[galaxy-commits] commit/galaxy-central: kanwei: update jquery to 1.5.2, pack scripts

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0f3a0c220945/ changeset: r5368:0f3a0c220945 user: kanwei date: 2011-04-12 18:10:48 summary: update jquery to 1.5.2, pack scripts affected #: 3 files (3.2 KB) --- a/static/scripts/jquery.js Tue Apr 12 09:35:36 2011 -0400 +++ b/static/scripts/jquery.js Tue Apr 12 12:10:48 2011 -0400 @@ -1,5 +1,5 @@ /*! - * jQuery JavaScript Library v1.5.1 + * jQuery JavaScript Library v1.5.2 * http://jquery.com/ * * Copyright 2011, John Resig @@ -11,7 +11,7 @@ * Copyright 2011, The Dojo Foundation * Released under the MIT, BSD, and GPL Licenses. * - * Date: Wed Feb 23 13:55:29 2011 -0500 + * Date: Thu Mar 31 15:28:23 2011 -0400 */ (function( window, undefined ) { @@ -69,15 +69,9 @@ // For matching the engine and version of the browser browserMatch, - // Has the ready events already been bound? - readyBound = false, - // The deferred used on DOM ready readyList, - // Promise methods - promiseMethods = "then done fail isResolved isRejected promise".split( " " ), - // The ready event handler DOMContentLoaded, @@ -202,7 +196,7 @@ selector: "", // The current version of jQuery being used - jquery: "1.5.1", + jquery: "1.5.2", // The default length of a jQuery object is 0 length: 0, @@ -427,11 +421,11 @@ }, bindReady: function() { - if ( readyBound ) { + if ( readyList ) { return; } - readyBound = true; + readyList = jQuery._Deferred(); // Catch cases where $(document).ready() is called after the // browser event has already occurred. @@ -811,6 +805,123 @@ return (new Date()).getTime(); }, + // Use of jQuery.browser is frowned upon. + // More details: http://docs.jquery.com/Utilities/jQuery.browser + uaMatch: function( ua ) { + ua = ua.toLowerCase(); + + var match = rwebkit.exec( ua ) || + ropera.exec( ua ) || + rmsie.exec( ua ) || + ua.indexOf("compatible") < 0 && rmozilla.exec( ua ) || + []; + + return { browser: match[1] || "", version: match[2] || "0" }; + }, + + sub: function() { + function jQuerySubclass( selector, context ) { + return new jQuerySubclass.fn.init( selector, context ); + } + jQuery.extend( true, jQuerySubclass, this ); + jQuerySubclass.superclass = this; + jQuerySubclass.fn = jQuerySubclass.prototype = this(); + jQuerySubclass.fn.constructor = jQuerySubclass; + jQuerySubclass.subclass = this.subclass; + jQuerySubclass.fn.init = function init( selector, context ) { + if ( context && context instanceof jQuery && !(context instanceof jQuerySubclass) ) { + context = jQuerySubclass(context); + } + + return jQuery.fn.init.call( this, selector, context, rootjQuerySubclass ); + }; + jQuerySubclass.fn.init.prototype = jQuerySubclass.fn; + var rootjQuerySubclass = jQuerySubclass(document); + return jQuerySubclass; + }, + + browser: {} +}); + +// Populate the class2type map +jQuery.each("Boolean Number String Function Array Date RegExp Object".split(" "), function(i, name) { + class2type[ "[object " + name + "]" ] = name.toLowerCase(); +}); + +browserMatch = jQuery.uaMatch( userAgent ); +if ( browserMatch.browser ) { + jQuery.browser[ browserMatch.browser ] = true; + jQuery.browser.version = browserMatch.version; +} + +// Deprecated, use jQuery.browser.webkit instead +if ( jQuery.browser.webkit ) { + jQuery.browser.safari = true; +} + +if ( indexOf ) { + jQuery.inArray = function( elem, array ) { + return indexOf.call( array, elem ); + }; +} + +// IE doesn't match non-breaking spaces with \s +if ( rnotwhite.test( "\xA0" ) ) { + trimLeft = /^[\s\xA0]+/; + trimRight = /[\s\xA0]+$/; +} + +// All jQuery objects should point back to these +rootjQuery = jQuery(document); + +// Cleanup functions for the document ready method +if ( document.addEventListener ) { + DOMContentLoaded = function() { + document.removeEventListener( "DOMContentLoaded", DOMContentLoaded, false ); + jQuery.ready(); + }; + +} else if ( document.attachEvent ) { + DOMContentLoaded = function() { + // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443). + if ( document.readyState === "complete" ) { + document.detachEvent( "onreadystatechange", DOMContentLoaded ); + jQuery.ready(); + } + }; +} + +// The DOM ready check for Internet Explorer +function doScrollCheck() { + if ( jQuery.isReady ) { + return; + } + + try { + // If IE is used, use the trick by Diego Perini + // http://javascript.nwbox.com/IEContentLoaded/ + document.documentElement.doScroll("left"); + } catch(e) { + setTimeout( doScrollCheck, 1 ); + return; + } + + // and execute any waiting functions + jQuery.ready(); +} + +// Expose jQuery to the global object +return jQuery; + +})(); + + +var // Promise methods + promiseMethods = "then done fail isResolved isRejected promise".split( " " ), + // Static reference to slice + sliceDeferred = [].slice; + +jQuery.extend({ // Create a simple deferred (one callbacks list) _Deferred: function() { var // callbacks list @@ -856,18 +967,14 @@ // resolve with given context and args resolveWith: function( context, args ) { if ( !cancelled && !fired && !firing ) { + // make sure args are available (#8421) + args = args || []; firing = 1; try { while( callbacks[ 0 ] ) { callbacks.shift().apply( context, args ); } } - // We have to add a catch block for - // IE prior to 8 or else the finally - // block will never get executed - catch (e) { - throw e; - } finally { fired = [ context, args ]; firing = 0; @@ -878,7 +985,7 @@ // resolve with this as context and given arguments resolve: function() { - deferred.resolveWith( jQuery.isFunction( this.promise ) ? this.promise() : this, arguments ); + deferred.resolveWith( this, arguments ); return this; }, @@ -941,153 +1048,44 @@ }, // Deferred helper - when: function( object ) { - var lastIndex = arguments.length, - deferred = lastIndex <= 1 && object && jQuery.isFunction( object.promise ) ? - object : - jQuery.Deferred(), - promise = deferred.promise(); - - if ( lastIndex > 1 ) { - var array = slice.call( arguments, 0 ), - count = lastIndex, - iCallback = function( index ) { - return function( value ) { - array[ index ] = arguments.length > 1 ? slice.call( arguments, 0 ) : value; - if ( !( --count ) ) { - deferred.resolveWith( promise, array ); - } - }; - }; - while( ( lastIndex-- ) ) { - object = array[ lastIndex ]; - if ( object && jQuery.isFunction( object.promise ) ) { - object.promise().then( iCallback(lastIndex), deferred.reject ); + when: function( firstParam ) { + var args = arguments, + i = 0, + length = args.length, + count = length, + deferred = length <= 1 && firstParam && jQuery.isFunction( firstParam.promise ) ? + firstParam : + jQuery.Deferred(); + function resolveFunc( i ) { + return function( value ) { + args[ i ] = arguments.length > 1 ? sliceDeferred.call( arguments, 0 ) : value; + if ( !( --count ) ) { + // Strange bug in FF4: + // Values changed onto the arguments object sometimes end up as undefined values + // outside the $.when method. Cloning the object into a fresh array solves the issue + deferred.resolveWith( deferred, sliceDeferred.call( args, 0 ) ); + } + }; + } + if ( length > 1 ) { + for( ; i < length; i++ ) { + if ( args[ i ] && jQuery.isFunction( args[ i ].promise ) ) { + args[ i ].promise().then( resolveFunc(i), deferred.reject ); } else { --count; } } if ( !count ) { - deferred.resolveWith( promise, array ); - } - } else if ( deferred !== object ) { - deferred.resolve( object ); - } - return promise; - }, - - // Use of jQuery.browser is frowned upon. - // More details: http://docs.jquery.com/Utilities/jQuery.browser - uaMatch: function( ua ) { - ua = ua.toLowerCase(); - - var match = rwebkit.exec( ua ) || - ropera.exec( ua ) || - rmsie.exec( ua ) || - ua.indexOf("compatible") < 0 && rmozilla.exec( ua ) || - []; - - return { browser: match[1] || "", version: match[2] || "0" }; - }, - - sub: function() { - function jQuerySubclass( selector, context ) { - return new jQuerySubclass.fn.init( selector, context ); - } - jQuery.extend( true, jQuerySubclass, this ); - jQuerySubclass.superclass = this; - jQuerySubclass.fn = jQuerySubclass.prototype = this(); - jQuerySubclass.fn.constructor = jQuerySubclass; - jQuerySubclass.subclass = this.subclass; - jQuerySubclass.fn.init = function init( selector, context ) { - if ( context && context instanceof jQuery && !(context instanceof jQuerySubclass) ) { - context = jQuerySubclass(context); - } - - return jQuery.fn.init.call( this, selector, context, rootjQuerySubclass ); - }; - jQuerySubclass.fn.init.prototype = jQuerySubclass.fn; - var rootjQuerySubclass = jQuerySubclass(document); - return jQuerySubclass; - }, - - browser: {} + deferred.resolveWith( deferred, args ); + } + } else if ( deferred !== firstParam ) { + deferred.resolveWith( deferred, length ? [ firstParam ] : [] ); + } + return deferred.promise(); + } }); -// Create readyList deferred -readyList = jQuery._Deferred(); - -// Populate the class2type map -jQuery.each("Boolean Number String Function Array Date RegExp Object".split(" "), function(i, name) { - class2type[ "[object " + name + "]" ] = name.toLowerCase(); -}); - -browserMatch = jQuery.uaMatch( userAgent ); -if ( browserMatch.browser ) { - jQuery.browser[ browserMatch.browser ] = true; - jQuery.browser.version = browserMatch.version; -} - -// Deprecated, use jQuery.browser.webkit instead -if ( jQuery.browser.webkit ) { - jQuery.browser.safari = true; -} - -if ( indexOf ) { - jQuery.inArray = function( elem, array ) { - return indexOf.call( array, elem ); - }; -} - -// IE doesn't match non-breaking spaces with \s -if ( rnotwhite.test( "\xA0" ) ) { - trimLeft = /^[\s\xA0]+/; - trimRight = /[\s\xA0]+$/; -} - -// All jQuery objects should point back to these -rootjQuery = jQuery(document); - -// Cleanup functions for the document ready method -if ( document.addEventListener ) { - DOMContentLoaded = function() { - document.removeEventListener( "DOMContentLoaded", DOMContentLoaded, false ); - jQuery.ready(); - }; - -} else if ( document.attachEvent ) { - DOMContentLoaded = function() { - // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443). - if ( document.readyState === "complete" ) { - document.detachEvent( "onreadystatechange", DOMContentLoaded ); - jQuery.ready(); - } - }; -} - -// The DOM ready check for Internet Explorer -function doScrollCheck() { - if ( jQuery.isReady ) { - return; - } - - try { - // If IE is used, use the trick by Diego Perini - // http://javascript.nwbox.com/IEContentLoaded/ - document.documentElement.doScroll("left"); - } catch(e) { - setTimeout( doScrollCheck, 1 ); - return; - } - - // and execute any waiting functions - jQuery.ready(); -} - -// Expose jQuery to the global object -return jQuery; - -})(); + (function() { @@ -1157,7 +1155,8 @@ boxModel: null, inlineBlockNeedsLayout: false, shrinkWrapBlocks: false, - reliableHiddenOffsets: true + reliableHiddenOffsets: true, + reliableMarginRight: true }; input.checked = true; @@ -1175,15 +1174,15 @@ script = document.createElement("script"), id = "script" + jQuery.now(); + // Make sure that the execution of code works by injecting a script + // tag with appendChild/createTextNode + // (IE doesn't support this, fails, and uses .text instead) try { script.appendChild( document.createTextNode( "window." + id + "=1;" ) ); } catch(e) {} root.insertBefore( script, root.firstChild ); - // Make sure that the execution of code works by injecting a script - // tag with appendChild/createTextNode - // (IE doesn't support this, fails, and uses .text instead) if ( window[ id ] ) { _scriptEval = true; delete window[ id ]; @@ -1192,8 +1191,6 @@ } root.removeChild( script ); - // release memory in IE - root = script = id = null; } return _scriptEval; @@ -1278,6 +1275,17 @@ jQuery.support.reliableHiddenOffsets = jQuery.support.reliableHiddenOffsets && tds[0].offsetHeight === 0; div.innerHTML = ""; + // Check if div with explicit width and no margin-right incorrectly + // gets computed margin-right based on width of container. For more + // info see bug #3333 + // Fails in WebKit before Feb 2011 nightlies + // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right + if ( document.defaultView && document.defaultView.getComputedStyle ) { + div.style.width = "1px"; + div.style.marginRight = "0"; + jQuery.support.reliableMarginRight = ( parseInt(document.defaultView.getComputedStyle(div, null).marginRight, 10) || 0 ) === 0; + } + body.removeChild( div ).style.display = "none"; div = tds = null; }); @@ -1301,8 +1309,6 @@ el.setAttribute(eventName, "return;"); isSupported = typeof el[eventName] === "function"; } - el = null; - return isSupported; }; @@ -2194,10 +2200,10 @@ } if ( !eventHandle ) { - elemData.handle = eventHandle = function() { + elemData.handle = eventHandle = function( e ) { // Handle the second event of a trigger and when // an event is called after a page has unloaded - return typeof jQuery !