits; } // decode length table codeLengthsTable = buildHuffmanTable(codeLengths); lengthTable = new Uint8Array(hlit + hdist); for (i = 0, il = hlit + hdist; i < il;) { code = this.readCodeByTable(codeLengthsTable); if (code < 0) { throw new Error('not enough input'); } switch (code) { case 16: if ((bits = this.readBits(2)) < 0) { throw new Error('not enough input'); } repeat = 3 + bits; while (repeat--) { lengthTable[i++] = prev; } break; case 17: if ((bits = this.readBits(3)) < 0) { throw new Error('not enough input'); } repeat = 3 + bits; while (repeat--) { lengthTable[i++] = 0; } prev = 0; break; case 18: if ((bits = this.readBits(7)) < 0) { throw new Error('not enough input'); } repeat = 11 + bits; while (repeat--) { lengthTable[i++] = 0; } prev = 0; break; default: lengthTable[i++] = code; prev = code; break; } } this.litlenTable = buildHuffmanTable(lengthTable.subarray(0, hlit)); this.distTable = buildHuffmanTable(lengthTable.subarray(hlit)); } this.status = Zlib.RawInflateStream.Status.BLOCK_BODY_END; return 0; }; /** * decode huffman code (dynamic) * @return {(number|undefined)} -1 is error. */ Zlib.RawInflateStream.prototype.decodeHuffman = function () { var output = this.output; var op = this.op; /** @type {number} huffman code. */ var code; /** @type {number} table index. */ var ti; /** @type {number} huffman code distination. */ var codeDist; /** @type {number} huffman code length. */ var codeLength; var litlen = this.litlenTable; var dist = this.distTable; var olength = output.length; var bits; this.status = Zlib.RawInflateStream.Status.DECODE_BLOCK_START; while (true) { this.save_(); code = this.readCodeByTable(litlen); if (code < 0) { this.op = op; this.restore_(); return -1; } if (code === 256) { break; } // literal if (code < 256) { if (op === olength) { output = this.expandBuffer(); olength = output.length; } output[op++] = code; continue; } // length code ti = code - 257; codeLength = Zlib.RawInflateStream.LengthCodeTable[ti]; if (Zlib.RawInflateStream.LengthExtraTable[ti] > 0) { bits = this.readBits(Zlib.RawInflateStream.LengthExtraTable[ti]); if (bits < 0) { this.op = op; this.restore_(); return -1; } codeLength += bits; } // dist code code = this.readCodeByTable(dist); if (code < 0) { this.op = op; this.restore_(); return -1; } codeDist = Zlib.RawInflateStream.DistCodeTable[code]; if (Zlib.RawInflateStream.DistExtraTable[code] > 0) { bits = this.readBits(Zlib.RawInflateStream.DistExtraTable[code]); if (bits < 0) { this.op = op; this.restore_(); return -1; } codeDist += bits; } // lz77 decode if (op + codeLength >= olength) { output = this.expandBuffer(); olength = output.length; } while (codeLength--) { output[op] = output[op++ - codeDist]; } // break if (this.ip === this.input.length) { this.op = op; return -1; } } while (this.bitsbuflen >= 8) { this.bitsbuflen -= 8; this.ip--; } this.op = op; this.status = Zlib.RawInflateStream.Status.DECODE_BLOCK_END; }; /** * expand output buffer. (dynamic) * @param {Object=} opt_param option parameters. * @return {!(Array|Uint8Array)} output buffer pointer. */ Zlib.RawInflateStream.prototype.expandBuffer = function (opt_param) { /** @type {!(Array|Uint8Array)} store buffer. */ var buffer; /** @type {number} expantion ratio. */ var ratio = this.input.length / this.ip + 1 | 0; /** @type {number} maximum number of huffman code. */ var maxHuffCode; /** @type {number} new output buffer size. */ var newSize; /** @type {number} max inflate size. */ var maxInflateSize; var input = this.input; var output = this.output; if (opt_param) { if (typeof opt_param.fixRatio === 'number') { ratio = opt_param.fixRatio; } if (typeof opt_param.addRatio === 'number') { ratio += opt_param.addRatio; } } // calculate new buffer size if (ratio < 2) { maxHuffCode = (input.length - this.ip) / this.litlenTable[2]; maxInflateSize = maxHuffCode / 2 * 258 | 0; newSize = maxInflateSize < output.length ? output.length + maxInflateSize : output.length << 1; } else { newSize = output.length * ratio; } // buffer expantion { buffer = new Uint8Array(newSize); buffer.set(output); } this.output = buffer; return this.output; }; /** * concat output buffer. (dynamic) * @return {!(Array|Uint8Array)} output buffer. */ Zlib.RawInflateStream.prototype.concatBuffer = function () { /** @type {!(Array|Uint8Array)} output buffer. */ var buffer; /** @type {number} */ var op = this.op; /** @type {Uint8Array} */ var tmp; if (this.resize) { { buffer = new Uint8Array(this.output.subarray(this.sp, op)); } } else { buffer = this.output.subarray(this.sp, op); } this.sp = op; // compaction if (op > Zlib.RawInflateStream.MaxBackwardLength + this.bufferSize) { this.op = this.sp = Zlib.RawInflateStream.MaxBackwardLength; { tmp = this.output; this.output = new Uint8Array(this.bufferSize + Zlib.RawInflateStream.MaxBackwardLength); this.output.set(tmp.subarray(op - Zlib.RawInflateStream.MaxBackwardLength, op)); } } return buffer; }; /** * @constructor * @param {!(Uint8Array|Array)} input deflated buffer. * @param {Object=} opt_params option parameters. * * opt_params は以下のプロパティを指定する事ができます。 * - index: input buffer の deflate コンテナの開始位置. * - blockSize: バッファのブロックサイズ. * - verify: 伸張が終わった後 adler-32 checksum の検証を行うか. * - bufferType: Zlib.Inflate.BufferType の値によってバッファの管理方法を指定する. * Zlib.Inflate.BufferType は Zlib.RawInflate.BufferType のエイリアス. */ Zlib.Inflate = function (input, opt_params) { /** @type {number} */ var cmf; /** @type {number} */ var flg; /** @type {!(Uint8Array|Array)} */ this.input = input; /** @type {number} */ this.ip = 0; /** @type {Zlib.RawInflate} */ this.rawinflate; /** @type {(boolean|undefined)} verify flag. */ this.verify; // option parameters if (opt_params || !(opt_params = {})) { if (opt_params['index']) { this.ip = opt_params['index']; } if (opt_params['verify']) { this.verify = opt_params['verify']; } } // Compression Method and Flags cmf = input[this.ip++]; flg = input[this.ip++]; // compression method switch (cmf & 0x0f) { case Zlib.CompressionMethod.DEFLATE: this.method = Zlib.CompressionMethod.DEFLATE; break; default: throw new Error('unsupported compression method'); } // fcheck if (((cmf << 8) + flg) % 31 !== 0) { throw new Error('invalid fcheck flag:' + ((cmf << 8) + flg) % 31); } // fdict (not supported) if (flg & 0x20) { throw new Error('fdict flag is not supported'); } // RawInflate this.rawinflate = new Zlib.RawInflate(input, { 'index': this.ip, 'bufferSize': opt_params['bufferSize'], 'bufferType': opt_params['bufferType'], 'resize': opt_params['resize'] }); }; /** * @enum {number} */ Zlib.Inflate.BufferType = Zlib.RawInflate.BufferType; /** * decompress. * @return {!(Uint8Array|Array)} inflated buffer. */ Zlib.Inflate.prototype.decompress = function () { /** @type {!(Array|Uint8Array)} input buffer. */ var input = this.input; /** @type {!(Uint8Array|Array)} inflated buffer. */ var buffer; /** @type {number} adler-32 checksum */ var adler32; buffer = this.rawinflate.decompress(); this.ip = this.rawinflate.ip; // verify adler-32 if (this.verify) { adler32 = (input[this.ip++] << 24 | input[this.ip++] << 16 | input[this.ip++] << 8 | input[this.ip++]) >>> 0; if (adler32 !== Zlib.Adler32(buffer)) { throw new Error('invalid adler-32 checksum'); } } return buffer; }; /* vim:set expandtab ts=2 sw=2 tw=80: */ /** * @param {!(Uint8Array|Array)} input deflated buffer. * @constructor */ Zlib.InflateStream = function (input) { /** @type {!(Uint8Array|Array)} */ this.input = input === void 0 ? new Uint8Array() : input; /** @type {number} */ this.ip = 0; /** @type {Zlib.RawInflateStream} */ this.rawinflate = new Zlib.RawInflateStream(this.input, this.ip); /** @type {Zlib.CompressionMethod} */ this.method; /** @type {!(Array|Uint8Array)} */ this.output = this.rawinflate.output; }; /** * decompress. * @return {!(Uint8Array|Array)} inflated buffer. */ Zlib.InflateStream.prototype.decompress = function (input) { /** @type {!(Uint8Array|Array)} inflated buffer. */ var buffer; // 新しい入力を入力バッファに結合する // XXX Array, Uint8Array のチェックを行うか確認する if (input !== void 0) { { var tmp = new Uint8Array(this.input.length + input.length); tmp.set(this.input, 0); tmp.set(input, this.input.length); this.input = tmp; } } if (this.method === void 0) { if (this.readHeader() < 0) { return new Uint8Array(); } } buffer = this.rawinflate.decompress(this.input, this.ip); if (this.rawinflate.ip !== 0) { this.input = this.input.subarray(this.rawinflate.ip); this.ip = 0; } // verify adler-32 /* if (this.verify) { adler32 = input[this.ip++] << 24 | input[this.ip++] << 16 | input[this.ip++] << 8 | input[this.ip++]; if (adler32 !== Zlib.Adler32(buffer)) { throw new Error('invalid adler-32 checksum'); } } */ return buffer; }; Zlib.InflateStream.prototype.readHeader = function () { var ip = this.ip; var input = this.input; // Compression Method and Flags var cmf = input[ip++]; var flg = input[ip++]; if (cmf === void 0 || flg === void 0) { return -1; } // compression method switch (cmf & 0x0f) { case Zlib.CompressionMethod.DEFLATE: this.method = Zlib.CompressionMethod.DEFLATE; break; default: throw new Error('unsupported compression method'); } // fcheck if (((cmf << 8) + flg) % 31 !== 0) { throw new Error('invalid fcheck flag:' + ((cmf << 8) + flg) % 31); } // fdict (not supported) if (flg & 0x20) { throw new Error('fdict flag is not supported'); } this.ip = ip; }; /** * @fileoverview GZIP (RFC1952) 展開コンテナ実装. */ /** * @constructor * @param {!(Array|Uint8Array)} input input buffer. * @param {Object=} opt_params option parameters. */ Zlib.Gunzip = function (input, opt_params) { /** @type {!(Array.|Uint8Array)} input buffer. */ this.input = input; /** @type {number} input buffer pointer. */ this.ip = 0; /** @type {Array.} */ this.member = []; /** @type {boolean} */ this.decompressed = false; }; /** * @return {Array.} */ Zlib.Gunzip.prototype.getMembers = function () { if (!this.decompressed) { this.decompress(); } return this.member.slice(); }; /** * inflate gzip data. * @return {!(Array.|Uint8Array)} inflated buffer. */ Zlib.Gunzip.prototype.decompress = function () { /** @type {number} input length. */ var il = this.input.length; while (this.ip < il) { this.decodeMember(); } this.decompressed = true; return this.concatMember(); }; /** * decode gzip member. */ Zlib.Gunzip.prototype.decodeMember = function () { /** @type {Zlib.GunzipMember} */ var member = new Zlib.GunzipMember(); /** @type {number} */ var isize; /** @type {Zlib.RawInflate} RawInflate implementation. */ var rawinflate; /** @type {!(Array.|Uint8Array)} inflated data. */ var inflated; /** @type {number} inflate size */ var inflen; /** @type {number} character code */ var c; /** @type {number} character index in string. */ var ci; /** @type {Array.} character array. */ var str; /** @type {number} modification time. */ var mtime; /** @type {number} */ var crc32; var input = this.input; var ip = this.ip; member.id1 = input[ip++]; member.id2 = input[ip++]; // check signature if (member.id1 !== 0x1f || member.id2 !== 0x8b) { throw new Error('invalid file signature:' + member.id1 + ',' + member.id2); } // check compression method member.cm = input[ip++]; switch (member.cm) { case 8: /* XXX: use Zlib const */ break; default: throw new Error('unknown compression method: ' + member.cm); } // flags member.flg = input[ip++]; // modification time mtime = input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24; member.mtime = new Date(mtime * 1000); // extra flags member.xfl = input[ip++]; // operating system member.os = input[ip++]; // extra if ((member.flg & Zlib.Gzip.FlagsMask.FEXTRA) > 0) { member.xlen = input[ip++] | input[ip++] << 8; ip = this.decodeSubField(ip, member.xlen); } // fname if ((member.flg & Zlib.Gzip.FlagsMask.FNAME) > 0) { for (str = [], ci = 0; (c = input[ip++]) > 0;) { str[ci++] = String.fromCharCode(c); } member.name = str.join(''); } // fcomment if ((member.flg & Zlib.Gzip.FlagsMask.FCOMMENT) > 0) { for (str = [], ci = 0; (c = input[ip++]) > 0;) { str[ci++] = String.fromCharCode(c); } member.comment = str.join(''); } // fhcrc if ((member.flg & Zlib.Gzip.FlagsMask.FHCRC) > 0) { member.crc16 = Zlib.CRC32.calc(input, 0, ip) & 0xffff; if (member.crc16 !== (input[ip++] | input[ip++] << 8)) { throw new Error('invalid header crc16'); } } // isize を事前に取得すると展開後のサイズが分かるため、 // inflate処理のバッファサイズが事前に分かり、高速になる isize = input[input.length - 4] | input[input.length - 3] << 8 | input[input.length - 2] << 16 | input[input.length - 1] << 24; // isize の妥当性チェック // ハフマン符号では最小 2-bit のため、最大で 1/4 になる // LZ77 符号では 長さと距離 2-Byte で最大 258-Byte を表現できるため、 // 1/128 になるとする // ここから入力バッファの残りが isize の 512 倍以上だったら // サイズ指定のバッファ確保は行わない事とする if (input.length - ip - /* CRC-32 */ 4 - /* ISIZE */ 4 < isize * 512) { inflen = isize; } // compressed block rawinflate = new Zlib.RawInflate(input, { 'index': ip, 'bufferSize': inflen }); member.data = inflated = rawinflate.decompress(); ip = rawinflate.ip; // crc32 member.crc32 = crc32 = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; if (Zlib.CRC32.calc(inflated) !== crc32) { throw new Error('invalid CRC-32 checksum: 0x' + Zlib.CRC32.calc(inflated).toString(16) + ' / 0x' + crc32.toString(16)); } // input size member.isize = isize = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; if ((inflated.length & 0xffffffff) !== isize) { throw new Error('invalid input size: ' + (inflated.length & 0xffffffff) + ' / ' + isize); } this.member.push(member); this.ip = ip; }; /** * サブフィールドのデコード * XXX: 現在は何もせずスキップする */ Zlib.Gunzip.prototype.decodeSubField = function (ip, length) { return ip + length; }; /** * @return {!(Array.|Uint8Array)} */ Zlib.Gunzip.prototype.concatMember = function () { /** @type {Array.} */ var member = this.member; /** @type {number} */ var i; /** @type {number} */ var il; /** @type {number} */ var p = 0; /** @type {number} */ var size = 0; /** @type {!(Array.|Uint8Array)} */ var buffer; for (i = 0, il = member.length; i < il; ++i) { size += member[i].data.length; } { buffer = new Uint8Array(size); for (i = 0; i < il; ++i) { buffer.set(member[i].data, p); p += member[i].data.length; } } return buffer; }; /** * @constructor */ Zlib.GunzipMember = function () { /** @type {number} signature first byte. */ this.id1; /** @type {number} signature second byte. */ this.id2; /** @type {number} compression method. */ this.cm; /** @type {number} flags. */ this.flg; /** @type {Date} modification time. */ this.mtime; /** @type {number} extra flags. */ this.xfl; /** @type {number} operating system number. */ this.os; /** @type {number} CRC-16 value for FHCRC flag. */ this.crc16; /** @type {number} extra length. */ this.xlen; /** @type {number} CRC-32 value for verification. */ this.crc32; /** @type {number} input size modulo 32 value. */ this.isize; /** @type {string} filename. */ this.name; /** @type {string} comment. */ this.comment; /** @type {!(Uint8Array|Array.)} */ this.data; }; Zlib.GunzipMember.prototype.getName = function () { return this.name; }; Zlib.GunzipMember.prototype.getData = function () { return this.data; }; Zlib.GunzipMember.prototype.getMtime = function () { return this.mtime; }; /** * @fileoverview GZIP (RFC1952) 実装. */ /** * @constructor * @param {!(Array|Uint8Array)} input input buffer. * @param {Object=} opt_params option parameters. */ Zlib.Gzip = function (input, opt_params) { /** @type {!(Array.|Uint8Array)} input buffer. */ this.input = input; /** @type {number} input buffer pointer. */ this.ip = 0; /** @type {!(Array.|Uint8Array)} output buffer. */ this.output; /** @type {number} output buffer. */ this.op = 0; /** @type {!Object} flags option flags. */ this.flags = {}; /** @type {!string} filename. */ this.filename; /** @type {!string} comment. */ this.comment; /** @type {!Object} deflate options. */ this.deflateOptions; // option parameters if (opt_params) { if (opt_params['flags']) { this.flags = opt_params['flags']; } if (typeof opt_params['filename'] === 'string') { this.filename = opt_params['filename']; } if (typeof opt_params['comment'] === 'string') { this.comment = opt_params['comment']; } if (opt_params['deflateOptions']) { this.deflateOptions = opt_params['deflateOptions']; } } if (!this.deflateOptions) { this.deflateOptions = {}; } }; /** * @type {number} * @const */ Zlib.Gzip.DefaultBufferSize = 0x8000; /** * encode gzip members. * @return {!(Array|Uint8Array)} gzip binary array. */ Zlib.Gzip.prototype.compress = function () { /** @type {number} flags. */ var flg; /** @type {number} modification time. */ var mtime; /** @type {number} CRC-16 value for FHCRC flag. */ var crc16; /** @type {number} CRC-32 value for verification. */ var crc32; /** @type {!Zlib.RawDeflate} raw deflate object. */ var rawdeflate; /** @type {number} character code */ var c; /** @type {number} loop counter. */ var i; /** @type {number} loop limiter. */ var il; /** @type {!(Array|Uint8Array)} output buffer. */ var output = new Uint8Array(Zlib.Gzip.DefaultBufferSize); /** @type {number} output buffer pointer. */ var op = 0; var input = this.input; var ip = this.ip; var filename = this.filename; var comment = this.comment; // check signature output[op++] = 0x1f; output[op++] = 0x8b; // check compression method output[op++] = 8; /* XXX: use Zlib const */ // flags flg = 0; if (this.flags['fname']) flg |= Zlib.Gzip.FlagsMask.FNAME; if (this.flags['fcomment']) flg |= Zlib.Gzip.FlagsMask.FCOMMENT; if (this.flags['fhcrc']) flg |= Zlib.Gzip.FlagsMask.FHCRC; // XXX: FTEXT // XXX: FEXTRA output[op++] = flg; // modification time mtime = (Date.now ? Date.now() : +new Date()) / 1000 | 0; output[op++] = mtime & 0xff; output[op++] = mtime >>> 8 & 0xff; output[op++] = mtime >>> 16 & 0xff; output[op++] = mtime >>> 24 & 0xff; // extra flags output[op++] = 0; // operating system output[op++] = Zlib.Gzip.OperatingSystem.UNKNOWN; // extra /* NOP */ // fname if (this.flags['fname'] !== void 0) { for (i = 0, il = filename.length; i < il; ++i) { c = filename.charCodeAt(i); if (c > 0xff) { output[op++] = c >>> 8 & 0xff; } output[op++] = c & 0xff; } output[op++] = 0; // null termination } // fcomment if (this.flags['comment']) { for (i = 0, il = comment.length; i < il; ++i) { c = comment.charCodeAt(i); if (c > 0xff) { output[op++] = c >>> 8 & 0xff; } output[op++] = c & 0xff; } output[op++] = 0; // null termination } // fhcrc if (this.flags['fhcrc']) { crc16 = Zlib.CRC32.calc(output, 0, op) & 0xffff; output[op++] = crc16 & 0xff; output[op++] = crc16 >>> 8 & 0xff; } // add compress option this.deflateOptions['outputBuffer'] = output; this.deflateOptions['outputIndex'] = op; // compress rawdeflate = new Zlib.RawDeflate(input, this.deflateOptions); output = rawdeflate.compress(); op = rawdeflate.op; // expand buffer { if (op + 8 > output.buffer.byteLength) { this.output = new Uint8Array(op + 8); this.output.set(new Uint8Array(output.buffer)); output = this.output; } else { output = new Uint8Array(output.buffer); } } // crc32 crc32 = Zlib.CRC32.calc(input); output[op++] = crc32 & 0xff; output[op++] = crc32 >>> 8 & 0xff; output[op++] = crc32 >>> 16 & 0xff; output[op++] = crc32 >>> 24 & 0xff; // input size il = input.length; output[op++] = il & 0xff; output[op++] = il >>> 8 & 0xff; output[op++] = il >>> 16 & 0xff; output[op++] = il >>> 24 & 0xff; this.ip = ip; if (op < output.length) { this.output = output = output.subarray(0, op); } return output; }; /** @enum {number} */ Zlib.Gzip.OperatingSystem = { FAT: 0, AMIGA: 1, VMS: 2, UNIX: 3, VM_CMS: 4, ATARI_TOS: 5, HPFS: 6, MACINTOSH: 7, Z_SYSTEM: 8, CP_M: 9, TOPS_20: 10, NTFS: 11, QDOS: 12, ACORN_RISCOS: 13, UNKNOWN: 255 }; /** @enum {number} */ Zlib.Gzip.FlagsMask = { FTEXT: 0x01, FHCRC: 0x02, FEXTRA: 0x04, FNAME: 0x08, FCOMMENT: 0x10 }; /** * @fileoverview Heap Sort 実装. ハフマン符号化で使用する. */ /** * カスタムハフマン符号で使用するヒープ実装 * @param {number} length ヒープサイズ. * @constructor */ Zlib.Heap = function (length) { this.buffer = new Uint16Array(length * 2); this.length = 0; }; /** * 親ノードの index 取得 * @param {number} index 子ノードの index. * @return {number} 親ノードの index. * */ Zlib.Heap.prototype.getParent = function (index) { return ((index - 2) / 4 | 0) * 2; }; /** * 子ノードの index 取得 * @param {number} index 親ノードの index. * @return {number} 子ノードの index. */ Zlib.Heap.prototype.getChild = function (index) { return 2 * index + 2; }; /** * Heap ã«å€¤ã‚’è¿½åŠ ã™ã‚‹ * @param {number} index キー index. * @param {number} value 値. * @return {number} 現在のヒープ長. */ Zlib.Heap.prototype.push = function (index, value) { var current, parent, heap = this.buffer, swap; current = this.length; heap[this.length++] = value; heap[this.length++] = index; // ルートノードにたどり着くまで入れ替えを試みる while (current > 0) { parent = this.getParent(current); // 親ノードと比較して親の方が小さければ入れ替える if (heap[current] > heap[parent]) { swap = heap[current]; heap[current] = heap[parent]; heap[parent] = swap; swap = heap[current + 1]; heap[current + 1] = heap[parent + 1]; heap[parent + 1] = swap; current = parent; // 入れ替えが必要なくなったらそこで抜ける } else { break; } } return this.length; }; /** * Heapから一番大きい値を返す * @return {{index: number, value: number, length: number}} {index: キーindex, * value: 値, length: ヒープ長} の Object. */ Zlib.Heap.prototype.pop = function () { var index, value, heap = this.buffer, swap, current, parent; value = heap[0]; index = heap[1]; // 後ろから値を取る this.length -= 2; heap[0] = heap[this.length]; heap[1] = heap[this.length + 1]; parent = 0; // ルートノードから下がっていく while (true) { current = this.getChild(parent); // 範囲チェック if (current >= this.length) { break; } // 隣のノードと比較して、隣の方が値が大きければ隣を現在ノードとして選択 if (current + 2 < this.length && heap[current + 2] > heap[current]) { current += 2; } // è¦ªãƒŽãƒ¼ãƒ‰ã¨æ¯”è¼ƒã—ã¦è¦ªã®æ–¹ãŒå°ã•ã„å ´åˆã¯å…¥ã‚Œæ›¿ãˆã‚‹ if (heap[current] > heap[parent]) { swap = heap[parent]; heap[parent] = heap[current]; heap[current] = swap; swap = heap[parent + 1]; heap[parent + 1] = heap[current + 1]; heap[current + 1] = swap; } else { break; } parent = current; } return { index: index, value: value, length: this.length }; }; /* vim:set expandtab ts=2 sw=2 tw=80: */ /** * @fileoverview Deflate (RFC1951) 符号化アルゴリズム実装. */ /** * Raw Deflate 実装 * * @constructor * @param {!(Array.|Uint8Array)} input 符号化する対象のバッファ. * @param {Object=} opt_params option parameters. * * typed array が使用可能なとき、outputBuffer が Array は自動的に Uint8Array に * 変換されます. * 別のオブジェクトになるため出力バッファを参照している変数などは * 更新する必要があります. */ Zlib.RawDeflate = function (input, opt_params) { /** @type {Zlib.RawDeflate.CompressionType} */ this.compressionType = Zlib.RawDeflate.CompressionType.DYNAMIC; /** @type {number} */ this.lazy = 0; /** @type {!(Array.|Uint32Array)} */ this.freqsLitLen; /** @type {!(Array.|Uint32Array)} */ this.freqsDist; /** @type {!(Array.|Uint8Array)} */ this.input = input instanceof Array ? new Uint8Array(input) : input; /** @type {!(Array.|Uint8Array)} output output buffer. */ this.output; /** @type {number} pos output buffer position. */ this.op = 0; // option parameters if (opt_params) { if (opt_params['lazy']) { this.lazy = opt_params['lazy']; } if (typeof opt_params['compressionType'] === 'number') { this.compressionType = opt_params['compressionType']; } if (opt_params['outputBuffer']) { this.output = opt_params['outputBuffer'] instanceof Array ? new Uint8Array(opt_params['outputBuffer']) : opt_params['outputBuffer']; } if (typeof opt_params['outputIndex'] === 'number') { this.op = opt_params['outputIndex']; } } if (!this.output) { this.output = new Uint8Array(0x8000); } }; /** * @enum {number} */ Zlib.RawDeflate.CompressionType = { NONE: 0, FIXED: 1, DYNAMIC: 2, RESERVED: 3 }; /** * LZ77 の最小マッチ長 * @const * @type {number} */ Zlib.RawDeflate.Lz77MinLength = 3; /** * LZ77 の最大マッチ長 * @const * @type {number} */ Zlib.RawDeflate.Lz77MaxLength = 258; /** * LZ77 のウィンドウサイズ * @const * @type {number} */ Zlib.RawDeflate.WindowSize = 0x8000; /** * 最長の符号長 * @const * @type {number} */ Zlib.RawDeflate.MaxCodeLength = 16; /** * ハフマン符号の最大数値 * @const * @type {number} */ Zlib.RawDeflate.HUFMAX = 286; /** * 固定ハフマン符号の符号化テーブル * @const * @type {Array.>} */ Zlib.RawDeflate.FixedHuffmanTable = function () { var table = [], i; for (i = 0; i < 288; i++) { switch (true) { case i <= 143: table.push([i + 0x030, 8]); break; case i <= 255: table.push([i - 144 + 0x190, 9]); break; case i <= 279: table.push([i - 256 + 0x000, 7]); break; case i <= 287: table.push([i - 280 + 0x0C0, 8]); break; default: throw 'invalid literal: ' + i; } } return table; }(); /** * DEFLATE ブロックの作成 * @return {!(Array.|Uint8Array)} 圧縮済み byte array. */ Zlib.RawDeflate.prototype.compress = function () { /** @type {!(Array.|Uint8Array)} */ var blockArray; /** @type {number} */ var position; /** @type {number} */ var length; var input = this.input; // compression switch (this.compressionType) { case Zlib.RawDeflate.CompressionType.NONE: // each 65535-Byte (length header: 16-bit) for (position = 0, length = input.length; position < length;) { blockArray = input.subarray(position, position + 0xffff); position += blockArray.length; this.makeNocompressBlock(blockArray, position === length); } break; case Zlib.RawDeflate.CompressionType.FIXED: this.output = this.makeFixedHuffmanBlock(input, true); this.op = this.output.length; break; case Zlib.RawDeflate.CompressionType.DYNAMIC: this.output = this.makeDynamicHuffmanBlock(input, true); this.op = this.output.length; break; default: throw 'invalid compression type'; } return this.output; }; /** * 非圧縮ブロックの作成 * @param {!(Array.|Uint8Array)} blockArray ブロックデータ byte array. * @param {!boolean} isFinalBlock 最後のブロックならばtrue. * @return {!(Array.|Uint8Array)} 非圧縮ブロック byte array. */ Zlib.RawDeflate.prototype.makeNocompressBlock = function (blockArray, isFinalBlock) { /** @type {number} */ var bfinal; /** @type {Zlib.RawDeflate.CompressionType} */ var btype; /** @type {number} */ var len; /** @type {number} */ var nlen; var output = this.output; var op = this.op; // expand buffer { output = new Uint8Array(this.output.buffer); while (output.length <= op + blockArray.length + 5) { output = new Uint8Array(output.length << 1); } output.set(this.output); } // header bfinal = isFinalBlock ? 1 : 0; btype = Zlib.RawDeflate.CompressionType.NONE; output[op++] = bfinal | btype << 1; // length len = blockArray.length; nlen = ~len + 0x10000 & 0xffff; output[op++] = len & 0xff; output[op++] = len >>> 8 & 0xff; output[op++] = nlen & 0xff; output[op++] = nlen >>> 8 & 0xff; // copy buffer { output.set(blockArray, op); op += blockArray.length; output = output.subarray(0, op); } this.op = op; this.output = output; return output; }; /** * 固定ハフマンブロックの作成 * @param {!(Array.|Uint8Array)} blockArray ブロックデータ byte array. * @param {!boolean} isFinalBlock 最後のブロックならばtrue. * @return {!(Array.|Uint8Array)} 固定ハフマン符号化ブロック byte array. */ Zlib.RawDeflate.prototype.makeFixedHuffmanBlock = function (blockArray, isFinalBlock) { /** @type {Zlib.BitStream} */ var stream = new Zlib.BitStream(new Uint8Array(this.output.buffer), this.op); /** @type {number} */ var bfinal; /** @type {Zlib.RawDeflate.CompressionType} */ var btype; /** @type {!(Array.|Uint16Array)} */ var data; // header bfinal = isFinalBlock ? 1 : 0; btype = Zlib.RawDeflate.CompressionType.FIXED; stream.writeBits(bfinal, 1, true); stream.writeBits(btype, 2, true); data = this.lz77(blockArray); this.fixedHuffman(data, stream); return stream.finish(); }; /** * 動的ハフマンブロックの作成 * @param {!(Array.|Uint8Array)} blockArray ブロックデータ byte array. * @param {!boolean} isFinalBlock 最後のブロックならばtrue. * @return {!(Array.|Uint8Array)} 動的ハフマン符号ブロック byte array. */ Zlib.RawDeflate.prototype.makeDynamicHuffmanBlock = function (blockArray, isFinalBlock) { /** @type {Zlib.BitStream} */ var stream = new Zlib.BitStream(new Uint8Array(this.output.buffer), this.op); /** @type {number} */ var bfinal; /** @type {Zlib.RawDeflate.CompressionType} */ var btype; /** @type {!(Array.|Uint16Array)} */ var data; /** @type {number} */ var hlit; /** @type {number} */ var hdist; /** @type {number} */ var hclen; /** @const @type {Array.} */ var hclenOrder = [16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15]; /** @type {!(Array.|Uint8Array)} */ var litLenLengths; /** @type {!(Array.|Uint16Array)} */ var litLenCodes; /** @type {!(Array.|Uint8Array)} */ var distLengths; /** @type {!(Array.|Uint16Array)} */ var distCodes; /** @type {{ * codes: !(Array.|Uint32Array), * freqs: !(Array.|Uint8Array) * }} */ var treeSymbols; /** @type {!(Array.|Uint8Array)} */ var treeLengths; /** @type {Array} */ var transLengths = new Array(19); /** @type {!(Array.|Uint16Array)} */ var treeCodes; /** @type {number} */ var code; /** @type {number} */ var bitlen; /** @type {number} */ var i; /** @type {number} */ var il; // header bfinal = isFinalBlock ? 1 : 0; btype = Zlib.RawDeflate.CompressionType.DYNAMIC; stream.writeBits(bfinal, 1, true); stream.writeBits(btype, 2, true); data = this.lz77(blockArray); // リテラル・長さ, 距離のハフマン符号と符号長の算出 litLenLengths = this.getLengths_(this.freqsLitLen, 15); litLenCodes = this.getCodesFromLengths_(litLenLengths); distLengths = this.getLengths_(this.freqsDist, 7); distCodes = this.getCodesFromLengths_(distLengths); // HLIT, HDIST の決定 for (hlit = 286; hlit > 257 && litLenLengths[hlit - 1] === 0; hlit--) {} for (hdist = 30; hdist > 1 && distLengths[hdist - 1] === 0; hdist--) {} // HCLEN treeSymbols = this.getTreeSymbols_(hlit, litLenLengths, hdist, distLengths); treeLengths = this.getLengths_(treeSymbols.freqs, 7); for (i = 0; i < 19; i++) { transLengths[i] = treeLengths[hclenOrder[i]]; } for (hclen = 19; hclen > 4 && transLengths[hclen - 1] === 0; hclen--) {} treeCodes = this.getCodesFromLengths_(treeLengths); // 出力 stream.writeBits(hlit - 257, 5, true); stream.writeBits(hdist - 1, 5, true); stream.writeBits(hclen - 4, 4, true); for (i = 0; i < hclen; i++) { stream.writeBits(transLengths[i], 3, true); } // ツリーの出力 for (i = 0, il = treeSymbols.codes.length; i < il; i++) { code = treeSymbols.codes[i]; stream.writeBits(treeCodes[code], treeLengths[code], true); // extra bits if (code >= 16) { i++; switch (code) { case 16: bitlen = 2; break; case 17: bitlen = 3; break; case 18: bitlen = 7; break; default: throw 'invalid code: ' + code; } stream.writeBits(treeSymbols.codes[i], bitlen, true); } } this.dynamicHuffman(data, [litLenCodes, litLenLengths], [distCodes, distLengths], stream); return stream.finish(); }; /** * 動的ハフマン符号化(カスタムハフマンテーブル) * @param {!(Array.|Uint16Array)} dataArray LZ77 符号化済み byte array. * @param {!Zlib.BitStream} stream 書き込み用ビットストリーム. * @return {!Zlib.BitStream} ハフマン符号化済みビットストリームオブジェクト. */ Zlib.RawDeflate.prototype.dynamicHuffman = function (dataArray, litLen, dist, stream) { /** @type {number} */ var index; /** @type {number} */ var length; /** @type {number} */ var literal; /** @type {number} */ var code; /** @type {number} */ var litLenCodes; /** @type {number} */ var litLenLengths; /** @type {number} */ var distCodes; /** @type {number} */ var distLengths; litLenCodes = litLen[0]; litLenLengths = litLen[1]; distCodes = dist[0]; distLengths = dist[1]; // 符号を BitStream に書き込んでいく for (index = 0, length = dataArray.length; index < length; ++index) { literal = dataArray[index]; // literal or length stream.writeBits(litLenCodes[literal], litLenLengths[literal], true); // 長さ・距離符号 if (literal > 256) { // length extra stream.writeBits(dataArray[++index], dataArray[++index], true); // distance code = dataArray[++index]; stream.writeBits(distCodes[code], distLengths[code], true); // distance extra stream.writeBits(dataArray[++index], dataArray[++index], true); // 終端 } else if (literal === 256) { break; } } return stream; }; /** * 固定ハフマン符号化 * @param {!(Array.|Uint16Array)} dataArray LZ77 符号化済み byte array. * @param {!Zlib.BitStream} stream 書き込み用ビットストリーム. * @return {!Zlib.BitStream} ハフマン符号化済みビットストリームオブジェクト. */ Zlib.RawDeflate.prototype.fixedHuffman = function (dataArray, stream) { /** @type {number} */ var index; /** @type {number} */ var length; /** @type {number} */ var literal; // 符号を BitStream に書き込んでいく for (index = 0, length = dataArray.length; index < length; index++) { literal = dataArray[index]; // 符号の書き込み Zlib.BitStream.prototype.writeBits.apply(stream, Zlib.RawDeflate.FixedHuffmanTable[literal]); // 長さ・距離符号 if (literal > 0x100) { // length extra stream.writeBits(dataArray[++index], dataArray[++index], true); // distance stream.writeBits(dataArray[++index], 5); // distance extra stream.writeBits(dataArray[++index], dataArray[++index], true); // 終端 } else if (literal === 0x100) { break; } } return stream; }; /** * ãƒžãƒƒãƒæƒ…å ± * @param {!number} length マッチした長さ. * @param {!number} backwardDistance マッチ位置との距離. * @constructor */ Zlib.RawDeflate.Lz77Match = function (length, backwardDistance) { /** @type {number} match length. */ this.length = length; /** @type {number} backward distance. */ this.backwardDistance = backwardDistance; }; /** * 長さ符号テーブル. * [コード, 拡張ビット, 拡張ビット長] の配列となっている. * @const * @type {!(Array.|Uint32Array)} */ Zlib.RawDeflate.Lz77Match.LengthCodeTable = function (table) { return new Uint32Array(table); }(function () { /** @type {!Array} */ var table = []; /** @type {number} */ var i; /** @type {!Array.} */ var c; for (i = 3; i <= 258; i++) { c = code(i); table[i] = c[2] << 24 | c[1] << 16 | c[0]; } /** * @param {number} length lz77 length. * @return {!Array.} lz77 codes. */ function code(length) { switch (true) { case length === 3: return [257, length - 3, 0]; case length === 4: return [258, length - 4, 0]; case length === 5: return [259, length - 5, 0]; case length === 6: return [260, length - 6, 0]; case length === 7: return [261, length - 7, 0]; case length === 8: return [262, length - 8, 0]; case length === 9: return [263, length - 9, 0]; case length === 10: return [264, length - 10, 0]; case length <= 12: return [265, length - 11, 1]; case length <= 14: return [266, length - 13, 1]; case length <= 16: return [267, length - 15, 1]; case length <= 18: return [268, length - 17, 1]; case length <= 22: return [269, length - 19, 2]; case length <= 26: return [270, length - 23, 2]; case length <= 30: return [271, length - 27, 2]; case length <= 34: return [272, length - 31, 2]; case length <= 42: return [273, length - 35, 3]; case length <= 50: return [274, length - 43, 3]; case length <= 58: return [275, length - 51, 3]; case length <= 66: return [276, length - 59, 3]; case length <= 82: return [277, length - 67, 4]; case length <= 98: return [278, length - 83, 4]; case length <= 114: return [279, length - 99, 4]; case length <= 130: return [280, length - 115, 4]; case length <= 162: return [281, length - 131, 5]; case length <= 194: return [282, length - 163, 5]; case length <= 226: return [283, length - 195, 5]; case length <= 257: return [284, length - 227, 5]; case length === 258: return [285, length - 258, 0]; default: throw 'invalid length: ' + length; } } return table; }()); /** * 距離符号テーブル * @param {!number} dist 距離. * @return {!Array.} コード、拡張ビット、拡張ビット長の配列. * @private */ Zlib.RawDeflate.Lz77Match.prototype.getDistanceCode_ = function (dist) { /** @type {!Array.} distance code table. */ var r; switch (true) { case dist === 1: r = [0, dist - 1, 0]; break; case dist === 2: r = [1, dist - 2, 0]; break; case dist === 3: r = [2, dist - 3, 0]; break; case dist === 4: r = [3, dist - 4, 0]; break; case dist <= 6: r = [4, dist - 5, 1]; break; case dist <= 8: r = [5, dist - 7, 1]; break; case dist <= 12: r = [6, dist - 9, 2]; break; case dist <= 16: r = [7, dist - 13, 2]; break; case dist <= 24: r = [8, dist - 17, 3]; break; case dist <= 32: r = [9, dist - 25, 3]; break; case dist <= 48: r = [10, dist - 33, 4]; break; case dist <= 64: r = [11, dist - 49, 4]; break; case dist <= 96: r = [12, dist - 65, 5]; break; case dist <= 128: r = [13, dist - 97, 5]; break; case dist <= 192: r = [14, dist - 129, 6]; break; case dist <= 256: r = [15, dist - 193, 6]; break; case dist <= 384: r = [16, dist - 257, 7]; break; case dist <= 512: r = [17, dist - 385, 7]; break; case dist <= 768: r = [18, dist - 513, 8]; break; case dist <= 1024: r = [19, dist - 769, 8]; break; case dist <= 1536: r = [20, dist - 1025, 9]; break; case dist <= 2048: r = [21, dist - 1537, 9]; break; case dist <= 3072: r = [22, dist - 2049, 10]; break; case dist <= 4096: r = [23, dist - 3073, 10]; break; case dist <= 6144: r = [24, dist - 4097, 11]; break; case dist <= 8192: r = [25, dist - 6145, 11]; break; case dist <= 12288: r = [26, dist - 8193, 12]; break; case dist <= 16384: r = [27, dist - 12289, 12]; break; case dist <= 24576: r = [28, dist - 16385, 13]; break; case dist <= 32768: r = [29, dist - 24577, 13]; break; default: throw 'invalid distance'; } return r; }; /** * ãƒžãƒƒãƒæƒ…å ±ã‚’ LZ77 符号化配列で返す. * なお、ここでは以下の内部仕様で符号化している * [ CODE, EXTRA-BIT-LEN, EXTRA, CODE, EXTRA-BIT-LEN, EXTRA ] * @return {!Array.} LZ77 符号化 byte array. */ Zlib.RawDeflate.Lz77Match.prototype.toLz77Array = function () { /** @type {number} */ var length = this.length; /** @type {number} */ var dist = this.backwardDistance; /** @type {Array} */ var codeArray = []; /** @type {number} */ var pos = 0; /** @type {!Array.} */ var code; // length code = Zlib.RawDeflate.Lz77Match.LengthCodeTable[length]; codeArray[pos++] = code & 0xffff; codeArray[pos++] = code >> 16 & 0xff; codeArray[pos++] = code >> 24; // distance code = this.getDistanceCode_(dist); codeArray[pos++] = code[0]; codeArray[pos++] = code[1]; codeArray[pos++] = code[2]; return codeArray; }; /** * LZ77 実装 * @param {!(Array.|Uint8Array)} dataArray LZ77 符号化するバイト配列. * @return {!(Array.|Uint16Array)} LZ77 符号化した配列. */ Zlib.RawDeflate.prototype.lz77 = function (dataArray) { /** @type {number} input position */ var position; /** @type {number} input length */ var length; /** @type {number} loop counter */ var i; /** @type {number} loop limiter */ var il; /** @type {number} chained-hash-table key */ var matchKey; /** @type {Object.>} chained-hash-table */ var table = {}; /** @const @type {number} */ var windowSize = Zlib.RawDeflate.WindowSize; /** @type {Array.} match list */ var matchList; /** @type {Zlib.RawDeflate.Lz77Match} longest match */ var longestMatch; /** @type {Zlib.RawDeflate.Lz77Match} previous longest match */ var prevMatch; /** @type {!(Array.|Uint16Array)} lz77 buffer */ var lz77buf = new Uint16Array(dataArray.length * 2); /** @type {number} lz77 output buffer pointer */ var pos = 0; /** @type {number} lz77 skip length */ var skipLength = 0; /** @type {!(Array.|Uint32Array)} */ var freqsLitLen = new Uint32Array(286); /** @type {!(Array.|Uint32Array)} */ var freqsDist = new Uint32Array(30); /** @type {number} */ var lazy = this.lazy; /** @type {*} temporary variable */ var tmp; freqsLitLen[256] = 1; // EOB の最低出現回数は 1 /** * マッチデータの書き込み * @param {Zlib.RawDeflate.Lz77Match} match LZ77 Match data. * @param {!number} offset スキップ開始位置(相対指定). * @private */ function writeMatch(match, offset) { /** @type {Array.} */ var lz77Array = match.toLz77Array(); /** @type {number} */ var i; /** @type {number} */ var il; for (i = 0, il = lz77Array.length; i < il; ++i) { lz77buf[pos++] = lz77Array[i]; } freqsLitLen[lz77Array[0]]++; freqsDist[lz77Array[3]]++; skipLength = match.length + offset - 1; prevMatch = null; } // LZ77 符号化 for (position = 0, length = dataArray.length; position < length; ++position) { // ハッシュキーの作成 for (matchKey = 0, i = 0, il = Zlib.RawDeflate.Lz77MinLength; i < il; ++i) { if (position + i === length) { break; } matchKey = matchKey << 8 | dataArray[position + i]; } // テーブルが未定義だったら作成する if (table[matchKey] === void 0) { table[matchKey] = []; } matchList = table[matchKey]; // skip if (skipLength-- > 0) { matchList.push(position); continue; } // マッチテーブルの更新 (最大戻り距離を超えているものを削除する) while (matchList.length > 0 && position - matchList[0] > windowSize) { matchList.shift(); } // ãƒ‡ãƒ¼ã‚¿æœ«å°¾ã§ãƒžãƒƒãƒã—ã‚ˆã†ãŒãªã„å ´åˆã¯ãã®ã¾ã¾æµã—ã“ã‚€ if (position + Zlib.RawDeflate.Lz77MinLength >= length) { if (prevMatch) { writeMatch(prevMatch, -1); } for (i = 0, il = length - position; i < il; ++i) { tmp = dataArray[position + i]; lz77buf[pos++] = tmp; ++freqsLitLen[tmp]; } break; } // マッチ候補から最長のものを探す if (matchList.length > 0) { longestMatch = this.searchLongestMatch_(dataArray, position, matchList); if (prevMatch) { // 現在のマッチの方が前回のマッチよりも長い if (prevMatch.length < longestMatch.length) { // write previous literal tmp = dataArray[position - 1]; lz77buf[pos++] = tmp; ++freqsLitLen[tmp]; // write current match writeMatch(longestMatch, 0); } else { // write previous match writeMatch(prevMatch, -1); } } else if (longestMatch.length < lazy) { prevMatch = longestMatch; } else { writeMatch(longestMatch, 0); } // 前回マッチしていて今回マッチがなかったら前回のを採用 } else if (prevMatch) { writeMatch(prevMatch, -1); } else { tmp = dataArray[position]; lz77buf[pos++] = tmp; ++freqsLitLen[tmp]; } matchList.push(position); // マッチテーブルに現在の位置を保存 } // 終端処理 lz77buf[pos++] = 256; freqsLitLen[256]++; this.freqsLitLen = freqsLitLen; this.freqsDist = freqsDist; return lz77buf.subarray(0, pos); }; /** * マッチした候補の中から最長一致を探す * @param {!Object} data plain data byte array. * @param {!number} position plain data byte array position. * @param {!Array.} matchList 候補となる位置の配列. * @return {!Zlib.RawDeflate.Lz77Match} 最長かつ最短距離のマッチオブジェクト. * @private */ Zlib.RawDeflate.prototype.searchLongestMatch_ = function (data, position, matchList) { var match, currentMatch, matchMax = 0, matchLength, i, j, l, dl = data.length; // 候補を後ろから 1 つずつ絞り込んでゆく permatch: for (i = 0, l = matchList.length; i < l; i++) { match = matchList[l - i - 1]; matchLength = Zlib.RawDeflate.Lz77MinLength; // 前回までの最長一致を末尾から一致検索する if (matchMax > Zlib.RawDeflate.Lz77MinLength) { for (j = matchMax; j > Zlib.RawDeflate.Lz77MinLength; j--) { if (data[match + j - 1] !== data[position + j - 1]) { continue permatch; } } matchLength = matchMax; } // 最長一致探索 while (matchLength < Zlib.RawDeflate.Lz77MaxLength && position + matchLength < dl && data[match + matchLength] === data[position + matchLength]) { ++matchLength; } // ãƒžãƒƒãƒé•·ãŒåŒã˜å ´åˆã¯å¾Œæ–¹ã‚’å„ªå…ˆ if (matchLength > matchMax) { currentMatch = match; matchMax = matchLength; } // 最長が確定したら後の処理は省略 if (matchLength === Zlib.RawDeflate.Lz77MaxLength) { break; } } return new Zlib.RawDeflate.Lz77Match(matchMax, position - currentMatch); }; /** * Tree-Transmit Symbols の算出 * reference: PuTTY Deflate implementation * @param {number} hlit HLIT. * @param {!(Array.|Uint8Array)} litlenLengths リテラルと長さ符号の符号長配列. * @param {number} hdist HDIST. * @param {!(Array.|Uint8Array)} distLengths 距離符号の符号長配列. * @return {{ * codes: !(Array.|Uint32Array), * freqs: !(Array.|Uint8Array) * }} Tree-Transmit Symbols. */ Zlib.RawDeflate.prototype.getTreeSymbols_ = function (hlit, litlenLengths, hdist, distLengths) { var src = new Uint32Array(hlit + hdist), i, j, runLength, l, result = new Uint32Array(286 + 30), nResult, rpt, freqs = new Uint8Array(19); j = 0; for (i = 0; i < hlit; i++) { src[j++] = litlenLengths[i]; } for (i = 0; i < hdist; i++) { src[j++] = distLengths[i]; } // 符号化 nResult = 0; for (i = 0, l = src.length; i < l; i += j) { // Run Length Encoding for (j = 1; i + j < l && src[i + j] === src[i]; ++j) {} runLength = j; if (src[i] === 0) { // 0 の繰り返しが 3 回未満ならばそのまま if (runLength < 3) { while (runLength-- > 0) { result[nResult++] = 0; freqs[0]++; } } else { while (runLength > 0) { // 繰り返しは最大 138 までなので切り詰める rpt = runLength < 138 ? runLength : 138; if (rpt > runLength - 3 && rpt < runLength) { rpt = runLength - 3; } // 3-10 回 -> 17 if (rpt <= 10) { result[nResult++] = 17; result[nResult++] = rpt - 3; freqs[17]++; // 11-138 回 -> 18 } else { result[nResult++] = 18; result[nResult++] = rpt - 11; freqs[18]++; } runLength -= rpt; } } } else { result[nResult++] = src[i]; freqs[src[i]]++; runLength--; // 繰り返し回数が3回未満ならばランレングス符号は要らない if (runLength < 3) { while (runLength-- > 0) { result[nResult++] = src[i]; freqs[src[i]]++; } // 3 回以上ならばランレングス符号化 } else { while (runLength > 0) { // runLengthã‚’ 3-6 で分割 rpt = runLength < 6 ? runLength : 6; if (rpt > runLength - 3 && rpt < runLength) { rpt = runLength - 3; } result[nResult++] = 16; result[nResult++] = rpt - 3; freqs[16]++; runLength -= rpt; } } } } return { codes: result.subarray(0, nResult), freqs: freqs }; }; /** * ハフマン符号の長さを取得する * @param {!(Array.|Uint8Array|Uint32Array)} freqs 出現カウント. * @param {number} limit 符号長の制限. * @return {!(Array.|Uint8Array)} 符号長配列. * @private */ Zlib.RawDeflate.prototype.getLengths_ = function (freqs, limit) { /** @type {number} */ var nSymbols = freqs.length; /** @type {Zlib.Heap} */ var heap = new Zlib.Heap(2 * Zlib.RawDeflate.HUFMAX); /** @type {!(Array.|Uint8Array)} */ var length = new Uint8Array(nSymbols); /** @type {Array} */ var nodes; /** @type {!(Array.|Uint32Array)} */ var values; /** @type {!(Array.|Uint8Array)} */ var codeLength; /** @type {number} */ var i; /** @type {number} */ var il; // ヒープの構築 for (i = 0; i < nSymbols; ++i) { if (freqs[i] > 0) { heap.push(i, freqs[i]); } } nodes = new Array(heap.length / 2); values = new Uint32Array(heap.length / 2); // 非 0 ã®è¦ç´ ãŒä¸€ã¤ã ã‘ã ã£ãŸå ´åˆã¯ã€ãã®ã‚·ãƒ³ãƒœãƒ«ã«ç¬¦å·é•· 1 を割り当てて終了 if (nodes.length === 1) { length[heap.pop().index] = 1; return length; } // Reverse Package Merge Algorithm による Canonical Huffman Code の符号長決定 for (i = 0, il = heap.length / 2; i < il; ++i) { nodes[i] = heap.pop(); values[i] = nodes[i].value; } codeLength = this.reversePackageMerge_(values, values.length, limit); for (i = 0, il = nodes.length; i < il; ++i) { length[nodes[i].index] = codeLength[i]; } return length; }; /** * Reverse Package Merge Algorithm. * @param {!(Array.|Uint32Array)} freqs sorted probability. * @param {number} symbols number of symbols. * @param {number} limit code length limit. * @return {!(Array.|Uint8Array)} code lengths. */ Zlib.RawDeflate.prototype.reversePackageMerge_ = function (freqs, symbols, limit) { /** @type {!(Array.|Uint16Array)} */ var minimumCost = new Uint16Array(limit); /** @type {!(Array.|Uint8Array)} */ var flag = new Uint8Array(limit); /** @type {!(Array.|Uint8Array)} */ var codeLength = new Uint8Array(symbols); /** @type {Array} */ var value = new Array(limit); /** @type {Array} */ var type = new Array(limit); /** @type {Array.} */ var currentPosition = new Array(limit); /** @type {number} */ var excess = (1 << limit) - symbols; /** @type {number} */ var half = 1 << limit - 1; /** @type {number} */ var i; /** @type {number} */ var j; /** @type {number} */ var t; /** @type {number} */ var weight; /** @type {number} */ var next; /** * @param {number} j */ function takePackage(j) { /** @type {number} */ var x = type[j][currentPosition[j]]; if (x === symbols) { takePackage(j + 1); takePackage(j + 1); } else { --codeLength[x]; } ++currentPosition[j]; } minimumCost[limit - 1] = symbols; for (j = 0; j < limit; ++j) { if (excess < half) { flag[j] = 0; } else { flag[j] = 1; excess -= half; } excess <<= 1; minimumCost[limit - 2 - j] = (minimumCost[limit - 1 - j] / 2 | 0) + symbols; } minimumCost[0] = flag[0]; value[0] = new Array(minimumCost[0]); type[0] = new Array(minimumCost[0]); for (j = 1; j < limit; ++j) { if (minimumCost[j] > 2 * minimumCost[j - 1] + flag[j]) { minimumCost[j] = 2 * minimumCost[j - 1] + flag[j]; } value[j] = new Array(minimumCost[j]); type[j] = new Array(minimumCost[j]); } for (i = 0; i < symbols; ++i) { codeLength[i] = limit; } for (t = 0; t < minimumCost[limit - 1]; ++t) { value[limit - 1][t] = freqs[t]; type[limit - 1][t] = t; } for (i = 0; i < limit; ++i) { currentPosition[i] = 0; } if (flag[limit - 1] === 1) { --codeLength[0]; ++currentPosition[limit - 1]; } for (j = limit - 2; j >= 0; --j) { i = 0; weight = 0; next = currentPosition[j + 1]; for (t = 0; t < minimumCost[j]; t++) { weight = value[j + 1][next] + value[j + 1][next + 1]; if (weight > freqs[i]) { value[j][t] = weight; type[j][t] = symbols; next += 2; } else { value[j][t] = freqs[i]; type[j][t] = i; ++i; } } currentPosition[j] = 0; if (flag[j] === 1) { takePackage(j); } } return codeLength; }; /** * 符号長配列からハフマン符号を取得する * reference: PuTTY Deflate implementation * @param {!(Array.|Uint8Array)} lengths 符号長配列. * @return {!(Array.|Uint16Array)} ハフマン符号配列. * @private */ Zlib.RawDeflate.prototype.getCodesFromLengths_ = function (lengths) { var codes = new Uint16Array(lengths.length), count = [], startCode = [], code = 0, i, il, j, m; // Count the codes of each length. for (i = 0, il = lengths.length; i < il; i++) { count[lengths[i]] = (count[lengths[i]] | 0) + 1; } // Determine the starting code for each length block. for (i = 1, il = Zlib.RawDeflate.MaxCodeLength; i <= il; i++) { startCode[i] = code; code += count[i] | 0; code <<= 1; } // Determine the code for each symbol. Mirrored, of course. for (i = 0, il = lengths.length; i < il; i++) { code = startCode[lengths[i]]; startCode[lengths[i]] += 1; codes[i] = 0; for (j = 0, m = lengths[i]; j < m; j++) { codes[i] = codes[i] << 1 | code & 1; code >>>= 1; } } return codes; }; /** * @param {!(Array.|Uint8Array)} input input buffer. * @param {Object=} opt_params options. * @constructor */ Zlib.Unzip = function (input, opt_params) { opt_params = opt_params || {}; /** @type {!(Array.|Uint8Array)} */ this.input = input instanceof Array ? new Uint8Array(input) : input; /** @type {number} */ this.ip = 0; /** @type {number} */ this.eocdrOffset; /** @type {number} */ this.numberOfThisDisk; /** @type {number} */ this.startDisk; /** @type {number} */ this.totalEntriesThisDisk; /** @type {number} */ this.totalEntries; /** @type {number} */ this.centralDirectorySize; /** @type {number} */ this.centralDirectoryOffset; /** @type {number} */ this.commentLength; /** @type {(Array.|Uint8Array)} */ this.comment; /** @type {Array.} */ this.fileHeaderList; /** @type {Object.} */ this.filenameToIndex; /** @type {boolean} */ this.verify = opt_params['verify'] || false; /** @type {(Array.|Uint8Array)} */ this.password = opt_params['password']; }; Zlib.Unzip.CompressionMethod = Zlib.Zip.CompressionMethod; /** * @type {Array.} * @const */ Zlib.Unzip.FileHeaderSignature = Zlib.Zip.FileHeaderSignature; /** * @type {Array.} * @const */ Zlib.Unzip.LocalFileHeaderSignature = Zlib.Zip.LocalFileHeaderSignature; /** * @type {Array.} * @const */ Zlib.Unzip.CentralDirectorySignature = Zlib.Zip.CentralDirectorySignature; /** * @param {!(Array.|Uint8Array)} input input buffer. * @param {number} ip input position. * @constructor */ Zlib.Unzip.FileHeader = function (input, ip) { /** @type {!(Array.|Uint8Array)} */ this.input = input; /** @type {number} */ this.offset = ip; /** @type {number} */ this.length; /** @type {number} */ this.version; /** @type {number} */ this.os; /** @type {number} */ this.needVersion; /** @type {number} */ this.flags; /** @type {number} */ this.compression; /** @type {number} */ this.time; /** @type {number} */ this.date; /** @type {number} */ this.crc32; /** @type {number} */ this.compressedSize; /** @type {number} */ this.plainSize; /** @type {number} */ this.fileNameLength; /** @type {number} */ this.extraFieldLength; /** @type {number} */ this.fileCommentLength; /** @type {number} */ this.diskNumberStart; /** @type {number} */ this.internalFileAttributes; /** @type {number} */ this.externalFileAttributes; /** @type {number} */ this.relativeOffset; /** @type {string} */ this.filename; /** @type {!(Array.|Uint8Array)} */ this.extraField; /** @type {!(Array.|Uint8Array)} */ this.comment; }; Zlib.Unzip.FileHeader.prototype.parse = function () { /** @type {!(Array.|Uint8Array)} */ var input = this.input; /** @type {number} */ var ip = this.offset; // central file header signature if (input[ip++] !== Zlib.Unzip.FileHeaderSignature[0] || input[ip++] !== Zlib.Unzip.FileHeaderSignature[1] || input[ip++] !== Zlib.Unzip.FileHeaderSignature[2] || input[ip++] !== Zlib.Unzip.FileHeaderSignature[3]) { throw new Error('invalid file header signature'); } // version made by this.version = input[ip++]; this.os = input[ip++]; // version needed to extract this.needVersion = input[ip++] | input[ip++] << 8; // general purpose bit flag this.flags = input[ip++] | input[ip++] << 8; // compression method this.compression = input[ip++] | input[ip++] << 8; // last mod file time this.time = input[ip++] | input[ip++] << 8; //last mod file date this.date = input[ip++] | input[ip++] << 8; // crc-32 this.crc32 = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // compressed size this.compressedSize = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // uncompressed size this.plainSize = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // file name length this.fileNameLength = input[ip++] | input[ip++] << 8; // extra field length this.extraFieldLength = input[ip++] | input[ip++] << 8; // file comment length this.fileCommentLength = input[ip++] | input[ip++] << 8; // disk number start this.diskNumberStart = input[ip++] | input[ip++] << 8; // internal file attributes this.internalFileAttributes = input[ip++] | input[ip++] << 8; // external file attributes this.externalFileAttributes = input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24; // relative offset of local header this.relativeOffset = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // file name this.filename = String.fromCharCode.apply(null, input.subarray(ip, ip += this.fileNameLength)); // extra field this.extraField = input.subarray(ip, ip += this.extraFieldLength); // file comment this.comment = input.subarray(ip, ip + this.fileCommentLength); this.length = ip - this.offset; }; /** * @param {!(Array.|Uint8Array)} input input buffer. * @param {number} ip input position. * @constructor */ Zlib.Unzip.LocalFileHeader = function (input, ip) { /** @type {!(Array.|Uint8Array)} */ this.input = input; /** @type {number} */ this.offset = ip; /** @type {number} */ this.length; /** @type {number} */ this.needVersion; /** @type {number} */ this.flags; /** @type {number} */ this.compression; /** @type {number} */ this.time; /** @type {number} */ this.date; /** @type {number} */ this.crc32; /** @type {number} */ this.compressedSize; /** @type {number} */ this.plainSize; /** @type {number} */ this.fileNameLength; /** @type {number} */ this.extraFieldLength; /** @type {string} */ this.filename; /** @type {!(Array.|Uint8Array)} */ this.extraField; }; Zlib.Unzip.LocalFileHeader.Flags = Zlib.Zip.Flags; Zlib.Unzip.LocalFileHeader.prototype.parse = function () { /** @type {!(Array.|Uint8Array)} */ var input = this.input; /** @type {number} */ var ip = this.offset; // local file header signature if (input[ip++] !== Zlib.Unzip.LocalFileHeaderSignature[0] || input[ip++] !== Zlib.Unzip.LocalFileHeaderSignature[1] || input[ip++] !== Zlib.Unzip.LocalFileHeaderSignature[2] || input[ip++] !== Zlib.Unzip.LocalFileHeaderSignature[3]) { throw new Error('invalid local file header signature'); } // version needed to extract this.needVersion = input[ip++] | input[ip++] << 8; // general purpose bit flag this.flags = input[ip++] | input[ip++] << 8; // compression method this.compression = input[ip++] | input[ip++] << 8; // last mod file time this.time = input[ip++] | input[ip++] << 8; //last mod file date this.date = input[ip++] | input[ip++] << 8; // crc-32 this.crc32 = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // compressed size this.compressedSize = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // uncompressed size this.plainSize = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // file name length this.fileNameLength = input[ip++] | input[ip++] << 8; // extra field length this.extraFieldLength = input[ip++] | input[ip++] << 8; // file name this.filename = String.fromCharCode.apply(null, input.subarray(ip, ip += this.fileNameLength)); // extra field this.extraField = input.subarray(ip, ip += this.extraFieldLength); this.length = ip - this.offset; }; Zlib.Unzip.prototype.searchEndOfCentralDirectoryRecord = function () { /** @type {!(Array.|Uint8Array)} */ var input = this.input; /** @type {number} */ var ip; for (ip = input.length - 12; ip > 0; --ip) { if (input[ip] === Zlib.Unzip.CentralDirectorySignature[0] && input[ip + 1] === Zlib.Unzip.CentralDirectorySignature[1] && input[ip + 2] === Zlib.Unzip.CentralDirectorySignature[2] && input[ip + 3] === Zlib.Unzip.CentralDirectorySignature[3]) { this.eocdrOffset = ip; return; } } throw new Error('End of Central Directory Record not found'); }; Zlib.Unzip.prototype.parseEndOfCentralDirectoryRecord = function () { /** @type {!(Array.|Uint8Array)} */ var input = this.input; /** @type {number} */ var ip; if (!this.eocdrOffset) { this.searchEndOfCentralDirectoryRecord(); } ip = this.eocdrOffset; // signature if (input[ip++] !== Zlib.Unzip.CentralDirectorySignature[0] || input[ip++] !== Zlib.Unzip.CentralDirectorySignature[1] || input[ip++] !== Zlib.Unzip.CentralDirectorySignature[2] || input[ip++] !== Zlib.Unzip.CentralDirectorySignature[3]) { throw new Error('invalid signature'); } // number of this disk this.numberOfThisDisk = input[ip++] | input[ip++] << 8; // number of the disk with the start of the central directory this.startDisk = input[ip++] | input[ip++] << 8; // total number of entries in the central directory on this disk this.totalEntriesThisDisk = input[ip++] | input[ip++] << 8; // total number of entries in the central directory this.totalEntries = input[ip++] | input[ip++] << 8; // size of the central directory this.centralDirectorySize = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // offset of start of central directory with respect to the starting disk number this.centralDirectoryOffset = (input[ip++] | input[ip++] << 8 | input[ip++] << 16 | input[ip++] << 24) >>> 0; // .ZIP file comment length this.commentLength = input[ip++] | input[ip++] << 8; // .ZIP file comment this.comment = input.subarray(ip, ip + this.commentLength); }; Zlib.Unzip.prototype.parseFileHeader = function () { /** @type {Array.} */ var filelist = []; /** @type {Object.} */ var filetable = {}; /** @type {number} */ var ip; /** @type {Zlib.Unzip.FileHeader} */ var fileHeader; /*: @type {number} */ var i; /*: @type {number} */ var il; if (this.fileHeaderList) { return; } if (this.centralDirectoryOffset === void 0) { this.parseEndOfCentralDirectoryRecord(); } ip = this.centralDirectoryOffset; for (i = 0, il = this.totalEntries; i < il; ++i) { fileHeader = new Zlib.Unzip.FileHeader(this.input, ip); fileHeader.parse(); ip += fileHeader.length; filelist[i] = fileHeader; filetable[fileHeader.filename] = i; } if (this.centralDirectorySize < ip - this.centralDirectoryOffset) { throw new Error('invalid file header size'); } this.fileHeaderList = filelist; this.filenameToIndex = filetable; }; /** * @param {number} index file header index. * @param {Object=} opt_params * @return {!(Array.|Uint8Array)} file data. */ Zlib.Unzip.prototype.getFileData = function (index, opt_params) { opt_params = opt_params || {}; /** @type {!(Array.|Uint8Array)} */ var input = this.input; /** @type {Array.} */ var fileHeaderList = this.fileHeaderList; /** @type {Zlib.Unzip.LocalFileHeader} */ var localFileHeader; /** @type {number} */ var offset; /** @type {number} */ var length; /** @type {!(Array.|Uint8Array)} */ var buffer; /** @type {number} */ var crc32; /** @type {Array.|Uint32Array|Object} */ var key; /** @type {number} */ var i; /** @type {number} */ var il; if (!fileHeaderList) { this.parseFileHeader(); } if (fileHeaderList[index] === void 0) { throw new Error('wrong index'); } offset = fileHeaderList[index].relativeOffset; localFileHeader = new Zlib.Unzip.LocalFileHeader(this.input, offset); localFileHeader.parse(); offset += localFileHeader.length; length = localFileHeader.compressedSize; // decryption if ((localFileHeader.flags & Zlib.Unzip.LocalFileHeader.Flags.ENCRYPT) !== 0) { if (!(opt_params['password'] || this.password)) { throw new Error('please set password'); } key = this.createDecryptionKey(opt_params['password'] || this.password); // encryption header for (i = offset, il = offset + 12; i < il; ++i) { this.decode(key, input[i]); } offset += 12; length -= 12; // decryption for (i = offset, il = offset + length; i < il; ++i) { input[i] = this.decode(key, input[i]); } } switch (localFileHeader.compression) { case Zlib.Unzip.CompressionMethod.STORE: buffer = this.input.subarray(offset, offset + length); break; case Zlib.Unzip.CompressionMethod.DEFLATE: buffer = new Zlib.RawInflate(this.input, { 'index': offset, 'bufferSize': localFileHeader.plainSize }).decompress(); break; default: throw new Error('unknown compression type'); } if (this.verify) { crc32 = Zlib.CRC32.calc(buffer); if (localFileHeader.crc32 !== crc32) { throw new Error('wrong crc: file=0x' + localFileHeader.crc32.toString(16) + ', data=0x' + crc32.toString(16)); } } return buffer; }; /** * @return {Array.} */ Zlib.Unzip.prototype.getFilenames = function () { /** @type {Array.} */ var filenameList = []; /** @type {number} */ var i; /** @type {number} */ var il; /** @type {Array.} */ var fileHeaderList; if (!this.fileHeaderList) { this.parseFileHeader(); } fileHeaderList = this.fileHeaderList; for (i = 0, il = fileHeaderList.length; i < il; ++i) { filenameList[i] = fileHeaderList[i].filename; } return filenameList; }; /** * @param {string} filename extract filename. * @param {Object=} opt_params * @return {!(Array.|Uint8Array)} decompressed data. */ Zlib.Unzip.prototype.decompress = function (filename, opt_params) { /** @type {number} */ var index; if (!this.filenameToIndex) { this.parseFileHeader(); } index = this.filenameToIndex[filename]; if (index === void 0) { throw new Error(filename + ' not found'); } return this.getFileData(index, opt_params); }; /** * @param {(Array.|Uint8Array)} password */ Zlib.Unzip.prototype.setPassword = function (password) { this.password = password; }; /** * @param {(Array.|Uint32Array|Object)} key * @param {number} n * @return {number} */ Zlib.Unzip.prototype.decode = function (key, n) { n ^= this.getByte(key); this.updateKeys(key, n); return n; }; // common method Zlib.Unzip.prototype.updateKeys = Zlib.Zip.prototype.updateKeys; Zlib.Unzip.prototype.createDecryptionKey = Zlib.Zip.prototype.createEncryptionKey; Zlib.Unzip.prototype.getByte = Zlib.Zip.prototype.getByte; /** * @fileoverview 雑多な関数群をまとめたモジュール実装. */ /** * Byte String から Byte Array に変換. * @param {!string} str byte string. * @return {!Array.} byte array. */ Zlib.Util.stringToByteArray = function (str) { /** @type {!Array.<(string|number)>} */ var tmp = str.split(''); /** @type {number} */ var i; /** @type {number} */ var il; for (i = 0, il = tmp.length; i < il; i++) { tmp[i] = (tmp[i].charCodeAt(0) & 0xff) >>> 0; } return tmp; }; /** * @fileoverview Adler32 checksum 実装. */ /** * Adler32 ハッシュ値の作成 * @param {!(Array|Uint8Array|string)} array 算出に使用する byte array. * @return {number} Adler32 ハッシュ値. */ Zlib.Adler32 = function (array) { if (typeof array === 'string') { array = Zlib.Util.stringToByteArray(array); } return Zlib.Adler32.update(1, array); }; /** * Adler32 ハッシュ値の更新 * @param {number} adler 現在のハッシュ値. * @param {!(Array|Uint8Array)} array 更新に使用する byte array. * @return {number} Adler32 ハッシュ値. */ Zlib.Adler32.update = function (adler, array) { /** @type {number} */ var s1 = adler & 0xffff; /** @type {number} */ var s2 = adler >>> 16 & 0xffff; /** @type {number} array length */ var len = array.length; /** @type {number} loop length (don't overflow) */ var tlen; /** @type {number} array index */ var i = 0; while (len > 0) { tlen = len > Zlib.Adler32.OptimizationParameter ? Zlib.Adler32.OptimizationParameter : len; len -= tlen; do { s1 += array[i++]; s2 += s1; } while (--tlen); s1 %= 65521; s2 %= 65521; } return (s2 << 16 | s1) >>> 0; }; /** * Adler32 最適化パラメータ * 現状では 1024 程度が最適. * @see http://jsperf.com/adler-32-simple-vs-optimized/3 * @define {number} */ Zlib.Adler32.OptimizationParameter = 1024; /** * ビットストリーム* @constructor * @param {!(Array|Uint8Array)=} buffer output buffer. * @param {number=} bufferPosition start buffer pointer. */ Zlib.BitStream = function (buffer, bufferPosition) { /** @type {number} buffer index. */ this.index = typeof bufferPosition === 'number' ? bufferPosition : 0; /** @type {number} bit index. */ this.bitindex = 0; /** @type {!(Array|Uint8Array)} bit-stream output buffer. */ this.buffer = buffer instanceof Uint8Array ? buffer : new Uint8Array(Zlib.BitStream.DefaultBlockSize); // 入力された index が足りなかったら拡張するが、倍にしてもダメなら不正とする if (this.buffer.length * 2 <= this.index) { throw new Error("invalid index"); } else if (this.buffer.length <= this.index) { this.expandBuffer(); } }; /** * デフォルトブロックサイズ. * @const * @type {number} */ Zlib.BitStream.DefaultBlockSize = 0x8000; /** * expand buffer. * @return {!(Array|Uint8Array)} new buffer. */ Zlib.BitStream.prototype.expandBuffer = function () { /** @type {!(Array|Uint8Array)} old buffer. */ var oldbuf = this.buffer; /** @type {number} loop limiter. */ var il = oldbuf.length; /** @type {!(Array|Uint8Array)} new buffer. */ var buffer = new Uint8Array(il << 1); // copy buffer { buffer.set(oldbuf); } return this.buffer = buffer; }; /** * 数値をビットで指定した数だけ書き込む. * @param {number} number 書き込む数値. * @param {number} n 書き込むビット数. * @param {boolean=} reverse é€†é †ã«æ›¸ãè¾¼ã‚€ãªã‚‰ã° true. */ Zlib.BitStream.prototype.writeBits = function (number, n, reverse) { var buffer = this.buffer; var index = this.index; var bitindex = this.bitindex; /** @type {number} current octet. */ var current = buffer[index]; /** @type {number} loop counter. */ var i; /** * 32-bit æ•´æ•°ã®ãƒ“ãƒƒãƒˆé †ã‚’é€†ã«ã™ã‚‹ * @param {number} n 32-bit integer. * @return {number} reversed 32-bit integer. * @private */ function rev32_(n) { return Zlib.BitStream.ReverseTable[n & 0xFF] << 24 | Zlib.BitStream.ReverseTable[n >>> 8 & 0xFF] << 16 | Zlib.BitStream.ReverseTable[n >>> 16 & 0xFF] << 8 | Zlib.BitStream.ReverseTable[n >>> 24 & 0xFF]; } if (reverse && n > 1) { number = n > 8 ? rev32_(number) >> 32 - n : Zlib.BitStream.ReverseTable[number] >> 8 - n; } // Byte 境界を超えないとき if (n + bitindex < 8) { current = current << n | number; bitindex += n; // Byte 境界を超えるとき } else { for (i = 0; i < n; ++i) { current = current << 1 | number >> n - i - 1 & 1; // next byte if (++bitindex === 8) { bitindex = 0; buffer[index++] = Zlib.BitStream.ReverseTable[current]; current = 0; // expand if (index === buffer.length) { buffer = this.expandBuffer(); } } } } buffer[index] = current; this.buffer = buffer; this.bitindex = bitindex; this.index = index; }; /** * ストリームの終端処理を行う * @return {!(Array|Uint8Array)} 終端処理後のバッファを byte array で返す. */ Zlib.BitStream.prototype.finish = function () { var buffer = this.buffer; var index = this.index; /** @type {!(Array|Uint8Array)} output buffer. */ var output; // bitindex が 0 の時は余分に index が進んでいる状態 if (this.bitindex > 0) { buffer[index] <<= 8 - this.bitindex; buffer[index] = Zlib.BitStream.ReverseTable[buffer[index]]; index++; } // array truncation { output = buffer.subarray(0, index); } return output; }; /** * 0-255 ã®ãƒ“ãƒƒãƒˆé †ã‚’åè»¢ã—ãŸãƒ†ãƒ¼ãƒ–ãƒ« * @const * @type {!(Uint8Array|Array.)} */ Zlib.BitStream.ReverseTable = function (table) { return table; }(function () { /** @type {!(Array|Uint8Array)} reverse table. */ var table = new Uint8Array(256); /** @type {number} loop counter. */ var i; // generate for (i = 0; i < 256; ++i) { table[i] = function (n) { var r = n; var s = 7; for (n >>>= 1; n; n >>>= 1) { r <<= 1; r |= n & 1; --s; } return (r << s & 0xff) >>> 0; }(i); } return table; }()); /** * CRC32 ハッシュ値を取得 * @param {!(Array.|Uint8Array)} data data byte array. * @param {number=} pos data position. * @param {number=} length data length. * @return {number} CRC32. */ Zlib.CRC32.calc = function (data, pos, length) { return Zlib.CRC32.update(data, 0, pos, length); }; /** * CRC32ハッシュ値を更新 * @param {!(Array.|Uint8Array)} data data byte array. * @param {number} crc CRC32. * @param {number=} pos data position. * @param {number=} length data length. * @return {number} CRC32. */ Zlib.CRC32.update = function (data, crc, pos, length) { var table = Zlib.CRC32.Table; var i = typeof pos === 'number' ? pos : pos = 0; var il = typeof length === 'number' ? length : data.length; crc ^= 0xffffffff; // loop unrolling for performance for (i = il & 7; i--; ++pos) { crc = crc >>> 8 ^ table[(crc ^ data[pos]) & 0xff]; } for (i = il >> 3; i--; pos += 8) { crc = crc >>> 8 ^ table[(crc ^ data[pos]) & 0xff]; crc = crc >>> 8 ^ table[(crc ^ data[pos + 1]) & 0xff]; crc = crc >>> 8 ^ table[(crc ^ data[pos + 2]) & 0xff]; crc = crc >>> 8 ^ table[(crc ^ data[pos + 3]) & 0xff]; crc = crc >>> 8 ^ table[(crc ^ data[pos + 4]) & 0xff]; crc = crc >>> 8 ^ table[(crc ^ data[pos + 5]) & 0xff]; crc = crc >>> 8 ^ table[(crc ^ data[pos + 6]) & 0xff]; crc = crc >>> 8 ^ table[(crc ^ data[pos + 7]) & 0xff]; } return (crc ^ 0xffffffff) >>> 0; }; /** * @param {number} num * @param {number} crc * @returns {number} */ Zlib.CRC32.single = function (num, crc) { return (Zlib.CRC32.Table[(num ^ crc) & 0xff] ^ num >>> 8) >>> 0; }; /** * @type {Array.} * @const * @private */ Zlib.CRC32.Table_ = [0x00000000, 0x77073096, 0xee0e612c, 0x990951ba, 0x076dc419, 0x706af48f, 0xe963a535, 0x9e6495a3, 0x0edb8832, 0x79dcb8a4, 0xe0d5e91e, 0x97d2d988, 0x09b64c2b, 0x7eb17cbd, 0xe7b82d07, 0x90bf1d91, 0x1db71064, 0x6ab020f2, 0xf3b97148, 0x84be41de, 0x1adad47d, 0x6ddde4eb, 0xf4d4b551, 0x83d385c7, 0x136c9856, 0x646ba8c0, 0xfd62f97a, 0x8a65c9ec, 0x14015c4f, 0x63066cd9, 0xfa0f3d63, 0x8d080df5, 0x3b6e20c8, 0x4c69105e, 0xd56041e4, 0xa2677172, 0x3c03e4d1, 0x4b04d447, 0xd20d85fd, 0xa50ab56b, 0x35b5a8fa, 0x42b2986c, 0xdbbbc9d6, 0xacbcf940, 0x32d86ce3, 0x45df5c75, 0xdcd60dcf, 0xabd13d59, 0x26d930ac, 0x51de003a, 0xc8d75180, 0xbfd06116, 0x21b4f4b5, 0x56b3c423, 0xcfba9599, 0xb8bda50f, 0x2802b89e, 0x5f058808, 0xc60cd9b2, 0xb10be924, 0x2f6f7c87, 0x58684c11, 0xc1611dab, 0xb6662d3d, 0x76dc4190, 0x01db7106, 0x98d220bc, 0xefd5102a, 0x71b18589, 0x06b6b51f, 0x9fbfe4a5, 0xe8b8d433, 0x7807c9a2, 0x0f00f934, 0x9609a88e, 0xe10e9818, 0x7f6a0dbb, 0x086d3d2d, 0x91646c97, 0xe6635c01, 0x6b6b51f4, 0x1c6c6162, 0x856530d8, 0xf262004e, 0x6c0695ed, 0x1b01a57b, 0x8208f4c1, 0xf50fc457, 0x65b0d9c6, 0x12b7e950, 0x8bbeb8ea, 0xfcb9887c, 0x62dd1ddf, 0x15da2d49, 0x8cd37cf3, 0xfbd44c65, 0x4db26158, 0x3ab551ce, 0xa3bc0074, 0xd4bb30e2, 0x4adfa541, 0x3dd895d7, 0xa4d1c46d, 0xd3d6f4fb, 0x4369e96a, 0x346ed9fc, 0xad678846, 0xda60b8d0, 0x44042d73, 0x33031de5, 0xaa0a4c5f, 0xdd0d7cc9, 0x5005713c, 0x270241aa, 0xbe0b1010, 0xc90c2086, 0x5768b525, 0x206f85b3, 0xb966d409, 0xce61e49f, 0x5edef90e, 0x29d9c998, 0xb0d09822, 0xc7d7a8b4, 0x59b33d17, 0x2eb40d81, 0xb7bd5c3b, 0xc0ba6cad, 0xedb88320, 0x9abfb3b6, 0x03b6e20c, 0x74b1d29a, 0xead54739, 0x9dd277af, 0x04db2615, 0x73dc1683, 0xe3630b12, 0x94643b84, 0x0d6d6a3e, 0x7a6a5aa8, 0xe40ecf0b, 0x9309ff9d, 0x0a00ae27, 0x7d079eb1, 0xf00f9344, 0x8708a3d2, 0x1e01f268, 0x6906c2fe, 0xf762575d, 0x806567cb, 0x196c3671, 0x6e6b06e7, 0xfed41b76, 0x89d32be0, 0x10da7a5a, 0x67dd4acc, 0xf9b9df6f, 0x8ebeeff9, 0x17b7be43, 0x60b08ed5, 0xd6d6a3e8, 0xa1d1937e, 0x38d8c2c4, 0x4fdff252, 0xd1bb67f1, 0xa6bc5767, 0x3fb506dd, 0x48b2364b, 0xd80d2bda, 0xaf0a1b4c, 0x36034af6, 0x41047a60, 0xdf60efc3, 0xa867df55, 0x316e8eef, 0x4669be79, 0xcb61b38c, 0xbc66831a, 0x256fd2a0, 0x5268e236, 0xcc0c7795, 0xbb0b4703, 0x220216b9, 0x5505262f, 0xc5ba3bbe, 0xb2bd0b28, 0x2bb45a92, 0x5cb36a04, 0xc2d7ffa7, 0xb5d0cf31, 0x2cd99e8b, 0x5bdeae1d, 0x9b64c2b0, 0xec63f226, 0x756aa39c, 0x026d930a, 0x9c0906a9, 0xeb0e363f, 0x72076785, 0x05005713, 0x95bf4a82, 0xe2b87a14, 0x7bb12bae, 0x0cb61b38, 0x92d28e9b, 0xe5d5be0d, 0x7cdcefb7, 0x0bdbdf21, 0x86d3d2d4, 0xf1d4e242, 0x68ddb3f8, 0x1fda836e, 0x81be16cd, 0xf6b9265b, 0x6fb077e1, 0x18b74777, 0x88085ae6, 0xff0f6a70, 0x66063bca, 0x11010b5c, 0x8f659eff, 0xf862ae69, 0x616bffd3, 0x166ccf45, 0xa00ae278, 0xd70dd2ee, 0x4e048354, 0x3903b3c2, 0xa7672661, 0xd06016f7, 0x4969474d, 0x3e6e77db, 0xaed16a4a, 0xd9d65adc, 0x40df0b66, 0x37d83bf0, 0xa9bcae53, 0xdebb9ec5, 0x47b2cf7f, 0x30b5ffe9, 0xbdbdf21c, 0xcabac28a, 0x53b39330, 0x24b4a3a6, 0xbad03605, 0xcdd70693, 0x54de5729, 0x23d967bf, 0xb3667a2e, 0xc4614ab8, 0x5d681b02, 0x2a6f2b94, 0xb40bbe37, 0xc30c8ea1, 0x5a05df1b, 0x2d02ef8d]; /** * @type {!(Array.|Uint32Array)} CRC-32 Table. * @const */ Zlib.CRC32.Table = new Uint32Array(Zlib.CRC32.Table_); /** * @fileoverview Deflate (RFC1951) 実装. * Deflateアルゴリズム本体は Zlib.RawDeflate で実装されている. */ /** * Zlib Deflate * @constructor * @param {!(Array|Uint8Array)} input 符号化する対象の byte array. * @param {Object=} opt_params option parameters. */ Zlib.Deflate = function (input, opt_params) { /** @type {!(Array|Uint8Array)} */ this.input = input; /** @type {!(Array|Uint8Array)} */ this.output = new Uint8Array(Zlib.Deflate.DefaultBufferSize); /** @type {Zlib.Deflate.CompressionType} */ this.compressionType = Zlib.Deflate.CompressionType.DYNAMIC; /** @type {Zlib.RawDeflate} */ this.rawDeflate; /** @type {Object} */ var rawDeflateOption = {}; /** @type {string} */ var prop; // option parameters if (opt_params || !(opt_params = {})) { if (typeof opt_params['compressionType'] === 'number') { this.compressionType = opt_params['compressionType']; } } // copy options for (prop in opt_params) { rawDeflateOption[prop] = opt_params[prop]; } // set raw-deflate output buffer rawDeflateOption['outputBuffer'] = this.output; this.rawDeflate = new Zlib.RawDeflate(this.input, rawDeflateOption); }; /** * @const * @type {number} デフォルトバッファサイズ. */ Zlib.Deflate.DefaultBufferSize = 0x8000; /** * @enum {number} */ Zlib.Deflate.CompressionType = Zlib.RawDeflate.CompressionType; /** * 直接圧縮に掛ける. * @param {!(Array|Uint8Array)} input target buffer. * @param {Object=} opt_params option parameters. * @return {!(Array|Uint8Array)} compressed data byte array. */ Zlib.Deflate.compress = function (input, opt_params) { return new Zlib.Deflate(input, opt_params).compress(); }; /** * Deflate Compression. * @return {!(Array|Uint8Array)} compressed data byte array. */ Zlib.Deflate.prototype.compress = function () { /** @type {Zlib.CompressionMethod} */ var cm; /** @type {number} */ var cinfo; /** @type {number} */ var cmf; /** @type {number} */ var flg; /** @type {number} */ var fcheck; /** @type {number} */ var fdict; /** @type {number} */ var flevel; /** @type {number} */ var adler; /** @type {!(Array|Uint8Array)} */ var output; /** @type {number} */ var pos = 0; output = this.output; // Compression Method and Flags cm = Zlib.CompressionMethod.DEFLATE; switch (cm) { case Zlib.CompressionMethod.DEFLATE: cinfo = Math.LOG2E * Math.log(Zlib.RawDeflate.WindowSize) - 8; break; default: throw new Error('invalid compression method'); } cmf = cinfo << 4 | cm; output[pos++] = cmf; // Flags fdict = 0; switch (cm) { case Zlib.CompressionMethod.DEFLATE: switch (this.compressionType) { case Zlib.Deflate.CompressionType.NONE: flevel = 0; break; case Zlib.Deflate.CompressionType.FIXED: flevel = 1; break; case Zlib.Deflate.CompressionType.DYNAMIC: flevel = 2; break; default: throw new Error('unsupported compression type'); } break; default: throw new Error('invalid compression method'); } flg = flevel << 6 | fdict << 5; fcheck = 31 - (cmf * 256 + flg) % 31; flg |= fcheck; output[pos++] = flg; // Adler-32 checksum adler = Zlib.Adler32(this.input); this.rawDeflate.op = pos; output = this.rawDeflate.compress(); pos = output.length; { // subarray 分を元にもどす output = new Uint8Array(output.buffer); // expand buffer if (output.length <= pos + 4) { this.output = new Uint8Array(output.length + 4); this.output.set(output); output = this.output; } output = output.subarray(0, pos + 4); } // adler32 output[pos++] = adler >> 24 & 0xff; output[pos++] = adler >> 16 & 0xff; output[pos++] = adler >> 8 & 0xff; output[pos++] = adler & 0xff; return output; }; // %23 %24 %25 %26 %27 %28 %29 %2A %2B %2C %2F %3A %3B %3D %3F %40 %5B %5D const encodings = new Map(); encodings.set("!", "%21"); encodings.set("#", "%23"); encodings.set("$", "%24"); encodings.set("%", "%25"); encodings.set("&", "%26"); encodings.set("'", "%27"); encodings.set("(", "%28"); encodings.set(")", "%29"); encodings.set("*", "%2A"); encodings.set("+", "%2B"); encodings.set(",", "%2C"); encodings.set("/", "%2F"); encodings.set(":", "%3A"); encodings.set(";", "%3B"); encodings.set("=", "%3D"); encodings.set("?", "%3F"); encodings.set("@", "%40"); encodings.set("[", "%5B"); encodings.set("]", "%5D"); encodings.set(" ", "%20"); if (typeof process === 'object' && typeof window === 'undefined') { global.atob = function (str) { return Buffer.from(str, 'base64').toString('binary'); }; } /** * Make the target element movable by clicking and dragging on the handle. This is not a general purprose function, * it makes several options specific to igv dialogs, the primary one being that the * target is absolutely positioned in pixel coordinates */ let dragData; // Its assumed we are only dragging one element at a time. function makeDraggable(target, handle) { handle.addEventListener('mousedown', dragStart.bind(target)); } function dragStart(event) { event.stopPropagation(); event.preventDefault(); offset(this); const dragFunction = drag.bind(this); const dragEndFunction = dragEnd.bind(this); const computedStyle = getComputedStyle(this); const top = parseInt(computedStyle.top.replace("px", "")); const left = parseInt(computedStyle.left.replace("px", "")); dragData = { dragFunction: dragFunction, dragEndFunction: dragEndFunction, screenX: event.screenX, screenY: event.screenY, top: top, left: left }; document.addEventListener('mousemove', dragFunction); document.addEventListener('mouseup', dragEndFunction); document.addEventListener('mouseleave', dragEndFunction); document.addEventListener('mouseexit', dragEndFunction); } function drag(event) { if (!dragData) { return; } event.stopPropagation(); event.preventDefault(); const dx = event.screenX - dragData.screenX; const dy = event.screenY - dragData.screenY; this.style.left = `${dragData.left + dx}px`; this.style.top = `${dragData.top + dy}px`; } function dragEnd(event) { if (!dragData) { return; } event.stopPropagation(); event.preventDefault(); const dragFunction = dragData.dragFunction; const dragEndFunction = dragData.dragEndFunction; document.removeEventListener('mousemove', dragFunction); document.removeEventListener('mouseup', dragEndFunction); document.removeEventListener('mouseleave', dragEndFunction); document.removeEventListener('mouseexit', dragEndFunction); dragData = undefined; } const appleCrayonPalette = { licorice: "#000000", lead: "#1e1e1e", tungsten: "#3a3a3a", iron: "#545453", steel: "#6e6e6e", tin: "#878687", nickel: "#888787", aluminum: "#a09fa0", magnesium: "#b8b8b8", silver: "#d0d0d0", mercury: "#e8e8e8", snow: "#ffffff", // cayenne: "#891100", mocha: "#894800", aspargus: "#888501", fern: "#458401", clover: "#028401", moss: "#018448", teal: "#008688", ocean: "#004a88", midnight: "#001888", eggplant: "#491a88", plum: "#891e88", maroon: "#891648", // maraschino: "#ff2101", tangerine: "#ff8802", lemon: "#fffa03", lime: "#83f902", spring: "#05f802", seam_foam: "#03f987", turquoise: "#00fdff", aqua: "#008cff", blueberry: "#002eff", grape: "#8931ff", magenta: "#ff39ff", strawberry: "#ff2987", // salmon: "#ff726e", cantaloupe: "#ffce6e", banana: "#fffb6d", honeydew: "#cefa6e", flora: "#68f96e", spindrift: "#68fbd0", ice: "#68fdff", sky: "#6acfff", orchid: "#6e76ff", lavender: "#d278ff", bubblegum: "#ff7aff", carnation: "#ff7fd3" }; // The MIT License (MIT) /** * @constructor * @param {Object} options A set op options to pass to the throttle function * @param {number} requestsPerSecond The amount of requests per second * the library will limit to */ class Throttle { constructor(options) { this.requestsPerSecond = options.requestsPerSecond || 10; this.lastStartTime = 0; this.queued = []; } /** * Adds a promise * @param {Function} async function to be executed * @param {Object} options A set of options. * @return {Promise} A promise */ add(asyncFunction, options) { var self = this; return new Promise(function (resolve, reject) { self.queued.push({ resolve: resolve, reject: reject, asyncFunction: asyncFunction }); self.dequeue(); }); } /** * Adds all the promises passed as parameters * @param {Function} promises An array of functions that return a promise * @param {Object} options A set of options. * @param {number} options.signal An AbortSignal object that can be used to abort the returned promise * @param {number} options.weight A "weight" of each operation resolving by array of promises * @return {Promise} A promise that succeeds when all the promises passed as options do */ addAll(promises, options) { var addedPromises = promises.map(function (promise) { return this.add(promise, options); }.bind(this)); return Promise.all(addedPromises); } /** * Dequeues a promise * @return {void} */ dequeue() { if (this.queued.length > 0) { var now = new Date(), inc = 1000 / this.requestsPerSecond + 1, elapsed = now - this.lastStartTime; if (elapsed >= inc) { this._execute(); } else { // we have reached the limit, schedule a dequeue operation setTimeout(function () { this.dequeue(); }.bind(this), inc - elapsed); } } } /** * Executes the promise * @private * @return {void} */ async _execute() { this.lastStartTime = new Date(); var candidate = this.queued.shift(); const f = candidate.asyncFunction; try { const r = await f(); candidate.resolve(r); } catch (e) { candidate.reject(e); } } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ new Throttle({ requestsPerSecond: 8 }); const httpMessages = { "401": "Access unauthorized", "403": "Access forbidden", "404": "Not found" }; class AlertDialog { constructor(parent) { // container this.container = div({ class: "igv-ui-alert-dialog-container" }); parent.appendChild(this.container); this.container.setAttribute('tabIndex', '-1'); // header const header = div(); this.container.appendChild(header); this.errorHeadline = div(); header.appendChild(this.errorHeadline); this.errorHeadline.textContent = ''; // body container let bodyContainer = div({ id: 'igv-ui-alert-dialog-body' }); this.container.appendChild(bodyContainer); // body copy this.body = div({ id: 'igv-ui-alert-dialog-body-copy' }); bodyContainer.appendChild(this.body); // ok container let ok_container = div(); this.container.appendChild(ok_container); // ok this.ok = div(); ok_container.appendChild(this.ok); this.ok.textContent = 'OK'; const okHandler = () => { if (typeof this.callback === 'function') { this.callback("OK"); this.callback = undefined; } this.body.innerHTML = ''; hide(this.container); }; this.ok.addEventListener('click', event => { event.stopPropagation(); okHandler(); }); this.container.addEventListener('keypress', event => { event.stopPropagation(); if ('Enter' === event.key) { okHandler(); } }); makeDraggable(this.container, header); hide(this.container); } present(alert, callback) { this.errorHeadline.textContent = alert.message ? 'ERROR' : ''; let string = alert.message || alert; if (httpMessages.hasOwnProperty(string)) { string = httpMessages[string]; } this.body.innerHTML = string; this.callback = callback; show(this.container); this.container.focus(); } } let alertDialog; const Alert = { init(root) { if (!alertDialog) { alertDialog = new AlertDialog(root); } }, presentAlert(alert, callback) { if (!alertDialog) { this.init(document.body); } alertDialog.present(alert, callback); } }; class InputDialog { constructor(parent) { this.parent = parent; // dialog container this.container = div({ class: 'igv-ui-generic-dialog-container' }); parent.appendChild(this.container); // const { x, y, width, height } = this.container.getBoundingClientRect(); // console.log(`InputDialog - x ${ x } y ${ y } width ${ width } height ${ height }`) // dialog header const header = div({ class: 'igv-ui-generic-dialog-header' }); this.container.appendChild(header); // dialog label this.label = div({ class: 'igv-ui-generic-dialog-one-liner' }); this.container.appendChild(this.label); this.label.text = 'Unlabeled'; // input container this.input_container = div({ class: 'igv-ui-generic-dialog-input' }); this.container.appendChild(this.input_container); // this.input = document.createElement("input"); this.input_container.appendChild(this.input); // ok | cancel const buttons = div({ class: 'igv-ui-generic-dialog-ok-cancel' }); this.container.appendChild(buttons); // ok this.ok = div(); buttons.appendChild(this.ok); this.ok.textContent = 'OK'; // cancel this.cancel = div(); buttons.appendChild(this.cancel); this.cancel.textContent = 'Cancel'; hide(this.container); this.input.addEventListener('keyup', e => { if (13 === e.keyCode) { if (typeof this.callback === 'function') { this.callback(this.input.value); this.callback = undefined; } this.input.value = undefined; hide(this.container); } }); this.ok.addEventListener('click', () => { if (typeof this.callback === 'function') { this.callback(this.input.value); this.callback = undefined; } this.input.value = undefined; hide(this.container); }); const cancel = () => { this.input.value = ''; hide(this.container); }; this.cancel.addEventListener('click', cancel); attachDialogCloseHandlerWithParent(header, cancel); makeDraggable(this.container, header); } present(options, e) { this.label.textContent = options.label; this.input.value = options.value; this.callback = options.callback || options.click; show(this.container); const { x, y } = pageCoordinates(e); this.clampLocation(x, y); } clampLocation(pageX, pageY) { const { width: w, height: h } = this.container.getBoundingClientRect(); const { x: px, y: py, width: pw, height: ph } = this.parent.getBoundingClientRect(); const y = Math.min(Math.max(pageY, py), py + ph - h); const x = Math.min(Math.max(pageX, px), px + pw - w); this.container.style.left = `${x}px`; this.container.style.top = `${y}px`; } } class GenericContainer { constructor({ parent, top, left, width, height, border, closeHandler }) { let container = div({ class: 'igv-ui-generic-container' }); parent.appendChild(container); hide(container); this.container = container; if (top !== undefined) { this.container.style.top = `${top}px`; } if (left !== undefined) { this.container.style.left = `${left}px`; } if (width !== undefined) { this.container.style.width = `${width}px`; } if (height !== undefined) { this.container.style.height = `${height}px`; } if (border) { this.container.style.border = border; } // // let bbox = parent.getBoundingClientRect(); // this.origin = {x: bbox.x, y: bbox.y}; // this.container.offset({left: this.origin.x, top: this.origin.y}); // header const header = div(); this.container.appendChild(header); // close button attachDialogCloseHandlerWithParent(header, e => { hide(this.container); if (typeof closeHandler === "function") { closeHandler(e); } }); makeDraggable(this.container, header); } show() { show(this.container); } hide() { hide(this.container); } dispose() { if (this.container.parent) { this.container.parent.removeChild(this.container); } } } class ColorPicker extends GenericContainer { constructor({ parent, top, left, width, height, defaultColors, colorHandler }) { super({ parent, top, left, width, height, border: '1px solid gray' }); createColorSwatchSelector(this.container, colorHandler, defaultColors); } } const createColorSwatchSelector = (container, colorHandler, defaultColors) => { const hexColorStrings = Object.values(appleCrayonPalette); for (let hexColorString of hexColorStrings) { const swatch = div({ class: 'igv-ui-color-swatch' }); container.appendChild(swatch); decorateSwatch(swatch, hexColorString, colorHandler); } if (defaultColors) { for (let hexColorString of defaultColors) { const swatch = div({ class: 'igv-ui-color-swatch' }); container.appendChild(swatch); decorateSwatch(swatch, hexColorString, colorHandler); } } }; const decorateSwatch = (swatch, hexColorString, colorHandler) => { swatch.style.backgroundColor = hexColorString; swatch.addEventListener('mouseenter', e => swatch.style.borderColor = hexColorString); swatch.addEventListener('mouseleave', e => swatch.style.borderColor = 'white'); swatch.addEventListener('click', event => { event.stopPropagation(); colorHandler(hexColorString); }); swatch.addEventListener('touchend', event => { event.stopPropagation(); colorHandler(hexColorString); }); }; class Popover { constructor(parent, title) { this.parent = parent; // popover this.popover = div({ class: "igv-ui-popover" }); parent.appendChild(this.popover); // header const popoverHeader = div(); this.popover.appendChild(popoverHeader); const titleElement = div(); popoverHeader.appendChild(titleElement); if (title) { titleElement.textContent = title; } attachDialogCloseHandlerWithParent(popoverHeader, () => this.hide()); makeDraggable(this.popover, popoverHeader); // content this.popoverContent = div(); this.popover.appendChild(this.popoverContent); this.popover.style.display = 'none'; } presentContentWithEvent(e, content) { this.popover.style.display = 'block'; this.popoverContent.innerHTML = content; present$1(e, this.popover); } presentMenu(e, menuItems) { if (0 === menuItems.length) { return; } this.popover.style.display = 'block'; const menuElements = createMenuElements$1(menuItems, this.popover); for (let item of menuElements) { this.popoverContent.appendChild(item.object); } present$1(e, this.popover); } hide() { this.popover.style.display = 'none'; this.dispose(); } dispose() { if (this.popover) { this.popover.parentNode.removeChild(this.popover); } const keys = Object.keys(this); for (let key of keys) { this[key] = undefined; } } } function present$1(e, popover) { const { x, y } = translateMouseCoordinates(e, popover.parentNode); // parent bbox const { width } = popover.parentNode.getBoundingClientRect(); const { width: w } = popover.getBoundingClientRect(); const xmax = x + w; popover.style.left = `${xmax > width ? x - (xmax - width) : x}px`; popover.style.top = `${y}px`; } function createMenuElements$1(itemList, popover) { const list = itemList.map(function (item, i) { let elem; if (typeof item === 'string') { elem = div(); elem.innerHTML = item; } else if (typeof item === 'Node') { elem = item; } else { if (typeof item.init === 'function') { item.init(); } if ("checkbox" === item.type) { elem = createCheckbox("Show all bases", item.value); } else if ("color" === item.type) { const colorPicker = new ColorPicker({ parent: popover.parentElement, width: 364, //defaultColor: 'aqua', colorHandler: color => item.click(color) }); elem = div(); if (typeof item.label === 'string') { elem.innerHTML = item.label; } const clickHandler = e => { colorPicker.show(); hide(popover); e.preventDefault(); e.stopPropagation(); }; elem.addEventListener('click', clickHandler); elem.addEventListener('touchend', clickHandler); elem.addEventListener('mouseup', function (e) { e.preventDefault(); e.stopPropagation(); }); } else { elem = div(); if (typeof item.label === 'string') { elem.innerHTML = item.label; } } if (item.click && "color" !== item.type) { elem.addEventListener('click', handleClick); elem.addEventListener('touchend', handleClick); elem.addEventListener('mouseup', function (e) { e.preventDefault(); e.stopPropagation(); }); // eslint-disable-next-line no-inner-declarations function handleClick(e) { item.click(); hide(popover); e.preventDefault(); e.stopPropagation(); } } } return { object: elem, init: item.init }; }); return list; } function embedCSS$1() { var css = '.igv-ui-popover {\n cursor: default;\n position: absolute;\n z-index: 2048;\n border-color: #7F7F7F;\n border-radius: 4px;\n border-style: solid;\n border-width: 1px;\n font-family: \"Open Sans\", sans-serif;\n font-size: small;\n background-color: white; }\n .igv-ui-popover > div:first-child {\n display: flex;\n flex-direction: row;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee; }\n .igv-ui-popover > div:first-child > div:first-child {\n margin-left: 4px; }\n .igv-ui-popover > div:first-child > div:last-child {\n margin-right: 4px;\n height: 12px;\n width: 12px;\n color: #7F7F7F; }\n .igv-ui-popover > div:first-child > div:last-child:hover {\n cursor: pointer;\n color: #444; }\n .igv-ui-popover > div:last-child {\n overflow-y: auto;\n overflow-x: hidden;\n max-height: 400px;\n max-width: 1500px;\n background-color: white; }\n .igv-ui-popover > div:last-child > div {\n -webkit-user-select: all;\n /* Chrome/Safari */\n -moz-user-select: all;\n /* Firefox */\n margin-left: 4px;\n margin-right: 4px;\n min-width: 220px;\n overflow-x: hidden;\n text-overflow: ellipsis;\n white-space: nowrap; }\n .igv-ui-popover > div:last-child > div > span {\n font-weight: bolder; }\n .igv-ui-popover > div:last-child hr {\n width: 100%; }\n\n.igv-ui-alert-dialog-container {\n box-sizing: content-box;\n position: absolute;\n z-index: 2048;\n top: 50%;\n left: 50%;\n width: 400px;\n height: 200px;\n border-color: #7F7F7F;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n outline: none;\n font-family: \"Open Sans\", sans-serif;\n font-size: 15px;\n font-weight: 400;\n background-color: white;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: space-between;\n align-items: center; }\n .igv-ui-alert-dialog-container > div:first-child {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee; }\n .igv-ui-alert-dialog-container > div:first-child div:first-child {\n padding-left: 8px; }\n .igv-ui-alert-dialog-container #igv-ui-alert-dialog-body {\n color: #373737;\n width: 100%;\n height: calc(100% - 24px - 64px);\n overflow-y: scroll; }\n .igv-ui-alert-dialog-container #igv-ui-alert-dialog-body #igv-ui-alert-dialog-body-copy {\n cursor: pointer;\n margin: 16px;\n width: auto;\n height: auto;\n overflow-wrap: break-word;\n word-break: break-word;\n background-color: white;\n border: unset; }\n .igv-ui-alert-dialog-container > div:last-child {\n width: 100%;\n margin-bottom: 10px;\n background-color: white;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: center;\n align-items: center; }\n .igv-ui-alert-dialog-container > div:last-child div {\n margin: unset;\n width: 40px;\n height: 30px;\n line-height: 30px;\n text-align: center;\n color: white;\n font-family: \"Open Sans\", sans-serif;\n font-size: small;\n font-weight: 400;\n border-color: #2B81AF;\n border-style: solid;\n border-width: thin;\n border-radius: 4px;\n background-color: #2B81AF; }\n .igv-ui-alert-dialog-container > div:last-child div:hover {\n cursor: pointer;\n border-color: #25597f;\n background-color: #25597f; }\n\n.igv-ui-color-swatch {\n position: relative;\n box-sizing: content-box;\n display: flex;\n flex-flow: row;\n flex-wrap: wrap;\n justify-content: center;\n align-items: center;\n width: 32px;\n height: 32px;\n border-style: solid;\n border-width: 2px;\n border-color: white;\n border-radius: 4px; }\n\n.igv-ui-color-swatch:hover {\n border-color: dimgray; }\n\n.igv-ui-colorpicker-menu-close-button {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n width: 100%;\n height: 32px;\n margin-top: 4px;\n margin-bottom: 4px;\n padding-right: 8px; }\n .igv-ui-colorpicker-menu-close-button i.fa {\n display: block;\n margin-left: 4px;\n margin-right: 4px;\n color: #5f5f5f; }\n .igv-ui-colorpicker-menu-close-button i.fa:hover,\n .igv-ui-colorpicker-menu-close-button i.fa:focus,\n .igv-ui-colorpicker-menu-close-button i.fa:active {\n cursor: pointer;\n color: #0f0f0f; }\n\n.igv-ui-generic-dialog-container {\n box-sizing: content-box;\n position: fixed;\n top: 0;\n left: 0;\n width: 300px;\n height: 200px;\n border-color: #7F7F7F;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n font-family: \"Open Sans\", sans-serif;\n font-size: medium;\n font-weight: 400;\n z-index: 2048;\n background-color: white;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-header {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-header div {\n margin-right: 4px;\n margin-bottom: 2px;\n height: 12px;\n width: 12px;\n color: #7F7F7F; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-header div:hover {\n cursor: pointer;\n color: #444; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-one-liner {\n color: #373737;\n width: 95%;\n height: 24px;\n line-height: 24px;\n text-align: left;\n margin-top: 8px;\n padding-left: 8px;\n overflow-wrap: break-word;\n background-color: white; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input {\n margin-top: 8px;\n width: 95%;\n height: 24px;\n color: #373737;\n line-height: 24px;\n padding-left: 8px;\n background-color: white;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-start;\n align-items: center; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input div {\n width: 30%;\n height: 100%;\n font-size: 16px;\n text-align: right;\n padding-right: 8px;\n background-color: white; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input input {\n display: block;\n height: 100%;\n width: 100%;\n padding-left: 4px;\n font-family: \"Open Sans\", sans-serif;\n font-weight: 400;\n color: #373737;\n text-align: left;\n outline: none;\n border-style: solid;\n border-width: thin;\n border-color: #7F7F7F;\n background-color: white; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-label-input input {\n width: 50%;\n font-size: 16px; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-input {\n margin-top: 8px;\n width: calc(100% - 16px);\n height: 24px;\n color: #373737;\n line-height: 24px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input {\n display: block;\n height: 100%;\n width: 100%;\n padding-left: 4px;\n font-family: \"Open Sans\", sans-serif;\n font-weight: 400;\n color: #373737;\n text-align: left;\n outline: none;\n border-style: solid;\n border-width: thin;\n border-color: #7F7F7F;\n background-color: white; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-input input {\n font-size: 16px; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel {\n width: 100%;\n height: 28px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div {\n margin-top: 32px;\n color: white;\n font-family: \"Open Sans\", sans-serif;\n font-size: 14px;\n font-weight: 400;\n width: 75px;\n height: 28px;\n line-height: 28px;\n text-align: center;\n border-color: transparent;\n border-style: solid;\n border-width: thin;\n border-radius: 2px; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div:first-child {\n margin-left: 32px;\n margin-right: 0;\n background-color: #5ea4e0; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div:last-child {\n margin-left: 0;\n margin-right: 32px;\n background-color: #c4c4c4; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div:first-child:hover {\n cursor: pointer;\n background-color: #3b5c7f; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok-cancel div:last-child:hover {\n cursor: pointer;\n background-color: #7f7f7f; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok {\n width: 100%;\n height: 36px;\n margin-top: 32px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok div {\n width: 98px;\n height: 36px;\n line-height: 36px;\n text-align: center;\n color: white;\n font-family: \"Open Sans\", sans-serif;\n font-size: medium;\n font-weight: 400;\n border-color: white;\n border-style: solid;\n border-width: thin;\n border-radius: 4px;\n background-color: #2B81AF; }\n .igv-ui-generic-dialog-container .igv-ui-generic-dialog-ok div:hover {\n cursor: pointer;\n background-color: #25597f; }\n\n.igv-ui-generic-container {\n box-sizing: content-box;\n position: absolute;\n z-index: 2048;\n background-color: white;\n cursor: pointer;\n display: flex;\n flex-direction: row;\n flex-wrap: wrap;\n justify-content: flex-start;\n align-items: center; }\n .igv-ui-generic-container div:first-child {\n cursor: move;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n height: 24px;\n width: 100%;\n background-color: #dddddd; }\n .igv-ui-generic-container div:first-child div {\n display: block;\n color: #5f5f5f;\n cursor: pointer;\n width: 14px;\n height: 14px;\n margin-right: 8px;\n margin-bottom: 4px; }\n\n.igv-ui-dialog {\n z-index: 2048;\n position: fixed;\n width: fit-content;\n height: fit-content;\n display: flex;\n flex-flow: column;\n flex-wrap: nowrap;\n justify-content: flex-start;\n background-color: white;\n border-color: #7F7F7F;\n border-radius: 4px;\n border-style: solid;\n border-width: thin;\n font-family: \"Open Sans\", sans-serif;\n font-size: medium;\n font-weight: 400; }\n .igv-ui-dialog .igv-ui-dialog-header {\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: flex-end;\n align-items: center;\n width: 100%;\n height: 24px;\n cursor: move;\n border-top-left-radius: 4px;\n border-top-right-radius: 4px;\n border-bottom-color: #7F7F7F;\n border-bottom-style: solid;\n border-bottom-width: thin;\n background-color: #eee; }\n .igv-ui-dialog .igv-ui-dialog-header div {\n margin-right: 4px;\n margin-bottom: 2px;\n height: 12px;\n width: 12px;\n color: #7F7F7F; }\n .igv-ui-dialog .igv-ui-dialog-header div:hover {\n cursor: pointer;\n color: #444; }\n .igv-ui-dialog .igv-ui-dialog-one-liner {\n width: 95%;\n height: 24px;\n line-height: 24px;\n text-align: left;\n margin: 8px;\n overflow-wrap: break-word;\n background-color: white;\n font-weight: bold; }\n .igv-ui-dialog .igv-ui-dialog-ok-cancel {\n width: 100%;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center; }\n .igv-ui-dialog .igv-ui-dialog-ok-cancel div {\n margin: 16px;\n margin-top: 32px;\n color: white;\n font-family: \"Open Sans\", sans-serif;\n font-size: 14px;\n font-weight: 400;\n width: 75px;\n height: 28px;\n line-height: 28px;\n text-align: center;\n border-color: transparent;\n border-style: solid;\n border-width: thin;\n border-radius: 2px; }\n .igv-ui-dialog .igv-ui-dialog-ok-cancel div:first-child {\n background-color: #5ea4e0; }\n .igv-ui-dialog .igv-ui-dialog-ok-cancel div:last-child {\n background-color: #c4c4c4; }\n .igv-ui-dialog .igv-ui-dialog-ok-cancel div:first-child:hover {\n cursor: pointer;\n background-color: #3b5c7f; }\n .igv-ui-dialog .igv-ui-dialog-ok-cancel div:last-child:hover {\n cursor: pointer;\n background-color: #7f7f7f; }\n .igv-ui-dialog .igv-ui-dialog-ok {\n width: 100%;\n height: 36px;\n margin-top: 32px;\n display: flex;\n flex-flow: row;\n flex-wrap: nowrap;\n justify-content: space-around;\n align-items: center; }\n .igv-ui-dialog .igv-ui-dialog-ok div {\n width: 98px;\n height: 36px;\n line-height: 36px;\n text-align: center;\n color: white;\n font-family: \"Open Sans\", sans-serif;\n font-size: medium;\n font-weight: 400;\n border-color: white;\n border-style: solid;\n border-width: thin;\n border-radius: 4px;\n background-color: #2B81AF; }\n .igv-ui-dialog .igv-ui-dialog-ok div:hover {\n cursor: pointer;\n background-color: #25597f; }\n\n.igv-ui-panel, .igv-ui-panel-column, .igv-ui-panel-row {\n z-index: 2048;\n background-color: white;\n font-family: \"Open Sans\", sans-serif;\n font-size: medium;\n font-weight: 400;\n display: flex;\n justify-content: flex-start;\n align-items: flex-start; }\n\n.igv-ui-panel-column {\n display: flex;\n flex-direction: column; }\n\n.igv-ui-panel-row {\n display: flex;\n flex-direction: row; }\n\n.igv-ui-textbox {\n background-color: white;\n font-family: \"Open Sans\", sans-serif;\n font-size: medium;\n font-weight: 400;\n display: flex;\n justify-content: flex-start;\n align-items: flex-start; }\n\n/*# sourceMappingURL=igv-ui.css.map */\n'; var style = document.createElement('style'); style.setAttribute('type', 'text/css'); style.innerHTML = css; document.head.insertBefore(style, document.head.childNodes[document.head.childNodes.length - 1]); } if (typeof document !== 'undefined') { if (!stylesheetExists("igv-ui.css")) { // console.log('igv-ui. will call embedCSS() ...'); embedCSS$1(); // console.log('... done.'); } function stylesheetExists(stylesheetName) { for (let ss of document.styleSheets) { ss = ss.href ? ss.href.replace(/^.*[\\\/]/, '') : ''; if (ss === stylesheetName) { return true; } } return false; } } /* * The MIT License (MIT) * * Copyright (c) 2016-2017 The Regents of the University of California * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ class DataRangeDialog { constructor($parent, alert) { // dialog container this.$container = $("
", { class: 'igv-generic-dialog-container' }); $parent.append(this.$container); this.$container.offset({ left: 0, top: 0 }); // dialog header const $header = $("
", { class: 'igv-generic-dialog-header' }); this.$container.append($header); attachDialogCloseHandlerWithParent$1($header[0], () => { this.$minimum_input.val(undefined); this.$maximum_input.val(undefined); this.$container.offset({ left: 0, top: 0 }); this.$container.hide(); }); // minimun this.$minimum = $("
", { class: 'igv-generic-dialog-label-input' }); this.$container.append(this.$minimum); const $mindiv = $('
'); $mindiv.text('Minimum'); this.$minimum.append($mindiv); this.$minimum_input = $(""); this.$minimum.append(this.$minimum_input); // maximum this.$maximum = $("
", { class: 'igv-generic-dialog-label-input' }); this.$container.append(this.$maximum); const $maxdiv = $('
'); $maxdiv.text('Maximum'); this.$maximum.append($maxdiv); this.$maximum_input = $(""); this.$maximum.append(this.$maximum_input); // ok | cancel const $buttons = $("
", { class: 'igv-generic-dialog-ok-cancel' }); this.$container.append($buttons); // ok this.$ok = $("
"); $buttons.append(this.$ok); this.$ok.text('OK'); // cancel this.$cancel = $("
"); $buttons.append(this.$cancel); this.$cancel.text('Cancel'); this.$cancel.on('click', () => { this.$minimum_input.val(undefined); this.$maximum_input.val(undefined); this.$container.offset({ left: 0, top: 0 }); this.$container.hide(); }); //this.$container.draggable({ handle:$header.get(0) }); makeDraggable$1(this.$container.get(0), $header.get(0)); this.$container.hide(); } configure(trackView) { const dataRange = trackView.dataRange(); let min; let max; if (dataRange) { min = dataRange.min; max = dataRange.max; } else { min = 0; max = 100; } this.$minimum_input.val(min); this.$maximum_input.val(max); this.$minimum_input.unbind(); this.$minimum_input.on('keyup', e => { if (13 === e.keyCode) { this.processResults(trackView); } }); this.$maximum_input.unbind(); this.$maximum_input.on('keyup', e => { if (13 === e.keyCode) { this.processResults(trackView); } }); this.$ok.unbind(); this.$ok.on('click', e => { this.processResults(trackView); }); } processResults(trackView) { const min = parseFloat(this.$minimum_input.val()); const max = parseFloat(this.$maximum_input.val()); if (isNaN(min) || isNaN(max)) { Alert.presentAlert(new Error('Must input numeric values'), undefined); } else { trackView.setDataRange(min, max); } this.$minimum_input.val(undefined); this.$maximum_input.val(undefined); this.$container.offset({ left: 0, top: 0 }); this.$container.hide(); } present($parent) { const offset_top = $parent.offset().top; const scroll_top = $('body').scrollTop(); this.$container.offset({ left: $parent.width() - this.$container.width(), top: offset_top + scroll_top }); this.$container.show(); } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of ctx software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and ctx permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const IGVGraphics = { configureHighDPICanvas: function (ctx, w, h) { const scaleFactor = window.devicePixelRatio; // const scaleFactor = 1 ctx.canvas.style.width = `${w}px`; ctx.canvas.width = Math.floor(scaleFactor * w); ctx.canvas.style.height = `${h}px`; ctx.canvas.height = Math.floor(scaleFactor * h); ctx.scale(scaleFactor, scaleFactor); }, setProperties: function (ctx, properties) { for (var key in properties) { if (properties.hasOwnProperty(key)) { var value = properties[key]; ctx[key] = value; } } }, strokeLine: function (ctx, x1, y1, x2, y2, properties) { x1 = Math.floor(x1) + 0.5; y1 = Math.floor(y1) + 0.5; x2 = Math.floor(x2) + 0.5; y2 = Math.floor(y2) + 0.5; if (properties) { ctx.save(); IGVGraphics.setProperties(ctx, properties); } ctx.beginPath(); ctx.moveTo(x1, y1); ctx.lineTo(x2, y2); ctx.stroke(); if (properties) ctx.restore(); }, fillRect: function (ctx, x, y, w, h, properties) { x = Math.round(x); y = Math.round(y); if (properties) { ctx.save(); IGVGraphics.setProperties(ctx, properties); } ctx.fillRect(x, y, w, h); if (properties) ctx.restore(); }, fillPolygon: function (ctx, x, y, properties) { if (properties) { ctx.save(); IGVGraphics.setProperties(ctx, properties); } doPath(ctx, x, y); ctx.fill(); if (properties) ctx.restore(); }, strokePolygon: function (ctx, x, y, properties) { if (properties) { ctx.save(); IGVGraphics.setProperties(ctx, properties); } doPath(ctx, x, y); ctx.stroke(); if (properties) ctx.restore(); }, fillText: function (ctx, text, x, y, properties, transforms) { if (properties || transforms) { ctx.save(); } if (properties) { IGVGraphics.setProperties(ctx, properties); } if (transforms) { // Slow path with context saving and extra translate ctx.translate(x, y); for (var transform in transforms) { var value = transforms[transform]; // TODO: Add error checking for robustness if (transform === 'translate') { ctx.translate(value['x'], value['y']); } if (transform === 'rotate') { ctx.rotate(value['angle'] * Math.PI / 180); } } ctx.fillText(text, 0, 0); } else { ctx.fillText(text, x, y); } if (properties || transforms) ctx.restore(); }, strokeText: function (ctx, text, x, y, properties, transforms) { if (properties || transforms) { ctx.save(); } if (properties) { IGVGraphics.setProperties(ctx, properties); } if (transforms) { ctx.translate(x, y); for (var transform in transforms) { var value = transforms[transform]; // TODO: Add error checking for robustness if (transform === 'translate') { ctx.translate(value['x'], value['y']); } if (transform === 'rotate') { ctx.rotate(value['angle'] * Math.PI / 180); } } ctx.strokeText(text, 0, 0); } else { ctx.strokeText(text, x, y); } if (properties || transforms) ctx.restore(); }, strokeCircle: function (ctx, x, y, radius, properties) { if (properties) { ctx.save(); IGVGraphics.setProperties(ctx, properties); } ctx.beginPath(); ctx.arc(x, y, radius, 0, 2 * Math.PI); ctx.stroke(); if (properties) ctx.restore(); }, fillCircle: function (ctx, x, y, radius, properties) { if (properties) { ctx.save(); IGVGraphics.setProperties(ctx, properties); } ctx.beginPath(); ctx.arc(x, y, radius, 0, 2 * Math.PI); ctx.fill(); if (properties) ctx.restore(); }, drawArrowhead: function (ctx, x, y, size, lineWidth) { ctx.save(); if (!size) { size = 5; } if (lineWidth) { ctx.lineWidth = lineWidth; } ctx.beginPath(); ctx.moveTo(x, y - size / 2); ctx.lineTo(x, y + size / 2); ctx.lineTo(x + size, y); ctx.lineTo(x, y - size / 2); ctx.closePath(); ctx.fill(); ctx.restore(); }, dashedLine: function (ctx, x1, y1, x2, y2, dashLen, properties = {}) { if (dashLen === undefined) dashLen = 2; ctx.setLineDash([dashLen, dashLen]); IGVGraphics.strokeLine(ctx, x1, y1, x2, y2, properties); ctx.setLineDash([]); }, roundRect: function (ctx, x, y, width, height, radius, fill, stroke) { if (typeof stroke == "undefined") { stroke = true; } if (typeof radius === "undefined") { radius = 5; } ctx.beginPath(); ctx.moveTo(x + radius, y); ctx.lineTo(x + width - radius, y); ctx.quadraticCurveTo(x + width, y, x + width, y + radius); ctx.lineTo(x + width, y + height - radius); ctx.quadraticCurveTo(x + width, y + height, x + width - radius, y + height); ctx.lineTo(x + radius, y + height); ctx.quadraticCurveTo(x, y + height, x, y + height - radius); ctx.lineTo(x, y + radius); ctx.quadraticCurveTo(x, y, x + radius, y); ctx.closePath(); if (stroke) { ctx.stroke(); } if (fill) { ctx.fill(); } }, polygon: function (ctx, x, y, fill, stroke) { if (typeof stroke == "undefined") { stroke = true; } ctx.beginPath(); var len = x.length; ctx.moveTo(x[0], y[0]); for (var i = 1; i < len; i++) { ctx.lineTo(x[i], y[i]); // this.moveTo(x[i], y[i]); } ctx.closePath(); if (stroke) { ctx.stroke(); } if (fill) { ctx.fill(); } } }; function doPath(ctx, x, y) { var i, len = x.length; for (i = 0; i < len; i++) { x[i] = Math.round(x[i]); y[i] = Math.round(y[i]); } ctx.beginPath(); ctx.moveTo(x[0], y[0]); for (i = 1; i < len; i++) { ctx.lineTo(x[i], y[i]); } ctx.closePath(); } // eslint-disable-next-line es/no-typed-arrays -- safe var arrayBufferNative = typeof ArrayBuffer !== 'undefined' && typeof DataView !== 'undefined'; var fails = function (exec) { try { return !!exec(); } catch (error) { return true; } }; var descriptors = !fails(function () { // eslint-disable-next-line es/no-object-defineproperty -- required for testing return Object.defineProperty({}, 1, { get: function () { return 7; } })[1] != 7; }); var commonjsGlobal = typeof globalThis !== 'undefined' ? globalThis : typeof window !== 'undefined' ? window : typeof global !== 'undefined' ? global : typeof self !== 'undefined' ? self : {}; function createCommonjsModule(fn) { var module = { exports: {} }; return fn(module, module.exports), module.exports; } var check = function (it) { return it && it.Math == Math && it; }; // https://github.com/zloirock/core-js/issues/86#issuecomment-115759028 var global$1 = // eslint-disable-next-line es/no-global-this -- safe check(typeof globalThis == 'object' && globalThis) || check(typeof window == 'object' && window) || // eslint-disable-next-line no-restricted-globals -- safe check(typeof self == 'object' && self) || check(typeof commonjsGlobal == 'object' && commonjsGlobal) || // eslint-disable-next-line no-new-func -- fallback function () { return this; }() || Function('return this')(); var isObject = function (it) { return typeof it === 'object' ? it !== null : typeof it === 'function'; }; // `RequireObjectCoercible` abstract operation // https://tc39.es/ecma262/#sec-requireobjectcoercible var requireObjectCoercible = function (it) { if (it == undefined) throw TypeError("Can't call method on " + it); return it; }; // https://tc39.es/ecma262/#sec-toobject var toObject = function (argument) { return Object(requireObjectCoercible(argument)); }; var hasOwnProperty = {}.hasOwnProperty; var has$1 = Object.hasOwn || function hasOwn(it, key) { return hasOwnProperty.call(toObject(it), key); }; var document$1 = global$1.document; // typeof document.createElement is 'object' in old IE var EXISTS = isObject(document$1) && isObject(document$1.createElement); var documentCreateElement = function (it) { return EXISTS ? document$1.createElement(it) : {}; }; var ie8DomDefine = !descriptors && !fails(function () { // eslint-disable-next-line es/no-object-defineproperty -- requied for testing return Object.defineProperty(documentCreateElement('div'), 'a', { get: function () { return 7; } }).a != 7; }); var anObject = function (it) { if (!isObject(it)) { throw TypeError(String(it) + ' is not an object'); } return it; }; // https://tc39.es/ecma262/#sec-toprimitive // instead of the ES6 spec version, we didn't implement @@toPrimitive case // and the second argument - flag - preferred type is a string var toPrimitive = function (input, PREFERRED_STRING) { if (!isObject(input)) return input; var fn, val; if (PREFERRED_STRING && typeof (fn = input.toString) == 'function' && !isObject(val = fn.call(input))) return val; if (typeof (fn = input.valueOf) == 'function' && !isObject(val = fn.call(input))) return val; if (!PREFERRED_STRING && typeof (fn = input.toString) == 'function' && !isObject(val = fn.call(input))) return val; throw TypeError("Can't convert object to primitive value"); }; var $defineProperty = Object.defineProperty; // `Object.defineProperty` method // https://tc39.es/ecma262/#sec-object.defineproperty var f$4 = descriptors ? $defineProperty : function defineProperty(O, P, Attributes) { anObject(O); P = toPrimitive(P, true); anObject(Attributes); if (ie8DomDefine) try { return $defineProperty(O, P, Attributes); } catch (error) { /* empty */ } if ('get' in Attributes || 'set' in Attributes) throw TypeError('Accessors not supported'); if ('value' in Attributes) O[P] = Attributes.value; return O; }; var objectDefineProperty = { f: f$4 }; var createPropertyDescriptor = function (bitmap, value) { return { enumerable: !(bitmap & 1), configurable: !(bitmap & 2), writable: !(bitmap & 4), value: value }; }; var createNonEnumerableProperty = descriptors ? function (object, key, value) { return objectDefineProperty.f(object, key, createPropertyDescriptor(1, value)); } : function (object, key, value) { object[key] = value; return object; }; var setGlobal = function (key, value) { try { createNonEnumerableProperty(global$1, key, value); } catch (error) { global$1[key] = value; } return value; }; var SHARED = '__core-js_shared__'; var store$1 = global$1[SHARED] || setGlobal(SHARED, {}); var sharedStore = store$1; var shared = createCommonjsModule(function (module) { (module.exports = function (key, value) { return sharedStore[key] || (sharedStore[key] = value !== undefined ? value : {}); })('versions', []).push({ version: '3.15.2', mode: 'global', copyright: '© 2021 Denis Pushkarev (zloirock.ru)' }); }); var id = 0; var postfix = Math.random(); var uid = function (key) { return 'Symbol(' + String(key === undefined ? '' : key) + ')_' + (++id + postfix).toString(36); }; var path = global$1; var aFunction$1 = function (variable) { return typeof variable == 'function' ? variable : undefined; }; var getBuiltIn = function (namespace, method) { return arguments.length < 2 ? aFunction$1(path[namespace]) || aFunction$1(global$1[namespace]) : path[namespace] && path[namespace][method] || global$1[namespace] && global$1[namespace][method]; }; var engineUserAgent = getBuiltIn('navigator', 'userAgent') || ''; var process$2 = global$1.process; var versions = process$2 && process$2.versions; var v8 = versions && versions.v8; var match, version$1; if (v8) { match = v8.split('.'); version$1 = match[0] < 4 ? 1 : match[0] + match[1]; } else if (engineUserAgent) { match = engineUserAgent.match(/Edge\/(\d+)/); if (!match || match[1] >= 74) { match = engineUserAgent.match(/Chrome\/(\d+)/); if (match) version$1 = match[1]; } } var engineV8Version = version$1 && +version$1; /* eslint-disable es/no-symbol -- required for testing */ var nativeSymbol = !!Object.getOwnPropertySymbols && !fails(function () { var symbol = Symbol(); // Chrome 38 Symbol has incorrect toString conversion // `get-own-property-symbols` polyfill symbols converted to object are not Symbol instances return !String(symbol) || !(Object(symbol) instanceof Symbol) || // Chrome 38-40 symbols are not inherited from DOM collections prototypes to instances !Symbol.sham && engineV8Version && engineV8Version < 41; }); /* eslint-disable es/no-symbol -- required for testing */ var useSymbolAsUid = nativeSymbol && !Symbol.sham && typeof Symbol.iterator == 'symbol'; var WellKnownSymbolsStore = shared('wks'); var Symbol$1 = global$1.Symbol; var createWellKnownSymbol = useSymbolAsUid ? Symbol$1 : Symbol$1 && Symbol$1.withoutSetter || uid; var wellKnownSymbol = function (name) { if (!has$1(WellKnownSymbolsStore, name) || !(nativeSymbol || typeof WellKnownSymbolsStore[name] == 'string')) { if (nativeSymbol && has$1(Symbol$1, name)) { WellKnownSymbolsStore[name] = Symbol$1[name]; } else { WellKnownSymbolsStore[name] = createWellKnownSymbol('Symbol.' + name); } } return WellKnownSymbolsStore[name]; }; var TO_STRING_TAG$2 = wellKnownSymbol('toStringTag'); var test = {}; test[TO_STRING_TAG$2] = 'z'; var toStringTagSupport = String(test) === '[object z]'; var toString = {}.toString; var classofRaw = function (it) { return toString.call(it).slice(8, -1); }; var TO_STRING_TAG$1 = wellKnownSymbol('toStringTag'); // ES3 wrong here var CORRECT_ARGUMENTS = classofRaw(function () { return arguments; }()) == 'Arguments'; // fallback for IE11 Script Access Denied error var tryGet = function (it, key) { try { return it[key]; } catch (error) { /* empty */ } }; // getting tag from ES6+ `Object.prototype.toString` var classof = toStringTagSupport ? classofRaw : function (it) { var O, tag, result; return it === undefined ? 'Undefined' : it === null ? 'Null' // @@toStringTag case : typeof (tag = tryGet(O = Object(it), TO_STRING_TAG$1)) == 'string' ? tag // builtinTag case : CORRECT_ARGUMENTS ? classofRaw(O) // ES3 arguments fallback : (result = classofRaw(O)) == 'Object' && typeof O.callee == 'function' ? 'Arguments' : result; }; var functionToString = Function.toString; // this helper broken in `core-js@3.4.1-3.4.4`, so we can't use `shared` helper if (typeof sharedStore.inspectSource != 'function') { sharedStore.inspectSource = function (it) { return functionToString.call(it); }; } var inspectSource = sharedStore.inspectSource; var WeakMap$1 = global$1.WeakMap; var nativeWeakMap = typeof WeakMap$1 === 'function' && /native code/.test(inspectSource(WeakMap$1)); var keys = shared('keys'); var sharedKey = function (key) { return keys[key] || (keys[key] = uid(key)); }; var hiddenKeys$1 = {}; var OBJECT_ALREADY_INITIALIZED = 'Object already initialized'; var WeakMap = global$1.WeakMap; var set$1, get, has; var enforce = function (it) { return has(it) ? get(it) : set$1(it, {}); }; var getterFor = function (TYPE) { return function (it) { var state; if (!isObject(it) || (state = get(it)).type !== TYPE) { throw TypeError('Incompatible receiver, ' + TYPE + ' required'); } return state; }; }; if (nativeWeakMap || sharedStore.state) { var store = sharedStore.state || (sharedStore.state = new WeakMap()); var wmget = store.get; var wmhas = store.has; var wmset = store.set; set$1 = function (it, metadata) { if (wmhas.call(store, it)) throw new TypeError(OBJECT_ALREADY_INITIALIZED); metadata.facade = it; wmset.call(store, it, metadata); return metadata; }; get = function (it) { return wmget.call(store, it) || {}; }; has = function (it) { return wmhas.call(store, it); }; } else { var STATE = sharedKey('state'); hiddenKeys$1[STATE] = true; set$1 = function (it, metadata) { if (has$1(it, STATE)) throw new TypeError(OBJECT_ALREADY_INITIALIZED); metadata.facade = it; createNonEnumerableProperty(it, STATE, metadata); return metadata; }; get = function (it) { return has$1(it, STATE) ? it[STATE] : {}; }; has = function (it) { return has$1(it, STATE); }; } var internalState = { set: set$1, get: get, has: has, enforce: enforce, getterFor: getterFor }; var redefine = createCommonjsModule(function (module) { var getInternalState = internalState.get; var enforceInternalState = internalState.enforce; var TEMPLATE = String(String).split('String'); (module.exports = function (O, key, value, options) { var unsafe = options ? !!options.unsafe : false; var simple = options ? !!options.enumerable : false; var noTargetGet = options ? !!options.noTargetGet : false; var state; if (typeof value == 'function') { if (typeof key == 'string' && !has$1(value, 'name')) { createNonEnumerableProperty(value, 'name', key); } state = enforceInternalState(value); if (!state.source) { state.source = TEMPLATE.join(typeof key == 'string' ? key : ''); } } if (O === global$1) { if (simple) O[key] = value;else setGlobal(key, value); return; } else if (!unsafe) { delete O[key]; } else if (!noTargetGet && O[key]) { simple = true; } if (simple) O[key] = value;else createNonEnumerableProperty(O, key, value); // add fake Function#toString for correct work wrapped methods / constructors with methods like LoDash isNative })(Function.prototype, 'toString', function toString() { return typeof this == 'function' && getInternalState(this).source || inspectSource(this); }); }); var correctPrototypeGetter = !fails(function () { function F() { /* empty */ } F.prototype.constructor = null; // eslint-disable-next-line es/no-object-getprototypeof -- required for testing return Object.getPrototypeOf(new F()) !== F.prototype; }); var IE_PROTO = sharedKey('IE_PROTO'); var ObjectPrototype$1 = Object.prototype; // `Object.getPrototypeOf` method // https://tc39.es/ecma262/#sec-object.getprototypeof // eslint-disable-next-line es/no-object-getprototypeof -- safe var objectGetPrototypeOf = correctPrototypeGetter ? Object.getPrototypeOf : function (O) { O = toObject(O); if (has$1(O, IE_PROTO)) return O[IE_PROTO]; if (typeof O.constructor == 'function' && O instanceof O.constructor) { return O.constructor.prototype; } return O instanceof Object ? ObjectPrototype$1 : null; }; var aPossiblePrototype = function (it) { if (!isObject(it) && it !== null) { throw TypeError("Can't set " + String(it) + ' as a prototype'); } return it; }; /* eslint-disable no-proto -- safe */ // https://tc39.es/ecma262/#sec-object.setprototypeof // Works with __proto__ only. Old v8 can't work with null proto objects. // eslint-disable-next-line es/no-object-setprototypeof -- safe var objectSetPrototypeOf = Object.setPrototypeOf || ('__proto__' in {} ? function () { var CORRECT_SETTER = false; var test = {}; var setter; try { // eslint-disable-next-line es/no-object-getownpropertydescriptor -- safe setter = Object.getOwnPropertyDescriptor(Object.prototype, '__proto__').set; setter.call(test, []); CORRECT_SETTER = test instanceof Array; } catch (error) { /* empty */ } return function setPrototypeOf(O, proto) { anObject(O); aPossiblePrototype(proto); if (CORRECT_SETTER) setter.call(O, proto);else O.__proto__ = proto; return O; }; }() : undefined); var defineProperty = objectDefineProperty.f; var Int8Array = global$1.Int8Array; var Int8ArrayPrototype = Int8Array && Int8Array.prototype; var Uint8ClampedArray = global$1.Uint8ClampedArray; var Uint8ClampedArrayPrototype = Uint8ClampedArray && Uint8ClampedArray.prototype; var TypedArray = Int8Array && objectGetPrototypeOf(Int8Array); var TypedArrayPrototype = Int8ArrayPrototype && objectGetPrototypeOf(Int8ArrayPrototype); var ObjectPrototype = Object.prototype; var isPrototypeOf = ObjectPrototype.isPrototypeOf; var TO_STRING_TAG = wellKnownSymbol('toStringTag'); var TYPED_ARRAY_TAG = uid('TYPED_ARRAY_TAG'); // Fixing native typed arrays in Opera Presto crashes the browser, see #595 var NATIVE_ARRAY_BUFFER_VIEWS = arrayBufferNative && !!objectSetPrototypeOf && classof(global$1.opera) !== 'Opera'; var TYPED_ARRAY_TAG_REQIRED = false; var NAME; var TypedArrayConstructorsList = { Int8Array: 1, Uint8Array: 1, Uint8ClampedArray: 1, Int16Array: 2, Uint16Array: 2, Int32Array: 4, Uint32Array: 4, Float32Array: 4, Float64Array: 8 }; var BigIntArrayConstructorsList = { BigInt64Array: 8, BigUint64Array: 8 }; var isView = function isView(it) { if (!isObject(it)) return false; var klass = classof(it); return klass === 'DataView' || has$1(TypedArrayConstructorsList, klass) || has$1(BigIntArrayConstructorsList, klass); }; var isTypedArray = function (it) { if (!isObject(it)) return false; var klass = classof(it); return has$1(TypedArrayConstructorsList, klass) || has$1(BigIntArrayConstructorsList, klass); }; var aTypedArray$1 = function (it) { if (isTypedArray(it)) return it; throw TypeError('Target is not a typed array'); }; var aTypedArrayConstructor = function (C) { if (objectSetPrototypeOf) { if (isPrototypeOf.call(TypedArray, C)) return C; } else for (var ARRAY in TypedArrayConstructorsList) if (has$1(TypedArrayConstructorsList, NAME)) { var TypedArrayConstructor = global$1[ARRAY]; if (TypedArrayConstructor && (C === TypedArrayConstructor || isPrototypeOf.call(TypedArrayConstructor, C))) { return C; } } throw TypeError('Target is not a typed array constructor'); }; var exportTypedArrayMethod$1 = function (KEY, property, forced) { if (!descriptors) return; if (forced) for (var ARRAY in TypedArrayConstructorsList) { var TypedArrayConstructor = global$1[ARRAY]; if (TypedArrayConstructor && has$1(TypedArrayConstructor.prototype, KEY)) try { delete TypedArrayConstructor.prototype[KEY]; } catch (error) { /* empty */ } } if (!TypedArrayPrototype[KEY] || forced) { redefine(TypedArrayPrototype, KEY, forced ? property : NATIVE_ARRAY_BUFFER_VIEWS && Int8ArrayPrototype[KEY] || property); } }; var exportTypedArrayStaticMethod = function (KEY, property, forced) { var ARRAY, TypedArrayConstructor; if (!descriptors) return; if (objectSetPrototypeOf) { if (forced) for (ARRAY in TypedArrayConstructorsList) { TypedArrayConstructor = global$1[ARRAY]; if (TypedArrayConstructor && has$1(TypedArrayConstructor, KEY)) try { delete TypedArrayConstructor[KEY]; } catch (error) { /* empty */ } } if (!TypedArray[KEY] || forced) { // V8 ~ Chrome 49-50 `%TypedArray%` methods are non-writable non-configurable try { return redefine(TypedArray, KEY, forced ? property : NATIVE_ARRAY_BUFFER_VIEWS && TypedArray[KEY] || property); } catch (error) { /* empty */ } } else return; } for (ARRAY in TypedArrayConstructorsList) { TypedArrayConstructor = global$1[ARRAY]; if (TypedArrayConstructor && (!TypedArrayConstructor[KEY] || forced)) { redefine(TypedArrayConstructor, KEY, property); } } }; for (NAME in TypedArrayConstructorsList) { if (!global$1[NAME]) NATIVE_ARRAY_BUFFER_VIEWS = false; } // WebKit bug - typed arrays constructors prototype is Object.prototype if (!NATIVE_ARRAY_BUFFER_VIEWS || typeof TypedArray != 'function' || TypedArray === Function.prototype) { // eslint-disable-next-line no-shadow -- safe TypedArray = function TypedArray() { throw TypeError('Incorrect invocation'); }; if (NATIVE_ARRAY_BUFFER_VIEWS) for (NAME in TypedArrayConstructorsList) { if (global$1[NAME]) objectSetPrototypeOf(global$1[NAME], TypedArray); } } if (!NATIVE_ARRAY_BUFFER_VIEWS || !TypedArrayPrototype || TypedArrayPrototype === ObjectPrototype) { TypedArrayPrototype = TypedArray.prototype; if (NATIVE_ARRAY_BUFFER_VIEWS) for (NAME in TypedArrayConstructorsList) { if (global$1[NAME]) objectSetPrototypeOf(global$1[NAME].prototype, TypedArrayPrototype); } } // WebKit bug - one more object in Uint8ClampedArray prototype chain if (NATIVE_ARRAY_BUFFER_VIEWS && objectGetPrototypeOf(Uint8ClampedArrayPrototype) !== TypedArrayPrototype) { objectSetPrototypeOf(Uint8ClampedArrayPrototype, TypedArrayPrototype); } if (descriptors && !has$1(TypedArrayPrototype, TO_STRING_TAG)) { TYPED_ARRAY_TAG_REQIRED = true; defineProperty(TypedArrayPrototype, TO_STRING_TAG, { get: function () { return isObject(this) ? this[TYPED_ARRAY_TAG] : undefined; } }); for (NAME in TypedArrayConstructorsList) if (global$1[NAME]) { createNonEnumerableProperty(global$1[NAME], TYPED_ARRAY_TAG, NAME); } } var arrayBufferViewCore = { NATIVE_ARRAY_BUFFER_VIEWS: NATIVE_ARRAY_BUFFER_VIEWS, TYPED_ARRAY_TAG: TYPED_ARRAY_TAG_REQIRED && TYPED_ARRAY_TAG, aTypedArray: aTypedArray$1, aTypedArrayConstructor: aTypedArrayConstructor, exportTypedArrayMethod: exportTypedArrayMethod$1, exportTypedArrayStaticMethod: exportTypedArrayStaticMethod, isView: isView, isTypedArray: isTypedArray, TypedArray: TypedArray, TypedArrayPrototype: TypedArrayPrototype }; var aFunction = function (it) { if (typeof it != 'function') { throw TypeError(String(it) + ' is not a function'); } return it; }; var ceil = Math.ceil; var floor$1 = Math.floor; // `ToInteger` abstract operation // https://tc39.es/ecma262/#sec-tointeger var toInteger = function (argument) { return isNaN(argument = +argument) ? 0 : (argument > 0 ? floor$1 : ceil)(argument); }; var min$1 = Math.min; // `ToLength` abstract operation // https://tc39.es/ecma262/#sec-tolength var toLength = function (argument) { return argument > 0 ? min$1(toInteger(argument), 0x1FFFFFFFFFFFFF) : 0; // 2 ** 53 - 1 == 9007199254740991 }; // TODO: use something more complex like timsort? var floor = Math.floor; var mergeSort = function (array, comparefn) { var length = array.length; var middle = floor(length / 2); return length < 8 ? insertionSort(array, comparefn) : merge(mergeSort(array.slice(0, middle), comparefn), mergeSort(array.slice(middle), comparefn), comparefn); }; var insertionSort = function (array, comparefn) { var length = array.length; var i = 1; var element, j; while (i < length) { j = i; element = array[i]; while (j && comparefn(array[j - 1], element) > 0) { array[j] = array[--j]; } if (j !== i++) array[j] = element; } return array; }; var merge = function (left, right, comparefn) { var llength = left.length; var rlength = right.length; var lindex = 0; var rindex = 0; var result = []; while (lindex < llength || rindex < rlength) { if (lindex < llength && rindex < rlength) { result.push(comparefn(left[lindex], right[rindex]) <= 0 ? left[lindex++] : right[rindex++]); } else { result.push(lindex < llength ? left[lindex++] : right[rindex++]); } } return result; }; var arraySort = mergeSort; var firefox = engineUserAgent.match(/firefox\/(\d+)/i); var engineFfVersion = !!firefox && +firefox[1]; var engineIsIeOrEdge = /MSIE|Trident/.test(engineUserAgent); var webkit = engineUserAgent.match(/AppleWebKit\/(\d+)\./); var engineWebkitVersion = !!webkit && +webkit[1]; var aTypedArray = arrayBufferViewCore.aTypedArray; var exportTypedArrayMethod = arrayBufferViewCore.exportTypedArrayMethod; var Uint16Array$1 = global$1.Uint16Array; var nativeSort = Uint16Array$1 && Uint16Array$1.prototype.sort; // WebKit var ACCEPT_INCORRECT_ARGUMENTS = !!nativeSort && !fails(function () { var array = new Uint16Array$1(2); array.sort(null); array.sort({}); }); var STABLE_SORT = !!nativeSort && !fails(function () { // feature detection can be too slow, so check engines versions if (engineV8Version) return engineV8Version < 74; if (engineFfVersion) return engineFfVersion < 67; if (engineIsIeOrEdge) return true; if (engineWebkitVersion) return engineWebkitVersion < 602; var array = new Uint16Array$1(516); var expected = Array(516); var index, mod; for (index = 0; index < 516; index++) { mod = index % 4; array[index] = 515 - index; expected[index] = index - 2 * mod + 3; } array.sort(function (a, b) { return (a / 4 | 0) - (b / 4 | 0); }); for (index = 0; index < 516; index++) { if (array[index] !== expected[index]) return true; } }); var getSortCompare = function (comparefn) { return function (x, y) { if (comparefn !== undefined) return +comparefn(x, y) || 0; // eslint-disable-next-line no-self-compare -- NaN check if (y !== y) return -1; // eslint-disable-next-line no-self-compare -- NaN check if (x !== x) return 1; if (x === 0 && y === 0) return 1 / x > 0 && 1 / y < 0 ? 1 : -1; return x > y; }; }; // `%TypedArray%.prototype.sort` method // https://tc39.es/ecma262/#sec-%typedarray%.prototype.sort exportTypedArrayMethod('sort', function sort(comparefn) { var array = this; if (comparefn !== undefined) aFunction(comparefn); if (STABLE_SORT) return nativeSort.call(array, comparefn); aTypedArray(array); var arrayLength = toLength(array.length); var items = Array(arrayLength); var index; for (index = 0; index < arrayLength; index++) { items[index] = array[index]; } items = arraySort(array, getSortCompare(comparefn)); for (index = 0; index < arrayLength; index++) { array[index] = items[index]; } return array; }, !STABLE_SORT || ACCEPT_INCORRECT_ARGUMENTS); const Cytoband = function (start, end, name, typestain) { this.start = start; this.end = end; this.name = name; this.stain = 0; // Set the type, either p, n, or c if (typestain === 'acen') { this.type = 'c'; } else { this.type = typestain.charAt(1); if (this.type === 'p') { this.stain = parseInt(typestain.substring(4)); } } }; const GenomicInterval = function (chr, start, end, features) { this.chr = chr; this.start = start; this.end = end; this.features = features; }; GenomicInterval.prototype.contains = function (chr, start, end) { return this.chr === chr && this.start <= start && this.end >= end; }; GenomicInterval.prototype.containsRange = function (range) { return this.chr === range.chr && this.start <= range.start && this.end >= range.end; }; const Chromosome = function (name, order, bpStart, bpLength, rangeLocus) { this.name = name; this.order = order; this.bpStart = bpStart; this.bpLength = bpLength; this.rangeLocus = rangeLocus; }; /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ /** * Test if the given value is a string or number. Not using typeof as it fails on boxed primitives. * * @param value * @returns boolean */ function isSimpleType(value) { const simpleTypes = new Set(["boolean", "number", "string", "symbol"]); const valueType = typeof value; return value !== undefined && (simpleTypes.has(valueType) || value.substring || value.toFixed); } function buildOptions(config, options) { var defaultOptions = { oauthToken: config.oauthToken, headers: config.headers, withCredentials: config.withCredentials, filename: config.filename }; return Object.assign(defaultOptions, options); } /** * isMobile test from http://detectmobilebrowsers.com * TODO -- improve UI design so this isn't neccessary * @returns {boolean} */ // igv.isMobile = function () { // // const a = (navigator.userAgent || navigator.vendor || window.opera); // return (/(android|bb\d+|meego).+mobile|avantgo|bada\/|blackberry|blazer|compal|elaine|fennec|hiptop|iemobile|ip(hone|od)|iris|kindle|lge |maemo|midp|mmp|mobile.+firefox|netfront|opera m(ob|in)i|palm( os)?|phone|p(ixi|re)\/|plucker|pocket|psp|series(4|6)0|symbian|treo|up\.(browser|link)|vodafone|wap|windows ce|xda|xiino/i.test(a) || // /1207|6310|6590|3gso|4thp|50[1-6]i|770s|802s|a wa|abac|ac(er|oo|s\-)|ai(ko|rn)|al(av|ca|co)|amoi|an(ex|ny|yw)|aptu|ar(ch|go)|as(te|us)|attw|au(di|\-m|r |s )|avan|be(ck|ll|nq)|bi(lb|rd)|bl(ac|az)|br(e|v)w|bumb|bw\-(n|u)|c55\/|capi|ccwa|cdm\-|cell|chtm|cldc|cmd\-|co(mp|nd)|craw|da(it|ll|ng)|dbte|dc\-s|devi|dica|dmob|do(c|p)o|ds(12|\-d)|el(49|ai)|em(l2|ul)|er(ic|k0)|esl8|ez([4-7]0|os|wa|ze)|fetc|fly(\-|_)|g1 u|g560|gene|gf\-5|g\-mo|go(\.w|od)|gr(ad|un)|haie|hcit|hd\-(m|p|t)|hei\-|hi(pt|ta)|hp( i|ip)|hs\-c|ht(c(\-| |_|a|g|p|s|t)|tp)|hu(aw|tc)|i\-(20|go|ma)|i230|iac( |\-|\/)|ibro|idea|ig01|ikom|im1k|inno|ipaq|iris|ja(t|v)a|jbro|jemu|jigs|kddi|keji|kgt( |\/)|klon|kpt |kwc\-|kyo(c|k)|le(no|xi)|lg( g|\/(k|l|u)|50|54|\-[a-w])|libw|lynx|m1\-w|m3ga|m50\/|ma(te|ui|xo)|mc(01|21|ca)|m\-cr|me(rc|ri)|mi(o8|oa|ts)|mmef|mo(01|02|bi|de|do|t(\-| |o|v)|zz)|mt(50|p1|v )|mwbp|mywa|n10[0-2]|n20[2-3]|n30(0|2)|n50(0|2|5)|n7(0(0|1)|10)|ne((c|m)\-|on|tf|wf|wg|wt)|nok(6|i)|nzph|o2im|op(ti|wv)|oran|owg1|p800|pan(a|d|t)|pdxg|pg(13|\-([1-8]|c))|phil|pire|pl(ay|uc)|pn\-2|po(ck|rt|se)|prox|psio|pt\-g|qa\-a|qc(07|12|21|32|60|\-[2-7]|i\-)|qtek|r380|r600|raks|rim9|ro(ve|zo)|s55\/|sa(ge|ma|mm|ms|ny|va)|sc(01|h\-|oo|p\-)|sdk\/|se(c(\-|0|1)|47|mc|nd|ri)|sgh\-|shar|sie(\-|m)|sk\-0|sl(45|id)|sm(al|ar|b3|it|t5)|so(ft|ny)|sp(01|h\-|v\-|v )|sy(01|mb)|t2(18|50)|t6(00|10|18)|ta(gt|lk)|tcl\-|tdg\-|tel(i|m)|tim\-|t\-mo|to(pl|sh)|ts(70|m\-|m3|m5)|tx\-9|up(\.b|g1|si)|utst|v400|v750|veri|vi(rg|te)|vk(40|5[0-3]|\-v)|vm40|voda|vulc|vx(52|53|60|61|70|80|81|83|85|98)|w3c(\-| )|webc|whit|wi(g |nc|nw)|wmlb|wonu|x700|yas\-|your|zeto|zte\-/i.test(a.substr(0, 4))) // // } const doAutoscale = function (features) { var min, max; if (features.length > 0) { min = Number.MAX_VALUE; max = -Number.MAX_VALUE; features.forEach(function (f) { if (!Number.isNaN(f.value)) { min = Math.min(min, f.value); max = Math.max(max, f.value); } }); // Insure we have a zero baseline if (max > 0) min = Math.min(0, min); if (max < 0) max = 0; } else { // No features -- default min = 0; max = 100; } return { min: min, max: max }; }; const validateLocusExtent = function (chromosomeLengthBP, extent, minimumBP) { let ss = extent.start; let ee = extent.end; if (undefined === ee) { ss -= minimumBP / 2; ee = ss + minimumBP; if (ee > chromosomeLengthBP) { ee = chromosomeLengthBP; ss = ee - minimumBP; } else if (ss < 0) { ss = 0; ee = minimumBP; } } else if (ee - ss < minimumBP) { const center = (ee + ss) / 2; if (center - minimumBP / 2 < 0) { ss = 0; ee = ss + minimumBP; } else if (center + minimumBP / 2 > chromosomeLengthBP) { ee = chromosomeLengthBP; ss = ee - minimumBP; } else { ss = center - minimumBP / 2; ee = ss + minimumBP; } } extent.start = Math.ceil(ss); extent.end = Math.floor(ee); }; /*! * is-number * * Copyright (c) 2014-present, Jon Schlinkert. * Released under the MIT License. */ const isNumber = function (num) { if (typeof num === 'number') { return num - num === 0; } if (typeof num === 'string' && num.trim() !== '') { return Number.isFinite ? Number.isFinite(+num) : isFinite(+num); } return false; }; function inferTrackType(config) { translateDeprecatedTypes(config); if (config.type) { return config.type; } if (config.format) { const format = config.format.toLowerCase(); switch (format) { case "bw": case "bigwig": case "wig": case "bedgraph": case "tdf": return "wig"; case "vcf": return "variant"; case "seg": return "seg"; case "mut": case "maf": return "mut"; case "bam": case "cram": return "alignment"; case "bedpe": case "bedpe-loop": return "interaction"; case "bp": return "arc"; case "gwas": return "gwas"; case "bed": case "bigbed": case "bb": return "bedtype"; default: return "annotation"; } } } function translateDeprecatedTypes(config) { if (config.featureType) { // Translate deprecated "feature" type config.type = config.type || config.featureType; config.featureType = undefined; } if ("junctions" === config.type) { config.type = "spliceJunctions"; } else if ("bed" === config.type) { config.type = "annotation"; config.format = config.format || "bed"; } else if ("annotations" === config.type) { config.type = "annotation"; } else if ("alignments" === config.type) { config.type = "alignment"; } else if ("bam" === config.type) { config.type = "alignment"; config.format = "bam"; } else if ("vcf" === config.type) { config.type = "variant"; config.format = "vcf"; } else if ("t2d" === config.type) { config.type = "gwas"; } else if ("FusionJuncSpan" === config.type && !config.format) { config.format = "fusionjuncspan"; } else if ("aed" === config.type) { config.type = "annotation"; config.format = config.format || "aed"; } } async function getFilename(url) { if (isString$6(url) && url.startsWith("https://drive.google.com")) { // This will fail if Google API key is not defined if (getApiKey() === undefined) { throw Error("Google drive is referenced, but API key is not defined. An API key is required for Google Drive access"); } const json = await getDriveFileInfo(url); return json.originalFileName || json.name; } else { return getFilename$2(url); } } const splitLines$2 = splitLines$3; const reservedProperties = new Set(['fastaURL', 'indexURL', 'cytobandURL', 'indexed']); class FastaSequence { constructor(reference) { if (typeof reference.fastaURL === 'string' && reference.fastaURL.startsWith('data:')) { this.file = decodeDataUri(reference.fastaURL); this.indexed = false; // dataURI is by definition not indexed this.isDataURI = true; } else { this.file = reference.fastaURL; this.indexed = reference.indexed !== false; // Indexed unless it explicitly is not if (this.indexed) { this.indexFile = reference.indexURL || reference.indexFile || this.file + ".fai"; } } this.withCredentials = reference.withCredentials; this.chromosomeNames = []; this.chromosomes = {}; this.sequences = {}; this.offsets = {}; // Build a track-like config object from the referenceObject const config = {}; for (let key in reference) { if (reference.hasOwnProperty(key) && !reservedProperties.has(key)) { config[key] = reference[key]; } } this.config = config; } async init() { if (this.indexed) { return this.getIndex(); } else { return this.loadAll(); } } async getSequence(chr, start, end) { if (this.indexed) { return this.getSequenceIndexed(chr, start, end); } else { return this.getSequenceNonIndexed(chr, start, end); } } async getSequenceIndexed(chr, start, end) { if (!