== "undefined" && !jQuery.event.triggered ? + return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ? jQuery.event.handle.apply( eventHandle.elem, arguments ) : undefined; }; @@ -2504,7 +2510,7 @@ target[ "on" + targetType ] = null; } - jQuery.event.triggered = true; + jQuery.event.triggered = event.type; target[ targetType ](); } @@ -2515,7 +2521,7 @@ target[ "on" + targetType ] = old; } - jQuery.event.triggered = false; + jQuery.event.triggered = undefined; } } }, @@ -2785,7 +2791,7 @@ // Chrome does something similar, the parentNode property // can be accessed but is null. - if ( parent !== document && !parent.parentNode ) { + if ( parent && parent !== document && !parent.parentNode ) { return; } // Traverse up the tree @@ -2992,19 +2998,33 @@ // Create "bubbling" focus and blur events if ( document.addEventListener ) { jQuery.each({ focus: "focusin", blur: "focusout" }, function( orig, fix ) { + + // Attach a single capturing handler while someone wants focusin/focusout + var attaches = 0; + jQuery.event.special[ fix ] = { setup: function() { - this.addEventListener( orig, handler, true ); + if ( attaches++ === 0 ) { + document.addEventListener( orig, handler, true ); + } }, teardown: function() { - this.removeEventListener( orig, handler, true ); + if ( --attaches === 0 ) { + document.removeEventListener( orig, handler, true ); + } } }; - function handler( e ) { - e = jQuery.event.fix( e ); + function handler( donor ) { + // Donor event is always a native one; fix it and switch its type. + // Let focusin/out handler cancel the donor focus/blur event. + var e = jQuery.event.fix( donor ); e.type = fix; - return jQuery.event.handle.call( this, e ); + e.originalEvent = {}; + jQuery.event.trigger( e, null, e.target ); + if ( e.isDefaultPrevented() ) { + donor.preventDefault(); + } } }); } @@ -3918,10 +3938,12 @@ }, text: function( elem ) { + var attr = elem.getAttribute( "type" ), type = elem.type; // IE6 and 7 will map elem.type to 'text' for new HTML5 types (search, etc) // use getAttribute instead to test this case - return "text" === elem.getAttribute( 'type' ); + return "text" === type && ( attr === type || attr === null ); }, + radio: function( elem ) { return "radio" === elem.type; }, @@ -4496,19 +4518,23 @@ (function(){ var html = document.documentElement, - matches = html.matchesSelector || html.mozMatchesSelector || html.webkitMatchesSelector || html.msMatchesSelector, - pseudoWorks = false; - - try { - // This should fail with an exception - // Gecko does not error, returns false instead - matches.call( document.documentElement, "[test!='']:sizzle" ); + matches = html.matchesSelector || html.mozMatchesSelector || html.webkitMatchesSelector || html.msMatchesSelector; + + if ( matches ) { + // Check to see if it's possible to do matchesSelector + // on a disconnected node (IE 9 fails this) + var disconnectedMatch = !matches.call( document.createElement( "div" ), "div" ), + pseudoWorks = false; + + try { + // This should fail with an exception + // Gecko does not error, returns false instead + matches.call( document.documentElement, "[test!='']:sizzle" ); - } catch( pseudoError ) { - pseudoWorks = true; - } - - if ( matches ) { + } catch( pseudoError ) { + pseudoWorks = true; + } + Sizzle.matchesSelector = function( node, expr ) { // Make sure that attribute selectors are quoted expr = expr.replace(/\=\s*([^'"\]]*)\s*\]/g, "='$1']"); @@ -4516,7 +4542,15 @@ if ( !Sizzle.isXML( node ) ) { try { if ( pseudoWorks || !Expr.match.PSEUDO.test( expr ) && !/!=/.test( expr ) ) { - return matches.call( node, expr ); + var ret = matches.call( node, expr ); + + // IE 9's matchesSelector returns false on disconnected nodes + if ( ret || !disconnectedMatch || + // As well, disconnected nodes are said to be in a document + // fragment in IE 9, so check for that + node.document && node.document.nodeType !== 11 ) { + return ret; + } } } catch(e) {} } @@ -5260,7 +5294,9 @@ } }); } else { - return this.pushStack( jQuery(jQuery.isFunction(value) ? value() : value), "replaceWith", value ); + return this.length ? + this.pushStack( jQuery(jQuery.isFunction(value) ? value() : value), "replaceWith", value ) : + this; } }, @@ -5707,7 +5743,8 @@ var ralpha = /alpha\([^)]*\)/i, ropacity = /opacity=([^)]*)/, rdashAlpha = /-([a-z])/ig, - rupper = /([A-Z])/g, + // fixed for IE9, see #8346 + rupper = /([A-Z]|^ms)/g, rnumpx = /^-?\d+(?:px)?$/i, rnum = /^-?\d/, @@ -5944,6 +5981,28 @@ }; } +jQuery(function() { + // This hook cannot be added until DOM ready because the support test + // for it is not run until after DOM ready + if ( !jQuery.support.reliableMarginRight ) { + jQuery.cssHooks.marginRight = { + get: function( elem, computed ) { + // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right + // Work around by temporarily setting element display to inline-block + var ret; + jQuery.swap( elem, { "display": "inline-block" }, function() { + if ( computed ) { + ret = curCSS( elem, "margin-right", "marginRight" ); + } else { + ret = elem.style.marginRight; + } + }); + return ret; + } + }; + } +}); + if ( document.defaultView && document.defaultView.getComputedStyle ) { getComputedStyle = function( elem, newName, name ) { var ret, defaultView, computedStyle; @@ -6048,7 +6107,7 @@ rheaders = /^(.*?):[ \t]*([^\r\n]*)\r?$/mg, // IE leaves an \r character at EOL rinput = /^(?:color|date|datetime|email|hidden|month|number|password|range|search|tel|text|time|url|week)$/i, // #7653, #8125, #8152: local protocol detection - rlocalProtocol = /(?:^file|^widget|\-extension):$/, + rlocalProtocol = /^(?:about|app|app\-storage|.+\-extension|file|widget):$/, rnoContent = /^(?:GET|HEAD)$/, rprotocol = /^\/\//, rquery = /\?/, @@ -6060,7 +6119,7 @@ rucHeadersFunc = function( _, $1, $2 ) { return $1 + $2.toUpperCase(); }, - rurl = /^([\w\+\.\-]+:)\/\/([^\/?#:]*)(?::(\d+))?/, + rurl = /^([\w\+\.\-]+:)(?:\/\/([^\/?#:]*)(?::(\d+))?)?/, // Keep a copy of the old load method _load = jQuery.fn.load, @@ -6102,7 +6161,7 @@ } // Segment location into parts -ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ); +ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ) || []; // Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport function addToPrefiltersOrTransports( structure ) { @@ -6360,7 +6419,6 @@ cache: null, traditional: false, headers: {}, - crossDomain: null, */ accepts: { @@ -6645,7 +6703,7 @@ s.dataTypes = jQuery.trim( s.dataType || "*" ).toLowerCase().split( rspacesAjax ); // Determine if a cross-domain request is in order - if ( !s.crossDomain ) { + if ( s.crossDomain == null ) { parts = rurl.exec( s.url.toLowerCase() ); s.crossDomain = !!( parts && ( parts[ 1 ] != ajaxLocParts[ 1 ] || parts[ 2 ] != ajaxLocParts[ 2 ] || @@ -7024,7 +7082,7 @@ var jsc = jQuery.now(), - jsre = /(\=)\?(&|$)|()\?\?()/i; + jsre = /(\=)\?(&|$)|\?\?/i; // Default jsonp settings jQuery.ajaxSetup({ @@ -7285,11 +7343,12 @@ xhr.overrideMimeType( s.mimeType ); } - // Requested-With header - // Not set for crossDomain requests with no content - // (see why at http://trac.dojotoolkit.org/ticket/9486) - // Won't change header if already provided - if ( !( s.crossDomain && !s.hasContent ) && !headers["X-Requested-With"] ) { + // X-Requested-With header + // For cross-domain requests, seeing as conditions for a preflight are + // akin to a jigsaw puzzle, we simply never set it to be sure. + // (it can always be set on a per-request basis or even using ajaxSetup) + // For same-domain requests, won't change header if already provided. + if ( !s.crossDomain && !headers["X-Requested-With"] ) { headers[ "X-Requested-With" ] = "XMLHttpRequest"; } @@ -7979,8 +8038,8 @@ win = getWindow(doc), clientTop = docElem.clientTop || body.clientTop || 0, clientLeft = docElem.clientLeft || body.clientLeft || 0, - scrollTop = (win.pageYOffset || jQuery.support.boxModel && docElem.scrollTop || body.scrollTop ), - scrollLeft = (win.pageXOffset || jQuery.support.boxModel && docElem.scrollLeft || body.scrollLeft), + scrollTop = win.pageYOffset || jQuery.support.boxModel && docElem.scrollTop || body.scrollTop, + scrollLeft = win.pageXOffset || jQuery.support.boxModel && docElem.scrollLeft || body.scrollLeft, top = box.top + scrollTop - clientTop, left = box.left + scrollLeft - clientLeft; @@ -8093,7 +8152,6 @@ this.doesNotIncludeMarginInBodyOffset = (body.offsetTop !== bodyMarginTop); body.removeChild( container ); - body = container = innerDiv = checkDiv = table = td = null; jQuery.offset.initialize = jQuery.noop; }, @@ -8123,10 +8181,10 @@ curOffset = curElem.offset(), curCSSTop = jQuery.css( elem, "top" ), curCSSLeft = jQuery.css( elem, "left" ), - calculatePosition = (position === "absolute" && jQuery.inArray('auto', [curCSSTop, curCSSLeft]) > -1), + calculatePosition = (position === "absolute" || position === "fixed") && jQuery.inArray('auto', [curCSSTop, curCSSLeft]) > -1, props = {}, curPosition = {}, curTop, curLeft; - // need to be able to calculate position if either top or left is auto and position is absolute + // 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(); } --- a/static/scripts/packed/jquery.js Tue Apr 12 09:35:36 2011 -0400 +++ b/static/scripts/packed/jquery.js Tue Apr 12 12:10:48 2011 -0400 @@ -1,5 +1,5 @@ /* - * jQuery JavaScript Library v1.5.1 + * jQuery JavaScript Library v1.5.2 * http://jquery.com/ * * Copyright 2011, John Resig @@ -11,13 +11,13 @@ * Copyright 2011, The Dojo Foundation * Released under the MIT, BSD, and GPL Licenses. * - * Date: Wed Feb 23 13:55:29 2011 -0500 + * Date: Thu Mar 31 15:28:23 2011 -0400 */ -(function(aY,H){var al=aY.document;var a=(function(){var bn=function(bI,bJ){return new bn.fn.init(bI,bJ,bl)},bD=aY.jQuery,bp=aY.$,bl,bH=/^(?:[^<]*(<[\w\W]+>)[^>]*$|#([\w\-]+)$)/,bv=/\S/,br=/^\s+/,bm=/\s+$/,bq=/\d/,bj=/^<(\w+)\s*\/?>(?:<\/\1>)?$/,bw=/^[\],:{}\s]*$/,bF=/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g,by=/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,bs=/(?:^|:|,)(?:\s*\[)+/g,bh=/(webkit)[ \/]([\w.]+)/,bA=/(opera)(?:.*version)?[ \/]([\w.]+)/,bz=/(msie) ([\w.]+)/,bB=/(mozilla)(?:.*? rv:([\w.]+))?/,bG=navigator.userAgent,bE,bC=false,bk,e="then done fail isResolved isRejected promise".split(" "),bd,bu=Object.prototype.toString,bo=Object.prototype.hasOwnProperty,bi=Array.prototype.push,bt=Array.prototype.slice,bx=String.prototype.trim,be=Array.prototype.indexOf,bg={};bn.fn=bn.prototype={constructor:bn,init:function(bI,bM,bL){var bK,bN,bJ,bO;if(!bI){return this}if(bI.nodeType){this.context=this[0]=bI;this.length=1;return this}if(bI==="body"&&!bM&&al.body){this.context=al;this[0]=al.body;this.selector="body";this.length=1;return this}if(typeof bI==="string"){bK=bH.exec(bI);if(bK&&(bK[1]||!bM)){if(bK[1]){bM=bM instanceof bn?bM[0]:bM;bO=(bM?bM.ownerDocument||bM:al);bJ=bj.exec(bI);if(bJ){if(bn.isPlainObject(bM)){bI=[al.createElement(bJ[1])];bn.fn.attr.call(bI,bM,true)}else{bI=[bO.createElement(bJ[1])]}}else{bJ=bn.buildFragment([bK[1]],[bO]);bI=(bJ.cacheable?bn.clone(bJ.fragment):bJ.fragment).childNodes}return bn.merge(this,bI)}else{bN=al.getElementById(bK[2]);if(bN&&bN.parentNode){if(bN.id!==bK[2]){return bL.find(bI)}this.length=1;this[0]=bN}this.context=al;this.selector=bI;return this}}else{if(!bM||bM.jquery){return(bM||bL).find(bI)}else{return this.constructor(bM).find(bI)}}}else{if(bn.isFunction(bI)){return bL.ready(bI)}}if(bI.selector!==H){this.selector=bI.selector;this.context=bI.context}return bn.makeArray(bI,this)},selector:"",jquery:"1.5.1",length:0,size:function(){return this.length},toArray:function(){return bt.call(this,0)},get:function(bI){return bI==null?this.toArray():(bI<0?this[this.length+bI]:this[bI])},pushStack:function(bJ,bL,bI){var bK=this.constructor();if(bn.isArray(bJ)){bi.apply(bK,bJ)}else{bn.merge(bK,bJ)}bK.prevObject=this;bK.context=this.context;if(bL==="find"){bK.selector=this.selector+(this.selector?" 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at end of file --- a/static/scripts/packed/trackster.js Tue Apr 12 09:35:36 2011 -0400 +++ b/static/scripts/packed/trackster.js Tue Apr 12 12:10:48 2011 -0400 @@ -1,1 +1,1 @@ -var extend=function(){var c=arguments[0];for(var b=1;b<arguments.length;b++){var a=arguments[b];for(key in a){c[key]=a[key]}}return c};var trackster_module=function(f,Q){var o=f("slotting"),G=f("painters");var V=function(W,X){this.document=W;this.default_font=X!==undefined?X:"9px Monaco, Lucida Console, 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Z=aa.children();var Y;for(Y=0;Y<Z.length;Y++){if(ac.offsetY<$(Z.get(Y)).position().top){break}}if(Y===Z.length){if(this!==Z.get(Y-1)){aa.append(this)}}else{if(this!==Z.get(Y)){$(this).insertBefore(Z.get(Y))}}})};var h=function(Y,W){var X=W-Y;return(X<=2?0.01:(X<=100?1:(X<=1000?5:10)))};var C=9,z=10,L=C+2,w=100,D=12000,J=200,r=10,F=5000,s=100,m="There was an error in indexing this dataset. 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Please check your datatypes_conf.xml file.",A="No data for this chrom/contig.",p="Currently indexing... please wait",u="Tool cannot be rerun: ",a="Loading data...",R="Ready for display",d=10,q=5,y=5;function t(W){return Math.round(W*1000)/1000}var c=function(W){this.num_elements=W;this.clear()};extend(c.prototype,{get:function(X){var W=this.key_ary.indexOf(X);if(W!==-1){this.move_key_to_end(X,W)}return this.obj_cache[X]},set:function(X,Y){if(!this.obj_cache[X]){if(this.key_ary.length>=this.num_elements){var W=this.key_ary.shift();delete this.obj_cache[W]}this.key_ary.push(X)}this.obj_cache[X]=Y;return Y},move_key_to_end:function(X,W){this.key_ary.splice(W,1);this.key_ary.push(X)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var K=function(X,W,Y){c.call(this,X);this.track=W;this.subset=(Y!==undefined?Y:true)};extend(K.prototype,c.prototype,{load_data:function(ad,ae,Z,ac,W,ab){var Y={chrom:ad,low:ae,high:Z,mode:ac,resolution:W,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(Y,ab);var af=[];for(var aa=0;aa<this.track.filters.length;aa++){af[af.length]=this.track.filters[aa].name}Y.filter_cols=JSON.stringify(af);var X=this;return $.getJSON(this.track.data_url,Y,function(ag){X.set_data(ae,Z,ac,ag)})},get_data:function(Y,W,ab,ac,X,aa){var Z=this.get(this.gen_key(W,ab,ac));if(Z){return Z}Z=this.load_data(Y,W,ab,ac,X,aa);this.set_data(W,ab,ac,Z);return Z},set_data:function(X,Y,Z,W){return this.set(this.gen_key(X,Y,Z),W)},gen_key:function(W,Y,Z){var X=W+"_"+Y+"_"+Z;return X},split_key:function(W){return W.split("_")}});var U=function(W,Z,Y,X,aa){this.container=W;this.chrom=null;this.vis_id=Y;this.dbkey=X;this.title=Z;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(aa);this.canvas_manager=new V(W.get(0).ownerDocument);this.reset()};extend(U.prototype,{init:function(Z){var Y=this.container,W=this;this.top_container=$("<div/>").addClass("top-container").appendTo(Y);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(Y);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(Y);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown 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Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var X=function(aa){if(aa.type==="focusout"||(aa.keyCode||aa.which)===13||(aa.keyCode||aa.which)===27){if((aa.keyCode||aa.which)!==27){W.go_to($(this).val())}$(this).hide();$(this).val("");W.location_span.show();W.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup 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ab=0,aa=W.tracks.length;ab<aa;ab++){W.tracks[ab].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",W.overview_box.height());W.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(aa,ab){if(aa.clientX>W.viewport_container.width()-16){return false}}).bind("dragstart",function(aa,ab){ab.original_low=W.low;ab.current_height=aa.clientY;ab.current_x=ab.offsetX}).bind("drag",function(ac,ae){var aa=$(this);var af=ae.offsetX-ae.current_x;var ab=aa.scrollTop()-(ac.clientY-ae.current_height);aa.scrollTop(ab);ae.current_height=ac.clientY;ae.current_x=ae.offsetX;var ad=Math.round(af/W.viewport_container.width()*(W.high-W.low));W.move_delta(ad)}).bind("mousewheel",function(ac,ae,ab,aa){if(ab){var ad=Math.round(-ab/W.viewport_container.width()*(W.high-W.low));W.move_delta(ad)}});this.top_labeltrack.bind("dragstart",function(aa,ab){return $("<div />").css({height:W.content_div.height()+W.top_labeltrack.height()+W.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ae,af){$(af.proxy).css({left:Math.min(ae.pageX,af.startX),width:Math.abs(ae.pageX-af.startX)});var ab=Math.min(ae.pageX,af.startX)-W.container.offset().left,aa=Math.max(ae.pageX,af.startX)-W.container.offset().left,ad=(W.high-W.low),ac=W.viewport_container.width();W.update_location(Math.round(ab/ac*ad)+W.low,Math.round(aa/ac*ad)+W.low)}).bind("dragend",function(af,ag){var ab=Math.min(af.pageX,ag.startX),aa=Math.max(af.pageX,ag.startX),ad=(W.high-W.low),ac=W.viewport_container.width(),ae=W.low;W.low=Math.round(ab/ac*ad)+ae;W.high=Math.round(aa/ac*ad)+ae;$(ag.proxy).remove();W.redraw()});this.add_label_track(new T(this,this.top_labeltrack));this.add_label_track(new T(this,this.nav_labeltrack));$(window).bind("resize",function(){W.resize_window()});$(document).bind("redraw",function(){W.redraw()});this.reset();$(window).trigger("resize")},update_location:function(W,X){this.location_span.text(commatize(W)+" - "+commatize(X));this.nav_input.val(this.chrom+":"+commatize(W)+"-"+commatize(X))},load_chroms:function(X,Y){X.num=s;$.extend(X,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var W=this;$.ajax({url:chrom_url,data:X,dataType:"json",success:function(aa){if(aa.chrom_info.length===0){alert("Invalid chromosome: "+X.chrom);return}if(aa.reference){W.add_label_track(new x(W))}W.chrom_data=aa.chrom_info;var ad='<option value="">Select Chrom/Contig</option>';for(var ac=0,Z=W.chrom_data.length;ac<Z;ac++){var ab=W.chrom_data[ac].chrom;ad+='<option value="'+ab+'">'+ab+"</option>"}if(aa.prev_chroms){ad+='<option value="previous">Previous '+s+"</option>"}if(aa.next_chroms){ad+='<option value="next">Next '+s+"</option>"}W.chrom_select.html(ad);if(Y){Y()}W.chrom_start_index=aa.start_index},error:function(){alert("Could not load chroms for this dbkey:",W.dbkey)}})},change_chrom:function(aa,X,ac){if(!aa||aa==="None"){return}var Z=this;if(aa==="previous"){Z.load_chroms({low:this.chrom_start_index-s});return}if(aa==="next"){Z.load_chroms({low:this.chrom_start_index+s});return}var ab=$.grep(Z.chrom_data,function(ae,af){return ae.chrom===aa})[0];if(ab===undefined){Z.load_chroms({chrom:aa},function(){Z.change_chrom(aa,X,ac)});return}else{if(aa!==Z.chrom){Z.chrom=aa;if(!Z.chrom){Z.intro_div.show()}else{Z.intro_div.hide()}Z.chrom_select.val(Z.chrom);Z.max_high=ab.len-1;Z.reset();Z.redraw(true);for(var ad=0,W=Z.tracks.length;ad<W;ad++){var Y=Z.tracks[ad];if(Y.init){Y.init()}}}if(X!==undefined&&ac!==undefined){Z.low=Math.max(X,0);Z.high=Math.min(ac,Z.max_high)}Z.reset_overview();Z.redraw()}},go_to:function(aa){var ae=this,W,Z,X=aa.split(":"),ac=X[0],ad=X[1];if(ad!==undefined){try{var ab=ad.split("-");W=parseInt(ab[0].replace(/,/g,""),10);Z=parseInt(ab[1].replace(/,/g,""),10)}catch(Y){return false}}ae.change_chrom(ac,W,Z)},move_fraction:function(Y){var W=this;var X=W.high-W.low;this.move_delta(Y*X)},move_delta:function(Y){var W=this;var X=W.high-W.low;if(W.low-Y<W.max_low){W.low=W.max_low;W.high=W.max_low+X}else{if(W.high-Y>W.max_high){W.high=W.max_high;W.low=W.max_high-X}else{W.high-=Y;W.low-=Y}}W.redraw()},add_track:function(W){W.view=this;W.track_id=this.track_id_counter;this.tracks.push(W);if(W.init){W.init()}W.container_div.attr("id","track_"+W.track_id);B(W.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(W){W.view=this;this.label_tracks.push(W)},remove_track:function(W){this.has_changes=true;W.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(W)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ad){var ac=this.high-this.low,ab=this.low,X=this.high;if(ab<this.max_low){ab=this.max_low}if(X>this.max_high){X=this.max_high}if(this.high!==0&&ac<this.min_separation){X=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(X);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(r,Math.max(0,Math.ceil(Math.log(this.resolution,r)/Math.log(r))));var W=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aa=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:W,width:Math.max(ae,aa)}).show();if(aa<ae){this.overview_box.css("left",W-(ae-aa)/2)}if(this.overview_highlight){this.overview_highlight.css({left:W,width:aa})}this.update_location(this.low,this.high);if(!ad){for(var Y=0,Z=this.tracks.length;Y<Z;Y++){if(this.tracks[Y]&&this.tracks[Y].enabled){this.tracks[Y].draw()}}for(Y=0,Z=this.label_tracks.length;Y<Z;Y++){this.label_tracks[Y].draw()}}},zoom_in:function(X,Y){if(this.max_high===0||this.high-this.low<this.min_separation){return}var Z=this.high-this.low,aa=Z/2+this.low,W=(Z/this.zoom_factor)/2;if(X){aa=X/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aa-W);this.high=Math.round(aa+W);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var X=this.high-this.low,Y=X/2+this.low,W=(X*this.zoom_factor)/2;this.low=Math.round(Y-W);this.high=Math.round(Y+W);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var n=function(X,aa){this.track=X;this.name=aa.name;this.params=[];var ai=aa.params;for(var Y=0;Y<ai.length;Y++){var ad=ai[Y],W=ad.name,ah=ad.label,Z=unescape(ad.html),af=ad.type;if(af==="number"){this.params[this.params.length]=new g(W,ah,Z,ad.min,ad.max)}else{if(af=="select"){this.params[this.params.length]=new I(W,ah,Z)}else{console.log("WARNING: unrecognized tool parameter type:",W,af)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ak){ak.stopPropagation()}).bind("click",function(ak){ak.stopPropagation()}).bind("dblclick",function(ak){ak.stopPropagation()});var ag=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ae=this.params;var ab=this;$.each(this.params,function(al,ao){var an=$("<div>").addClass("param-row").appendTo(ab.parent_div);var ak=$("<div>").addClass("param-label").text(ao.label).appendTo(an);var am=$("<div/>").addClass("slider").html(ao.html).appendTo(an);$("<div style='clear: both;'/>").appendTo(an)});this.parent_div.find("input").click(function(){$(this).select()});var aj=$("<div>").addClass("slider-row").appendTo(this.parent_div);var ac=$("<input type='submit'>").attr("value","Run").appendTo(aj);var ab=this;ac.click(function(){ab.run()})};extend(n.prototype,{get_param_values_dict:function(){var W={};this.parent_div.find(":input").each(function(){var X=$(this).attr("name"),Y=$(this).val();W[X]=JSON.stringify(Y)});return W},get_param_values:function(){var X=[];var W={};this.parent_div.find(":input").each(function(){var Y=$(this).attr("name"),Z=$(this).val();if(Y){X[X.length]=Z}});return X},run:function(){var X={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name};$.extend(X,this.get_param_values_dict());var Z=this.track,Y=X.tool_id+Z.tool_region_and_parameters_str(X.chrom,X.low,X.high),aa;if(Z.track_type==="FeatureTrack"){aa=new N(Y,view,Z.hda_ldda,undefined,{},{},Z)}this.track.add_track(aa);aa.content_div.text("Starting job.");var W=function(){$.getJSON(run_tool_url,X,function(ab){if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(E)}else{if(ab.error){aa.container_div.addClass("error");aa.content_div.text(u+ab.message)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text("Converting input data so that it can be easily reused.");setTimeout(W,2000)}else{aa.dataset_id=ab.dataset_id;aa.content_div.text("Running job.");aa.init()}}}})};W()}});var I=function(X,W,Y){this.name=X;this.label=W;this.html=Y};var g=function(Y,X,aa,Z,W){I.call(this,Y,X,aa);this.min=Z;this.max=W};var j=function(X,W,Y){this.name=X;this.index=W;this.value=Y};var O=function(X,W){this.name=X;this.index=W;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};extend(O.prototype,{applies_to:function(W){if(W.length>this.index){return true}return false},keep:function(W){if(!this.applies_to(W)){return true}return(W[this.index]>=this.low&&W[this.index]<=this.high)},update_attrs:function(X){var W=false;if(!this.applies_to(X)){return W}if(X[this.index]<this.min){this.min=Math.floor(X[this.index]);W=true}if(X[this.index]>this.max){this.max=Math.ceil(X[this.index]);W=true}return W},update_ui_elt:function(){var X=this.slider.slider("option","min"),W=this.slider.slider("option","max");if(this.min<X||this.max>W){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",h(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var v=function(W){var ac=[];for(var Z=0;Z<W.length;Z++){var ab=W[Z];var Y=ab.name,aa=ab.type,X=ab.index;if(aa==="int"||aa==="float"){ac[Z]=new O(Y,X)}else{ac[Z]=new j(Y,X,aa)}}return ac};var S=function(W){this.track=W.track;this.params=W.params;this.values={};if(W.saved_values){this.restore_values(W.saved_values)}this.onchange=W.onchange};extend(S.prototype,{restore_values:function(W){var X=this;$.each(this.params,function(Y,Z){if(W[Z.key]!==undefined){X.values[Z.key]=W[Z.key]}else{X.values[Z.key]=Z.default_value}})},build_form:function(){var X=this;var W=$("<div />");$.each(this.params,function(ab,Z){if(!Z.hidden){var Y="param_"+ab;var ag=$("<div class='form-row' />").appendTo(W);ag.append($("<label />").attr("for",Y).text(Z.label+":"));if(Z.type==="bool"){ag.append($('<input type="checkbox" />').attr("id",Y).attr("name",Y).attr("checked",X.values[Z.key]))}else{if(Z.type==="color"){var ad=X.values[Z.key];var ac=$("<input />").attr("id",Y).attr("name",Y).val(ad);var ae=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var aa=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ae);var af=$("<div/>").appendTo(aa).farbtastic({width:100,height:100,callback:ac,color:ad});$("<div />").append(ac).append(ae).appendTo(ag).bind("click",function(ah){ae.css({left:$(this).position().left+($(ac).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ae.hide();$(document).unbind("click.color-picker")});ah.stopPropagation()})}else{ag.append($("<input />").attr("id",Y).attr("name",Y).val(X.values[Z.key]))}}}});return W},update_from_form:function(W){var Y=this;var X=false;$.each(this.params,function(Z,ab){if(!ab.hidden){var ac="param_"+Z;var aa=W.find("#"+ac).val();if(ab.type==="float"){aa=parseFloat(aa)}else{if(ab.type==="int"){aa=parseInt(aa)}else{if(ab.type==="bool"){aa=W.find("#"+ac).is(":checked")}}}if(aa!