(this.interval && this.interval.contains(chr, start, end))) { // Expand query, to minimum of 50kb let qstart = start; let qend = end; if (end - start < 50000) { const w = end - start; const center = Math.round(start + w / 2); qstart = Math.max(0, center - 25000); qend = center + 25000; } const seqBytes = await this.readSequence(chr, qstart, qend); this.interval = new GenomicInterval(chr, qstart, qend, seqBytes); } const offset = start - this.interval.start; const n = end - start; const seq = this.interval.features ? this.interval.features.substr(offset, n) : null; return seq; } async getSequenceNonIndexed(chr, start, end) { if (this.offsets[chr]) { start -= this.offsets[chr]; end -= this.offsets[chr]; } let prefix = ""; if (start < 0) { for (let i = start; i < Math.min(end, 0); i++) { prefix += "*"; } } if (end <= 0) { return Promise.resolve(prefix); } const seq = this.sequences[chr]; const seqEnd = Math.min(end, seq.length); return prefix + seq.substring(start, seqEnd); } async getIndex() { if (this.index) { return this.index; } else { const data = await igvxhr.load(this.indexFile, buildOptions(this.config)); const lines = splitLines$2(data); const len = lines.length; let lineNo = 0; let order = 0; this.index = {}; while (lineNo < len) { const tokens = lines[lineNo++].split("\t"); const nTokens = tokens.length; if (nTokens === 5) { // Parse the index line. const chr = tokens[0]; const size = parseInt(tokens[1]); const position = parseInt(tokens[2]); const basesPerLine = parseInt(tokens[3]); const bytesPerLine = parseInt(tokens[4]); const indexEntry = { size: size, position: position, basesPerLine: basesPerLine, bytesPerLine: bytesPerLine }; this.chromosomeNames.push(chr); this.index[chr] = indexEntry; this.chromosomes[chr] = new Chromosome(chr, order++, 0, size); } } return this.index; } } async loadAll() { let data; if (this.isDataURI) { data = this.file; // <= Strange convention, revisit. } else { data = await igvxhr.load(this.file, buildOptions(this.config)); } const lines = splitLines$2(data); const len = lines.length; let lineNo = 0; let currentSeq; let currentRangeLocus; let currentOffset = 0; let order = 0; let nextLine; let currentChr; while (lineNo < len) { nextLine = lines[lineNo++].trim(); if (nextLine.startsWith("#") || nextLine.length === 0) ; else if (nextLine.startsWith(">")) { // Start the next sequence if (currentSeq) { this.chromosomeNames.push(currentChr); this.sequences[currentChr] = currentSeq; this.chromosomes[currentChr] = new Chromosome(currentChr, order++, currentOffset, currentOffset + currentSeq.length, currentRangeLocus); } const parts = nextLine.substr(1).split(/\s+/); // Check for samtools style locus string. This is not perfect, and could fail on weird sequence names const nameParts = parts[0].split(':'); currentChr = nameParts[0]; currentSeq = ""; currentOffset = 0; currentRangeLocus = undefined; if (nameParts.length > 1 && nameParts[1].indexOf('-') > 0) { const locusParts = nameParts[1].split('-'); if (locusParts.length === 2 && /^[0-9]+$/.test(locusParts[0]) && /^[0-9]+$/.test(locusParts[1])) ; const from = Number.parseInt(locusParts[0]); const to = Number.parseInt(locusParts[1]); if (to > from) { currentOffset = from - 1; this.offsets[currentChr] = currentOffset; currentRangeLocus = nameParts[1]; } } } else { currentSeq += nextLine; } } // add last seq if (currentSeq) { this.chromosomeNames.push(currentChr); this.sequences[currentChr] = currentSeq; this.chromosomes[currentChr] = new Chromosome(currentChr, order++, currentOffset, currentOffset + currentSeq.length, currentRangeLocus); } } async readSequence(chr, qstart, qend) { // let offset; // let start; // let end; // let basesPerLine; // let nEndBytes; await this.getIndex(); const idxEntry = this.index[chr]; if (!idxEntry) { // Tag interval with null so we don't try again this.interval = new GenomicInterval(chr, qstart, qend, null); return null; } else { const start = Math.max(0, qstart); // qstart should never be < 0 const end = Math.min(idxEntry.size, qend); const bytesPerLine = idxEntry.bytesPerLine; const basesPerLine = idxEntry.basesPerLine; const position = idxEntry.position; const nEndBytes = bytesPerLine - basesPerLine; const startLine = Math.floor(start / basesPerLine); const endLine = Math.floor(end / basesPerLine); const base0 = startLine * basesPerLine; // Base at beginning of start line const offset = start - base0; const startByte = position + startLine * bytesPerLine + offset; const base1 = endLine * basesPerLine; const offset1 = end - base1; const endByte = position + endLine * bytesPerLine + offset1 - 1; const byteCount = endByte - startByte + 1; let allBytes; if (byteCount <= 0) { console.error("No sequence for " + chr + ":" + qstart + "-" + qend); } else { allBytes = await igvxhr.load(this.file, buildOptions(this.config, { range: { start: startByte, size: byteCount } })); } if (!allBytes) { return null; } else { let nBases, seqBytes = "", srcPos = 0, allBytesLength = allBytes.length; if (offset > 0) { nBases = Math.min(end - start, basesPerLine - offset); seqBytes += allBytes.substr(srcPos, nBases); srcPos += nBases + nEndBytes; } while (srcPos < allBytesLength) { nBases = Math.min(basesPerLine, allBytesLength - srcPos); seqBytes += allBytes.substr(srcPos, nBases); srcPos += nBases + nEndBytes; } return seqBytes; } } } } function decodeDataUri(dataUri) { const split = dataUri.split(','); const info = split[0].split(':')[1]; let dataString = split[1]; if (info.indexOf('base64') >= 0) { dataString = atob(dataString); } else { dataString = decodeURI(dataString); } const bytes = new Uint8Array(dataString.length); for (let i = 0; i < dataString.length; i++) { bytes[i] = dataString.charCodeAt(i); } const inflate = new Zlib$1.Gunzip(bytes); const plain = inflate.decompress(); let s = ""; const len = plain.length; for (let i = 0; i < len; i++) s += String.fromCharCode(plain[i]); return s; } const _version = "2.9.3"; function version() { return _version; } const DEFAULT_GENOMES_URL = "https://igv.org/genomes/genomes.json"; const BACKUP_GENOMES_URL = "https://s3.amazonaws.com/igv.org.genomes/genomes.json"; const splitLines$1 = splitLines$3; const GenomeUtils = { loadGenome: async function (options) { const cytobandUrl = options.cytobandURL; const aliasURL = options.aliasURL; const sequence = new FastaSequence(options); await sequence.init(); let cytobands; if (cytobandUrl) { cytobands = await loadCytobands(cytobandUrl, sequence.config); } let aliases; if (aliasURL) { aliases = await loadAliases(aliasURL, sequence.config); } return new Genome(options, sequence, cytobands, aliases); }, initializeGenomes: async function (config) { if (!GenomeUtils.KNOWN_GENOMES) { const table = {}; // Get default genomes if (config.loadDefaultGenomes !== false) { try { const url = DEFAULT_GENOMES_URL + `?randomSeed=${Math.random().toString(36)}&version=${version()}`; // prevent caching const jsonArray = await igvxhr.loadJson(url, { timeout: 3000 }); processJson(jsonArray); } catch (e) { console.error(e); const url = BACKUP_GENOMES_URL + `?randomSeed=${Math.random().toString(36)}&version=${version()}`; // prevent caching const jsonArray = await igvxhr.loadJson(url, {}); processJson(jsonArray); } } // Add user-defined genomes const genomeList = config.genomeList || config.genomes; if (genomeList) { if (typeof genomeList === 'string') { const jsonArray = await igvxhr.loadJson(genomeList, {}); processJson(jsonArray); } else { processJson(genomeList); } } GenomeUtils.KNOWN_GENOMES = table; function processJson(jsonArray) { jsonArray.forEach(function (json) { table[json.id] = json; }); return table; } } }, isWholeGenomeView: function (chr) { return 'all' === chr.toLowerCase(); }, // Expand a genome id to a reference object, if needed expandReference: function (idOrConfig) { // idOrConfig might be json if (isString$6(idOrConfig) && idOrConfig.startsWith("{")) { try { idOrConfig = JSON.parse(idOrConfig); } catch (e) {// Apparently its not json, could be an ID starting with "{". Unusual but legal. } } let genomeID; if (isString$6(idOrConfig)) { genomeID = idOrConfig; } else if (idOrConfig.genome) { genomeID = idOrConfig.genome; } else if (idOrConfig.id !== undefined && idOrConfig.fastaURL === undefined) { // Backward compatibility genomeID = idOrConfig.id; } if (genomeID) { const knownGenomes = GenomeUtils.KNOWN_GENOMES; const reference = knownGenomes[genomeID]; if (!reference) { Alert.presentAlert(new Error(`Unknown genome id: ${genomeID}`), undefined); } return reference; } else { return idOrConfig; } } }; class Genome { constructor(config, sequence, ideograms, aliases) { this.config = config; this.id = config.id; this.sequence = sequence; this.chromosomeNames = sequence.chromosomeNames; this.chromosomes = sequence.chromosomes; // An object (functions as a dictionary) this.ideograms = ideograms; this.featureDB = {}; // Hash of name -> feature, used for search function. this.wholeGenomeView = config.wholeGenomeView === undefined || config.wholeGenomeView; if (this.wholeGenomeView && Object.keys(sequence.chromosomes).length > 1) { constructWG(this, config); } else { this.wgChromosomeNames = sequence.chromosomeNames; } /** * Return the official chromosome name for the (possibly) alias. Deals with * 1 <-> chr1, chrM <-> MT, IV <-> chr4, etc. * @param str */ var chrAliasTable = {}, self = this; // The standard mappings chrAliasTable["all"] = "all"; this.chromosomeNames.forEach(function (name) { var alias = name.startsWith("chr") ? name.substring(3) : "chr" + name; chrAliasTable[alias.toLowerCase()] = name; if (name === "chrM") chrAliasTable["mt"] = "chrM"; if (name === "MT") chrAliasTable["chrm"] = "MT"; chrAliasTable[name.toLowerCase()] = name; }); // Custom mappings if (aliases) { aliases.forEach(function (array) { // Find the official chr name var defName, i; for (i = 0; i < array.length; i++) { if (self.chromosomes[array[i]]) { defName = array[i]; break; } } if (defName) { array.forEach(function (alias) { if (alias !== defName) { chrAliasTable[alias.toLowerCase()] = defName; chrAliasTable[alias] = defName; // Should not be needed } }); } }); } this.chrAliasTable = chrAliasTable; } showWholeGenomeView() { return this.config.wholeGenomeView !== false; } toJSON() { return Object.assign({}, this.config, { tracks: undefined }); } getInitialLocus() {} getHomeChromosomeName() { if (this.showWholeGenomeView() && this.chromosomes.hasOwnProperty("all")) { return "all"; } else { const chromosome = this.chromosomes[this.chromosomeNames[0]]; if (chromosome.rangeLocus) { return chromosome.name + ":" + chromosome.rangeLocus; } else { return this.chromosomeNames[0]; } } } getChromosomeName(str) { var chr = this.chrAliasTable[str.toLowerCase()]; return chr ? chr : str; } getChromosome(chr) { chr = this.getChromosomeName(chr); return this.chromosomes[chr]; } getCytobands(chr) { return this.ideograms ? this.ideograms[chr] : null; } getLongestChromosome() { var longestChr, chromosomes = this.chromosomes; for (let key in chromosomes) { if (chromosomes.hasOwnProperty(key)) { var chr = chromosomes[key]; if (longestChr === undefined || chr.bpLength > longestChr.bpLength) { longestChr = chr; } } return longestChr; } } getChromosomes() { return this.chromosomes; } /** * Return the genome coordinate in kb for the give chromosome and position. * NOTE: This might return undefined if the chr is filtered from whole genome view. */ getGenomeCoordinate(chr, bp) { var offset = this.getCumulativeOffset(chr); if (offset === undefined) return undefined; return offset + bp; } /** * Return the chromosome and coordinate in bp for the given genome coordinate */ getChromosomeCoordinate(genomeCoordinate) { if (this.cumulativeOffsets === undefined) { this.cumulativeOffsets = computeCumulativeOffsets.call(this); } let lastChr = undefined; let lastCoord = 0; for (let name of this.wgChromosomeNames) { const cumulativeOffset = this.cumulativeOffsets[name]; if (cumulativeOffset > genomeCoordinate) { const position = genomeCoordinate - lastCoord; return { chr: lastChr, position: position }; } lastChr = name; lastCoord = cumulativeOffset; } // If we get here off the end return { chr: this.chromosomeNames[this.chromosomeNames.length - 1], position: 0 }; } /** * Return the offset in genome coordinates (kb) of the start of the given chromosome * NOTE: This might return undefined if the chromosome is filtered from whole genome view. */ getCumulativeOffset(chr) { if (this.cumulativeOffsets === undefined) { this.cumulativeOffsets = computeCumulativeOffsets.call(this); } const queryChr = this.getChromosomeName(chr); return this.cumulativeOffsets[queryChr]; function computeCumulativeOffsets() { let self = this; let acc = {}; let offset = 0; for (let name of self.wgChromosomeNames) { acc[name] = Math.floor(offset); const chromosome = self.getChromosome(name); offset += chromosome.bpLength; } return acc; } } /** * Return the nominal genome length, this is the length of the main chromosomes (no scaffolds, etc). */ getGenomeLength() { let self = this; if (!this.bpLength) { let bpLength = 0; self.wgChromosomeNames.forEach(function (cname) { let c = self.chromosomes[cname]; bpLength += c.bpLength; }); this.bpLength = bpLength; } return this.bpLength; } } function loadCytobands(cytobandUrl, config) { if (cytobandUrl.startsWith("data:")) { var data = decodeDataUri(cytobandUrl); return Promise.resolve(getCytobands(data)); } else { return igvxhr.loadString(cytobandUrl, buildOptions(config)).then(function (data) { return getCytobands(data); }); } function getCytobands(data) { var bands = [], lastChr, n = 0, lines = splitLines$1(data), len = lines.length, cytobands = {}; for (var i = 0; i < len; i++) { var tokens = lines[i].split("\t"); var chr = tokens[0]; if (!lastChr) lastChr = chr; if (chr !== lastChr) { cytobands[lastChr] = bands; bands = []; lastChr = chr; n = 0; } if (tokens.length === 5) { //10 0 3000000 p15.3 gneg var start = parseInt(tokens[1]); var end = parseInt(tokens[2]); var name = tokens[3]; var stain = tokens[4]; bands[n++] = new Cytoband(start, end, name, stain); } } return cytobands; } function decodeDataUri(dataUri) { let plain; if (dataUri.startsWith("data:application/gzip;base64")) { plain = decodeDataURI$1(dataUri); } else { let bytes, split = dataUri.split(','), info = split[0].split(':')[1], dataString = split[1]; if (info.indexOf('base64') >= 0) { dataString = atob(dataString); } else { dataString = decodeURI(dataString); } bytes = new Uint8Array(dataString.length); for (let i = 0; i < dataString.length; i++) { bytes[i] = dataString.charCodeAt(i); } var inflate = new Zlib$1.Gunzip(bytes); plain = inflate.decompress(); } let s = ""; const len = plain.length; for (let i = 0; i < len; i++) { s += String.fromCharCode(plain[i]); } return s; } } function loadAliases(aliasURL, config) { return igvxhr.loadString(aliasURL, buildOptions(config)).then(function (data) { var lines = splitLines$1(data), aliases = []; lines.forEach(function (line) { if (!line.startsWith("#") && line.length > 0) aliases.push(line.split("\t")); }); return aliases; }); } function constructWG(genome, config) { let wgChromosomes; if (config.chromosomeOrder) { genome.wgChromosomeNames = config.chromosomeOrder.split(',').map(nm => nm.trim()); wgChromosomes = genome.wgChromosomeNames.map(nm => genome.chromosomes[nm]).filter(chr => chr !== undefined); } else { // Trim small chromosomes. const lengths = Object.keys(genome.chromosomes).map(key => genome.chromosomes[key].bpLength); const median = lengths.reduce((a, b) => Math.max(a, b)); const threshold = median / 50; wgChromosomes = Object.values(genome.chromosomes).filter(chr => chr.bpLength > threshold); // Sort chromosomes. First segregate numeric and alpha names, sort numeric, leave alpha as is const numericChromosomes = wgChromosomes.filter(chr => isDigit(chr.name.replace('chr', ''))); const alphaChromosomes = wgChromosomes.filter(chr => !isDigit(chr.name.replace('chr', ''))); numericChromosomes.sort((a, b) => Number.parseInt(a.name.replace('chr', '')) - Number.parseInt(b.name.replace('chr', ''))); const wgChromosomeNames = numericChromosomes.map(chr => chr.name); for (let chr of alphaChromosomes) { wgChromosomeNames.push(chr.name); } genome.wgChromosomeNames = wgChromosomeNames; } // Compute psuedo-chromosome "all" const l = wgChromosomes.reduce((accumulator, currentValue) => accumulator += currentValue.bpLength, 0); genome.chromosomes["all"] = { name: "all", bpLength: l }; function isDigit(val) { return /^\d+$/.test(val); } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ class ViewportBase { constructor(trackView, $viewportContainer, referenceFrame, width) { this.guid = guid(); this.trackView = trackView; this.referenceFrame = referenceFrame; this.browser = trackView.browser; this.$viewport = $('
'); $viewportContainer.append(this.$viewport); // store the viewport GUID for later use this.$viewport.data('viewportGUID', this.guid); this.$content = $("
", { class: 'igv-viewport-content' }); this.$viewport.append(this.$content); this.$content.height(this.$viewport.height()); this.contentDiv = this.$content.get(0); this.$canvas = $(''); this.$content.append(this.$canvas); this.canvas = this.$canvas.get(0); this.ctx = this.canvas.getContext("2d"); this.setWidth(width); this.initializationHelper(); } initializationHelper() {} showMessage(message) { if (!this.messageDiv) { this.messageDiv = document.createElement('div'); this.messageDiv.className = 'igv-viewport-message'; this.contentDiv.append(this.messageDiv); } this.messageDiv.textContent = message; this.messageDiv.style.display = 'inline-block'; } hideMessage(message) { if (this.messageDiv) this.messageDiv.style.display = 'none'; } setTrackLabel(label) {} startSpinner() {} stopSpinner() {} checkZoomIn() { return true; } shift() {} setTop(contentTop) { const viewportHeight = this.$viewport.height(); const viewTop = -contentTop; const viewBottom = viewTop + viewportHeight; this.$content.css('top', `${contentTop}px`); if (undefined === this.canvasVerticalRange || this.canvasVerticalRange.bottom < viewBottom || this.canvasVerticalRange.top > viewTop) { this.repaint(); } } async loadFeatures() { return undefined; } async repaint() {} draw(drawConfiguration, features, roiFeatures) {} checkContentHeight() { let track = this.trackView.track; if ("FILL" === track.displayMode) { this.setContentHeight(this.$viewport.height()); } else if (typeof track.computePixelHeight === 'function') { let features = this.cachedFeatures; if (features && features.length > 0) { let requiredContentHeight = track.computePixelHeight(features); let currentContentHeight = this.$content.height(); if (requiredContentHeight !== currentContentHeight) { this.setContentHeight(requiredContentHeight); } } } } getContentHeight() { return this.$content.height(); } setContentHeight(contentHeight) { // Maximum height of a canvas is ~32,000 pixels on Chrome, possibly smaller on other platforms contentHeight = Math.min(contentHeight, 32000); this.$content.height(contentHeight); if (this.tile) this.tile.invalidate = true; } isLoading() { return false; } saveSVG() {} renderSVGContext(context, offset) {} drawSVGWithContext(context) {} isVisible() { return this.$viewport.width(); } setWidth(width) { this.$viewport.width(width); this.canvas.style.width = `${width}px`; this.canvas.setAttribute('width', width); } getWidth() { return this.$viewport.width(); } getContentTop() { return this.contentDiv.offsetTop; } containsPosition(chr, position) {} /** * Called when the associated track is removed. Do any needed cleanup here. */ dispose() { if (this.popover) { this.popover.dispose(); } this.$canvas.off(); this.$canvas.empty(); this.$content.off(); this.$content.empty(); this.$viewport.off(); this.$viewport.empty(); // Null out all properties -- this should not be neccessary, but just in case there is a // reference to self somewhere we want to free memory. for (let key of Object.keys(this)) { this[key] = undefined; } } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const trackMenuItemListHelper = MenuUtils.trackMenuItemListHelper; const MenuPopup = function ($parent) { // popover container this.$popover = $('
', { class: 'igv-menu-popup' }); $parent.append(this.$popover); // popover header let $popoverHeader = $('
', { class: 'igv-menu-popup-header' }); this.$popover.append($popoverHeader); attachDialogCloseHandlerWithParent$1($popoverHeader.get(0), () => this.$popover.hide()); this.$popoverContent = $('
'); this.$popover.append(this.$popoverContent); makeDraggable$1(this.$popover.get(0), $popoverHeader.get(0)); $popoverHeader.on('click.menu-popup-dismiss', function (e) { e.stopPropagation(); e.preventDefault(); // absorb click to prevent it leaking through to parent DOM element }); }; MenuPopup.prototype.presentMenuList = function (dx, dy, list) { hideAllMenuPopups(); if (list.length > 0) { this.$popoverContent.empty(); list = trackMenuItemListHelper(list, this.$popover); for (let item of list) { if (item.init) { item.init(); } let $e = item.object; if (0 === list.indexOf(item)) { $e.removeClass('igv-track-menu-border-top'); } if ($e.hasClass('igv-track-menu-border-top') || $e.hasClass('igv-menu-popup-check-container')) ; else if ($e.is('div')) { $e.addClass('igv-menu-popup-shim'); } this.$popoverContent.append($e); } this.$popover.css({ left: dx + 'px', top: dy + 'px' }); this.$popover.show(); } }; MenuPopup.prototype.presentTrackContextMenu = function (e, menuItems) { this.$popoverContent.empty(); const menuElements = createMenuElements(menuItems, this.$popover.get(0)); for (let item of menuElements) { this.$popoverContent.get(0).appendChild(item.object); } present(e, this.$popover.get(0)); this.$popover.show(); }; MenuPopup.prototype.dispose = function () { this.$popover.empty(); this.$popoverContent.empty(); Object.keys(this).forEach(function (key) { this[key] = undefined; }); }; function createMenuElements(itemList, popover) { return itemList.map(item => { let elem; if (typeof item === 'string' && '
' === item) { elem = document.createElement('hr'); } else if (typeof item === 'string') { elem = div$1({ class: 'context-menu' }); elem.innerHTML = item; } else if (typeof item === 'Node') { elem = item; } else { if (typeof item.init === 'function') { item.init(); } if ("checkbox" === item.type) { elem = Icon.createCheckbox("Show all bases", item.value); } else if ("color" === item.type) { const colorPicker = new ColorPicker({ parent: popover.parentElement, width: 364, //defaultColor: 'aqua', colorHandler: color => item.click(color) }); elem = div$1({ class: 'context-menu' }); if (typeof item.label === 'string') { elem.innerHTML = item.label; } const clickHandler = e => { colorPicker.show(); hide$1(popover); e.preventDefault(); e.stopPropagation(); }; elem.addEventListener('click', clickHandler); elem.addEventListener('touchend', clickHandler); elem.addEventListener('mouseup', function (e) { e.preventDefault(); e.stopPropagation(); }); } else { elem = div$1({ class: 'context-menu' }); if (typeof item.label === 'string') { elem.innerHTML = item.label; } } if (item.click && "color" !== item.type) { elem.addEventListener('click', handleClick); elem.addEventListener('touchend', handleClick); elem.addEventListener('mouseup', function (e) { e.preventDefault(); e.stopPropagation(); }); // eslint-disable-next-line no-inner-declarations function handleClick(e) { item.click(); hide$1(popover); e.preventDefault(); e.stopPropagation(); } } } return { object: elem, init: item.init }; }); } function present(e, popover) { const { x, y } = translateMouseCoordinates$1(e, popover.parentNode); // parent bbox const { width } = popover.parentNode.getBoundingClientRect(); const { width: w } = popover.getBoundingClientRect(); const xmax = x + w; popover.style.left = `${xmax > width ? x - (xmax - width) : x}px`; popover.style.top = `${y}px`; } const hideAllMenuPopups = () => $('.igv-menu-popup').hide(); /*!! * Canvas 2 Svg v1.0.19 * A low level canvas to SVG converter. Uses a mock canvas context to build an SVG document. * * Licensed under the MIT license: * http://www.opensource.org/licenses/mit-license.php * * Author: * Kerry Liu * * Copyright (c) 2014 Gliffy Inc. */ var STYLES, ctx, CanvasGradient, CanvasPattern, namedEntities; //helper function to format a string function format(str, args) { var keys = Object.keys(args), i; for (i = 0; i < keys.length; i++) { str = str.replace(new RegExp("\\{" + keys[i] + "\\}", "gi"), args[keys[i]]); } return str; } //helper function that generates a random string function randomString(holder) { var chars, randomstring, i; if (!holder) { throw new Error("cannot create a random attribute name for an undefined object"); } chars = "ABCDEFGHIJKLMNOPQRSTUVWXTZabcdefghiklmnopqrstuvwxyz"; randomstring = ""; do { randomstring = ""; for (i = 0; i < 12; i++) { randomstring += chars[Math.floor(Math.random() * chars.length)]; } } while (holder[randomstring]); return randomstring; } //helper function to map named to numbered entities function createNamedToNumberedLookup(items, radix) { var i, entity, lookup = {}, base10; items = items.split(','); radix = radix || 10; // Map from named to numbered entities. for (i = 0; i < items.length; i += 2) { entity = '&' + items[i + 1] + ';'; base10 = parseInt(items[i], radix); lookup[entity] = '&#' + base10 + ';'; } //FF and IE need to create a regex from hex values ie   == \xa0 lookup["\\xa0"] = ' '; return lookup; } //helper function to map canvas-textAlign to svg-textAnchor function getTextAnchor(textAlign) { //TODO: support rtl languages var mapping = { "left": "start", "right": "end", "center": "middle", "start": "start", "end": "end" }; return mapping[textAlign] || mapping.start; } //helper function to map canvas-textBaseline to svg-dominantBaseline function getDominantBaseline(textBaseline) { //INFO: not supported in all browsers var mapping = { "alphabetic": "alphabetic", "hanging": "hanging", "top": "text-before-edge", "bottom": "text-after-edge", "middle": "central" }; return mapping[textBaseline] || mapping.alphabetic; } // Unpack entities lookup where the numbers are in radix 32 to reduce the size // entity mapping courtesy of tinymce namedEntities = createNamedToNumberedLookup('50,nbsp,51,iexcl,52,cent,53,pound,54,curren,55,yen,56,brvbar,57,sect,58,uml,59,copy,' + '5a,ordf,5b,laquo,5c,not,5d,shy,5e,reg,5f,macr,5g,deg,5h,plusmn,5i,sup2,5j,sup3,5k,acute,' + '5l,micro,5m,para,5n,middot,5o,cedil,5p,sup1,5q,ordm,5r,raquo,5s,frac14,5t,frac12,5u,frac34,' + '5v,iquest,60,Agrave,61,Aacute,62,Acirc,63,Atilde,64,Auml,65,Aring,66,AElig,67,Ccedil,' + '68,Egrave,69,Eacute,6a,Ecirc,6b,Euml,6c,Igrave,6d,Iacute,6e,Icirc,6f,Iuml,6g,ETH,6h,Ntilde,' + '6i,Ograve,6j,Oacute,6k,Ocirc,6l,Otilde,6m,Ouml,6n,times,6o,Oslash,6p,Ugrave,6q,Uacute,' + '6r,Ucirc,6s,Uuml,6t,Yacute,6u,THORN,6v,szlig,70,agrave,71,aacute,72,acirc,73,atilde,74,auml,' + '75,aring,76,aelig,77,ccedil,78,egrave,79,eacute,7a,ecirc,7b,euml,7c,igrave,7d,iacute,7e,icirc,' + '7f,iuml,7g,eth,7h,ntilde,7i,ograve,7j,oacute,7k,ocirc,7l,otilde,7m,ouml,7n,divide,7o,oslash,' + '7p,ugrave,7q,uacute,7r,ucirc,7s,uuml,7t,yacute,7u,thorn,7v,yuml,ci,fnof,sh,Alpha,si,Beta,' + 'sj,Gamma,sk,Delta,sl,Epsilon,sm,Zeta,sn,Eta,so,Theta,sp,Iota,sq,Kappa,sr,Lambda,ss,Mu,' + 'st,Nu,su,Xi,sv,Omicron,t0,Pi,t1,Rho,t3,Sigma,t4,Tau,t5,Upsilon,t6,Phi,t7,Chi,t8,Psi,' + 't9,Omega,th,alpha,ti,beta,tj,gamma,tk,delta,tl,epsilon,tm,zeta,tn,eta,to,theta,tp,iota,' + 'tq,kappa,tr,lambda,ts,mu,tt,nu,tu,xi,tv,omicron,u0,pi,u1,rho,u2,sigmaf,u3,sigma,u4,tau,' + 'u5,upsilon,u6,phi,u7,chi,u8,psi,u9,omega,uh,thetasym,ui,upsih,um,piv,812,bull,816,hellip,' + '81i,prime,81j,Prime,81u,oline,824,frasl,88o,weierp,88h,image,88s,real,892,trade,89l,alefsym,' + '8cg,larr,8ch,uarr,8ci,rarr,8cj,darr,8ck,harr,8dl,crarr,8eg,lArr,8eh,uArr,8ei,rArr,8ej,dArr,' + '8ek,hArr,8g0,forall,8g2,part,8g3,exist,8g5,empty,8g7,nabla,8g8,isin,8g9,notin,8gb,ni,8gf,prod,' + '8gh,sum,8gi,minus,8gn,lowast,8gq,radic,8gt,prop,8gu,infin,8h0,ang,8h7,and,8h8,or,8h9,cap,8ha,cup,' + '8hb,int,8hk,there4,8hs,sim,8i5,cong,8i8,asymp,8j0,ne,8j1,equiv,8j4,le,8j5,ge,8k2,sub,8k3,sup,8k4,' + 'nsub,8k6,sube,8k7,supe,8kl,oplus,8kn,otimes,8l5,perp,8m5,sdot,8o8,lceil,8o9,rceil,8oa,lfloor,8ob,' + 'rfloor,8p9,lang,8pa,rang,9ea,loz,9j0,spades,9j3,clubs,9j5,hearts,9j6,diams,ai,OElig,aj,oelig,b0,' + 'Scaron,b1,scaron,bo,Yuml,m6,circ,ms,tilde,802,ensp,803,emsp,809,thinsp,80c,zwnj,80d,zwj,80e,lrm,' + '80f,rlm,80j,ndash,80k,mdash,80o,lsquo,80p,rsquo,80q,sbquo,80s,ldquo,80t,rdquo,80u,bdquo,810,dagger,' + '811,Dagger,81g,permil,81p,lsaquo,81q,rsaquo,85c,euro', 32); //Some basic mappings for attributes and default values. STYLES = { "strokeStyle": { svgAttr: "stroke", //corresponding svg attribute canvas: "#000000", //canvas default svg: "none", //svg default apply: "stroke" //apply on stroke() or fill() }, "fillStyle": { svgAttr: "fill", canvas: "#000000", svg: null, //svg default is black, but we need to special case this to handle canvas stroke without fill apply: "fill" }, "lineCap": { svgAttr: "stroke-linecap", canvas: "butt", svg: "butt", apply: "stroke" }, "lineJoin": { svgAttr: "stroke-linejoin", canvas: "miter", svg: "miter", apply: "stroke" }, "miterLimit": { svgAttr: "stroke-miterlimit", canvas: 10, svg: 4, apply: "stroke" }, "lineWidth": { svgAttr: "stroke-width", canvas: 1, svg: 1, apply: "stroke" }, "globalAlpha": { svgAttr: "opacity", canvas: 1, svg: 1, apply: "fill stroke" }, "font": { //font converts to multiple svg attributes, there is custom logic for this canvas: "10px sans-serif" }, "shadowColor": { canvas: "#000000" }, "shadowOffsetX": { canvas: 0 }, "shadowOffsetY": { canvas: 0 }, "shadowBlur": { canvas: 0 }, "textAlign": { canvas: "start" }, "textBaseline": { canvas: "alphabetic" }, "lineDash": { svgAttr: "stroke-dasharray", canvas: [], svg: null, apply: "stroke" } }; /** * * @param gradientNode - reference to the gradient * @constructor */ CanvasGradient = function (gradientNode, ctx) { this.__root = gradientNode; this.__ctx = ctx; }; /** * Adds a color stop to the gradient root */ CanvasGradient.prototype.addColorStop = function (offset, color) { var stop = this.__ctx.__createElement("stop"), regex, matches; stop.setAttribute("offset", offset); if (color && color.indexOf("rgba") !== -1) { //separate alpha value, since webkit can't handle it regex = /rgba\(\s*(\d+)\s*,\s*(\d+)\s*,\s*(\d+)\s*,\s*(\d?\.?\d*)\s*\)/gi; matches = regex.exec(color); stop.setAttribute("stop-color", format("rgb({r},{g},{b})", { r: matches[1], g: matches[2], b: matches[3] })); stop.setAttribute("stop-opacity", matches[4]); } else { stop.setAttribute("stop-color", color); } this.__root.appendChild(stop); }; CanvasPattern = function (pattern, ctx) { this.__root = pattern; this.__ctx = ctx; }; /** * The mock canvas context * @param config - options include: * ctx - existing Context2D to wrap around * width - width of your canvas (defaults to 500) * height - height of your canvas (defaults to 500) * enableMirroring - enables canvas mirroring (get image data) (defaults to false) * document - the document object (defaults to the current document) */ ctx = function (config) { if (!(this instanceof ctx)) { //did someone call this without new? return new ctx(config); } // clone config this.config = config; //setup options this.width = config.width; this.height = config.height; this.enableMirroring = config.enableMirroring || false; this.canvas = this; ///point back to this instance! this.__document = document; // allow passing in an existing context to wrap around // if a context is passed in, we know a canvas already exist if (config.ctx) { this.__ctx = config.ctx; } else { this.__canvas = this.__document.createElement("canvas"); this.__ctx = this.__canvas.getContext("2d"); } // give this canvas a type this.isSVG = true; this.__setDefaultStyles(); this.__stack = [this.__getStyleState()]; this.__groupStack = []; // root svg element this.__root = this.__createElement("svg"); this.__root.setAttribute("width", this.width); this.__root.setAttribute("height", this.height); // allow contents to overflow svg bbox this.__root.setAttribute('overflow', 'visible'); // viewbox if (config.viewbox) { const str = config.viewbox.x + ' ' + config.viewbox.y + ' ' + config.viewbox.width + ' ' + config.viewbox.height; this.__root.setAttribute("viewBox", str); this.viewbox = config.viewbox; } // make sure we don't generate the same ids in defs this.__ids = {}; // defs this.__defs = this.__createElement("defs"); this.__root.appendChild(this.__defs); this.multiLocusGap = config.multiLocusGap; // svg background color let backdropConfig = { id: 'svg_output_backdrop', width: '100%', height: '100%', fill: config.backdropColor || 'white' }; let backdropRect = this.__createElement('rect', backdropConfig); this.__root.appendChild(backdropRect); // root group this.__rootGroup = this.__createElement('g', { id: 'root-group' }); this.__root.appendChild(this.__rootGroup); // point current element to root group this.__currentElement = this.__rootGroup; }; ctx.prototype.setWidth = function (width) { this.width = width; this.__root.setAttribute("width", this.width); const str = this.config.viewbox.x + ' ' + this.config.viewbox.y + ' ' + width + ' ' + this.config.viewbox.height; this.__root.setAttribute("viewBox", str); }; ctx.prototype.setHeight = function (height) { this.height = height; this.__root.setAttribute("height", this.height); const str = this.config.viewbox.x + ' ' + this.config.viewbox.y + ' ' + this.config.viewbox.width + ' ' + height; this.__root.setAttribute("viewBox", str); }; /** * Creates the specified svg element * @private */ ctx.prototype.__createElement = function (elementName, properties, resetFill) { if (typeof properties === "undefined") { properties = {}; } let element = this.__document.createElementNS("http://www.w3.org/2000/svg", elementName); if (resetFill) { //if fill or stroke is not specified, the svg element should not display. By default SVG's fill is black. element.setAttribute("fill", "none"); element.setAttribute("stroke", "none"); } for (let key of Object.keys(properties)) { element.setAttribute(key, properties[key]); } return element; }; /** * Applies default canvas styles to the context * @private */ ctx.prototype.__setDefaultStyles = function () { //default 2d canvas context properties see:http://www.w3.org/TR/2dcontext/ var keys = Object.keys(STYLES), i, key; for (i = 0; i < keys.length; i++) { key = keys[i]; this[key] = STYLES[key].canvas; } }; /** * Applies styles on restore * @param styleState * @private */ ctx.prototype.__applyStyleState = function (styleState) { var keys = Object.keys(styleState), i, key; for (i = 0; i < keys.length; i++) { key = keys[i]; this[key] = styleState[key]; } }; /** * Gets the current style state * @return {Object} * @private */ ctx.prototype.__getStyleState = function () { var i, styleState = {}, keys = Object.keys(STYLES), key; for (i = 0; i < keys.length; i++) { key = keys[i]; styleState[key] = this[key]; } return styleState; }; /** * Apples the current styles to the current SVG element. On "ctx.fill" or "ctx.stroke" * @param type * @private */ ctx.prototype.__applyStyleToCurrentElement = function (type) { var currentElement = this.__currentElement; var currentStyleGroup = this.__currentElementsToStyle; if (currentStyleGroup) { currentElement.setAttribute(type, ""); currentElement = currentStyleGroup.element; currentStyleGroup.children.forEach(function (node) { node.setAttribute(type, ""); }); } var keys = Object.keys(STYLES), i, style, value, id, regex, matches; for (i = 0; i < keys.length; i++) { style = STYLES[keys[i]]; value = this[keys[i]]; if (style.apply) { //is this a gradient or pattern? if (value instanceof CanvasPattern) { //pattern if (value.__ctx) { //copy over defs while (value.__ctx.__defs.childNodes.length) { id = value.__ctx.__defs.childNodes[0].getAttribute("id"); this.__ids[id] = id; this.__defs.appendChild(value.__ctx.__defs.childNodes[0]); } } currentElement.setAttribute(style.apply, format("url(#{id})", { id: value.__root.getAttribute("id") })); } else if (value instanceof CanvasGradient) { //gradient currentElement.setAttribute(style.apply, format("url(#{id})", { id: value.__root.getAttribute("id") })); } else if (style && style.apply.indexOf(type) !== -1 && style.svg !== value) { if ((style.svgAttr === "stroke" || style.svgAttr === "fill") && value && value.indexOf("rgba") !== -1) { //separate alpha value, since illustrator can't handle it regex = /rgba\(\s*(\d+)\s*,\s*(\d+)\s*,\s*(\d+)\s*,\s*(\d?\.?\d*)\s*\)/gi; matches = regex.exec(value); currentElement.setAttribute(style.svgAttr, format("rgb({r},{g},{b})", { r: matches[1], g: matches[2], b: matches[3] })); //should take globalAlpha here var opacity = matches[4]; var globalAlpha = this.globalAlpha; if (globalAlpha != null) { opacity *= globalAlpha; } currentElement.setAttribute(style.svgAttr + "-opacity", opacity); } else { var attr = style.svgAttr; if (keys[i] === 'globalAlpha') { attr = type + '-' + style.svgAttr; if (currentElement.getAttribute(attr)) { //fill-opacity or stroke-opacity has already been set by stroke or fill. continue; } } //otherwise only update attribute if right type, and not svg default currentElement.setAttribute(attr, value); } } } } }; /** * Will return the closest group or svg node. May return the current element. * @private */ ctx.prototype.__closestGroupOrSvg = function (node) { node = node || this.__currentElement; if (node.nodeName === "g" || node.nodeName === "svg") { return node; } else { return this.__closestGroupOrSvg(node.parentNode); } }; /** * Returns the serialized value of the svg so far * @param fixNamedEntities - Standalone SVG doesn't support named entities, which document.createTextNode encodes. * If true, we attempt to find all named entities and encode it as a numeric entity. * @return serialized svg */ ctx.prototype.getSerializedSvg = function (fixNamedEntities) { var serialized = new XMLSerializer().serializeToString(this.__root), keys, i, key, value, regexp; //IE search for a duplicate xmnls because they didn't implement setAttributeNS correctly // xmlns = /xmlns="http:\/\/www\.w3\.org\/2000\/svg".+xmlns="http:\/\/www\.w3\.org\/2000\/svg/gi; // if (xmlns.test(serialized)) { // serialized = serialized.replace('xmlns="http://www.w3.org/2000/svg','xmlns:xlink="http://www.w3.org/1999/xlink'); // } if (fixNamedEntities) { keys = Object.keys(namedEntities); //loop over each named entity and replace with the proper equivalent. for (i = 0; i < keys.length; i++) { key = keys[i]; value = namedEntities[key]; regexp = new RegExp(key, "gi"); if (regexp.test(serialized)) { serialized = serialized.replace(regexp, value); } } } return serialized; }; /** * Returns the root svg * @return */ ctx.prototype.getSvg = function () { return this.__root; }; /** * Will generate a group tag. */ ctx.prototype.saveWithTranslationAndClipRect = function (id, tx, ty, width, height, clipYOffset) { // clip rect const clip_id = `${id}_clip_rect`; let clipPath = this.__createElement('clipPath', { id: clip_id }); this.__defs.appendChild(clipPath); const config = { x: '0', y: clipYOffset.toString(), width: width.toString(), height: height.toString() }; clipPath.appendChild(this.__createElement('rect', config)); const group = this.__createElement("g"); group.setAttribute('transform', format('translate({x},{y})', { x: tx, y: ty })); group.setAttribute('clip-path', format('url(#{id})', { id: clip_id })); const parent = this.__closestGroupOrSvg(); parent.appendChild(group); this.__groupStack.push(parent); this.__currentElement = group; this.__stack.push(this.__getStyleState()); }; ctx.prototype.save = function () { var group = this.__createElement("g"); var parent = this.__closestGroupOrSvg(); this.__groupStack.push(parent); parent.appendChild(group); this.__currentElement = group; this.__stack.push(this.__getStyleState()); }; /** * Sets current element to parent, or just root if already root */ ctx.prototype.restore = function () { this.__currentElement = this.__groupStack.pop(); this.__currentElementsToStyle = null; //Clearing canvas will make the poped group invalid, currentElement is set to the root group node. if (!this.__currentElement) { this.__currentElement = this.__root.childNodes[1]; } var state = this.__stack.pop(); this.__applyStyleState(state); }; /** * Helper method to add transform * @private */ ctx.prototype.__addTransform = function (t) { //if the current element has siblings, add another group var parent = this.__closestGroupOrSvg(); if (parent.childNodes.length > 0) { if (this.__currentElement.nodeName === "path") { if (!this.__currentElementsToStyle) this.__currentElementsToStyle = { element: parent, children: [] }; this.__currentElementsToStyle.children.push(this.__currentElement); this.__applyCurrentDefaultPath(); } var group = this.__createElement("g"); parent.appendChild(group); this.__currentElement = group; } var transform = this.__currentElement.getAttribute("transform"); if (transform) { transform += " "; } else { transform = ""; } transform += t; this.__currentElement.setAttribute("transform", transform); }; ctx.prototype.addTrackGroupWithTranslationAndClipRect = function (id, tx, ty, width, height, clipYOffset) { // clip rect const clip_id = id + '_clip_rect'; let clipPath = this.__createElement('clipPath', { id: clip_id }); this.__defs.appendChild(clipPath); clipPath.appendChild(this.__createElement('rect', { x: '0', y: clipYOffset.toString(), width: width.toString(), height: height.toString() })); let group = this.__createElement('g'); this.__rootGroup.appendChild(group); group.setAttribute('transform', format('translate({x},{y})', { x: tx, y: ty })); group.setAttribute('id', id + '_group'); // add clip rect group.setAttribute('clip-path', format('url(#{id})', { id: clip_id })); this.__currentElement = group; }; /** * scales the current element */ ctx.prototype.scale = function (x, y) { if (y === undefined) { y = x; } this.__addTransform(format("scale({x},{y})", { x: x, y: y })); }; /** * rotates the current element */ ctx.prototype.rotate = function (angle) { var degrees = angle * 180 / Math.PI; this.__addTransform(format("rotate({angle},{cx},{cy})", { angle: degrees, cx: 0, cy: 0 })); }; /** * translates the current element */ ctx.prototype.translate = function (x, y) { this.__addTransform(format("translate({x},{y})", { x: x, y: y })); }; /** * applies a transform to the current element */ ctx.prototype.transform = function (a, b, c, d, e, f) { this.__addTransform(format("matrix({a},{b},{c},{d},{e},{f})", { a: a, b: b, c: c, d: d, e: e, f: f })); }; /** * Create a new Path Element */ ctx.prototype.beginPath = function () { var path, parent; // Note that there is only one current default path, it is not part of the drawing state. // See also: https://html.spec.whatwg.org/multipage/scripting.html#current-default-path this.__currentDefaultPath = ""; this.__currentPosition = {}; path = this.__createElement("path", {}, true); parent = this.__closestGroupOrSvg(); parent.appendChild(path); this.__currentElement = path; }; /** * Helper function to apply currentDefaultPath to current path element * @private */ ctx.prototype.__applyCurrentDefaultPath = function () { var currentElement = this.__currentElement; if (currentElement.nodeName === "path") { currentElement.setAttribute("d", this.__currentDefaultPath); } else { console.error("Attempted to apply path command to node", currentElement.nodeName); } }; /** * Helper function to add path command * @private */ ctx.prototype.__addPathCommand = function (command) { this.__currentDefaultPath += " "; this.__currentDefaultPath += command; }; /** * Adds the move command to the current path element, * if the currentPathElement is not empty create a new path element */ ctx.prototype.moveTo = function (x, y) { if (this.__currentElement.nodeName !== "path") { this.beginPath(); } // creates a new subpath with the given point this.__currentPosition = { x: x, y: y }; this.__addPathCommand(format("M {x} {y}", { x: x, y: y })); }; /** * Closes the current path */ ctx.prototype.closePath = function () { if (this.__currentDefaultPath) { this.__addPathCommand("Z"); } }; /** * Adds a line to command */ ctx.prototype.lineTo = function (x, y) { this.__currentPosition = { x: x, y: y }; if (this.__currentDefaultPath && this.__currentDefaultPath.indexOf('M') > -1) { this.__addPathCommand(format("L {x} {y}", { x: x, y: y })); } else { this.__addPathCommand(format("M {x} {y}", { x: x, y: y })); } }; /** * Add a bezier command */ ctx.prototype.bezierCurveTo = function (cp1x, cp1y, cp2x, cp2y, x, y) { this.__currentPosition = { x: x, y: y }; this.__addPathCommand(format("C {cp1x} {cp1y} {cp2x} {cp2y} {x} {y}", { cp1x: cp1x, cp1y: cp1y, cp2x: cp2x, cp2y: cp2y, x: x, y: y })); }; /** * Adds a quadratic curve to command */ ctx.prototype.quadraticCurveTo = function (cpx, cpy, x, y) { this.__currentPosition = { x: x, y: y }; this.__addPathCommand(format("Q {cpx} {cpy} {x} {y}", { cpx: cpx, cpy: cpy, x: x, y: y })); }; /** * Return a new normalized vector of given vector */ var normalize$1 = function (vector) { var len = Math.sqrt(vector[0] * vector[0] + vector[1] * vector[1]); return [vector[0] / len, vector[1] / len]; }; /** * Adds the arcTo to the current path * * @see http://www.w3.org/TR/2015/WD-2dcontext-20150514/#dom-context-2d-arcto */ ctx.prototype.arcTo = function (x1, y1, x2, y2, radius) { // Let the point (x0, y0) be the last point in the subpath. var x0 = this.__currentPosition && this.__currentPosition.x; var y0 = this.__currentPosition && this.__currentPosition.y; // First ensure there is a subpath for (x1, y1). if (typeof x0 == "undefined" || typeof y0 == "undefined") { return; } // Negative values for radius must cause the implementation to throw an IndexSizeError exception. if (radius < 0) { throw new Error("IndexSizeError: The radius provided (" + radius + ") is negative."); } // If the point (x0, y0) is equal to the point (x1, y1), // or if the point (x1, y1) is equal to the point (x2, y2), // or if the radius radius is zero, // then the method must add the point (x1, y1) to the subpath, // and connect that point to the previous point (x0, y0) by a straight line. if (x0 === x1 && y0 === y1 || x1 === x2 && y1 === y2 || radius === 0) { this.lineTo(x1, y1); return; } // Otherwise, if the points (x0, y0), (x1, y1), and (x2, y2) all lie on a single straight line, // then the method must add the point (x1, y1) to the subpath, // and connect that point to the previous point (x0, y0) by a straight line. var unit_vec_p1_p0 = normalize$1([x0 - x1, y0 - y1]); var unit_vec_p1_p2 = normalize$1([x2 - x1, y2 - y1]); if (unit_vec_p1_p0[0] * unit_vec_p1_p2[1] === unit_vec_p1_p0[1] * unit_vec_p1_p2[0]) { this.lineTo(x1, y1); return; } // Otherwise, let The Arc be the shortest arc given by circumference of the circle that has radius radius, // and that has one point tangent to the half-infinite line that crosses the point (x0, y0) and ends at the point (x1, y1), // and that has a different point tangent to the half-infinite line that ends at the point (x1, y1), and crosses the point (x2, y2). // The points at which this circle touches these two lines are called the start and end tangent points respectively. // note that both vectors are unit vectors, so the length is 1 var cos = unit_vec_p1_p0[0] * unit_vec_p1_p2[0] + unit_vec_p1_p0[1] * unit_vec_p1_p2[1]; var theta = Math.acos(Math.abs(cos)); // Calculate origin var unit_vec_p1_origin = normalize$1([unit_vec_p1_p0[0] + unit_vec_p1_p2[0], unit_vec_p1_p0[1] + unit_vec_p1_p2[1]]); var len_p1_origin = radius / Math.sin(theta / 2); var x = x1 + len_p1_origin * unit_vec_p1_origin[0]; var y = y1 + len_p1_origin * unit_vec_p1_origin[1]; // Calculate start angle and end angle // rotate 90deg clockwise (note that y axis points to its down) var unit_vec_origin_start_tangent = [-unit_vec_p1_p0[1], unit_vec_p1_p0[0]]; // rotate 90deg counter clockwise (note that y axis points to its down) var unit_vec_origin_end_tangent = [unit_vec_p1_p2[1], -unit_vec_p1_p2[0]]; var getAngle = function (vector) { // get angle (clockwise) between vector and (1, 0) var x = vector[0]; var y = vector[1]; if (y >= 0) { // note that y axis points to its down return Math.acos(x); } else { return -Math.acos(x); } }; var startAngle = getAngle(unit_vec_origin_start_tangent); var endAngle = getAngle(unit_vec_origin_end_tangent); // Connect the point (x0, y0) to the start tangent point by a straight line this.lineTo(x + unit_vec_origin_start_tangent[0] * radius, y + unit_vec_origin_start_tangent[1] * radius); // Connect the start tangent point to the end tangent point by arc // and adding the end tangent point to the subpath. this.arc(x, y, radius, startAngle, endAngle); }; /** * Sets the stroke property on the current element */ ctx.prototype.stroke = function () { if (this.__currentElement.nodeName === "path") { this.__currentElement.setAttribute("paint-order", "fill stroke markers"); } this.__applyCurrentDefaultPath(); this.__applyStyleToCurrentElement("stroke"); }; /** * Sets fill properties on the current element */ ctx.prototype.fill = function () { if (this.__currentElement.nodeName === "path") { this.__currentElement.setAttribute("paint-order", "stroke fill markers"); } this.__applyCurrentDefaultPath(); this.__applyStyleToCurrentElement("fill"); }; /** * Adds a rectangle to the path. */ ctx.prototype.rect = function (x, y, width, height) { if (this.__currentElement.nodeName !== "path") { this.beginPath(); } this.moveTo(x, y); this.lineTo(x + width, y); this.lineTo(x + width, y + height); this.lineTo(x, y + height); this.lineTo(x, y); this.closePath(); }; /** * adds a rectangle element */ ctx.prototype.fillRect = function (x, y, width, height) { if (height < 0) { y += height; height = -height; } if (width < 0) { x += width; width = -width; } // See if rect instersects current viewbox var r2 = { x: x, y: y, width: width, height: height }; if (this.viewbox) { if (!intersectRect(this.viewbox, r2)) { return; } } var rect, parent; rect = this.__createElement("rect", r2, true); parent = this.__closestGroupOrSvg(); parent.appendChild(rect); this.__currentElement = rect; this.__applyStyleToCurrentElement("fill"); }; function intersectRect(rect1, rect2) { return rect1.x < rect2.x + rect2.width && rect1.x + rect1.width > rect2.x && rect1.y < rect2.y + rect2.height && rect1.y + rect1.height > rect2.y; } /** * Draws a rectangle with no fill * @param x * @param y * @param width * @param height */ ctx.prototype.strokeRect = function (x, y, width, height) { var rect, parent; rect = this.__createElement("rect", { x: x, y: y, width: width, height: height }, true); parent = this.__closestGroupOrSvg(); parent.appendChild(rect); this.__currentElement = rect; this.__applyStyleToCurrentElement("stroke"); }; /** * Clear entire canvas: * 1. save current transforms * 2. remove all the childNodes of the root g element */ ctx.prototype.__clearCanvas = function () { var current = this.__closestGroupOrSvg(), transform = current.getAttribute("transform"); var rootGroup = this.__root.childNodes[1]; var childNodes = rootGroup.childNodes; for (var i = childNodes.length - 1; i >= 0; i--) { if (childNodes[i]) { rootGroup.removeChild(childNodes[i]); } } this.__currentElement = rootGroup; //reset __groupStack as all the child group nodes are all removed. this.__groupStack = []; if (transform) { this.__addTransform(transform); } }; /** * "Clears" a canvas by just drawing a white rectangle in the current group. */ ctx.prototype.clearRect = function (x, y, width, height) { //clear entire canvas if (x === 0 && y === 0 && width === this.width && height === this.height) { this.__clearCanvas(); return; } var rect, parent = this.__closestGroupOrSvg(); rect = this.__createElement("rect", { x: x, y: y, width: width, height: height, fill: "#FFFFFF" }, true); parent.appendChild(rect); }; /** * Adds a linear gradient to a defs tag. * Returns a canvas gradient object that has a reference to it's parent def */ ctx.prototype.createLinearGradient = function (x1, y1, x2, y2) { var grad = this.__createElement("linearGradient", { id: randomString(this.__ids), x1: x1 + "px", x2: x2 + "px", y1: y1 + "px", y2: y2 + "px", "gradientUnits": "userSpaceOnUse" }, false); this.__defs.appendChild(grad); return new CanvasGradient(grad, this); }; /** * Adds a radial gradient to a defs tag. * Returns a canvas gradient object that has a reference to it's parent def */ ctx.prototype.createRadialGradient = function (x0, y0, r0, x1, y1, r1) { var grad = this.__createElement("radialGradient", { id: randomString(this.__ids), cx: x1 + "px", cy: y1 + "px", r: r1 + "px", fx: x0 + "px", fy: y0 + "px", "gradientUnits": "userSpaceOnUse" }, false); this.__defs.appendChild(grad); return new CanvasGradient(grad, this); }; /** * Parses the font string and returns svg mapping * @private */ ctx.prototype.__parseFont = function () { var regex = /^\s*(?=(?:(?:[-a-z]+\s*){0,2}(italic|oblique))?)(?=(?:(?:[-a-z]+\s*){0,2}(small-caps))?)(?=(?:(?:[-a-z]+\s*){0,2}(bold(?:er)?|lighter|[1-9]00))?)(?:(?:normal|\1|\2|\3)\s*){0,3}((?:xx?-)?(?:small|large)|medium|smaller|larger|[.\d]+(?:\%|in|[cem]m|ex|p[ctx]))(?:\s*\/\s*(normal|[.\d]+(?:\%|in|[cem]m|ex|p[ctx])))?\s*([-,\'\"\sa-z0-9]+?)\s*$/i; var fontPart = regex.exec(this.font); var data = { style: fontPart[1] || 'normal', size: fontPart[4] || '10px', family: fontPart[6] || 'sans-serif', weight: fontPart[3] || 'normal', decoration: fontPart[2] || 'normal', href: null }; //canvas doesn't support underline natively, but we can pass this attribute if (this.__fontUnderline === "underline") { data.decoration = "underline"; } //canvas also doesn't support linking, but we can pass this as well if (this.__fontHref) { data.href = this.__fontHref; } return data; }; /** * Helper to link text fragments * @param font * @param element * @return {*} * @private */ ctx.prototype.__wrapTextLink = function (font, element) { if (font.href) { var a = this.__createElement("a"); a.setAttributeNS("http://www.w3.org/1999/xlink", "xlink:href", font.href); a.appendChild(element); return a; } return element; }; /** * Fills or strokes text * @param text * @param x * @param y * @param action - stroke or fill * @private */ ctx.prototype.__applyText = function (text, x, y, action) { var font = this.__parseFont(), parent = this.__closestGroupOrSvg(), textElement = this.__createElement("text", { "font-family": font.family, "font-size": font.size, "font-style": font.style, "font-weight": font.weight, "text-decoration": font.decoration, "x": x, "y": y, "text-anchor": getTextAnchor(this.textAlign), "dominant-baseline": getDominantBaseline(this.textBaseline) }, true); textElement.appendChild(this.__document.createTextNode(text)); this.__currentElement = textElement; this.__applyStyleToCurrentElement(action); parent.appendChild(this.__wrapTextLink(font, textElement)); }; /** * Creates a text element * @param text * @param x * @param y */ ctx.prototype.fillText = function (text, x, y) { this.__applyText(text, x, y, "fill"); }; /** * Strokes text * @param text * @param x * @param y */ ctx.prototype.strokeText = function (text, x, y) { this.__applyText(text, x, y, "stroke"); }; /** * No need to implement this for svg. * @param text * @return {TextMetrics} */ ctx.prototype.measureText = function (text) { this.__ctx.font = this.font; return this.__ctx.measureText(text); }; /** * Arc command! */ ctx.prototype.arc = function (x, y, radius, startAngle, endAngle, counterClockwise) { // in canvas no circle is drawn if no angle is provided. if (startAngle === endAngle) { return; } startAngle = startAngle % (2 * Math.PI); endAngle = endAngle % (2 * Math.PI); if (startAngle === endAngle) { //circle time! subtract some of the angle so svg is happy (svg elliptical arc can't draw a full circle) endAngle = (endAngle + 2 * Math.PI - 0.001 * (counterClockwise ? -1 : 1)) % (2 * Math.PI); } var endX = x + radius * Math.cos(endAngle), endY = y + radius * Math.sin(endAngle), startX = x + radius * Math.cos(startAngle), startY = y + radius * Math.sin(startAngle), sweepFlag = counterClockwise ? 0 : 1, largeArcFlag = 0, diff = endAngle - startAngle; // https://github.com/gliffy/canvas2svg/issues/4 if (diff < 0) { diff += 2 * Math.PI; } if (counterClockwise) { largeArcFlag = diff > Math.PI ? 0 : 1; } else { largeArcFlag = diff > Math.PI ? 1 : 0; } this.lineTo(startX, startY); this.__addPathCommand(format("A {rx} {ry} {xAxisRotation} {largeArcFlag} {sweepFlag} {endX} {endY}", { rx: radius, ry: radius, xAxisRotation: 0, largeArcFlag: largeArcFlag, sweepFlag: sweepFlag, endX: endX, endY: endY })); this.__currentPosition = { x: endX, y: endY }; }; /** * Generates a ClipPath from the clip command. */ ctx.prototype.clip = function () { var group = this.__closestGroupOrSvg(), clipPath = this.__createElement("clipPath"), id = randomString(this.__ids), newGroup = this.__createElement("g"); this.__applyCurrentDefaultPath(); group.removeChild(this.__currentElement); clipPath.setAttribute("id", id); clipPath.appendChild(this.__currentElement); this.__defs.appendChild(clipPath); //set the clip path to this group group.setAttribute("clip-path", format("url(#{id})", { id: id })); //clip paths can be scaled and transformed, we need to add another wrapper group to avoid later transformations // to this path group.appendChild(newGroup); this.__currentElement = newGroup; }; /** * Draws a canvas, image or mock context to this canvas. * Note that all svg dom manipulation uses node.childNodes rather than node.children for IE support. * http://www.whatwg.org/specs/web-apps/current-work/multipage/the-canvas-element.html#dom-context-2d-drawimage */ ctx.prototype.drawImage = function () { //convert arguments to a real array var args = Array.prototype.slice.call(arguments), image = args[0], dx, dy, dw, dh, sx = 0, sy = 0, sw, sh, parent, svg, defs, group, svgImage, canvas, context, id; if (args.length === 3) { dx = args[1]; dy = args[2]; sw = image.width; sh = image.height; dw = sw; dh = sh; } else if (args.length === 5) { dx = args[1]; dy = args[2]; dw = args[3]; dh = args[4]; sw = image.width; sh = image.height; } else if (args.length === 9) { sx = args[1]; sy = args[2]; sw = args[3]; sh = args[4]; dx = args[5]; dy = args[6]; dw = args[7]; dh = args[8]; } else { throw new Error("Invalid number of arguments passed to drawImage: " + arguments.length); } parent = this.__closestGroupOrSvg(); var translateDirective = "translate(" + dx + ", " + dy + ")"; if (image instanceof ctx) { //canvas2svg mock canvas context. In the future we may want to clone nodes instead. //also I'm currently ignoring dw, dh, sw, sh, sx, sy for a mock context. svg = image.getSvg().cloneNode(true); if (svg.childNodes && svg.childNodes.length > 1) { defs = svg.childNodes[0]; while (defs.childNodes.length) { id = defs.childNodes[0].getAttribute("id"); this.__ids[id] = id; this.__defs.appendChild(defs.childNodes[0]); } group = svg.childNodes[1]; if (group) { //save original transform var originTransform = group.getAttribute("transform"); var transformDirective; if (originTransform) { transformDirective = originTransform + " " + translateDirective; } else { transformDirective = translateDirective; } group.setAttribute("transform", transformDirective); parent.appendChild(group); } } } else if (image.nodeName === "CANVAS" || image.nodeName === "IMG") { //canvas or image svgImage = this.__createElement("image"); svgImage.setAttribute("width", dw); svgImage.setAttribute("height", dh); svgImage.setAttribute("preserveAspectRatio", "none"); if (sx || sy || sw !== image.width || sh !== image.height) { //crop the image using a temporary canvas canvas = this.__document.createElement("canvas"); canvas.width = dw; canvas.height = dh; context = canvas.getContext("2d"); context.drawImage(image, sx, sy, sw, sh, 0, 0, dw, dh); image = canvas; } svgImage.setAttribute("transform", translateDirective); svgImage.setAttributeNS("http://www.w3.org/1999/xlink", "xlink:href", image.nodeName === "CANVAS" ? image.toDataURL() : image.getAttribute("src")); parent.appendChild(svgImage); } }; /** * Generates a pattern tag */ ctx.prototype.createPattern = function (image, repetition) { let pattern = this.__document.__createElement("pattern"); let id = randomString(this.__ids); let img; pattern.setAttribute("id", id); pattern.setAttribute("width", image.width); pattern.setAttribute("height", image.height); if (image.nodeName === "CANVAS" || image.nodeName === "IMG") { img = this.__createElement("image"); img.setAttribute("width", image.width); img.setAttribute("height", image.height); img.setAttributeNS("http://www.w3.org/1999/xlink", "xlink:href", image.nodeName === "CANVAS" ? image.toDataURL() : image.getAttribute("src")); pattern.appendChild(img); this.__defs.appendChild(pattern); } else if (image instanceof ctx) { pattern.appendChild(image.__root.childNodes[1]); this.__defs.appendChild(pattern); } return new CanvasPattern(pattern, this); }; ctx.prototype.setLineDash = function (dashArray) { if (dashArray && dashArray.length > 0) { this.lineDash = dashArray.join(","); } else { this.lineDash = null; } }; /** * Not yet implemented */ ctx.prototype.drawFocusRing = function () {}; ctx.prototype.createImageData = function () {}; ctx.prototype.getImageData = function () {}; ctx.prototype.putImageData = function () {}; ctx.prototype.globalCompositeOperation = function () {}; ctx.prototype.setTransform = function () {}; var C2S = ctx; /** * Created by dat on 9/16/16. */ const NOT_LOADED_MESSAGE = 'Error loading track data'; class ViewPort extends ViewportBase { constructor(trackView, $viewportContainer, referenceFrame, width) { super(trackView, $viewportContainer, referenceFrame, width); } initializationHelper() { this.menuPopup = new MenuPopup(this.trackView.$viewportContainer); this.menuPopup.$popover.hide(); this.addMouseHandlers(); this.$spinner = $('
'); this.$spinner.append(createIcon$1("spinner")); this.$viewport.append(this.$spinner); this.stopSpinner(); const { track } = this.trackView; if ('sequence' !== track.type) { this.$zoomInNotice = this.createZoomInNotice(this.$content); } if (track.name && "sequence" !== track.config.type) { this.$trackLabel = $('
'); this.$viewport.append(this.$trackLabel); this.setTrackLabel(track.name); if (false === this.browser.trackLabelsVisible) { this.$trackLabel.hide(); } this.$trackLabel.click(e => { let str; e.stopPropagation(); if (typeof track.description === 'function') { str = track.description(); } else if (track.description) { str = `
${track.description}
`; } else { if (track.url) { if (track.url instanceof File) { str = `
Filename: ${track.url.name}`; } else { str = `
URL: ${track.url}`; } } else { str = track.name; } } if (this.popover) this.popover.dispose(); this.popover = new Popover(this.trackView.$viewportContainer.get(0), track.name || 'unnamed'); this.popover.presentContentWithEvent(e, str); }); this.$trackLabel.mousedown(function (e) { // Prevent bubbling e.stopPropagation(); }); this.$trackLabel.mouseup(function (e) { // Prevent bubbling e.stopPropagation(); }); this.$trackLabel.mousemove(function (e) { // Prevent bubbling e.stopPropagation(); }); } } setTrackLabel(label) { this.trackView.track.name = this.trackView.track.config.name = label; this.$trackLabel.empty(); this.$trackLabel.html(label); const txt = this.$trackLabel.text(); this.$trackLabel.attr('title', txt); } startSpinner() { const $spinner = this.$spinner; if ($spinner) { $spinner.addClass("igv-fa5-spin"); $spinner.show(); } } stopSpinner() { const $spinner = this.$spinner; if ($spinner) { $spinner.hide(); $spinner.removeClass("igv-fa5-spin"); } } checkZoomIn() { const showZoomInNotice = () => { const referenceFrame = this.referenceFrame; if (this.referenceFrame.chr.toLowerCase() === "all" && !this.trackView.track.supportsWholeGenome()) { return true; } else { const visibilityWindow = typeof this.trackView.track.getVisibilityWindow === 'function' ? this.trackView.track.getVisibilityWindow() : this.trackView.track.visibilityWindow; return visibilityWindow !== undefined && visibilityWindow > 0 && referenceFrame.bpPerPixel * this.$viewport.width() > visibilityWindow; } }; if (!this.viewIsReady()) { return false; } if (this.$zoomInNotice) { if (showZoomInNotice()) { // Out of visibility window if (this.canvas) { this.ctx.clearRect(0, 0, this.canvas.width, this.canvas.height); this.tile = undefined; } this.$zoomInNotice.show(); if (this.trackView.track.autoHeight) { const minHeight = this.trackView.minHeight || 0; this.setContentHeight(minHeight); } return false; } else { this.$zoomInNotice.hide(); return true; } } return true; } shift() { const self = this; const referenceFrame = self.referenceFrame; if (self.canvas && self.tile && self.tile.chr === self.referenceFrame.chr && self.tile.bpPerPixel === referenceFrame.bpPerPixel) { const pixelOffset = Math.round((self.tile.startBP - referenceFrame.start) / referenceFrame.bpPerPixel); self.canvas.style.left = pixelOffset + "px"; } } async loadFeatures() { const referenceFrame = this.referenceFrame; const chr = referenceFrame.chr; // Expand the requested range so we can pan a bit without reloading. But not beyond chromosome bounds const chrLength = this.browser.genome.getChromosome(chr).bpLength; const pixelWidth = this.$content.width() * 3; const bpWidth = pixelWidth * referenceFrame.bpPerPixel; const bpStart = Math.floor(Math.max(0, referenceFrame.start - bpWidth / 3)); const bpEnd = Math.ceil(Math.min(chrLength, bpStart + bpWidth)); if (this.loading && this.loading.start === bpStart && this.loading.end === bpEnd) { return undefined; } this.loading = { start: bpStart, end: bpEnd }; this.startSpinner(); // console.log('get features'); try { const features = await this.getFeatures(this.trackView.track, chr, bpStart, bpEnd, referenceFrame.bpPerPixel); let roiFeatures = []; const roi = mergeArrays(this.browser.roi, this.trackView.track.roi); if (roi) { for (let r of roi) { const f = await r.getFeatures(chr, bpStart, bpEnd, referenceFrame.bpPerPixel); roiFeatures.push({ track: r, features: f }); } } this.tile = new Tile(chr, bpStart, bpEnd, referenceFrame.bpPerPixel, features, roiFeatures); this.loading = false; this.hideMessage(); this.stopSpinner(); return this.tile; } catch (error) { // Track might have been removed during load if (this.trackView && this.trackView.disposed !== true) { this.showMessage(NOT_LOADED_MESSAGE); Alert.presentAlert(error); console.error(error); } } finally { this.loading = false; this.stopSpinner(); } } async repaint() { if (undefined === this.tile) { return; } let { features, roiFeatures, bpPerPixel, startBP, endBP } = this.tile; const isWGV = GenomeUtils.isWholeGenomeView(this.browser.referenceFrameList[0].chr); let pixelWidth; if (isWGV) { bpPerPixel = this.referenceFrame.initialEnd / this.$viewport.width(); startBP = 0; endBP = this.referenceFrame.initialEnd; pixelWidth = this.$viewport.width(); } else { pixelWidth = Math.ceil((endBP - startBP) / bpPerPixel); } // For deep tracks we paint a canvas == 3*viewportHeight centered on the current vertical scroll position const viewportHeight = this.$viewport.height(); const contentHeight = this.getContentHeight(); const minHeight = roiFeatures ? Math.max(contentHeight, viewportHeight) : contentHeight; // Need to fill viewport for ROIs. let pixelHeight = Math.min(minHeight, 3 * viewportHeight); if (0 === pixelWidth || 0 === pixelHeight) { if (this.canvas) { $(this.canvas).remove(); } return; } const canvasTop = Math.max(0, -this.$content.position().top - viewportHeight); // Always use high DPI if in compressed display mode, otherwise use preference setting; let devicePixelRatio; if ("FILL" === this.trackView.track.displayMode) { devicePixelRatio = window.devicePixelRatio; } else { devicePixelRatio = this.trackView.track.supportHiDPI === false ? 1 : window.devicePixelRatio; } const pixelXOffset = Math.round((startBP - this.referenceFrame.start) / this.referenceFrame.bpPerPixel); const newCanvas = $('').get(0); const ctx = newCanvas.getContext("2d"); newCanvas.style.width = pixelWidth + "px"; newCanvas.style.height = pixelHeight + "px"; newCanvas.width = devicePixelRatio * pixelWidth; newCanvas.height = devicePixelRatio * pixelHeight; ctx.scale(devicePixelRatio, devicePixelRatio); newCanvas.style.left = pixelXOffset + "px"; newCanvas.style.top = canvasTop + "px"; ctx.translate(0, -canvasTop); const drawConfiguration = { context: ctx, pixelXOffset, pixelWidth, pixelHeight, pixelTop: canvasTop, bpStart: startBP, bpEnd: endBP, bpPerPixel, referenceFrame: this.referenceFrame, selection: this.selection, viewport: this, viewportWidth: this.$viewport.width() //viewportContainerX: this.referenceFrame.toPixels(this.referenceFrame.start - startBP), //viewportContainerWidth: this.browser.getViewportContainerWidth() }; this.draw(drawConfiguration, features, roiFeatures); this.canvasVerticalRange = { top: canvasTop, bottom: canvasTop + pixelHeight }; if (this.$canvas) { this.$canvas.remove(); } this.$canvas = $(newCanvas); this.$content.append(this.$canvas); this.canvas = newCanvas; this.ctx = ctx; } draw(drawConfiguration, features, roiFeatures) { // console.log(`${ Date.now() } viewport draw(). track ${ this.trackView.track.type }. content-css-top ${ this.$content.css('top') }. canvas-top ${ drawConfiguration.pixelTop }.`) if (features) { drawConfiguration.features = features; this.trackView.track.draw(drawConfiguration); } if (roiFeatures) { for (let r of roiFeatures) { drawConfiguration.features = r.features; r.track.draw(drawConfiguration); } } } // TODO: Nolonger used. Will discard async toSVG(tile) { // Nothing to do if zoomInNotice is active if (this.$zoomInNotice && this.$zoomInNotice.is(":visible")) { return; } const referenceFrame = this.referenceFrame; const bpPerPixel = tile.bpPerPixel; const features = tile.features; const roiFeatures = tile.roiFeatures; const pixelWidth = this.$viewport.width(); const pixelHeight = this.$viewport.height(); const bpStart = referenceFrame.start; const bpEnd = referenceFrame.start + pixelWidth * referenceFrame.bpPerPixel; const ctx = new C2S({ // svg width: pixelWidth, height: pixelHeight, viewbox: { x: 0, y: -this.$content.position().top, width: pixelWidth, height: pixelHeight } }); const drawConfiguration = { viewport: this, context: ctx, top: -this.$content.position().top, pixelTop: 0, // for compatibility with canvas draw pixelWidth, pixelHeight, bpStart, bpEnd, bpPerPixel, referenceFrame: this.referenceFrame, selection: this.selection, viewportWidth: pixelWidth, viewportContainerX: 0, viewportContainerWidth: this.browser.getViewportContainerWidth() }; this.draw(drawConfiguration, features, roiFeatures); return ctx.getSerializedSvg(true); } containsPosition(chr, position) { if (this.referenceFrame.chr === chr && position >= this.referenceFrame.start) { return position <= this.referenceFrame.calculateEnd(this.getWidth()); } else { return false; } } isLoading() { return this.loading; } saveImage() { if (!this.ctx) return; const canvasTop = this.canvasVerticalRange ? this.canvasVerticalRange.top : 0; const devicePixelRatio = window.devicePixelRatio; const w = this.$viewport.width() * devicePixelRatio; const h = this.$viewport.height() * devicePixelRatio; const x = -$(this.canvas).position().left * devicePixelRatio; const y = (-this.$content.position().top - canvasTop) * devicePixelRatio; const imageData = this.ctx.getImageData(x, y, w, h); const exportCanvas = document.createElement('canvas'); const exportCtx = exportCanvas.getContext('2d'); exportCanvas.width = imageData.width; exportCanvas.height = imageData.height; exportCtx.putImageData(imageData, 0, 0); // filename = this.trackView.track.name + ".png"; const filename = (this.$trackLabel.text() ? this.$trackLabel.text() : "image") + ".png"; const data = exportCanvas.toDataURL("image/png"); download(filename, data); } saveSVG() { const { width, height } = this.$viewport.get(0).getBoundingClientRect(); const config = { width, height, viewbox: { x: 0, y: -this.$content.position().top, width, height } }; const context = new C2S(config); const str = (this.trackView.track.name || this.trackView.track.id).replace(/\W/g, ''); const index = this.browser.referenceFrameList.indexOf(this.referenceFrame); const id = `${str}_referenceFrame_${index}_guid_${guid()}`; this.drawSVGWithContext(context, width, height, id, 0, 0, 0); const svg = context.getSerializedSvg(true); const data = URL.createObjectURL(new Blob([svg], { type: "application/octet-stream" })); download(`${id}.svg`, data); } // called by trackView.renderSVGContext() when rendering // entire browser as SVG renderSVGContext(context, { deltaX, deltaY }) { // Nothing to do if zoomInNotice is active if (this.$zoomInNotice && this.$zoomInNotice.is(":visible")) { return; } const str = (this.trackView.track.name || this.trackView.track.id).replace(/\W/g, ''); const index = this.browser.referenceFrameList.indexOf(this.referenceFrame); const id = `${str}_referenceFrame_${index}_guid_${guid()}`; const yScrollDelta = $(this.contentDiv).position().top; const dx = deltaX + index * context.multiLocusGap; const dy = deltaY + yScrollDelta; const { width, height } = this.$viewport.get(0).getBoundingClientRect(); this.drawSVGWithContext(context, width, height, id, dx, dy, -yScrollDelta); if (this.$trackLabel && true === this.browser.trackLabelsVisible) { const { x: xTrackLabel, y: yTrackLabel, width: wTracklabel, height: hTrackLabel } = relativeDOMBBox(this.$viewport.get(0), this.$trackLabel.get(0)); this.renderTrackLabelSVG(context, deltaX + xTrackLabel, deltaY + yTrackLabel, wTracklabel, hTrackLabel); } } // render track label element called from renderSVGContext() renderTrackLabelSVG(context, tx, ty, width, height) { const str = (this.trackView.track.name || this.trackView.track.id).replace(/\W/g, ''); const id = `${str}_track_label_guid_${guid()}`; context.saveWithTranslationAndClipRect(id, tx, ty, width, height, 0); context.fillStyle = "white"; context.fillRect(0, 0, width, height); context.font = "12px Arial"; context.fillStyle = 'rgb(68, 68, 68)'; const { width: stringWidth } = context.measureText(this.$trackLabel.text()); const dx = 0.25 * (width - stringWidth); const dy = 0.7 * (height - 12); context.fillText(this.$trackLabel.text(), dx, height - dy); context.strokeStyle = 'rgb(68, 68, 68)'; context.strokeRect(0, 0, width, height); context.restore(); } // called by renderSVGContext() drawSVGWithContext(context, width, height, id, tx, ty, clipYOffset) { let { start, bpPerPixel } = this.referenceFrame; context.saveWithTranslationAndClipRect(id, tx, ty, width, height, clipYOffset); const top = -this.$content.position().top; const config = { context, viewport: this, referenceFrame: this.referenceFrame, top, pixelTop: top, pixelWidth: width, pixelHeight: height, bpStart: start, bpEnd: start + width * bpPerPixel, bpPerPixel, viewportWidth: width, // viewportContainerX: 0, // viewportContainerWidth: this.browser.getViewportContainerWidth(), selection: this.selection }; const features = this.tile ? this.tile.features : []; const roiFeatures = this.tile ? this.tile.roiFeatures : undefined; this.draw(config, features, roiFeatures); context.restore(); } getCachedFeatures() { return this.tile ? this.tile.features : []; } async getFeatures(track, chr, start, end, bpPerPixel) { if (this.tile && this.tile.containsRange(chr, start, end, bpPerPixel)) { return this.tile.features; } else if (typeof track.getFeatures === "function") { const features = await track.getFeatures(chr, start, end, bpPerPixel, this); this.cachedFeatures = features; this.checkContentHeight(); return features; } else { return undefined; } } createZoomInNotice($parent) { const $notice = $('