==Y.values[ab.key]){Y.values[ab.key]=aa;X=true}}});if(X){this.onchange()}}});var b=function(W,X){this.track=W;this.canvas=X};var k=function(X,W,aa,Y,Z){this.name=X;this.view=W;this.parent_element=aa;this.data_url=(Y?Y:default_data_url);this.data_url_extra_params={};this.data_query_wait=(Z?Z:F);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};extend(k.prototype,{init:function(){var W=this;W.enabled=false;W.tile_cache.clear();W.data_cache.clear();W.initial_canvas=undefined;W.content_div.css("height","auto");W.container_div.removeClass("nodata error pending");if(!W.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:W.hda_ldda,dataset_id:W.dataset_id,chrom:W.view.chrom},function(X){if(!X||X==="error"||X.kind==="error"){W.container_div.addClass("error");W.content_div.text(m);if(X.message){var Z=W.view.tracks.indexOf(W);var Y=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+X.message+"</pre>",{Close:hide_modal})});W.content_div.append(Y)}}else{if(X==="no converter"){W.container_div.addClass("error");W.content_div.text(E)}else{if(X==="no data"||(X.data!==undefined&&(X.data===null||X.data.length===0))){W.container_div.addClass("nodata");W.content_div.text(A)}else{if(X==="pending"){W.container_div.addClass("pending");W.content_div.text(p);setTimeout(function(){W.init()},W.data_query_wait)}else{if(X.status==="data"){if(X.valid_chroms){W.valid_chroms=X.valid_chroms;W.make_name_popup_menu()}W.content_div.text(R);if(W.view.chrom){W.content_div.text("");W.content_div.css("height",W.height_px+"px");W.enabled=true;$.when(W.predraw_init()).done(function(){W.container_div.removeClass("nodata error pending");W.draw()})}}}}}}})},predraw_init:function(){},update_name:function(W){this.old_name=this.name;this.name=W;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var H=function(X,ad,ag){var Y=this,ah=Y.view;this.filters=(X!==undefined?v(X):[]);this.filters_available=false;this.filters_visible=false;this.tool=(ad!==undefined&&obj_length(ad)>0?new n(this,ad):undefined);this.parent_track=ag;this.child_tracks=[];if(Y.hidden){return}var af=function(ai,aj,ak){ai.click(function(){var al=aj.text();max=parseFloat(ak.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ak.slider("option","values")){input_size=2*input_size+1;multi_value=true}aj.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",al).appendTo(aj).focus().select().click(function(am){am.stopPropagation()}).blur(function(){$(this).remove();aj.text(al)}).keyup(function(aq){if(aq.keyCode===27){$(this).trigger("blur")}else{if(aq.keyCode===13){var ao=ak.slider("option","min"),am=ak.slider("option","max"),ap=function(ar){return(isNaN(ar)||ar>am||ar<ao)},an=$(this).val();if(!multi_value){an=parseFloat(an);if(ap(an)){alert("Parameter value must be in the range ["+ao+"-"+am+"]");return $(this)}}else{an=an.split("-");an=[parseFloat(an[0]),parseFloat(an[1])];if(ap(an[0])||ap(an[1])){alert("Parameter value must be in the range ["+ao+"-"+am+"]");return $(this)}}ak.slider((multi_value?"values":"value"),an)}}})})};if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(ai){ai.stopPropagation()}).bind("click",function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()});$.each(this.filters,function(ao,aj){var al=$("<div/>").addClass("slider-row").appendTo(Y.filters_div);var ai=$("<div/>").addClass("slider-label").appendTo(al);var aq=$("<span/>").addClass("slider-name").text(aj.name+" ").appendTo(ai);var ak=$("<span/>");var am=$("<span/>").addClass("slider-value").appendTo(ai).append("[").append(ak).append("]");var ap=$("<div/>").addClass("slider").appendTo(al);aj.control_element=$("<div/>").attr("id",aj.name+"-filter-control").appendTo(ap);var an=[0,0];aj.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ar,at){an=at.values;ak.text(at.values[0]+"-"+at.values[1]);setTimeout(function(){if(at.values[0]==an[0]&&at.values[1]==an[1]){var au=at.values;ak.text(au[0]+"-"+au[1]);aj.low=au[0];aj.high=au[1];Y.draw(true,true)}},50)},change:function(ar,at){aj.control_element.slider("option","slide").call(aj.control_element,ar,at)}});aj.slider=aj.control_element;aj.slider_label=ak;af(am,ak,aj.control_element);$("<div style='clear: both;'/>").appendTo(al)});if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}Y.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();Y.container_div.append(Y.child_tracks_container);if(Y.display_modes!==undefined){if(Y.mode_div===undefined){Y.mode_div=$("<div class='right-float menubutton popup' />").appendTo(Y.header_div);var aa=(Y.track_config&&Y.track_config.values.mode?Y.track_config.values.mode:Y.display_modes[0]);Y.mode=aa;Y.mode_div.text(aa);var Z=function(ai){Y.mode_div.text(ai);Y.mode=ai;Y.track_config.values.mode=ai;Y.tile_cache.clear();Y.draw()};var W={};for(var ab=0,ae=Y.display_modes.length;ab<ae;ab++){var ac=Y.display_modes[ab];W[ac]=function(ai){return function(){Z(ai)}}(ac)}make_popupmenu(Y.mode_div,W)}else{Y.mode_div.hide()}}this.make_name_popup_menu()};extend(H.prototype,k.prototype,{make_name_popup_menu:function(){var X=this;var W={};W["Edit configuration"]=function(){var ad=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(){X.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(ae){if((ae.keyCode||ae.which)===27){ad()}else{if((ae.keyCode||ae.which)===13){ab()}}};$(window).bind("keypress.check_enter_esc",ac);show_modal("Configure Track",X.track_config.build_form(),{Cancel:ad,OK:ab})};if(X.filters_available>0){var aa=(X.filters_div.is(":visible")?"Hide filters":"Show filters");W[aa]=function(){X.filters_visible=(X.filters_div.is(":visible"));X.filters_div.toggle();X.make_name_popup_menu()}}if(X.tool){var aa=(X.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");W[aa]=function(){if(!X.dynamic_tool_div.is(":visible")){X.update_name(X.name+X.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";X.revert_name()}X.dynamic_tool_div.toggle();X.make_name_popup_menu()}}if(X.valid_chroms){W["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+X.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var Y=view;var Z=function(){$("#no-tracks").show()};if(this.parent_track){Y=this.parent_track;Z=function(){}}W.Remove=function(){Y.remove_track(X);if(Y.num_tracks===0){Z()}};make_popupmenu(X.name_div,W)},draw:function(W,Z){var an=this.view.low,ac=this.view.high,ae=ac-an,ag=this.view.container.width(),ab=ag/ae,ah=this.view.resolution,aa=$("<div style='position: relative;'></div>");if(!Z){this.content_div.children().remove()}this.content_div.append(aa);this.max_height=0;var aj=Math.floor(an/ah/J);var Y={};while((aj*J*ah)<ac){var am=ag+"_"+ab+"_"+aj;var ad=this.tile_cache.get(am);var ak=aj*J*this.view.resolution;var X=ak+J*this.view.resolution;if(!W&&ad){this.show_tile(ad,aa,ak,ab)}else{this.delayed_draw(W,am,ak,X,aj,ah,aa,ab,Y)}aj+=1}var af=this;var al=setInterval(function(){if(obj_length(Y)===0){clearInterval(al);if(Z){var aq=af.content_div.children();var ap=false;for(var ar=aq.length-1,ao=0;ar>=ao;ar--){var av=$(aq[ar]);if(ap){av.remove()}else{if(av.children().length!==0){ap=true}}}}for(var au=0;au<af.filters.length;au++){af.filters[au].update_ui_elt()}var at=false;if(af.example_feature){for(var au=0;au<af.filters.length;au++){if(af.filters[au].applies_to(af.example_feature)){at=true;break}}}if(af.filters_available!==at){af.filters_available=at;if(!af.filters_available){af.filters_div.hide()}af.make_name_popup_menu()}}},50);for(var ai=0;ai<this.child_tracks.length;ai++){this.child_tracks[ai].draw(W,Z)}},delayed_draw:function(X,ae,ac,ag,Y,aa,af,ah,ab){var Z=this;var ad=function(ap,ai,ak,aj,an,ao,al){returned_tile=Z.draw_tile(ai,ak,aj,an,ao,al);var am=$("<div class='track-tile'>").prepend(returned_tile);tile_element=am;Z.tile_cache.set(ae,tile_element);Z.show_tile(tile_element,an,ac,ao);delete ab[ap]};var W=setTimeout(function(){if(ac<=Z.view.high&&ag>=Z.view.low){var ai=(X?undefined:Z.tile_cache.get(ae));if(ai){Z.show_tile(ai,af,ac,ah);delete ab[W]}else{$.when(Z.data_cache.get_data(view.chrom,ac,ag,Z.mode,aa,Z.data_url_extra_params)).then(function(aj){if(view.reference_track&&ah>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,ac,ag,Z.mode,aa,view.reference_track.data_url_extra_params)).then(function(ak){ad(W,aj,aa,Y,af,ah,ak)})}else{ad(W,aj,aa,Y,af,ah)}})}}},50);ab[W]=true},show_tile:function(W,ab,Z,ac){var X=this;var Y=this.view.high-this.view.low,aa=(Z-this.view.low)*ac;if(this.left_offset){aa-=this.left_offset}W.css({position:"absolute",top:0,left:aa,height:""});ab.append(W);X.max_height=Math.max(X.max_height,W.height());X.content_div.css("height",X.max_height+"px");ab.children().css("height",X.max_height+"px")},set_overview:function(){var W=this.view;if(this.initial_canvas&&this.is_overview){W.overview_close.show();W.overview_viewport.append(this.initial_canvas);W.overview_highlight.show().height(this.initial_canvas.height());W.overview_viewport.height(this.initial_canvas.height()+W.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(Y,W,Z){var X=this,aa=(Y!==undefined&&W!==undefined&&Z!==undefined?Y+":"+W+"-"+Z:"all");return" - region=["+aa+"], parameters=["+X.tool.get_param_values().join(", ")+"]"},add_track:function(W){W.track_id=this.track_id+"_"+this.child_tracks.length;W.container_div.attr("id","track_"+W.track_id);this.child_tracks_container.append(W.container_div);B(W.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(W);this.view.has_changes=true},remove_track:function(W){W.container_div.fadeOut("slow",function(){$(this).remove()})}});var T=function(W,X){this.track_type="LabelTrack";this.hidden=true;k.call(this,null,W,X);this.container_div.addClass("label-track")};extend(T.prototype,k.prototype,{draw:function(){var Y=this.view,Z=Y.high-Y.low,ac=Math.floor(Math.pow(10,Math.floor(Math.log(Z)/Math.log(10)))),W=Math.floor(Y.low/ac)*ac,aa=this.view.container.width(),X=$("<div style='position: relative; height: 1.3em;'></div>");while(W<Y.high){var ab=(W-Y.low)/Z*aa;X.append($("<div class='label'>"+commatize(W)+"</div>").css({position:"absolute",left:ab-1}));W+=ac}this.content_div.children(":first").remove();this.content_div.append(X)}});var x=function(W){this.track_type="ReferenceTrack";this.hidden=true;k.call(this,null,W,W.top_labeltrack);H.call(this);W.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:W.dbkey};this.data_cache=new K(y,this,false);this.tile_cache=new c(q)};extend(x.prototype,H.prototype,{draw_tile:function(ag,ab,X,ad,ah){var aa=this,Y=J*ab;if(ah>this.view.canvas_manager.char_width_px){if(ag===null){aa.content_div.css("height","0px");return}var Z=this.view.canvas_manager.new_canvas();var af=Z.getContext("2d");Z.width=Math.ceil(Y*ah+aa.left_offset);Z.height=aa.height_px;af.font=af.canvas.manager.default_font;af.textAlign="center";for(var ac=0,ae=ag.length;ac<ae;ac++){var W=Math.round(ac*ah);af.fillText(ag[ac],W+aa.left_offset,10)}return Z}this.content_div.css("height","0px")}});var l=function(aa,Y,ab,W,Z){var X=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";k.call(this,aa,Y,Y.viewport_container);H.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ab;this.dataset_id=W;this.original_dataset_id=W;this.data_cache=new K(y,this);this.tile_cache=new c(q);this.track_config=new S({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:Z,onchange:function(){X.vertical_range=X.prefs.max_value-X.prefs.min_value;$("#linetrack_"+X.track_id+"_minval").text(X.prefs.min_value);$("#linetrack_"+X.track_id+"_maxval").text(X.prefs.max_value);X.tile_cache.clear();X.