'); $parent.append($notice); const $e = $('
'); $notice.append($e); $e.text('Zoom in to see features'); $notice.hide(); return $notice; } viewIsReady() { return this.browser && this.browser.referenceFrameList && this.referenceFrame; } addMouseHandlers() { const self = this; const browser = this.browser; let popupTimerID; let lastClickTime = 0; this.$viewport.on("contextmenu", function (e) { // Ignore if we are doing a drag. This can happen with touch events. if (self.browser.dragObject) { return false; } const clickState = createClickState(e, self); if (undefined === clickState) { return false; } e.preventDefault(); // Track specific items let menuItems = []; if (typeof self.trackView.track.contextMenuItemList === "function") { const trackMenuItems = self.trackView.track.contextMenuItemList(clickState); if (trackMenuItems) { menuItems = trackMenuItems; } } // Add items common to all tracks if (menuItems.length > 0) { menuItems.push({ label: $('
') }); } menuItems.push({ label: 'Save Image (PNG)', click: () => self.saveImage() }); menuItems.push({ label: 'Save Image (SVG)', click: () => self.saveSVG() }); self.menuPopup.presentTrackContextMenu(e, menuItems); }); /** * Mouse click down, notify browser for potential drag (pan), and record position for potential click. */ this.$viewport.on('mousedown', function (e) { self.enableClick = true; browser.mouseDownOnViewport(e, self); pageCoordinates$1(e); }); this.$viewport.on('touchstart', function (e) { self.enableClick = true; browser.mouseDownOnViewport(e, self); pageCoordinates$1(e); }); /** * Mouse is released. Ignore if this is a context menu click, or the end of a drag action. If neither of * those, it is a click. */ this.$viewport.on('mouseup', handleMouseUp); this.$viewport.on('touchend', handleMouseUp); this.$viewport.on('click', function (e) { if (self.enableClick) { handleClick(e); } }); function handleMouseUp(e) { // Any mouse up cancels drag and scrolling if (self.browser.dragObject || self.browser.isScrolling) { self.browser.cancelTrackPan(); e.preventDefault(); e.stopPropagation(); self.enableClick = false; // Until next mouse down return; } else { self.browser.cancelTrackPan(); self.browser.endTrackDrag(); } } function handleClick(e) { if (3 === e.which || e.ctrlKey) { return; } // Close any currently open popups $('.igv-popover').hide(); if (browser.dragObject || browser.isScrolling) { return; } // // Interpret mouseDown + mouseUp < 5 pixels as a click. // if(!mouseDownCoords) { // return; // } // const coords = pageCoordinates(e); // const dx = coords.x - mouseDownCoords.x; // const dy = coords.y - mouseDownCoords.y; // const dist2 = dx*dx + dy*dy; // if(dist2 > 25) { // mouseDownCoords = undefined; // return; // } // Treat as a mouse click, its either a single or double click. // Handle here and stop propogation / default e.preventDefault(); e.stopPropagation(); const mouseX = translateMouseCoordinates$1(e, self.$viewport.get(0)).x; const mouseXCanvas = translateMouseCoordinates$1(e, self.canvas).x; const referenceFrame = self.referenceFrame; const xBP = Math.floor(referenceFrame.start + referenceFrame.toBP(mouseXCanvas)); const time = Date.now(); if (time - lastClickTime < browser.constants.doubleClickDelay) { // double-click if (popupTimerID) { window.clearTimeout(popupTimerID); popupTimerID = undefined; } const centerBP = Math.round(referenceFrame.start + referenceFrame.toBP(mouseX)); let string; if ('all' === self.referenceFrame.chr.toLowerCase()) { const chr = browser.genome.getChromosomeCoordinate(centerBP).chr; if (1 === browser.referenceFrameList.length) { string = chr; } else { let loci = browser.referenceFrameList.map(function (g) { return g.locusSearchString; }); loci[browser.referenceFrameList.indexOf(self.referenceFrame)] = chr; string = loci.join(' '); } browser.search(string); } else { browser.zoomWithScaleFactor(0.5, centerBP, self); } } else { // single-click if (e.shiftKey && typeof self.trackView.track.shiftClick === "function") { self.trackView.track.shiftClick(xBP, e); } else if (typeof self.trackView.track.popupData === "function") { popupTimerID = setTimeout(function () { const content = getPopupContent(e, self); if (content) { if (self.popover) self.popover.dispose(); self.popover = new Popover(self.trackView.$viewportContainer.get(0)); self.popover.presentContentWithEvent(e, content); } clearTimeout(popupTimerID); popupTimerID = undefined; }, browser.constants.doubleClickDelay); } } lastClickTime = time; } function createClickState(e, viewport) { const referenceFrame = viewport.referenceFrame; const viewportCoords = translateMouseCoordinates$1(e, viewport.contentDiv); const canvasCoords = translateMouseCoordinates$1(e, viewport.canvas); const genomicLocation = referenceFrame.start + referenceFrame.toBP(viewportCoords.x); if (undefined === genomicLocation || null === viewport.tile) { return undefined; } return { event: e, viewport: viewport, referenceFrame: referenceFrame, genomicLocation: genomicLocation, x: viewportCoords.x, y: viewportCoords.y, canvasX: canvasCoords.x, canvasY: canvasCoords.y }; } /** * Return markup for popup info window * * @param e * @param viewport * @returns {*} */ function getPopupContent(e, viewport) { const clickState = createClickState(e, viewport); if (undefined === clickState) { return; } let track = viewport.trackView.track; const dataList = track.popupData(clickState); const popupClickHandlerResult = browser.fireEvent('trackclick', [track, dataList]); let content; if (undefined === popupClickHandlerResult || true === popupClickHandlerResult) { // Indicates handler did not handle the result, or the handler wishes default behavior to occur if (dataList && dataList.length > 0) { content = formatPopoverText(dataList); } } else if (typeof popupClickHandlerResult === 'string') { content = popupClickHandlerResult; } return content; } /** * Format markup for popover text from an array of name value pairs [{name, value}] */ function formatPopoverText(nameValues) { const rows = nameValues.map(nameValue => { if (nameValue.name) { const str = `${nameValue.name}   ${nameValue.value}`; return `
${str}
`; } else if ('
' === nameValue) { // this can be retired if nameValue.html is allowed. return nameValue; } else if (nameValue.html) { return nameValue.html; } else { return `
${nameValue}
`; } }); return rows.join(''); } } } var Tile = function (chr, tileStart, tileEnd, bpPerPixel, features, roiFeatures) { this.chr = chr; this.startBP = tileStart; this.endBP = tileEnd; this.bpPerPixel = bpPerPixel; this.features = features; this.roiFeatures = roiFeatures; }; Tile.prototype.containsRange = function (chr, start, end, bpPerPixel) { return this.bpPerPixel === bpPerPixel && start >= this.startBP && end <= this.endBP && chr === this.chr; }; Tile.prototype.overlapsRange = function (chr, start, end) { return this.chr === chr && end >= this.startBP && start <= this.endBP; }; /** * Merge 2 arrays. a and/or b can be undefined. If both are undefined, return undefined * @param a An array or undefined * @param b An array or undefined */ function mergeArrays(a, b) { if (a && b) return a.concat(b);else if (a) return a;else return b; } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ class IdeogramViewport extends ViewPort { constructor(trackView, $viewportContainer, referenceFrame, width) { super(trackView, $viewportContainer, referenceFrame, width); } initializationHelper() { this.$ideogramCanvas = $('', { class: 'igv-ideogram-canvas' }); this.$ideogramCanvas.insertBefore(this.$canvas); const canvas = this.$ideogramCanvas.get(0); this.ideogram_ctx = canvas.getContext('2d'); this.$canvas.remove(); this.canvas = undefined; this.ctx = undefined; this.$viewport.on('click.ideogram', e => { clickHandler(e, canvas, this.browser, this.referenceFrame); }); } setWidth(width) { this.$viewport.width(width); } drawSVGWithContext(context, width, height, id, tx, ty, clipYOffset) { context.saveWithTranslationAndClipRect(id, tx, ty, width, height, clipYOffset); this.trackView.track.draw({ context, referenceFrame: this.referenceFrame, pixelWidth: width, pixelHeight: height }); context.restore(); } async repaint() { this.draw({ referenceFrame: this.referenceFrame }); } draw({ referenceFrame }) { this.$canvas.hide(); IGVGraphics.configureHighDPICanvas(this.ideogram_ctx, this.$viewport.width(), this.$viewport.height()); this.trackView.track.draw({ context: this.ideogram_ctx, referenceFrame, pixelWidth: this.$viewport.width(), pixelHeight: this.$viewport.height() }); } } function clickHandler(e, canvas, browser, referenceFrame) { const { xNormalized, width } = translateMouseCoordinates$1(e, canvas); const { bpLength } = browser.genome.getChromosome(referenceFrame.chr); const locusLength = referenceFrame.bpPerPixel * width; const chrCoveragePercentage = locusLength / bpLength; let xPercentage = xNormalized; if (xPercentage - chrCoveragePercentage / 2.0 < 0) { xPercentage = chrCoveragePercentage / 2.0; } if (xPercentage + chrCoveragePercentage / 2.0 > 1.0) { xPercentage = 1.0 - chrCoveragePercentage / 2.0; } const ss = Math.round((xPercentage - chrCoveragePercentage / 2.0) * bpLength); const ee = Math.round((xPercentage + chrCoveragePercentage / 2.0) * bpLength); referenceFrame.start = ss; referenceFrame.initialEnd = ee; referenceFrame.bpPerPixel = (ee - ss) / width; browser.updateLocusSearchWidget(browser.referenceFrameList > 1 ? browser.referenceFrameList : [referenceFrame]); browser.updateViews(referenceFrame, browser.trackViews, true); } /* * The MIT License (MIT) * * Copyright (c) 2016-2017 The Regents of the University of California * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ class RulerSweeper { constructor(viewport) { this.viewport = viewport; this.browser = viewport.browser; this.$rulerSweeper = $('
'); $(viewport.contentDiv).append(this.$rulerSweeper); this.namespace = '.sweeper_' + guid(); this.addMouseHandlers(); } disableMouseHandlers() { $(document).off(this.namespace); this.viewport.$viewport.off(this.namespace); } addMouseHandlers() { const browser = this.browser; const self = this; var isMouseDown, isMouseIn, mouseDown, left, threshold, width, dx; this.disableMouseHandlers(); isMouseDown = isMouseIn = mouseDown = undefined; threshold = 1; $(this.browser.$root).on('mousedown' + this.namespace, function (e) { isMouseIn = true; mouseDown = translateMouseCoordinates$1(e, self.viewport.$viewport.get(0)).x; if (true === isMouseDown) { self.$rulerSweeper.show(); width = threshold; left = mouseDown; self.$rulerSweeper.css({ left: left + 'px' }); self.$rulerSweeper.width(width); } }); $(this.browser.$root).on('mousemove' + this.namespace, function (e) { var mouseCurrent; if (isMouseDown && isMouseIn) { mouseCurrent = translateMouseCoordinates$1(e, self.viewport.$viewport.get(0)).x; mouseCurrent = Math.min(mouseCurrent, self.viewport.$viewport.width()); mouseCurrent = Math.max(mouseCurrent, 0); dx = mouseCurrent - mouseDown; width = Math.abs(dx); self.$rulerSweeper.width(width); if (dx < 0) { left = mouseDown + dx; self.$rulerSweeper.css({ left: left + 'px' }); } } }); $(this.browser.$root).on('mouseup' + this.namespace, function (e) { let extent; if (true === isMouseDown && true === isMouseIn) { isMouseDown = isMouseIn = undefined; self.$rulerSweeper.hide(); extent = {}; extent.start = self.bp(left); extent.end = self.bp(left + width); if (width > threshold) { validateLocusExtent(browser.genome.getChromosome(self.viewport.referenceFrame.chr).bpLength, extent, browser.minimumBases()); self.viewport.referenceFrame.bpPerPixel = (Math.round(extent.end) - Math.round(extent.start)) / self.viewport.$viewport.width(); self.viewport.referenceFrame.start = Math.round(extent.start); self.viewport.referenceFrame.initialEnd = Math.round(extent.end); browser.updateViews(self.viewport.referenceFrame); } } }); this.viewport.$viewport.on('mousedown' + this.namespace, function (e) { isMouseDown = true; }); } dispose() { this.disableMouseHandlers(); } bp(pixel) { return this.viewport.referenceFrame.start + pixel * this.viewport.referenceFrame.bpPerPixel; } } let timer; let currentViewport = undefined; const toolTipTimeout = 1e4; class RulerViewport extends ViewPort { constructor(trackView, $viewportContainer, referenceFrame, width) { super(trackView, $viewportContainer, referenceFrame, width); } initializationHelper() { this.rulerSweeper = new RulerSweeper(this); appendMultiPanelCloseButton(this.browser, this.$viewport, this.referenceFrame); this.$rulerLabel = $('
'); this.$content.append(this.$rulerLabel); this.$rulerLabel.click(() => this.browser.selectMultiLocusPanelWithReferenceFrame(this.referenceFrame)); this.$tooltip = $('
', { class: 'igv-ruler-tooltip' }); this.$tooltip.height(this.$viewport.height()); this.$viewport.append(this.$tooltip); this.$tooltipContent = $('
'); this.$tooltip.append(this.$tooltipContent); this.attachMouseHandlers(GenomeUtils.isWholeGenomeView(this.browser.referenceFrameList[0].chr)); this.$tooltip.hide(); } updateLocusLabel() { const str = this.referenceFrame.presentLocus(this.$viewport.width()); this.$rulerLabel.text(str); } attachMouseHandlers(isWholeGenomeView) { this.namespace = `.ruler_track_viewport_${this.browser.referenceFrameList.indexOf(this.referenceFrame)}`; this.$viewport.off(this.namespace); if (true === isWholeGenomeView) { const index = this.browser.referenceFrameList.indexOf(this.referenceFrame); const click = `click${this.namespace}`; this.$viewport.on(click, e => { const { x: pixel } = translateMouseCoordinates$1(e, this.$viewport.get(0)); const bp = Math.round(this.referenceFrame.start + this.referenceFrame.toBP(pixel)); let searchString; const { chr } = this.browser.genome.getChromosomeCoordinate(bp); if (1 === this.browser.referenceFrameList.length) { searchString = chr; } else { let loci = this.browser.referenceFrameList.map(({ locusSearchString }) => locusSearchString); loci[index] = chr; searchString = loci.join(' '); } this.browser.search(searchString); }); } } mouseMove(event) { if (true === this.browser.cursorGuideVisible) { if (undefined === currentViewport) { currentViewport = this; this.$tooltip.show(); } else if (currentViewport.guid !== this.guid) { currentViewport.$tooltip.hide(); this.$tooltip.show(); currentViewport = this; } else { this.$tooltip.show(); } const isWholeGenome = this.browser.isMultiLocusWholeGenomeView() || GenomeUtils.isWholeGenomeView(this.browser.referenceFrameList[0].chr); if (isWholeGenome) { this.$tooltip.hide(); return; } const { x } = translateMouseCoordinates$1(event, this.$viewport.get(0)); const { start, bpPerPixel } = this.referenceFrame; const bp = Math.round(0.5 + start + Math.max(0, x) * bpPerPixel); this.$tooltipContent.text(numberFormatter$1(bp)); const { width: ww } = this.$tooltipContent.get(0).getBoundingClientRect(); const { width: w } = this.$viewport.get(0).getBoundingClientRect(); this.$tooltip.css({ left: `${IGVMath.clamp(x, 0, w - ww)}px` }); // hide tooltip when movement stops clearTimeout(timer); timer = setTimeout(() => this.$tooltip.hide(), toolTipTimeout); } } } function appendMultiPanelCloseButton(browser, $viewport, referenceFrame) { $viewport.addClass('igv-viewport-ruler'); const $close = $('
'); $viewport.append($close); $close.append(createIcon$1("times-circle")); $close.click(() => browser.removeMultiLocusPanelWithReferenceFrame(referenceFrame, true)); } const createViewport = (trackView, referenceFrameList, index, width) => { if ('ruler' === trackView.track.type) { return new RulerViewport(trackView, trackView.$viewportContainer, referenceFrameList[index], width); } else if ('ideogram' === trackView.track.type) { return new IdeogramViewport(trackView, trackView.$viewportContainer, referenceFrameList[index], width); } else { return new ViewPort(trackView, trackView.$viewportContainer, referenceFrameList[index], width); } }; /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const numberFormatter = numberFormatter$1; class RulerTrack { constructor(browser) { this.browser = browser; this.height = 40; this.name = ""; this.id = "ruler"; this.disableButtons = true; this.ignoreTrackMenu = true; this.order = Number.MIN_SAFE_INTEGER * 1e-2; this.removable = false; this.type = 'ruler'; } updateLocusLabel() { for (let viewport of this.trackView.viewports) { viewport.updateLocusLabel(); } } async getFeatures(chr, start, end) { return []; } computePixelHeight(ignore) { return this.height; } draw(options) { if (GenomeUtils.isWholeGenomeView(options.referenceFrame.chr)) { options.viewport.rulerSweeper.disableMouseHandlers(); this.drawWholeGenome(options); } else { options.viewport.rulerSweeper.addMouseHandlers(); const tickHeight = 6; const shim = 2; const pixelWidthBP = 1 + Math.floor(options.referenceFrame.toBP(options.pixelWidth)); const tick = new Tick(pixelWidthBP, options); tick.drawTicks(options, tickHeight, shim, this.height); IGVGraphics.strokeLine(options.context, 0, this.height - shim, options.pixelWidth, this.height - shim); } } drawWholeGenome(options) { options.context.save(); IGVGraphics.fillRect(options.context, 0, 0, options.pixelWidth, options.pixelHeight, { 'fillStyle': 'white' }); let y = 0; let h = options.pixelHeight; for (let name of this.browser.genome.wgChromosomeNames) { let xBP = this.browser.genome.getCumulativeOffset(name); let wBP = this.browser.genome.getChromosome(name).bpLength; let x = Math.round(xBP / options.bpPerPixel); let w = Math.round(wBP / options.bpPerPixel); this.renderChromosomeRect(options.context, x, y, w, h, name); } options.context.restore(); } renderChromosomeRect(ctx, x, y, w, h, name) { ctx.textAlign = 'center'; ctx.textBaseline = 'middle'; ctx.font = '12px sans-serif'; // IGVGraphics.fillRect(ctx, x, y, w, h, { 'fillStyle' : toggleColor(this.browser.genome.wgChromosomeNames.indexOf(name)) }); IGVGraphics.strokeLine(ctx, x + w, y, x + w, y + h, { strokeStyle: IGVColor.greyScale(191) }); const shortName = name.startsWith("chr") ? name.substring(3) : name; if (w > ctx.measureText(shortName).width) { IGVGraphics.fillText(ctx, shortName, x + w / 2, y + h / 2, { fillStyle: IGVColor.greyScale(68) }); } } supportsWholeGenome() { return true; } dispose() {// do stuff } } class Tick { constructor(pixelWidthBP, options) { initialize.call(this, pixelWidthBP, options); function initialize(pixelWidthBP, options) { var numberOfZeroes, majorUnit, unitMultiplier, numberOfMajorTicks, str; const isSVGContext = options.context.isSVG || false; if (pixelWidthBP < 10) { set.call(this, 1, "bp", 1, isSVGContext); } numberOfZeroes = Math.floor(Math.log10(pixelWidthBP)); if (numberOfZeroes > 9) { majorUnit = "gb"; unitMultiplier = 1e9; } else if (numberOfZeroes > 6) { majorUnit = "mb"; unitMultiplier = 1e6; } else if (numberOfZeroes > 3) { majorUnit = "kb"; unitMultiplier = 1e3; } else { majorUnit = "bp"; unitMultiplier = 1; } str = numberFormatter(Math.floor(pixelWidthBP / unitMultiplier)) + " " + majorUnit; this.labelWidthBP = Math.round(options.referenceFrame.toBP(options.context.measureText(str).width)); numberOfMajorTicks = pixelWidthBP / Math.pow(10, numberOfZeroes - 1); if (numberOfMajorTicks < 25) { set.call(this, Math.pow(10, numberOfZeroes - 1), majorUnit, unitMultiplier, isSVGContext); } else { set.call(this, Math.pow(10, numberOfZeroes) / 2, majorUnit, unitMultiplier, isSVGContext); } } function set(majorTick, majorUnit, unitMultiplier, isSVGContext) { // reduce label frequency by half for SVG rendering this.majorTick = true === isSVGContext ? 2 * majorTick : majorTick; this.majorUnit = majorUnit; this.halfTick = majorTick / 2; this.unitMultiplier = unitMultiplier; } } drawTicks(options, tickHeight, shim, height) { var numberOfTicks, bp, pixel, label, labelWidth, labelX, numer, floored; numberOfTicks = Math.floor(options.bpStart / this.majorTick) - 1; labelWidth = 0; labelX = 0; pixel = 0; while (pixel < options.pixelWidth) { bp = Math.floor(numberOfTicks * this.majorTick); pixel = Math.round(options.referenceFrame.toPixels(bp - 1 - options.bpStart + 0.5)); label = numberFormatter(Math.floor(bp / this.unitMultiplier)) + " " + this.majorUnit; labelWidth = options.context.measureText(label).width; labelX = Math.round(pixel - labelWidth / 2); IGVGraphics.fillText(options.context, label, labelX, height - tickHeight / 0.75); IGVGraphics.strokeLine(options.context, pixel, height - tickHeight, pixel, height - shim); ++numberOfTicks; } numberOfTicks = Math.floor(options.bpStart / this.halfTick) - 1; pixel = 0; while (pixel < options.pixelWidth) { bp = Math.floor(numberOfTicks * this.halfTick); pixel = Math.round(options.referenceFrame.toPixels(bp - 1 - options.bpStart + 0.5)); numer = bp / this.unitMultiplier; floored = Math.floor(numer); if (numer === floored && this.majorTick / this.labelWidthBP > 8) { label = numberFormatter(Math.floor(numer)) + " " + this.majorUnit; labelWidth = options.context.measureText(label).width; labelX = pixel - labelWidth / 2; IGVGraphics.fillText(options.context, label, labelX, height - tickHeight / 0.75); } IGVGraphics.strokeLine(options.context, pixel, height - tickHeight, pixel, height - shim); ++numberOfTicks; } } description(blurb) {} } const appleCrayonRGBPalette = { cantaloupe: { r: 255, g: 206, b: 110 }, honeydew: { r: 206, g: 250, b: 110 }, spindrift: { r: 104, g: 251, b: 208 }, sky: { r: 106, g: 207, b: 255 }, lavender: { r: 210, g: 120, b: 255 }, carnation: { r: 255, g: 127, b: 211 }, licorice: { r: 0, g: 0, b: 0 }, snow: { r: 255, g: 255, b: 255 }, salmon: { r: 255, g: 114, b: 110 }, banana: { r: 255, g: 251, b: 109 }, flora: { r: 104, g: 249, b: 110 }, ice: { r: 104, g: 253, b: 255 }, orchid: { r: 110, g: 118, b: 255 }, bubblegum: { r: 255, g: 122, b: 255 }, lead: { r: 30, g: 30, b: 30 }, mercury: { r: 232, g: 232, b: 232 }, tangerine: { r: 255, g: 136, b: 2 }, lime: { r: 131, g: 249, b: 2 }, sea_foam: { r: 3, g: 249, b: 135 }, aqua: { r: 0, g: 140, b: 255 }, grape: { r: 137, g: 49, b: 255 }, strawberry: { r: 255, g: 41, b: 135 }, tungsten: { r: 58, g: 58, b: 58 }, silver: { r: 208, g: 208, b: 208 }, maraschino: { r: 255, g: 33, b: 1 }, lemon: { r: 255, g: 250, b: 3 }, spring: { r: 5, g: 248, b: 2 }, turquoise: { r: 0, g: 253, b: 255 }, blueberry: { r: 0, g: 46, b: 255 }, magenta: { r: 255, g: 57, b: 255 }, iron: { r: 84, g: 84, b: 83 }, magnesium: { r: 184, g: 184, b: 184 }, mocha: { r: 137, g: 72, b: 0 }, fern: { r: 69, g: 132, b: 1 }, moss: { r: 1, g: 132, b: 72 }, ocean: { r: 0, g: 74, b: 136 }, eggplant: { r: 73, g: 26, b: 136 }, maroon: { r: 137, g: 22, b: 72 }, steel: { r: 110, g: 110, b: 110 }, aluminum: { r: 160, g: 159, b: 160 }, cayenne: { r: 137, g: 17, b: 0 }, aspargus: { r: 136, g: 133, b: 1 }, clover: { r: 2, g: 132, b: 1 }, teal: { r: 0, g: 134, b: 136 }, midnight: { r: 0, g: 24, b: 136 }, plum: { r: 137, g: 30, b: 136 }, tin: { r: 135, g: 134, b: 135 }, nickel: { r: 136, g: 135, b: 135 } }; function appleCrayonRGB(name) { const { r, g, b } = appleCrayonRGBPalette[name]; return `rgb(${r},${g},${b})`; } const colorPalettes = { Set1: ["rgb(228,26,28)", "rgb(55,126,184)", "rgb(77,175,74)", "rgb(166,86,40)", "rgb(152,78,163)", "rgb(255,127,0)", "rgb(247,129,191)", "rgb(153,153,153)", "rgb(255,255,51)"], Dark2: ["rgb(27,158,119)", "rgb(217,95,2)", "rgb(117,112,179)", "rgb(231,41,138)", "rgb(102,166,30)", "rgb(230,171,2)", "rgb(166,118,29)", "rgb(102,102,102)"], Set2: ["rgb(102, 194,165)", "rgb(252,141,98)", "rgb(141,160,203)", "rgb(231,138,195)", "rgb(166,216,84)", "rgb(255,217,47)", "rgb(229,196,148)", "rgb(179,179,179)"], Set3: ["rgb(141,211,199)", "rgb(255,255,179)", "rgb(190,186,218)", "rgb(251,128,114)", "rgb(128,177,211)", "rgb(253,180,98)", "rgb(179,222,105)", "rgb(252,205,229)", "rgb(217,217,217)", "rgb(188,128,189)", "rgb(204,235,197)", "rgb(255,237,111)"], Pastel1: ["rgb(251,180,174)", "rgb(179,205,227)", "rgb(204,235,197)", "rgb(222,203,228)", "rgb(254,217,166)", "rgb(255,255,204)", "rgb(229,216,189)", "rgb(253,218,236)"], Pastel2: ["rgb(173,226,207)", "rgb(253,205,172)", "rgb(203,213,232)", "rgb(244,202,228)", "rgb(230,245,201)", "rgb(255,242,174)", "rgb(243,225,206)"], Accent: ["rgb(127,201,127)", "rgb(190,174,212)", "rgb(253,192,134)", "rgb(255,255,153)", "rgb(56,108,176)", "rgb(240,2,127)", "rgb(191,91,23)"] }; class PaletteColorTable { constructor(palette) { this.colors = colorPalettes[palette]; if (!Array.isArray(this.colors)) this.colors = []; this.colorTable = {}; this.nextIdx = 0; this.colorGenerator = new RandomColorGenerator(); } getColor(key) { if (!this.colorTable.hasOwnProperty(key)) { if (this.nextIdx < this.colors.length) { this.colorTable[key] = this.colors[this.nextIdx]; } else { this.colorTable[key] = this.colorGenerator.get(); } this.nextIdx++; } return this.colorTable[key]; } } class ColorTable { constructor(colors) { this.colorTable = colors || {}; this.nextIdx = 0; this.colorGenerator = new RandomColorGenerator(); } getColor(key) { if (!this.colorTable.hasOwnProperty(key)) { if (this.colorTable.hasOwnProperty("*")) { return this.colorTable["*"]; } this.colorTable[key] = this.colorGenerator.get(); } return this.colorTable[key]; } } // Random color generator from https://github.com/sterlingwes/RandomColor/blob/master/rcolor.js // Free to use & distribute under the MIT license // Wes Johnson (@SterlingWes) // // inspired by http://martin.ankerl.com/2009/12/09/how-to-create-random-colors-programmatically/ function RandomColorGenerator() { this.hue = Math.random(); this.goldenRatio = 0.618033988749895; this.hexwidth = 2; } RandomColorGenerator.prototype.hsvToRgb = function (h, s, v) { var h_i = Math.floor(h * 6), f = h * 6 - h_i, p = v * (1 - s), q = v * (1 - f * s), t = v * (1 - (1 - f) * s), r = 255, g = 255, b = 255; switch (h_i) { case 0: r = v, g = t, b = p; break; case 1: r = q, g = v, b = p; break; case 2: r = p, g = v, b = t; break; case 3: r = p, g = q, b = v; break; case 4: r = t, g = p, b = v; break; case 5: r = v, g = p, b = q; break; } return [Math.floor(r * 256), Math.floor(g * 256), Math.floor(b * 256)]; }; RandomColorGenerator.prototype.padHex = function (str) { if (str.length > this.hexwidth) return str; return new Array(this.hexwidth - str.length + 1).join('0') + str; }; RandomColorGenerator.prototype.get = function (saturation, value) { this.hue += this.goldenRatio; this.hue %= 1; if (typeof saturation !== "number") saturation = 0.5; if (typeof value !== "number") value = 0.95; var rgb = this.hsvToRgb(this.hue, saturation, value); return "#" + this.padHex(rgb[0].toString(16)) + this.padHex(rgb[1].toString(16)) + this.padHex(rgb[2].toString(16)); }; const randomColorGenerator = new RandomColorGenerator(); function randomColor() { return randomColorGenerator.get(); } // Returns a random number between min (inclusive) and max (exclusive) const maxFontSize = 10; const fontConfigureTemplate = { // font: '2pt sans-serif', textAlign: 'start', textBaseline: 'bottom', strokeStyle: 'black', fillStyle: 'black' }; class SampleNameViewport { constructor(trackView, $viewportContainer, referenceFrame, width) { this.guid = guid(); this.trackView = trackView; this.referenceFrame = referenceFrame; this.browser = trackView.browser; this.$viewport = $('
'); $viewportContainer.append(this.$viewport); this.$canvas = $(''); this.$viewport.append(this.$canvas); this.canvas = this.$canvas.get(0); this.ctx = this.canvas.getContext("2d"); this.contentTop = 0; this.setWidth(width); this.$viewport.get(0).addEventListener('contextmenu', e => { e.preventDefault(); e.stopPropagation(); const config = { label: 'Name Panel Width', value: this.browser.sampleNameViewportWidth, callback: width => { this.browser.sampleNameViewportWidth = width; for (let { sampleNameViewport } of this.browser.trackViews) { sampleNameViewport.setWidth(this.browser.sampleNameViewportWidth); } this.browser.resize(); } }; this.browser.inputDialog.present(config, e); }); } checkCanvas() { const dpi = window.devicePixelRatio; const requiredHeight = this.$viewport.height(); const requiredWidth = this.browser.sampleNameViewportWidth; if (this.canvas.width !== requiredWidth * dpi || this.canvas.height !== requiredHeight * dpi) { const canvas = this.canvas; canvas.width = requiredWidth * dpi; canvas.height = requiredHeight * dpi; canvas.style.width = `${requiredWidth}px`; canvas.style.height = `${requiredHeight}px`; this.ctx = this.canvas.getContext("2d"); this.ctx.scale(dpi, dpi); } } setTop(contentTop) { if (typeof this.trackView.track.getSamples === 'function') { this.contentTop = contentTop; const samples = this.trackView.track.getSamples(); this.repaint(samples); } } setWidth(width) { this.$viewport.width(width); this.checkCanvas(); } show() { this.$viewport.show(); } hide() { this.$viewport.hide(); } async repaint(samples) { this.checkCanvas(); this.draw({ context: this.ctx, samples }); } draw({ context, samples }) { if (!samples || samples.names.length === 0 || samples.height < 1) { return; } configureFont(context, fontConfigureTemplate, samples.height); const sampleNameXShim = 4; context.clearRect(0, 0, context.canvas.width, context.canvas.height); context.fillStyle = appleCrayonRGB('lead'); const viewportHeight = this.$viewport.get(0).getBoundingClientRect().height; let y = (samples.yOffset || 0) + this.contentTop; // contentTop will always be a negative number (top relative to viewport) for (let name of samples.names) { if (y > viewportHeight) break; if (y + samples.height > 0) { const text = name.toUpperCase(); const yFont = getYFont(context, text, y, samples.height); context.fillText(text, sampleNameXShim, yFont); } y += samples.height; } } renderSVGContext(context, { deltaX, deltaY }) { if (typeof this.trackView.track.getSamples === 'function') { const samples = this.trackView.track.getSamples(); const yScrollDelta = 0; // This is not relevant, scrolling is handled in "draw" const { width, height } = this.$viewport.get(0).getBoundingClientRect(); const str = (this.trackView.track.name || this.trackView.track.id).replace(/\W/g, ''); const id = `${str}_sample_names_guid_${guid()}`; context.saveWithTranslationAndClipRect(id, deltaX, deltaY + yScrollDelta, width, height, -yScrollDelta); this.draw({ context, samples }); context.restore(); } } addMouseHandler(context, pixelTop, samples) { this.canvas.addEventListener('click', e => { if ('block' === this.hover.style.display) { this.hover.style.display = 'none'; this.hover.textContent = ''; } else { const { currentTarget, clientY } = e; const { y: target_bbox_min_y } = currentTarget.getBoundingClientRect(); const y = clientY - target_bbox_min_y + pixelTop; let yMin = 0; for (let name of samples.names) { const yMax = getYFont(context, name.toUpperCase(), yMin, samples.height); if (y < yMin || y > yMax) ; else { this.hover.style.top = `${yMin + this.contentTop}px`; this.hover.style.right = '0px'; this.hover.textContent = name.toUpperCase(); this.hover.style.display = 'block'; } yMin += samples.height; } } }); this.canvas.addEventListener('mouseleave', () => { this.hover.style.display = 'none'; this.hover.textContent = ''; }); } } function getYFont(context, text, y, height) { return y + height - getSampleNameYShim(context, text, height); } function getSampleNameYShim(context, text, h) { const { fontBoundingBoxAscent, fontBoundingBoxDescent } = context.measureText(text); return (h - (fontBoundingBoxAscent + fontBoundingBoxDescent)) / 2; } function configureFont(ctx, { textAlign, textBaseline, strokeStyle, fillStyle }, sampleHeight) { const pixels = Math.min(sampleHeight, maxFontSize); ctx.font = `${pixels}px sans-serif`; ctx.textAlign = textAlign; ctx.textBaseline = textBaseline; ctx.fillStyle = fillStyle; } const namespace = '.trackscrollbar' + guid(); class TrackScrollbar { constructor($viewportContainer, viewports, sampleNameViewport) { let lastY; // Define mouse events first, use arrow function so "this" is in scope const mouseMove = event => { event.preventDefault(); event.stopPropagation(); const page = pageCoordinates$1(event); this.moveScrollerBy(page.y - lastY); lastY = page.y; }; const mouseUp = event => { $(document).off(this.namespace); }; const mouseDown = event => { event.preventDefault(); const page = pageCoordinates$1(event); lastY = page.y; $(document).on('mousemove' + namespace, mouseMove); $(document).on('mouseup' + namespace, mouseUp); $(document).on('mouseleave' + namespace, mouseUp); // prevents start of horizontal track panning) event.stopPropagation(); }; this.namespace = namespace; this.$outerScroll = $('
'); this.$innerScroll = $('
'); this.$outerScroll.append(this.$innerScroll); this.$viewportContainer = $viewportContainer; this.viewports = viewports; this.sampleNameViewport = sampleNameViewport; this.$innerScroll.on("mousedown", mouseDown); this.$innerScroll.on("click", event => { event.stopPropagation(); }); this.$outerScroll.on("click", event => { this.moveScrollerBy(event.offsetY - this.$innerScroll.height() / 2); event.stopPropagation(); }); } disableMouseHandlers() { $(document).off(namespace); this.$innerScroll.off(); this.$outerScroll.off(); } moveScrollerBy(delta) { const y = this.$innerScroll.position().top + delta; this.moveScrollerTo(y); } moveScrollerTo(y) { const outerScrollHeight = this.$outerScroll.height(); const innerScrollHeight = this.$innerScroll.height(); const newTop = Math.min(Math.max(0, y), outerScrollHeight - innerScrollHeight); const contentDivHeight = maxViewportContentHeight(this.viewports); const contentTop = -Math.round(newTop * (contentDivHeight / this.$viewportContainer.height())); this.$innerScroll.css("top", newTop + "px"); for (let viewport of [...this.viewports, this.sampleNameViewport]) { viewport.setTop(contentTop); } } dispose() { $(window).off(this.namespace); this.$innerScroll.off(); } update() { const viewportContainerHeight = this.$viewportContainer.height(); const viewportContentHeight = maxViewportContentHeight(this.viewports); const innerScrollHeight = Math.round(viewportContainerHeight / viewportContentHeight * viewportContainerHeight); if (viewportContentHeight > viewportContainerHeight) { this.$innerScroll.show(); this.$innerScroll.height(innerScrollHeight); } else { this.$innerScroll.hide(); } } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const defaultSequenceTrackOrder = Number.MIN_SAFE_INTEGER; const translationDict = { 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'TAT': 'Y', 'TAC': 'Y', 'TAA': 'STOP', 'TAG': 'STOP', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'TGT': 'C', 'TGC': 'C', 'TGA': 'STOP', 'TGG': 'W', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G' }; const complement = {}; const t1 = ['A', 'G', 'C', 'T', 'Y', 'R', 'W', 'S', 'K', 'M', 'D', 'V', 'H', 'B', 'N', 'X']; const t2 = ['T', 'C', 'G', 'A', 'R', 'Y', 'W', 'S', 'M', 'K', 'H', 'B', 'D', 'V', 'N', 'X']; for (let i = 0; i < t1.length; i++) { complement[t1[i]] = t2[i]; complement[t1[i].toLowerCase()] = t2[i].toLowerCase(); } class SequenceTrack { constructor(config, browser) { this.type = "sequence"; this.browser = browser; this.removable = false; this.config = config; this.name = "Sequence"; this.id = "sequence"; this.sequenceType = config.sequenceType || "dna"; // dna | rna | prot this.height = 25; this.disableButtons = false; this.order = config.order || defaultSequenceTrackOrder; this.ignoreTrackMenu = false; this.reversed = false; this.frameTranslate = false; } menuItemList() { return [{ name: this.reversed ? "Forward" : "Reverse", click: () => { this.reversed = !this.reversed; this.trackView.repaintViews(); } }, { name: this.frameTranslate ? "Close Translation" : "Three-frame Translate", click: () => { this.frameTranslate = !this.frameTranslate; if (this.frameTranslate) { for (let vp of this.trackView.viewports) { vp.setContentHeight(115); } this.trackView.setTrackHeight(115); } else { for (let vp of this.trackView.viewports) { vp.setContentHeight(25); } this.trackView.setTrackHeight(25); } this.trackView.repaintViews(); } }]; } contextMenuItemList(clickState) { const viewport = clickState.viewport; if (viewport.referenceFrame.bpPerPixel <= 1) { return [{ label: 'Copy visible sequence...', click: async () => { const pixelWidth = viewport.getWidth(); const bpWindow = pixelWidth * viewport.referenceFrame.bpPerPixel; const chr = viewport.referenceFrame.chr; const start = viewport.referenceFrame.start; const end = start + bpWindow; const sequence = await this.browser.genome.sequence.getSequence(chr, start, end); if (viewport.trackView.alert) { viewport.trackView.alert.present(sequence); } else { Alert.presentAlert(sequence); } } }, '
']; } else { return undefined; } } translateSequence(seq) { const threeFrame = [[], [], []]; for (let fNum of [0, 1, 2]) { let idx = fNum; while (seq.length - idx >= 3) { let st = seq.slice(idx, idx + 3); if (this.reversed) { st = st.split('').reverse().join(''); } const aa = translationDict[st.toUpperCase()] || ""; threeFrame[fNum].push({ codons: st, aminoA: aa }); idx += 3; } } return threeFrame; } async getFeatures(chr, start, end, bpPerPixel) { if (bpPerPixel && bpPerPixel > 1) { return null; } else { const sequence = await this.browser.genome.sequence.getSequence(chr, start, end); return { bpStart: start, sequence: sequence }; } } draw(options) { const ctx = options.context; if (options.features) { const sequence = options.features.sequence; const sequenceBpStart = options.features.bpStart; const bpEnd = 1 + options.bpStart + options.pixelWidth * options.bpPerPixel; let height = 15; for (let bp = sequenceBpStart; bp <= bpEnd; bp++) { let seqOffsetBp = Math.floor(bp - sequenceBpStart); if (seqOffsetBp < sequence.length) { let letter = sequence[seqOffsetBp]; if (this.reversed) { letter = complement[letter] || ""; } let offsetBP = bp - options.bpStart; let aPixel = offsetBP / options.bpPerPixel; let bPixel = (offsetBP + 1) / options.bpPerPixel; let color = this.fillColor(letter); if (options.bpPerPixel > 1 / 10) { IGVGraphics.fillRect(ctx, aPixel, 5, bPixel - aPixel, height - 5, { fillStyle: color }); } else { let xPixel = 0.5 * (aPixel + bPixel - ctx.measureText(letter).width); IGVGraphics.strokeText(ctx, letter, xPixel, height, { strokeStyle: color }); } } } if (this.frameTranslate) { let transSeq; if (this.reversed) { transSeq = sequence.split('').map(function (cv) { return complement[cv]; }); transSeq = transSeq.join(''); } else { transSeq = sequence; } let y = height; let translatedSequence = this.translateSequence(transSeq); for (let arr of translatedSequence) { let i = translatedSequence.indexOf(arr); let fNum = i; let h = 25; y = i === 0 ? y + 10 : y + 30; //Little less room at first. for (let cv of arr) { let aaS; let idx = arr.indexOf(cv); let xSeed = idx + fNum + 2 * idx; let color = 0 === idx % 2 ? 'rgb(160,160,160)' : 'rgb(224,224,224)'; let p0 = Math.floor(xSeed / options.bpPerPixel); let p1 = Math.floor((xSeed + 3) / options.bpPerPixel); let pc = Math.round((p0 + p1) / 2); if (cv.aminoA.indexOf('STOP') > -1) { color = 'rgb(255, 0, 0)'; aaS = 'STOP'; //Color blind accessible } else { aaS = cv.aminoA; } if (cv.aminoA === 'M') { color = 'rgb(0, 153, 0)'; aaS = 'START'; //Color blind accessible } IGVGraphics.fillRect(ctx, p0, y, p1 - p0, h, { fillStyle: color }); if (options.bpPerPixel <= 1 / 10) { IGVGraphics.strokeText(ctx, aaS, pc - ctx.measureText(aaS).width / 2, y + 15); } } } } } } supportsWholeGenome() { return false; } computePixelHeight(ignore) { return this.height; } fillColor(index) { if (this.color) { return this.color; } else if ("dna" === this.sequenceType) { return this.browser.nucleotideColors[index] || 'gray'; } else { return 'rgb(0, 0, 150)'; } } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const axisContainerWidth = 50; class TrackView { constructor(browser, $container, track) { this.browser = browser; this.track = track; track.trackView = this; const $track = $('
'); this.trackDiv = $track.get(0); $container.append($track); this.namespace = '.trackview_' + guid(); if (track instanceof RulerTrack) { this.trackDiv.dataset.rulerTrack = "rulerTrack"; } // Create an alert dialog for the sequence track to copy ref sequence to. Obviously a little hacky. if (track instanceof SequenceTrack) { this.alert = new AlertDialog(this.trackDiv); } if (track.height) { this.trackDiv.style.height = track.height + "px"; } this.$viewportContainer = $('
'); $track.append(this.$viewportContainer); // add axis to viewportContainer this.$axis = this.createAxis(this.$viewportContainer); // add viewport(s) to viewportContainer. One viewport per reference frame this.populateViewportContainer(browser, browser.referenceFrameList); // Track drag handle if ('ideogram' === track.type || 'ruler' === track.type) ; else { this.attachDragWidget($track, this.$viewportContainer); } // right hand gutter if (true === track.ignoreTrackMenu) ; else { this.appendRightHandGutter($track); } // color picker const trackColors = []; const color = track.color || track.defaultColor; if (isString$6(color)) { trackColors.push(color); } if (track.altColor && isString$6(track.altColor)) { trackColors.push(track.altColor); } const defaultColors = trackColors.map(c => { return c.startsWith("#") ? c : c.startsWith("rgb(") ? IGVColor.rgbToHex(c) : IGVColor.colorNameToHex(c); }); const options = { parent: this.trackDiv, top: undefined, left: undefined, width: 432, height: undefined, defaultColors, colorHandler: color => { this.track.color = color; this.repaintViews(); } }; this.colorPicker = new ColorPicker(options); // alt color picker -- TODO pass handler in at "show" time and use 1 color picker options.colorHandler = color => { this.track.altColor = color; this.repaintViews(); }; this.altColorPicker = new ColorPicker(options); } populateViewportContainer(browser, referenceFrameList) { const width = browser.computeViewportWidth(referenceFrameList.length, browser.getViewportContainerWidth()); this.viewports = []; for (let referenceFrame of referenceFrameList) { const viewport = createViewport(this, referenceFrameList, referenceFrameList.indexOf(referenceFrame), width); this.viewports.push(viewport); } this.sampleNameViewport = new SampleNameViewport(this, this.$viewportContainer, undefined, browser.sampleNameViewportWidth); if (false === browser.showSampleNames) { this.sampleNameViewport.$viewport.hide(); } else { this.sampleNameViewport.$viewport.show(); } updateViewportShims(this.viewports, this.$viewportContainer); this.updateViewportForMultiLocus(); this.attachScrollbar($(this.trackDiv), this.$viewportContainer, this.viewports, this.sampleNameViewport); } renderSVGContext(context, { deltaX, deltaY }) { renderSVGAxis(context, this.track, this.axisCanvas, deltaX, deltaY); const { width: axisWidth } = this.$axis.get(0).getBoundingClientRect(); const { y } = this.viewports[0].$viewport.get(0).getBoundingClientRect(); let delta = { deltaX: axisWidth + deltaX, deltaY: y + deltaY }; for (let viewport of this.viewports) { viewport.renderSVGContext(context, delta); const { width } = viewport.$viewport.get(0).getBoundingClientRect(); delta.deltaX += width; } if (true === this.browser.showSampleNames) { this.sampleNameViewport.renderSVGContext(context, delta); } } attachScrollbar($track, $viewportContainer, viewports, sampleNameViewport) { if ("hidden" === $viewportContainer.find('.igv-viewport').css("overflow-y")) { this.scrollbar = new TrackScrollbar($viewportContainer, viewports, sampleNameViewport); this.scrollbar.$outerScroll.insertAfter($viewportContainer); if ('ruler' === this.track.type || 'ideogram' === this.track.type) { this.scrollbar.disableMouseHandlers(); } } } removeViewportForReferenceFrame(referenceFrame) { let index = -1; for (let i = 0; i < this.viewports.length; i++) { if (this.viewports[i].referenceFrame === referenceFrame) { index = i; break; } } if (index >= 0) { this.viewports[index].$viewport.remove(); this.viewports.splice(index, 1); this.updateViewportForMultiLocus(); } } updateViewportForMultiLocus() { if ('ruler' === this.track.type) { if (this.viewports.length > 1) { this.$viewportContainer.find('.igv-multi-locus-panel-close-container').show(); this.$viewportContainer.find('.igv-multi-locus-panel-label-div').show(); this.track.updateLocusLabel(); } else { this.$viewportContainer.find('.igv-multi-locus-panel-close-container').hide(); this.$viewportContainer.find('.igv-multi-locus-panel-label-div').hide(); } } } createAxis($viewportContainer) { const $axis = $('
'); $viewportContainer.append($axis); if (typeof this.track.paintAxis === 'function') { if (this.track.dataRange) { $axis.click(() => { this.browser.dataRangeDialog.configure(this); this.browser.dataRangeDialog.present($(this.trackDiv)); }); $axis.addClass('igv-clickable'); } this.resizeAxisCanvas($axis, $axis.outerWidth(), $axis.outerHeight()); } return $axis; } dataRange() { return this.track.dataRange ? this.track.dataRange : undefined; } setDataRange(min, max) { if (min !== undefined) { this.track.dataRange.min = min; } if (max !== undefined) { this.track.dataRange.max = max; } this.track.autoscale = false; this.repaintViews(); } presentColorPicker(option) { if (option === "altColor") { this.altColorPicker.show(); } else { this.colorPicker.show(); } } setTrackHeight(newHeight, force) { if (!force) { if (this.track.minHeight) { newHeight = Math.max(this.track.minHeight, newHeight); } if (this.track.maxHeight) { newHeight = Math.min(this.track.maxHeight, newHeight); } } this.track.height = newHeight; this.track.config.height = newHeight; $(this.trackDiv).height(newHeight); // If the track does not manage its own content height set it here if (typeof this.track.computePixelHeight !== "function") { for (let vp of this.viewports) { vp.setContentHeight(newHeight); } } this.repaintViews(); this.resizeAxisCanvas(this.$axis, this.$axis.outerWidth(), newHeight); if (this.track.paintAxis) { this.track.paintAxis(this.axisCanvasContext, this.axisCanvasContext.canvas.width, this.axisCanvasContext.canvas.height); } if (this.scrollbar) { this.scrollbar.update(); } } isLoading() { for (let i = 0; i < this.viewports.length; i++) { if (this.viewports[i].isLoading()) return true; } } resize(viewportWidth) { for (let viewport of this.viewports) { viewport.setWidth(viewportWidth); } this.resizeAxisCanvas(this.$axis, this.$axis.outerWidth(), this.$axis.outerHeight()); this.updateViews(true); } /** * Repaint all viewports without loading any new data. Use this for events that change visual aspect of data, * e.g. color, sort order, etc, but do not change the genomic state. */ repaintViews() { for (let viewport of this.viewports) { viewport.repaint(); } if (this.track.paintAxis) { this.track.paintAxis(this.axisCanvasContext, this.axisCanvasContext.canvas.width, this.axisCanvasContext.canvas.height); } // Repaint sample names last this.repaintSamples(); } repaintSamples() { if (typeof this.track.getSamples === 'function') { const samples = this.track.getSamples(); this.sampleNameViewport.repaint(samples); } } /** * Update viewports to reflect current genomic state, possibly loading additional data. */ async updateViews(force) { if (!(this.browser && this.browser.referenceFrameList)) return; const visibleViewports = this.viewports.filter(vp => vp.isVisible()); // Shift viewports left/right to current genomic state (pans canvas) visibleViewports.forEach(function (viewport) { viewport.shift(); }); // rpv: viewports whose image (canvas) does not fully cover current genomic range const rpV = this.viewportsToReload(force); // Trigger viewport to load features needed to cover current genomic range for (let vp of rpV) { await vp.loadFeatures(); } // Very special case for variant tracks in multilocus view. The # of rows to allocate to the variant (site) // section depends on data from all the views. if (typeof this.track.variantRowCount === 'function') { let maxRow = 0; for (let vp of this.viewports) { if (vp.tile && vp.tile.features) { maxRow = Math.max(maxRow, vp.tile.features.reduce((a, f) => Math.max(a, f.row || 0), 0)); } } const current = this.track.nVariantRows; if (current !== maxRow + 1) { this.track.variantRowCount(maxRow + 1); for (let vp of this.viewports) { vp.checkContentHeight(); } } } if (this.disposed) return; // Track was removed during load const isDragging = this.browser.dragObject; if (!isDragging && this.track.autoscale) { let allFeatures = []; for (let vp of visibleViewports) { const referenceFrame = vp.referenceFrame; const start = referenceFrame.start; const end = start + referenceFrame.toBP($(vp.contentDiv).width()); if (vp.tile && vp.tile.features) { if (typeof vp.tile.features.getMax === 'function') { const max = vp.tile.features.getMax(start, end); allFeatures.push({ value: max }); } else { allFeatures = allFeatures.concat(FeatureUtils.findOverlapping(vp.tile.features, start, end)); } } } if (typeof this.track.doAutoscale === 'function') { this.track.dataRange = this.track.doAutoscale(allFeatures); } else { this.track.dataRange = doAutoscale(allFeatures); } } // Must repaint all viewports if autoscaling if (!isDragging && (this.track.autoscale || this.track.autoscaleGroup)) { for (let vp of visibleViewports) { vp.repaint(); } } else { for (let vp of rpV) { vp.repaint(); } } this.adjustTrackHeight(); // Repaint sample names last this.repaintSamples(); } /** * Return a promise to get all in-view features. Used for group autoscaling. */ async getInViewFeatures(force) { if (!(this.browser && this.browser.referenceFrameList)) { return []; } // List of viewports that need reloading const rpV = this.viewportsToReload(force); const promises = rpV.map(function (vp) { return vp.loadFeatures(); }); await Promise.all(promises); let allFeatures = []; for (let vp of this.viewports) { if (vp.tile && vp.tile.features) { const referenceFrame = vp.referenceFrame; const start = referenceFrame.start; const end = start + referenceFrame.toBP($(vp.contentDiv).width()); if (typeof vp.tile.features.getMax === 'function') { const max = vp.tile.features.getMax(start, end); allFeatures.push({ value: max }); } else { allFeatures = allFeatures.concat(FeatureUtils.findOverlapping(vp.tile.features, start, end)); } } } return allFeatures; } checkContentHeight() { for (let viewport of this.viewports) { viewport.checkContentHeight(); } this.adjustTrackHeight(); } adjustTrackHeight() { var maxHeight = maxViewportContentHeight(this.viewports); if (this.track.autoHeight) { this.setTrackHeight(maxHeight, false); } else if (this.track.paintAxis) { // Avoid duplication, paintAxis is already called in setTrackHeight this.track.paintAxis(this.axisCanvasContext, this.axisCanvasContext.canvas.width, this.axisCanvasContext.canvas.height); } if (this.scrollbar) { const currentTop = this.viewports[0].getContentTop(); const viewports = [...this.viewports, this.sampleNameViewport]; const heights = this.viewports.map(viewport => viewport.getContentHeight()); const minContentHeight = Math.min(...heights); const newTop = Math.min(0, this.$viewportContainer.height() - minContentHeight); if (currentTop < newTop) { for (let viewport of viewports) { viewport.$content.css("top", `${newTop}px`); } } this.scrollbar.update(); } } resizeAxisCanvas($axis, width, height) { if ($axis) { if (this.axisCanvas) { $(this.axisCanvas).remove(); } const $canvas = $(''); $axis.append($canvas); this.axisCanvas = $canvas.get(0); this.axisCanvasContext = this.axisCanvas.getContext('2d'); this.axisCanvas.style.height = `${height}px`; this.axisCanvas.style.width = `${width}px`; this.axisCanvas.height = window.devicePixelRatio * height; this.axisCanvas.width = window.devicePixelRatio * width; this.axisCanvasContext.scale(window.devicePixelRatio, window.devicePixelRatio); } } attachDragWidget($track, $viewportContainer) { const self = this; const browser = this.browser; this.$trackDragScrim = $('
'); $viewportContainer.append(this.$trackDragScrim); this.$trackDragScrim.hide(); self.$trackManipulationHandle = $('
'); $track.append(self.$trackManipulationHandle); self.$trackManipulationHandle.on('mousedown', function (e) { e.preventDefault(); e.stopPropagation(); self.$trackDragScrim.show(); browser.startTrackDrag(self); }); self.$trackManipulationHandle.on('mouseup', function (e) { e.preventDefault(); e.stopPropagation(); browser.endTrackDrag(); self.$trackDragScrim.hide(); }); $track.on('mouseenter', function (e) { if (browser.dragTrack) { e.preventDefault(); e.stopPropagation(); browser.updateTrackDrag(self); } }); self.$trackManipulationHandle.on('mouseleave', function (e) { if (!browser.dragTrack) { e.preventDefault(); e.stopPropagation(); self.$trackDragScrim.hide(); } }); } viewportsToReload(force) { // List of viewports that need reloading const rpV = this.viewports.filter(function (viewport) { if (!viewport.isVisible()) { return false; } if (!viewport.checkZoomIn()) { return false; } else { const referenceFrame = viewport.referenceFrame; const chr = viewport.referenceFrame.chr; const start = referenceFrame.start; const end = start + referenceFrame.toBP($(viewport.contentDiv).width()); const bpPerPixel = referenceFrame.bpPerPixel; return force || !viewport.tile || viewport.tile.invalidate || !viewport.tile.containsRange(chr, start, end, bpPerPixel); } }); return rpV; } /** * Do any cleanup here */ dispose() { const self = this; if (this.$trackManipulationHandle) { this.$trackManipulationHandle.off(); } if (this.scrollbar) { this.scrollbar.dispose(); } $(document).off(this.namespace); if (typeof this.track.dispose === "function") { this.track.dispose(); } var track = this.track; if (typeof track.dispose === 'function') { track.dispose(); } Object.keys(track).forEach(function (key) { track[key] = undefined; }); this.viewports.forEach(function (viewport) { viewport.dispose(); }); Object.keys(this).forEach(function (key) { self[key] = undefined; }); if (this.alert) { this.alert.container.remove(); // This is quite obviously a hack, need a "dispose" method on AlertDialog } this.disposed = true; } scrollBy(delta) { this.scrollbar.moveScrollerBy(delta); } appendRightHandGutter($parent) { let $div = $('
'); $parent.append($div); this.createTrackGearPopup($div); } createTrackGearPopup($parent) { let $container = $("
", { class: 'igv-trackgear-container' }); $parent.append($container); $container.append(createIcon$1('cog')); this.trackGearPopup = new MenuPopup($parent); this.trackGearPopup.$popover.hide(); $container.click(e => { e.preventDefault(); e.stopPropagation(); this.trackGearPopup.presentMenuList(-this.trackGearPopup.$popover.width(), 0, MenuUtils.trackMenuItemList(this)); }); } static computeViewportWidth(browser, viewportContainerWidth) { return viewportContainerWidth - axisContainerWidth - browser.getSampleNameViewportWidth(); } } function renderSVGAxis(context, track, axisCanvas, deltaX, deltaY) { if (typeof track.paintAxis === 'function') { const { y, width, height } = axisCanvas.getBoundingClientRect(); const str = (track.name || track.id).replace(/\W/g, ''); const id = `${str}_axis_guid_${guid()}`; context.saveWithTranslationAndClipRect(id, deltaX, y + deltaY, width, height, 0); track.paintAxis(context, width, height); context.restore(); } } function emptyViewportContainers(trackViews) { for (let trackView of trackViews) { if (trackView.scrollbar) { trackView.scrollbar.$outerScroll.remove(); trackView.scrollbar = null; trackView.scrollbar = undefined; } for (let viewport of [...trackView.viewports, trackView.sampleNameViewport]) { if (viewport.rulerSweeper) { viewport.rulerSweeper.$rulerSweeper.remove(); } if (viewport.popover) { viewport.popover.dispose(); } viewport.$viewport.remove(); } delete trackView.sampleNameViewport; delete trackView.viewports; delete trackView.scrollbar; } } function updateViewportShims(viewports, $viewportContainer) { const $trackContainer = $('.igv-track-container'); $trackContainer.find('.igv-multi-locus-separator').remove(); const { x: tx } = documentOffset($trackContainer.get(0)); $viewportContainer.find('.igv-viewport-multi-locus-gap-shim').remove(); if (viewports.length > 1) { for (let viewport of viewports) { if (viewports.indexOf(viewport) <= viewports.length - 2) { const { $viewport } = viewport; const $shim = $('
'); $shim.insertAfter($viewport); const { x: sx } = documentOffset($shim.get(0)); // console.log(`trackContainer x ${ tx }. shim x ${ sx }`) const $multilLocusSeparator = $('
'); $trackContainer.append($multilLocusSeparator); $multilLocusSeparator.get(0).style.left = `${sx - tx}px`; } } } } function documentOffset(el) { const { x, y } = el.getBoundingClientRect(); const scrollX = window.pageXOffset || document.documentElement.scrollLeft; const scrollY = window.pageYOffset || document.documentElement.scrollTop; return { x: x + scrollX, y: y + scrollY }; } function maxViewportContentHeight(viewports) { const heights = viewports.filter(viewport => !(viewport.trackView.sampleNameViewport === viewport)).map(viewport => viewport.getContentHeight()); return Math.max(...heights); } /** * Decoder for bedpe records. * * Bedpe format was created by Aaron Quinlan et al as part of the bedtools project. * The spec is here: https://bedtools.readthedocs.io/en/latest/content/general-usage.html, however there * are off spec variants, an important one being a 7 column format with score in place of the standard * name column. * * Another common variant is a "hiccups" output file, which is standard bedpe with the exception of a header line * of the form * chr1 x1 x2 chr2 y1 y2 name score strand1 strand2 color observed expectedBL expectedDonut expectedH expectedV fdrBL fdrDonut fdrH fdrV * * @param tokens * @param ignore * @returns {{start1: number, end2: number, end1: number, chr1: *, chr2: *, start2: number}|undefined} */ function decodeBedpe(tokens, header) { if (tokens.length < 6) { return undefined; } var feature = { chr1: tokens[0], start1: Number.parseInt(tokens[1]), end1: Number.parseInt(tokens[2]), chr2: tokens[3], start2: Number.parseInt(tokens[4]), end2: Number.parseInt(tokens[5]) }; if (isNaN(feature.start1) || isNaN(feature.end1) || isNaN(feature.start2) || isNaN(feature.end2)) { //throw Error(`Error parsing line: ${tokens.join('\t')}`); return undefined; } if (tokens.length > 6 && tokens[6] !== ".") { feature.name = tokens[6]; } if (tokens.length > 7 && tokens[7] !== ".") { feature.score = parseFloat(tokens[7]); } if (tokens.length > 8 && tokens[8] !== ".") { feature.strand1 = tokens[8]; } if (tokens.length > 9 && tokens[9] !== ".") { feature.strand2 = tokens[9]; } // Optional extra columns if (header) { const colorColumn = header.colorColumn; if (colorColumn && colorColumn < tokens.length) { feature.color = IGVColor.createColorString(tokens[colorColumn]); } const thicknessColumn = header.thicknessColumn; if (thicknessColumn && thicknessColumn < tokens.length) { feature.thickness = tokens[thicknessColumn]; } if (tokens.length > 10 && header.columnNames && header.columnNames.length === tokens.length) { feature.extras = tokens.slice(10); } } // Set total extent of feature if (feature.chr1 === feature.chr2) { feature.chr = feature.chr1; feature.start = Math.min(feature.start1, feature.start2); feature.end = Math.max(feature.end1, feature.end2); } return feature; } /** * Hack for non-standard bedPE formats, where numeric score can be in column 7 (name field from spec) * @param features */ function fixBedPE(features) { if (features.length == 0) return; // Assume all features have same properties const firstFeature = features[0]; if (firstFeature.score === undefined && firstFeature.name !== undefined) { // Name field (col 7) is sometimes used for score. for (let f of features) { if (!(isNumber(f.name) || f.name === '.')) return; } for (let f of features) { f.score = parseFloat(f.name); delete f.name; } } // Make copies of inter-chr features, one for each chromosome const interChrFeatures = features.filter(f => f.chr1 !== f.chr2); for (let f1 of interChrFeatures) { const f2 = Object.assign({}, f1); f2.dup = true; features.push(f2); f1.chr = f1.chr1; f1.start = f1.start1; f1.end = f1.end1; f2.chr = f2.chr2; f2.start = f2.start2; f2.end = f2.end2; } } /** * Special decoder for Hic Domain files. In these files feature1 == feature2, they are really bed records. * @param tokens * @param ignore * @returns {*} */ function decodeBedpeDomain(tokens, header) { if (tokens.length < 8) return undefined; return { chr: tokens[0], start: Number.parseInt(tokens[1]), end: Number.parseInt(tokens[2]), color: IGVColor.createColorString(tokens[6]), value: Number.parseFloat(tokens[7]) }; } /** * Decode UCSC "interact" files. See https://genome.ucsc.edu/goldenpath/help/interact.html * 0 string chrom; "Chromosome (or contig, scaffold, etc.). For interchromosomal, use 2 records" 1 uint chromStart; "Start position of lower region. For interchromosomal, set to chromStart of this region" 2 uint chromEnd; "End position of upper region. For interchromosomal, set to chromEnd of this region" 3 string name; "Name of item, for display. Usually 'sourceName/targetName/exp' or empty" 4 uint score; "Score (0-1000)" 5 double value; "Strength of interaction or other data value. Typically basis for score" 6 string exp; "Experiment name (metadata for filtering). Use . if not applicable" 7 string color; "Item color. Specified as r,g,b or hexadecimal #RRGGBB or html color name, as in //www.w3.org/TR/css3-color/#html4. Use 0 and spectrum setting to shade by score" 8 string sourceChrom; "Chromosome of source region (directional) or lower region. For non-directional interchromosomal, chrom of this region." 9 uint sourceStart; "Start position in chromosome of source/lower/this region" 10 uint sourceEnd; "End position in chromosome of source/lower/this region" 11 string sourceName; "Identifier of source/lower/this region" 12 string sourceStrand; "Orientation of source/lower/this region: + or -. Use . if not applicable" 13 string targetChrom; "Chromosome of target region (directional) or upper region. For non-directional interchromosomal, chrom of other region" 14 uint targetStart; "Start position in chromosome of target/upper/this region" 15 uint targetEnd; "End position in chromosome of target/upper/this region" 16 string targetName; "Identifier of target/upper/this region" 17 string targetStrand; "Orientation of target/upper/this region: + or -. Use . if not applicable" * * @param tokens * @param ignore * @returns {*} */ function decodeInteract(tokens, header) { if (tokens.length < 6) { return undefined; } var feature = { chr: tokens[0], start: tokens[1], end: tokens[2], chr1: tokens[8], start1: Number.parseInt(tokens[9]), end1: Number.parseInt(tokens[10]), chr2: tokens[13], start2: Number.parseInt(tokens[14]), end2: Number.parseInt(tokens[15]), name: tokens[3], score: Number.parseFloat(tokens[4]), value: Number.parseFloat(tokens[5]), color: tokens[7] === '.' ? undefined : tokens[7] === "0" ? "rgb(0,0,0)" : tokens[7] }; return feature; } const gffNameFields = ["Name", "gene_name", "gene", "gene_id", "alias", "locus", "name"]; /** * Decode a single gff record (1 line in file). Aggregations such as gene models are constructed at a higher level. * ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001 * @param tokens * @param ignore * @returns {*} */ function decodeGFF(tokens, header) { var tokenCount, chr, start, end, strand, type, score, attributeString, color, name, i, format = header.format; tokenCount = tokens.length; if (tokenCount < 9) { return null; // Not a valid gff record } chr = tokens[0]; type = tokens[2]; start = parseInt(tokens[3]) - 1; end = parseInt(tokens[4]); score = "." === tokens[5] ? 0 : parseFloat(tokens[5]); strand = tokens[6]; "." === tokens[7] ? 0 : parseInt(tokens[7]); attributeString = tokens[8]; // Find ID and Parent, or transcript_id var delim = 'gff3' === format ? '=' : /\s+/; var attributes = parseAttributeString(attributeString, delim); for (let [key, value] of Object.entries(attributes)) { const keyLower = key.toLowerCase(); if ("color" === keyLower || "colour" === keyLower) { color = IGVColor.createColorString(value); } else if ('gff3' === format) try { attributes[key] = unescape(value); } catch (e) { attributes[key] = value; // Invalid console.error(`Malformed gff3 attibute value: ${value}`); } } // Find name (label) property if (header.nameField) { name = attributes[header.nameField]; } else { for (i = 0; i < gffNameFields.length; i++) { if (attributes.hasOwnProperty(gffNameFields[i])) { header.nameField = gffNameFields[i]; name = attributes[header.nameField]; break; } } } const id = attributes["ID"] || attributes["transcript_id"]; const parent = attributes["Parent"]; return { id: id, parent: parent, name: name, type: type, chr: chr, start: start, end: end, score: score, strand: strand, color: color, attributeString: attributeString, delim: delim, popupData: popupData }; } function parseAttributeString(attributeString, keyValueDelim) { // parse 'attributes' string (see column 9 docs in https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md) var attributes = {}; for (let kv of attributeString.split(';')) { const t = kv.trim().split(keyValueDelim, 2); if (t.length === 2) { const key = t[0].trim(); let value = t[1].trim(); //Strip off quotes, if any if (value.startsWith('"') && value.endsWith('"')) { value = value.substr(1, value.length - 2); } attributes[key] = value; } } return attributes; } function popupData(genomicLocation) { const kvs = this.attributeString.split(';'); const pd = []; if (this.name) { pd.push({ name: 'name:', value: this.name }); } pd.push({ name: 'type:', value: this.type }); for (let kv of kvs) { const t = kv.trim().split(this.delim, 2); if (t.length === 2 && t[1] !== undefined) { const key = t[0].trim(); if ('name' === key.toLowerCase()) continue; let value = t[1].trim(); //Strip off quotes, if any if (value.startsWith('"') && value.endsWith('"')) { value = value.substr(1, value.length - 2); } pd.push({ name: key + ":", value: value }); } } pd.push({ name: 'position:', value: `${this.chr}:${numberFormatter$1(this.start + 1)}-${numberFormatter$1(this.end)}` }); return pd; } /** * Wrapper class to record a decoding error. */ class DecodeError { constructor(message) { this.message = message; } } /** * Decode the UCSC bed format. Only the first 3 columns (chr, start, end) are required. The remaining columns * must follow standard bed order, but we will tolerate deviations after column 3. * * @param tokens * @param ignore * @returns decoded feature, or null if this is not a valid record */ function decodeBed(tokens, header) { if (tokens.length < 3) return undefined; header && header.gffTags; const chr = tokens[0]; const start = parseInt(tokens[1]); const end = tokens.length > 2 ? parseInt(tokens[2]) : start + 1; if (isNaN(start) || isNaN(end)) { return new DecodeError(`Unparsable bed record.`); } const feature = { chr: chr, start: start, end: end, score: 1000 }; try { if (tokens.length > 3) { // Note: these are very special rules for the gencode gene files. // tmp = tokens[3].replace(/"/g, ''); // idName = tmp.split(';'); // for (var i = 0; i < idName.length; i++) { // var kv = idName[i].split('='); // if (kv[0] == "gene_id") { // id = kv[1]; // } // if (kv[0] == "gene_name") { // name = kv[1]; // } // } // feature.id = id ? id : tmp; // feature.name = name ? name : tmp; //parse gffTags in the name field if (tokens[3].indexOf(';') > 0 && tokens[3].indexOf('=') > 0) { const attributes = parseAttributeString(tokens[3], '='); for (let nmField of gffNameFields) { if (attributes.hasOwnProperty(nmField)) { feature.name = attributes[nmField]; delete attributes[nmField]; break; } } feature.attributes = attributes; } if (!feature.name) { feature.name = tokens[3] === '.' ? '' : tokens[3]; } } if (tokens.length > 4) { feature.score = tokens[4] === '.' ? 0 : parseFloat(tokens[4]); if (isNaN(feature.score)) { return feature; } } if (tokens.length > 5) { feature.strand = tokens[5]; if (!(feature.strand === '.' || feature.strand === '+' || feature.strand === '-')) { return feature; } } if (tokens.length > 6) { feature.cdStart = parseInt(tokens[6]); if (isNaN(feature.cdStart)) { return feature; } } if (tokens.length > 7) { feature.cdEnd = parseInt(tokens[7]); if (isNaN(feature.cdEnd)) { return feature; } } if (tokens.length > 8) { if (tokens[8] !== "." && tokens[8] !== "0") feature.color = IGVColor.createColorString(tokens[8]); } if (tokens.length > 11) { const exonCount = parseInt(tokens[9]); // Some basic validation if (exonCount > 1000) { // unlikely return feature; } const exonSizes = tokens[10].replace(/,$/, '').split(','); const exonStarts = tokens[11].replace(/,$/, '').split(','); if (!(exonSizes.length === exonStarts.length && exonCount === exonSizes.length)) { return feature; } const exons = []; for (let i = 0; i < exonCount; i++) { const eStart = start + parseInt(exonStarts[i]); const eEnd = eStart + parseInt(exonSizes[i]); exons.push({ start: eStart, end: eEnd }); } findUTRs(exons, feature.cdStart, feature.cdEnd); feature.exons = exons; } // Optional extra columns if (header) { let thicknessColumn = header.thicknessColumn; let colorColumn = header.colorColumn; if (colorColumn && colorColumn < tokens.length) { feature.color = IGVColor.createColorString(tokens[colorColumn]); } if (thicknessColumn && thicknessColumn < tokens.length) { feature.thickness = tokens[thicknessColumn]; } } } catch (e) {} return feature; } /** * Decode a UCSC repeat masker record. * * Columns, from UCSC documentation * * 0 bin 585 smallint(5) unsigned Indexing field to speed chromosome range queries. * 1 swScore 1504 int(10) unsigned Smith Waterman alignment score * 2 milliDiv 13 int(10) unsigned Base mismatches in parts per thousand * 3 milliDel 4 int(10) unsigned Bases deleted in parts per thousand * 4 milliIns 13 int(10) unsigned Bases inserted in parts per thousand * 5 genoName chr1 varchar(255) Genomic sequence name * 6 genoStart 10000 int(10) unsigned Start in genomic sequence * 7 genoEnd 10468 int(10) unsigned End in genomic sequence * 8 genoLeft -249240153 int(11) -#bases after match in genomic sequence * 9 strand + char(1) Relative orientation + or - * 10 repName (CCCTAA)n varchar(255) Name of repeat * 11 repClass Simple_repeat varchar(255) Class of repeat * 12 repFamily Simple_repeat varchar(255) Family of repeat * 13 repStart 1 int(11) Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence * 14 repEnd 463 int(11) End in repeat sequence * 15 repLeft 0 int(11) -#bases after match (if strand is +) or start (if strand is -) in repeat sequence * 16 id 1 char(1) First digit of id field in RepeatMasker .out file. Best ignored. */ function decodeRepeatMasker(tokens, header) { if (tokens.length <= 15) return undefined; const feature = { swScore: Number.parseInt(tokens[1]), milliDiv: Number.parseInt(tokens[2]), milliDel: Number.parseInt(tokens[3]), milliIns: Number.parseInt(tokens[4]), chr: tokens[5], start: Number.parseInt(tokens[6]), end: Number.parseInt(tokens[7]), //genoLeft: tokens[8], strand: tokens[9], repName: tokens[10], repClass: tokens[11], repFamily: tokens[12], repStart: Number.parseInt(tokens[13]), repEnd: Number.parseInt(tokens[14]), repLeft: Number.parseInt(tokens[15]) }; return feature; } /** * Decode a UCSC "genePred" record. * * @param tokens * @param ignore * @returns {*} */ function decodeGenePred(tokens, header) { var shift = header.shift === undefined ? 0 : 1; if (tokens.length <= 9 + shift) return undefined; const cdStart = parseInt(tokens[5 + shift]); const cdEnd = parseInt(tokens[6 + shift]); var feature = { name: tokens[0 + shift], chr: tokens[1 + shift], strand: tokens[2 + shift], start: parseInt(tokens[3 + shift]), end: parseInt(tokens[4 + shift]), cdStart: cdStart, cdEnd: cdEnd, id: tokens[0 + shift] }, exonCount = parseInt(tokens[7 + shift]), exonStarts = tokens[8 + shift].split(','), exonEnds = tokens[9 + shift].split(','), exons = []; for (let i = 0; i < exonCount; i++) { const start = parseInt(exonStarts[i]); const end = parseInt(exonEnds[i]); exons.push({ start: start, end: end }); } findUTRs(exons, cdStart, cdEnd); feature.exons = exons; return feature; } /** * Decode a UCSC "genePredExt" record. refGene files are in this format. * * @param tokens * @param ignore * @returns {*} */ function decodeGenePredExt(tokens, header) { var shift = header.shift === undefined ? 0 : 1; if (tokens.length <= 11 + shift) return undefined; const cdStart = parseInt(tokens[5 + shift]); const cdEnd = parseInt(tokens[6 + shift]); const feature = { name: tokens[11 + shift], chr: tokens[1 + shift], strand: tokens[2 + shift], start: parseInt(tokens[3 + shift]), end: parseInt(tokens[4 + shift]), cdStart: cdStart, cdEnd: cdEnd, id: tokens[0 + shift] }, exonCount = parseInt(tokens[7 + shift]), exonStarts = tokens[8 + shift].split(','), exonEnds = tokens[9 + shift].split(','), exons = []; for (let i = 0; i < exonCount; i++) { const start = parseInt(exonStarts[i]); const end = parseInt(exonEnds[i]); exons.push({ start: start, end: end }); } findUTRs(exons, cdStart, cdEnd); feature.exons = exons; return feature; } /** * Decode a UCSC "refFlat" record * @param tokens * @param ignore * @returns {*} */ function decodeReflat(tokens, header) { var shift = header.shift === undefined ? 0 : 1; if (tokens.length <= 10 + shift) return undefined; const cdStart = parseInt(tokens[6 + shift]); const cdEnd = parseInt(tokens[7 + shift]); var feature = { name: tokens[0 + shift], id: tokens[1 + shift], chr: tokens[2 + shift], strand: tokens[3 + shift], start: parseInt(tokens[4 + shift]), end: parseInt(tokens[5 + shift]), cdStart: cdStart, cdEnd: cdEnd }, exonCount = parseInt(tokens[8 + shift]), exonStarts = tokens[9 + shift].split(','), exonEnds = tokens[10 + shift].split(','), exons = []; for (let i = 0; i < exonCount; i++) { const start = parseInt(exonStarts[i]); const end = parseInt(exonEnds[i]); exons.push({ start: start, end: end }); } findUTRs(exons, cdStart, cdEnd); feature.exons = exons; return feature; } function findUTRs(exons, cdStart, cdEnd) { for (let exon of exons) { const end = exon.end; const start = exon.start; if (end < cdStart || start > cdEnd) { exon.utr = true; } else { if (cdStart >= start && cdStart <= end) { exon.cdStart = cdStart; } if (cdEnd >= start && cdEnd <= end) { exon.cdEnd = cdEnd; } } } } function decodePeak(tokens, header) { var tokenCount, chr, start, end, strand, name, score, qValue, signal, pValue; tokenCount = tokens.length; if (tokenCount < 9) { return undefined; } chr = tokens[0]; start = parseInt(tokens[1]); end = parseInt(tokens[2]); name = tokens[3]; score = parseFloat(tokens[4]); strand = tokens[5].trim(); signal = parseFloat(tokens[6]); pValue = parseFloat(tokens[7]); qValue = parseFloat(tokens[8]); if (score === 0) score = signal; return { chr: chr, start: start, end: end, name: name, score: score, strand: strand, signal: signal, pValue: pValue, qValue: qValue }; } function decodeBedGraph(tokens, header) { var chr, start, end, value; if (tokens.length <= 3) return undefined; chr = tokens[0]; start = parseInt(tokens[1]); end = parseInt(tokens[2]); value = parseFloat(tokens[3]); const feature = { chr: chr, start: start, end: end, value: value }; // Optional extra columns if (header) { let colorColumn = header.colorColumn; if (colorColumn && colorColumn < tokens.length) { feature.color = IGVColor.createColorString(tokens[colorColumn]); } } return feature; } function decodeWig(tokens, header) { const wig = header.wig; if (wig && wig.format === "fixedStep") { const ss = wig.index * wig.step + wig.start; const ee = ss + wig.span; const value = parseFloat(tokens[0]); ++wig.index; return isNaN(value) ? null : { chr: wig.chrom, start: ss, end: ee, value: value }; } else if (wig && wig.format === "variableStep") { if (tokens.length < 2) return null; const ss = parseInt(tokens[0], 10) - 1; const ee = ss + wig.span; const value = parseFloat(tokens[1]); return isNaN(value) ? null : { chr: wig.chrom, start: ss, end: ee, value: value }; } else { return decodeBedGraph(tokens); } } function decodeSNP(tokens, header) { if (tokens.length < 6) return undefined; const autoSql = ['bin', 'chr', 'start', 'end', 'name', 'score', 'strand', 'refNCBI', 'refUCSC', 'observed', 'molType', 'class', 'valid', 'avHet', 'avHetSE', 'func', 'locType', 'weight', 'exceptions', 'submitterCount', 'submitters', 'alleleFreqCount', 'alleles', 'alleleNs', 'alleleFreqs', 'bitfields']; const feature = { chr: tokens[1], start: Number.parseInt(tokens[2]), end: Number.parseInt(tokens[3]), name: tokens[4], score: Number.parseInt(tokens[5]) }; const n = Math.min(tokens.length, autoSql.length); for (let i = 6; i < n; i++) { feature[autoSql[i]] = tokens[i]; } return feature; } function decodeFusionJuncSpan(tokens, header) { /* Format: 0 #scaffold 1 fusion_break_name 2 break_left 3 break_right 4 num_junction_reads 5 num_spanning_frags 6 spanning_frag_coords 0 B3GNT1--NPSR1 1 B3GNT1--NPSR1|2203-10182 2 2203 3 10182 4 189 5 1138 6 1860-13757,1798-13819,1391-18127,1443-17174,... */ if (tokens.length < 7) return undefined; var chr = tokens[0]; var fusion_name = tokens[1]; var junction_left = parseInt(tokens[2]); var junction_right = parseInt(tokens[3]); var num_junction_reads = parseInt(tokens[4]); var num_spanning_frags = parseInt(tokens[5]); var spanning_frag_coords_text = tokens[6]; var feature = { chr: chr, name: fusion_name, junction_left: junction_left, junction_right: junction_right, num_junction_reads: num_junction_reads, num_spanning_frags: num_spanning_frags, spanning_frag_coords: [], start: -1, end: -1 }; // set start and end later based on min/max of span coords var min_coord = junction_left; var max_coord = junction_right; if (num_spanning_frags > 0) { var coord_pairs = spanning_frag_coords_text.split(','); for (var i = 0; i < coord_pairs.length; i++) { var split_coords = coord_pairs[i].split('-'); var span_left = split_coords[0]; var span_right = split_coords[1]; if (span_left < min_coord) { min_coord = span_left; } if (span_right > max_coord) { max_coord = span_right; } feature.spanning_frag_coords.push({ left: span_left, right: span_right }); } } feature.start = min_coord; feature.end = max_coord; return feature; } function decodeGtexGWAS(tokens, header) { //chrom chromStart chromEnd Strongest SNP-risk allele Disease/Phenotype P-value Odds ratio or beta PUBMEDID //1 1247493 1247494 rs12103-A Inflammatory bowel disease 8.00E-13 1.1 23128233 const tokenCount = tokens.length; if (tokenCount < 7) { return null; } const feature = { chr: tokens[0], start: parseInt(tokens[1]) - 1, end: parseInt(tokens[2]), 'Strongest SNP-risk allele': tokens[3], 'Disease/Phenotype': tokens[4], 'P-value': tokens[5], 'Odds ratio or beta': tokens[6] }; if (tokens.length > 6) { feature['PUBMEDID'] = `${tokens[7]}`; } return feature; } /** * Decode a custom columnar format. Required columns are 'chr' and 'start' * * @param tokens * @param ignore * @returns decoded feature, or null if this is not a valid record */ function decodeCustom(tokens, header) { const format = header.customFormat; if (tokens.length < format.fields.length) return undefined; const coords = format.coords || 0; const chr = tokens[format.chr]; const start = parseInt(tokens[format.start]) - coords; const end = format.end !== undefined ? parseInt(tokens[format.end]) : start + 1; const feature = { chr: chr, start: start, end: end }; if (format.fields) { format.fields.forEach(function (field, index) { if (index !== format.chr && index !== format.start && index !== format.end) { feature[field] = tokens[index]; } }); } return feature; } // function expandFormat(format) { /** * Decode a gcnv record, a bed style format encoding copy number variation * * @param tokens * @param header */ function decodeGcnv(tokens, header) { const columnNames = header.columnNames; if (!columnNames) { throw Error("Sample names are not defined. Missing column headers?"); } const sampleCount = columnNames.length - 3; const chr = tokens[0]; const start = parseInt(tokens[1]); const end = parseInt(tokens[2]); const values = tokens.slice(3).map(parseFloat); if (values.length == sampleCount) { return { chr: chr, start: start, end: end, values: values }; } else { // TODO Throw error? console.warn(`${chr}:${start}-${end} row contains ${values.length} sample columns instead of the expected ${sampleCount} columns. Skipping...`); return undefined; } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ /** * Parser for column style (tab delimited, etc) text file formats (bed, gff, vcf, etc). * * */ /** * Return a parser for the given file format. */ class FeatureParser { constructor(config) { this.config = config; this.header = {}; if (config.nameField) { this.header.nameField = config.nameField; } this.skipRows = 0; // The number of fixed header rows to skip. Override for specific types as needed if (config.decode) { this.decode = config.decode; this.delimiter = config.delimiter || "\t"; } else if (config.format) { this.header.format = config.format.toLowerCase(); this.setDecoder(this.header.format); } if (!this.delimiter) { this.delimiter = "\t"; } } /** * Parse metadata from the file. A variety of conventions are in use to supply metadata about file contents * through header lines (e.g. 'track') and # directives. This method unifies metadata as properties of a * 'header' object. * * @param data * @returns {{}} */ async parseHeader(dataWrapper) { let header = this.header; let columnNames; let line; while ((line = await dataWrapper.nextLine()) !== undefined) { if (line.startsWith("track") || line.startsWith("#track")) { let h = parseTrackLine$1(line); Object.assign(header, h); } else if (line.startsWith("browser")) ; else if (line.startsWith("#columns")) { let h = parseColumnsDirective$1(line); Object.assign(header, h); } else if (line.startsWith("##gff-version 3")) { header.format = "gff3"; } else if (line.startsWith("#gffTags")) { header.gffTags = true; } else if (line.startsWith("fixedStep") || line.startsWith("variableStep")) { // Wig directives -- we are in the data section break; } else if (line.startsWith("#")) { const tokens = line.split(this.delimiter || "\t"); if (tokens.length > 1) { columnNames = tokens; // Possible column names } } else { // All directives that could change the format, and thus decoder, should have been read by now. this.setDecoder(header.format); // If the line can be parsed as a feature assume we are beyond the header, if any const tokens = line.split(this.delimiter || "\t"); try { const tmpHeader = Object.assign({ columnNames }, header); if (this.decode(tokens, tmpHeader)) { break; } else { if (tokens.length > 1) { columnNames = tokens; // possible column names } } } catch (e) { // Not a feature if (tokens.length > 1) { columnNames = tokens; // possible column names } } } } if (columnNames) { header.columnNames = columnNames; for (let n = 0; n < columnNames.length; n++) { if (columnNames[n] === "color" || columnNames[n] === "colour") { header.colorColumn = n; } else if (columnNames[n] === "thickness") { header.thicknessColumn = n; } } } this.header = header; // Directives might be needed for parsing lines return header; } async parseFeatures(dataWrapper) { const allFeatures = []; const decode = this.decode; const format = this.header.format; const delimiter = this.delimiter || "\t"; let i = 0; let errorCount = 0; let line; while ((line = await dataWrapper.nextLine()) !== undefined) { i++; if (i <= this.skipRows) continue; if (!line || line.startsWith("track") || line.startsWith("#") || line.startsWith("browser")) { continue; } else if (format === "wig" && line.startsWith("fixedStep")) { this.header.wig = parseFixedStep(line); continue; } else if (format === "wig" && line.startsWith("variableStep")) { this.header.wig = parseVariableStep(line); continue; } const tokens = line.split(delimiter); if (tokens.length < 1) { continue; } const feature = decode(tokens, this.header); if (feature instanceof DecodeError) { errorCount++; if (errorCount > 0) { console.error(`Error parsing line '${line}': ${feature.message}`); } continue; } if (feature) { allFeatures.push(feature); } } // Special hack for bedPE if (decode === decodeBedpe) { fixBedPE(allFeatures); } return allFeatures; } setDecoder(format) { switch (format) { case "narrowpeak": case "broadpeak": case "regionpeak": case "peaks": this.decode = decodePeak; this.delimiter = this.config.delimiter || /\s+/; break; case "bedgraph": this.decode = decodeBedGraph; this.delimiter = /\s+/; break; case "wig": this.decode = decodeWig; this.delimiter = this.config.delimiter || /\s+/; break; case "gff3": case "gff": case "gtf": this.decode = decodeGFF; this.delimiter = "\t"; break; case "fusionjuncspan": // bhaas, needed for FusionInspector view this.decode = decodeFusionJuncSpan; this.delimiter = this.config.delimiter || /\s+/; break; case "gtexgwas": this.skipRows = 1; this.decode = decodeGtexGWAS; this.delimiter = "\t"; break; case "refflat": this.decode = decodeReflat; this.delimiter = this.config.delimiter || /\s+/; break; case "genepred": this.decode = decodeGenePred; this.delimiter = this.config.delimiter || /\s+/; break; case "genepredext": this.decode = decodeGenePredExt; this.delimiter = this.config.delimiter || /\s+/; break; case "ensgene": this.decode = decodeGenePred; this.header.shift = 1; this.delimiter = this.config.delimiter || /\s+/; break; case "refgene": this.decode = decodeGenePredExt; this.delimiter = this.config.delimiter || /\s+/; this.header.shift = 1; break; case "bed": this.decode = decodeBed; this.delimiter = this.config.delimiter || /\s+/; break; case "bedpe": this.decode = decodeBedpe; this.delimiter = this.config.delimiter || "\t"; break; case "bedpe-domain": this.decode = decodeBedpeDomain; this.headerLine = true; this.delimiter = this.config.delimiter || "\t"; break; case "bedpe-loop": this.decode = decodeBedpe; this.delimiter = this.config.delimiter || "\t"; this.header = { colorColumn: 7 }; break; case "interact": this.decode = decodeInteract; this.delimiter = this.config.delimiter || /\s+/; break; case "snp": this.decode = decodeSNP; this.delimiter = "\t"; break; case "rmsk": this.decode = decodeRepeatMasker; this.delimiter = "\t"; break; case "gcnv": this.decode = decodeGcnv; this.delimiter = "\t"; break; default: const customFormat = getFormat(format); if (customFormat !== undefined) { this.decode = decodeCustom; this.header.customFormat = customFormat; this.delimiter = customFormat.delimiter || "\t"; } else { this.decode = decodeBed; this.delimiter = this.config.delimiter || /\s+/; } } } } function parseTrackLine$1(line) { const properties = {}; const tokens = line.split(/(?:")([^"]+)(?:")|([^\s"]+)(?=\s+|$)/g); // Clean up tokens array let curr; const tmp = []; for (let tk of tokens) { if (!tk || tk.trim().length === 0) continue; if (tk.endsWith("=")) { curr = tk; } else if (curr) { tmp.push(curr + tk); curr = undefined; } else { tmp.push(tk); } } for (let str of tmp) { if (!str) return; var kv = str.split('=', 2); if (kv.length === 2) { const key = kv[0].trim(); const value = kv[1].trim(); if (properties.hasOwnProperty(key)) { let currentValue = properties[key]; if (Array.isArray(currentValue)) { currentValue.push(value); } else { properties[key] = [currentValue, value]; } } else { properties[key] = value; } } } if ("interact" == properties["type"]) { properties["format"] = "interact"; } else if ("gcnv" === properties["type"]) { properties["format"] = "gcnv"; } return properties; } function parseColumnsDirective$1(line) { let properties = {}; let t1 = line.split(/\s+/); if (t1.length === 2) { let t2 = t1[1].split(";"); t2.forEach(function (keyValue) { let t = keyValue.split("="); if (t[0] === "color") { properties.colorColumn = Number.parseInt(t[1]) - 1; } else if (t[0] === "thickness") { properties.thicknessColumn = Number.parseInt(t[1]) - 1; } }); } return properties; } function parseFixedStep(line) { const tokens = line.split(/\s+/); const chrom = tokens[1].split("=")[1]; const start = parseInt(tokens[2].split("=")[1], 10) - 1; const step = parseInt(tokens[3].split("=")[1], 10); const span = tokens.length > 4 ? parseInt(tokens[4].split("=")[1], 10) : 1; return { format: "fixedStep", chrom, start, step, span, index: 0 }; } function parseVariableStep(line) { const tokens = line.split(/\s+/); const chrom = tokens[1].split("=")[1]; const span = tokens.length > 2 ? parseInt(tokens[2].split("=")[1], 10) : 1; return { format: "variableStep", chrom, span }; } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ /** * Define parser for seg files (.bed, .gff, .vcf, etc). A parser should implement 2 methods * * parseHeader(data) - return an object representing a header. Details are format specific * * parseFeatures(data) - return a list of features * */ class SegParser { constructor(type) { this.type = type || 'seg'; // One of seg, mut, or maf switch (this.type) { case 'mut': this.sampleColumn = 3; this.chrColumn = 0; this.startColumn = 1; this.endColumn = 2; this.dataColumn = 4; break; case 'maf': this.sampleColumn = 15; this.chrColumn = 4; this.startColumn = 5; this.endColumn = 6; this.dataColumn = 8; break; default: this.sampleColumn = 0; this.chrColumn = 1; this.startColumn = 2; this.endColumn = 3; // Data column determined after reading header } } async parseHeader(dataWrapper) { let line; while ((line = await dataWrapper.nextLine()) !== undefined) { if (line.startsWith("#")) ; else { const tokens = line.split("\t"); this.header = { headings: tokens }; break; } } return this.header; } async parseFeatures(dataWrapper) { const allFeatures = []; let extraHeaders; if (!this.header) { this.header = await this.parseHeader(dataWrapper); // This will only work for non-indexed files } if ('seg' === this.type) { this.dataColumn = this.header.headings.length - 1; } if (this.header.headings.length > 5) { extraHeaders = this.extractExtraColumns(this.header.headings); } const valueColumnName = this.header.headings[this.dataColumn]; let line; while ((line = await dataWrapper.nextLine()) !== undefined) { const tokens = line.split("\t"); const value = 'seg' === this.type ? parseFloat(tokens[this.dataColumn]) : tokens[this.dataColumn]; if (tokens.length > this.dataColumn) { const feature = new SegFeature({ sample: tokens[this.sampleColumn], chr: tokens[this.chrColumn], start: parseInt(tokens[this.startColumn]) - 1, end: parseInt(tokens[this.endColumn]), value, valueColumnName }); if (extraHeaders) { const extraValues = this.extractExtraColumns(tokens); feature.setAttributes({ names: extraHeaders, values: extraValues }); } allFeatures.push(feature); } } return allFeatures; } extractExtraColumns(tokens) { const extras = []; for (let i = 0; i < tokens.length; i++) { if (i !== this.chrColumn && i !== this.startColumn && i !== this.endColumn) { extras.push(tokens[i]); } } return extras; } } class SegFeature { constructor({ sample, chr, start, end, value, valueColumnName }) { this.sample = sample; this.chr = chr; this.start = start; this.end = end; this.value = value; this.valueColumnName = valueColumnName; } setAttributes({ names, values }) { this.attributeNames = names; this.attributeValues = values; } getAttribute(name) { if (this.attributeNames) { const idx = this.attributeNames.indexOf(name); if (idx >= 0) { return this.attributeValues[idx]; } } return undefined; } popupData() { const locationString = this.chr + ":" + numberFormatter$1(this.start + 1) + "-" + numberFormatter$1(this.end); const pd = [{ name: "Sample", value: this.sample }, { name: "Location", value: locationString }, { name: this.valueColumnName ? this.valueColumnName : "Value", value: this.value }]; if (this.attributeNames && this.attributeNames.length > 0) { pd.push("
"); for (let i = 0; i < this.attributeNames.length; i++) { pd.push({ name: this.attributeNames[i], value: this.attributeValues[i] }); } pd.push("
"); // In case there are multiple features selected } return pd; } } /* * The MIT License (MIT) * * Copyright (c) 2018 Regents of the University of California * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ /** * A collection of properties and methods shared by all (or most) track types. * * @param config * @param browser * @constructor */ class TrackBase { constructor(config, browser) { this.browser = browser; this.init(config); } /** * Initialize track properties from the config object. This method is typically overriden in subclasses, which * will call this implementation as super.init(config). * * @param config */ init(config) { if (config.displayMode) { config.displayMode = config.displayMode.toUpperCase(); } this.config = config; this.url = config.url; this.type = config.type; this.description = config.description; this.supportHiDPI = config.supportHiDPI === undefined ? true : config.supportHiDPI; if (config.name || config.label) { this.name = config.name || config.label; } else { if (isFilePath(config.url)) this.name = config.url.name;else this.name = config.url; } this.id = this.config.id === undefined ? this.name : this.config.id; this.order = config.order; this.color = config.color; this.altColor = config.altColor; if ("civic-ws" === config.sourceType) { // Ugly proxy for specialized track type this.defaultColor = "rgb(155,20,20)"; } else { this.defaultColor = "rgb(0,0,150)"; } this.autoscaleGroup = config.autoscaleGroup; this.removable = config.removable === undefined ? true : config.removable; // Defaults to true this.height = config.height || 100; this.autoHeight = config.autoHeight; this.minHeight = config.minHeight || Math.min(25, this.height); this.maxHeight = config.maxHeight || Math.max(1000, this.height); this.visibilityWindow = config.visibilityWindow; this.trackView = undefined; } /** * Update track properties from the config object. * * @param config */ updateConfig(config) { this.init(config); } /** * Default implementation -- update config with current values. * to create session object for bookmarking, sharing. Updates the track "config" object to reflect the * current state. Only simple properties (string, number, boolean) are updated. */ getState() { // Create copy of config, minus transient properties (convention is name starts with '_') const state = {}; for (let key of Object.keys(this.config)) { if (!key.startsWith("_")) { state[key] = this.config[key]; } } // Update original config values with any changes for (let key of Object.keys(state)) { if (key.startsWith("_")) continue; // transient property const value = this[key]; if (value && (isSimpleType(value) || typeof value === "boolean")) { state[key] = value; } } if (this.color) state.color = this.color; if (this.altColor) state.altColor = this.altColor; // Flatten dataRange if present if (!this.autoscale && this.dataRange) { state.min = this.dataRange.min; state.max = this.dataRange.max; } // Check for non-json-if-yable properties. Perhaps we should test what can be saved. for (let key of Object.keys(state)) { if (typeof state[key] === 'function') { throw Error(`Property '${key}' of track '${this.name} is a function. Functions cannot be saved in sessions.`); } if (state[key] instanceof File) { const str = `Track ${this.name} is a local file. Sessions cannot be saved with local file references.`; throw Error(str); } if (state[key] instanceof Promise) { throw Error(`Property '${key}' of track '${this.name} is a Promise. Promises cannot be saved in sessions.`); } } return state; } supportsWholeGenome() { return false; } /** * Does the track support sample names. Current sample aware tracks include VCF (with genotypes), MUT, MAF, and SEG * @returns {boolean} */ hasSamples() { return false; } getGenomeId() { return this.browser.genome ? this.browser.genome.id : undefined; } /** * Set certain track properties, usually from a "track" line. Not all UCSC properties are supported. * * Track configuration settings have precendence over track line properties, so if both are present ignore the * track line. * * @param properties */ setTrackProperties(properties) { const tracklineConfg = {}; let tokens; for (let key of Object.keys(properties)) { switch (key.toLowerCase()) { case "usescore": tracklineConfg.useScore = properties[key] === 1 || properties[key] === "1" || properties[key] === "on" || properties[key] === true; break; case "visibility": //0 - hide, 1 - dense, 2 - full, 3 - pack, and 4 - squish switch (properties[key]) { case "2": case "3": case "pack": case "full": tracklineConfg.displayMode = "EXPANDED"; break; case "4": case "squish": tracklineConfg.displayMode = "SQUISHED"; break; case "1": case "dense": tracklineConfg.displayMode = "COLLAPSED"; } break; case "color": case "altcolor": tracklineConfg[key] = properties[key].startsWith("rgb(") ? properties[key] : "rgb(" + properties[key] + ")"; break; case "featurevisiblitywindow": case "visibilitywindow": tracklineConfg.visibilityWindow = Number.parseInt(properties[key]); break; case "maxheightpixels": tokens = properties[key].split(":"); if (tokens.length === 3) { tracklineConfg.minHeight = Number.parseInt(tokens[2]); tracklineConfg.height = Number.parseInt(tokens[1]); tracklineConfg.maxHeight = Number.parseInt(tokens[0]); } break; case "viewlimits": if (!this.config.autoscale) { // autoscale in the config has precedence tokens = properties[key].split(":"); let min = 0; let max; if (tokens.length == 1) { max = Number.parseFloat(tokens[0]); } else if (tokens.length == 2) { min = Number.parseFloat(tokens[0]); max = Number.parseFloat(tokens[1]); } tracklineConfg.autoscale = false; tracklineConfg.dataRange = { min, max }; } case "name": tracklineConfg[key] = properties[key]; break; case "url": tracklineConfg["infoURL"] = properties[key]; } } // Track configuration objects have precendence over track line properties for (let key of Object.keys(tracklineConfg)) { if (!this.config.hasOwnProperty(key)) { this[key] = tracklineConfg[key]; } } } getVisibilityWindow() { return this.visibilityWindow; } clickedFeatures(clickState, features) { // We use the cached features rather than method to avoid async load. If the // feature is not already loaded this won't work, but the user wouldn't be mousing over it either. if (!features) features = clickState.viewport.getCachedFeatures(); if (!features || features.length === 0) { return []; } const genomicLocation = clickState.genomicLocation; // When zoomed out we need some tolerance around genomicLocation const tolerance = clickState.referenceFrame.bpPerPixel > 0.2 ? 3 * clickState.referenceFrame.bpPerPixel : 0.2; const ss = genomicLocation - tolerance; const ee = genomicLocation + tolerance; return FeatureUtils.findOverlapping(features, ss, ee); } /** * Default popup text function -- just extracts string and number properties in random order. * @param feature * @returns {Array} */ extractPopupData(feature, genomeId) { const filteredProperties = new Set(['row', 'color', 'chr', 'start', 'end', 'cdStart', 'cdEnd', 'strand', 'alpha']); const data = []; let alleles, alleleFreqs; for (var property in feature) { if (feature.hasOwnProperty(property) && !filteredProperties.has(property) && isSimpleType(feature[property])) { let value = feature[property]; data.push({ name: capitalize(property), value: value }); if (property === "alleles") { alleles = feature[property]; } else if (property === "alleleFreqs") { alleleFreqs = feature[property]; } } } //const genomeId = this.getGenomeId() if (alleles && alleleFreqs) { if (alleles.endsWith(",")) { alleles = alleles.substr(0, alleles.length - 1); } if (alleleFreqs.endsWith(",")) { alleleFreqs = alleleFreqs.substr(0, alleleFreqs.length - 1); } let a = alleles.split(","); let af = alleleFreqs.split(","); if (af.length > 1) { let b = []; for (let i = 0; i < af.length; i++) { b.push({ a: a[i], af: Number.parseFloat(af[i]) }); } b.sort(function (x, y) { return x.af - y.af; }); let ref = b[b.length - 1].a; if (ref.length === 1) { for (let i = b.length - 2; i >= 0; i--) { let alt = b[i].a; if (alt.length === 1) { const cravatLink = TrackBase.getCravatLink(feature.chr, feature.start + 1, ref, alt, genomeId); if (cravatLink) { data.push("
"); data.push({ html: cravatLink }); data.push("
"); } } } } } } if (feature.attributes) { for (let key of Object.keys(feature.attributes)) { data.push({ name: key, value: feature.attributes[key] }); } } // final chr position let posString = `${feature.chr}:${numberFormatter$1(feature.start + 1)}-${numberFormatter$1(feature.end)}`; if (feature.strand) { posString += ` (${feature.strand})`; } data.push({ name: 'Location', value: posString }); if (this.infoURL) { data.push("
"); const href = this.infoURL.replace("$$", feature.name); data.push({ html: `${href}` }); } return data; } static getCravatLink(chr, position, ref, alt, genomeID) { if ("hg38" === genomeID || "GRCh38" === genomeID) { const cravatChr = chr.startsWith("chr") ? chr : "chr" + chr; return `Cravat ${ref}->${alt}`; // return "Cravat " + ref + "->" + alt + "" } else { return undefined; } } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const knownAltBases = new Set(["A", "C", "T", "G"].map(c => c.charCodeAt(0))); function createVCFVariant(tokens) { return new Variant(tokens); } class Variant { constructor(tokens) { this.chr = tokens[0]; // TODO -- use genome aliases this.pos = parseInt(tokens[1]); this.names = tokens[2]; // id in VCF this.referenceBases = tokens[3]; this.alternateBases = tokens[4]; this.quality = tokens[5]; this.filter = tokens[6]; this.info = getInfoObject(tokens[7]); this.init(); } init() { const ref = this.referenceBases; const altBases = this.alternateBases; if (this.info) { if (this.info["VT"]) { this.type = this.info["VT"]; } else if (this.info["SVTYPE"]) { this.type = "SV"; } else if (this.info["PERIOD"]) { this.type = "STR"; } } if (this.type === undefined) { this.type = determineType(ref, altBases); } if (this.type === "NONVARIANT") { this.heterozygosity = 0; } // Determine start/end coordinates -- these are the coordinates representing the actual variant, // not the leading or trailing reference if (this.info["END"]) { this.start = this.pos - 1; if (this.info["CHR2"] && this.info["CHR2"] !== this.chr) { this.end = this.start + 1; } else { this.end = Number.parseInt(this.info["END"]); } } else { if (this.type === "NONVARIANT") { this.start = this.pos - 1; // convert to 0-based coordinate convention this.end = this.start + ref.length; } else { const altTokens = altBases.split(",").filter(token => token.length > 0); this.alleles = []; this.start = undefined; this.end = undefined; for (let alt of altTokens) { this.alleles.push(alt); // We don't yet handle SV and other special alt representations if ("SV" !== this.type && isKnownAlt(alt)) { let altLength = alt.length; let lengthOnRef = ref.length; const lmin = Math.min(altLength, lengthOnRef); // Trim off matching bases. Try first match, then right -> left, then any remaining left -> right let s = 0; while (s < lmin && ref.charCodeAt(s) === alt.charCodeAt(s)) { s++; altLength--; lengthOnRef--; } // right -> left from end while (altLength > 0 && lengthOnRef > 0) { const altIdx = s + altLength - 1; const refIdx = s + lengthOnRef - 1; if (alt.charCodeAt(altIdx) === ref.charCodeAt(refIdx)) { altLength--; lengthOnRef--; } else { break; } } // if any remaining, left -> right while (altLength > 0 && lengthOnRef > 0) { const altIdx = s; const refIdx = s; if (alt.charCodeAt(altIdx) === ref.charCodeAt(refIdx)) { s++; altLength--; lengthOnRef--; } else { break; } } const alleleStart = this.pos + s - 1; // -1 for zero based coordinates const alleleEnd = alleleStart + lengthOnRef; this.start = this.start === undefined ? alleleStart : Math.min(this.start, alleleStart); this.end = this.end === undefined ? alleleEnd : Math.max(this.end, alleleEnd); } } // Default to single base representation @ position for variant types not otherwise handled if (this.start === undefined) { this.start = this.pos - 1; this.end = this.pos; } } } } popupData(genomicLocation, genomeId) { const posString = `${numberFormatter$1(this.pos)}`; const locString = this.start === this.end ? `${numberFormatter$1(this.start)} | ${numberFormatter$1(this.start + 1)}` : `${numberFormatter$1(this.start + 1)}-${numberFormatter$1(this.end)}`; const fields = [{ name: "Chr", value: this.chr }, { name: "Pos", value: posString }, { name: "Loc", value: locString }, { name: "Names", value: this.names ? this.names : "" }, { name: "Ref", value: this.referenceBases }, { name: "Alt", value: this.alternateBases.replace("<", "<") }, { name: "Qual", value: this.quality }, { name: "Filter", value: this.filter }]; if ("SNP" === this.type) { let ref = this.referenceBases; if (ref.length === 1) { let altArray = this.alternateBases.split(","); for (let alt of altArray) { if (alt.length === 1) { let l = TrackBase.getCravatLink(this.chr, this.pos, ref, alt, genomeId); if (l) { fields.push("
"); fields.push({ html: l }); } } } } } if (this.hasOwnProperty("heterozygosity")) { fields.push({ name: "Heterozygosity", value: this.heterozygosity }); } if (this.info) { fields.push({ html: '
' }); for (let key of Object.keys(this.info)) { fields.push({ name: key, value: arrayToString(decodeURIComponent(this.info[key])) }); } } return fields; } isRefBlock() { return "NONVARIANT" === this.type; } } function getInfoObject(infoStr) { var info = {}; if (infoStr) { infoStr.split(';').forEach(function (elem) { var element = elem.split('='); info[element[0]] = element[1]; }); } return info; } function isKnownAlt(alt) { for (let i = 0; i < alt.length; i++) { if (!knownAltBases.has(alt.charCodeAt(i))) { return false; } } return true; } function determineType(ref, altAlleles) { const refLength = ref.length; if (altAlleles === undefined) { return "UNKNOWN"; } else if (altAlleles.trim().length === 0 || altAlleles === "" || altAlleles === "<*>" || altAlleles === ".") { return "NONVARIANT"; } else { const alleles = altAlleles.split(","); const types = alleles.map(function (a) { if (refLength === 1 && a.length === 1) { return "SNP"; } else { return "" === a ? "NONVARIANT" : "OTHER"; } }); let type = types[0]; for (let t of types) { if (t !== type) { return "MIXED"; } } return type; } } function arrayToString(value, delim) { if (delim === undefined) delim = ","; if (!Array.isArray(value)) { return value; } return value.join(delim); } /** * @deprecated - the GA4GH API has been deprecated. This code no longer maintained. * @param json * @returns {Variant} */ function createGAVariant(json) { var variant = new Variant(); variant.chr = json.referenceName; variant.start = parseInt(json.start); // Might get overriden below variant.end = parseInt(json.end); // Might get overriden below variant.pos = variant.start + 1; // GA4GH is 0 based. variant.names = arrayToString(json.names, "; "); variant.referenceBases = json.referenceBases; variant.alternateBases = arrayToString(json.alternateBases); variant.quality = json.quality; variant.filter = arrayToString(json.filter); // Flatten GA4GH attributes array variant.info = {}; if (json.info) { Object.keys(json.info).forEach(function (key) { var value, valueArray = json.info[key]; if (Array.isArray(valueArray)) { value = valueArray.join(","); } else { value = valueArray; } variant.info[key] = value; }); } // Need to build a hash of calls for fast lookup // Note from the GA4GH spec on call ID: // // The ID of the call set this variant call belongs to. If this field is not present, // the ordering of the call sets from a SearchCallSetsRequest over this GAVariantSet // is guaranteed to match the ordering of the calls on this GAVariant. // The number of results will also be the same. variant.calls = {}; var id; if (json.calls) { json.calls.forEach(function (call) { id = call.callSetId; variant.calls[id] = call; }); } init(variant); return variant; } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ /** * Parser for VCF files. */ class VcfParser { construtor() {} async parseHeader(dataWrapper, genome) { const header = {}; header.chrAliasTable = new Map(); // First line must be file format let line = await dataWrapper.nextLine(); if (line.startsWith("##fileformat")) { header.version = line.substr(13); } else { throw new Error("Invalid VCF file: missing fileformat line"); } while ((line = await dataWrapper.nextLine()) !== undefined) { if (line.startsWith("#")) { let id; const values = {}; if (line.startsWith("##")) { if (line.startsWith("##INFO") || line.startsWith("##FILTER") || line.startsWith("##FORMAT")) { const ltIdx = line.indexOf("<"); const gtIdx = line.lastIndexOf(">"); if (!(ltIdx > 2 && gtIdx > 0)) { continue; } const type = line.substring(2, ltIdx - 1); if (!header[type]) header[type] = {}; //##INFO= // ##FILTER= // ##FORMAT= const tokens = splitStringRespectingQuotes(line.substring(ltIdx + 1, gtIdx - 1), ","); for (let token of tokens) { var kv = token.split("="); if (kv.length > 1) { if (kv[0] === "ID") { id = kv[1]; } else { values[kv[0]] = kv[1]; } } } if (id) { header[type][id] = values; } } else if (line.startsWith("##contig") && genome) { const idx1 = line.indexOf("", idx1); } const chr = line.substring(idx1 + 4, idx2); const canonicalChromosome = genome.getChromosomeName(chr); header.chrAliasTable.set(canonicalChromosome, chr); } else ; } else if (line.startsWith("#CHROM")) { const tokens = line.split("\t"); if (tokens.length > 8) { // call set names -- use column index for id header.callSets = []; for (let j = 9; j < tokens.length; j++) { header.callSets.push({ id: j, name: tokens[j] }); } } } } else { break; } } this.header = header; // Will need to intrepret genotypes and info field return header; } /** * Parse data as a collection of Variant objects. * * @param data * @returns {Array} */ async parseFeatures(dataWrapper) { const allFeatures = []; const callSets = this.header.callSets; const nExpectedColumns = 8 + (callSets ? callSets.length + 1 : 0); let line; while ((line = await dataWrapper.nextLine()) !== undefined) { if (line && !line.startsWith("#")) { const tokens = line.split("\t"); if (tokens.length === nExpectedColumns) { const variant = createVCFVariant(tokens); variant.header = this.header; // Keep a pointer to the header to interpret fields for popup text allFeatures.push(variant); if (tokens.length > 9) { // Format const callFields = extractCallFields(tokens[8].split(":")); variant.calls = {}; for (let index = 9; index < tokens.length; index++) { const token = tokens[index]; const callSet = callSets[index - 9]; const call = { callSetName: callSet.name, info: {} }; variant.calls[callSet.id] = call; token.split(":").forEach(function (callToken, idx) { switch (idx) { case callFields.genotypeIndex: call.genotype = []; callToken.split(/[\|\/]/).forEach(function (s) { call.genotype.push('.' === s ? s : parseInt(s)); }); break; default: call.info[callFields.fields[idx]] = callToken; } }); } } } } } return allFeatures; } } function extractCallFields(tokens) { const callFields = { genotypeIndex: -1, fields: tokens }; for (let i = 0; i < tokens.length; i++) { if ("GT" === tokens[i]) { callFields.genotypeIndex = i; } } return callFields; } /* * The MIT License (MIT) * * Copyright (c) 2016-2017 The Regents of the University of California * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ function getDataWrapper(data) { if (typeof data == 'string' || data instanceof String) { return new StringDataWrapper(data); } else { return new ByteArrayDataWrapper(data); } } // Data might be a string, or an UInt8Array class StringDataWrapper { constructor(string) { this.data = string; this.ptr = 0; } nextLine() { var start = this.ptr, idx = this.data.indexOf('\n', start), data = this.data; if (idx > 0) { this.ptr = idx + 1; // Advance pointer for next line if (idx > start && data.charAt(idx - 1) === '\r') { // Trim CR manually in CR/LF sequence return data.substring(start, idx - 1); } return data.substring(start, idx); } else { var length = data.length; this.ptr = length; // Return undefined only at the very end of the data return start >= length ? undefined : data.substring(start); } } } class ByteArrayDataWrapper { constructor(array) { this.data = array; this.length = this.data.length; this.ptr = 0; } nextLine() { var c, result; result = ""; if (this.ptr >= this.length) return undefined; for (var i = this.ptr; i < this.length; i++) { c = String.fromCharCode(this.data[i]); if (c === '\r') continue; if (c === '\n') break; result = result + c; } this.ptr = i + 1; return result; } } /** * Parser for IGV desktop GWAS files. See http://software.broadinstitute.org/software/igv/GWAS */ class GWASParser { constructor(config) { // Defaults - can be overriden by header this.config = config; if (config.columns) { if (config.columns.chromosome === undefined || config.columns.position === undefined || config.columns.value === undefined) { throw Error("columns property must define chrCol, posCol, and valueCol"); } this.posCol = config.columns.position - 1; this.chrCol = config.columns.chromosome - 1; this.pvalueCol = config.columns.value - 1; } else { // Defaults -- can be overriden in header this.posCol = 2; this.chrCol = 1; this.pvalueCol = 3; } } async parseHeader(dataWrapper) { const headerLine = await dataWrapper.nextLine(); return this.parseHeaderLine(headerLine); } parseHeaderLine(headerLine) { this.columns = headerLine.split(/\t/); if (!this.config.columns) { for (let i = 0; i < this.columns.length; i++) { const c = this.columns[i].toLowerCase(); switch (c) { case 'chr': case 'chromosome': case 'chr_id': this.chrCol = i; break; case 'bp': case 'pos': case 'position': case 'chr_pos': this.posCol = i; break; case 'p': case 'pval': case 'pvalue': case 'p-value': case 'p.value': this.pvalueCol = i; break; } } } return this.columns; } async parseFeatures(dataWrapper) { const allFeatures = []; const headerLine = dataWrapper.nextLine(); if (!this.columns) { this.parseHeaderLine(headerLine); } let line; while ((line = dataWrapper.nextLine()) !== undefined) { const tokens = line.split(/\t/); if (tokens.length === this.columns.length) { const chr = tokens[this.chrCol]; const start = parseInt(tokens[this.posCol]) - 1; const end = start + 1; const value = parseFloat(tokens[this.pvalueCol]); allFeatures.push(new GWASFeature({ chr: chr, start: start, end: end, value: value, line: line, columns: this.columns })); } } return allFeatures; } } class GWASFeature { constructor({ chr, start, end, value, line, columns }) { this.chr = chr; this.start = start; this.end = end; this.value = value; this.line = line; this.columns = columns; } popupData() { const tokens = this.line.split(/\t/); return this.columns.map(function (c, index) { return { name: c, value: tokens[index] }; }); } getAttribute(attrName) { const tokens = this.line.split(/\t/); for (let i = 0; i < this.columns.length; i++) { if (this.columns[i] === attrName) { return tokens[i]; } } return undefined; } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ /** * Define parsers for bed-like files (.bed, .gff, .vcf, etc). A parser should implement 2 methods * * parseHeader(data) - return an object representing a header or metadata. Details are format specific * * parseFeatures(data) - return an array of features * */ var aedRegexpNoNamespace = new RegExp("([^:]*)\\(([^)]*)\\)"); // name(type) for AED parsing (namespace undefined) var aedRegexpNamespace = new RegExp("([^:]*):([^(]*)\\(([^)]*)\\)"); // namespace:name(type) for AED parsing class AEDParser { constructor(config) { const decode = config ? config.decode : undefined; this.nameField = config ? config.nameField : undefined; this.skipRows = 0; // The number of fixed header rows to skip. Override for specific types as needed if (decode) { this.decode = decode; } else { this.decode = decodeAed; } this.delimiter = "\t"; } async parseHeader(dataWrapper) { let line; let header; while (line = await dataWrapper.nextLine()) { if (line.startsWith("track") || line.startsWith("#") || line.startsWith("browser")) { if (line.startsWith("track") || line.startsWith("#track")) { let h = parseTrackLine(line); if (header) { Object.assign(header, h); } else { header = h; } } else if (line.startsWith("#columns")) { let h = parseColumnsDirective(line); if (header) { Object.assign(header, h); } else { header = h; } } else if (line.startsWith("##gff-version 3")) { this.format = "gff3"; if (!header) header = {}; header["format"] = "gff3"; } } else { break; } } this.header = header; // Directives might be needed for parsing lines return header; } async parseFeatures(dataWrapper) { const allFeatures = []; const decode = this.decode; const delimiter = this.delimiter || "\t"; let i = 0; let line; let wig; while ((line = dataWrapper.nextLine()) !== undefined) { i++; if (i <= this.skipRows || line.startsWith("track") || line.startsWith("#") || line.startsWith("browser")) { continue; } let tokens = readTokensAed(); if (tokens.length < 1) { continue; } if (!this.aed) { // Store information about the aed header in the parser itself // This is done only once - on the first row this.aed = parseAedHeaderRow(tokens); continue; } const feature = decode.call(this, tokens, wig); if (feature) { allFeatures.push(feature); } } return allFeatures; // Double quoted strings can contain newlines in AED // "" is an escape for a ". // Parse all this, clean it up, split into tokens in a custom way function readTokensAed() { var tokens = [], token = "", quotedString = false, n, c; while (line || line === '') { for (n = 0; n < line.length; n++) { c = line.charAt(n); if (c === delimiter) { if (!quotedString) { tokens.push(token); token = ""; } else { token += c; } } else if (c === "\"") { // Look ahead to the next character if (n + 1 < line.length && line.charAt(n + 1) === "\"") { if (quotedString) { // Turn "" into a single " in the output string token += "\""; } // Skip the next double quote n++; } else { // We know the next character is NOT a double quote, flip our state quotedString = !quotedString; } } else { token += c; } } // We are at the end of the line if (quotedString) { token += '\n'; // Add newline to the token line = nextLine(); // Keep going } else { // We can end the loop break; } } // Push the last token tokens.push(token); return tokens; } } } function parseAedToken(value) { // Example: refseq:accessionNumber(aed:String) // refseq - namespace, will be declared later // accessionNumber - name of the field // aed:String - type of the field // The namespace part may be missing var match = aedRegexpNamespace.exec(value); if (match) { return { namespace: match[1], name: match[2], type: match[3] }; } match = aedRegexpNoNamespace.exec(value); if (match) { return { namespace: '?', name: match[1], type: match[2] }; } else { throw new Error("Error parsing the header row of AED file - column not in ns:name(ns:type) format"); } } function parseAedHeaderRow(tokens) { // First row of AED file defines column names // Each header item is an aed token - see parseAedToken var aed, k, token, aedToken; // Initialize aed section to be filled in aed = { columns: [// Information about the namespace, name and type of each column // Example entry: // { namespace: 'bio', name: 'start', type: 'aed:Integer' } ], metadata: {// Metadata about the entire AED file // Example: // { // aed: { // application: { value: "CHaS Browser 3.3.0.139 (r10838)", type: "aed:String" }, // created: { value: "2018-01-02T10:20:30.123+01:00", type: "aed:DateTime" }, // modified: { value: "2018-03-04T11:22:33.456+01:00", type: "aed:DateTime" }, // } // affx: { // ucscGenomeVersion: { value: "hg19", type: "aed:String" } // }, // namespace: { // omim: { value: "http://affymetrix.com/ontology/www.ncbi.nlm.nih.gov/omim/", type: "aed:URI" }, // affx: { value: "http://affymetrix.com/ontology/", type: "aed:URI" }, // refseq: { value: "http://affymetrix.com/ontology/www.ncbi.nlm.nih.gov/RefSeq/", type: "aed:URI" } // } // } } }; for (k = 0; k < tokens.length; k++) { token = tokens[k]; aedToken = parseAedToken(token); aed.columns.push(aedToken); } return aed; } function parseTrackLine(line) { const properties = {}; const tokens = line.split(/(?:")([^"]+)(?:")|([^\s"]+)(?=\s+|$)/g); // Clean up tokens array let curr; const tmp = []; for (let tk of tokens) { if (!tk || tk.trim().length === 0) continue; if (tk.endsWith("=") > 0) { curr = tk; } else if (curr) { tmp.push(curr + tk); curr = undefined; } else { tmp.push(tk); } } for (let str of tmp) { if (!str) return; var kv = str.split('=', 2); if (kv.length === 2) { const key = kv[0].trim(); const value = kv[1].trim(); properties[key] = value; } } return properties; } function parseColumnsDirective(line) { let properties = {}; let t1 = line.split(/\s+/); if (t1.length === 2) { let t2 = t1[1].split(";"); t2.forEach(function (keyValue) { let t = keyValue.split("="); if (t[0] === "color") { properties.colorColumn = Number.parseInt(t[1]) - 1; } else if (t[0] === "thickness") { properties.thicknessColumn = Number.parseInt(t[1]) - 1; } }); } return properties; } /** * AED file feature. * * @param aed link to the AED file object containing file-level metadata and column descriptors * @param allColumns All columns as parsed from the AED * * Other values are parsed one by one */ function AedFeature(aed, allColumns) { var token, aedColumn, aedColumns = aed.columns; // Link to AED file (for metadata) this.aed = aed; // Unparsed columns from AED file this.allColumns = allColumns; // Prepare space for the parsed values this.chr = null; this.start = null; this.end = null; this.score = 1000; this.strand = '.'; this.cdStart = null; this.cdEnd = null; this.name = null; this.color = null; for (let i = 0; i < allColumns.length; i++) { token = allColumns[i]; if (!token) { // Skip empty fields continue; } aedColumn = aedColumns[i]; if (aedColumn.type === 'aed:Integer') { token = parseInt(token); } var arr = []; if (aedColumn.namespace.length > 0) { for (let j = 0; j < aedColumn.namespace.length; j++) { arr.push(aedColumn.namespace.charCodeAt(j)); } } if (aedColumn.namespace.trim() === 'bio') { if (aedColumn.name === 'sequence') { this.chr = token; } else if (aedColumn.name === 'start') { this.start = token; } else if (aedColumn.name === 'end') { this.end = token; } else if (aedColumn.name === 'cdsMin') { this.cdStart = token; } else if (aedColumn.name === 'cdsMax') { this.cdEnd = token; } else if (aedColumn.name === 'strand') { this.strand = token; } } else if (aedColumn.namespace === 'aed') { if (aedColumn.name === 'name') { this.name = token; } } else if (aedColumn.namespace === 'style') { if (aedColumn.name === 'color') { this.color = IGVColor.createColorString(token); } } } } AedFeature.prototype.popupData = function () { var data = [], aed = this.aed; // Just dump everything we have for now for (var i = 0; i < this.allColumns.length; i++) { var featureValue = this.allColumns[i]; var name = aed.columns[i].name; // Skip columns that are not interesting - you know the sequence, and you can see color if (name !== 'sequence' && name !== 'color') { if (featureValue) { data.push({ name: name, value: featureValue }); } } } return data; }; /** * Decode the AED file format * @param tokens * @param ignore * @returns decoded feature, or null if this is not a valid record */ function decodeAed(tokens, ignore) { var name, value, token, nonEmptyTokens = 0, aedColumns = this.aed.columns, aedColumn, aedKey, i; // Each aed row must match the exact number of columns or we skip it if (tokens.length !== aedColumns.length) { return undefined; } for (i = 0; i < tokens.length; i++) { aedColumn = aedColumns[i]; token = tokens[i]; if (token !== '') { nonEmptyTokens++; } if (aedColumn.name === 'name' && aedColumn.namespace === 'aed') { name = token; } else if (aedColumn.name === 'value' && aedColumn.namespace === 'aed') { value = token; } } if (nonEmptyTokens === 2 && name && value) { // Special row that defines metadata for the entire file aedKey = parseAedToken(name); // Store in the metadata section if (!this.aed.metadata[aedKey.namespace]) { this.aed.metadata[aedKey.namespace] = {}; } if (!this.aed.metadata[aedKey.namespace][aedKey.name]) { this.aed.metadata[aedKey.namespace][aedKey.name] = { type: aedKey.type, value: value }; } // Ignore this value return undefined; } var feature = new AedFeature(this.aed, tokens); if (!feature.chr || !feature.start && feature.start !== 0 || !feature.end) { return undefined; } return feature; } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ // TODO -- big endian? class BinaryParser { constructor(dataView, littleEndian) { this.littleEndian = littleEndian !== undefined ? littleEndian : true; this.position = 0; this.view = dataView; this.length = dataView.byteLength; } available() { return this.length - this.position; } remLength() { return this.length - this.position; } hasNext() { return this.position < this.length - 1; } getByte() { var retValue = this.view.getUint8(this.position, this.littleEndian); this.position++; return retValue; } getShort() { var retValue = this.view.getInt16(this.position, this.littleEndian); this.position += 2; return retValue; } getUShort() { // var byte1 = this.getByte(), // byte2 = this.getByte(), // retValue = ((byte2 << 24 >>> 16) + (byte1 << 24 >>> 24)); // return retValue; // var retValue = this.view.getUint16(this.position, this.littleEndian); this.position += 2; return retValue; } getInt() { var retValue = this.view.getInt32(this.position, this.littleEndian); this.position += 4; return retValue; } getUInt() { var retValue = this.view.getUint32(this.position, this.littleEndian); this.position += 4; return retValue; } getLong() { // DataView doesn't support long. So we'll try manually var b = []; b[0] = this.view.getUint8(this.position); b[1] = this.view.getUint8(this.position + 1); b[2] = this.view.getUint8(this.position + 2); b[3] = this.view.getUint8(this.position + 3); b[4] = this.view.getUint8(this.position + 4); b[5] = this.view.getUint8(this.position + 5); b[6] = this.view.getUint8(this.position + 6); b[7] = this.view.getUint8(this.position + 7); var value = 0; if (this.littleEndian) { for (let i = b.length - 1; i >= 0; i--) { value = value * 256 + b[i]; } } else { for (let i = 0; i < b.length; i++) { value = value * 256 + b[i]; } } this.position += 8; return value; } getString(len) { var s = ""; var c; while ((c = this.view.getUint8(this.position++)) !== 0) { s += String.fromCharCode(c); if (len && s.length === len) break; } return s; } getFixedLengthString(len) { var s = ""; var i; var c; for (i = 0; i < len; i++) { c = this.view.getUint8(this.position++); if (c > 0) { s += String.fromCharCode(c); } } return s; } getFixedLengthTrimmedString(len) { var s = ""; var i; var c; for (i = 0; i < len; i++) { c = this.view.getUint8(this.position++); if (c > 32) { s += String.fromCharCode(c); } } return s; } getFloat() { var retValue = this.view.getFloat32(this.position, this.littleEndian); this.position += 4; return retValue; } getDouble() { var retValue = this.view.getFloat64(this.position, this.littleEndian); this.position += 8; return retValue; } skip(n) { this.position += n; return this.position; } /** * Return a BGZip (bam and tabix) virtual pointer * TODO -- why isn't 8th byte used ? * @returns {*} */ getVPointer() { var position = this.position, offset = this.view.getUint8(position + 1) << 8 | this.view.getUint8(position), byte6 = (this.view.getUint8(position + 6) & 0xff) * 0x100000000, byte5 = (this.view.getUint8(position + 5) & 0xff) * 0x1000000, byte4 = (this.view.getUint8(position + 4) & 0xff) * 0x10000, byte3 = (this.view.getUint8(position + 3) & 0xff) * 0x100, byte2 = this.view.getUint8(position + 2) & 0xff, block = byte6 + byte5 + byte4 + byte3 + byte2; this.position += 8; // if (block == 0 && offset == 0) { // return null; // } else { return new VPointer(block, offset); // } } } class VPointer { constructor(block, offset) { this.block = block; this.offset = offset; } isLessThan(vp) { return this.block < vp.block || this.block === vp.block && this.offset < vp.offset; } isGreaterThan(vp) { return this.block > vp.block || this.block === vp.block && this.offset > vp.offset; } print() { return "" + this.block + ":" + this.offset; } } const CSI1_MAGIC$1 = 21582659; // CSI\1 const CSI2_MAGIC$1 = 38359875; // CSI\2 async function parseCsiIndex(arrayBuffer, genome) { const idx = new CSIIndex(); idx.parse(arrayBuffer, genome); return idx; } class CSIIndex { constructor(tabix) { this.tabix = true; // Means whatever is indexed is BGZipped } parse(arrayBuffer, genome) { const parser = new BinaryParser(new DataView(arrayBuffer)); const magic = parser.getInt(); if (magic !== CSI1_MAGIC$1) { if (magic === CSI2_MAGIC$1) { throw Error("CSI version 2 is not supported. Please enter an issue at https://github.com/igvteam/igv.js"); } else { throw Error("Not a CSI index"); } } this.indices = []; this.blockMin = Number.MAX_SAFE_INTEGER; this.blockMax = 0; this.sequenceIndexMap = {}; this.minShift = parser.getInt(); this.depth = parser.getInt(); const lAux = parser.getInt(); if (lAux >= 28) { // Tabix header parameters aren't used, but they must be read to advance the pointer parser.getInt(); parser.getInt(); parser.getInt(); parser.getInt(); parser.getInt(); parser.getInt(); const l_nm = parser.getInt(); const nameEndPos = parser.position + l_nm; let i = 0; while (parser.position < nameEndPos) { let seq_name = parser.getString(); // Translate to "official" chr name. if (genome) { seq_name = genome.getChromosomeName(seq_name); } this.sequenceIndexMap[seq_name] = i; i++; } } const MAX_BIN = this.bin_limit() + 1; const nref = parser.getInt(); for (let ref = 0; ref < nref; ref++) { const binIndex = []; const loffset = []; const nbin = parser.getInt(); for (let b = 0; b < nbin; b++) { const binNumber = parser.getInt(); loffset[binNumber] = parser.getVPointer(); if (binNumber > MAX_BIN) { // This is a psuedo bin, not used but we have to consume the bytes parser.getInt(); // # of chunks for this bin parser.getVPointer(); // unmapped beg parser.getVPointer(); // unmapped end parser.getLong(); parser.getLong(); } else { binIndex[binNumber] = []; const nchnk = parser.getInt(); // # of chunks for this bin for (let i = 0; i < nchnk; i++) { const cs = parser.getVPointer(); //chunk_beg const ce = parser.getVPointer(); //chunk_end if (cs && ce) { if (cs.block < this.blockMin) { this.blockMin = cs.block; // Block containing first alignment } if (ce.block > this.blockMax) { this.blockMax = ce.block; } binIndex[binNumber].push([cs, ce]); } } } } if (nbin > 0) { this.indices[ref] = { binIndex: binIndex, loffset: loffset }; } } } /** * Fetch blocks for a particular genomic range. This method is public so it can be unit-tested. * * @param refId the sequence dictionary index of the chromosome * @param min genomic start position * @param max genomic end position * @param return an array of {minv: {filePointer, offset}, {maxv: {filePointer, offset}} */ blocksForRange(refId, min, max) { const ba = this.indices[refId]; if (!ba) { return []; } else { const overlappingBins = this.reg2bins(min, max); // List of bin #s that overlap min, max if (overlappingBins.length == 0) return []; const chunks = []; // Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned for (let binRange of overlappingBins) { for (let bin = binRange[0]; bin <= binRange[1]; bin++) { if (ba.binIndex[bin]) { const binChunks = ba.binIndex[bin]; const nchnk = binChunks.length; for (let c = 0; c < nchnk; ++c) { const cs = binChunks[c][0]; const ce = binChunks[c][1]; chunks.push({ minv: cs, maxv: ce, bin: bin }); } } } } const lowestOffset = ba.loffset[overlappingBins[0]]; return optimizeChunks$1(chunks, lowestOffset); } } // reg2bins implementation adapted from GMOD/tabix-js https://github.com/GMOD/tabix-js/blob/master/src/csi.ts reg2bins(beg, end) { beg -= 1; // < convert to 1-based closed if (beg < 1) beg = 1; if (end > 2 ** 50) end = 2 ** 34; // 17 GiB ought to be enough for anybody end -= 1; let l = 0; let t = 0; let s = this.minShift + this.depth * 3; const bins = []; for (; l <= this.depth; s -= 3, t += 1 << l * 3, l += 1) { const b = t + (beg >> s); const e = t + (end >> s); if (e - b + bins.length > this.maxBinNumber) throw new Error(`query ${beg}-${end} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`); //for (let i = b; i <= e; i += 1) bins.push(i) bins.push([b, e]); } return bins; } // function reg2bins(beg, end, min_shift, depth) { // let l, t, n, s = min_shift + depth * 3; // const bins = []; // for (--end, l = n = t = 0; l <= depth; s -= 3, t += 1 << l * 3, ++l) { // let b = t + (beg >> s), e = t + (end >> s), i; // for (i = b; i <= e; ++i) bins[n++] = i; // } // return bins; // } bin_limit() { return ((1 << (this.depth + 1) * 3) - 1) / 7; } } function optimizeChunks$1(chunks, lowest) { const mergedChunks = []; let lastChunk = null; if (chunks.length === 0) return chunks; chunks.sort(function (c0, c1) { const dif = c0.minv.block - c1.minv.block; if (dif !== 0) { return dif; } else { return c0.minv.offset - c1.minv.offset; } }); chunks.forEach(function (chunk) { if (!lowest || chunk.maxv.isGreaterThan(lowest)) { if (lastChunk === null) { mergedChunks.push(chunk); lastChunk = chunk; } else { if (canMerge$1(lastChunk, chunk)) { if (chunk.maxv.isGreaterThan(lastChunk.maxv)) { lastChunk.maxv = chunk.maxv; } } else { mergedChunks.push(chunk); lastChunk = chunk; } } } }); return mergedChunks; } function canMerge$1(chunk1, chunk2) { return chunk2.minv.block - chunk1.maxv.block < 65000 && chunk2.maxv.block - chunk1.minv.block < 5000000; // lastChunk.minv.block === lastChunk.maxv.block && // lastChunk.maxv.block === chunk.minv.block && // chunk.minv.block === chunk.maxv.block } const BAI_MAGIC$1 = 21578050; const TABIX_MAGIC$1 = 21578324; async function parseBamIndex(arrayBuffer, genome) { return parseIndex(arrayBuffer, false, genome); } async function parseTabixIndex(arrayBuffer, genome) { return parseIndex(arrayBuffer, true, genome); } async function parseIndex(arrayBuffer, tabix, genome) { const indices = []; let blockMin = Number.MAX_SAFE_INTEGER; let blockMax = 0; const parser = new BinaryParser(new DataView(arrayBuffer)); const magic = parser.getInt(); const sequenceIndexMap = {}; if (magic === BAI_MAGIC$1 || tabix && magic === TABIX_MAGIC$1) { const nref = parser.getInt(); if (tabix) { // Tabix header parameters aren't used, but they must be read to advance the pointer parser.getInt(); parser.getInt(); parser.getInt(); parser.getInt(); parser.getInt(); parser.getInt(); parser.getInt(); for (let i = 0; i < nref; i++) { let seq_name = parser.getString(); // Translate to "official" chr name. if (genome) { seq_name = genome.getChromosomeName(seq_name); } sequenceIndexMap[seq_name] = i; } } for (let ref = 0; ref < nref; ref++) { const binIndex = {}; const linearIndex = []; const nbin = parser.getInt(); for (let b = 0; b < nbin; b++) { const binNumber = parser.getInt(); if (binNumber === 37450) { // This is a psuedo bin, not used but we have to consume the bytes parser.getInt(); // # of chunks for this bin parser.getVPointer(); // unmapped beg parser.getVPointer(); // unmapped end parser.getLong(); parser.getLong(); } else { binIndex[binNumber] = []; const nchnk = parser.getInt(); // # of chunks for this bin for (let i = 0; i < nchnk; i++) { const cs = parser.getVPointer(); //chunk_beg const ce = parser.getVPointer(); //chunk_end if (cs && ce) { if (cs.block < blockMin) { blockMin = cs.block; // Block containing first alignment } if (ce.block > blockMax) { blockMax = ce.block; } binIndex[binNumber].push([cs, ce]); } } } } const nintv = parser.getInt(); for (let i = 0; i < nintv; i++) { const cs = parser.getVPointer(); linearIndex.push(cs); // Might be null } if (nbin > 0) { indices[ref] = { binIndex: binIndex, linearIndex: linearIndex }; } } } else { throw new Error(indexURL + " is not a " + (tabix ? "tabix" : "bai") + " file"); } return new BamIndex(indices, blockMin, blockMax, sequenceIndexMap, tabix); } class BamIndex { constructor(indices, blockMin, blockMax, sequenceIndexMap, tabix) { this.firstAlignmentBlock = blockMin; this.lastAlignmentBlock = blockMax; this.indices = indices; this.sequenceIndexMap = sequenceIndexMap; this.tabix = tabix; } /** * Fetch blocks for a particular genomic range. This method is public so it can be unit-tested. * * @param refId the sequence dictionary index of the chromosome * @param min genomic start position * @param max genomic end position * @param return an array of {minv: {filePointer, offset}, {maxv: {filePointer, offset}} */ blocksForRange(refId, min, max) { const bam = this; const ba = bam.indices[refId]; if (!ba) { return []; } else { const overlappingBins = reg2bins(min, max); // List of bin #s that overlap min, max const chunks = []; // Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned for (let binRange of overlappingBins) { for (let bin = binRange[0]; bin <= binRange[1]; bin++) { if (ba.binIndex[bin]) { const binChunks = ba.binIndex[bin], nchnk = binChunks.length; for (let c = 0; c < nchnk; ++c) { const cs = binChunks[c][0]; const ce = binChunks[c][1]; chunks.push({ minv: cs, maxv: ce, bin: bin }); } } } } // Use the linear index to find minimum file position of chunks that could contain alignments in the region const nintv = ba.linearIndex.length; let lowest = null; const minLin = Math.min(min >> 14, nintv - 1); const maxLin = Math.min(max >> 14, nintv - 1); for (let i = minLin; i <= maxLin; ++i) { const vp = ba.linearIndex[i]; if (vp) { // todo -- I think, but am not sure, that the values in the linear index have to be in increasing order. So the first non-null should be minimum if (!lowest || vp.isLessThan(lowest)) { lowest = vp; } } } return optimizeChunks(chunks, lowest); } } } function optimizeChunks(chunks, lowest) { const mergedChunks = []; let lastChunk = null; if (chunks.length === 0) return chunks; chunks.sort(function (c0, c1) { const dif = c0.minv.block - c1.minv.block; if (dif !