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};extend(l.prototype,H.prototype,{add_resize_handle:function(){var W=this;var Z=false;var Y=false;var X=$("<div class='track-resize'>");$(W.container_div).hover(function(){Z=true;X.show()},function(){Z=false;if(!Y){X.hide()}});X.hide().bind("dragstart",function(aa,ab){Y=true;ab.original_height=$(W.content_div).height()}).bind("drag",function(ab,ac){var aa=Math.min(Math.max(ac.original_height+ac.deltaY,W.min_height_px),W.max_height_px);$(W.content_div).css("height",aa);W.height_px=aa;W.draw(true)}).bind("dragend",function(aa,ab){W.tile_cache.clear();Y=false;if(!Z){X.hide()}W.track_config.values.height=W.height_px}).appendTo(W.container_div)},predraw_init:function(){var W=this,X=W.view.tracks.indexOf(W);W.vertical_range=undefined;return $.getJSON(W.data_url,{stats:true,chrom:W.view.chrom,low:null,high:null,hda_ldda:W.hda_ldda,dataset_id:W.dataset_id},function(Y){W.container_div.addClass("line-track");var aa=Y.data;if(isNaN(parseFloat(W.prefs.min_value))||isNaN(parseFloat(W.prefs.max_value))){W.prefs.min_value=aa.min;W.prefs.max_value=aa.max;$("#track_"+X+"_minval").val(W.prefs.min_value);$("#track_"+X+"_maxval").val(W.prefs.max_value)}W.vertical_range=W.prefs.max_value-W.prefs.min_value;W.total_frequency=aa.total_frequency;W.container_div.find(".yaxislabel").remove();var ab=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+X+"_minval").text(t(W.prefs.min_value));var Z=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+X+"_maxval").text(t(W.prefs.max_value));Z.css({position:"absolute",top:"24px",left:"10px"});Z.prependTo(W.container_div);ab.css({position:"absolute",bottom:"2px",left:"10px"});ab.prependTo(W.container_div)})},draw_tile:function(ah,aa,X,ae,ag){if(this.vertical_range===undefined){return}var ab=X*J*aa,Z=J*aa,W=Math.ceil(Z*ag),ad=this.height_px;var Y=this.view.canvas_manager.new_canvas();Y.width=W,Y.height=ad;var af=Y.getContext("2d");var ac=new G.LinePainter(ah.data,ab,ab+Z,this.prefs,this.mode);ac.draw(af,W,ad);return Y}});var e=function(W,ab,aa,ae,ad,Y,Z,ac){var X=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new S({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ad,onchange:function(){X.tile_cache.clear();X.draw()}});this.prefs=this.track_config.values;k.call(this,W,ab,ab.viewport_container);H.call(this,Y,Z,ac);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=aa;this.dataset_id=ae;this.original_dataset_id=ae;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_cache=new K(20,this);this.left_offset=200;this.painter=G.LinkedFeaturePainter};extend(e.prototype,H.prototype,{update_auto_mode:function(W){if(this.mode=="Auto"){if(W=="no_detail"){W="feature spans"}else{if(W=="summary_tree"){W="coverage histogram"}}this.mode_div.text("Auto ("+W+")")}},incremental_slots:function(aa,X,Z){var Y=this.view.canvas_manager.dummy_context,W=this.inc_slots[aa];if(!W||(W.mode!==Z)){W=new (o.FeatureSlotter)(aa,Z==="Pack",w,function(ab){return Y.measureText(ab)});W.mode=Z;this.inc_slots[aa]=W}return W.slot_features(X)},draw_tile:function(ai,aq,av,ae,ag,Z){var an=this,ax=av*J*aq,X=(av+1)*J*aq,ak=X-ax,ao=Math.ceil(ak*ag),am=this.mode,aB=25,aa=this.left_offset,aj,ab;if(am==="Auto"){if(ai.dataset_type==="summary_tree"){am=ai.dataset_type}else{if(ai.extra_info==="no_detail"){am="no_detail"}else{var aA=ai.data;if(this.view.high-this.view.low>D){am="Squish"}else{am="Pack"}}}this.update_auto_mode(am)}if(am==="summary_tree"){ab=this.summary_draw_height;ae.parent().css("height",Math.max(this.height_px,ab)+"px");this.container_div.find(".yaxislabel").remove();var W=$("<div />").addClass("yaxislabel");W.text(ai.max);W.css({position:"absolute",top:"22px",left:"10px"});W.prependTo(this.container_div);var Y=this.view.canvas_manager.new_canvas();Y.width=ao+aa;Y.height=ab+L;var ay=new G.SummaryTreePainter(ai,ax,X,this.prefs);var ap=Y.getContext("2d");ap.translate(aa,L);ay.draw(ap,ao,ab);return Y}var aj,ad=1;if(am==="no_detail"||am==="Squish"||am==="Pack"){ad=this.incremental_slots(ag,ai.data,am);aj=this.inc_slots[ag].slots}var af=[];if(ai.data){for(var ar=0,au=ai.data.length;ar<au;ar++){var ac=ai.data[ar];var at=false;var ah;for(var aw=0,az=this.filters.length;aw<az;aw++){ah=this.filters[aw];ah.update_attrs(ac);if(!ah.keep(ac)){at=true;break}}if(!at){af.push(ac)}}}var ay=new (this.painter)(af,ax,X,this.prefs,am,Z);var ab=ay.get_required_height(ad)+z;var Y=this.view.canvas_manager.new_canvas();Y.width=ao+aa;Y.height=ab;ae.parent().css("height",Math.max(this.height_px,ab)+"px");var ap=Y.getContext("2d");ap.fillStyle=this.prefs.block_color;ap.font=ap.canvas.manager.default_font;ap.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ai.message){$(Y).css({"border-top":"1px solid red"});ap.fillStyle="red";ap.textAlign="left";var al=ap.textBaseline;ap.textBaseline="top";ap.fillText(ai.message,aa,0);ap.textBaseline=al;if(!ai.data){return Y}}this.example_feature=(ai.data.length?ai.data[0]:undefined);ap.translate(aa,z);ay.draw(ap,ao,ab,aj);return Y}});var M=function(Z,X,ab,W,Y,aa){e.call(this,Z,X,ab,W,Y,aa);this.track_type="VcfTrack";this.painter=G.VariantPainter};extend(M.prototype,H.prototype,e.prototype);var P=function(Z,X,ab,W,Y,aa){e.call(this,Z,X,ab,W,Y,aa);this.track_config=new S({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:Y,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=G.ReadPainter;this.make_name_popup_menu()};extend(P.prototype,H.prototype,e.prototype);var N=function(aa,Y,ac,W,Z,ab,X){e.call(this,aa,Y,ac,W,Z,ab,{},X);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};extend(N.prototype,H.prototype,e.prototype,{predraw_init:function(){var X=this;var W=function(){if(X.data_cache.size()===0){setTimeout(W,300)}else{X.data_url=default_data_url;X.data_query_wait=F;X.dataset_state_url=converted_datasets_state_url;$.getJSON(X.dataset_state_url,{dataset_id:X.dataset_id,hda_ldda:X.hda_ldda},function(Y){})}};W()}});Q.View=U;Q.LineTrack=l;Q.FeatureTrack=e;Q.ReadTrack=P};var slotting_module=function(c,b){var d=2,a=5;b.FeatureSlotter=function(h,g,e,f){this.slots={};this.start_end_dct={};this.w_scale=h;this.include_label=g;this.max_rows=e;this.measureText=f};extend(b.FeatureSlotter.prototype,{slot_features:function(l){var o=this.w_scale,r=this.slots,g=this.start_end_dct,x=[],z=[],m=0,y=this.max_rows;for(var v=0,w=l.length;v<w;v++){var k=l[v],n=k[0];if(r[n]!==undefined){m=Math.max(m,r[n]);z.push(r[n])}else{x.push(v)}}var p=function(F,G){for(var E=0;E<=y;E++){var C=false,H=g[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var A=H[B];if(G>A[0]&&F<A[1]){C=true;break}}}if(!C){return E}}return -1};for(var v=0,w=x.length;v<w;v++){var k=l[x[v]],n=k[0],t=k[1],e=k[2],q=k[3],f=Math.floor(t*o),j=Math.ceil(e*o),u=this.measureText(q).width,h;if(q!==undefined&&this.include_label){u+=(d+a);if(f-u>=0){f-=u;h="left"}else{j+=u;h="right"}}var s=p(f,j);if(s>=0){if(g[s]===undefined){g[s]=[]}g[s].push([f,j]);r[n]=s;m=Math.max(m,s)}else{}}return m+1}})};var painters_module=function(k,B){var r=function(M,E,K,D,J,H){if(H===undefined){H=4}var G=D-E;var F=J-K;var I=Math.floor(Math.sqrt(G*G+F*F)/H);var N=G/I;var L=F/I;var C;for(C=0;C<I;C++,E+=N,K+=L){if(C%2!==0){continue}M.fillRect(E,K,H,1)}};var s=function(E,D,C,H){var G=D-H/2,F=D+H/2,I=C-Math.sqrt(H*3/2);E.beginPath();E.moveTo(G,I);E.lineTo(F,I);E.lineTo(D,C);E.lineTo(G,I);E.strokeStyle=this.fillStyle;E.fill();E.stroke();E.closePath()};var o=function(E,G,C,D,F){this.data=E;this.view_start=G;this.view_end=C;this.prefs=extend({},this.default_prefs,D);this.mode=F};o.prototype.default_prefs={};var w=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};w.prototype.default_prefis={show_counts:false};w.prototype.draw=function(P,C,O){var H=this.view_start,R=this.view_end-this.view_start,Q=C/R;var M=this.data.data,L=this.data.delta,J=this.data.max,E=O;delta_x_px=Math.ceil(L*Q);P.save();for(var F=0,G=M.length;F<G;F++){var K=Math.floor((M[F][0]-H)*Q);var I=M[F][1];if(!I){continue}var N=I/J*O;P.fillStyle="black";P.fillRect(K,E-N,delta_x_px,N);var D=4;if(this.prefs.show_counts&&(P.measureText(I).width+D)<delta_x_px){P.fillStyle="#666";P.textAlign="center";P.fillText(I,K+(delta_x_px/2),10)}}P.restore()};var c=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(R,Q,O){var J=false,K=this.prefs.min_value,H=this.prefs.max_value,N=H-K,D=O,E=this.view_start,P=this.view_end-this.view_start,F=Q/P,L=this.mode,V=this.data;R.save();var W=Math.round(O+K/N*O);if(L!=="Intensity"){R.fillStyle="#aaa";R.fillRect(0,W,Q,1)}R.beginPath();R.fillStyle=this.prefs.color;var U,I,G;if(V.length>1){G=Math.ceil((V[1][0]-V[0][0])*F)}else{G=10}for(var S=0,T=V.length;S<T;S++){U=Math.round((V[S][0]-E)*F);I=V[S][1];if(I===null){if(J&&L==="Filled"){R.lineTo(U,D)}J=false;continue}if(I<K){I=K}else{if(I>H){I=H}}if(L==="Histogram"){I=Math.round(I/N*D);R.fillRect(U,W,G,-I)}else{if(L==="Intensity"){I=255-Math.floor((I-K)/N*255);R.fillStyle="rgb("+I+","+I+","+I+")";R.fillRect(U,0,G,D)}else{I=Math.round(D-(I-K)/N*D);if(J){R.lineTo(U,I)}else{J=true;if(L==="Filled"){R.moveTo(U,D);R.lineTo(U,I)}else{R.moveTo(U,I)}}}}}if(L==="Filled"){if(J){R.lineTo(U,W);R.lineTo(0,W)}R.fill()}else{R.stroke()}var C=-1,M=-1;R.fillStyle=this.prefs.overflow_color;for(var S=0,T=V.length;S<T;S++){I=V[S][1];U=Math.round((V[S][0]-E)*F);x_minus_scaled=Math.round((V[S][0]-1-E)*F);if(M>=0&&(I===null||I<H)){R.fillRect(M,0,x_minus_scaled-M+1,2);M=-1}else{if(C>=0&&(I===null||I>K)){R.fillRect(C,O-2,x_minus_scaled-C+1,2);C=-1}}if(I!==null&&I>H&&M<0){M=U}else{if(I!==null&&I<K&&C<0){C=U}}}R.restore()};var q=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};q.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(q.prototype,{get_required_height:function(D){var C=y_scale=this.get_row_height(),E=this.mode;if(E==="no_detail"||E==="Squish"||E==="Pack"){C=D*y_scale}return C+Math.max(Math.round(y_scale/2),5)},draw:function(O,F,N,K){var I=this.data,L=this.view_start,P=this.view_end;O.save();O.fillStyle=this.prefs.block_color;O.textAlign="right";var S=this.view_end-this.view_start,R=F/S,E=this.get_row_height();for(var H=0,J=I.length;H<J;H++){var Q=I[H],G=Q[0],C=Q[1],D=Q[2],M=(K&&K[G]!==undefined?K[G]:null);if((C<P&&D>L)&&(this.mode=="Dense"||M!==null)){this.draw_element(O,this.mode,Q,M,L,P,R,E,F)}}O.restore()}});var d=10,j=3,n=5,A=10,g=1,u=3,f=3,a=9,p=2,h="#ccc";var t=function(E,G,C,D,F){q.call(this,E,G,C,D,F)};extend(t.prototype,q.prototype,{get_row_height:function(){var D=this.mode,C;if(D==="Dense"){C=d}else{if(D==="no_detail"){C=j}else{if(D==="Squish"){C=n}else{C=A}}}return C},draw_element:function(O,H,W,J,Q,ag,ak,al,C){var T=W[0],ai=W[1],aa=W[2]-1,R=W[3],ab=Math.floor(Math.max(0,(ai-Q)*ak)),P=Math.ceil(Math.min(C,Math.max(0,(aa-Q)*ak))),Z=(H==="Dense"?0:(0+J))*al,N,ae,S=null,am=null,F=this.prefs.block_color,ad=this.prefs.label_color;if(H=="Dense"){J=1}if(H==="no_detail"){O.fillStyle=F;O.fillRect(ab,Z+5,P-ab,g)}else{var M=W[4],Y=W[5],ac=W[6],G=W[7];if(Y&&ac){S=Math.floor(Math.max(0,(Y-Q)*ak));am=Math.ceil(Math.min(C,Math.max(0,(ac-Q)*ak)))}var aj,U;if(H==="Squish"||H==="Dense"){aj=1;U=f}else{aj=5;U=a}if(!G){if(W.strand){if(W.strand==="+"){O.fillStyle=O.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){O.fillStyle=O.canvas.manager.get_pattern("left_strand_inv")}}}else{O.fillStyle=F}O.fillRect(ab,Z,P-ab,U)}else{var L,V;if(H==="Squish"||H==="Dense"){O.fillStyle=h;L=Z+Math.floor(f/2)+1;V=1}else{if(M){var L=Z;var V=U;if(M==="+"){O.fillStyle=O.canvas.manager.get_pattern("right_strand")}else{if(M==="-"){O.fillStyle=O.canvas.manager.get_pattern("left_strand")}}}else{O.fillStyle=h;L+=(f/2)+1;V=1}}O.fillRect(ab,L,P-ab,V);for(var ah=0,E=G.length;ah<E;ah++){var I=G[ah],D=Math.floor(Math.max(0,(I[0]-Q)*ak)),X=Math.ceil(Math.min(C,Math.max((I[1]-1-Q)*ak)));if(D>X){continue}O.fillStyle=F;O.fillRect(D,Z+(U-aj)/2+1,X-D,aj);if(S!==undefined&&ac>Y&&!(D>am||X<S)){var af=Math.max(D,S),K=Math.min(X,am);O.fillRect(af,Z+1,K-af,U);if(G.length==1&&H=="Pack"){if(M==="+"){O.fillStyle=O.canvas.manager.get_pattern("right_strand_inv")}else{if(M==="-"){O.fillStyle=O.canvas.manager.get_pattern("left_strand_inv")}}if(af+14<K){af+=2;K-=2}O.fillRect(af,Z+1,K-af,U)}}}}if(H==="Pack"&&ai>Q){O.fillStyle=ad;if(Q===0&&ab-O.measureText(R).width<0){O.textAlign="left";O.fillText(R,P+p,Z+8)}else{O.textAlign="right";O.fillText(R,ab-p,Z+8)}O.fillStyle=F}}}});var b=function(E,G,C,D,F){q.call(this,E,G,C,D,F)};extend(b.prototype,q.prototype,{draw_element:function(V,Q,K,G,Y,E,N,W,T){var K=data[i],M=K[0],U=K[1],F=K[2]-1,P=K[3],I=Math.floor(Math.max(0,(U-Y)*N)),L=Math.ceil(Math.min(T,Math.max(0,(F-Y)*N))),H=(Q==="Dense"?0:(0+G))*W,C,Z,D=null,O=null;if(no_label){V.fillStyle=block_color;V.fillRect(I+left_offset,H+5,L-I,1)}else{var X=K[4],S=K[5],J=K[6];C=9;Z=1;V.fillRect(I+left_offset,H,L-I,C);if(Q!=="Dense"&&P!==undefined&&U>Y){V.fillStyle=label_color;if(Y===0&&I-V.measureText(P).width<0){V.textAlign="left";V.fillText(P,L+2+left_offset,H+8)}else{V.textAlign="right";V.fillText(P,I-2+left_offset,H+8)}V.fillStyle=block_color}var R=X+" / "+S;if(U>Y&&V.measureText(R).width<(L-I)){V.fillStyle="white";V.textAlign="center";V.fillText(R,left_offset+I+(L-I)/2,H+8);V.fillStyle=block_color}}}});var z=1001,m=1002,e=1003,y=1004,l=1005;var x=function(G,D){var I=G[0],H=G[1],F=D[0],E=D[1],C;if(I<F){if(H<F){C=z}else{if(H<=E){C=e}else{C=m}}}else{if(I>E){C=z}else{if(H<=E){C=l}else{C=y}}}return C};var v=function(F,H,C,E,G,D){q.call(this,F,H,C,E,G);this.ref_seq=D};v.prototype.default_prefs=extend({},q.prototype.default_prefs,{show_insertions:false});extend(v.prototype,q.prototype,{get_row_height:function(){var C,D=this.mode;if(D==="Dense"){C=d}else{if(D==="Squish"){C=n}else{C=A;if(this.prefs.show_insertions){C*=2}}}return C},draw_read:function(Z,U,P,ae,E,Y,M,J,I){Z.textAlign="center";var X=this,D=[ae,E],S=0,aa=0,W=0;ref_seq=this.ref_seq,char_width_px=Z.canvas.manager.char_width_px;var aj=[];if((U==="Pack"||this.mode==="Auto")&&J!==undefined&&P>char_width_px){W=Math.round(P/2)}if(!M){M=[[0,J.length]]}for(var Q=0,ac=M.length;Q<ac;Q++){var N=M[Q],F="MIDNSHP=X"[N[0]],R=N[1];if(F==="H"||F==="S"){S-=R}var K=Y+S,ai=Math.floor(Math.max(0,(K-ae)*P)),L=Math.floor(Math.max(0,(K+R-ae)*P));if(ai===L){L+=1}switch(F){case"H":break;case"S":case"M":case"=":var T=x([K,K+R],D);if(T!==z){var V=J.slice(aa,aa+R);if(W>0){Z.fillStyle=this.prefs.block_color;Z.fillRect(ai-W,I+1,L-ai,9);Z.fillStyle=h;for(var ag=0,C=V.length;ag<C;ag++){if(this.prefs.show_differences&&ref_seq){var O=ref_seq[K-ae+ag];if(!O||O.toLowerCase()===V[ag].toLowerCase()){continue}}if(K+ag>=ae&&K+ag<=E){var ah=Math.floor(Math.max(0,(K+ag-ae)*P));Z.fillText(V[ag],ah,I+9)}}}else{Z.fillStyle=this.prefs.block_color;Z.fillRect(ai,I+4,L-ai,f)}}aa+=R;S+=R;break;case"N":Z.fillStyle=h;Z.fillRect(ai-W,I+5,L-ai,1);S+=R;break;case"D":Z.fillStyle="red";Z.fillRect(ai-W,I+4,L-ai,3);S+=R;break;case"P":break;case"I":var T=x([K,K+R],D),ad=ai-W;if(T!==z){var V=J.slice(aa,aa+R);if(this.prefs.show_insertions){var H=ai-(L-ai)/2;if((U==="Pack"||this.mode==="Auto")&&J!==undefined&&P>char_width_px){Z.fillStyle="yellow";Z.fillRect(H-W,I-9,L-ai,9);aj[aj.length]={type:"triangle",data:[ad,I+4,5]};Z.fillStyle=h;switch(T){case (e):V=V.slice(ae-K);break;case (y):V=V.slice(0,K-E);break;case (l):break;case (m):V=V.slice(ae-K,K-E);break}for(var ag=0,C=V.length;ag<C;ag++){var ah=Math.floor(Math.max(0,(K+ag-ae)*P));Z.fillText(V[ag],ah-(L-ai)/2,I)}}else{Z.fillStyle="yellow";Z.fillRect(H,I+(this.mode!=="Dense"?2:5),L-ai,(U!=="Dense"?f:u))}}else{if((U==="Pack"||this.mode==="Auto")&&J!==undefined&&P>char_width_px){aj[aj.length]={type:"text",data:[V.length,ad,I+9]}}else{}}}aa+=R;break;case"X":aa+=R;break}}Z.fillStyle="yellow";var af,G,ak;for(var ab=0;ab<aj.length;ab++){af=aj[ab];G=af.type;ak=af.data;if(G==="text"){Z.save();Z.font="bold "+Z.font;Z.fillText(ak[0],ak[1],ak[2]);Z.restore()}else{if(G=="triangle"){s(Z,ak[0],ak[1],ak[2])}}}},draw_element:function(V,Q,I,F,Y,D,M,W,T){var L=I[0],U=I[1],E=I[2],N=I[3],H=Math.floor(Math.max(0,(U-Y)*M)),J=Math.ceil(Math.min(T,Math.max(0,(E-Y)*M))),G=(Q==="Dense"?0:(0+F))*W,Z=this.prefs.block_color,K=this.prefs.label_color,S=0;if((Q==="Pack"||this.mode==="Auto")&&M>V.canvas.manager.char_width_px){var S=Math.round(M/2)}V.fillStyle=Z;if(I[5] instanceof Array){var R=Math.floor(Math.max(0,(I[4][0]-Y)*M)),P=Math.ceil(Math.min(T,Math.max(0,(I[4][1]-Y)*M))),O=Math.floor(Math.max(0,(I[5][0]-Y)*M)),C=Math.ceil(Math.min(T,Math.max(0,(I[5][1]-Y)*M)));if(I[4][1]>=Y&&I[4][0]<=D&&I[4][2]){this.draw_read(V,Q,M,Y,D,I[4][0],I[4][2],I[4][3],G)}if(I[5][1]>=Y&&I[5][0]<=D&&I[5][2]){this.draw_read(V,Q,M,Y,D,I[5][0],I[5][2],I[5][3],G)}if(O>P){V.fillStyle=h;r(V,P-S,G+5,O-S,G+5)}}else{V.fillStyle=Z;this.draw_read(V,Q,M,Y,D,U,I[4],I[5],G)}if(Q==="Pack"&&U>Y){V.fillStyle=this.prefs.label_color;var X=1;if(X===0&&H-V.measureText(N).width<0){V.textAlign="left";V.fillText(N,J+p-S,G+8)}else{V.textAlign="right";V.fillText(N,H-p-S,G+8)}V.fillStyle=Z}}});B.SummaryTreePainter=w;B.LinePainter=c;B.LinkedFeaturePainter=t;B.ReadPainter=v;B.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var extend=function(){var c=arguments[0];for(var b=1;b<arguments.length;b++){var a=arguments[b];for(key in a){c[key]=a[key]}}return c};var trackster_module=function(f,P){var o=f("slotting"),F=f("painters");var V=function(W,X){this.document=W;this.default_font=X!==undefined?X:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};extend(V.prototype,{load_pattern:function(W,aa){var X=this.patterns,Y=this.dummy_context,Z=new Image();Z.src=image_path+aa;Z.onload=function(){X[W]=Y.createPattern(Z,"repeat")}},get_pattern:function(W){return this.patterns[W]},new_canvas:function(){var W=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(W)}W.manager=this;return W}});var A=function(W,X){W.bind("drag",{handle:X,relative:true},function(ab,ac){var aa=$(this).parent();var Z=aa.children();var Y;for(Y=0;Y<Z.length;Y++){if(ac.offsetY<$(Z.get(Y)).position().top){break}}if(Y===Z.length){if(this!==Z.get(Y-1)){aa.append(this)}}else{if(this!==Z.get(Y)){$(this).insertBefore(Z.get(Y))}}})};var h=function(Y,W){var X=W-Y;return(X<=2?0.01:(X<=100?1:(X<=1000?5:10)))};var B=9,y=10,K=B+2,v=100,C=12000,I=200,r=10,E=5000,s=100,m="There was an error in indexing this dataset. ",D="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",z="No data for this chrom/contig.",p="Currently indexing... please wait",u="Tool cannot be rerun: ",a="Loading data...",Q="Ready for display",d=10,q=5,x=5;function t(W){return Math.round(W*1000)/1000}var c=function(W){this.num_elements=W;this.clear()};extend(c.prototype,{get:function(X){var W=this.key_ary.indexOf(X);if(W!==-1){this.move_key_to_end(X,W)}return this.obj_cache[X]},set:function(X,Y){if(!this.obj_cache[X]){if(this.key_ary.length>=this.num_elements){var W=this.key_ary.shift();delete this.obj_cache[W]}this.key_ary.push(X)}this.obj_cache[X]=Y;return Y},move_key_to_end:function(X,W){this.key_ary.splice(W,1);this.key_ary.push(X)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var J=function(X,W,Y){c.call(this,X);this.track=W;this.subset=(Y!==undefined?Y:true)};extend(J.prototype,c.prototype,{load_data:function(ae,af,aa,ad,X,ac){var Z={chrom:ae,low:af,high:aa,mode:ad,resolution:X,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(Z,ac);if(this.track.filters_manager){var ag=[];var W=this.track.filters_manager.filters;for(var ab=0;ab<W.length;ab++){ag[ag.length]=W[ab].name}Z.filter_cols=JSON.stringify(ag)}var Y=this;return $.getJSON(this.track.data_url,Z,function(ah){Y.set_data(af,aa,ad,ah)})},get_data:function(Y,W,ab,ac,X,aa){var Z=this.get(this.gen_key(W,ab,ac));if(Z){return Z}Z=this.load_data(Y,W,ab,ac,X,aa);this.set_data(W,ab,ac,Z);return Z},set_data:function(X,Y,Z,W){return this.set(this.gen_key(X,Y,Z),W)},gen_key:function(W,Y,Z){var X=W+"_"+Y+"_"+Z;return X},split_key:function(W){return W.split("_")}});var U=function(W,Z,Y,X,aa){this.container=W;this.chrom=null;this.vis_id=Y;this.dbkey=X;this.title=Z;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(aa);this.canvas_manager=new V(W.get(0).ownerDocument);this.reset()};extend(U.prototype,{init:function(Z){var Y=this.container,W=this;this.top_container=$("<div/>").addClass("top-container").appendTo(Y);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(Y);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(Y);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var X=function(aa){if(aa.type==="focusout"||(aa.keyCode||aa.which)===13||(aa.keyCode||aa.which)===27){if((aa.keyCode||aa.which)!==27){W.go_to($(this).val())}$(this).hide();$(this).val("");W.location_span.show();W.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",X).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){W.location_span.hide();W.chrom_select.hide();W.nav_input.val(W.chrom+":"+W.low+"-"+W.high);W.nav_input.css("display","inline-block");W.nav_input.select();W.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){W.zoom_out();W.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){W.zoom_in();W.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},Z);this.chrom_select.bind("change",function(){W.change_chrom(W.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(aa){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(aa){W.zoom_in(aa.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aa,ab){this.current_x=ab.offsetX}).bind("drag",function(aa,ac){var ad=ac.offsetX-this.current_x;this.current_x=ac.offsetX;var ab=Math.round(ad/W.viewport_container.width()*(W.max_high-W.max_low));W.move_delta(-ab)});this.overview_close.bind("click",function(){for(var ab=0,aa=W.tracks.length;ab<aa;ab++){W.tracks[ab].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",W.overview_box.height());W.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(aa,ab){if(aa.clientX>W.viewport_container.width()-16){return false}}).bind("dragstart",function(aa,ab){ab.original_low=W.low;ab.current_height=aa.clientY;ab.current_x=ab.offsetX}).bind("drag",function(ac,ae){var aa=$(this);var af=ae.offsetX-ae.current_x;var ab=aa.scrollTop()-(ac.clientY-ae.current_height);aa.scrollTop(ab);ae.current_height=ac.clientY;ae.current_x=ae.offsetX;var ad=Math.round(af/W.viewport_container.width()*(W.high-W.low));W.move_delta(ad)}).bind("mousewheel",function(ac,ae,ab,aa){if(ab){var ad=Math.round(-ab/W.viewport_container.width()*(W.high-W.low));W.move_delta(ad)}});this.top_labeltrack.bind("dragstart",function(aa,ab){return $("<div />").css({height:W.content_div.height()+W.top_labeltrack.height()+W.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ae,af){$(af.proxy).css({left:Math.min(ae.pageX,af.startX),width:Math.abs(ae.pageX-af.startX)});var ab=Math.min(ae.pageX,af.startX)-W.container.offset().left,aa=Math.max(ae.pageX,af.startX)-W.container.offset().left,ad=(W.high-W.low),ac=W.viewport_container.width();W.update_location(Math.round(ab/ac*ad)+W.low,Math.round(aa/ac*ad)+W.low)}).bind("dragend",function(af,ag){var ab=Math.min(af.pageX,ag.startX),aa=Math.max(af.pageX,ag.startX),ad=(W.high-W.low),ac=W.viewport_container.width(),ae=W.low;W.low=Math.round(ab/ac*ad)+ae;W.high=Math.round(aa/ac*ad)+ae;$(ag.proxy).remove();W.redraw()});this.add_label_track(new T(this,this.top_labeltrack));this.add_label_track(new T(this,this.nav_labeltrack));$(window).bind("resize",function(){W.resize_window()});$(document).bind("redraw",function(){W.redraw()});this.reset();$(window).trigger("resize")},update_location:function(W,X){this.location_span.text(commatize(W)+" - "+commatize(X));this.nav_input.val(this.chrom+":"+commatize(W)+"-"+commatize(X))},load_chroms:function(X,Y){X.num=s;$.extend(X,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var W=this;$.ajax({url:chrom_url,data:X,dataType:"json",success:function(aa){if(aa.chrom_info.length===0){alert("Invalid chromosome: "+X.chrom);return}if(aa.reference){W.add_label_track(new w(W))}W.chrom_data=aa.chrom_info;var ad='<option value="">Select Chrom/Contig</option>';for(var ac=0,Z=W.chrom_data.length;ac<Z;ac++){var ab=W.chrom_data[ac].chrom;ad+='<option value="'+ab+'">'+ab+"</option>"}if(aa.prev_chroms){ad+='<option value="previous">Previous '+s+"</option>"}if(aa.next_chroms){ad+='<option value="next">Next '+s+"</option>"}W.chrom_select.html(ad);if(Y){Y()}W.chrom_start_index=aa.start_index},error:function(){alert("Could not load chroms for this dbkey:",W.dbkey)}})},change_chrom:function(aa,X,ac){if(!aa||aa==="None"){return}var Z=this;if(aa==="previous"){Z.load_chroms({low:this.chrom_start_index-s});return}if(aa==="next"){Z.load_chroms({low:this.chrom_start_index+s});return}var ab=$.grep(Z.chrom_data,function(ae,af){return ae.chrom===aa})[0];if(ab===undefined){Z.load_chroms({chrom:aa},function(){Z.change_chrom(aa,X,ac)});return}else{if(aa!==Z.chrom){Z.chrom=aa;if(!Z.chrom){Z.intro_div.show()}else{Z.intro_div.hide()}Z.chrom_select.val(Z.chrom);Z.max_high=ab.len-1;Z.reset();Z.redraw(true);for(var ad=0,W=Z.tracks.length;ad<W;ad++){var Y=Z.tracks[ad];if(Y.init){Y.init()}}}if(X!==undefined&&ac!==undefined){Z.low=Math.max(X,0);Z.high=Math.min(ac,Z.max_high)}Z.reset_overview();Z.redraw()}},go_to:function(aa){var ae=this,W,Z,X=aa.split(":"),ac=X[0],ad=X[1];if(ad!==undefined){try{var ab=ad.split("-");W=parseInt(ab[0].replace(/,/g,""),10);Z=parseInt(ab[1].replace(/,/g,""),10)}catch(Y){return false}}ae.change_chrom(ac,W,Z)},move_fraction:function(Y){var W=this;var X=W.high-W.low;this.move_delta(Y*X)},move_delta:function(Y){var W=this;var X=W.high-W.low;if(W.low-Y<W.max_low){W.low=W.max_low;W.high=W.max_low+X}else{if(W.high-Y>W.max_high){W.high=W.max_high;W.low=W.max_high-X}else{W.high-=Y;W.low-=Y}}W.redraw()},add_track:function(W){W.view=this;W.track_id=this.track_id_counter;this.tracks.push(W);if(W.init){W.init()}W.container_div.attr("id","track_"+W.track_id);A(W.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(W){W.view=this;this.label_tracks.push(W)},remove_track:function(W){this.has_changes=true;W.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(W)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ad){var ac=this.high-this.low,ab=this.low,X=this.high;if(ab<this.max_low){ab=this.max_low}if(X>this.max_high){X=this.max_high}if(this.high!