== 0) { return dif; } else { return c0.minv.offset - c1.minv.offset; } }); chunks.forEach(function (chunk) { if (!lowest || chunk.maxv.isGreaterThan(lowest)) { if (lastChunk === null) { mergedChunks.push(chunk); lastChunk = chunk; } else { if (canMerge(lastChunk, chunk)) { if (chunk.maxv.isGreaterThan(lastChunk.maxv)) { lastChunk.maxv = chunk.maxv; } } else { mergedChunks.push(chunk); lastChunk = chunk; } } } }); return mergedChunks; } function canMerge(chunk1, chunk2) { return chunk2.minv.block - chunk1.maxv.block < 65000 && chunk2.maxv.block - chunk1.minv.block < 5000000; // lastChunk.minv.block === lastChunk.maxv.block && // lastChunk.maxv.block === chunk.minv.block && // chunk.minv.block === chunk.maxv.block } /** * Calculate the list of bins that overlap with region [beg, end] * */ function reg2bins(beg, end) { const list = []; if (end >= 1 << 29) end = 1 << 29; --end; list.push([0, 0]); list.push([1 + (beg >> 26), 1 + (end >> 26)]); list.push([9 + (beg >> 23), 9 + (end >> 23)]); list.push([73 + (beg >> 20), 73 + (end >> 20)]); list.push([585 + (beg >> 17), 585 + (end >> 17)]); list.push([4681 + (beg >> 14), 4681 + (end >> 14)]); // for (k = 1 + (beg >> 26); k <= 1 + (end >> 26); ++k) list.push(k); // for (k = 9 + (beg >> 23); k <= 9 + (end >> 23); ++k) list.push(k); // for (k = 73 + (beg >> 20); k <= 73 + (end >> 20); ++k) list.push(k); // for (k = 585 + (beg >> 17); k <= 585 + (end >> 17); ++k) list.push(k); // for (k = 4681 + (beg >> 14); k <= 4681 + (end >> 14); ++k) list.push(k); return list; } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ async function parseTribbleIndex(arrayBuffer, genome) { const index = {}; const parser = new BinaryParser(new DataView(arrayBuffer)); readHeader(parser); let nChrs = parser.getInt(); while (nChrs-- > 0) { // todo -- support interval tree index, we're assuming its a linear index const chrIdx = readLinear(parser); index[chrIdx.chr] = chrIdx; } return new TribbleIndex(index); /** * Read the header file. Data here is not used in igv.js but we need to read it to advance the pointer. * @param parser */ function readHeader(parser) { parser.getInt(); // view._getInt32(offset += 32, true); parser.getInt(); const version = parser.getInt(); parser.getString(); parser.getLong(); parser.getLong(); parser.getString(); parser.getInt(); if (version >= 3) { let nProperties = parser.getInt(); while (nProperties-- > 0) { parser.getString(); parser.getString(); } } } function readLinear(parser) { let chr = parser.getString(); if (genome) chr = genome.getChromosomeName(chr); const binWidth = parser.getInt(); const nBins = parser.getInt(); const longestFeature = parser.getInt(); parser.getInt() > 0; parser.getInt(); // note the code below accounts for > 60% of the total time to read an index let pos = parser.getLong(); const blocks = new Array(); for (let binNumber = 0; binNumber < nBins; binNumber++) { const nextPos = parser.getLong(); blocks.push({ min: pos, max: nextPos }); // {position: pos, size: size}); pos = nextPos; } return { chr: chr, blocks: blocks, longestFeature: longestFeature, binWidth: binWidth }; } } class TribbleIndex { constructor(chrIndexTable) { this.chrIndex = chrIndexTable; // Dictionary of chr -> tribble index } /** * Fetch blocks for a particular genomic range. * * @param queryChr the sequence dictionary index of the chromosome * @param min genomic start position * @param max genomic end position */ blocksForRange(queryChr, min, max) { const chrIdx = this.chrIndex[queryChr]; if (chrIdx) { const blocks = chrIdx.blocks; const longestFeature = chrIdx.longestFeature; const binWidth = chrIdx.binWidth; const adjustedPosition = Math.max(min - longestFeature, 0); const startBinNumber = Math.floor(adjustedPosition / binWidth); if (startBinNumber >= blocks.length) // are we off the end of the bin list, so return nothing return [];else { const endBinNumber = Math.min(Math.floor((max - 1) / binWidth), blocks.length - 1); // By definition blocks are adjacent in the file for the liner index. Combine them into one merged block const startPos = blocks[startBinNumber].min; const endPos = blocks[endBinNumber].max; const size = endPos - startPos; if (size === 0) { return []; } else { const mergedBlock = { minv: { block: startPos, offset: 0 }, maxv: { block: endPos, offset: 0 } }; return [mergedBlock]; } } } else { return undefined; } } } const CSI1_MAGIC = 21582659; // CSI\1 const CSI2_MAGIC = 38359875; // CSI\2 const BAI_MAGIC = 21578050; const TABIX_MAGIC = 21578324; const TRIBBLE_MAGIC = 1480870228; // byte[]{'T', 'I', 'D', 'X'}; /** * @param indexURL * @param config * @param tabix * */ async function loadIndex(indexURL, config, genome) { let arrayBuffer = await igvxhr.loadArrayBuffer(indexURL, buildOptions(config)); let dv = new DataView(arrayBuffer); // Some indexs are gzipped, specifically tabix, and csi. Bam (bai) are not. Tribble is usually not. // Check first 2 bytes of file for gzip magic number, and inflate if neccessary if (dv.getUint8(0) === 0x1f && dv.getUint8(1) === 0x8b) { // gzipped const inflate = new Zlib$1.Gunzip(new Uint8Array(arrayBuffer)); arrayBuffer = inflate.decompress().buffer; dv = new DataView(arrayBuffer); } const magic = dv.getInt32(0, true); switch (magic) { case BAI_MAGIC: return parseBamIndex(arrayBuffer, genome); case TABIX_MAGIC: return parseTabixIndex(arrayBuffer, genome); case CSI1_MAGIC: return parseCsiIndex(arrayBuffer, genome); case TRIBBLE_MAGIC: return parseTribbleIndex(arrayBuffer, genome); case CSI2_MAGIC: throw Error("CSI version 2 is not supported."); default: throw Error(`Unrecognized index type: ${indexURL}`); } } class BGZipLineReader { constructor(config) { this.config = config; this.filePtr = 0; this.bufferPtr = 0; this.buffer; } async nextLine() { let result = undefined; try { while (true) { const length = this.buffer ? this.buffer.length : 0; while (this.bufferPtr < length) { const c = String.fromCharCode(this.buffer[this.bufferPtr++]); if (c === '\r') continue; if (c === '\n') { return result; } result = result ? result + c : c; } if (this.eof) { return result; } else { await this.readNextBlock(); } } } catch (e) { console.warn(e); this.eof = true; return result; } } async readNextBlock() { const bsizeOptions = buildOptions(this.config, { range: { start: this.filePtr, size: 26 } }); const abuffer = await igvxhr.loadArrayBuffer(this.config.url, bsizeOptions); const bufferSize = bgzBlockSize(abuffer); //console.log(`next block ${this.filePtr} ${bufferSize}`); if (bufferSize === 0) { this.eof = true; this.buffer = undefined; } else { const options = buildOptions(this.config, { range: { start: this.filePtr, size: bufferSize } }); const data = await igvxhr.loadArrayBuffer(this.config.url, options); if (data.byteLength < bufferSize) { this.eof = true; // Assumption } this.buffer = unbgzf(data); this.bufferPtr = 0; this.filePtr += data.byteLength; //data.byteLength; } } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const isString$5 = isString$6; /** * Reader for "bed like" files (tab delimited files with 1 feature per line: bed, gff, vcf, etc) * * @param config * @constructor */ class FeatureFileReader { constructor(config, genome) { var uriParts; this.config = config || {}; this.genome = genome; this.indexURL = config.indexURL; this.indexed = config.indexed; if (isFilePath(this.config.url)) { this.filename = this.config.url.name; } else if (isString$5(this.config.url) && this.config.url.startsWith('data:')) { this.indexed = false; // by definition this.dataURI = config.url; } else { uriParts = parseUri(this.config.url); this.filename = config.filename || uriParts.file; } this.parser = this.getParser(this.config); if (this.config.format === "vcf" && !this.config.indexURL) { console.warn("Warning: index file not specified. The entire vcf file will be loaded."); } } /** * Return a promise to load features for the genomic interval * @param chr * @param start * @param end */ async readFeatures(chr, start, end) { const index = await this.getIndex(); if (index) { this.indexed = true; return this.loadFeaturesWithIndex(chr, start, end); } else if (this.dataURI) { this.indexed = false; return this.loadFeaturesFromDataURI(); } else { this.indexed = false; return this.loadFeaturesNoIndex(); } } async readHeader() { if (this.dataURI) { await this.loadFeaturesFromDataURI(this.dataURI); return this.header; } else { if (this.config.indexURL) { const index = await this.getIndex(); if (!index) { // Note - it should be impossible to get here throw new Error("Unable to load index: " + this.config.indexURL); } let dataWrapper; if (index.tabix) { dataWrapper = new BGZipLineReader(this.config); } else { // Tribble const maxSize = Object.values(index.chrIndex).flatMap(chr => chr.blocks).map(block => block.max).reduce((previous, current) => Math.min(previous, current), Number.MAX_SAFE_INTEGER); const options = buildOptions(this.config, { bgz: index.tabix, range: { start: 0, size: maxSize } }); const data = await igvxhr.loadString(this.config.url, options); dataWrapper = getDataWrapper(data); } this.header = await this.parser.parseHeader(dataWrapper); // Cache header, might be needed to parse features return this.header; } else { // If this is a non-indexed file we will load all features in advance const options = buildOptions(this.config); const data = await igvxhr.loadString(this.config.url, options); let dataWrapper = getDataWrapper(data); this.header = await this.parser.parseHeader(dataWrapper); // Reset data wrapper and parse features dataWrapper = getDataWrapper(data); this.features = await this.parser.parseFeatures(dataWrapper); // cache features return this.header; } } } getParser(config) { switch (config.format) { case "vcf": return new VcfParser(config); case "seg": return new SegParser("seg"); case "mut": return new SegParser("mut"); case "maf": return new SegParser("maf"); case "gwas": return new GWASParser(config); case "aed": return new AEDParser(config); default: return new FeatureParser(config); } } async loadFeaturesNoIndex() { if (this.features) { // An optimization hack for non-indexed files, features are temporarily cached when header is read. const tmp = this.features; delete this.features; return tmp; } else { const options = buildOptions(this.config); // Add oauth token, if any const data = await igvxhr.loadString(this.config.url, options); if (!this.header) { const dataWrapper = getDataWrapper(data); this.header = await this.parser.parseHeader(dataWrapper); } const dataWrapper = getDataWrapper(data); const features = await this.parser.parseFeatures(dataWrapper); // <= PARSING DONE HERE return features; } } async loadFeaturesWithIndex(chr, start, end) { //console.log("Using index" const config = this.config; const parser = this.parser; const tabix = this.index.tabix; const refId = tabix ? this.index.sequenceIndexMap[chr] : chr; if (refId === undefined) { return []; } const genome = this.genome; const blocks = this.index.blocksForRange(refId, start, end); if (!blocks || blocks.length === 0) { return []; } else { const allFeatures = []; for (let block of blocks) { const startPos = block.minv.block; const startOffset = block.minv.offset; const endOffset = block.maxv.offset; let endPos; if (tabix) { let lastBlockSize = 0; if (endOffset > 0) { const bsizeOptions = buildOptions(config, { range: { start: block.maxv.block, size: 26 } }); const abuffer = await igvxhr.loadArrayBuffer(config.url, bsizeOptions); lastBlockSize = bgzBlockSize(abuffer); } endPos = block.maxv.block + lastBlockSize; } else { endPos = block.maxv.block; } const options = buildOptions(config, { range: { start: startPos, size: endPos - startPos + 1 } }); let inflated; if (tabix) { const data = await igvxhr.loadArrayBuffer(config.url, options); inflated = unbgzf(data); } else { inflated = await igvxhr.loadString(config.url, options); } const slicedData = startOffset ? inflated.slice(startOffset) : inflated; const dataWrapper = getDataWrapper(slicedData); const slicedFeatures = await parser.parseFeatures(dataWrapper); // Filter features not in requested range. let inInterval = false; for (let i = 0; i < slicedFeatures.length; i++) { const f = slicedFeatures[i]; const canonicalChromosome = genome ? genome.getChromosomeName(f.chr) : f.chr; if (canonicalChromosome !== chr) { if (allFeatures.length === 0) { continue; //adjacent chr to the left } else { break; //adjacent chr to the right } } if (f.start > end) { allFeatures.push(f); // First feature beyond interval break; } if (f.end >= start && f.start <= end) { if (!inInterval) { inInterval = true; if (i > 0) { allFeatures.push(slicedFeatures[i - 1]); } } allFeatures.push(f); } } } allFeatures.sort(function (a, b) { return a.start - b.start; }); return allFeatures; } } async getIndex() { if (this.index || !this.config.indexURL) { return this.index; } else { this.index = await this.loadIndex(); return this.index; } } /** * Return a Promise for the async loaded index */ async loadIndex() { const indexURL = this.config.indexURL; return loadIndex(indexURL, this.config, this.genome); } async loadFeaturesFromDataURI() { if (this.features) { // An optimization hack for non-indexed files, features are temporarily cached when header is read. const tmp = this.features; delete this.features; return tmp; } else { const plain = decodeDataURI$1(this.dataURI); let dataWrapper = getDataWrapper(plain); this.header = await this.parser.parseHeader(dataWrapper); if (this.header instanceof String && this.header.startsWith("##gff-version 3")) { this.format = 'gff3'; } dataWrapper = getDataWrapper(plain); this.features = await this.parser.parseFeatures(dataWrapper); return this.features; } } } /* * The MIT License (MIT) * * Copyright (c) 2016 University of California San Diego * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const isString$4 = isString$6; class CustomServiceReader { constructor(config) { this.config = config; } async readFeatures(chr, start, end) { let url; if (typeof this.config.url === 'function') { url = this.config.url({ chr, start, end }); } else { url = this.config.url.replace("$CHR", chr).replace("$START", start).replace("$END", end); } let config = Object.assign({}, this.config); if (this.config.body !== undefined) { if (typeof this.config.body === 'function') { config.body = this.config.body({ chr, start, end }); } else { config.body = this.config.body.replace("$CHR", chr).replace("$START", start).replace("$END", end); } } let features; const data = await igvxhr.load(url, config); if (data) { if (typeof this.config.parser === "function") { features = this.config.parser(data); } else if (isString$4(data)) { features = JSON.parse(data); } else { features = data; } } if (this.config.mappings) { let mappingKeys = Object.keys(this.config.mappings); for (let f of features) { for (let key of mappingKeys) { f[key] = f[this.config.mappings[key]]; } } } return features; } } /* * The MIT License (MIT) * * Copyright (c) 2016-2017 The Regents of the University of California * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const UCSCServiceReader = function (config, genome) { this.config = config; this.genome = genome; this.expandQueryInterval = false; }; UCSCServiceReader.prototype.readFeatures = function (chr, start, end) { const s = Math.max(0, Math.floor(start)); let e = Math.ceil(end); if (this.genome) { const c = this.genome.getChromosome(chr); if (c && e > c.bpLength) { e = c.bpLength; } } const url = this.config.url + '?db=' + this.config.db + '&table=' + this.config.tableName + '&chr=' + chr + '&start=' + s + '&end=' + e; return igvxhr.loadJson(url, this.config).then(function (data) { if (data) { data.forEach(function (sample) { if (sample.hasOwnProperty('exonStarts') && sample.hasOwnProperty('exonEnds') && sample.hasOwnProperty('exonCount') && sample.hasOwnProperty('cdsStart') && sample.hasOwnProperty('cdsEnd')) { addExons(sample); } }); return data; } else { return null; } }); }; function addExons(sample) { var exonCount, exonStarts, exonEnds, exons, eStart, eEnd; exonCount = sample['exonCount']; exonStarts = sample['exonStarts'].split(','); exonEnds = sample['exonEnds'].split(','); exons = []; for (var i = 0; i < exonCount; i++) { eStart = parseInt(exonStarts[i]); eEnd = parseInt(exonEnds[i]); var exon = { start: eStart, end: eEnd }; if (sample.cdsStart > eEnd || sample.cdsEnd < sample.cdsStart) exon.utr = true; // Entire exon is UTR if (sample.cdsStart >= eStart && sample.cdsStart <= eEnd) exon.cdStart = sample.cdsStart; if (sample.cdsEnd >= eStart && sample.cdsEnd <= eEnd) exon.cdEnd = sample.cdsEnd; exons.push(exon); } sample.exons = exons; } /* * The MIT License (MIT) * * Copyright (c) 2016 University of California San Diego * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ /** * Created by jrobinson on 4/7/16. */ const transcriptTypes = new Set(['transcript', 'primary_transcript', 'processed_transcript', 'mRNA', 'mrna']); const cdsTypes = new Set(['CDS', 'cds']); const codonTypes = new Set(['start_codon', 'stop_codon']); const utrTypes = new Set(['5UTR', '3UTR', 'UTR', 'five_prime_UTR', 'three_prime_UTR', "3'-UTR", "5'-UTR"]); const exonTypes = new Set(['exon', 'coding-exon']); const intronType = 'intron'; const transcriptModelTypes = new Set(); for (let cltn of [transcriptTypes, cdsTypes, codonTypes, utrTypes, exonTypes]) { for (let t of cltn) { transcriptModelTypes.add(t); } } class GFFHelper { constructor(options) { this.format = options.format; this.filterTypes = options.filterTypes === undefined ? new Set(['chromosome']) : new Set(options.filterTypes); } combineFeatures(features) { let combinedFeatures; if ("gff3" === this.format) { const tmp = this.combineFeaturesById(features); combinedFeatures = this.combineFeaturesGFF(tmp); } else { combinedFeatures = this.combineFeaturesGTF(features); } combinedFeatures.sort(function (a, b) { return a.start - b.start; }); return combinedFeatures; } combineFeaturesById(features) { const combinedFeatures = []; const chrIdHash = {}; for (let f of features) { if (f.id === undefined) { combinedFeatures.push(f); } else { let idHash = chrIdHash[f.chr]; if (!idHash) { idHash = {}; chrIdHash[f.chr] = idHash; } if (idHash.hasOwnProperty(f.id)) { const sf = idHash[f.id]; if (sf.hasOwnProperty("exons")) { sf.start = Math.min(sf.start, f.start); sf.end = Math.max(sf.end, f.end); sf.exons.push(f); } else { const cf = { id: f.id, type: f.type, chr: f.chr, strand: f.strand, start: Math.min(f.start, sf.start), end: Math.max(f.end, sf.end), exons: [sf, f] }; if (f.parent && f.parent.trim() !== "") { cf.parent = f.parent; } idHash[f.id] = cf; } } else { idHash[f.id] = f; } } } for (let key of Object.keys(chrIdHash)) { const idHash = chrIdHash[key]; for (let id of Object.keys(idHash)) { combinedFeatures.push(idHash[id]); } } return combinedFeatures; } combineFeaturesGTF(features) { const transcripts = Object.create(null); const combinedFeatures = []; const consumedFeatures = new Set(); const filterTypes = this.filterTypes; features = features.filter(f => filterTypes === undefined || !filterTypes.has(f.type)); // 1. Build dictionary of transcripts for (let f of features) { if (transcriptTypes.has(f.type)) { const transcriptId = f.id; if (undefined !== transcriptId) { const gffTranscript = new GFFTranscript(f); transcripts[transcriptId] = gffTranscript; combinedFeatures.push(gffTranscript); consumedFeatures.add(f); } } } // Add exons for (let f of features) { if (exonTypes.has(f.type)) { const id = f.id; // transcript_id, GTF groups all features with the same ID, does not have a parent/child hierarchy if (id) { let transcript = transcripts[id]; if (transcript === undefined) { transcript = new GFFTranscript(f); // GTF does not require an explicit transcript record transcripts[id] = transcript; combinedFeatures.push(transcript); } transcript.addExon(f); consumedFeatures.add(f); } } } // Apply CDS and UTR for (let f of features) { if (cdsTypes.has(f.type) || utrTypes.has(f.type) || codonTypes.has(f.type)) { const id = f.id; if (id) { let transcript = transcripts[id]; if (transcript === undefined) { transcript = new GFFTranscript(f); transcripts[id] = transcript; combinedFeatures.push(transcript); } if (utrTypes.has(f.type)) { transcript.addUTR(f); } else if (cdsTypes.has(f.type)) { transcript.addCDS(f); } else if (codonTypes.has(f.type)) ; consumedFeatures.add(f); } } } // Finish transcripts for (let f of combinedFeatures) { if (typeof f.finish === "function") { f.finish(); } } // Add other features const others = features.filter(f => !consumedFeatures.has(f)); for (let f of others) { combinedFeatures.push(f); } return combinedFeatures; } combineFeaturesGFF(features) { // Build dictionary of genes (optional) const genes = features.filter(f => "gene" === f.type); const geneMap = Object.create(null); for (let g of genes) { geneMap[g.id] = g; } // 1. Build dictionary of transcripts const transcripts = Object.create(null); const combinedFeatures = []; const consumedFeatures = new Set(); const filterTypes = this.filterTypes; features = features.filter(f => filterTypes === undefined || !filterTypes.has(f.type)); for (let f of features) { if (transcriptTypes.has(f.type)) { const transcriptId = f.id; // getAttribute(f.attributeString, "transcript_id", /\s+/); if (undefined !== transcriptId) { const gffTranscript = new GFFTranscript(f); transcripts[transcriptId] = gffTranscript; combinedFeatures.push(gffTranscript); consumedFeatures.add(f); const g = geneMap[f.parent]; if (g) { gffTranscript.gene = geneMap[f.parent]; consumedFeatures.add(g); } } } } // Remove assigned genes // Add exons for (let f of features) { if (exonTypes.has(f.type)) { const parents = getParents(f); if (parents) { for (let id of parents) { let transcript = transcripts[id]; if (transcript !== undefined) { transcript.addExon(f); consumedFeatures.add(f); } } } } } // Apply CDS and UTR for (let f of features) { if (cdsTypes.has(f.type) || utrTypes.has(f.type) || codonTypes.has(f.type)) { const parents = getParents(f); if (parents) { for (let id of parents) { let transcript = transcripts[id]; if (transcript !== undefined) { if (utrTypes.has(f.type)) { transcript.addUTR(f); } else if (cdsTypes.has(f.type)) { transcript.addCDS(f); } else if (codonTypes.has(f.type)) ; consumedFeatures.add(f); } } } } } // Introns are ignored, but are consumed const introns = features.filter(f => intronType === f.type); for (let i of introns) { const parents = getParents(i); for (let id of parents) { if (transcripts[id]) { consumedFeatures.add(i); break; } } } // Finish transcripts combinedFeatures.forEach(function (f) { if (typeof f.finish === "function") { f.finish(); } }); // Add other features const others = features.filter(f => !consumedFeatures.has(f)); for (let f of others) { combinedFeatures.push(f); } return combinedFeatures; function getParents(f) { if (f.parent && f.parent.trim() !== "") { return f.parent.trim().split(","); } else { return null; } } } } var GFFTranscript = function (feature) { Object.assign(this, feature); this.exons = []; }; GFFTranscript.prototype.addExon = function (feature) { this.exons.push(feature); // Expand feature -- for transcripts not explicitly represented in the file this.start = Math.min(this.start, feature.start); this.end = Math.max(this.end, feature.end); }; GFFTranscript.prototype.addCDS = function (cds) { let exon; const exons = this.exons; // Find exon containing CDS for (let i = 0; i < exons.length; i++) { if (exons[i].start <= cds.start && exons[i].end >= cds.end) { exon = exons[i]; break; } } if (exon) { exon.cdStart = exon.cdStart ? Math.min(cds.start, exon.cdStart) : cds.start; exon.cdEnd = exon.cdEnd ? Math.max(cds.end, exon.cdEnd) : cds.end; if (!exon.children) { exon.children = []; } exon.children.push(cds); } else { cds.cdStart = cds.start; cds.cdEnd = cds.end; exons.push(cds); } // Expand feature -- for transcripts not explicitly represented in the file (gtf files) this.start = Math.min(this.start, cds.start); this.end = Math.max(this.end, cds.end); this.cdStart = this.cdStart ? Math.min(cds.start, this.cdStart) : cds.start; this.cdEnd = this.cdEnd ? Math.max(cds.end, this.cdEnd) : cds.end; }; GFFTranscript.prototype.addUTR = function (utr) { let exon; const exons = this.exons; // Find exon containing CDS for (let i = 0; i < exons.length; i++) { if (exons[i].start <= utr.start && exons[i].end >= utr.end) { exon = exons[i]; break; } } if (exon) { if (utr.start === exon.start && utr.end === exon.end) { exon.utr = true; } else { if (utr.end < exon.end) { exon.cdStart = utr.end; } if (utr.start > exon.start) { exon.cdEnd = utr.start; } } if (!exon.children) { exon.children = []; } exon.children.push(utr); } else { utr.utr = true; exons.push(utr); } // Expand feature -- for transcripts not explicitly represented in the file this.start = Math.min(this.start, utr.start); this.end = Math.max(this.end, utr.end); }; GFFTranscript.prototype.finish = function () { var cdStart = this.cdStart; var cdEnd = this.cdEnd; this.exons.sort(function (a, b) { return a.start - b.start; }); // Search for UTR exons that were not explicitly tagged if (cdStart) { this.exons.forEach(function (exon) { if (exon.end < cdStart || exon.start > cdEnd) exon.utr = true; }); } }; GFFTranscript.prototype.popupData = function (genomicLocation) { const kvs = this.attributeString.split(';'); const pd = []; // If feature has an associated gene list its attributes first if (this.gene && typeof this.gene.popupData === 'function') { const gd = this.gene.popupData(genomicLocation); for (let e of gd) { pd.push(e); } pd.push("
"); } if (this.name) { pd.push({ name: 'name', value: this.name }); } pd.push({ name: 'type', value: this.type }); for (let kv of kvs) { var t = kv.trim().split(this.delim, 2); if (t.length === 2 && t[1] !== undefined) { const key = t[0].trim(); if ('name' === key.toLowerCase()) continue; let value = t[1].trim(); //Strip off quotes, if any if (value.startsWith('"') && value.endsWith('"')) { value = value.substr(1, value.length - 2); } pd.push({ name: key, value: value }); } } pd.push({ name: 'position', value: `${this.chr}:${numberFormatter$1(this.start + 1)}-${numberFormatter$1(this.end)}` }); // If clicked over an exon add its attributes for (let exon of this.exons) { if (genomicLocation >= exon.start && genomicLocation < exon.end && typeof exon.popupData === 'function') { pd.push("
"); const exonData = exon.popupData(genomicLocation); for (let att of exonData) { pd.push(att); } if (exon.children) { for (let c of exon.children) { pd.push("
"); const exonData = c.popupData(genomicLocation); for (let att of exonData) { pd.push(att); } } } } } return pd; }; /* * The MIT License (MIT) * * Copyright (c) 2015 UC San Diego * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const GtexReader = function (config) { this.config = config; this.url = config.url; this.tissueId = config.tissueSiteDetailId; this.indexed = true; this.datasetId = config.datasetId || "gtex_v8"; }; GtexReader.prototype.readFeatures = async function (chr, bpStart, bpEnd) { let self = this, queryChr = chr.startsWith("chr") ? chr : "chr" + chr, queryStart = Math.floor(bpStart), queryEnd = Math.ceil(bpEnd), datasetId = this.datasetId, queryURL = this.url + "?chromosome=" + queryChr + "&start=" + queryStart + "&end=" + queryEnd + "&tissueSiteDetailId=" + this.tissueId + "&datasetId=" + datasetId; const json = await igvxhr.loadJson(queryURL, { withCredentials: self.config.withCredentials }); if (json && json.singleTissueEqtl) { //variants = json.variants; //variants.sort(function (a, b) { // return a.POS - b.POS; //}); //source.cache = new FeatureCache(chr, queryStart, queryEnd, variants); json.singleTissueEqtl.forEach(function (eqtl) { eqtl.chr = eqtl.chromosome; eqtl.position = eqtl.pos; eqtl.start = eqtl.pos - 1; eqtl.end = eqtl.start + 1; eqtl.snp = eqtl.snpId; eqtl.geneName = eqtl.geneSymbol; eqtl.geneId = eqtl.gencodeId; }); return json.singleTissueEqtl; } else { return undefined; } }; /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ // http://immvar.broadinstitute.org:3000/load_data?chromosome=&start=&end=&categories= const ImmVarReader = function (config) { this.config = config; this.url = config.url; this.cellConditionId = config.cellConditionId; this.valueThreshold = config.valueThreshold ? config.valueThreshold : 5E-2; }; ImmVarReader.prototype.readFeatures = function (queryChr, queryStart, queryEnd) { var self = this, queryURL = this.url + "?chromosome=" + queryChr + "&start=" + queryStart + "&end=" + queryEnd + "&cell_condition_id=" + this.cellConditionId; return new Promise(function (fulfill, reject) { igvxhr.loadJson(queryURL, { withCredentials: self.config.withCredentials }).then(function (json) { if (json) { //variants = json.variants; //variants.sort(function (a, b) { // return a.POS - b.POS; //}); //source.cache = new FeatureCache(chr, queryStart, queryEnd, variants); json.eqtls.forEach(function (eqtl) { eqtl.chr = eqtl.chromosome; eqtl.start = eqtl.position; eqtl.end = eqtl.position + 1; }); fulfill(json.eqtls); } else { fulfill(null); } }).catch(function (error) { reject(error); }); }); }; /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const apiKey = igvxhr.apiKey; function ga4ghGet(options) { var url = options.url + "/" + options.entity + "/" + options.entityId; options.headers = ga4ghHeaders(); return igvxhr.loadJson(url, options); // Returns a promise } function ga4ghSearch(options) { return new Promise(function (fulfill, reject) { var results = options.results ? options.results : [], url = options.url, body = options.body, decode = options.decode, paramSeparator = "?", fields = options.fields; // Partial response if (apiKey) { url = url + paramSeparator + "key=" + apiKey; paramSeparator = "&"; } if (fields) { url = url + paramSeparator + "fields=" + fields; } // Start the recursive load cycle. Data is fetched in chunks, if more data is available a "nextPageToken" is returned. return loadChunk(); function loadChunk(pageToken) { if (pageToken) { body.pageToken = pageToken; } else { if (body.pageToken !== undefined) delete body.pageToken; // Remove previous page token, if any } var sendData = JSON.stringify(body); igvxhr.loadJson(url, { sendData: sendData, contentType: "application/json", headers: ga4ghHeaders() // oauthToken: ga4ghToken() }).then(function (json) { var nextPageToken, tmp; if (json) { tmp = decode ? decode(json) : json; if (tmp) { tmp.forEach(function (a) { { results.push(a); } }); } nextPageToken = json["nextPageToken"]; if (nextPageToken) { loadChunk(nextPageToken); } else { fulfill(results); } } else { fulfill(results); } }).catch(function (error) { reject(error); }); } }); } function ga4ghHeaders() { return { "Cache-Control": "no-cache" }; } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const Ga4ghVariantReader = function (config, genome) { this.config = config; this.genome = genome; this.url = config.url; this.variantSetId = config.variantSetId; this.callSetIds = config.callSetIds; this.includeCalls = config.includeCalls === undefined ? true : config.includeCalls; }; // Simulate a VCF file header Ga4ghVariantReader.prototype.readHeader = function () { var self = this; if (self.header) { return Promise.resolve(self.header); } else { self.header = {}; if (self.includeCalls === false) { return Promise.resolve(self.header); } else { var readURL = self.url + "/callsets/search"; return ga4ghSearch({ url: readURL, fields: "nextPageToken,callSets(id,name)", body: { "variantSetIds": Array.isArray(self.variantSetId) ? self.variantSetId : [self.variantSetId], "pageSize": "10000" }, decode: function (json) { // If specific callSetIds are specified filter to those if (self.callSetIds) { var callSets = [], csIdSet = new Set(); self.callSetIds.forEach(function (csid) { csIdSet.add(csid); }); json.callSets.forEach(function (cs) { if (csIdSet.has(cs.id)) { callSets.push(cs); } }); return callSets; } else { return json.callSets; } } }).then(function (callSets) { self.header.callSets = callSets; return self.header; }); } } }; Ga4ghVariantReader.prototype.readFeatures = function (chr, bpStart, bpEnd) { const self = this; const genome = this.genome; return self.readHeader().then(function (header) { return getChrAliasTable(); }).then(function (chrAliasTable) { var queryChr = chrAliasTable.hasOwnProperty(chr) ? chrAliasTable[chr] : chr, readURL = self.url + "/variants/search"; return ga4ghSearch({ url: readURL, fields: self.includeCalls ? undefined : "nextPageToken,variants(id,variantSetId,names,referenceName,start,end,referenceBases,alternateBases,quality,filter,info)", body: { "variantSetIds": Array.isArray(self.variantSetId) ? self.variantSetId : [self.variantSetId], "callSetIds": self.callSetIds ? self.callSetIds : undefined, "referenceName": queryChr, "start": bpStart.toString(), "end": bpEnd.toString(), "pageSize": "10000" }, decode: function (json) { var v; var variants = []; json.variants.forEach(function (json) { v = createGAVariant(json); if (!v.isRefBlock()) { variants.push(v); } }); return variants; } }); }); function getChrAliasTable() { return new Promise(function (fulfill, reject) { if (self.chrAliasTable) { fulfill(self.chrAliasTable); } else { self.readMetadata().then(function (json) { self.metadata = json.metadata; self.chrAliasTable = {}; if (json.referenceBounds && genome) { json.referenceBounds.forEach(function (rb) { var refName = rb.referenceName, alias = genome.getChromosomeName(refName); self.chrAliasTable[alias] = refName; }); } fulfill(self.chrAliasTable); }); } }); } }; Ga4ghVariantReader.prototype.readMetadata = function () { return ga4ghGet({ url: this.url, entity: "variantsets", entityId: this.variantSetId }); }; class CivicReader { constructor(config) { this.config = config; } async readFeatures(chr, start, end) { const json = await igvxhr.loadJson(this.config.url + "/variants/?count=50000"); const records = json.records; const features = []; for (let record of records) { if (record.coordinates) { record.id; const coordinates = record.coordinates; if (coordinates.chromosome) { features.push(new CivicVariant(coordinates.chromosome, coordinates.start - 1, // UCSC 0 convention coordinates.stop, record)); } if (coordinates.chromosome2) { features.push(new CivicVariant(coordinates.chromosome2, coordinates.start2 - 1, // UCSC 0 convention coordinates.stop2, record)); } } } return features; } } class CivicVariant { constructor(chr, start, end, record) { this.chr = chr; this.start = start; this.end = end; this.id = record.id; this.entrezName = record.entrez_name; this.name = record.name; this.actionabilityScore = record.civic_actionability_score; if (record.coordinates.reference_bases) { this.refBases = record.coordinates.reference_bases; } if (record.coordinates.variant_bases) { this.altBases = record.coordinates.variant_bases; } if (record.variant_types) { this.variant_types = record.variant_types; } this.locationString = this.chr + ":" + numberFormatter$1(this.start + 1) + "-" + numberFormatter$1(this.end); // Color based on actionability score if (this.actionabilityScore !== undefined) { let alpha; if (this.actionabilityScore <= 10) { alpha = 0.2; } else { const v = Math.min(30, this.actionabilityScore); alpha = 0.2 + 0.8 * Math.log10((v - 10) / 2); } this.alpha = alpha; } } popupData() { const link = createLink("CIViC", "https://civicdb.org/links/variants/" + this.id); this.refBases !== this.altBases && this.refBases && this.refBases.length === 1 && this.altBases && this.altBases.length === 1; const pd = [link]; pd.push({ name: "Entrez", value: createLink(this.entrezName, "https://ghr.nlm.nih.gov/gene/" + this.entrezName) }); pd.push({ name: "Name", value: this.name }); if (this.variant_types && this.variant_types.length > 0) { const name = this.variant_types.length === 1 ? "Type" : "Types"; let typeString; for (let vt of this.variant_types) { if (!typeString) typeString = vt.display_name;else typeString += ", " + vt.display_name; } pd.push({ name: name, value: typeString }); } pd.push({ name: "Actionability", value: this.actionabilityScore }); pd.push({ name: "Location", value: this.locationString }); return pd; function createLink(text, href) { return "" + text + ""; } } } // Assigns a row # to each feature. If the feature does not fit in any row and #rows == maxRows no // row number is assigned. function pack(featureList, maxRows) { maxRows = maxRows || Number.MAX_SAFE_INTEGER; const rows = []; featureList.sort(function (a, b) { return a.start - b.start; }); rows.push(-1000); for (let feature of featureList) { let r = 0; const len = Math.min(rows.length, maxRows); for (r = 0; r < len; r++) { if (feature.start > rows[r]) { feature.row = r; rows[r] = feature.end; break; } } feature.row = r; rows[r] = feature.end; } } class HtsgetReader { constructor(config, genome) { this.config = config; this.genome = genome; this.format = config.format ? config.format.toUpperCase() : "BAM"; // Backward compatibility if (!(this.format === "BAM" || this.format === "VCF")) { throw Error(`htsget format ${config.format} is not supported`); } } async readHeaderData() { const url = `${getUrl(this.config)}?class=header&format=${this.format}`; const ticket = await igvxhr.loadJson(url, buildOptions(this.config)); return await this.loadUrls(ticket.htsget.urls); } async readData(chr, start, end) { const url = `${getUrl(this.config)}?format=${this.format}&referenceName=${chr}&start=${Math.floor(start)}&end=${Math.ceil(end)}`; const ticket = await igvxhr.loadJson(url, buildOptions(this.config)); return this.loadUrls(ticket.htsget.urls); } async loadUrls(urls) { const promiseArray = []; for (let urlData of urls) { if (urlData.url.startsWith('data:')) { // this is a data-uri promiseArray.push(Promise.resolve(dataUriToBytes(urlData.url))); } else { const options = buildOptions(this.config || {}); if (urlData.headers) { options.headers = Object.assign(options.headers || {}, urlData.headers); } promiseArray.push(igvxhr.loadArrayBuffer(urlData.url, options)); } } const arrayBuffers = await Promise.all(promiseArray); return concatArrays(arrayBuffers); } static async inferFormat(config) { try { const url = getUrl(config); const headerURL = `${url}${url.includes("?") ? "&" : "?"}class=header`; const ticket = await igvxhr.loadJson(headerURL, buildOptions(config)); if (ticket.htsget) { const format = ticket.htsget.format; if (!(format === "BAM" || format === "VCF")) { throw Error(`htsget format ${format} is not supported`); } config.format = format.toLowerCase(); config.sourceType = "htsget"; if (!config.name) { config.name = await getFilename(config.url); } } } catch (e) {// Errors => this is not an htsget source, not an application error. Ignore } } } /** * Extract the full url from the config. Striving for backward compatibility, "endpoint" and "id" are deprecated. * * @param config */ function getUrl(config) { if (config.url && config.endpoint && config.id) { return config.url + config.endpoint + config.id; // Deprecated } else if (config.endpoint && config.id) { return config.endpoint + config.id; // Deprecated } else if (config.url) { if (config.url.startsWith("htsget://")) { return config.url.replace("htsget://", "https://"); // htsget -> http not supported } else { return config.url; } } else { throw Error("Must specify either 'url', or 'endpoint' and 'id"); } } /** * Concatenate a list of array buffers, returning an UInt8Array * @param arrayBuffers */ function concatArrays(arrayBuffers) { let len = 0; for (let a of arrayBuffers) { len += a.byteLength; } let offset = 0; const newArray = new Uint8Array(len); for (let buf of arrayBuffers) { const a = new Uint8Array(buf); newArray.set(a, offset); offset += a.length; } return newArray; } function dataUriToBytes(dataUri) { const split = dataUri.split(','); const info = split[0].split(':')[1]; let dataString = split[1]; if (info.indexOf('base64') >= 0) { dataString = atob(dataString); } else { dataString = decodeURI(dataString); } const bytes = new Uint8Array(dataString.length); for (var i = 0; i < dataString.length; i++) { bytes[i] = dataString.charCodeAt(i); } return bytes; } /* * The MIT License (MIT) * * Copyright (c) 2016-2017 The Regents of the University of California * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ class HtsgetVariantReader extends HtsgetReader { constructor(config, genome) { super(config, genome); this.parser = new VcfParser(); } async readHeader() { if (!this.header) { const data = await this.readHeaderData(); const dataWrapper = getDataWrapper(data); this.header = await this.parser.parseHeader(dataWrapper, this.genome); this.chrAliasTable = this.header.chrAliasTable; } return this.header; } async readFeatures(chr, start, end) { if (this.config.format && this.config.format.toUpperCase() !== "VCF") { throw Error(`htsget format ${this.config.format} is not supported`); } if (!this.chrAliasTable) { await this.readHeader(); } let queryChr = this.chrAliasTable.has(chr) ? this.chrAliasTable.get(chr) : chr; const data = await this.readData(queryChr, start, end); const dataWrapper = getDataWrapper(data); return this.parser.parseFeatures(dataWrapper); // return dataWrapper; } } /* * The MIT License (MIT) * * Copyright (c) 2014-2015 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ /** * feature source for "bed like" files (tab or whitespace delimited files with 1 feature per line: bed, gff, vcf, etc) * * @param config * @constructor */ class TextFeatureSource { constructor(config, genome) { this.config = config || {}; this.genome = genome; this.sourceType = config.sourceType === undefined ? "file" : config.sourceType; this.visibilityWindow = config.visibilityWindow; const queryableFormats = new Set(["bigwig", "bw", "bigbed", "bb", "tdf"]); if (config.features && Array.isArray(config.features)) { let features = fixFeatures(config.features, genome); packFeatures(features); if (config.mappings) { mapProperties(features, config.mappings); } this.queryable = false; this.featureCache = new FeatureCache(features, genome); } else if (config.reader) { this.reader = config.reader; this.queryable = config.queryable !== undefined ? config.queryable : true; this.expandQuery = config.expandQuery ? true : false; } else if (config.sourceType === "ga4gh") { this.reader = new Ga4ghVariantReader(config, genome); this.queryable = true; } else if (config.sourceType === "immvar") { this.reader = new ImmVarReader(config); this.queryable = true; } else if (config.type === "eqtl" && config.sourceType === "gtex-ws") { this.reader = new GtexReader(config); this.queryable = true; this.expandQuery = config.expandQuery ? true : false; } else if ("htsget" === config.sourceType) { this.reader = new HtsgetVariantReader(config, genome); } else if (config.sourceType === 'ucscservice') { this.reader = new UCSCServiceReader(config.source); this.queryable = true; } else if (config.sourceType === 'custom' || config.source !== undefined) { // Second test for backward compatibility this.reader = new CustomServiceReader(config.source); this.queryable = config.source.queryable !== undefined ? config.source.queryable : true; this.expandQuery = config.expandQuery ? true : false; } else if ("civic-ws" === config.sourceType) { this.reader = new CivicReader(config); this.queryable = false; this.expandQuery = config.expandQuery ? true : false; } else { this.reader = new FeatureFileReader(config, genome); if (config.queryable !== undefined) { this.queryable = config.queryable; } else if (queryableFormats.has(config.format)) { this.queryable = queryableFormats.has(config.format) || this.reader.indexed; } else ; } } supportsWholeGenome() { return !this.queryable && (this.visibilityWindow === undefined || this.visibilityWindow <= 0); } async trackType() { const header = await this.getHeader(); if (header) { return header.type; } else { return undefined; // Convention for unknown or unspecified } } async getHeader() { if (!this.header) { if (this.reader && typeof this.reader.readHeader === "function") { const header = await this.reader.readHeader(); if (header) { this.header = header; if (header.format) { this.config.format = header.format; } } else { this.header = {}; } } else { this.header = {}; } } return this.header; } /** * Required function for all data source objects. Fetches features for the * range requested. * * This function is quite complex due to the variety of reader types backing it, some indexed, some queryable, * some not. The whole scheme could use a refactoring. * * @param chr * @param start * @param end * @param bpPerPixel */ async getFeatures({ chr, start, end, bpPerPixel, visibilityWindow }) { const genome = this.genome; const queryChr = genome ? genome.getChromosomeName(chr) : chr; const isWholeGenome = "all" === queryChr.toLowerCase(); // Various conditions that can create a feature load // * view is "whole genome" but no features are loaded // * cache is disabled // * cache does not contain requested range if (isWholeGenome && !this.getWGFeatures || this.config.disableCache || !this.featureCache || !this.featureCache.containsRange(new GenomicInterval(queryChr, start, end))) { await this.loadFeatures(start, end, visibilityWindow, queryChr); } if (isWholeGenome) { if (!this.wgFeatures) { if (this.queryable) { // queryable sources don't support whole genome view this.wgFeatures = []; } else { this.wgFeatures = this.getWGFeatures(this.featureCache.getAllFeatures()); } } return this.wgFeatures; } else { return this.featureCache.queryFeatures(queryChr, start, end); } } async loadFeatures(start, end, visibilityWindow, queryChr) { const reader = this.reader; let intervalStart = start; let intervalEnd = end; // Use visibility window to potentially expand query interval. // This can save re-queries as we zoom out. Visibility window <= 0 is a special case // indicating whole chromosome should be read at once. if ((!visibilityWindow || visibilityWindow <= 0) && this.expandQuery !== false) { // Whole chromosome const chromosome = this.genome ? this.genome.getChromosome(queryChr) : undefined; intervalStart = 0; intervalEnd = chromosome ? chromosome.bpLength : Number.MAX_SAFE_INTEGER; } else if (visibilityWindow > end - start && this.expandQuery !== false) { const expansionWindow = Math.min(4.1 * (end - start), visibilityWindow); intervalStart = Math.max(0, (start + end) / 2 - expansionWindow); intervalEnd = start + expansionWindow; } let features = await reader.readFeatures(queryChr, intervalStart, intervalEnd); if (this.queryable === undefined) { this.queryable = reader.indexed; } const genomicInterval = this.queryable ? new GenomicInterval(queryChr, intervalStart, intervalEnd) : undefined; if (features) { if ("gtf" === this.config.format || "gff3" === this.config.format || "gff" === this.config.format) { features = new GFFHelper(this.config).combineFeatures(features); } // Assign overlapping features to rows if (this.config.format !== "wig" && this.config.type !== "junctions") { const maxRows = this.config.maxRows || Number.MAX_SAFE_INTEGER; packFeatures(features, maxRows); } // Note - replacing previous cache with new one. genomicInterval is optional (might be undefined => includes all features) this.featureCache = new FeatureCache(features, this.genome, genomicInterval); // If track is marked "searchable"< cache features by name -- use this with caution, memory intensive if (this.config.searchable) { this.addFeaturesToDB(features); } } else { this.featureCache = new FeatureCache([], genomicInterval); // Empty cache } } addFeaturesToDB(featureList) { for (let feature of featureList) { if (feature.name) { this.genome.featureDB[feature.name.toUpperCase()] = feature; } if (feature.gene && feature.gene.name) { this.genome.featureDB[feature.gene.name.toUpperCase()] = feature; } } } // TODO -- filter by pixel size getWGFeatures(allFeatures) { const genome = this.genome; const wgChromosomeNames = new Set(genome.wgChromosomeNames); const wgFeatures = []; for (let c of genome.wgChromosomeNames) { const features = allFeatures[c]; if (features) { for (let f of features) { let queryChr = genome.getChromosomeName(f.chr); if (wgChromosomeNames.has(queryChr)) { const wg = Object.assign({}, f); wg.chr = "all"; wg.start = genome.getGenomeCoordinate(f.chr, f.start); wg.end = genome.getGenomeCoordinate(f.chr, f.end); wg._f = f; // Don't draw exons in whole genome view if (wg["exons"]) delete wg["exons"]; wgFeatures.push(wg); } } } } wgFeatures.sort(function (a, b) { return a.start - b.start; }); return wgFeatures; } } function packFeatures(features, maxRows) { maxRows = maxRows || 1000; if (features == null || features.length === 0) { return; } // Segregate by chromosome const chrFeatureMap = {}; const chrs = []; for (let feature of features) { const chr = feature.chr; let flist = chrFeatureMap[chr]; if (!flist) { flist = []; chrFeatureMap[chr] = flist; chrs.push(chr); } flist.push(feature); } // Loop through chrosomosomes and pack features; for (let chr of chrs) { pack(chrFeatureMap[chr], maxRows); } } /** * This function is used to apply properties normally added during parsing to features supplied directly in the * config as an array of objects. At the moment the only application is bedpe type features. * @param features */ function fixFeatures(features, genome) { if (!features || features.length === 0) return []; const isBedPE = features[0].chr === undefined && features[0].chr1 !== undefined; if (isBedPE) { const interChrFeatures = []; for (let feature of features) { if (genome) { feature.chr1 = genome.getChromosomeName(feature.chr1); feature.chr2 = genome.getChromosomeName(feature.chr2); } // Set total extent of feature if (feature.chr1 === feature.chr2) { feature.chr = feature.chr1; feature.start = Math.min(feature.start1, feature.start2); feature.end = Math.max(feature.end1, feature.end2); } else { interChrFeatures.push(feature); } } // Make copies of inter-chr features, one for each chromosome for (let f1 of interChrFeatures) { const f2 = Object.assign({ dup: true }, f1); features.push(f2); f1.chr = f1.chr1; f1.start = f1.start1; f1.end = f1.end1; f2.chr = f2.chr2; f2.start = f2.start2; f2.end = f2.end2; } } else if (genome) { for (let feature of features) { feature.chr = genome.getChromosomeName(feature.chr); } } return features; } function mapProperties(features, mappings) { let mappingKeys = Object.keys(mappings); features.forEach(function (f) { mappingKeys.forEach(function (key) { f[key] = f[mappings[key]]; }); }); } class BufferedReader { constructor(config, contentLength, bufferSize) { this.path = config.url; this.bufferSize = bufferSize ? bufferSize : 512000; this.range = { start: -1, size: -1 }; this.config = config; } /** * * @param requestedRange - byte rangeas {start, size} * @param fulfill - function to receive result * @param asUint8 - optional flag to return result as an UInt8Array */ async dataViewForRange(requestedRange, asUint8) { const hasData = this.data && this.range.start <= requestedRange.start && this.range.start + this.range.size >= requestedRange.start + requestedRange.size; if (!hasData) { let bufferSize; // If requested range size is specified, potentially expand buffer size if (requestedRange.size) { bufferSize = Math.max(this.bufferSize, requestedRange.size); } else { bufferSize = this.bufferSize; } const loadRange = { start: requestedRange.start, size: bufferSize }; const arrayBuffer = await igvxhr.loadArrayBuffer(this.path, buildOptions(this.config, { range: loadRange })); this.data = arrayBuffer; this.range = loadRange; } const len = this.data.byteLength; const bufferStart = requestedRange.start - this.range.start; return asUint8 ? new Uint8Array(this.data, bufferStart, len - bufferStart) : new DataView(this.data, bufferStart, len - bufferStart); } } function scoreShade(score, color) { const alpha = Math.min(1, 0.11 + 0.89 * (score / 779)); return alpha.toString(); } function parseAutoSQL(str) { let table; const fields = []; let startDecoding = false; const lines = str.trim().split(/\s*[\r\n]+\s*/g); for (let line of lines) { if (line.startsWith('table')) { table = line.split(/\s+/)[1].trim(); } else if (line.startsWith('(')) { startDecoding = true; } else if (line.startsWith(')')) ; else if (startDecoding) { if (line.length > 0) { const idx = line.indexOf(';'); const tokens = line.substr(0, idx).split(/\s+/); const description = line.substr(idx + 1).replace(/"/g, '').trim(); fields.push({ type: tokens[0], name: tokens[1], description: description }); } } } return { table: table, fields: fields }; } //table chromatinInteract function getDecoder(definedFieldCount, fieldCount, autoSql) { if (autoSql && 'chromatinInteract' === autoSql.table) { return decodeInteract; } else { const standardFieldCount = definedFieldCount - 3; return function (feature, tokens) { if (standardFieldCount > 0) { feature.name = tokens[0]; } if (standardFieldCount > 1) { feature.score = parseFloat(tokens[1]); } if (standardFieldCount > 2) { feature.strand = tokens[2]; } if (standardFieldCount > 3) { feature.cdStart = parseInt(tokens[3]); } if (standardFieldCount > 4) { feature.cdEnd = parseInt(tokens[4]); } if (standardFieldCount > 5) { if (tokens[5] !== "." && tokens[5] !== "0" && tokens[5] !== "-1") { const c = IGVColor.createColorString(tokens[5]); feature.color = c.startsWith("rgb") ? c : undefined; } } if (standardFieldCount > 8) { const exonCount = parseInt(tokens[6]); const exonSizes = tokens[7].split(','); const exonStarts = tokens[8].split(','); const exons = []; for (let i = 0; i < exonCount; i++) { const eStart = feature.start + parseInt(exonStarts[i]); const eEnd = eStart + parseInt(exonSizes[i]); exons.push({ start: eStart, end: eEnd }); } feature.exons = exons; } if (autoSql) { // TODO -- these should be equal, validate? fieldCount-definedFieldCount, as.fields.length, tokens.length-3 const extraStart = definedFieldCount; for (let i = extraStart; i < fieldCount; i++) { if (i < autoSql.fields.length) { const name = autoSql.fields[i].name; const value = tokens[i - 3]; feature[name] = value; } } } }; } function decodeInteract(feature, tokens) { feature.chr1 = tokens[5]; feature.start1 = Number.parseInt(tokens[6]); feature.end1 = Number.parseInt(tokens[7]); feature.chr2 = tokens[10]; feature.start2 = Number.parseInt(tokens[11]); feature.end2 = Number.parseInt(tokens[12]); feature.name = tokens[0]; feature.score = Number.parseFloat(tokens[1]); feature.value = Number.parseFloat(tokens[2]); feature.color = tokens[4] === '.' ? undefined : tokens[4] === "0" ? "rgb(0,0,0)" : tokens[4]; return feature; } } let BIGWIG_MAGIC_LTH = 0x888FFC26; // BigWig Magic Low to High let BIGWIG_MAGIC_HTL = 0x26FC8F66; // BigWig Magic High to Low let BIGBED_MAGIC_LTH = 0x8789F2EB; // BigBed Magic Low to High let BIGBED_MAGIC_HTL = 0xEBF28987; // BigBed Magic High to Low let BBFILE_HEADER_SIZE = 64; let RPTREE_HEADER_SIZE = 48; let RPTREE_NODE_LEAF_ITEM_SIZE = 32; // leaf item size let RPTREE_NODE_CHILD_ITEM_SIZE = 24; // child item size let BUFFER_SIZE = 512000; // buffer class BWReader { constructor(config, genome) { this.path = config.url; this.genome = genome; this.rpTreeCache = {}; this.config = config; } async readWGFeatures(bpPerPixel, windowFunction) { await this.loadHeader(); const chrIdx1 = 0; const chrIdx2 = this.chromTree.idToChrom.length - 1; const chr1 = this.chromTree.idToChrom[chrIdx1]; const chr2 = this.chromTree.idToChrom[chrIdx2]; return this.readFeatures(chr1, 0, chr2, Number.MAX_VALUE, bpPerPixel, windowFunction); } async readFeatures(chr1, bpStart, chr2, bpEnd, bpPerPixel, windowFunction) { await this.loadHeader(); const chrIdx1 = this.chromTree.chromToID[chr1]; const chrIdx2 = this.chromTree.chromToID[chr2]; if (chrIdx1 === undefined || chrIdx2 === undefined) { return []; } let treeOffset; let decodeFunction; if (this.type === "bigwig") { // Select a biwig "zoom level" appropriate for the current resolution. const zoomLevelHeaders = await this.getZoomHeaders(); let zoomLevelHeader = bpPerPixel ? zoomLevelForScale$1(bpPerPixel, zoomLevelHeaders) : undefined; if (zoomLevelHeader) { treeOffset = zoomLevelHeader.indexOffset; decodeFunction = decodeZoomData; } else { treeOffset = this.header.fullIndexOffset; decodeFunction = decodeWigData; } } else { // bigbed, zoom data is not currently used in igv for bed type features treeOffset = this.header.fullIndexOffset; decodeFunction = getBedDataDecoder.call(this); } // Load the R Tree and fine leaf items const rpTree = await this.loadRPTree(treeOffset); const leafItems = await rpTree.findLeafItemsOverlapping(chrIdx1, bpStart, chrIdx2, bpEnd); if (!leafItems || leafItems.length === 0) { return []; } else { // Consolidate leaf items and get all data at once let start = Number.MAX_VALUE; let end = 0; for (let item of leafItems) { start = Math.min(start, item.dataOffset); end = Math.max(end, item.dataOffset + item.dataSize); } const size = end - start; const arrayBuffer = await igvxhr.loadArrayBuffer(this.config.url, buildOptions(this.config, { range: { start: start, size: size } })); // Parse data and return features const allFeatures = []; const buffer = new Uint8Array(arrayBuffer); for (let item of leafItems) { const uint8Array = buffer.subarray(item.dataOffset - start, item.dataOffset + item.dataSize); let plain; const isCompressed = this.header.uncompressBuffSize > 0; if (isCompressed) { const inflate = new Zlib$1.Inflate(uint8Array); plain = inflate.decompress(); } else { plain = uint8Array; } decodeFunction.call(this, new DataView(plain.buffer), chrIdx1, bpStart, chrIdx2, bpEnd, allFeatures, this.chromTree.idToChrom, windowFunction); } allFeatures.sort(function (a, b) { return a.start - b.start; }); return allFeatures; } } async getZoomHeaders() { if (this.zoomLevelHeaders) { return this.zoomLevelHeaders; } else { await this.loadHeader(); return this.zoomLevelHeaders; } } async loadHeader() { if (this.header) { return this.header; } else { let data = await igvxhr.loadArrayBuffer(this.path, buildOptions(this.config, { range: { start: 0, size: BBFILE_HEADER_SIZE } })); let header; // Assume low-to-high unless proven otherwise this.littleEndian = true; let binaryParser = new BinaryParser(new DataView(data)); let magic = binaryParser.getUInt(); if (magic === BIGWIG_MAGIC_LTH) { this.type = "bigwig"; } else if (magic === BIGBED_MAGIC_LTH) { this.type = "bigbed"; } else { //Try big endian order this.littleEndian = false; binaryParser.littleEndian = false; binaryParser.position = 0; let magic = binaryParser.getUInt(); if (magic === BIGWIG_MAGIC_HTL) { this.type = "bigwig"; } else if (magic === BIGBED_MAGIC_HTL) { this.type = "bigbed"; } else ; } // Table 5 "Common header for bigwig and bigbed files" header = { bwVersion: binaryParser.getUShort(), nZoomLevels: binaryParser.getUShort(), chromTreeOffset: binaryParser.getLong(), fullDataOffset: binaryParser.getLong(), fullIndexOffset: binaryParser.getLong(), fieldCount: binaryParser.getUShort(), definedFieldCount: binaryParser.getUShort(), autoSqlOffset: binaryParser.getLong(), totalSummaryOffset: binaryParser.getLong(), uncompressBuffSize: binaryParser.getInt(), extensionOffset: binaryParser.getLong() }; /////////// const startOffset = BBFILE_HEADER_SIZE; let range = { start: startOffset, size: header.fullDataOffset - startOffset + 5 }; data = await igvxhr.loadArrayBuffer(this.path, buildOptions(this.config, { range: range })); const nZooms = header.nZoomLevels; binaryParser = new BinaryParser(new DataView(data)); this.zoomLevelHeaders = []; this.firstZoomDataOffset = Number.MAX_SAFE_INTEGER; for (let i = 1; i <= nZooms; i++) { const zoomNumber = nZooms - i; const zlh = new ZoomLevelHeader(zoomNumber, binaryParser); this.firstZoomDataOffset = Math.min(zlh.dataOffset, this.firstZoomDataOffset); this.zoomLevelHeaders[zoomNumber] = zlh; } // Autosql if (header.autoSqlOffset > 0) { binaryParser.position = header.autoSqlOffset - startOffset; const autoSqlString = binaryParser.getString(); if (autoSqlString) { this.autoSql = parseAutoSQL(autoSqlString); } } // Total summary if (header.totalSummaryOffset > 0) { binaryParser.position = header.totalSummaryOffset - startOffset; this.totalSummary = new BWTotalSummary(binaryParser); } // Chrom data index if (header.chromTreeOffset > 0) { binaryParser.position = header.chromTreeOffset - startOffset; this.chromTree = new BPTree(binaryParser, startOffset, this.genome); } else { // TODO -- this is an error, not expected throw "BigWig chromosome tree offset <= 0"; } //Finally total data count binaryParser.position = header.fullDataOffset - startOffset; header.dataCount = binaryParser.getInt(); /////////// this.setDefaultVisibilityWindow(header); this.header = header; return this.header; } } async loadRPTree(offset) { let rpTree = this.rpTreeCache[offset]; if (rpTree) { return rpTree; } else { rpTree = new RPTree(offset, this.config, this.littleEndian); await rpTree.load(); this.rpTreeCache[offset] = rpTree; return rpTree; } } async getType() { await this.loadHeader(); return this.type; } async getTrackType() { await this.loadHeader(); if (this.type === "bigwig") { return "wig"; } else { return this.autoSql && this.autoSql.table === "chromatinInteract" ? "interact" : "annotation"; } } setDefaultVisibilityWindow(header) { if (this.type === "bigwig") { this.visibilityWindow = -1; } else { // bigbed let genomeSize = this.genome ? this.genome.getGenomeLength() : 3088286401; // Estimate window size to return ~ 1,000 features, assuming even distribution across the genome this.visibilityWindow = header.dataCount < 1000 ? -1 : 1000 * (genomeSize / header.dataCount); } } } class ZoomLevelHeader { constructor(index, byteBuffer) { this.index = index; this.reductionLevel = byteBuffer.getInt(); this.reserved = byteBuffer.getInt(); this.dataOffset = byteBuffer.getLong(); this.indexOffset = byteBuffer.getLong(); } } class RPTree { constructor(fileOffset, config, littleEndian) { this.config = config; this.fileOffset = fileOffset; // File offset to beginning of tree this.path = config.url; this.littleEndian = littleEndian; } async load() { const rootNodeOffset = this.fileOffset + RPTREE_HEADER_SIZE; const bufferedReader = new BufferedReader(this.config, BUFFER_SIZE); this.rootNode = await this.readNode(rootNodeOffset, bufferedReader); return this; } async readNode(filePosition, bufferedReader) { let dataView = await bufferedReader.dataViewForRange({ start: filePosition, size: 4 }, false); let binaryParser = new BinaryParser(dataView, this.littleEndian); const type = binaryParser.getByte(); const isLeaf = type === 1; binaryParser.getByte(); const count = binaryParser.getUShort(); filePosition += 4; let bytesRequired = count * (isLeaf ? RPTREE_NODE_LEAF_ITEM_SIZE : RPTREE_NODE_CHILD_ITEM_SIZE); let range2 = { start: filePosition, size: bytesRequired }; dataView = await bufferedReader.dataViewForRange(range2, false); const items = new Array(count); binaryParser = new BinaryParser(dataView); if (isLeaf) { for (let i = 0; i < count; i++) { let item = { isLeaf: true, startChrom: binaryParser.getInt(), startBase: binaryParser.getInt(), endChrom: binaryParser.getInt(), endBase: binaryParser.getInt(), dataOffset: binaryParser.getLong(), dataSize: binaryParser.getLong() }; items[i] = item; } return new RPTreeNode(items); } else { // non-leaf for (let i = 0; i < count; i++) { let item = { isLeaf: false, startChrom: binaryParser.getInt(), startBase: binaryParser.getInt(), endChrom: binaryParser.getInt(), endBase: binaryParser.getInt(), childOffset: binaryParser.getLong() }; items[i] = item; } return new RPTreeNode(items); } } async findLeafItemsOverlapping(chrIdx1, startBase, chrIdx2, endBase) { let self = this; return new Promise(function (fulfill, reject) { let leafItems = [], processing = new Set(), bufferedReader = new BufferedReader(self.config, BUFFER_SIZE); processing.add(0); // Zero represents the root node findLeafItems(self.rootNode, 0); function findLeafItems(node, nodeId) { if (overlaps(node, chrIdx1, startBase, chrIdx2, endBase)) { let items = node.items; items.forEach(function (item) { if (overlaps(item, chrIdx1, startBase, chrIdx2, endBase)) { if (item.isLeaf) { leafItems.push(item); } else { if (item.childNode) { findLeafItems(item.childNode); } else { processing.add(item.childOffset); // Represent node to-be-loaded by its file position self.readNode(item.childOffset, bufferedReader).then(function (node) { item.childNode = node; findLeafItems(node, item.childOffset); }).catch(reject); } } } }); } if (nodeId !== undefined) processing.delete(nodeId); // Wait until all nodes are processed if (processing.size === 0) { fulfill(leafItems); } } }); } } class RPTreeNode { constructor(items) { this.items = items; let minChromId = Number.MAX_SAFE_INTEGER, maxChromId = 0, minStartBase = Number.MAX_SAFE_INTEGER, maxEndBase = 0, i, item; for (i = 0; i < items.length; i++) { item = items[i]; minChromId = Math.min(minChromId, item.startChrom); maxChromId = Math.max(maxChromId, item.endChrom); minStartBase = Math.min(minStartBase, item.startBase); maxEndBase = Math.max(maxEndBase, item.endBase); } this.startChrom = minChromId; this.endChrom = maxChromId; this.startBase = minStartBase; this.endBase = maxEndBase; } } class BPTree { constructor(binaryParser, startOffset, genome) { let magic = binaryParser.getInt(); let blockSize = binaryParser.getInt(); let keySize = binaryParser.getInt(); let valSize = binaryParser.getInt(); let itemCount = binaryParser.getLong(); let reserved = binaryParser.getLong(); let chromToId = {}; let idToChrom = []; this.header = { magic: magic, blockSize: blockSize, keySize: keySize, valSize: valSize, itemCount: itemCount, reserved: reserved }; this.chromToID = chromToId; this.idToChrom = idToChrom; // Recursively walk tree to populate dictionary readTreeNode(binaryParser, -1); function readTreeNode(byteBuffer, offset) { if (offset >= 0) byteBuffer.position = offset; let type = byteBuffer.getByte(); byteBuffer.getByte(); let count = byteBuffer.getUShort(), i, key, chromId, childOffset, bufferOffset, currOffset; if (type === 1) { for (i = 0; i < count; i++) { key = byteBuffer.getFixedLengthTrimmedString(keySize); chromId = byteBuffer.getInt(); byteBuffer.getInt(); if (genome) key = genome.getChromosomeName(key); // Translate to canonical chr name chromToId[key] = chromId; idToChrom[chromId] = key; } } else { // non-leaf for (i = 0; i < count; i++) { key = byteBuffer.getFixedLengthTrimmedString(keySize); childOffset = byteBuffer.getLong(); bufferOffset = childOffset - startOffset; currOffset = byteBuffer.position; readTreeNode(byteBuffer, bufferOffset); byteBuffer.position = currOffset; } } } } } /** * Return true if {chrIdx1:startBase-chrIdx2:endBase} overlaps item's interval * @returns {boolean} */ function overlaps(item, chrIdx1, startBase, chrIdx2, endBase) { if (!item) { return false; } return (chrIdx2 > item.startChrom || chrIdx2 === item.startChrom && endBase >= item.startBase) && (chrIdx1 < item.endChrom || chrIdx1 === item.endChrom && startBase <= item.endBase); } class BWTotalSummary { constructor(byteBuffer) { if (byteBuffer) { this.basesCovered = byteBuffer.getLong(); this.minVal = byteBuffer.getDouble(); this.maxVal = byteBuffer.getDouble(); this.sumData = byteBuffer.getDouble(); this.sumSquares = byteBuffer.getDouble(); computeStats.call(this); } else { this.basesCovered = 0; this.minVal = 0; this.maxVal = 0; this.sumData = 0; this.sumSquares = 0; this.mean = 0; this.stddev = 0; } } } function computeStats() { let n = this.basesCovered; if (n > 0) { this.mean = this.sumData / n; this.stddev = Math.sqrt(this.sumSquares / (n - 1)); let min = this.minVal < 0 ? this.mean - 2 * this.stddev : 0, max = this.maxVal > 0 ? this.mean + 2 * this.stddev : 0; this.defaultRange = { min: min, max: max }; } } function zoomLevelForScale$1(bpPerPixel, zoomLevelHeaders) { let level; for (let i = 0; i < zoomLevelHeaders.length; i++) { const zl = zoomLevelHeaders[i]; if (zl.reductionLevel < bpPerPixel) { level = zl; break; } } return level; } function decodeWigData(data, chrIdx1, bpStart, chrIdx2, bpEnd, featureArray, chrDict) { const binaryParser = new BinaryParser(data); const chromId = binaryParser.getInt(); let chromStart = binaryParser.getInt(); let chromEnd = binaryParser.getInt(); const itemStep = binaryParser.getInt(); const itemSpan = binaryParser.getInt(); const type = binaryParser.getByte(); binaryParser.getByte(); let itemCount = binaryParser.getUShort(); if (chromId >= chrIdx1 && chromId <= chrIdx2) { while (itemCount-- > 0) { let value; switch (type) { case 1: chromStart = binaryParser.getInt(); chromEnd = binaryParser.getInt(); value = binaryParser.getFloat(); break; case 2: chromStart = binaryParser.getInt(); value = binaryParser.getFloat(); chromEnd = chromStart + itemSpan; break; case 3: // Fixed step value = binaryParser.getFloat(); chromEnd = chromStart + itemSpan; chromStart += itemStep; break; } if (chromId < chrIdx1 || chromId === chrIdx1 && chromEnd < bpStart) continue;else if (chromId > chrIdx2 || chromId === chrIdx2 && chromStart >= bpEnd) break; if (Number.isFinite(value)) { const chr = chrDict[chromId]; featureArray.push({ chr: chr, start: chromStart, end: chromEnd, value: value }); } } } } function getBedDataDecoder() { const minSize = 3 * 4 + 1; // Minimum # of bytes required for a bed record const decoder = getDecoder(this.header.definedFieldCount, this.header.fieldCount, this.autoSql); return function (data, chrIdx1, bpStart, chrIdx2, bpEnd, featureArray, chrDict) { const binaryParser = new BinaryParser(data); while (binaryParser.remLength() >= minSize) { const chromId = binaryParser.getInt(); const chr = chrDict[chromId]; const chromStart = binaryParser.getInt(); const chromEnd = binaryParser.getInt(); const rest = binaryParser.getString(); if (chromId < chrIdx1 || chromId === chrIdx1 && chromEnd < bpStart) continue;else if (chromId > chrIdx2 || chromId === chrIdx2 && chromStart >= bpEnd) break; if (chromEnd > 0) { const feature = { chr: chr, start: chromStart, end: chromEnd }; featureArray.push(feature); const tokens = rest.split("\t"); decoder(feature, tokens); } } }; } function decodeZoomData(data, chrIdx1, bpStart, chrIdx2, bpEnd, featureArray, chrDict, windowFunction) { const binaryParser = new BinaryParser(data); const minSize = 8 * 4; // Minimum # of bytes required for a zoom record while (binaryParser.remLength() >= minSize) { const chromId = binaryParser.getInt(); const chr = chrDict[chromId]; const chromStart = binaryParser.getInt(); const chromEnd = binaryParser.getInt(); const validCount = binaryParser.getInt(); const minVal = binaryParser.getFloat(); const maxVal = binaryParser.getFloat(); const sumData = binaryParser.getFloat(); binaryParser.getFloat(); let value; switch (windowFunction) { case "min": value = minVal; break; case "max": value = maxVal; break; default: value = validCount === 0 ? 0 : sumData / validCount; } if (chromId < chrIdx1 || chromId === chrIdx1 && chromEnd < bpStart) continue;else if (chromId > chrIdx2 || chromId === chrIdx2 && chromStart >= bpEnd) break; if (Number.isFinite(value)) { featureArray.push({ chr: chr, start: chromStart, end: chromEnd, value: value }); } } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ class BWSource { constructor(config, genome) { this.reader = new BWReader(config, genome); this.genome = genome; this.format = config.format || "bigwig"; this.wgValues = {}; } async getFeatures({ chr, start, end, bpPerPixel, windowFunction }) { const features = chr.toLowerCase() === "all" ? await this.getWGValues(windowFunction) : await this.reader.readFeatures(chr, start, chr, end, bpPerPixel, windowFunction); const isBigWig = this.reader.type === "bigwig"; if (!isBigWig) { pack(features); } return features; } async getHeader() { return this.reader.loadHeader(); } getDefaultRange() { if (this.reader.totalSummary !== undefined) { return this.reader.totalSummary.defaultRange; } else { return undefined; } } async defaultVisibilityWindow() { return this.reader.defaultVisibilityWindow; } async getWGValues(windowFunction) { const nominalScreenWidth = 1000; // This doesn't need to be precise const genome = this.genome; if (this.wgValues[windowFunction]) { return this.wgValues[windowFunction]; } else { const bpPerPixel = genome.getGenomeLength() / nominalScreenWidth; const features = await this.reader.readWGFeatures(bpPerPixel, windowFunction); let wgValues = []; for (let f of features) { const chr = f.chr; const offset = genome.getCumulativeOffset(chr); const wgFeature = Object.assign({}, f); wgFeature.chr = "all"; wgFeature.start = offset + f.start; wgFeature.end = offset + f.end; wgValues.push(wgFeature); } this.wgValues[windowFunction] = wgValues; return wgValues; } } supportsWholeGenome() { return this.reader.type === "bigwig" || this.defaultVisibilityWindow() <= 0; } async trackType() { return this.reader.getTrackType(); } } const GZIP_FLAG = 0x1; class TDFReader { constructor(config, genome) { this.config = config; this.genome = genome; this.path = config.url; this.groupCache = {}; this.datasetCache = {}; } async readHeader() { if (this.magic !== undefined) { return this; // Already read } let data = await igvxhr.loadArrayBuffer(this.path, buildOptions(this.config, { range: { start: 0, size: 64000 } })); let binaryParser = new BinaryParser(new DataView(data)); this.magic = binaryParser.getInt(); this.version = binaryParser.getInt(); this.indexPos = binaryParser.getLong(); this.indexSize = binaryParser.getInt(); binaryParser.getInt(); if (this.version >= 2) { let nWindowFunctions = binaryParser.getInt(); this.windowFunctions = []; while (nWindowFunctions-- > 0) { this.windowFunctions.push(binaryParser.getString()); } } this.trackType = binaryParser.getString(); this.trackLine = binaryParser.getString(); let nTracks = binaryParser.getInt(); this.trackNames = []; while (nTracks-- > 0) { this.trackNames.push(binaryParser.getString()); } this.genomeID = binaryParser.getString(); this.flags = binaryParser.getInt(); this.compressed = (this.flags & GZIP_FLAG) !