==0&&ac<this.min_separation){X=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(X);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(r,Math.max(0,Math.ceil(Math.log(this.resolution,r)/Math.log(r))));var W=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aa=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:W,width:Math.max(ae,aa)}).show();if(aa<ae){this.overview_box.css("left",W-(ae-aa)/2)}if(this.overview_highlight){this.overview_highlight.css({left:W,width:aa})}this.update_location(this.low,this.high);if(!ad){for(var Y=0,Z=this.tracks.length;Y<Z;Y++){if(this.tracks[Y]&&this.tracks[Y].enabled){this.tracks[Y].draw()}}for(Y=0,Z=this.label_tracks.length;Y<Z;Y++){this.label_tracks[Y].draw()}}},zoom_in:function(X,Y){if(this.max_high===0||this.high-this.low<this.min_separation){return}var Z=this.high-this.low,aa=Z/2+this.low,W=(Z/this.zoom_factor)/2;if(X){aa=X/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aa-W);this.high=Math.round(aa+W);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var X=this.high-this.low,Y=X/2+this.low,W=(X*this.zoom_factor)/2;this.low=Math.round(Y-W);this.high=Math.round(Y+W);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var n=function(X,aa){this.track=X;this.name=aa.name;this.params=[];var ai=aa.params;for(var Y=0;Y<ai.length;Y++){var ad=ai[Y],W=ad.name,ah=ad.label,Z=unescape(ad.html),af=ad.type;if(af==="number"){this.params[this.params.length]=new g(W,ah,Z,ad.min,ad.max)}else{if(af=="select"){this.params[this.params.length]=new H(W,ah,Z)}else{console.log("WARNING: unrecognized tool parameter type:",W,af)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ak){ak.stopPropagation()}).bind("click",function(ak){ak.stopPropagation()}).bind("dblclick",function(ak){ak.stopPropagation()});var ag=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ae=this.params;var ab=this;$.each(this.params,function(al,ao){var an=$("<div>").addClass("param-row").appendTo(ab.parent_div);var ak=$("<div>").addClass("param-label").text(ao.label).appendTo(an);var am=$("<div/>").addClass("slider").html(ao.html).appendTo(an);$("<div style='clear: both;'/>").appendTo(an)});this.parent_div.find("input").click(function(){$(this).select()});var aj=$("<div>").addClass("slider-row").appendTo(this.parent_div);var ac=$("<input type='submit'>").attr("value","Run").appendTo(aj);var ab=this;ac.click(function(){ab.run()})};extend(n.prototype,{get_param_values_dict:function(){var W={};this.parent_div.find(":input").each(function(){var X=$(this).attr("name"),Y=$(this).val();W[X]=JSON.stringify(Y)});return W},get_param_values:function(){var X=[];var W={};this.parent_div.find(":input").each(function(){var Y=$(this).attr("name"),Z=$(this).val();if(Y){X[X.length]=Z}});return X},run:function(){var X={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name};$.extend(X,this.get_param_values_dict());var Z=this.track,Y=X.tool_id+Z.tool_region_and_parameters_str(X.chrom,X.low,X.high),aa;if(Z.track_type==="FeatureTrack"){aa=new M(Y,view,Z.hda_ldda,undefined,{},{},Z)}this.track.add_track(aa);aa.content_div.text("Starting job.");var W=function(){$.getJSON(run_tool_url,X,function(ab){if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(D)}else{if(ab.error){aa.container_div.addClass("error");aa.content_div.text(u+ab.message)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text("Converting input data so that it can be easily reused.");setTimeout(W,2000)}else{aa.dataset_id=ab.dataset_id;aa.content_div.text("Running job.");aa.init()}}}})};W()}});var H=function(X,W,Y){this.name=X;this.label=W;this.html=Y};var g=function(Y,X,aa,Z,W){H.call(this,Y,X,aa);this.min=Z;this.max=W};var j=function(X,W,Y){this.name=X;this.index=W;this.value=Y};var N=function(X,W){this.name=X;this.index=W;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};extend(N.prototype,{applies_to:function(W){if(W.length>this.index){return true}return false},keep:function(W){if(!this.applies_to(W)){return true}return(W[this.index]>=this.low&&W[this.index]<=this.high)},update_attrs:function(X){var W=false;if(!this.applies_to(X)){return W}if(X[this.index]<this.min){this.min=Math.floor(X[this.index]);W=true}if(X[this.index]>this.max){this.max=Math.ceil(X[this.index]);W=true}return W},update_ui_elt:function(){var X=this.slider.slider("option","min"),W=this.slider.slider("option","max");if(this.min<X||this.max>W){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",h(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var S=function(Y,ae){this.track=Y;this.filters=[];for(var aa=0;aa<ae.length;aa++){var W=ae[aa];var X=W.name,ad=W.type,ab=W.index;if(ad==="int"||ad==="float"){this.filters[aa]=new N(X,ab)}else{this.filters[aa]=new j(X,ab,ad)}}var ac=function(af,ag,ah){af.click(function(){var ai=ag.text();max=parseFloat(ah.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ah.slider("option","values")){input_size=2*input_size+1;multi_value=true}ag.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ai).appendTo(ag).focus().select().click(function(aj){aj.stopPropagation()}).blur(function(){$(this).remove();ag.text(ai)}).keyup(function(an){if(an.keyCode===27){$(this).trigger("blur")}else{if(an.keyCode===13){var al=ah.slider("option","min"),aj=ah.slider("option","max"),am=function(ao){return(isNaN(ao)||ao>aj||ao<al)},ak=$(this).val();if(!multi_value){ak=parseFloat(ak);if(am(ak)){alert("Parameter value must be in the range ["+al+"-"+aj+"]");return $(this)}}else{ak=ak.split("-");ak=[parseFloat(ak[0]),parseFloat(ak[1])];if(am(ak[0])||am(ak[1])){alert("Parameter value must be in the range ["+al+"-"+aj+"]");return $(this)}}ah.slider((multi_value?"values":"value"),ak)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(af){af.stopPropagation()}).bind("click",function(af){af.stopPropagation()}).bind("dblclick",function(af){af.stopPropagation()});var Z=this;$.each(this.filters,function(al,ag){var ai=$("<div/>").addClass("slider-row").appendTo(Z.parent_div);var af=$("<div/>").addClass("slider-label").appendTo(ai);var an=$("<span/>").addClass("slider-name").text(ag.name+" ").appendTo(af);var ah=$("<span/>");var aj=$("<span/>").addClass("slider-value").appendTo(af).append("[").append(ah).append("]");var am=$("<div/>").addClass("slider").appendTo(ai);ag.control_element=$("<div/>").attr("id",ag.name+"-filter-control").appendTo(am);var ak=[0,0];ag.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ao,ap){ak=ap.values;ah.text(ap.values[0]+"-"+ap.values[1]);setTimeout(function(){if(ap.values[0]==ak[0]&&ap.values[1]==ak[1]){var aq=ap.values;ah.text(aq[0]+"-"+aq[1]);ag.low=aq[0];ag.high=aq[1];Z.track.draw(true,true)}},50)},change:function(ao,ap){ag.control_element.slider("option","slide").call(ag.control_element,ao,ap)}});ag.slider=ag.control_element;ag.slider_label=ah;ac(aj,ah,ag.control_element);$("<div style='clear: both;'/>").appendTo(ai)})};var R=function(W){this.track=W.track;this.params=W.params;this.values={};if(W.saved_values){this.restore_values(W.saved_values)}this.onchange=W.onchange};extend(R.prototype,{restore_values:function(W){var X=this;$.each(this.params,function(Y,Z){if(W[Z.key]!==undefined){X.values[Z.key]=W[Z.key]}else{X.values[Z.key]=Z.default_value}})},build_form:function(){var X=this;var W=$("<div />");$.each(this.params,function(ab,Z){if(!Z.hidden){var Y="param_"+ab;var ag=$("<div class='form-row' />").appendTo(W);ag.append($("<label />").attr("for",Y).text(Z.label+":"));if(Z.type==="bool"){ag.append($('<input type="checkbox" />').attr("id",Y).attr("name",Y).attr("checked",X.values[Z.key]))}else{if(Z.type==="color"){var ad=X.values[Z.key];var ac=$("<input />").attr("id",Y).attr("name",Y).val(ad);var ae=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var aa=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ae);var af=$("<div/>").appendTo(aa).farbtastic({width:100,height:100,callback:ac,color:ad});$("<div />").append(ac).append(ae).appendTo(ag).bind("click",function(ah){ae.css({left:$(this).position().left+($(ac).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ae.hide();$(document).unbind("click.color-picker")});ah.stopPropagation()})}else{ag.append($("<input />").attr("id",Y).attr("name",Y).val(X.values[Z.key]))}}}});return W},update_from_form:function(W){var Y=this;var X=false;$.each(this.params,function(Z,ab){if(!ab.hidden){var ac="param_"+Z;var aa=W.find("#"+ac).val();if(ab.type==="float"){aa=parseFloat(aa)}else{if(ab.type==="int"){aa=parseInt(aa)}else{if(ab.type==="bool"){aa=W.find("#"+ac).is(":checked")}}}if(aa!==Y.values[ab.key]){Y.values[ab.key]=aa;X=true}}});if(X){this.onchange()}}});var b=function(W,X){this.track=W;this.canvas=X};var k=function(X,W,aa,Y,Z){this.name=X;this.view=W;this.parent_element=aa;this.data_url=(Y?Y:default_data_url);this.data_url_extra_params={};this.data_query_wait=(Z?Z:E);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};extend(k.prototype,{init:function(){var W=this;W.enabled=false;W.tile_cache.clear();W.data_cache.clear();W.initial_canvas=undefined;W.content_div.css("height","auto");W.container_div.removeClass("nodata error pending");if(!W.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:W.hda_ldda,dataset_id:W.dataset_id,chrom:W.view.chrom},function(X){if(!X||X==="error"||X.kind==="error"){W.container_div.addClass("error");W.content_div.text(m);if(X.message){var Z=W.view.tracks.indexOf(W);var Y=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+X.message+"</pre>",{Close:hide_modal})});W.content_div.append(Y)}}else{if(X==="no converter"){W.container_div.addClass("error");W.content_div.text(D)}else{if(X==="no data"||(X.data!==undefined&&(X.data===null||X.data.length===0))){W.container_div.addClass("nodata");W.content_div.text(z)}else{if(X==="pending"){W.container_div.addClass("pending");W.content_div.text(p);setTimeout(function(){W.init()},W.data_query_wait)}else{if(X.status==="data"){if(X.valid_chroms){W.valid_chroms=X.valid_chroms;W.make_name_popup_menu()}W.content_div.text(Q);if(W.view.chrom){W.content_div.text("");W.content_div.css("height",W.height_px+"px");W.enabled=true;$.when(W.predraw_init()).done(function(){W.container_div.removeClass("nodata error pending");W.draw()})}}}}}}})},predraw_init:function(){},update_name:function(W){this.old_name=this.name;this.name=W;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var G=function(ae,ac,af){var X=this,ag=X.view;this.filters_manager=(ae!==undefined?new S(this,ae):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(ac!==undefined&&obj_length(ac)>0?new n(this,ac):undefined);this.parent_track=af;this.child_tracks=[];if(X.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}X.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();X.container_div.append(X.child_tracks_container);if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(X.display_modes!==undefined){if(X.mode_div===undefined){X.mode_div=$("<div class='right-float menubutton popup' />").appendTo(X.header_div);var Z=(X.track_config&&X.track_config.values.mode?X.track_config.values.mode:X.display_modes[0]);X.mode=Z;X.mode_div.text(Z);var Y=function(ah){X.mode_div.text(ah);X.mode=ah;X.track_config.values.mode=ah;X.tile_cache.clear();X.draw()};var W={};for(var aa=0,ad=X.display_modes.length;aa<ad;aa++){var ab=X.display_modes[aa];W[ab]=function(ah){return function(){Y(ah)}}(ab)}make_popupmenu(X.mode_div,W)}else{X.mode_div.hide()}}this.make_name_popup_menu()};extend(G.prototype,k.prototype,{make_name_popup_menu:function(){var X=this;var W={};W["Edit configuration"]=function(){var ad=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(){X.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(ae){if((ae.keyCode||ae.which)===27){ad()}else{if((ae.keyCode||ae.which)===13){ab()}}};$(window).bind("keypress.check_enter_esc",ac);show_modal("Configure Track",X.track_config.build_form(),{Cancel:ad,OK:ab})};if(X.filters_available>0){var aa=(X.filters_div.is(":visible")?"Hide filters":"Show filters");W[aa]=function(){X.filters_visible=(X.filters_div.is(":visible"));X.filters_div.toggle();X.make_name_popup_menu()}}if(X.tool){var aa=(X.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");W[aa]=function(){if(!X.dynamic_tool_div.is(":visible")){X.update_name(X.name+X.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";X.revert_name()}X.dynamic_tool_div.toggle();X.make_name_popup_menu()}}if(X.valid_chroms){W["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+X.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var Y=view;var Z=function(){$("#no-tracks").show()};if(this.parent_track){Y=this.parent_track;Z=function(){}}W.Remove=function(){Y.remove_track(X);if(Y.num_tracks===0){Z()}};make_popupmenu(X.name_div,W)},draw:function(W,Z){var an=this.view.low,ac=this.view.high,ae=ac-an,ag=this.view.container.width(),ab=ag/ae,ah=this.view.resolution,aa=$("<div style='position: relative;'></div>");if(!Z){this.content_div.children().remove()}this.content_div.append(aa);this.max_height=0;var aj=Math.floor(an/ah/I);var Y={};while((aj*I*ah)<ac){var am=ag+"_"+ab+"_"+aj;var ad=this.tile_cache.get(am);var ak=aj*I*this.view.resolution;var X=ak+I*this.view.resolution;if(!W&&ad){this.show_tile(ad,aa,ak,ab)}else{this.delayed_draw(W,am,ak,X,aj,ah,aa,ab,Y)}aj+=1}var af=this;var al=setInterval(function(){if(obj_length(Y)===0){clearInterval(al);if(Z){var aq=af.content_div.children();var ap=false;for(var ar=aq.length-1,ao=0;ar>=ao;ar--){var aw=$(aq[ar]);if(ap){aw.remove()}else{if(aw.children().length!==0){ap=true}}}}if(af.filters_manager){var au=af.filters_manager.filters;for(var av=0;av<au.length;av++){au[av].update_ui_elt()}var at=false;if(af.example_feature){for(var av=0;av<au.length;av++){if(au[av].applies_to(af.example_feature)){at=true;break}}}if(af.filters_available!