== 0; // Now read index data = await igvxhr.loadArrayBuffer(this.path, buildOptions(this.config, { range: { start: this.indexPos, size: this.indexSize } })); binaryParser = new BinaryParser(new DataView(data)); this.datasetIndex = {}; let nEntries = binaryParser.getInt(); while (nEntries-- > 0) { const name = binaryParser.getString(); const pos = binaryParser.getLong(); const size = binaryParser.getInt(); this.datasetIndex[name] = { position: pos, size: size }; } this.groupIndex = {}; nEntries = binaryParser.getInt(); while (nEntries-- > 0) { const name = binaryParser.getString(); const pos = binaryParser.getLong(); const size = binaryParser.getInt(); this.groupIndex[name] = { position: pos, size: size }; } return this; } async readDataset(chr, windowFunction, zoom) { const key = chr + "_" + windowFunction + "_" + zoom; if (this.datasetCache[key]) { return this.datasetCache[key]; } else { await this.readHeader(); const wf = this.version < 2 ? "" : "/" + windowFunction; const zoomString = chr.toLowerCase() === "all" || zoom === undefined ? "0" : zoom.toString(); let dsName; if (windowFunction === "raw") { dsName = "/" + chr + "/raw"; } else { dsName = "/" + chr + "/z" + zoomString + wf; } const indexEntry = this.datasetIndex[dsName]; if (indexEntry === undefined) { return undefined; } const data = await igvxhr.loadArrayBuffer(this.path, buildOptions(this.config, { range: { start: indexEntry.position, size: indexEntry.size } })); if (!data) { return undefined; } const binaryParser = new BinaryParser(new DataView(data)); let nAttributes = binaryParser.getInt(); const attributes = {}; while (nAttributes-- > 0) { attributes[binaryParser.getString()] = binaryParser.getString(); } const dataType = binaryParser.getString(); const tileWidth = binaryParser.getFloat(); let nTiles = binaryParser.getInt(); const tiles = []; while (nTiles-- > 0) { tiles.push({ position: binaryParser.getLong(), size: binaryParser.getInt() }); } const dataset = { name: dsName, attributes: attributes, dataType: dataType, tileWidth: tileWidth, tiles: tiles }; this.datasetCache[key] = dataset; return dataset; } } async readRootGroup() { const genome = this.genome; const rootGroup = this.groupCache["/"]; if (rootGroup) { return rootGroup; } else { const group = await this.readGroup("/"); const names = group["chromosomes"]; const maxZoomString = group["maxZoom"]; // Now parse out interesting attributes. if (maxZoomString) { this.maxZoom = Number(maxZoomString); } const totalCountString = group["totalCount"]; if (totalCountString) { group.totalCount = Number.parseFloat(totalCountString); } // Chromosome names const chrAliasTable = {}; if (names) { names.split(",").forEach(function (chr) { const canonicalName = genome.getChromosomeName(chr); chrAliasTable[canonicalName] = chr; }); } this.chrAliasTable = chrAliasTable; this.groupCache["/"] = group; return group; } } async readGroup(name) { const group = this.groupCache[name]; if (group) { return group; } else { await this.readHeader(); const indexEntry = this.groupIndex[name]; if (indexEntry === undefined) { return undefined; } const data = await igvxhr.loadArrayBuffer(this.path, buildOptions(this.config, { range: { start: indexEntry.position, size: indexEntry.size } })); if (!data) { return undefined; } const binaryParser = new BinaryParser(new DataView(data)); const group = { name: name }; let nAttributes = binaryParser.getInt(); while (nAttributes-- > 0) { const key = binaryParser.getString(); const value = binaryParser.getString(); group[key] = value; } this.groupCache[name] = group; return group; } } async readTiles(tileIndeces, nTracks) { tileIndeces.sort(function (a, b) { return a.position - b.position; }); tileIndeces = tileIndeces.filter(function (idx) { return idx.size > 0; }); if (tileIndeces.length === 0) { return Promise.resolve([]); } const firstEntry = tileIndeces[0]; const lastEntry = tileIndeces[tileIndeces.length - 1]; const position = firstEntry.position; const size = lastEntry.position + lastEntry.size - position; const data = await igvxhr.loadArrayBuffer(this.path, buildOptions(this.config, { range: { start: position, size: size } })); const tiles = []; // Loop through and decode tiles for (let indexEntry of tileIndeces) { const start = indexEntry.position - position; const size = indexEntry.size; if (size > 0) { let tileData; if (this.compressed) { const inflate = new Zlib$1.Inflate(new Uint8Array(data, start, size)); const plain = inflate.decompress(); tileData = plain.buffer; } else { tileData = data.slice(start, start + size); } const binaryParser = new BinaryParser(new DataView(tileData)); const type = binaryParser.getString(); let tile; switch (type) { case "fixedStep": tile = createFixedStep(binaryParser, nTracks); break; case "variableStep": tile = createVariableStep(binaryParser, nTracks); break; case "bed": case "bedWithName": tile = createBed(binaryParser, nTracks, type); break; default: throw "Unknown tile type: " + type; } tiles.push(tile); } } return tiles; } async readTile(indexEntry, nTracks) { let data = await igvxhr.loadArrayBuffer(this.path, buildOptions(this.config, { range: { start: indexEntry.position, size: indexEntry.size } })); if (this.compressed) { const inflate = new Zlib$1.Inflate(new Uint8Array(data)); const plain = inflate.decompress(); data = plain.buffer; } const binaryParser = new BinaryParser(new DataView(data)); const type = binaryParser.getString(); switch (type) { case "fixedStep": return createFixedStep(binaryParser, nTracks); case "variableStep": return createVariableStep(binaryParser, nTracks); case "bed": case "bedWithName": return createBed(binaryParser, nTracks, type); default: throw "Unknown tile type: " + type; } } } function createFixedStep(binaryParser, nTracks) { const nPositions = binaryParser.getInt(); const start = binaryParser.getInt(); const span = binaryParser.getFloat(); const data = []; let nt = nTracks; while (nt-- > 0) { let np = nPositions; const dtrack = []; while (np-- > 0) { dtrack.push(binaryParser.getFloat()); } data.push(dtrack); } return { type: "fixedStep", start: start, span: span, data: data, nTracks: nTracks, nPositions: nPositions }; } function createVariableStep(binaryParser, nTracks) { const tileStart = binaryParser.getInt(); const span = binaryParser.getFloat(); const nPositions = binaryParser.getInt(); const start = []; let np = nPositions; while (np-- > 0) { start.push(binaryParser.getInt()); } binaryParser.getInt(); // # of samples, ignored but should === nTracks const data = []; let nt = nTracks; while (nt-- > 0) { np = nPositions; const dtrack = []; while (np-- > 0) { dtrack.push(binaryParser.getFloat()); } data.push(dtrack); } return { type: "variableStep", tileStart: tileStart, span: span, start: start, data: data, nTracks: nTracks, nPositions: nPositions }; } function createBed(binaryParser, nTracks, type) { const nPositions = binaryParser.getInt(); let n = nPositions; const start = []; while (n-- > 0) { start.push(binaryParser.getInt()); } n = nPositions; const end = []; while (n-- > 0) { end.push(binaryParser.getInt()); } binaryParser.getInt(); // # of samples, ignored but should === nTracks const data = []; let nt = nTracks; while (nt-- > 0) { let np = nPositions; const dtrack = []; while (np-- > 0) { dtrack.push(binaryParser.getFloat()); } data.push(dtrack); } if (type === "bedWithName") { n = nPositions; const name = []; while (n-- > 0) { name.push(binaryParser.getString()); } } return { type: type, start: start, end: end, data: data, nTracks: nTracks, nPositions: nPositions }; } /* * The MIT License (MIT) * * Copyright (c) 2016 University of California San Diego * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ class TDFSource { constructor(config, genome) { this.genome = genome; this.windowFunction = config.windowFunction || "mean"; this.reader = new TDFReader(config, genome); } async getFeatures({ chr, start, end, bpPerPixel }) { const genomicInterval = new GenomicInterval(chr, start, end); const genome = this.genome; if (!this.rootGroup) { this.rootGroup = await this.reader.readRootGroup(); if (!this.normalizationFactor) { const totalCount = this.rootGroup.totalCount; if (totalCount) { this.normalizationFactor = 1.0e6 / totalCount; } } } if (chr.toLowerCase() === "all") { return []; // Whole genome view not yet supported } genomicInterval.bpPerPixel = bpPerPixel; const zoom = zoomLevelForScale(chr, bpPerPixel, genome); let queryChr = this.reader.chrAliasTable[chr]; let maxZoom = this.reader.maxZoom; if (queryChr === undefined) queryChr = chr; if (maxZoom === undefined) maxZoom = -1; const wf = zoom > maxZoom ? "raw" : this.windowFunction; const dataset = await this.reader.readDataset(queryChr, wf, zoom); if (dataset == null) { return []; } const tileWidth = dataset.tileWidth; const startTile = Math.floor(start / tileWidth); const endTile = Math.floor(end / tileWidth); const NTRACKS = 1; // TODO read this const tiles = await this.reader.readTiles(dataset.tiles.slice(startTile, endTile + 1), NTRACKS); const features = []; for (let tile of tiles) { switch (tile.type) { case "bed": decodeBedTile(tile, chr, start, end, bpPerPixel, features); break; case "variableStep": decodeVaryTile(tile, chr, start, end, bpPerPixel, features); break; case "fixedStep": decodeFixedTile(tile, chr, start, end, bpPerPixel, features); break; default: throw "Unknown tile type: " + tile.type; } } features.sort(function (a, b) { return a.start - b.start; }); return features; } supportsWholeGenome() { return false; } } function decodeBedTile(tile, chr, bpStart, bpEnd, bpPerPixel, features) { const nPositions = tile.nPositions; const starts = tile.start; const ends = tile.end; const data = tile.data[0]; // Single track for now for (let i = 0; i < nPositions; i++) { const s = starts[i]; const e = ends[i]; if (e < bpStart) continue; if (s > bpEnd) break; features.push({ chr: chr, start: s, end: e, value: data[i] }); } } function decodeVaryTile(tile, chr, bpStart, bpEnd, bpPerPixel, features) { const nPositions = tile.nPositions; const starts = tile.start; const span = tile.span; const data = tile.data[0]; // Single track for now for (let i = 0; i < nPositions; i++) { const s = starts[i]; const e = s + span; if (e < bpStart) continue; if (s > bpEnd) break; features.push({ chr: chr, start: s, end: e, value: data[i] }); } } function decodeFixedTile(tile, chr, bpStart, bpEnd, bpPerPixel, features) { const nPositions = tile.nPositions; let s = tile.start; const span = tile.span; const data = tile.data[0]; // Single track for now for (let i = 0; i < nPositions; i++) { const e = s + span; if (s > bpEnd) break; if (e >= bpStart) { if (!Number.isNaN(data[i])) { features.push({ chr: chr, start: s, end: e, value: data[i] }); } } s = e; } } var log2 = Math.log(2); function zoomLevelForScale(chr, bpPerPixel, genome) { // Convert bpPerPixel to IGV "zoom" level. This is a bit convoluted, IGV computes zoom levels assuming // display in a 700 pixel window. The fully zoomed out view of a chromosome is zoom level "0". // Zoom level 1 is magnified 2X, and so forth var chrSize = genome.getChromosome(chr).bpLength; return Math.ceil(Math.log(Math.max(0, chrSize / (bpPerPixel * 700))) / log2); } /* * The MIT License (MIT) * * Copyright (c) 2014-2015 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ function FeatureSource(config, genome) { const format = config.format ? config.format.toLowerCase() : undefined; if ('bigwig' === format || 'bigbed' === format || 'bb' === format) { return new BWSource(config, genome); } else if ("tdf" === format) { return new TDFSource(config, genome); } else { return new TextFeatureSource(config, genome); } } const GtexUtils = { getTissueInfo: function (datasetId, baseURL) { datasetId = datasetId || 'gtex_v8'; baseURL = baseURL || 'https://gtexportal.org/rest/v1'; let url = baseURL + '/dataset/tissueInfo?datasetId=' + datasetId; return igvxhr.loadJson(url, {}); }, //https://gtexportal.org/rest/v1/association/singleTissueEqtlByLocation?chromosome=7&start=98358766&end=101523798&tissueName=Liver&datasetId=gtex_v7 //https://gtexportal.org/rest/v1/association/singleTissueEqtlByLocation?chromosome=7&start=98358766&end=101523798&tissueSiteDetailId=Liver&datasetId=gtex_v8 trackConfiguration: function (tissueSummary, baseURL) { baseURL = baseURL || 'https://gtexportal.org/rest/v1'; return { type: "eqtl", sourceType: "gtex-ws", url: baseURL + '/association/singleTissueEqtlByLocation', tissueSiteDetailId: tissueSummary.tissueSiteDetailId, name: tissueSummary.tissueSiteDetailId.split('_').join(' '), visibilityWindow: 250000 }; } }; /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ let JUNCTION_MOTIF_PALETTE = new PaletteColorTable("Dark2"); // Lock in color-to-motif mapping so it's independent of data loading order. This list may not include all possible // motif values as this varies depending on the RNA-seq pipeline. The current list is based on STAR v2.4 docs. const someMotifValues = ['GT/AG', 'CT/AC', 'GC/AG', 'CT/GC', 'AT/AC', 'GT/AT', 'non-canonical']; someMotifValues.forEach(motif => { JUNCTION_MOTIF_PALETTE.getColor(motif); }); // rendering context with values that only need to be computed once per render, rather than for each splice junction const junctionRenderingContext = {}; class FeatureTrack extends TrackBase { constructor(config, browser) { super(config, browser); } init(config) { super.init(config); this.type = config.type || "annotation"; // Set maxRows -- protects against pathological feature packing cases (# of rows of overlapping feaures) this.maxRows = config.maxRows === undefined ? 1000 : config.maxRows; this.displayMode = config.displayMode || "EXPANDED"; // COLLAPSED | EXPANDED | SQUISHED this.labelDisplayMode = config.labelDisplayMode; if (config._featureSource) { this.featureSource = config._featureSource; delete config._featureSource; } else { this.featureSource = config.featureSource ? config.featureSource : FeatureSource(config, this.browser.genome); } // Set default heights this.autoHeight = config.autoHeight; this.margin = config.margin === undefined ? 10 : config.margin; this.featureHeight = config.featureHeight || 14; if ("FusionJuncSpan" === config.type) { this.squishedRowHeight = config.squishedRowHeight || 50; this.expandedRowHeight = config.expandedRowHeight || 50; this.height = config.height || this.margin + 2 * this.expandedRowHeight; } else if ('snp' === config.type) { this.expandedRowHeight = config.expandedRowHeight || 10; this.squishedRowHeight = config.squishedRowHeight || 5; this.height = config.height || 30; } else { this.squishedRowHeight = config.squishedRowHeight || 15; this.expandedRowHeight = config.expandedRowHeight || 30; this.height = config.height || this.margin + 2 * this.expandedRowHeight; } if (this.height === undefined || !this.height) { this.height = 100; } //set defaults if ('spliceJunctions' === config.type && config.colorByNumReadsThreshold === undefined) { config.colorByNumReadsThreshold = 5; } // Set the render function. This can optionally be passed in the config if (config.render) { this.render = config.render; } else if ("FusionJuncSpan" === config.type) { this.render = renderFusionJuncSpan; } else if ('spliceJunctions' === config.type) { this.render = renderJunctions; this.displayMode = "COLLAPSED"; // needed for this.clickedFeatures(..) to work } else if ('snp' === config.type) { this.render = renderSnp; // colors ordered based on priority least to greatest this.snpColors = ['rgb(0,0,0)', 'rgb(0,0,255)', 'rgb(0,255,0)', 'rgb(255,0,0)']; this.colorBy = 'function'; } else { this.render = renderFeature; this.arrowSpacing = 30; // adjust label positions to make sure they're always visible monitorTrackDrag(this); } //UCSC useScore option this.useScore = config.useScore; } async postInit() { if (typeof this.featureSource.getHeader === "function") { this.header = await this.featureSource.getHeader(); } // Set properties from track line if (this.header) { this.setTrackProperties(this.header); } if (this.visibilityWindow === undefined && typeof this.featureSource.defaultVisibilityWindow === 'function') { this.visibilityWindow = await this.featureSource.defaultVisibilityWindow(); this.featureSource.visibilityWindow = this.visibilityWindow; // <- this looks odd } return this; } supportsWholeGenome() { return (this.config.indexed === false || !this.config.indexURL) && this.config.supportsWholeGenome !== false; } async getFeatures(chr, start, end, bpPerPixel) { const visibilityWindow = this.visibilityWindow; return this.featureSource.getFeatures({ chr, start, end, bpPerPixel, visibilityWindow }); } /** * The required height in pixels required for the track content. This is not the visible track height, which * can be smaller (with a scrollbar) or larger. * * @param features * @returns {*} */ computePixelHeight(features) { if (this.type === 'spliceJunctions') { return this.height; } else if (this.displayMode === "COLLAPSED") { return this.margin + this.expandedRowHeight; } else { let maxRow = 0; if (features && typeof features.forEach === "function") { for (let feature of features) { if (feature.row && feature.row > maxRow) { maxRow = feature.row; } } } const height = this.margin + (maxRow + 1) * ("SQUISHED" === this.displayMode ? this.squishedRowHeight : this.expandedRowHeight); return height; } } draw(options) { const featureList = options.features; const ctx = options.context; const bpPerPixel = options.bpPerPixel; const bpStart = options.bpStart; const pixelWidth = options.pixelWidth; const pixelHeight = options.pixelHeight; const bpEnd = bpStart + pixelWidth * bpPerPixel + 1; if (!this.config.isMergedTrack) { IGVGraphics.fillRect(ctx, 0, options.pixelTop, pixelWidth, pixelHeight, { 'fillStyle': "rgb(255, 255, 255)" }); } if (featureList) { const rowFeatureCount = []; options.rowLastX = []; for (let feature of featureList) { const row = feature.row || 0; if (rowFeatureCount[row] === undefined) { rowFeatureCount[row] = 1; } else { rowFeatureCount[row]++; } options.rowLastX[row] = -Number.MAX_SAFE_INTEGER; } if (this.config.type == 'spliceJunctions') { junctionRenderingContext.referenceFrame = options.viewport.referenceFrame; junctionRenderingContext.referenceFrameStart = junctionRenderingContext.referenceFrame.start; junctionRenderingContext.referenceFrameEnd = junctionRenderingContext.referenceFrameStart + junctionRenderingContext.referenceFrame.toBP($(options.viewport.contentDiv).width()); // For a given viewport, records where features that are < 2px in width have been rendered already. // This prevents wasteful rendering of multiple such features onto the same pixels. junctionRenderingContext.featureZoomOutTracker = {}; } let lastPxEnd = []; for (let feature of featureList) { if (feature.end < bpStart) continue; if (feature.start > bpEnd) break; const row = this.displayMode === 'COLLAPSED' ? 0 : feature.row; const featureDensity = pixelWidth / rowFeatureCount[row]; options.drawLabel = options.labelAllFeatures || featureDensity > 10; const pxEnd = Math.ceil((feature.end - bpStart) / bpPerPixel); const last = lastPxEnd[row]; if (!last || pxEnd > last || this.config.type === 'spliceJunctions') { this.render.call(this, feature, bpStart, bpPerPixel, pixelHeight, ctx, options); if (this.config.type !== 'spliceJunctions') { // Ensure a visible gap between features const pxStart = Math.floor((feature.start - bpStart) / bpPerPixel); if (last && pxStart - last <= 0) { ctx.globalAlpha = 0.5; IGVGraphics.strokeLine(ctx, pxStart, 0, pxStart, pixelHeight, { 'strokeStyle': "rgb(255, 255, 255)" }); ctx.globalAlpha = 1.0; } lastPxEnd[row] = pxEnd; } } } } } clickedFeatures(clickState, features) { const y = clickState.y - this.margin; const allFeatures = super.clickedFeatures(clickState, features); let row; switch (this.displayMode) { case 'SQUISHED': row = Math.floor(y / this.squishedRowHeight); break; case 'EXPANDED': row = Math.floor(y / this.expandedRowHeight); break; default: row = undefined; } return allFeatures.filter(function (feature) { return row === undefined || feature.row === undefined || row === feature.row; }); } /** * Return "popup data" for feature @ genomic location. Data is an array of key-value pairs */ popupData(clickState, features) { features = this.clickedFeatures(clickState, features); const genomicLocation = clickState.genomicLocation; const data = []; for (let feature of features) { if (this.config.type === 'spliceJunctions') { if (!feature.isVisible || !feature.attributes) { continue; } } const featureData = typeof feature.popupData === "function" ? feature.popupData(genomicLocation) : this.extractPopupData(feature._f || feature, this.getGenomeId()); if (featureData) { if (data.length > 0) { data.push("

"); } Array.prototype.push.apply(data, featureData); } } return data; } menuItemList() { const self = this; const menuItems = []; if (this.render === renderSnp) { ["function", "class"].forEach(function (colorScheme) { menuItems.push({ object: createCheckbox$1('Color by ' + colorScheme, colorScheme === self.colorBy), click: function () { self.colorBy = colorScheme; self.trackView.repaintViews(); } }); }); menuItems.push({ object: $('
') }); } menuItems.push({ object: $('
') }); ["COLLAPSED", "SQUISHED", "EXPANDED"].forEach(function (displayMode) { const lut = { "COLLAPSED": "Collapse", "SQUISHED": "Squish", "EXPANDED": "Expand" }; menuItems.push({ object: createCheckbox$1(lut[displayMode], displayMode === self.displayMode), click: function () { self.displayMode = displayMode; self.config.displayMode = displayMode; self.trackView.checkContentHeight(); self.trackView.repaintViews(); } }); }); return menuItems; } description() { // if('snp' === this.type) { if (renderSnp === this.render) { let desc = "" + this.name + "
"; desc += 'Color By Function:
'; desc += 'Red: Coding-Non-Synonymous, Splice Site
'; desc += 'Green: Coding-Synonymous
'; desc += 'Blue: Untranslated
'; desc += 'Black: Intron, Locus, Unknown

'; desc += 'Color By Class:
'; desc += 'Red: Deletion
'; desc += 'Green: MNP
'; desc += 'Blue: Microsatellite, Named
'; desc += 'Black: Indel, Insertion, SNP'; desc += ""; return desc; } else { return this.name; } } /** * Called when the track is removed. Do any needed cleanup here */ dispose() { this.trackView = undefined; } } /** * Monitors track drag events, updates label position to ensure that they're always visible. * @param track */ function monitorTrackDrag(track) { if (track.browser.on) { track.browser.on('trackdragend', onDragEnd); track.browser.on('trackremoved', unSubscribe); } function onDragEnd() { if (track.trackView && track.displayMode !== "SQUISHED") { track.trackView.repaintViews(); // TODO -- refine this to the viewport that was dragged after DOM refactor } } function unSubscribe(removedTrack) { if (track.browser.un && track === removedTrack) { track.browser.un('trackdrag', onDragEnd); track.browser.un('trackremoved', unSubscribe); } } } /** * @param feature * @param bpStart genomic location of the left edge of the current canvas * @param xScale scale in base-pairs per pixel * @returns {{px: number, px1: number, pw: number, h: number, py: number}} */ function calculateFeatureCoordinates(feature, bpStart, xScale) { let px = (feature.start - bpStart) / xScale; let px1 = (feature.end - bpStart) / xScale; //px = Math.round((feature.start - bpStart) / xScale), //px1 = Math.round((feature.end - bpStart) / xScale), let pw = px1 - px; if (pw < 3) { pw = 3; px -= 1.5; } return { px: px, px1: px1, pw: pw }; } /** * Return color for feature. Called in the context of a FeatureTrack instance. * @param feature * @returns {string} */ function getColorForFeature(feature) { let color; if (this.altColor && "-" === feature.strand) { color = this.altColor; } else if (this.color) { color = this.color; // Explicit setting via menu, or possibly track line if !config.color } else if (this.config.colorBy) { const colorByValue = feature[this.config.colorBy.field]; if (colorByValue) { color = this.config.colorBy.pallete[colorByValue]; // This is an undocumented option, and its not clear if its used } } else if (feature.color) { color = feature.color; // Explicit color for feature } else { color = this.defaultColor; // Track default } if (feature.alpha && feature.alpha !== 1) { color = IGVColor.addAlpha(color, feature.alpha); } else if (this.useScore && feature.score && !Number.isNaN(feature.score)) { // UCSC useScore option, for scores between 0-1000. See https://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK const min = this.config.min ? this.config.min : 0; //getViewLimitMin(track); const max = this.config.max ? this.config.max : 1000; //getViewLimitMax(track); const alpha = getAlpha(min, max, feature.score); feature.alpha = alpha; // Avoid computing again color = IGVColor.addAlpha(color, alpha); } function getAlpha(min, max, score) { const binWidth = (max - min) / 9; const binNumber = Math.floor((score - min) / binWidth); return Math.min(1.0, 0.2 + binNumber * 0.8 / 9); } return color; } /** * * @param feature * @param bpStart genomic location of the left edge of the current canvas * @param xScale scale in base-pairs per pixel * @param pixelHeight pixel height of the current canvas * @param ctx the canvas 2d context * @param options genomic state */ function renderFeature(feature, bpStart, xScale, pixelHeight, ctx, options) { let color = getColorForFeature.call(this, feature); ctx.fillStyle = color; ctx.strokeStyle = color; let h; let py; if (this.displayMode === "SQUISHED" && feature.row !== undefined) { h = this.featureHeight / 2; py = this.margin + this.squishedRowHeight * feature.row; } else if (this.displayMode === "EXPANDED" && feature.row !== undefined) { h = this.featureHeight; py = this.margin + this.expandedRowHeight * feature.row; } else { // collapsed h = this.featureHeight; py = this.margin; } const cy = py + h / 2; const h2 = h / 2; const py2 = cy - h2 / 2; const exonCount = feature.exons ? feature.exons.length : 0; const coord = calculateFeatureCoordinates(feature, bpStart, xScale); const step = this.arrowSpacing; const direction = feature.strand === '+' ? 1 : feature.strand === '-' ? -1 : 0; if (exonCount === 0) { // single-exon transcript ctx.fillRect(coord.px, py, coord.pw, h); // Arrows // Do not draw if strand is not +/- if (direction !== 0) { ctx.fillStyle = "white"; ctx.strokeStyle = "white"; for (let x = coord.px + step / 2; x < coord.px1; x += step) { // draw arrowheads along central line indicating transcribed orientation IGVGraphics.strokeLine(ctx, x - direction * 2, cy - 2, x, cy); IGVGraphics.strokeLine(ctx, x - direction * 2, cy + 2, x, cy); } ctx.fillStyle = color; ctx.strokeStyle = color; } } else { // multi-exon transcript IGVGraphics.strokeLine(ctx, coord.px + 1, cy, coord.px1 - 1, cy); // center line for introns const pixelWidth = options.pixelWidth; const xLeft = Math.max(0, coord.px) + step / 2; const xRight = Math.min(pixelWidth, coord.px1); for (let x = xLeft; x < xRight; x += step) { // draw arrowheads along central line indicating transcribed orientation IGVGraphics.strokeLine(ctx, x - direction * 2, cy - 2, x, cy); IGVGraphics.strokeLine(ctx, x - direction * 2, cy + 2, x, cy); } for (let e = 0; e < exonCount; e++) { // draw the exons const exon = feature.exons[e]; let ePx = Math.round((exon.start - bpStart) / xScale); let ePx1 = Math.round((exon.end - bpStart) / xScale); let ePw = Math.max(1, ePx1 - ePx); let ePxU; if (ePx + ePw < 0) { continue; // Off the left edge } if (ePx > pixelWidth) { break; // Off the right edge } if (exon.utr) { ctx.fillRect(ePx, py2, ePw, h2); // Entire exon is UTR } else { if (exon.cdStart) { ePxU = Math.round((exon.cdStart - bpStart) / xScale); ctx.fillRect(ePx, py2, ePxU - ePx, h2); // start is UTR ePw -= ePxU - ePx; ePx = ePxU; } if (exon.cdEnd) { ePxU = Math.round((exon.cdEnd - bpStart) / xScale); ctx.fillRect(ePxU, py2, ePx1 - ePxU, h2); // start is UTR ePw -= ePx1 - ePxU; ePx1 = ePxU; } ctx.fillRect(ePx, py, ePw, h); // Arrows if (ePw > step + 5 && direction !== 0) { ctx.fillStyle = "white"; ctx.strokeStyle = "white"; for (let x = ePx + step / 2; x < ePx1; x += step) { // draw arrowheads along central line indicating transcribed orientation IGVGraphics.strokeLine(ctx, x - direction * 2, cy - 2, x, cy); IGVGraphics.strokeLine(ctx, x - direction * 2, cy + 2, x, cy); } ctx.fillStyle = color; ctx.strokeStyle = color; } } } } if (options.drawLabel && this.displayMode !== "SQUISHED") { renderFeatureLabel.call(this, ctx, feature, coord.px, coord.px1, py, options.referenceFrame, options); } } /** * @param ctx the canvas 2d context * @param feature * @param featureX feature start x-coordinate * @param featureX1 feature end x-coordinate * @param featureY feature y-coordinate * @param windowX visible window start x-coordinate * @param windowX1 visible window end x-coordinate * @param referenceFrame genomic state * @param options options */ function renderFeatureLabel(ctx, feature, featureX, featureX1, featureY, referenceFrame, options) { let name = feature.name; if (name === undefined && feature.gene) name = feature.gene.name; if (name === undefined) name = feature.id || feature.ID; if (!name || name === '.') return; let pixelXOffset = options.pixelXOffset || 0; const t1 = Math.max(featureX, -pixelXOffset); const t2 = Math.min(featureX1, -pixelXOffset + options.viewportWidth); const centerX = (t1 + t2) / 2; let transform; if (this.displayMode === "COLLAPSED" && this.labelDisplayMode === "SLANT") { transform = { rotate: { angle: 45 } }; } const labelY = getFeatureLabelY(featureY, transform); let color = getColorForFeature.call(this, feature); let geneColor; let gtexSelection = false; if (referenceFrame.selection && GtexUtils.gtexLoaded) { // TODO -- for gtex, figure out a better way to do this gtexSelection = true; geneColor = referenceFrame.selection.colorForGene(name); } const geneFontStyle = { textAlign: "SLANT" === this.labelDisplayMode ? undefined : 'center', fillStyle: geneColor || color, strokeStyle: geneColor || color }; const textBox = ctx.measureText(name); const xleft = centerX - textBox.width / 2; const xright = centerX + textBox.width / 2; if (options.labelAllFeatures || xleft > options.rowLastX[feature.row] || gtexSelection) { options.rowLastX[feature.row] = xright; IGVGraphics.fillText(ctx, name, centerX, labelY, geneFontStyle, transform); } } function getFeatureLabelY(featureY, transform) { return transform ? featureY + 20 : featureY + 25; } /** * * @param feature * @param bpStart genomic location of the left edge of the current canvas * @param xScale scale in base-pairs per pixel * @param pixelHeight pixel height of the current canvas * @param ctx the canvas 2d context */ function renderFusionJuncSpan(feature, bpStart, xScale, pixelHeight, ctx) { var py; var rowHeight = this.displayMode === "EXPANDED" ? this.expandedRowHeight : this.squishedRowHeight; if (this.display === "COLLAPSED") { py = this.margin; } if (this.displayMode === "SQUISHED" && feature.row !== undefined) { py = this.margin + rowHeight * feature.row; } else if (this.displayMode === "EXPANDED" && feature.row !== undefined) { py = this.margin + rowHeight * feature.row; } var cy = py + 0.5 * rowHeight; var topY = cy - 0.5 * rowHeight; var bottomY = cy + 0.5 * rowHeight; // draw the junction arc var junctionLeftPx = Math.round((feature.junction_left - bpStart) / xScale); var junctionRightPx = Math.round((feature.junction_right - bpStart) / xScale); ctx.beginPath(); ctx.moveTo(junctionLeftPx, cy); ctx.bezierCurveTo(junctionLeftPx, topY, junctionRightPx, topY, junctionRightPx, cy); ctx.lineWidth = 1 + Math.log(feature.num_junction_reads) / Math.log(2); ctx.strokeStyle = 'blue'; ctx.stroke(); // draw the spanning arcs var spanningCoords = feature.spanning_frag_coords; for (var i = 0; i < spanningCoords.length; i++) { var spanningInfo = spanningCoords[i]; var spanLeftPx = Math.round((spanningInfo.left - bpStart) / xScale); var spanRightPx = Math.round((spanningInfo.right - bpStart) / xScale); ctx.beginPath(); ctx.moveTo(spanLeftPx, cy); ctx.bezierCurveTo(spanLeftPx, bottomY, spanRightPx, bottomY, spanRightPx, cy); ctx.lineWidth = 1; ctx.strokeStyle = 'purple'; ctx.stroke(); } } /** * * @param feature * @param bpStart genomic location of the left edge of the current canvas * @param xScale scale in base-pairs per pixel * @param pixelHeight pixel height of the current canvas * @param ctx the canvas 2d context */ function renderJunctions(feature, bpStart, xScale, pixelHeight, ctx) { // cache whether this junction is rendered or filtered out. Use later to exclude non-rendered junctions from click detection. feature.isVisible = false; const junctionLeftPx = Math.round((feature.start - bpStart) / xScale); const junctionRightPx = Math.round((feature.end - bpStart) / xScale); const junctionMiddlePx = (junctionLeftPx + junctionRightPx) / 2; if (junctionRightPx - junctionLeftPx <= 3) { if (junctionMiddlePx in junctionRenderingContext.featureZoomOutTracker) { return; } junctionRenderingContext.featureZoomOutTracker[junctionMiddlePx] = true; } // TODO: cache filter and pixel calculations by doing them earlier when features are initially parsed? if (this.config.hideAnnotatedJunctions && feature.attributes.annotated_junction === "true") { return; } if (this.config.hideUnannotatedJunctions && feature.attributes.annotated_junction === "false") { return; } if (this.config.hideMotifs && this.config.hideMotifs.includes(feature.attributes.motif)) { return; } if (this.config.hideStrand === feature.strand) { return; } // check if splice junction is inside viewport if (this.config.minJunctionEndsVisible) { let numJunctionEndsVisible = 0; if (feature.start >= junctionRenderingContext.referenceFrameStart && feature.start <= junctionRenderingContext.referenceFrameEnd) { numJunctionEndsVisible += 1; } if (feature.end >= junctionRenderingContext.referenceFrameStart && feature.end <= junctionRenderingContext.referenceFrameEnd) { numJunctionEndsVisible += 1; } if (numJunctionEndsVisible < this.config.minJunctionEndsVisible) { return; } } let uniquelyMappedReadCount; let multiMappedReadCount; let totalReadCount; if (feature.attributes.uniquely_mapped) { uniquelyMappedReadCount = parseInt(feature.attributes.uniquely_mapped); if (uniquelyMappedReadCount < this.config.minUniquelyMappedReads) { return; } multiMappedReadCount = parseInt(feature.attributes.multi_mapped); totalReadCount = uniquelyMappedReadCount + multiMappedReadCount; if (totalReadCount < this.config.minTotalReads) { return; } if (totalReadCount > 0 && multiMappedReadCount / totalReadCount > this.config.maxFractionMultiMappedReads) { return; } if (feature.attributes.maximum_spliced_alignment_overhang && parseInt(feature.attributes.maximum_spliced_alignment_overhang) < this.config.minSplicedAlignmentOverhang) { return; } } let numSamplesWithThisJunction; if (feature.attributes.num_samples_with_this_junction) { numSamplesWithThisJunction = parseInt(feature.attributes.num_samples_with_this_junction); if (this.config.minSamplesWithThisJunction && numSamplesWithThisJunction < this.config.minSamplesWithThisJunction) { return; } if (this.config.maxSamplesWithThisJunction && numSamplesWithThisJunction > this.config.maxSamplesWithThisJunction) { return; } if (feature.attributes.num_samples_total) { feature.attributes.percent_samples_with_this_junction = 100 * numSamplesWithThisJunction / parseFloat(feature.attributes.num_samples_total); if (this.config.minPercentSamplesWithThisJunction) { if (feature.attributes.percent_samples_with_this_junction < this.config.minPercentSamplesWithThisJunction || feature.attributes.percent_samples_with_this_junction > this.config.maxPercentSamplesWithThisJunction) { return; } } } } const py = this.margin; const rowHeight = this.height; const cy = py + 0.5 * rowHeight; let topY = py; const bottomY = py + rowHeight; const bezierBottomY = bottomY - 10; // draw the junction arc const bezierControlLeftPx = (junctionLeftPx + junctionMiddlePx) / 2; const bezierControlRightPx = (junctionMiddlePx + junctionRightPx) / 2; let lineWidth = 1; if (feature.attributes.line_width) { lineWidth = parseFloat(feature.attributes.line_width); } else { if (this.config.thicknessBasedOn === undefined || this.config.thicknessBasedOn === 'numUniqueReads') { lineWidth = uniquelyMappedReadCount; } else if (this.config.thicknessBasedOn === 'numReads') { lineWidth = totalReadCount; } else if (this.config.thicknessBasedOn === 'numSamplesWithThisJunction') { if (numSamplesWithThisJunction !== undefined) { lineWidth = numSamplesWithThisJunction; } } lineWidth = 1 + Math.log(lineWidth + 1) / Math.log(12); } let bounceHeight; if (this.config.bounceHeightBasedOn === undefined || this.config.bounceHeightBasedOn === 'random') { // randomly but deterministically stagger topY coordinates to reduce overlap bounceHeight = (feature.start + feature.end) % 7; } else if (this.config.bounceHeightBasedOn === 'distance') { bounceHeight = 6 * (feature.end - feature.start) / (junctionRenderingContext.referenceFrameEnd - junctionRenderingContext.referenceFrameStart); } else if (this.config.bounceHeightBasedOn === 'thickness') { bounceHeight = 2 * lineWidth; } topY += rowHeight * Math.max(7 - bounceHeight, 0) / 10; let color; if (feature.attributes.color) { color = feature.attributes.color; // Explicit setting } else if (this.config.colorBy === undefined || this.config.colorBy === 'numUniqueReads') { color = uniquelyMappedReadCount > this.config.colorByNumReadsThreshold ? 'blue' : '#AAAAAA'; // color gradient? } else if (this.config.colorBy === 'numReads') { color = totalReadCount > this.config.colorByNumReadsThreshold ? 'blue' : '#AAAAAA'; } else if (this.config.colorBy === 'isAnnotatedJunction') { color = feature.attributes.annotated_junction === "true" ? '#b0b0ec' : 'orange'; } else if (this.config.colorBy === 'strand') { color = feature.strand === "+" ? '#b0b0ec' : '#ecb0b0'; } else if (this.config.colorBy === 'motif') { color = JUNCTION_MOTIF_PALETTE.getColor(feature.attributes.motif); } else { color = '#AAAAAA'; } let label = ""; if (feature.attributes.label) { label = feature.attributes.label.replace(/_/g, " "); } else if (this.config.labelWith === undefined || this.config.labelWith === 'uniqueReadCount') { //default label label = uniquelyMappedReadCount; } else if (this.config.labelWith === 'totalReadCount') { label = totalReadCount; } else if (this.config.labelWith === 'numSamplesWithThisJunction') { if (numSamplesWithThisJunction !== undefined) { label = numSamplesWithThisJunction; } } else if (this.config.labelWith === 'percentSamplesWithThisJunction') { if (feature.attributes.percent_samples_with_this_junction !== undefined) { label = feature.attributes.percent_samples_with_this_junction.toFixed(0) + '%'; } } else if (this.config.labelWith === 'motif') { if (feature.attributes.motif !== undefined) { label += feature.attributes.motif; } } if (this.config.labelWithInParen === 'uniqueReadCount') { label += ' (' + uniquelyMappedReadCount + ')'; } else if (this.config.labelWithInParen === 'totalReadCount') { label += ' (' + totalReadCount + ')'; } else if (this.config.labelWithInParen === 'multiMappedReadCount') { if (multiMappedReadCount > 0) { label += ' (+' + multiMappedReadCount + ')'; } } else if (this.config.labelWithInParen === 'numSamplesWithThisJunction') { if (numSamplesWithThisJunction !== undefined) { label += ' (' + numSamplesWithThisJunction + ')'; } } else if (this.config.labelWithInParen === 'percentSamplesWithThisJunction') { if (feature.attributes.percent_samples_with_this_junction !== undefined) { label += ' (' + feature.attributes.percent_samples_with_this_junction.toFixed(0) + '%)'; } } else if (this.config.labelWithInParen === 'motif') { if (feature.attributes.motif !== undefined) { label += ` ${feature.attributes.motif}`; } } // data source: STAR splice junctions (eg. SJ.out.tab file converted to bed). // .bed "name" field used to store unique + multi-mapped read counts, so: // feature.score: unique spanning read counts // feature.name: unique + multi-mapped spanning read counts //example feature: { chr: "chr17", start: 39662344, end: 39662803, name: "59", row: 0, score: 38, strand: "+"} feature.isVisible = true; ctx.beginPath(); ctx.moveTo(junctionLeftPx, bezierBottomY); ctx.bezierCurveTo(bezierControlLeftPx, topY, bezierControlRightPx, topY, junctionRightPx, bezierBottomY); ctx.lineWidth = lineWidth; ctx.strokeStyle = color; ctx.stroke(); const drawArrowhead = (ctx, x, y, size) => { //TODO draw better arrow heads: https://stackoverflow.com/questions/21052972/curved-thick-arrows-on-canvas ctx.beginPath(); ctx.moveTo(x, y); ctx.lineTo(x - size / 2, y - size); ctx.lineTo(x + size / 2, y - size); ctx.lineTo(x, y); ctx.closePath(); ctx.fill(); }; if (feature.attributes.left_shape || feature.attributes.right_shape) { ctx.fillStyle = color; const arrowSize = ctx.lineWidth > 2 ? 10 : 7; if (feature.attributes.left_shape) { drawArrowhead(ctx, junctionLeftPx, bezierBottomY, arrowSize); } if (feature.attributes.right_shape) { drawArrowhead(ctx, junctionRightPx, bezierBottomY, arrowSize); } } ctx.fillText(label, junctionMiddlePx - ctx.measureText(label).width / 2, (7 * topY + cy) / 8); } // SNP constants const codingNonSynonSet = new Set(['nonsense', 'missense', 'stop-loss', 'frameshift', 'cds-indel']); const codingSynonSet = new Set(['coding-synon']); const spliceSiteSet = new Set(['splice-3', 'splice-5']); const untranslatedSet = new Set(['untranslated-5', 'untranslated-3']); /** * Renderer for a UCSC snp track * * @param snp * @param bpStart genomic location of the left edge of the current canvas * @param xScale scale in base-pairs per pixel * @param pixelHeight pixel height of the current canvas * @param ctx the canvas 2d context */ function renderSnp(snp, bpStart, xScale, pixelHeight, ctx) { var coord = calculateFeatureCoordinates(snp, bpStart, xScale), py = this.margin, h, colorArrLength = this.snpColors.length, colorPriority; h = this.displayMode === "squished" ? this.squishedRowHeight : this.expandedRowHeight; switch (this.colorBy) { case 'function': colorPriority = colorByFunc(snp.func); break; case 'class': colorPriority = colorByClass(snp['class']); } ctx.fillStyle = this.snpColors[colorPriority]; ctx.fillRect(coord.px, py, coord.pw, h); // Coloring functions, convert a value to a priority function colorByFunc(theFunc) { var priorities; var funcArray = theFunc.split(','); // possible func values priorities = funcArray.map(function (func) { if (codingNonSynonSet.has(func) || spliceSiteSet.has(func)) { return colorArrLength - 1; } else if (codingSynonSet.has(func)) { return colorArrLength - 2; } else if (untranslatedSet.has(func)) { return colorArrLength - 3; } else { // locusSet.has(func) || intronSet.has(func) return 0; } }); return priorities.reduce(function (a, b) { return Math.max(a, b); }); } function colorByClass(cls) { if (cls === 'deletion') { return colorArrLength - 1; } else if (cls === 'mnp') { return colorArrLength - 2; } else if (cls === 'microsatellite' || cls === 'named') { return colorArrLength - 3; } else { // cls === 'single' || cls === 'in-del' || cls === 'insertion' return 0; } } } function paintAxis(ctx, pixelWidth, pixelHeight) { var x1, x2, y1, y2, a, b, reference, shim, font = { 'font': 'normal 10px Arial', 'textAlign': 'right', 'strokeStyle': "black" }; if (undefined === this.dataRange || undefined === this.dataRange.max || undefined === this.dataRange.min) { return; } IGVGraphics.fillRect(ctx, 0, 0, pixelWidth, pixelHeight, { 'fillStyle': "rgb(255, 255, 255)" }); reference = 0.95 * pixelWidth; x1 = reference - 8; x2 = reference; //shim = 0.5 * 0.125; shim = .01; y1 = y2 = shim * pixelHeight; a = { x: x2, y: y1 }; // tick IGVGraphics.strokeLine(ctx, x1, y1, x2, y2, font); IGVGraphics.fillText(ctx, prettyPrint(this.dataRange.max), x1 + 4, y1 + 12, font); //shim = 0.25 * 0.125; y1 = y2 = (1.0 - shim) * pixelHeight; b = { x: x2, y: y1 }; // tick IGVGraphics.strokeLine(ctx, x1, y1, x2, y2, font); IGVGraphics.fillText(ctx, prettyPrint(this.dataRange.min), x1 + 4, y1 - 4, font); IGVGraphics.strokeLine(ctx, a.x, a.y, b.x, b.y, font); function prettyPrint(number) { // if number >= 100, show whole number // if >= 1 show 1 significant digits // if < 1 show 2 significant digits if (number === 0) { return "0"; } else if (Math.abs(number) >= 10) { return number.toFixed(); } else if (Math.abs(number) >= 1) { return number.toFixed(1); } else { return number.toFixed(2); } } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const DEFAULT_COLOR = "rgb(150,150,150)"; class WigTrack extends TrackBase { constructor(config, browser) { super(config, browser); } init(config) { super.init(config); this.type = "wig"; this.height = config.height || 50; this.featureType = 'numeric'; this.paintAxis = paintAxis; const format = config.format ? config.format.toLowerCase() : config.format; if ("bigwig" === format) { this.featureSource = new BWSource(config, this.browser.genome); } else if ("tdf" === format) { this.featureSource = new TDFSource(config, this.browser.genome); } else { this.featureSource = FeatureSource(config, this.browser.genome); } this.autoscale = config.autoscale || config.max === undefined; if (!this.autoscale) { this.dataRange = { min: config.min || 0, max: config.max }; } this.windowFunction = config.windowFunction || "mean"; this.graphType = config.graphType || "bar"; this.normalize = config.normalize; // boolean, for use with "TDF" files this.scaleFactor = config.scaleFactor; // optional scale factor, ignored if normalize === true; } async postInit() { const header = await this.getHeader(); if (header) this.setTrackProperties(header); } async getFeatures(chr, start, end, bpPerPixel) { const features = await this.featureSource.getFeatures({ chr, start, end, bpPerPixel, windowFunction: this.windowFunction }); if (this.normalize && this.featureSource.normalizationFactor) { const scaleFactor = this.featureSource.normalizationFactor; for (let f of features) { f.value *= scaleFactor; } } if (this.scaleFactor) { const scaleFactor = this.scaleFactor; for (let f of features) { f.value *= scaleFactor; } } return features; } menuItemList() { return MenuUtils.numericDataMenuItems(this.trackView); } async getHeader() { if (typeof this.featureSource.getHeader === "function") { this.header = await this.featureSource.getHeader(); } return this.header; } draw(options) { const features = options.features; const ctx = options.context; const bpPerPixel = options.bpPerPixel; const bpStart = options.bpStart; const pixelWidth = options.pixelWidth; const pixelHeight = options.pixelHeight; const bpEnd = bpStart + pixelWidth * bpPerPixel + 1; let lastPixelEnd = -1; let lastValue = -1; let lastNegValue = 1; const posColor = this.color || DEFAULT_COLOR; let baselineColor; if (typeof posColor === "string" && posColor.startsWith("rgb(")) { baselineColor = IGVColor.addAlpha(posColor, 0.1); } const yScale = yValue => { return (this.dataRange.max - yValue) / (this.dataRange.max - this.dataRange.min) * pixelHeight; }; if (features && features.length > 0) { if (this.dataRange.min === undefined) this.dataRange.min = 0; // Max can be less than min if config.min is set but max left to autoscale. If that's the case there is // nothing to paint. if (this.dataRange.max > this.dataRange.min) { const y0 = this.dataRange.min == 0 ? pixelHeight : yScale(0); for (let f of features) { if (f.end < bpStart) continue; if (f.start > bpEnd) break; const x = Math.floor((f.start - bpStart) / bpPerPixel); if (isNaN(x)) continue; let y = yScale(f.value); const rectEnd = Math.ceil((f.end - bpStart) / bpPerPixel); const width = Math.max(1, rectEnd - x); let c = f.value < 0 && this.altColor ? this.altColor : posColor; const color = typeof c === "function" ? c(f.value) : c; if (this.graphType === "points") { const pointSize = this.config.pointSize || 3; const px = x + width / 2; IGVGraphics.fillCircle(ctx, px, y, pointSize / 2, { "fillStyle": color, "strokeStyle": color }); } else { let height = y - y0; if (Math.abs(height) < 1) { height = height < 0 ? -1 : 1; } const pixelEnd = x + width; if (pixelEnd > lastPixelEnd || f.value >= 0 && f.value > lastValue || f.value < 0 && f.value < lastNegValue) { IGVGraphics.fillRect(ctx, x, y0, width, height, { fillStyle: color }); } lastValue = f.value; lastPixelEnd = pixelEnd; } } // If the track includes negative values draw a baseline if (this.dataRange.min < 0) { const basepx = this.dataRange.max / (this.dataRange.max - this.dataRange.min) * options.pixelHeight; IGVGraphics.strokeLine(ctx, 0, basepx, options.pixelWidth, basepx, { strokeStyle: baselineColor }); } } } // Draw guidelines if (this.config.hasOwnProperty('guideLines')) { for (let line of this.config.guideLines) { if (line.hasOwnProperty('color') && line.hasOwnProperty('y') && line.hasOwnProperty('dotted')) { let y = yScale(line.y); let props = { 'strokeStyle': line['color'], 'strokeWidth': 2 }; if (line['dotted']) IGVGraphics.dashedLine(options.context, 0, y, options.pixelWidth, y, 5, props);else IGVGraphics.strokeLine(options.context, 0, y, options.pixelWidth, y, props); } } } } popupData(clickState, features) { // We use the featureCache property rather than method to avoid async load. If the // feature is not already loaded this won't work, but the user wouldn't be mousing over it either. features = this.clickedFeatures(clickState, features); if (features && features.length > 0) { const genomicLocation = clickState.genomicLocation; const popupData = []; // Sort features based on distance from click features.sort(function (a, b) { const distA = Math.abs((a.start + a.end) / 2 - genomicLocation); const distB = Math.abs((b.start + b.end) / 2 - genomicLocation); return distA - distB; }); // Display closest 10 const displayFeatures = features.length > 10 ? features.slice(0, 10) : features; // Resort in ascending order displayFeatures.sort(function (a, b) { return a.start - b.start; }); for (let selectedFeature of displayFeatures) { if (selectedFeature) { if (popupData.length > 0) { popupData.push("
"); } let posString = selectedFeature.end - selectedFeature.start === 1 ? numberFormatter$1(selectedFeature.start + 1) : numberFormatter$1(selectedFeature.start + 1) + "-" + numberFormatter$1(selectedFeature.end); popupData.push({ name: "Position:", value: posString }); popupData.push({ name: "Value:     ", value: numberFormatter$1(selectedFeature.value) }); } } if (displayFeatures.length < features.length) { popupData.push("
..."); } return popupData; } else { return []; } } supportsWholeGenome() { if (typeof this.featureSource.supportsWholeGenome === 'function') { return this.featureSource.supportsWholeGenome(); } else { return false; } } /** * Called when the track is removed. Do any needed cleanup here */ dispose() { this.trackView = undefined; } } /** * * @param cs - object containing * 1) array of threshold values defining bin boundaries in ascending order * 2) array of colors for bins (length == thresholds.length + 1) * @constructor */ function BinnedColorScale(cs) { this.thresholds = cs.thresholds; this.colors = cs.colors; } BinnedColorScale.prototype.getColor = function (value) { for (let threshold of this.thresholds) { if (value < threshold) { return this.colors[this.thresholds.indexOf(threshold)]; } } return this.colors[this.colors.length - 1]; }; /** * * @param scale - object with the following properties * low * lowR * lowG * lowB * high * highR * highG * highB * * @constructor */ function GradientColorScale(scale) { this.scale = scale; this.lowColor = "rgb(" + scale.lowR + "," + scale.lowG + "," + scale.lowB + ")"; this.highColor = "rgb(" + scale.highR + "," + scale.highG + "," + scale.highB + ")"; this.diff = scale.high - scale.low; } GradientColorScale.prototype.getColor = function (value) { var scale = this.scale, r, g, b, frac; if (value <= scale.low) return this.lowColor;else if (value >= scale.high) return this.highColor; frac = (value - scale.low) / this.diff; r = Math.floor(scale.lowR + frac * (scale.highR - scale.lowR)); g = Math.floor(scale.lowG + frac * (scale.highG - scale.lowG)); b = Math.floor(scale.lowB + frac * (scale.highB - scale.lowB)); return "rgb(" + r + "," + g + "," + b + ")"; }; class ConstantColorScale { constructor(color) { this.color = color; } getColor() { return this.color; } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ class SegTrack extends TrackBase { constructor(config, browser) { super(config, browser); } init(config) { super.init(config); this.type = config.type || "seg"; this.isLog = config.isLog; this.displayMode = config.displayMode || "EXPANDED"; // EXPANDED | SQUISHED -- TODO perhaps set his based on sample count this.height = config.height || 300; this.maxHeight = config.maxHeight || 500; this.squishedRowHeight = config.sampleSquishHeight || config.squishedRowHeight || 2; this.expandedRowHeight = config.sampleExpandHeight || config.expandedRowHeight || 13; this.sampleHeight = this.squishedRowHeight; // Initial value, will get overwritten when rendered if (config.color) { this.color = config.color; } else { // Color scales for "seg" (copy number) tracks. this.posColorScale = config.posColorScale || new GradientColorScale({ low: 0.1, lowR: 255, lowG: 255, lowB: 255, high: 1.5, highR: 255, highG: 0, highB: 0 }); this.negColorScale = config.negColorScale || new GradientColorScale({ low: -1.5, lowR: 0, lowG: 0, lowB: 255, high: -0.1, highR: 255, highG: 255, highB: 255 }); // Color table for mutation (mut and maf) tracks this.colorTable = new ColorTable(config.colorTable || MUT_COLORS); } this.sampleKeys = []; this.sampleNames = new Map(); if (config.samples) { // Explicit setting, keys == names for (let s of config.samples) { this.sampleKeys.push(s); this.sampleNames.set(s, s); } this.explicitSamples = true; } // this.featureSource = config.sourceType === "bigquery" ? // new igv.BigQueryFeatureSource(this.config) : this.featureSource = FeatureSource(this.config, this.browser.genome); this.initialSort = config.sort; } async postInit() { if (typeof this.featureSource.getHeader === "function") { this.header = await this.featureSource.getHeader(); } // Set properties from track line if (this.header) { this.setTrackProperties(this.header); } } menuItemList() { const menuItems = []; const lut = { "SQUISHED": "Squish", "EXPANDED": "Expand", "FILL": "Fill" }; menuItems.push("
"); menuItems.push("Sample Height:"); const displayOptions = this.type === 'seg' ? ["SQUISHED", "EXPANDED", "FILL"] : ["SQUISHED", "EXPANDED"]; for (let displayMode of displayOptions) { menuItems.push({ object: createCheckbox$1(lut[displayMode], displayMode === this.displayMode), click: () => { this.displayMode = displayMode; this.config.displayMode = displayMode; this.trackView.checkContentHeight(); this.trackView.repaintViews(); } }); } return menuItems; } hasSamples() { return true; // SEG, MUT, and MAF tracks have samples by definition } getSamples() { return { names: this.sampleKeys.map(key => this.sampleNames.get(key)), height: this.sampleHeight, yOffset: 0 }; } async getFeatures(chr, start, end) { const features = await this.featureSource.getFeatures({ chr, start, end }); if (this.initialSort) { const sort = this.initialSort; this.sortSamples(sort.chr, sort.start, sort.end, sort.direction, features); this.initialSort = undefined; // Sample order is sorted, } return features; } draw({ context, renderSVG, pixelTop, pixelWidth, pixelHeight, features, bpPerPixel, bpStart }) { IGVGraphics.fillRect(context, 0, 0, pixelWidth, pixelHeight, { 'fillStyle': "rgb(255, 255, 255)" }); if (features && features.length > 0) { this.checkForLog(features); // New segments could conceivably add new samples this.updateSampleKeys(features); // Create a map for fast id -> row lookup const samples = {}; this.sampleKeys.forEach(function (id, index) { samples[id] = index; }); let border; switch (this.displayMode) { case "FILL": this.sampleHeight = pixelHeight / this.sampleKeys.length; border = 0; break; case "SQUISHED": this.sampleHeight = this.squishedRowHeight; border = 0; break; default: // EXPANDED this.sampleHeight = this.expandedRowHeight; border = 1; } const rowHeight = this.sampleHeight; // this.featureMap = new Map() for (let segment of features) { segment.pixelRect = undefined; // !important, reset this in case segment is not drawn } const pixelBottom = pixelTop + pixelHeight; const bpEnd = bpStart + pixelWidth * bpPerPixel + 1; const xScale = bpPerPixel; this.sampleYStart = undefined; for (let f of features) { if (f.end < bpStart) continue; if (f.start > bpEnd) break; const sampleKey = f.sampleKey || f.sample; f.row = samples[sampleKey]; const y = f.row * rowHeight + border; if (undefined === this.sampleYStart) { this.sampleYStart = y; } const bottom = y + rowHeight; if (bottom < pixelTop || y > pixelBottom) { continue; } const segmentStart = Math.max(f.start, bpStart); // const segmentStart = segment.start; let x = Math.round((segmentStart - bpStart) / xScale); const segmentEnd = Math.min(f.end, bpEnd); // const segmentEnd = segment.end; const x1 = Math.round((segmentEnd - bpStart) / xScale); let w = Math.max(1, x1 - x); let color; let h; if (this.color) { if (typeof this.color === "function") { color = this.color(f); } else { color = this.color; } } else if ("mut" === this.type) { color = this.colorTable.getColor(f.value.toLowerCase()); h = rowHeight - 2 * border; if (w < 3) { w = 3; x -= 1; } } else { // Assume seg track let value = f.value; if (!this.isLog) { value = IGVMath.log2(value / 2); } if (value < -0.1) { color = this.negColorScale.getColor(value); } else if (value > 0.1) { color = this.posColorScale.getColor(value); } else { color = "white"; } let sh = rowHeight; if (rowHeight < 0.25) { const f = 0.1 + 2 * Math.abs(value); sh = Math.min(1, f * rowHeight); } h = sh - 2 * border; } f.pixelRect = { x, y, w, h }; // Use for diagnostic rendering // context.fillStyle = randomRGB(180, 240) // context.fillStyle = randomGrey(200, 255) context.fillStyle = color; context.fillRect(x, y, w, h); } } } checkForLog(features) { if (this.isLog === undefined) { this.isLog = false; for (let feature of features) { if (feature.value < 0) { this.isLog = true; return; } } } } /** * Optional method to compute pixel height to accomodate the list of features. The implementation below * has side effects (modifiying the samples hash). This is unfortunate, but harmless. * * @param features * @returns {number} */ computePixelHeight(features) { if (!features) return 0; const sampleHeight = "SQUISHED" === this.displayMode ? this.squishedRowHeight : this.expandedRowHeight; this.updateSampleKeys(features); return this.sampleKeys.length * sampleHeight; } /** * Sort samples by the average value over the genomic range in the direction indicated (1 = ascending, -1 descending) */ async sortSamples(chr, start, end, direction, featureList) { if (!featureList) { featureList = await this.featureSource.getFeatures({ chr, start, end }); } if (!featureList) return; this.updateSampleKeys(featureList); const scores = {}; const d2 = direction === "ASC" ? 1 : -1; const sortSeg = () => { // Compute weighted average score for each sample const bpLength = end - start + 1; for (let segment of featureList) { if (segment.end < start) continue; if (segment.start > end) break; const min = Math.max(start, segment.start); const max = Math.min(end, segment.end); const f = (max - min) / bpLength; const sampleKey = segment.sampleKey || segment.sample; const s = scores[sampleKey] || 0; scores[sampleKey] = s + f * segment.value; } // Now sort sample names by score this.sampleKeys.sort(function (a, b) { let s1 = scores[a]; let s2 = scores[b]; if (!s1) s1 = d2 * Number.MAX_VALUE; if (!s2) s2 = d2 * Number.MAX_VALUE; if (s1 === s2) return 0;else if (s1 > s2) return d2;else return d2 * -1; }); }; const sortMut = () => { // Compute weighted average score for each sample for (let segment of featureList) { if (segment.end < start) continue; if (segment.start > end) break; const sampleKey = segment.sampleKey || segment.sample; if (!scores.hasOwnProperty(sampleKey) || segment.value.localeCompare(scores[sampleKey]) > 0) { scores[sampleKey] = segment.value; } } // Now sort sample names by score this.sampleKeys.sort(function (a, b) { let sa = scores[a] || ""; let sb = scores[b] || ""; return d2 * sa.localeCompare(sb); }); }; if ("mut" === this.type) { sortMut(); } else { sortSeg(); } this.trackView.repaintViews(); // self.trackView.$viewport.scrollTop(0); } clickedFeatures(clickState, features) { const allFeatures = super.clickedFeatures(clickState, features); return filterByRow(allFeatures, clickState.y); function filterByRow(features, y) { return features.filter(function (feature) { const rect = feature.pixelRect; return rect && y >= rect.y && y <= rect.y + rect.h; }); } } popupData(clickState, featureList) { featureList = this.clickedFeatures(clickState); const items = []; for (let feature of featureList) { if (items.length > 0) { items.push("
"); } if (typeof feature.popupData === 'function') { const data = feature.popupData(); Array.prototype.push.apply(items, data); } else { const filteredProperties = new Set(['chr', 'start', 'end', 'sample', 'value', 'row', 'color', 'sampleKey', 'uniqueSampleKey', 'sampleId', 'chromosome', 'uniquePatientKey']); // hack for whole genome features, which save the original feature as "_f" const f = feature._f || feature; items.push({ name: 'Sample', value: f.sample }); const valueString = this.type === 'seg' ? numberFormatter$1(f.value) : f.value; items.push({ name: 'Value', value: valueString }); const locus = `${f.chr}:${numberFormatter$1(f.start + 1)}-${numberFormatter$1(f.end)}`; items.push({ name: 'Locus', value: locus }); items.push('
'); for (let property of Object.keys(f)) { if (!filteredProperties.has(property) && isSimpleType(f[property])) { items.push({ name: property, value: f[property] }); } } } } return items; } contextMenuItemList(clickState) { const referenceFrame = clickState.viewport.referenceFrame; const genomicLocation = clickState.genomicLocation; // Define a region 5 "pixels" wide in genomic coordinates const sortDirection = this.config.sort ? this.config.sort.direction === "ASC" ? "DESC" : "ASC" : // Toggle from previous sort "DESC"; const bpWidth = referenceFrame.toBP(2.5); const sortHandler = sort => { const viewport = clickState.viewport; const features = viewport.getCachedFeatures(); this.sortSamples(sort.chr, sort.start, sort.end, sort.direction, features); }; const sortLabel = this.type === 'seg' ? 'Sort by value' : 'Sort by type'; return [{ label: sortLabel, click: e => { const sort = { direction: sortDirection, chr: clickState.viewport.referenceFrame.chr, start: genomicLocation - bpWidth, end: genomicLocation + bpWidth }; sortHandler(sort); this.config.sort = sort; } }]; } supportsWholeGenome() { return (this.config.indexed === false || !this.config.indexURL) && this.config.supportsWholeGenome !== false; } updateSampleKeys(featureList) { if (this.explicitSamples) return; for (let feature of featureList) { const sampleKey = feature.sampleKey || feature.sample; if (!this.sampleNames.has(sampleKey)) { this.sampleNames.set(sampleKey, feature.sample); this.sampleKeys.push(sampleKey); } } } } // Mut and MAF file default color table const MUT_COLORS = { "indel": "rgb(0,200,0)", "targeted region": "rgb(236,155,43)", "truncating": "rgb( 150,0,0)", "non-coding transcript": "rgb(0,0,150)", // Colors from https://www.nature.com/articles/nature11404 "synonymous": "rgb(109,165,95)", "silent": "rgb(109,135,80)", "missense_mutation": "rgb(72,130,187)", "missense": "rgb(72,130,187)", "splice site": "rgb(143,83,155)", "splice_region": "rgb(143,83,155)", "nonsense": "rgb(216, 57,81)", "nonsense_mutation": "rgb(216, 57,81)", "frame_shift_del": "rgb(226,135,65)", "frame_shift_ins": "rgb(226,135,65)", "in_frame_del": "rgb(247,235,94)", "in_frame_ins": "rgb(247,235,94)", "*other*": "rgb(159,91,50)" // // 3'Flank // 3'UTR // 5'Flank // 5'UTR // Frame_Shift_Del // Frame_Shift_Ins // IGR // In_Frame_Del // In_Frame_Ins // Intron // Missense_Mutation // Nonsense_Mutation // Nonstop_Mutation // RNA // Silent // Splice_Region // Splice_Site // Translation_Start_Site // Variant_Classification }; /* * The MIT License (MIT) * * Copyright (c) 2016-2017 The Regents of the University of California * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ class MergedTrack extends TrackBase { constructor(config, browser) { super(config, browser); } init(config) { if (!config.tracks) { throw Error("Error: no tracks defined for merged track" + config); } super.init(config); } async postInit() { this.tracks = []; for (let tconf of this.config.tracks) { if (!tconf.type) inferTrackType(tconf); tconf.isMergedTrack = true; const t = await this.browser.createTrack(tconf); if (t) { t.autoscale = false; // Scaling done from merged track this.tracks.push(t); } else { console.warn("Could not create track " + tconf); } } Object.defineProperty(this, "height", { get() { return this._height; }, set(h) { this._height = h; for (let t of this.tracks) { t.height = h; t.config.height = h; } } }); this.height = this.config.height || 100; } async getFeatures(chr, bpStart, bpEnd, bpPerPixel) { const promises = this.tracks.map(t => t.getFeatures(chr, bpStart, bpEnd, bpPerPixel)); return Promise.all(promises); } draw(options) { var i, len, mergedFeatures, trackOptions, dataRange; mergedFeatures = options.features; // Array of feature arrays, 1 for each track dataRange = autoscale(options.referenceFrame.chr, mergedFeatures); //IGVGraphics.fillRect(options.context, 0, options.pixelTop, options.pixelWidth, options.pixelHeight, {'fillStyle': "rgb(255, 255, 255)"}); for (i = 0, len = this.tracks.length; i < len; i++) { trackOptions = Object.assign({}, options); trackOptions.features = mergedFeatures[i]; this.tracks[i].dataRange = dataRange; this.tracks[i].draw(trackOptions); } } paintAxis(ctx, pixelWidth, pixelHeight) { var i, len, autoscale, track; autoscale = true; // Hardcoded for now for (i = 0, len = this.tracks.length; i < len; i++) { track = this.tracks[i]; if (typeof track.paintAxis === 'function') { track.paintAxis(ctx, pixelWidth, pixelHeight); if (autoscale) break; } } } popupData(clickState, features) { const featuresArray = features || clickState.viewport.getCachedFeatures(); if (featuresArray && featuresArray.length === this.tracks.length) { // Array of feature arrays, 1 for each track const popupData = []; for (let i = 0; i < this.tracks.length; i++) { if (i > 0) popupData.push("
"); popupData.push(`
${this.tracks[i].name}
`); const trackPopupData = this.tracks[i].popupData(clickState, featuresArray[i]); popupData.push(...trackPopupData); } return popupData; } } } function autoscale(chr, featureArrays) { var min = 0, max = -Number.MAX_VALUE; // if (chr === 'all') { // allValues = []; // featureArrays.forEach(function (features) { // features.forEach(function (f) { // if (!Number.isNaN(f.value)) { // allValues.push(f.value); // } // }); // }); // // min = Math.min(0, IGVMath.percentile(allValues, .1)); // max = IGVMath.percentile(allValues, 99.9); // // } // else { featureArrays.forEach(function (features, i) { features.forEach(function (f) { if (typeof f.value !== 'undefined' && !Number.isNaN(f.value)) { min = Math.min(min, f.value); max = Math.max(max, f.value); } }); }); // } return { min: min, max: max }; } /* * The MIT License (MIT) * * Copyright (c) 2016 University of California San Diego * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ class PairedAlignment { constructor(firstAlignment) { this.paired = true; this.firstAlignment = firstAlignment; this.chr = firstAlignment.chr; this.readName = firstAlignment.readName; if (firstAlignment.start < firstAlignment.mate.position) { this.start = firstAlignment.start; this.scStart = firstAlignment.scStart; this.connectingStart = firstAlignment.start + firstAlignment.lengthOnRef; this.connectingEnd = firstAlignment.mate.position; } else { this.start = firstAlignment.mate.position; this.scStart = this.start; this.connectingStart = firstAlignment.mate.position; this.connectingEnd = firstAlignment.start; } this.end = Math.max(firstAlignment.mate.position, firstAlignment.start + firstAlignment.lengthOnRef); // Approximate this.lengthOnRef = this.end - this.start; let scEnd = Math.max(this.end, firstAlignment.scStart + firstAlignment.scLengthOnRef); this.scLengthOnRef = scEnd - this.scStart; } setSecondAlignment(secondAlignment) { // TODO -- check the chrs are equal, error otherwise this.secondAlignment = secondAlignment; const firstAlignment = this.firstAlignment; if (secondAlignment.start > firstAlignment.start) { this.connectingEnd = secondAlignment.start; } else { this.connectingStart = secondAlignment.start + secondAlignment.lengthOnRef; } this.start = Math.min(firstAlignment.start, secondAlignment.start); this.end = Math.max(firstAlignment.start + firstAlignment.lengthOnRef, secondAlignment.start + secondAlignment.lengthOnRef); this.lengthOnRef = this.end - this.start; this.scStart = Math.min(firstAlignment.scStart, secondAlignment.scStart); const scEnd = Math.max(firstAlignment.scStart + firstAlignment.scLengthOnRef, secondAlignment.scStart + secondAlignment.scLengthOnRef); this.scLengthOnRef = scEnd - this.scStart; } containsLocation(genomicLocation, showSoftClips) { const s = showSoftClips ? this.scStart : this.start; const l = showSoftClips ? this.scLengthOnRef : this.lengthOnRef; return genomicLocation >= s && genomicLocation <= s + l; } alignmentContaining(genomicLocation, showSoftClips) { if (this.firstAlignment.containsLocation(genomicLocation, showSoftClips)) { return this.firstAlignment; } else if (this.secondAlignment && this.secondAlignment.containsLocation(genomicLocation, showSoftClips)) { return this.secondAlignment; } else { return undefined; } } popupData(genomicLocation) { let nameValues = this.firstAlignment.popupData(genomicLocation); if (this.secondAlignment) { nameValues.push("-------------------------------"); nameValues = nameValues.concat(this.secondAlignment.popupData(genomicLocation)); } return nameValues; } isPaired() { return true; // By definition } firstOfPairStrand() { if (this.firstAlignment.isFirstOfPair()) { return this.firstAlignment.strand; } else if (this.secondAlignment && this.secondAlignment.isFirstOfPair()) { return this.secondAlignment.strand; } else { return this.firstAlignment.mate.strand; // Assumption is mate is first-of-pair } } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const isString$3 = isString$6; const hashCode = hashCode$1; class BamAlignmentRow { constructor() { this.alignments = []; this.score = undefined; } findAlignment(genomicLocation) { const alignmentContains = (a, genomicLocation) => { return genomicLocation >= a.start && genomicLocation < a.start + a.lengthOnRef; }; // find single alignment that overlaps sort location let centerAlignment; for (let i = 0; i < this.alignments.length; i++) { const a = this.alignments[i]; if (genomicLocation >= a.start && genomicLocation < a.start + a.lengthOnRef) { if (a.paired) { if (a.firstAlignment && alignmentContains(a.firstAlignment, genomicLocation)) { centerAlignment = a.firstAlignment; } else if (a.secondAlignment && alignmentContains(a.secondAlignment, genomicLocation)) { centerAlignment = a.secondAlignment; } } else { centerAlignment = a; } break; } } return centerAlignment; } updateScore(options, alignmentContainer) { this.score = this.calculateScore(options, alignmentContainer); } calculateScore({ position, option, direction, tag }, alignmentContainer) { if (!option) option = "BASE"; const alignment = this.findAlignment(position); if (undefined === alignment) { return Number.MAX_VALUE * (direction ? 1 : -1); } let mate; switch (option) { case "NUCLEOTIDE": case "BASE": { return calculateBaseScore(alignment, alignmentContainer, position); } case "STRAND": return alignment.strand ? 1 : -1; case "START": return alignment.start; case "TAG": { const tagValue = alignment.tags()[tag]; if (tagValue !== undefined) { return isString$3(tagValue) ? hashCode(tagValue) : tagValue; } else { return Number.MAX_VALUE; } } case "READ_NAME": return hashCode(alignment.readName); case "INSERT_SIZE": return -Math.abs(alignment.fragmentLength); case "GAP_SIZE": return -alignment.gapSizeAt(position); case "MATE_CHR": mate = alignment.mate; if (!mate) { return Number.MAX_VALUE; } else { if (mate.chr === alignment.chr) { return Number.MAX_VALUE - 1; } else { return hashCode(mate.chr); } } case "MQ": return alignment.mq === undefined ? Number.MAX_VALUE : -alignment.mq; default: return Number.MAX_VALUE; } function calculateBaseScore(alignment, alignmentContainer, genomicLocation) { let reference; const idx = Math.floor(genomicLocation) - alignmentContainer.start; if (idx < alignmentContainer.sequence.length) { reference = alignmentContainer.sequence.charAt(idx); } if (!reference) { return 0; } const base = alignment.readBaseAt(genomicLocation); const quality = alignment.readBaseQualityAt(genomicLocation); const coverageMap = alignmentContainer.coverageMap; const coverageMapIndex = Math.floor(genomicLocation - coverageMap.bpStart); const coverage = coverageMap.coverage[coverageMapIndex]; // Insertions. These are additive with base scores as they occur between bases, so you can have a // base mismatch AND an insertion let baseScore = 0; if (alignment.insertions) { for (let ins of alignment.insertions) { if (ins.start === genomicLocation) { baseScore = -coverage.ins; } } } if (!base) { // Either deletion or skipped (splice junction) const delCount = coverage.del; if (delCount > 0) { baseScore -= delCount; } else if (baseScore === 0) { // Don't modify insertion score, if any baseScore = 1; } } else { reference = reference.toUpperCase(); if ('N' === base && baseScore === 0) { baseScore = 2; } else if ((reference === base || '=' === base) && baseScore === 0) { baseScore = 4 - quality / 1000; } else if ("X" === base || reference !== base) { const count = coverage["pos" + base] + coverage["neg" + base]; baseScore -= count + quality / 1000; } } return baseScore; } } } function canBePaired(alignment) { return alignment.isPaired() && alignment.mate && alignment.isMateMapped() && alignment.chr === alignment.mate.chr && (alignment.isFirstOfPair() || alignment.isSecondOfPair()) && !(alignment.isSecondary() || alignment.isSupplementary()); } function pairAlignments(rows) { const pairCache = {}; const result = []; for (let row of rows) { for (let alignment of row.alignments) { if (canBePaired(alignment)) { let pairedAlignment = pairCache[alignment.readName]; if (pairedAlignment) { pairedAlignment.setSecondAlignment(alignment); pairCache[alignment.readName] = undefined; // Don't need to track this anymore. } else { pairedAlignment = new PairedAlignment(alignment); pairCache[alignment.readName] = pairedAlignment; result.push(pairedAlignment); } } else { result.push(alignment); } } } return result; } function unpairAlignments(rows) { const result = []; for (let row of rows) { for (let alignment of row.alignments) { if (alignment instanceof PairedAlignment) { if (alignment.firstAlignment) result.push(alignment.firstAlignment); // shouldn't need the null test if (alignment.secondAlignment) result.push(alignment.secondAlignment); } else { result.push(alignment); } } } return result; } function packAlignmentRows(alignments, start, end, showSoftClips) { if (!alignments) { return undefined; } else if (alignments.length === 0) { return []; } else { alignments.sort(function (a, b) { return showSoftClips ? a.scStart - b.scStart : a.start - b.start; }); // bucketStart = Math.max(start, alignments[0].start); const firstAlignment = alignments[0]; let bucketStart = Math.max(start, showSoftClips ? firstAlignment.scStart : firstAlignment.start); let nextStart = bucketStart; const bucketList = []; for (let alignment of alignments) { //var buckListIndex = Math.max(0, alignment.start - bucketStart); const s = showSoftClips ? alignment.scStart : alignment.start; const buckListIndex = Math.max(0, s - bucketStart); if (bucketList[buckListIndex] === undefined) { bucketList[buckListIndex] = []; } bucketList[buckListIndex].push(alignment); } let allocatedCount = 0; let lastAllocatedCount = 0; const packedAlignmentRows = []; const alignmentSpace = 2; try { while (allocatedCount < alignments.length) { const alignmentRow = new BamAlignmentRow(); while (nextStart <= end) { let bucket = undefined; let index; while (!bucket && nextStart <= end) { index = nextStart - bucketStart; if (bucketList[index] === undefined) { ++nextStart; // No alignments at this index } else { bucket = bucketList[index]; } } // while (bucket) if (!bucket) { break; } const alignment = bucket.pop(); if (0 === bucket.length) { bucketList[index] = undefined; } alignmentRow.alignments.push(alignment); nextStart = showSoftClips ? alignment.scStart + alignment.scLengthOnRef + alignmentSpace : alignment.start + alignment.lengthOnRef + alignmentSpace; ++allocatedCount; } // while (nextStart) if (alignmentRow.alignments.length > 0) { packedAlignmentRows.push(alignmentRow); } nextStart = bucketStart; if (allocatedCount === lastAllocatedCount) break; // Protect from infinite loops lastAllocatedCount = allocatedCount; } // while (allocatedCount) } catch (e) { console.error(e); throw e; } return packedAlignmentRows; } } /* * The MIT License (MIT) * * Copyright (c) 2016 University of California San Diego * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ class AlignmentContainer { constructor(chr, start, end, samplingWindowSize, samplingDepth, pairsSupported, alleleFreqThreshold) { this.chr = chr; this.start = Math.floor(start); this.end = Math.ceil(end); this.length = end - start; this.alleleFreqThreshold = alleleFreqThreshold === undefined ? 0.2 : alleleFreqThreshold; this.coverageMap = new CoverageMap(chr, start, end, this.alleleFreqThreshold); this.alignments = []; this.downsampledIntervals = []; this.samplingWindowSize = samplingWindowSize === undefined ? 100 : samplingWindowSize; this.samplingDepth = samplingDepth === undefined ? 1000 : samplingDepth; this.pairsSupported = pairsSupported === undefined ? true : pairsSupported; this.paired = false; // false until proven otherwise this.pairsCache = {}; // working cache of paired alignments by read name this.downsampledReads = new Set(); this.currentBucket = new DownsampleBucket(this.start, this.start + this.samplingWindowSize, this); this.filter = function filter(alignment) { // TODO -- pass this in return alignment.isMapped() && !alignment.isFailsVendorQualityCheck(); }; this.pairedEndStats = new PairedEndStats(); } push(alignment) { if (this.filter(alignment) === false) return; if (alignment.isPaired()) { this.pairedEndStats.push(alignment); } this.coverageMap.incCounts(alignment); // Count coverage before any downsampling if (this.pairsSupported && this.downsampledReads.has(alignment.readName)) { return; // Mate already downsampled -- pairs are treated as a single alignment for downsampling } if (alignment.start >= this.currentBucket.end) { this.finishBucket(); this.currentBucket = new DownsampleBucket(alignment.start, alignment.start + this.samplingWindowSize, this); } this.currentBucket.addAlignment(alignment); } forEach(callback) { this.alignments.forEach(callback); } finish() { if (this.currentBucket !== undefined) { this.finishBucket(); } this.alignments.sort(function (a, b) { return a.start - b.start; }); this.pairsCache = undefined; this.downsampledReads = undefined; this.pairedEndStats.compute(); } contains(chr, start, end) { return this.chr === chr && this.start <= start && this.end >= end; } hasDownsampledIntervals() { return this.downsampledIntervals && this.downsampledIntervals.length > 0; } finishBucket() { this.alignments = this.alignments.concat(this.currentBucket.alignments); if (this.currentBucket.downsampledCount > 0) { this.downsampledIntervals.push(new DownsampledInterval(this.currentBucket.start, this.currentBucket.end, this.currentBucket.downsampledCount)); } this.paired = this.paired || this.currentBucket.paired; } setViewAsPairs(bool) { let alignments; if (bool) { alignments = pairAlignments(this.packedAlignmentRows); } else { alignments = unpairAlignments(this.packedAlignmentRows); } this.packedAlignmentRows = packAlignmentRows(alignments, this.start, this.end); } setShowSoftClips(bool) { const alignments = this.allAlignments(); this.packedAlignmentRows = packAlignmentRows(alignments, this.start, this.end, bool); } allAlignments() { const alignments = []; for (let row of this.packedAlignmentRows) { for (let alignment of row.alignments) { alignments.push(alignment); } } return alignments; } getMax(start, end) { return this.coverageMap.getMax(start, end); } } class DownsampleBucket { constructor(start, end, alignmentContainer) { this.start = start; this.end = end; this.alignments = []; this.downsampledCount = 0; this.samplingDepth = alignmentContainer.samplingDepth; this.pairsSupported = alignmentContainer.pairsSupported; this.downsampledReads = alignmentContainer.downsampledReads; this.pairsCache = alignmentContainer.pairsCache; } addAlignment(alignment) { var idx, replacedAlignment, pairedAlignment; if (this.pairsSupported && canBePaired(alignment)) { pairedAlignment = this.pairsCache[alignment.readName]; if (pairedAlignment) { // Not subject to downsampling, just update the existing alignment pairedAlignment.setSecondAlignment(alignment); this.pairsCache[alignment.readName] = undefined; // Don't need to track this anymore. NOTE: Don't "delete", causes runtime performance issues return; } } if (this.alignments.length < this.samplingDepth) { if (this.pairsSupported && canBePaired(alignment)) { // First alignment in a pair pairedAlignment = new PairedAlignment(alignment); this.paired = true; this.pairsCache[alignment.readName] = pairedAlignment; this.alignments.push(pairedAlignment); } else { this.alignments.push(alignment); } } else { idx = Math.floor(Math.random() * (this.samplingDepth + this.downsampledCount - 1)); if (idx < this.samplingDepth) { // Keep the new item // idx = Math.floor(Math.random() * (this.alignments.length - 1)); replacedAlignment = this.alignments[idx]; // To be replaced if (this.pairsSupported && canBePaired(alignment)) { if (this.pairsCache[replacedAlignment.readName] !== undefined) { this.pairsCache[replacedAlignment.readName] = undefined; } pairedAlignment = new PairedAlignment(alignment); this.paired = true; this.pairsCache[alignment.readName] = pairedAlignment; this.alignments[idx] = pairedAlignment; } else { this.alignments[idx] = alignment; } this.downsampledReads.add(replacedAlignment.readName); } else { this.downsampledReads.add(alignment.readName); } this.downsampledCount++; } } } class CoverageMap { constructor(chr, start, end, alleleFreqThreshold) { this.chr = chr; this.bpStart = start; this.length = end - start; this.coverage = new Array(this.length); this.maximum = 0; this.threshold = alleleFreqThreshold; this.qualityWeight = true; } /** * Return the maximum coverage value between start and end. This is used for autoscaling. * @param start * @param end */ getMax(start, end) { let max = 0; const len = this.coverage.length; for (let i = 0; i < len; i++) { const pos = this.bpStart + i; if (pos > end) break; const cov = this.coverage[i]; if (pos >= start && cov) { max = Math.max(max, cov.total); } } return max; } incCounts(alignment) { var self = this; if (alignment.blocks === undefined) { incBlockCount(alignment); } else { alignment.blocks.forEach(function (block) { incBlockCount(block); }); } if (alignment.gaps) { for (let del of alignment.gaps) { if (del.type === 'D') { const offset = del.start - self.bpStart; for (let i = offset; i < offset + del.len; i++) { if (i < 0) continue; if (!this.coverage[i]) { this.coverage[i] = new Coverage(self.threshold); } this.coverage[i].del++; } } } } if (alignment.insertions) { for (let del of alignment.insertions) { const i = del.start - this.bpStart; if (i < 0) continue; if (!this.coverage[i]) { this.coverage[i] = new Coverage(self.threshold); } this.coverage[i].ins++; } } function incBlockCount(block) { if ('S' === block.type) return; const seq = alignment.seq; const qual = alignment.qual; const seqOffset = block.seqOffset; for (let i = block.start - self.bpStart, j = 0; j < block.len; i++, j++) { if (!self.coverage[i]) { self.coverage[i] = new Coverage(self.threshold); } const base = seq == undefined ? "N" : seq.charAt(seqOffset + j); const key = alignment.strand ? "pos" + base : "neg" + base; const q = qual && seqOffset + j < qual.length ? qual[seqOffset + j] : 30; self.coverage[i][key] += 1; self.coverage[i]["qual" + base] += q; self.coverage[i].total += 1; self.coverage[i].qual += q; self.maximum = Math.max(self.coverage[i].total, self.maximum); } } } } class Coverage { constructor(alleleThreshold) { this.qualityWeight = true; this.posA = 0; this.negA = 0; this.posT = 0; this.negT = 0; this.posC = 0; this.negC = 0; this.posG = 0; this.negG = 0; this.posN = 0; this.negN = 0; this.pos = 0; this.neg = 0; this.qualA = 0; this.qualT = 0; this.qualC = 0; this.qualG = 0; this.qualN = 0; this.qual = 0; this.total = 0; this.del = 0; this.ins = 0; this.threshold = alleleThreshold; } isMismatch(refBase) { const threshold = this.threshold * (this.qualityWeight && this.qual ? this.qual : this.total); let mismatchQualitySum = 0; for (let base of ["A", "T", "C", "G"]) { if (base !== refBase) { mismatchQualitySum += this.qualityWeight && this.qual ? this["qual" + base] : this["pos" + base] + this["neg" + base]; } } return mismatchQualitySum >= threshold; } } class DownsampledInterval { constructor(start, end, counts) { this.start = start; this.end = end; this.counts = counts; } popupData(genomicLocation) { return [{ name: "start", value: this.start + 1 }, { name: "end", value: this.end }, { name: "# downsampled:", value: this.counts }]; } } class PairedEndStats { constructor(lowerPercentile, upperPercentile) { this.totalCount = 0; this.frCount = 0; this.rfCount = 0; this.ffCount = 0; this.sumF = 0; this.sumF2 = 0; //this.lp = lowerPercentile === undefined ? 0.005 : lowerPercentile; //this.up = upperPercentile === undefined ? 0.995 : upperPercentile; //this.digest = new Digest(); } push(alignment) { if (alignment.isProperPair()) { var fragmentLength = Math.abs(alignment.fragmentLength); //this.digest.push(fragmentLength); this.sumF += fragmentLength; this.sumF2 += fragmentLength * fragmentLength; var po = alignment.pairOrientation; if (typeof po === "string" && po.length === 4) { var tmp = '' + po.charAt(0) + po.charAt(2); switch (tmp) { case 'FF': case 'RR': this.ffCount++; break; case "FR": this.frCount++; break; case "RF": this.rfCount++; } } this.totalCount++; } } compute() { if (this.totalCount > 100) { if (this.ffCount / this.totalCount > 0.9) this.orienation = "ff";else if (this.frCount / this.totalCount > 0.9) this.orienation = "fr";else if (this.rfCount / this.totalCount > 0.9) this.orienation = "rf"; var fMean = this.sumF / this.totalCount; var stdDev = Math.sqrt((this.totalCount * this.sumF2 - this.sumF * this.sumF) / (this.totalCount * this.totalCount)); this.lowerFragmentLength = fMean - 3 * stdDev; this.upperFragmentLength = fMean + 3 * stdDev; //this.lowerFragmentLength = this.digest.percentile(this.lp); //this.upperFragmentLength = this.digest.percentile(this.up); //this.digest = undefined; } } } /* * The MIT License (MIT) * * Copyright (c) 2014 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ const READ_PAIRED_FLAG = 0x1; const PROPER_PAIR_FLAG = 0x2; const READ_UNMAPPED_FLAG = 0x4; const MATE_UNMAPPED_FLAG = 0x8; const READ_STRAND_FLAG$2 = 0x10; const MATE_STRAND_FLAG$2 = 0x20; const FIRST_OF_PAIR_FLAG = 0x40; const SECOND_OF_PAIR_FLAG = 0x80; const SECONDARY_ALIGNMNET_FLAG = 0x100; const READ_FAILS_VENDOR_QUALITY_CHECK_FLAG = 0x200; const DUPLICATE_READ_FLAG = 0x400; const SUPPLEMENTARY_ALIGNMENT_FLAG = 0x800; const ELEMENT_SIZE = { c: 1, C: 1, s: 2, S: 2, i: 4, I: 4, f: 4 }; /** * readName * chr * cigar * lengthOnRef * start * seq * qual * mq * strand * blocks */ class BamAlignment { constructor() { this.hidden = false; } isMapped() { return (this.flags & READ_UNMAPPED_FLAG) === 0; } isPaired() { return (this.flags & READ_PAIRED_FLAG) !== 0; } isProperPair() { return (this.flags & PROPER_PAIR_FLAG) !== 0; } isFirstOfPair() { return (this.flags & FIRST_OF_PAIR_FLAG) !== 0; } isSecondOfPair() { return (this.flags & SECOND_OF_PAIR_FLAG) !== 0; } isSecondary() { return (this.flags & SECONDARY_ALIGNMNET_FLAG) !== 0; } isSupplementary() { return (this.flags & SUPPLEMENTARY_ALIGNMENT_FLAG) !== 0; } isFailsVendorQualityCheck() { return (this.flags & READ_FAILS_VENDOR_QUALITY_CHECK_FLAG) !== 0; } isDuplicate() { return (this.flags & DUPLICATE_READ_FLAG) !== 0; } isMateMapped() { return (this.flags & MATE_UNMAPPED_FLAG) === 0; } isNegativeStrand() { return (this.flags & READ_STRAND_FLAG$2) !== 0; } isMateNegativeStrand() { return (this.flags & MATE_STRAND_FLAG$2) !== 0; } tags() { if (!this.tagDict) { if (this.tagBA) { this.tagDict = decodeTags(this.tagBA); this.tagBA = undefined; } else { this.tagDict = {}; // Mark so we don't try again. The record has no tags } } return this.tagDict; function decodeTags(ba) { let p = 0; const len = ba.length; const tags = {}; while (p < len) { const tag = String.fromCharCode(ba[p]) + String.fromCharCode(ba[p + 1]); p += 2; const type = String.fromCharCode(ba[p++]); let value; if (type === 'A') { value = String.fromCharCode(ba[p]); p++; } else if (type === 'i' || type === 'I') { value = readInt$1(ba, p); p += 4; } else if (type === 'c') { value = readInt8(ba, p); p++; } else if (type === 'C') { value = readUInt8(ba, p); p++; } else if (type === 's' || type === 'S') { value = readShort(ba, p); p += 2; } else if (type === 'f') { value = readFloat(ba, p); p += 4; } else if (type === 'Z') { value = ''; for (;;) { var cc = ba[p++]; if (cc === 0) { break; } else { value += String.fromCharCode(cc); } } } else if (type === 'B') { const elementType = String.fromCharCode(ba[p++]); let elementSize = ELEMENT_SIZE[elementType]; if (elementSize === undefined) { tags[tag] = `Error: unknown element type '${elementType}'`; break; } const numElements = readInt$1(ba, p); p += 4 + numElements * elementSize; value = '[not shown]'; } else { //'Unknown type ' + type; value = 'Error unknown type: ' + type; tags[tag] = value; break; } tags[tag] = value; } return tags; } } /** * Does alignment (or alignment extended by soft clips) contain the genomic location? * * @param genomicLocation * @param showSoftClips * @returns {boolean|boolean} */ containsLocation(genomicLocation, showSoftClips) { const s = showSoftClips ? this.scStart : this.start; const l = showSoftClips ? this.scLengthOnRef : this.lengthOnRef; return genomicLocation >= s && genomicLocation <= s + l; } popupData(genomicLocation) { // if the user clicks on a base next to an insertion, show just the // inserted bases in a popup (like in desktop IGV). const nameValues = []; // Consert genomic location to int genomicLocation = Math.floor(genomicLocation); if (this.insertions) { const seq = this.seq; for (let insertion of this.insertions) { var ins_start = insertion.start; if (genomicLocation === ins_start || genomicLocation === ins_start - 1) { nameValues.push({ name: 'Insertion', value: seq.substr(insertion.seqOffset, insertion.len) }); nameValues.push({ name: 'Location', value: ins_start }); return nameValues; } } } nameValues.push({ name: 'Read Name', value: this.readName }); // Sample // Read group nameValues.push("
"); // Add 1 to genomic location to map from 0-based computer units to user-based units nameValues.push({ name: 'Alignment Start', value: numberFormatter$1(1 + this.start), borderTop: true }); nameValues.push({ name: 'Read Strand', value: true === this.strand ? '(+)' : '(-)', borderTop: true }); nameValues.push({ name: 'Cigar', value: this.cigar }); nameValues.push({ name: 'Mapped', value: yesNo(this.isMapped()) }); nameValues.push({ name: 'Mapping Quality', value: this.mq }); nameValues.push({ name: 'Secondary', value: yesNo(this.isSecondary()) }); nameValues.push({ name: 'Supplementary', value: yesNo(this.isSupplementary()) }); nameValues.push({ name: 'Duplicate', value: yesNo(this.isDuplicate()) }); nameValues.push({ name: 'Failed QC', value: yesNo(this.isFailsVendorQualityCheck()) }); if (this.isPaired()) { nameValues.push("
"); nameValues.push({ name: 'First in Pair', value: !this.isSecondOfPair(), borderTop: true }); nameValues.push({ name: 'Mate is Mapped', value: yesNo(this.isMateMapped()) }); if (this.pairOrientation) { nameValues.push({ name: 'Pair Orientation', value: this.pairOrientation }); } if (this.isMateMapped()) { nameValues.push({ name: 'Mate Chromosome', value: this.mate.chr }); nameValues.push({ name: 'Mate Start', value: this.mate.position + 1 }); nameValues.push({ name: 'Mate Strand', value: true === this.mate.strand ? '(+)' : '(-)' }); nameValues.push({ name: 'Insert Size', value: this.fragmentLength }); // Mate Start // Mate Strand // Insert Size } // First in Pair // Pair Orientation } nameValues.push("
"); const tagDict = this.tags(); let isFirst = true; for (let key in tagDict) { if (tagDict.hasOwnProperty(key)) { if (isFirst) { nameValues.push({ name: key, value: tagDict[key], borderTop: true }); isFirst = false; } else { nameValues.push({ name: key, value: tagDict[key] }); } } } nameValues.push("
"); nameValues.push({ name: 'Genomic Location: ', value: numberFormatter$1(1 + genomicLocation) }); nameValues.push({ name: 'Read Base:', value: this.readBaseAt(genomicLocation) }); nameValues.push({ name: 'Base Quality:', value: this.readBaseQualityAt(genomicLocation) }); return nameValues; function yesNo(bool) { return bool ? 'Yes' : 'No'; } } readBaseAt(genomicLocation) { const block = blockAtGenomicLocation(this.blocks, genomicLocation); if (block) { if ("*" === this.seq) { return "*"; } else { const idx = block.seqIndexAt(genomicLocation); // if (idx >= 0 && idx < this.seq.length) { return this.seq[idx]; // } } } else { return undefined; } } readBaseQualityAt(genomicLocation) { const block = blockAtGenomicLocation(this.blocks, genomicLocation); if (block) { if ("*" === this.qual) { return 30; } else { const idx = block.seqIndexAt(genomicLocation); if (idx >= 0 && this.qual && idx < this.qual.length) { return this.qual[idx]; } else { return 30; } } } else { return undefined; } } gapSizeAt(genomicLocation) { if (this.gaps) { for (let gap of this.gaps) { if (genomicLocation >= gap.start && genomicLocation < gap.start + gap.len) { return gap.len; } } } return 0; } } function blockAtGenomicLocation(blocks, genomicLocation) { for (let i = 0; i < blocks.length; i++) { const block = blocks[i]; if (genomicLocation >= block.start && genomicLocation < block.start + block.len) { return block; } } return undefined; } function readInt$1(ba, offset) { return ba[offset + 3] << 24 | ba[offset + 2] << 16 | ba[offset + 1] << 8 | ba[offset]; } function readShort(ba, offset) { return ba[offset + 1] << 8 | ba[offset]; } function readFloat(ba, offset) { const dataView = new DataView(ba.buffer); return dataView.getFloat32(offset); } function readInt8(ba, offset) { const dataView = new DataView(ba.buffer); return dataView.getInt8(offset); } function readUInt8(ba, offset) { const dataView = new DataView(ba.buffer); return dataView.getUint8(offset); } /* * The MIT License (MIT) * * Copyright (c) 2016-2017 The Regents of the University of California * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ /** * Created by jrobinso on 4/5/18. */ class AlignmentBlock { constructor(b) { if (b) { Object.assign(this, b); } } seqIndexAt(genomicLocation) { return Math.floor(genomicLocation) - this.start + this.seqOffset; } } class BamFilter { constructor(options) { if (!options) options = {}; this.vendorFailed = options.vendorFailed === undefined ? true : options.vendorFailed; this.duplicates = options.duplicates === undefined ? true : options.duplicates; this.secondary = options.secondary || false; this.supplementary = options.supplementary || false; this.mqThreshold = options.mqThreshold === undefined ? 0 : options.mqThreshold; if (options.readgroups) { this.readgroups = new Set(options.readgroups); } } pass(alignment) { if (this.vendorFailed && alignment.isFailsVendorQualityCheck()) return false; if (this.duplicates && alignment.isDuplicate()) return false; if (this.secondary && alignment.isSecondary()) return false; if (this.supplementary && alignment.isSupplementary()) return false; if (alignment.mq < this.mqThreshold) return false; if (this.readgroups) { var rg = alignment.tags()['RG']; return this.readgroups.has(rg); } return true; } } /** * This code is based on the Biodalliance BAM reader by Thomas Down, 2011 * * https://github.com/dasmoth/dalliance/blob/master/js/bam.js */ const SEQ_DECODER = ['=', 'A', 'C', 'x', 'G', 'x', 'x', 'x', 'T', 'x', 'x', 'x', 'x', 'x', 'x', 'N']; const CIGAR_DECODER = ['M', 'I', 'D', 'N', 'S', 'H', 'P', '=', 'X', '?', '?', '?', '?', '?', '?', '?']; const READ_STRAND_FLAG$1 = 0x10; const MATE_STRAND_FLAG$1 = 0x20; const BAM1_MAGIC_BYTES = new Uint8Array([0x42, 0x41, 0x4d, 0x01]); // BAM\1 const BAM1_MAGIC_NUMBER = readInt(BAM1_MAGIC_BYTES, 0); const DEFAULT_ALLELE_FREQ_THRESHOLD = 0.2; const DEFAULT_SAMPLING_WINDOW_SIZE = 100; const DEFAULT_SAMPLING_DEPTH = 500; const MAXIMUM_SAMPLING_DEPTH = 10000; const BamUtils = { readHeader: function (url, options, genome) { return igvxhr.loadArrayBuffer(url, options).then(function (compressedBuffer) { var header, unc, uncba; unc = unbgzf(compressedBuffer); uncba = unc; header = BamUtils.decodeBamHeader(uncba, genome); return header; }); }, /** * * @param ba bytes to decode as a UInt8Array * @param genome optional igv genome object * @returns {{ magicNumer: number, size: number, chrNames: Array, chrToIndex: ({}|*), chrAliasTable: ({}|*) }} */ decodeBamHeader: function (ba, genome) { var magic, samHeaderLen, samHeader, chrToIndex, chrNames, chrAliasTable, alias; magic = readInt(ba, 0); if (magic !== BAM1_MAGIC_NUMBER) { throw new Error('BAM header errror: bad magic number. This could be caused by either a corrupt or missing file.'); } samHeaderLen = readInt(ba, 4); samHeader = ''; for (var i = 0; i < samHeaderLen; ++i) { samHeader += String.fromCharCode(ba[i + 8]); } var nRef = readInt(ba, samHeaderLen + 8); var p = samHeaderLen + 12; chrToIndex = {}; chrNames = []; chrAliasTable = {}; for (i = 0; i < nRef; ++i) { var lName = readInt(ba, p); var name = ''; for (var j = 0; j < lName - 1; ++j) { name += String.fromCharCode(ba[p + 4 + j]); } readInt(ba, p + lName + 4); //dlog(name + ': ' + lRef); chrToIndex[name] = i; chrNames[i] = name; if (genome) { alias = genome.getChromosomeName(name); chrAliasTable[alias] = name; } p = p + 8 + lName; } return { magicNumber: magic, size: p, chrNames: chrNames, chrToIndex: chrToIndex, chrAliasTable: chrAliasTable }; }, bam_tag2cigar: function (ba, block_end, seq_offset, lseq, al, cigarArray) { function type2size(x) { if (x === 'C' || x === 'c' || x === 'A') return 1;else if (x === 'S' || x === 's') return 2;else if (x === 'I' || x === 'i' || x === 'f') return 4;else return 0; } // test if the real CIGAR is encoded in a CG:B,I tag if (cigarArray.length !== 1 || al.start < 0) return false; var p = seq_offset + (lseq + 1 >> 1) + lseq; while (p + 4 < block_end) { var tag = String.fromCharCode(ba[p]) + String.fromCharCode(ba[p + 1]); if (tag === 'CG') break; var type = String.fromCharCode(ba[p + 2]); if (type === 'B') { // the binary array type type = String.fromCharCode(ba[p + 3]); var size = type2size(type); var len = readInt(ba, p + 4); p += 8 + size * len; } else if (type === 'Z' || type === 'H') { // 0-terminated string p += 3; while (ba[p++] !== 0) {} } else { // other atomic types p += 3 + type2size(type); } } if (p >= block_end) return false; // no CG tag if (String.fromCharCode(ba[p + 2]) !== 'B' || String.fromCharCode(ba[p + 3]) !== 'I') return false; // not of type B,I // now we know the real CIGAR length and its offset in the binary array var cigar_len = readInt(ba, p + 4); var cigar_offset = p + 8; // 4 for "CGBI" and 4 for length if (cigar_offset + cigar_len * 4 > block_end) return false; // out of bound // decode CIGAR var cigar = ''; var lengthOnRef = 0; cigarArray.length = 0; // empty the old array p = cigar_offset; for (var k = 0; k < cigar_len; ++k, p += 4) { var cigop = readInt(ba, p); var opLen = cigop >> 4; var opLtr = CIGAR_DECODER[cigop & 0xf]; if (opLtr === 'M' || opLtr === 'EQ' || opLtr === 'X' || opLtr === 'D' || opLtr === 'N' || opLtr === '=') lengthOnRef += opLen; cigar = cigar + opLen + opLtr; cigarArray.push({ len: opLen, ltr: opLtr }); } // update alignment record. We are not updating bin, as apparently it is not used. al.cigar = cigar; al.lengthOnRef = lengthOnRef; return true; }, /** * * @param ba bytes to decode as an UInt8Array * @param offset offset position of ba array to start decoding * @param alignmentContainer container to receive the decoded alignments * @param min minimum genomic position * @param max maximum genomic position * @param chrIdx chromosome index * @param chrNames array of chromosome names * @param filter a BamFilter object * * @return true if we have moved beyond the right end of the genomic range. */ decodeBamRecords: function (ba, offset, alignmentContainer, chrNames, chrIdx, min, max, filter) { while (offset < ba.length) { const blockSize = readInt(ba, offset); const blockEnd = offset + blockSize + 4; const alignment = new BamAlignment(); const refID = readInt(ba, offset + 4); const pos = readInt(ba, offset + 8); if (blockEnd > ba.length) { return; } if (refID < 0) { offset = blockEnd; continue; // unmapped read } else if (chrIdx !== undefined && (refID > chrIdx || pos > max)) { return true; // off right edge, we're done } else if (chrIdx !== undefined && refID < chrIdx) { offset = blockEnd; continue; // ref ID to left of start, not sure this is possible } const bin_mq_nl = readInt(ba, offset + 12); const mq = (bin_mq_nl & 0xff00) >> 8; const nl = bin_mq_nl & 0xff; const flag_nc = readInt(ba, offset + 16); const flag = (flag_nc & 0xffff0000) >> 16; const nc = flag_nc & 0xffff; const lseq = readInt(ba, offset + 20); const mateChrIdx = readInt(ba, offset + 24); const matePos = readInt(ba, offset + 28); const tlen = readInt(ba, offset + 32); let readName = []; for (let j = 0; j < nl - 1; ++j) { readName.push(String.fromCharCode(ba[offset + 36 + j])); } readName = readName.join(''); let lengthOnRef = 0; let cigar = ''; let p = offset + 36 + nl; const cigarArray = []; // concatenate M,=,EQ,and X let lastCigRecord; for (let c = 0; c < nc; ++c) { var cigop = readInt(ba, p); var opLen = cigop >> 4; var opLtr = CIGAR_DECODER[cigop & 0xf]; if (opLtr === 'M' || opLtr === 'EQ' || opLtr === 'X' || opLtr === 'D' || opLtr === 'N' || opLtr === '=') lengthOnRef += opLen; cigar = cigar + opLen + opLtr; p += 4; // if(mOperators.has(opLtr) && mOperators.has(lastCigRecord.ltr)) { // lastCigRecord.len += opLen; // lastCigRecord.ltr = 'M' // } // else { lastCigRecord = { len: opLen, ltr: opLtr }; cigarArray.push(lastCigRecord); //} } alignment.chr = chrNames[refID]; alignment.start = pos; alignment.flags = flag; alignment.strand = !(flag & READ_STRAND_FLAG$1); alignment.readName = readName; alignment.cigar = cigar; alignment.lengthOnRef = lengthOnRef; alignment.fragmentLength = tlen; alignment.mq = mq; BamUtils.bam_tag2cigar(ba, blockEnd, p, lseq, alignment, cigarArray); alignment.end = alignment.start + alignment.lengthOnRef; if (alignment.end < min) { offset = blockEnd; continue; } // Record out-of-range "to the left", skip to next one let seq = []; const seqBytes = lseq + 1 >> 1; for (let j = 0; j < seqBytes; ++j) { var sb = ba[p + j]; seq.push(SEQ_DECODER[(sb & 0xf0) >> 4]); seq.push(SEQ_DECODER[sb & 0x0f]); } seq = seq.slice(0, lseq).join(''); // seq might have one extra character (if lseq is an odd number) p += seqBytes; const qualArray = []; for (let j = 0; j < lseq; ++j) { qualArray.push(ba[p + j]); } p += lseq; if (mateChrIdx >= 0) { alignment.mate = { chr: chrNames[mateChrIdx], position: matePos, strand: !(flag & MATE_STRAND_FLAG$1) }; } alignment.seq = seq; alignment.qual = qualArray; alignment.tagBA = new Uint8Array(ba.buffer.slice(p, blockEnd)); // decode these on demand this.setPairOrientation(alignment); if (undefined === filter || filter.pass(alignment)) { makeBlocks(alignment, cigarArray); alignmentContainer.push(alignment); } offset = blockEnd; } }, decodeSamRecords: function (sam, alignmentContainer, chr, min, max, filter) { var lines, i, j, len, tokens, qualString, rnext, lengthOnRef, alignment, cigarArray, started; lines = splitLines$3(sam); len = lines.length; started = false; for (i = 0; i < len; i++) { tokens = lines[i].split('\t'); alignment = new BamAlignment(); alignment.chr = tokens[2]; alignment.start = Number.parseInt(tokens[3]) - 1; alignment.flags = Number.parseInt(tokens[1]); alignment.readName = tokens[0]; alignment.strand = !(alignment.flags & READ_STRAND_FLAG$1); alignment.mq = Number.parseInt(tokens[4]); alignment.cigar = tokens[5]; alignment.fragmentLength = Number.parseInt(tokens[8]); alignment.seq = tokens[9]; if (alignment.chr === '*' || !alignment.isMapped()) continue; // Unmapped if (alignment.chr !== chr) { if (started) break; // Off the right edge, we're done else continue; // Possibly to the left, skip but keep looping } else if (alignment.start > max) { break; // off right edge, we're done } lengthOnRef = 0; cigarArray = buildOperators(alignment.cigar); cigarArray.forEach(function (op) { var opLen = op.len; var opLtr = op.ltr; if (opLtr === 'M' || opLtr === 'EQ' || opLtr === 'X' || opLtr === 'D' || opLtr === 'N' || opLtr === '=') lengthOnRef += opLen; }); alignment.lengthOnRef = lengthOnRef; // TODO for lh3: parse the CG:B,I tag in SAM here if (alignment.start + lengthOnRef < min) { continue; // To the left, skip and continue } qualString = tokens[10]; alignment.qual = []; for (j = 0; j < qualString.length; j++) { alignment.qual[j] = qualString.charCodeAt(j) - 33; } alignment.tagDict = tokens.length < 11 ? {} : decodeSamTags(tokens.slice(11)); if (alignment.isMateMapped()) { rnext = tokens[6]; alignment.mate = { chr: rnext === '=' ? alignment.chr : rnext, position: Number.parseInt(tokens[7]), strand: !(alignment.flags & MATE_STRAND_FLAG$1) }; } this.setPairOrientation(alignment); if (undefined === filter || filter.pass(alignment)) { makeBlocks(alignment, cigarArray); alignmentContainer.push(alignment); } } }, setReaderDefaults: function (reader, config) { reader.filter = new BamFilter(config.filter); if (config.readgroup) { reader.filter.readgroups = new Set([config.readgroup]); } reader.alleleFreqThreshold = config.alleleFreqThreshold === undefined ? DEFAULT_ALLELE_FREQ_THRESHOLD : config.alleleFreqThreshold; reader.samplingWindowSize = config.samplingWindowSize === undefined ? DEFAULT_SAMPLING_WINDOW_SIZE : config.samplingWindowSize; reader.samplingDepth = config.samplingDepth === undefined ? DEFAULT_SAMPLING_DEPTH : config.samplingDepth; if (reader.samplingDepth > MAXIMUM_SAMPLING_DEPTH) { reader.samplingDepth = MAXIMUM_SAMPLING_DEPTH; } if (config.viewAsPairs) { reader.pairsSupported = true; } else { reader.pairsSupported = config.pairsSupported === undefined ? true : config.pairsSupported; } }, setPairOrientation: function (alignment) { if (alignment.isMapped() && alignment.mate && alignment.isMateMapped() && alignment.mate.chr === alignment.chr) { var s1 = alignment.strand ? 'F' : 'R'; var mate = alignment.mate; var s2 = mate.strand ? 'F' : 'R'; var o1 = ' '; var o2 = ' '; if (alignment.isFirstOfPair()) { o1 = '1'; o2 = '2'; } else if (alignment.isSecondOfPair()) { o1 = '2'; o2 = '1'; } var tmp = []; var isize = alignment.fragmentLength; var estReadLen = alignment.end - alignment.start; if (isize === 0) { //isize not recorded. Need to estimate. This calculation was validated against an Illumina // -> <- library bam. var estMateEnd = alignment.start < mate.position ? mate.position + estReadLen : mate.position - estReadLen; isize = estMateEnd - alignment.start; } //if (isize > estReadLen) { if (isize > 0) { tmp[0] = s1; tmp[1] = o1; tmp[2] = s2; tmp[3] = o2; } else { tmp[2] = s1; tmp[3] = o1; tmp[0] = s2; tmp[1] = o2; } // } alignment.pairOrientation = tmp.join(''); } } }; /** * Split the alignment record into blocks as specified in the cigarArray. Each aligned block contains * its portion of the read sequence and base quality strings. A read sequence or base quality string * of "*" indicates the value is not recorded. In all other cases the length of the block sequence (block.seq) * and quality string (block.qual) must == the block length. * * @param alignment * @param cigarArray * @returns array of blocks */ function makeBlocks(alignment, cigarArray) { const blocks = []; let insertions; let gaps; let seqOffset = 0; let pos = alignment.start; alignment.scStart = alignment.start; alignment.scLengthOnRef = alignment.lengthOnRef; for (let c of cigarArray) { let scPos; switch (c.ltr) { case 'H': break; // ignore hard clips case 'P': break; // ignore pads case 'S': scPos = pos; alignment.scLengthOnRef += c.len; if (blocks.length === 0) { alignment.scStart -= c.len; scPos -= c.len; } blocks.push(new AlignmentBlock({ start: scPos, seqOffset: seqOffset, len: c.len, type: 'S' })); seqOffset += c.len; break; // soft clip read bases case 'N': case 'D': if (gaps === undefined) { gaps = []; } gaps.push({ start: pos, len: c.len, type: c.ltr }); pos += c.len; break; case 'I': if (insertions === undefined) { insertions = []; } insertions.push(new AlignmentBlock({ start: pos, len: c.len, seqOffset: seqOffset, type: 'I' })); seqOffset += c.len; break; case 'M': case 'EQ': case '=': case 'X': blocks.push(new AlignmentBlock({ start: pos, seqOffset: seqOffset, len: c.len, type: 'M' })); seqOffset += c.len; pos += c.len; break; } } alignment.blocks = blocks; alignment.insertions = insertions; alignment.gaps = gaps; } function readInt(ba, offset) { return ba[offset + 3] << 24 | ba[offset + 2] << 16 | ba[offset + 1] << 8 | ba[offset]; } /** * Build a list of cigar operators from a cigarString. Removes padding operators and concatenates consecutive * operators of the same type * * @param cigarString * @return */ function buildOperators(cigarString) { var operators, buffer, i, len, prevOp, next, op, nBases; operators = []; buffer = []; // Create list of cigar operators prevOp = null; len = cigarString.length; for (i = 0; i < len; i++) { next = cigarString.charAt(i); if (isDigit(next)) { buffer.push(next); } else { op = next; nBases = Number.parseInt(buffer.join('')); buffer = []; if (prevOp !== null && prevOp.ltr === op) { prevOp.len += nBases; } else { prevOp = { len: nBases, ltr: op }; operators.push(prevOp); } } } return operators; } function isDigit(a) { var charCode = a.charCodeAt(0); return charCode >= 48 && charCode <= 57; // 0-9 } function decodeSamTags(tags) { var tagDict = {}; tags.forEach(function (tag) { var tokens = tag.split(':'); tagDict[tokens[0]] = tokens[2]; }); return tagDict; } const isString$2 = isString$6; /** * Class for reading a bam file * * @param config * @constructor */ class BamReaderNonIndexed { constructor(config, genome) { this.config = config; this.genome = genome; this.bamPath = config.url; this.isDataUri = isString$2(config.url) && config.url.startsWith("data:"); BamUtils.setReaderDefaults(this, config); } // Return an alignment container async readAlignments(chr, bpStart, bpEnd) { this.genome; if (this.alignmentCache) { const header = this.header; const queryChr = header.chrAliasTable.hasOwnProperty(chr) ? header.chrAliasTable[chr] : chr; const qAlignments = this.alignmentCache.queryFeatures(queryChr, bpStart, bpEnd); const alignmentContainer = new AlignmentContainer(chr, bpStart, bpEnd, this.samplingWindowSize, this.samplingDepth, this.pairsSupported, this.alleleFreqThreshold); for (let a of qAlignments) { alignmentContainer.push(a); } alignmentContainer.finish(); return alignmentContainer; } else { if (this.isDataUri) { const data = decodeDataURI(this.bamPath); const unc = unbgzf(data.buffer); this.parseAlignments(this, unc); return this.fetchAlignments(chr, bpStart, bpEnd); } else { const arrayBuffer = await igvxhr.loadArrayBuffer(this.bamPath, buildOptions(this.config)); const unc = unbgzf(arrayBuffer); this.parseAlignments(unc); return this.fetchAlignments(chr, bpStart, bpEnd); } } } } function decodeDataURI(dataURI) { const split = dataURI.split(','); const info = split[0].split(':')[1]; let dataString = split[1]; if (info.indexOf('base64') >= 0) { dataString = atob(dataString); } else { dataString = decodeURI(dataString); } const bytes = new Uint8Array(dataString.length); for (var i = 0; i < dataString.length; i++) { bytes[i] = dataString.charCodeAt(i); } return bytes; } /* * The MIT License (MIT) * * Copyright (c) 2016-2017 The Regents of the University of California * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ /** * Class for reading a bam file * * @param config * @constructor */ class BamReader { constructor(config, genome) { this.config = config; this.genome = genome; this.bamPath = config.url; // Todo - deal with Picard convention. WHY DOES THERE HAVE TO BE 2? this.baiPath = config.indexURL; if (!this.baiPath && config.indexed !== false && !(this.bamPath instanceof File)) { this.baiPath = inferIndexPath(this.bamPath, "bai"); console.error(`Warning: no indexURL specified for ${this.config.url}. Guessing ${this.baiPath}`); } BamUtils.setReaderDefaults(this, config); } async readAlignments(chr, bpStart, bpEnd) { const chrToIndex = await this.getChrIndex(); const queryChr = this.chrAliasTable.hasOwnProperty(chr) ? this.chrAliasTable[chr] : chr; const chrId = chrToIndex[queryChr]; const alignmentContainer = new AlignmentContainer(chr, bpStart, bpEnd, this.config.samplingWindowSize, this.config.samplingDepth, this.config.pairsSupported, this.config.alleleFreqThreshold); if (chrId === undefined) { return alignmentContainer; } else { const bamIndex = await this.getIndex(); const chunks = bamIndex.blocksForRange(chrId, bpStart, bpEnd); if (!chunks || chunks.length === 0) { return alignmentContainer; } for (let c of chunks) { let lastBlockSize; if (c.maxv.offset === 0) { lastBlockSize = 0; // Don't need to read the last block. } else { const bsizeOptions = buildOptions(this.config, { range: { start: c.maxv.block, size: 26 } }); const abuffer = await igvxhr.loadArrayBuffer(this.bamPath, bsizeOptions); lastBlockSize = bgzBlockSize(abuffer); } const fetchMin = c.minv.block; const fetchMax = c.maxv.block + lastBlockSize; const range = { start: fetchMin, size: fetchMax - fetchMin + 1 }; const compressed = await igvxhr.loadArrayBuffer(this.bamPath, buildOptions(this.config, { range: range })); var ba = unbgzf(compressed); //new Uint8Array(BGZip.unbgzf(compressed)); //, c.maxv.block - c.minv.block + 1)); const done = BamUtils.decodeBamRecords(ba, c.minv.offset, alignmentContainer, this.indexToChr, chrId, bpStart, bpEnd, this.filter); if (done) { break; } } alignmentContainer.finish(); return alignmentContainer; } } async getHeader() { if (!this.header) { const genome = this.genome; const index = await this.getIndex(); let len; if (index.firstAlignmentBlock) { const bsizeOptions = buildOptions(this.config, { range: { start: index.firstAlignmentBlock, size: 26 } }); const abuffer = await igvxhr.loadArrayBuffer(this.bamPath, bsizeOptions); const bsize = bgzBlockSize(abuffer); len = index.firstAlignmentBlock + bsize; // Insure we get the complete compressed block containing the header } else { len = 64000; } const options = buildOptions(this.config, { range: { start: 0, size: len } }); this.header = await BamUtils.readHeader(this.bamPath, options, genome); } return this.header; } async getIndex() { const genome = this.genome; if (!this.index) { this.index = await loadIndex(this.baiPath, this.config, genome); } return this.index; } async getChrIndex() { if (this.chrToIndex) { return this.chrToIndex; } else { const header = await this.getHeader(); this.chrToIndex = header.chrToIndex; this.indexToChr = header.chrNames; this.chrAliasTable = header.chrAliasTable; return this.chrToIndex; } } } /* * The MIT License (MIT) * * Copyright (c) 2016-2017 The Regents of the University of California * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ class ShardedBamReader { constructor(config, genome) { this.config = config; this.genome = genome; const bamReaders = {}; const chrAliasTable = {}; config.sources.sequences.forEach(function (chr) { bamReaders[chr] = null; // Placeholder if (genome) { const alias = genome.getChromosomeName(chr); chrAliasTable[alias] = chr; } }); this.chrAliasTable = chrAliasTable; this.bamReaders = bamReaders; BamUtils.setReaderDefaults(this, config); } async readAlignments(chr, start, end) { this.genome; const self = this; const queryChr = self.chrAliasTable.hasOwnProperty(chr) ? self.chrAliasTable[chr] : chr; if (!this.bamReaders.hasOwnProperty(queryChr) || "none" === this.bamReaders[queryChr]) { return Promise.resolve(new AlignmentContainer(chr, start, end)); } else { let reader = self.bamReaders[queryChr]; let tmp; if (!reader) { tmp = { url: self.config.sources.url.replace("$CHR", queryChr) }; if (self.config.sources.indexURL) { tmp.indexURL = self.config.sources.indexURL.replace("$CHR", queryChr); } const bamConfig = Object.assign(self.config, tmp); reader = new BamReader(bamConfig); self.bamReaders[queryChr] = reader; } return reader.readAlignments(queryChr, start, end).catch(function (error) { console.error(error); const str = `Error reading BAM or index file for: ${tmp ? tmp.url : ''}`; Alert.presentAlert(new Error(str)); self.bamReaders[queryChr] = "none"; return new AlignmentContainer(chr, start, end); // Empty alignment container }); } } } /* * The MIT License (MIT) * * Copyright (c) 2016-2017 The Regents of the University of California * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ /** * Class for reading bam records from an igv.js-flask server backed by pysam. Deprecated. * * @param config * @constructor */ const BamWebserviceReader = function (config, genome) { this.config = config; this.genome = genome; BamUtils.setReaderDefaults(this, config); }; // Example http://localhost:5000/alignments/?reference=/Users/jrobinso/hg19mini.fa&file=/Users/jrobinso/cram_with_crai_index.cram®ion=1:100-2000 BamWebserviceReader.prototype.readAlignments = function (chr, bpStart, bpEnd) { var self = this; return getHeader.call(self).then(function (header) { var queryChr, url; queryChr = header.chrAliasTable.hasOwnProperty(chr) ? header.chrAliasTable[chr] : chr; url = self.config.url + "?reference=" + self.config.referenceFile + "&file=" + self.config.alignmentFile + "" + "®ion=" + queryChr + ":" + bpStart + "-" + bpEnd; return igvxhr.loadString(url, buildOptions(self.config)).then(function (sam) { var alignmentContainer; header.chrToIndex[queryChr]; alignmentContainer = new AlignmentContainer(chr, bpStart, bpEnd, self.samplingWindowSize, self.samplingDepth, self.pairsSupported, self.alleleFreqThreshold); BamUtils.decodeSamRecords(sam, alignmentContainer, queryChr, bpStart, bpEnd, self.filter); return alignmentContainer; }); }); }; // Example http://localhost:5000/alignments/?reference=/Users/jrobinso/hg19mini.fa&file=/Users/jrobinso/cram_with_crai_index.cram&options=-b%20-H function getHeader() { const self = this; const genome = this.genome; if (this.header) { return Promise.resolve(this.header); } else { const url = this.config.url + "?file=" + this.config.alignmentFile + "&options=-b,-H"; const options = buildOptions(this.config); return BamUtils.readHeader(url, options, genome).then(function (header) { self.header = header; return header; }); } } /* * The MIT License (MIT) * * Copyright (c) 2016-2017 The Regents of the University of California * Author: Jim Robinson * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ class HtsgetBamReader extends HtsgetReader { constructor(config, genome) { super(config, genome); BamUtils.setReaderDefaults(this, config); } async readAlignments(chr, start, end) { if (!this.header) { const compressedData = await this.readHeaderData(); const ba = unbgzf(compressedData.buffer); this.header = BamUtils.decodeBamHeader(ba, this.genome); this.chrAliasTable = new Map(); for (let key of Object.keys(this.header.chrAliasTable)) { this.chrAliasTable.set(key, this.header.chrAliasTable[key]); } } let queryChr = this.chrAliasTable.has(chr) ? this.chrAliasTable.get(chr) : chr; const compressedData = await this.readData(queryChr, start, end); // BAM decoding const ba = unbgzf(compressedData.buffer); const chrIdx = this.header.chrToIndex[chr]; const alignmentContainer = new AlignmentContainer(chr, start, end, this.samplingWindowSize, this.samplingDepth, this.pairsSupported, this.alleleFreqThreshold); BamUtils.decodeBamRecords(ba, this.header.size, alignmentContainer, this.header.chrNames, chrIdx, start, end); alignmentContainer.finish(); return alignmentContainer; } } var $propertyIsEnumerable = {}.propertyIsEnumerable; // eslint-disable-next-line es/no-object-getownpropertydescriptor -- safe var getOwnPropertyDescriptor$1 = Object.getOwnPropertyDescriptor; // Nashorn ~ JDK8 bug var NASHORN_BUG = getOwnPropertyDescriptor$1 && !$propertyIsEnumerable.call({ 1: 2 }, 1); // `Object.prototype.propertyIsEnumerable` method implementation // https://tc39.es/ecma262/#sec-object.prototype.propertyisenumerable var f$3 = NASHORN_BUG ? function propertyIsEnumerable(V) { var descriptor = getOwnPropertyDescriptor$1(this, V); return !!descriptor && descriptor.enumerable; } : $propertyIsEnumerable; var objectPropertyIsEnumerable = { f: f$3 }; var split = ''.split; // fallback for non-array-like ES3 and non-enumerable old V8 strings var indexedObject = fails(function () { // throws an error in rhino, see https://github.com/mozilla/rhino/issues/346 // eslint-disable-next-line no-prototype-builtins -- safe return !Object('z').propertyIsEnumerable(0); }) ? function (it) { return classofRaw(it) == 'String' ? split.call(it, '') : Object(it); } : Object; var toIndexedObject = function (it) { return indexedObject(requireObjectCoercible(it)); }; var $getOwnPropertyDescriptor = Object.getOwnPropertyDescriptor; // `Object.getOwnPropertyDescriptor` method // https://tc39.es/ecma262/#sec-object.getownpropertydescriptor var f$2 = descriptors ? $getOwnPropertyDescriptor : function getOwnPropertyDescriptor(O, P) { O = toIndexedObject(O); P = toPrimitive(P, true); if (ie8DomDefine) try { return $getOwnPropertyDescriptor(O, P); } catch (error) { /* empty */ } if (has$1(O, P)) return createPropertyDescriptor(!objectPropertyIsEnumerable.f.call(O, P), O[P]); }; var objectGetOwnPropertyDescriptor = { f: f$2 }; var max = Math.max; var min = Math.min; // Helper for a popular repeating case of the spec: // Let integer be ? ToInteger(index). // If integer < 0, let result be max((length + integer), 0); else let result be min(integer, length). var toAbsoluteIndex = function (index, length) { var integer = toInteger(index); return integer < 0 ? max(integer + length, 0) : min(integer, length); }; var createMethod = function (IS_INCLUDES) { return function ($this, el, fromIndex) { var O = toIndexedObject($this); var length = toLength(O.length); var index = toAbsoluteIndex(fromIndex, length); var value; // Array#includes uses SameValueZero equality algorithm // eslint-disable-next-line no-self-compare -- NaN check if (IS_INCLUDES && el != el) while (length > index) { value = O[index++]; // eslint-disable-next-line no-self-compare -- NaN check if (value != value) return true; // Array#indexOf ignores holes, Array#includes - not } else for (; length > index; index++) { if ((IS_INCLUDES || index in O) && O[index] === el) return IS_INCLUDES || index || 0; } return !IS_INCLUDES && -1; }; }; var arrayIncludes = { // `Array.prototype.includes` method // https://tc39.es/ecma262/#sec-array.prototype.includes includes: createMethod(true), // `Array.prototype.indexOf` method // https://tc39.es/ecma262/#sec-array.prototype.indexof indexOf: createMethod(false) }; var indexOf = arrayIncludes.indexOf; var objectKeysInternal = function (object, names) { var O = toIndexedObject(object); var i = 0; var result = []; var key; for (key in O) !has$1(hiddenKeys$1, key) && has$1(O, key) && result.push(key); // Don't enum bug & hidden keys while (names.length > i) if (has$1(O, key = names[i++])) { ~indexOf(result, key) || result.push(key); } return result; }; // IE8- don't enum bug keys var enumBugKeys = ['constructor', 'hasOwnProperty', 'isPrototypeOf', 'propertyIsEnumerable', 'toLocaleString', 'toString', 'valueOf']; var hiddenKeys = enumBugKeys.concat('length', 'prototype'); // `Object.getOwnPropertyNames` method // https://tc39.es/ecma262/#sec-object.getownpropertynames // eslint-disable-next-line es/no-object-getownpropertynames -- safe var f$1 = Object.getOwnPropertyNames || function getOwnPropertyNames(O) { return objectKeysInternal(O, hiddenKeys); }; var objectGetOwnPropertyNames = { f: f$1 }; // eslint-disable-next-line es/no-object-getownpropertysymbols -- safe var f = Object.getOwnPropertySymbols; var objectGetOwnPropertySymbols = { f: f }; var ownKeys = getBuiltIn('Reflect', 'ownKeys') || function ownKeys(it) { var keys = objectGetOwnPropertyNames.f(anObject(it)); var getOwnPropertySymbols = objectGetOwnPropertySymbols.f; return getOwnPropertySymbols ? keys.concat(getOwnPropertySymbols(it)) : keys; }; var copyConstructorProperties = function (target, source) { var keys = ownKeys(source); var defineProperty = objectDefineProperty.f; var getOwnPropertyDescriptor = objectGetOwnPropertyDescriptor.f; for (var i = 0; i < keys.length; i++) { var key = keys[i]; if (!has$1(target, key)) defineProperty(target, key, getOwnPropertyDescriptor(source, key)); } }; var replacement = /#|\.prototype\./; var isForced = function (feature, detection) { var value = data[normalize(feature)]; return value == POLYFILL ? true : value == NATIVE ? false : typeof detection == 'function' ? fails(detection) : !!detection; }; var normalize = isForced.normalize = function (string) { return String(string).replace(replacement, '.').toLowerCase(); }; var data = isForced.data = {}; var NATIVE = isForced.NATIVE = 'N'; var POLYFILL = isForced.POLYFILL = 'P'; var isForced_1 = isForced; var getOwnPropertyDescriptor = objectGetOwnPropertyDescriptor.f; /* options.target - name of the target object options.global - target is the global object options.stat - export as static methods of target options.proto - export as prototype methods of target options.real - real prototype method for the `pure` version options.forced - export even if the native feature is available options.bind - bind methods to the target, required for the `pure` version options.wrap - wrap constructors to preventing global pollution, required for the `pure` version options.unsafe - use the simple assignment of property instead of delete + defineProperty options.sham - add a flag to not completely full polyfills options.enumerable - export as enumerable property options.noTargetGet - prevent calling a getter on target */ var _export = function (options, source) { var TARGET = options.target; var GLOBAL = options.global; var STATIC = options.stat; var FORCED, target, key, targetProperty, sourceProperty, descriptor; if (GLOBAL) { target = global$1; } else if (STATIC) { target = global$1[TARGET] || setGlobal(TARGET, {}); } else { target = (global$1[TARGET] || {}).prototype; } if (target) for (key in source) { sourceProperty = source[key]; if (options.noTargetGet) { descriptor = getOwnPropertyDescriptor(target, key); targetProperty = descriptor && descriptor.value; } else targetProperty = target[key]; FORCED = isForced_1(GLOBAL ? key : TARGET + (STATIC ? '.' : '#') + key, options.forced); // contained in target if (!FORCED && targetProperty !== undefined) { if (typeof sourceProperty === typeof targetProperty) continue; copyConstructorProperties(sourceProperty, targetProperty); } // add a flag to not completely full polyfills if (options.sham || targetProperty && targetProperty.sham) { createNonEnumerableProperty(sourceProperty, 'sham', true); } // extend global redefine(target, key, sourceProperty, options); } }; var functionBindContext = function (fn, that, length) { aFunction(fn); if (that === undefined) return fn; switch (length) { case 0: return function () { return fn.call(that); }; case 1: return function (a) { return fn.call(that, a); }; case 2: return function (a, b) { return fn.call(that, a, b); }; case 3: return function (a, b, c) { return fn.call(that, a, b, c); }; } return function () { return fn.apply(that, arguments); }; }; var html = getBuiltIn('document', 'documentElement'); var engineIsIos = /(?:iphone|ipod|ipad).*applewebkit/i.test(engineUserAgent); var engineIsNode = classofRaw(global$1.process) == 'process'; var location = global$1.location; var set = global$1.setImmediate; var clear = global$1.clearImmediate; var process$1 = global$1.process; var MessageChannel$1 = global$1.MessageChannel; var Dispatch = global$1.Dispatch; var counter = 0; var queue = {}; var ONREADYSTATECHANGE = 'onreadystatechange'; var defer, channel, port; var run = function (id) { // eslint-disable-next-line no-prototype-builtins -- safe if (queue.hasOwnProperty(id)) { var fn = queue[id]; delete queue[id]; fn(); } }; var runner = function (id) { return function () { run(id); }; }; var listener = function (event) { run(event.data); }; var post = function (id) { // old engines have not location.origin global$1.postMessage(id + '', location.protocol + '//' + location.host); }; // Node.js 0.9+ & IE10+ has setImmediate, otherwise: if (!set || !clear) { set = function setImmediate(fn) { var args = []; var i = 1; while (arguments.length > i) args.push(arguments[i++]); queue[++counter] = function () { // eslint-disable-next-line no-new-func -- spec requirement (typeof fn == 'function' ? fn : Function(fn)).apply(undefined, args); }; defer(counter); return counter; }; clear = function clearImmediate(id) { delete queue[id]; }; // Node.js 0.8- if (engineIsNode) { defer = function (id) { process$1.nextTick(runner(id)); }; // Sphere (JS game engine) Dispatch API } else if (Dispatch && Dispatch.now) { defer = function (id) { Dispatch.now(runner(id)); }; // Browsers with MessageChannel, includes WebWorkers // except iOS - https://github.com/zloirock/core-js/issues/624 } else if (MessageChannel$1 && !engineIsIos) { channel = new MessageChannel$1(); port = channel.port2; channel.port1.onmessage = listener; defer = functionBindContext(port.postMessage, port, 1); // Browsers with postMessage, skip WebWorkers // IE8 has postMessage, but it's sync & typeof its postMessage is 'object' } else if (global$1.addEventListener && typeof postMessage == 'function' && !global$1.importScripts && location && location.protocol !== 'file:' && !fails(post)) { defer = post; global$1.addEventListener('message', listener, false); // IE8- } else if (ONREADYSTATECHANGE in documentCreateElement('script')) { defer = function (id) { html.appendChild(documentCreateElement('script'))[ONREADYSTATECHANGE] = function () { html.removeChild(this); run(id); }; }; // Rest old browsers } else { defer = function (id) { setTimeout(runner(id), 0); }; } } var task = { set: set, clear: clear }; var FORCED = !global$1.setImmediate || !global$1.clearImmediate; // http://w3c.github.io/setImmediate/ _export({ global: true, bind: true, enumerable: true, forced: FORCED }, { // `setImmediate` method // http://w3c.github.io/setImmediate/#si-setImmediate setImmediate: task.set, // `clearImmediate` method // http://w3c.github.io/setImmediate/#si-clearImmediate clearImmediate: task.clear }); const eval2 = eval; const gmodCRAM = function (t) { var e = {}; function r(n) { if (e[n]) return e[n].exports; var i = e[n] = { i: n, l: !1, exports: {} }; return t[n].call(i.exports, i, i.exports, r), i.l = !0, i.exports; } return r.m = t, r.c = e, r.d = function (t, e, n) { r.o(t, e) || Object.defineProperty(t, e, { enumerable: !0, get: n }); }, r.r = function (t) { "undefined" != typeof Symbol && Symbol.toStringTag && Object.defineProperty(t, Symbol.toStringTag, { value: "Module" }), Object.defineProperty(t, "__esModule", { value: !0 }); }, r.t = function (t, e) { if (1 & e && (t = r(t)), 8 & e) return t; if (4 & e && "object" == typeof t && t && t.__esModule) return t; var n = Object.create(null); if (r.r(n), Object.defineProperty(n, "default", { enumerable: !0, value: t }), 2 & e && "string" != typeof t) for (var i in t) r.d(n, i, function (e) { return t[e]; }.bind(null, i)); return n; }, r.n = function (t) { var e = t && t.__esModule ? 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Uint8Array.prototype.indexOf.call(t, e, r) : Uint8Array.prototype.lastIndexOf.call(t, e, r) : m(t, [e], r, n, i); throw new TypeError("val must be string, number or Buffer"); } function m(t, e, r, n, i) { var o, a = 1, s = t.length, u = e.length; if (void 0 !== n && ("ucs2" === (n = String(n).toLowerCase()) || "ucs-2" === n || "utf16le" === n || "utf-16le" === n)) { if (t.length < 2 || e.length < 2) return -1; a = 2, s /= 2, u /= 2, r /= 2; } function f(t, e) { return 1 === a ? t[e] : t.readUInt16BE(e * a); } if (i) { var c = -1; for (o = r; o < s; o++) if (f(t, o) === f(e, -1 === c ? 0 : o - c)) { if (-1 === c && (c = o), o - c + 1 === u) return c * a; } else -1 !== c && (o -= o - c), c = -1; } else for (r + u > s && (r = s - u), o = r; o >= 0; o--) { for (var l = !0, h = 0; h < u; h++) if (f(t, o + h) !== f(e, h)) { l = !1; break; } if (l) return o; } return -1; } function b(t, e, r, n) { r = Number(r) || 0; var i = t.length - r; n ? (n = Number(n)) > i && (n = i) : n = i; var o = e.length; if (o % 2 != 0) throw new TypeError("Invalid hex string"); n > o / 2 && (n = o / 2); for (var a = 0; a < n; ++a) { var s = parseInt(e.substr(2 * a, 2), 16); if (isNaN(s)) return a; t[r + a] = s; } return a; } function _(t, e, r, n) { return Z(D(e, t.length - r), t, r, n); } function w(t, e, r, n) { return Z(function (t) { for (var e = [], r = 0; r < t.length; ++r) e.push(255 & t.charCodeAt(r)); return e; }(e), t, r, n); } function x(t, e, r, n) { return w(t, e, r, n); } function E(t, e, r, n) { return Z(q(e), t, r, n); } function S(t, e, r, n) { return Z(function (t, e) { for (var r, n, i, o = [], a = 0; a < t.length && !((e -= 2) < 0); ++a) r = t.charCodeAt(a), n = r >> 8, i = r % 256, o.push(i), o.push(n); return o; }(e, t.length - r), t, r, n); } function k(t, e, r) { return 0 === e && r === t.length ? n.fromByteArray(t) : n.fromByteArray(t.slice(e, r)); } function A(t, e, r) { r = Math.min(t.length, r); for (var n = [], i = e; i < r;) { var o, a, s, u, f = t[i], c = null, l = f > 239 ? 4 : f > 223 ? 3 : f > 191 ? 2 : 1; if (i + l <= r) switch (l) { case 1: f < 128 && (c = f); break; case 2: 128 == (192 & (o = t[i + 1])) && (u = (31 & f) << 6 | 63 & o) > 127 && (c = u); break; case 3: o = t[i + 1], a = t[i + 2], 128 == (192 & o) && 128 == (192 & a) && (u = (15 & f) << 12 | (63 & o) << 6 | 63 & a) > 2047 && (u < 55296 || u > 57343) && (c = u); break; case 4: o = t[i + 1], a = t[i + 2], s = t[i + 3], 128 == (192 & o) && 128 == (192 & a) && 128 == (192 & s) && (u = (15 & f) << 18 | (63 & o) << 12 | (63 & a) << 6 | 63 & s) > 65535 && u < 1114112 && (c = u); } null === c ? (c = 65533, l = 1) : c > 65535 && (c -= 65536, n.push(c >>> 10 & 1023 | 55296), c = 56320 | 1023 & c), n.push(c), i += l; } return function (t) { var e = t.length; if (e <= C) return String.fromCharCode.apply(String, t); var r = "", n = 0; for (; n < e;) r += String.fromCharCode.apply(String, t.slice(n, n += C)); return r; }(n); } e.Buffer = u, e.SlowBuffer = function (t) { +t != t && (t = 0); return u.alloc(+t); }, e.INSPECT_MAX_BYTES = 50, u.TYPED_ARRAY_SUPPORT = void 0 !== t.TYPED_ARRAY_SUPPORT ? t.TYPED_ARRAY_SUPPORT : function () { try { var t = new Uint8Array(1); return t.__proto__ = { __proto__: Uint8Array.prototype, foo: function () { return 42; } }, 42 === t.foo() && "function" == typeof t.subarray && 0 === t.subarray(1, 1).byteLength; } catch (t) { return !1; } }(), e.kMaxLength = a(), u.poolSize = 8192, u._augment = function (t) { return t.__proto__ = u.prototype, t; }, u.from = function (t, e, r) { return f(null, t, e, r); }, u.TYPED_ARRAY_SUPPORT && (u.prototype.__proto__ = Uint8Array.prototype, u.__proto__ = Uint8Array, "undefined" != typeof Symbol && Symbol.species && u[Symbol.species] === u && Object.defineProperty(u, Symbol.species, { value: null, configurable: !0 })), u.alloc = function (t, e, r) { return function (t, e, r, n) { return c(e), e <= 0 ? s(t, e) : void 0 !== r ? "string" == typeof n ? s(t, e).fill(r, n) : s(t, e).fill(r) : s(t, e); }(null, t, e, r); }, u.allocUnsafe = function (t) { return l(null, t); }, u.allocUnsafeSlow = function (t) { return l(null, t); }, u.isBuffer = function (t) { return !(null == t || !t._isBuffer); }, u.compare = function (t, e) { if (!u.isBuffer(t) || !u.isBuffer(e)) throw new TypeError("Arguments must be Buffers"); if (t === e) return 0; for (var r = t.length, n = e.length, i = 0, o = Math.min(r, n); i < o; ++i) if (t[i] !== e[i]) { r = t[i], n = e[i]; break; } return r < n ? -1 : n < r ? 1 : 0; }, u.isEncoding = function (t) { switch (String(t).toLowerCase()) { case "hex": case "utf8": case "utf-8": case "ascii": case "latin1": case "binary": case "base64": case "ucs2": case "ucs-2": case "utf16le": case "utf-16le": return !0; default: return !1; } }, u.concat = function (t, e) { if (!o(t)) throw new TypeError('"list" argument must be an Array of Buffers'); if (0 === t.length) return u.alloc(0); var r; if (void 0 === e) for (e = 0, r = 0; r < t.length; ++r) e += t[r].length; var n = u.allocUnsafe(e), i = 0; for (r = 0; r < t.length; ++r) { var a = t[r]; if (!u.isBuffer(a)) throw new TypeError('"list" argument must be an Array of Buffers'); a.copy(n, i), i += a.length; } return n; }, u.byteLength = p, u.prototype._isBuffer = !0, u.prototype.swap16 = function () { var t = this.length; if (t % 2 != 0) throw new RangeError("Buffer size must be a multiple of 16-bits"); for (var e = 0; e < t; e += 2) v(this, e, e + 1); return this; }, u.prototype.swap32 = function () { var t = this.length; if (t % 4 != 0) throw new RangeError("Buffer size must be a multiple of 32-bits"); for (var e = 0; e < t; e += 4) v(this, e, e + 3), v(this, e + 1, e + 2); return this; }, u.prototype.swap64 = function () { var t = this.length; if (t % 8 != 0) throw new RangeError("Buffer size must be a multiple of 64-bits"); for (var e = 0; e < t; e += 8) v(this, e, e + 7), v(this, e + 1, e + 6), v(this, e + 2, e + 5), v(this, e + 3, e + 4); return this; }, u.prototype.toString = function () { var t = 0 | this.length; return 0 === t ? "" : 0 === arguments.length ? A(this, 0, t) : g.apply(this, arguments); }, u.prototype.equals = function (t) { if (!u.isBuffer(t)) throw new TypeError("Argument must be a Buffer"); return this === t || 0 === u.compare(this, t); }, u.prototype.inspect = function () { var t = "", r = e.INSPECT_MAX_BYTES; return this.length > 0 && (t = this.toString("hex", 0, r).match(/.{2}/g).join(" "), this.length > r && (t += " ... ")), ""; }, u.prototype.compare = function (t, e, r, n, i) { if (!u.isBuffer(t)) throw new TypeError("Argument must be a Buffer"); if (void 0 === e && (e = 0), void 0 === r && (r = t ? t.length : 0), void 0 === n && (n = 0), void 0 === i && (i = this.length), e < 0 || r > t.length || n < 0 || i > this.length) throw new RangeError("out of range index"); if (n >= i && e >= r) return 0; if (n >= i) return -1; if (e >= r) return 1; if (this === t) return 0; for (var o = (i >>>= 0) - (n >>>= 0), a = (r >>>= 0) - (e >>>= 0), s = Math.min(o, a), f = this.slice(n, i), c = t.slice(e, r), l = 0; l < s; ++l) if (f[l] !== c[l]) { o = f[l], a = c[l]; break; } return o < a ? -1 : a < o ? 1 : 0; }, u.prototype.includes = function (t, e, r) { return -1 !== this.indexOf(t, e, r); }, u.prototype.indexOf = function (t, e, r) { return y(this, t, e, r, !0); }, u.prototype.lastIndexOf = function (t, e, r) { return y(this, t, e, r, !1); }, u.prototype.write = function (t, e, r, n) { if (void 0 === e) n = "utf8", r = this.length, e = 0;else if (void 0 === r && "string" == typeof e) n = e, r = this.length, e = 0;else { if (!isFinite(e)) throw new Error("Buffer.write(string, encoding, offset[, length]) is no longer supported"); e |= 0, isFinite(r) ? (r |= 0, void 0 === n && (n = "utf8")) : (n = r, r = void 0); } var i = this.length - e; if ((void 0 === r || r > i) && (r = i), t.length > 0 && (r < 0 || e < 0) || e > this.length) throw new RangeError("Attempt to write outside buffer bounds"); n || (n = "utf8"); for (var o = !1;;) switch (n) { case "hex": return b(this, t, e, r); case "utf8": case "utf-8": return _(this, t, e, r); case "ascii": return w(this, t, e, r); case "latin1": case "binary": return x(this, t, e, r); case "base64": return E(this, t, e, r); case "ucs2": case "ucs-2": case "utf16le": case "utf-16le": return S(this, t, e, r); default: if (o) throw new TypeError("Unknown encoding: " + n); n = ("" + n).toLowerCase(), o = !0; } }, u.prototype.toJSON = function () { return { type: "Buffer", data: Array.prototype.slice.call(this._arr || this, 0) }; }; var C = 4096; function T(t, e, r) { var n = ""; r = Math.min(t.length, r); for (var i = e; i < r; ++i) n += String.fromCharCode(127 & t[i]); return n; } function R(t, e, r) { var n = ""; r = Math.min(t.length, r); for (var i = e; i < r; ++i) n += String.fromCharCode(t[i]); return n; } function O(t, e, r) { var n = t.length; (!e || e < 0) && (e = 0), (!r || r < 0 || r > n) && (r = n); for (var i = "", o = e; o < r; ++o) i += U(t[o]); return i; } function I(t, e, r) { for (var n = t.slice(e, r), i = "", o = 0; o < n.length; o += 2) i += String.fromCharCode(n[o] + 256 * n[o + 1]); return i; } function L(t, e, r) { if (t % 1 != 0 || t < 0) throw new RangeError("offset is not uint"); if (t + e > r) throw new RangeError("Trying to access beyond buffer length"); } function B(t, e, r, n, i, o) { if (!u.isBuffer(t)) throw new TypeError('"buffer" argument must be a Buffer instance'); if (e > i || e < o) throw new RangeError('"value" argument is out of bounds'); if (r + n > t.length) throw new RangeError("Index out of range"); } function P(t, e, r, n) { e < 0 && (e = 65535 + e + 1); for (var i = 0, o = Math.min(t.length - r, 2); i < o; ++i) t[r + i] = (e & 255 << 8 * (n ? i : 1 - i)) >>> 8 * (n ? i : 1 - i); } function F(t, e, r, n) { e < 0 && (e = 4294967295 + e + 1); for (var i = 0, o = Math.min(t.length - r, 4); i < o; ++i) t[r + i] = e >>> 8 * (n ? i : 3 - i) & 255; } function N(t, e, r, n, i, o) { if (r + n > t.length) throw new RangeError("Index out of range"); if (r < 0) throw new RangeError("Index out of range"); } function M(t, e, r, n, o) { return o || N(t, 0, r, 4), i.write(t, e, r, n, 23, 4), r + 4; } function j(t, e, r, n, o) { return o || N(t, 0, r, 8), i.write(t, e, r, n, 52, 8), r + 8; } u.prototype.slice = function (t, e) { var r, n = this.length; if ((t = ~~t) < 0 ? (t += n) < 0 && (t = 0) : t > n && (t = n), (e = void 0 === e ? n : ~~e) < 0 ? (e += n) < 0 && (e = 0) : e > n && (e = n), e < t && (e = t), u.TYPED_ARRAY_SUPPORT) (r = this.subarray(t, e)).__proto__ = u.prototype;else { var i = e - t; r = new u(i, void 0); for (var o = 0; o < i; ++o) r[o] = this[o + t]; } return r; }, u.prototype.readUIntLE = function (t, e, r) { t |= 0, e |= 0, r || L(t, e, this.length); for (var n = this[t], i = 1, o = 0; ++o < e && (i *= 256);) n += this[t + o] * i; return n; }, u.prototype.readUIntBE = function (t, e, r) { t |= 0, e |= 0, r || L(t, e, this.length); for (var n = this[t + --e], i = 1; e > 0 && (i *= 256);) n += this[t + --e] * i; return n; }, u.prototype.readUInt8 = function (t, e) { return e || L(t, 1, this.length), this[t]; }, u.prototype.readUInt16LE = function (t, e) { return e || L(t, 2, this.length), this[t] | this[t + 1] << 8; }, u.prototype.readUInt16BE = function (t, e) { return e || L(t, 2, this.length), this[t] << 8 | this[t + 1]; }, u.prototype.readUInt32LE = function (t, e) { return e || L(t, 4, this.length), (this[t] | this[t + 1] << 8 | this[t + 2] << 16) + 16777216 * this[t + 3]; }, u.prototype.readUInt32BE = function (t, e) { return e || L(t, 4, this.length), 16777216 * this[t] + (this[t + 1] << 16 | this[t + 2] << 8 | this[t + 3]); }, u.prototype.readIntLE = function (t, e, r) { t |= 0, e |= 0, r || L(t, e, this.length); for (var n = this[t], i = 1, o = 0; ++o < e && (i *= 256);) n += this[t + o] * i; return n >= (i *= 128) && (n -= Math.pow(2, 8 * e)), n; }, u.prototype.readIntBE = function (t, e, r) { t |= 0, e |= 0, r || L(t, e, this.length); for (var n = e, i = 1, o = this[t + --n]; n > 0 && (i *= 256);) o += this[t + --n] * i; return o >= (i *= 128) && (o -= Math.pow(2, 8 * e)), o; }, u.prototype.readInt8 = function (t, e) { return e || L(t, 1, this.length), 128 & this[t] ? -1 * (255 - this[t] + 1) : this[t]; }, u.prototype.readInt16LE = function (t, e) { e || L(t, 2, this.length); var r = this[t] | this[t + 1] << 8; return 32768 & r ? 4294901760 | r : r; }, u.prototype.readInt16BE = function (t, e) { e || L(t, 2, this.length); var r = this[t + 1] | this[t] << 8; return 32768 & r ? 4294901760 | r : r; }, u.prototype.readInt32LE = function (t, e) { return e || L(t, 4, this.length), this[t] | this[t + 1] << 8 | this[t + 2] << 16 | this[t + 3] << 24; }, u.prototype.readInt32BE = function (t, e) { return e || L(t, 4, this.length), this[t] << 24 | this[t + 1] << 16 | this[t + 2] << 8 | this[t + 3]; }, u.prototype.readFloatLE = function (t, e) { return e || L(t, 4, this.length), i.read(this, t, !0, 23, 4); }, u.prototype.readFloatBE = function (t, e) { return e || L(t, 4, this.length), i.read(this, t, !1, 23, 4); }, u.prototype.readDoubleLE = function (t, e) { return e || L(t, 8, this.length), i.read(this, t, !0, 52, 8); }, u.prototype.readDoubleBE = function (t, e) { return e || L(t, 8, this.length), i.read(this, t, !1, 52, 8); }, u.prototype.writeUIntLE = function (t, e, r, n) { (t = +t, e |= 0, r |= 0, n) || B(this, t, e, r, Math.pow(2, 8 * r) - 1, 0); var i = 1, o = 0; for (this[e] = 255 & t; ++o < r && (i *= 256);) this[e + o] = t / i & 255; return e + r; }, u.prototype.writeUIntBE = function (t, e, r, n) { (t = +t, e |= 0, r |= 0, n) || B(this, t, e, r, Math.pow(2, 8 * r) - 1, 0); var i = r - 1, o = 1; for (this[e + i] = 255 & t; --i >= 0 && (o *= 256);) this[e + i] = t / o & 255; return e + r; }, u.prototype.writeUInt8 = function (t, e, r) { return t = +t, e |= 0, r || B(this, t, e, 1, 255, 0), u.TYPED_ARRAY_SUPPORT || (t = Math.floor(t)), this[e] = 255 & t, e + 1; }, u.prototype.writeUInt16LE = function (t, e, r) { return t = +t, e |= 0, r || B(this, t, e, 2, 65535, 0), u.TYPED_ARRAY_SUPPORT ? (this[e] = 255 & t, this[e + 1] = t >>> 8) : P(this, t, e, !0), e + 2; }, u.prototype.writeUInt16BE = function (t, e, r) { return t = +t, e |= 0, r || B(this, t, e, 2, 65535, 0), u.TYPED_ARRAY_SUPPORT ? (this[e] = t >>> 8, this[e + 1] = 255 & t) : P(this, t, e, !1), e + 2; }, u.prototype.writeUInt32LE = function (t, e, r) { return t = +t, e |= 0, r || B(this, t, e, 4, 4294967295, 0), u.TYPED_ARRAY_SUPPORT ? (this[e + 3] = t >>> 24, this[e + 2] = t >>> 16, this[e + 1] = t >>> 8, this[e] = 255 & t) : F(this, t, e, !0), e + 4; }, u.prototype.writeUInt32BE = function (t, e, r) { return t = +t, e |= 0, r || B(this, t, e, 4, 4294967295, 0), u.TYPED_ARRAY_SUPPORT ? (this[e] = t >>> 24, this[e + 1] = t >>> 16, this[e + 2] = t >>> 8, this[e + 3] = 255 & t) : F(this, t, e, !1), e + 4; }, u.prototype.writeIntLE = function (t, e, r, n) { if (t = +t, e |= 0, !n) { var i = Math.pow(2, 8 * r - 1); B(this, t, e, r, i - 1, -i); } var o = 0, a = 1, s = 0; for (this[e] = 255 & t; ++o < r && (a *= 256);) t < 0 && 0 === s && 0 !== this[e + o - 1] && (s = 1), this[e + o] = (t / a >> 0) - s & 255; return e + r; }, u.prototype.writeIntBE = function (t, e, r, n) { if (t = +t, e |= 0, !n) { var i = Math.pow(2, 8 * r - 1); B(this, t, e, r, i - 1, -i); } var o = r - 1, a = 1, s = 0; for (this[e + o] = 255 & t; --o >= 0 && (a *= 256);) t < 0 && 0 === s && 0 !== this[e + o + 1] && (s = 1), this[e + o] = (t / a >> 0) - s & 255; return e + r; }, u.prototype.writeInt8 = function (t, e, r) { return t = +t, e |= 0, r || B(this, t, e, 1, 127, -128), u.TYPED_ARRAY_SUPPORT || (t = Math.floor(t)), t < 0 && (t = 255 + t + 1), this[e] = 255 & t, e + 1; }, u.prototype.writeInt16LE = function (t, e, r) { return t = +t, e |= 0, r || B(this, t, e, 2, 32767, -32768), u.TYPED_ARRAY_SUPPORT ? 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