==at){af.filters_available=at;if(!af.filters_available){af.filters_div.hide()}af.make_name_popup_menu()}}}},50);for(var ai=0;ai<this.child_tracks.length;ai++){this.child_tracks[ai].draw(W,Z)}},delayed_draw:function(X,ae,ac,ag,Y,aa,af,ah,ab){var Z=this;var ad=function(ap,ai,ak,aj,an,ao,al){returned_tile=Z.draw_tile(ai,ak,aj,an,ao,al);var am=$("<div class='track-tile'>").prepend(returned_tile);tile_element=am;Z.tile_cache.set(ae,tile_element);Z.show_tile(tile_element,an,ac,ao);delete ab[ap]};var W=setTimeout(function(){if(ac<=Z.view.high&&ag>=Z.view.low){var ai=(X?undefined:Z.tile_cache.get(ae));if(ai){Z.show_tile(ai,af,ac,ah);delete ab[W]}else{$.when(Z.data_cache.get_data(view.chrom,ac,ag,Z.mode,aa,Z.data_url_extra_params)).then(function(aj){if(view.reference_track&&ah>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,ac,ag,Z.mode,aa,view.reference_track.data_url_extra_params)).then(function(ak){ad(W,aj,aa,Y,af,ah,ak)})}else{ad(W,aj,aa,Y,af,ah)}})}}},50);ab[W]=true},show_tile:function(W,ab,Z,ac){var X=this;var Y=this.view.high-this.view.low,aa=(Z-this.view.low)*ac;if(this.left_offset){aa-=this.left_offset}W.css({position:"absolute",top:0,left:aa,height:""});ab.append(W);X.max_height=Math.max(X.max_height,W.height());X.content_div.css("height",X.max_height+"px");ab.children().css("height",X.max_height+"px")},set_overview:function(){var W=this.view;if(this.initial_canvas&&this.is_overview){W.overview_close.show();W.overview_viewport.append(this.initial_canvas);W.overview_highlight.show().height(this.initial_canvas.height());W.overview_viewport.height(this.initial_canvas.height()+W.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(Y,W,Z){var X=this,aa=(Y!==undefined&&W!==undefined&&Z!==undefined?Y+":"+W+"-"+Z:"all");return" - region=["+aa+"], parameters=["+X.tool.get_param_values().join(", ")+"]"},add_track:function(W){W.track_id=this.track_id+"_"+this.child_tracks.length;W.container_div.attr("id","track_"+W.track_id);this.child_tracks_container.append(W.container_div);A(W.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(W);this.view.has_changes=true},remove_track:function(W){W.container_div.fadeOut("slow",function(){$(this).remove()})}});var T=function(W,X){this.track_type="LabelTrack";this.hidden=true;k.call(this,null,W,X);this.container_div.addClass("label-track")};extend(T.prototype,k.prototype,{draw:function(){var Y=this.view,Z=Y.high-Y.low,ac=Math.floor(Math.pow(10,Math.floor(Math.log(Z)/Math.log(10)))),W=Math.floor(Y.low/ac)*ac,aa=this.view.container.width(),X=$("<div style='position: relative; height: 1.3em;'></div>");while(W<Y.high){var ab=(W-Y.low)/Z*aa;X.append($("<div class='label'>"+commatize(W)+"</div>").css({position:"absolute",left:ab-1}));W+=ac}this.content_div.children(":first").remove();this.content_div.append(X)}});var w=function(W){this.track_type="ReferenceTrack";this.hidden=true;k.call(this,null,W,W.top_labeltrack);G.call(this);W.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:W.dbkey};this.data_cache=new J(x,this,false);this.tile_cache=new c(q)};extend(w.prototype,G.prototype,{draw_tile:function(ag,ab,X,ad,ah){var aa=this,Y=I*ab;if(ah>this.view.canvas_manager.char_width_px){if(ag===null){aa.content_div.css("height","0px");return}var Z=this.view.canvas_manager.new_canvas();var af=Z.getContext("2d");Z.width=Math.ceil(Y*ah+aa.left_offset);Z.height=aa.height_px;af.font=af.canvas.manager.default_font;af.textAlign="center";for(var ac=0,ae=ag.length;ac<ae;ac++){var W=Math.round(ac*ah);af.fillText(ag[ac],W+aa.left_offset,10)}return Z}this.content_div.css("height","0px")}});var l=function(aa,Y,ab,W,Z){var X=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";k.call(this,aa,Y,Y.viewport_container);G.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ab;this.dataset_id=W;this.original_dataset_id=W;this.data_cache=new J(x,this);this.tile_cache=new c(q);this.track_config=new R({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:Z,onchange:function(){X.vertical_range=X.prefs.max_value-X.prefs.min_value;$("#linetrack_"+X.track_id+"_minval").text(X.prefs.min_value);$("#linetrack_"+X.track_id+"_maxval").text(X.prefs.max_value);X.tile_cache.clear();X.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};extend(l.prototype,G.prototype,{add_resize_handle:function(){var W=this;var Z=false;var Y=false;var X=$("<div class='track-resize'>");$(W.container_div).hover(function(){Z=true;X.show()},function(){Z=false;if(!Y){X.hide()}});X.hide().bind("dragstart",function(aa,ab){Y=true;ab.original_height=$(W.content_div).height()}).bind("drag",function(ab,ac){var aa=Math.min(Math.max(ac.original_height+ac.deltaY,W.min_height_px),W.max_height_px);$(W.content_div).css("height",aa);W.height_px=aa;W.draw(true)}).bind("dragend",function(aa,ab){W.tile_cache.clear();Y=false;if(!Z){X.hide()}W.track_config.values.height=W.height_px}).appendTo(W.container_div)},predraw_init:function(){var W=this,X=W.view.tracks.indexOf(W);W.vertical_range=undefined;return $.getJSON(W.data_url,{stats:true,chrom:W.view.chrom,low:null,high:null,hda_ldda:W.hda_ldda,dataset_id:W.dataset_id},function(Y){W.container_div.addClass("line-track");var aa=Y.data;if(isNaN(parseFloat(W.prefs.min_value))||isNaN(parseFloat(W.prefs.max_value))){W.prefs.min_value=aa.min;W.prefs.max_value=aa.max;$("#track_"+X+"_minval").val(W.prefs.min_value);$("#track_"+X+"_maxval").val(W.prefs.max_value)}W.vertical_range=W.prefs.max_value-W.prefs.min_value;W.total_frequency=aa.total_frequency;W.container_div.find(".yaxislabel").remove();var ab=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+X+"_minval").text(t(W.prefs.min_value));var Z=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+X+"_maxval").text(t(W.prefs.max_value));Z.css({position:"absolute",top:"24px",left:"10px"});Z.prependTo(W.container_div);ab.css({position:"absolute",bottom:"2px",left:"10px"});ab.prependTo(W.container_div)})},draw_tile:function(ah,aa,X,ae,ag){if(this.vertical_range===undefined){return}var ab=X*I*aa,Z=I*aa,W=Math.ceil(Z*ag),ad=this.height_px;var Y=this.view.canvas_manager.new_canvas();Y.width=W,Y.height=ad;var af=Y.getContext("2d");var ac=new F.LinePainter(ah.data,ab,ab+Z,this.prefs,this.mode);ac.draw(af,W,ad);return Y}});var e=function(W,ab,aa,ae,ad,Y,Z,ac){var X=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new R({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ad,onchange:function(){X.tile_cache.clear();X.draw()}});this.prefs=this.track_config.values;k.call(this,W,ab,ab.viewport_container);G.call(this,Y,Z,ac);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=aa;this.dataset_id=ae;this.original_dataset_id=ae;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_cache=new J(20,this);this.left_offset=200;this.painter=F.LinkedFeaturePainter};extend(e.prototype,G.prototype,{update_auto_mode:function(W){if(this.mode=="Auto"){if(W=="no_detail"){W="feature spans"}else{if(W=="summary_tree"){W="coverage histogram"}}this.mode_div.text("Auto ("+W+")")}},incremental_slots:function(aa,X,Z){var Y=this.view.canvas_manager.dummy_context,W=this.inc_slots[aa];if(!W||(W.mode!==Z)){W=new (o.FeatureSlotter)(aa,Z==="Pack",v,function(ab){return Y.measureText(ab)});W.mode=Z;this.inc_slots[aa]=W}return W.slot_features(X)},draw_tile:function(aj,ar,aw,ae,ag,Z){var ao=this,ay=aw*I*ar,X=(aw+1)*I*ar,al=X-ay,ap=Math.ceil(al*ag),an=this.mode,aC=25,aa=this.left_offset,ak,ab;if(an==="Auto"){if(aj.dataset_type==="summary_tree"){an=aj.dataset_type}else{if(aj.extra_info==="no_detail"){an="no_detail"}else{var aB=aj.data;if(this.view.high-this.view.low>C){an="Squish"}else{an="Pack"}}}this.update_auto_mode(an)}if(an==="summary_tree"){ab=this.summary_draw_height;ae.parent().css("height",Math.max(this.height_px,ab)+"px");this.container_div.find(".yaxislabel").remove();var W=$("<div />").addClass("yaxislabel");W.text(aj.max);W.css({position:"absolute",top:"22px",left:"10px"});W.prependTo(this.container_div);var Y=this.view.canvas_manager.new_canvas();Y.width=ap+aa;Y.height=ab+K;var az=new F.SummaryTreePainter(aj,ay,X,this.prefs);var aq=Y.getContext("2d");aq.translate(aa,K);az.draw(aq,ap,ab);return Y}var ak,ad=1;if(an==="no_detail"||an==="Squish"||an==="Pack"){ad=this.incremental_slots(ag,aj.data,an);ak=this.inc_slots[ag].slots}var af=[];if(aj.data){var ah=this.filters_manager.filters;for(var at=0,av=aj.data.length;at<av;at++){var ac=aj.data[at];var au=false;var ai;for(var ax=0,aA=ah.length;ax<aA;ax++){ai=ah[ax];ai.update_attrs(ac);if(!ai.keep(ac)){au=true;break}}if(!au){af.push(ac)}}}var az=new (this.painter)(af,ay,X,this.prefs,an,Z);var ab=az.get_required_height(ad)+y;var Y=this.view.canvas_manager.new_canvas();Y.width=ap+aa;Y.height=ab;ae.parent().css("height",Math.max(this.height_px,ab)+"px");var aq=Y.getContext("2d");aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aj.message){$(Y).css({"border-top":"1px solid red"});aq.fillStyle="red";aq.textAlign="left";var am=aq.textBaseline;aq.textBaseline="top";aq.fillText(aj.message,aa,0);aq.textBaseline=am;if(!aj.data){return Y}}this.example_feature=(aj.data.length?aj.data[0]:undefined);aq.translate(aa,y);az.draw(aq,ap,ab,ak);return Y}});var L=function(Z,X,ab,W,Y,aa){e.call(this,Z,X,ab,W,Y,aa);this.track_type="VcfTrack";this.painter=F.VariantPainter};extend(L.prototype,G.prototype,e.prototype);var O=function(Z,X,ab,W,Y,aa){e.call(this,Z,X,ab,W,Y,aa);this.track_config=new R({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:Y,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=F.ReadPainter;this.make_name_popup_menu()};extend(O.prototype,G.prototype,e.prototype);var M=function(aa,Y,ac,W,Z,ab,X){e.call(this,aa,Y,ac,W,Z,ab,{},X);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};extend(M.prototype,G.prototype,e.prototype,{predraw_init:function(){var X=this;var W=function(){if(X.data_cache.size()===0){setTimeout(W,300)}else{X.data_url=default_data_url;X.data_query_wait=E;X.dataset_state_url=converted_datasets_state_url;$.getJSON(X.dataset_state_url,{dataset_id:X.dataset_id,hda_ldda:X.hda_ldda},function(Y){})}};W()}});P.View=U;P.LineTrack=l;P.FeatureTrack=e;P.ReadTrack=O};var slotting_module=function(c,b){var d=2,a=5;b.FeatureSlotter=function(h,g,e,f){this.slots={};this.start_end_dct={};this.w_scale=h;this.include_label=g;this.max_rows=e;this.measureText=f};extend(b.FeatureSlotter.prototype,{slot_features:function(l){var o=this.w_scale,r=this.slots,g=this.start_end_dct,x=[],z=[],m=0,y=this.max_rows;for(var v=0,w=l.length;v<w;v++){var k=l[v],n=k[0];if(r[n]!==undefined){m=Math.max(m,r[n]);z.push(r[n])}else{x.push(v)}}var p=function(F,G){for(var E=0;E<=y;E++){var C=false,H=g[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var A=H[B];if(G>A[0]&&F<A[1]){C=true;break}}}if(!C){return E}}return -1};for(var v=0,w=x.length;v<w;v++){var k=l[x[v]],n=k[0],t=k[1],e=k[2],q=k[3],f=Math.floor(t*o),j=Math.ceil(e*o),u=this.measureText(q).width,h;if(q!==undefined&&this.include_label){u+=(d+a);if(f-u>=0){f-=u;h="left"}else{j+=u;h="right"}}var s=p(f,j);if(s>=0){if(g[s]===undefined){g[s]=[]}g[s].push([f,j]);r[n]=s;m=Math.max(m,s)}else{}}return m+1}})};var painters_module=function(k,B){var r=function(M,E,K,D,J,H){if(H===undefined){H=4}var G=D-E;var F=J-K;var I=Math.floor(Math.sqrt(G*G+F*F)/H);var N=G/I;var L=F/I;var C;for(C=0;C<I;C++,E+=N,K+=L){if(C%2!==0){continue}M.fillRect(E,K,H,1)}};var s=function(E,D,C,H){var G=D-H/2,F=D+H/2,I=C-Math.sqrt(H*3/2);E.beginPath();E.moveTo(G,I);E.lineTo(F,I);E.lineTo(D,C);E.lineTo(G,I);E.strokeStyle=this.fillStyle;E.fill();E.stroke();E.closePath()};var o=function(E,G,C,D,F){this.data=E;this.view_start=G;this.view_end=C;this.prefs=extend({},this.default_prefs,D);this.mode=F};o.prototype.default_prefs={};var w=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};w.prototype.default_prefis={show_counts:false};w.prototype.draw=function(P,C,O){var H=this.view_start,R=this.view_end-this.view_start,Q=C/R;var M=this.data.data,L=this.data.delta,J=this.data.max,E=O;delta_x_px=Math.ceil(L*Q);P.save();for(var F=0,G=M.length;F<G;F++){var K=Math.floor((M[F][0]-H)*Q);var I=M[F][1];if(!I){continue}var N=I/J*O;P.fillStyle="black";P.fillRect(K,E-N,delta_x_px,N);var D=4;if(this.prefs.show_counts&&(P.measureText(I).width+D)<delta_x_px){P.fillStyle="#666";P.textAlign="center";P.fillText(I,K+(delta_x_px/2),10)}}P.restore()};var c=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(R,Q,O){var J=false,K=this.prefs.min_value,H=this.prefs.max_value,N=H-K,D=O,E=this.view_start,P=this.view_end-this.view_start,F=Q/P,L=this.mode,V=this.data;R.save();var W=Math.round(O+K/N*O);if(L!=="Intensity"){R.fillStyle="#aaa";R.fillRect(0,W,Q,1)}R.beginPath();R.fillStyle=this.prefs.color;var U,I,G;if(V.length>1){G=Math.ceil((V[1][0]-V[0][0])*F)}else{G=10}for(var S=0,T=V.length;S<T;S++){U=Math.round((V[S][0]-E)*F);I=V[S][1];if(I===null){if(J&&L==="Filled"){R.lineTo(U,D)}J=false;continue}if(I<K){I=K}else{if(I>H){I=H}}if(L==="Histogram"){I=Math.round(I/N*D);R.fillRect(U,W,G,-I)}else{if(L==="Intensity"){I=255-Math.floor((I-K)/N*255);R.fillStyle="rgb("+I+","+I+","+I+")";R.fillRect(U,0,G,D)}else{I=Math.round(D-(I-K)/N*D);if(J){R.lineTo(U,I)}else{J=true;if(L==="Filled"){R.moveTo(U,D);R.lineTo(U,I)}else{R.moveTo(U,I)}}}}}if(L==="Filled"){if(J){R.lineTo(U,W);R.lineTo(0,W)}R.fill()}else{R.stroke()}var C=-1,M=-1;R.fillStyle=this.prefs.overflow_color;for(var S=0,T=V.length;S<T;S++){I=V[S][1];U=Math.round((V[S][0]-E)*F);x_minus_scaled=Math.round((V[S][0]-1-E)*F);if(M>=0&&(I===null||I<H)){R.fillRect(M,0,x_minus_scaled-M+1,2);M=-1}else{if(C>=0&&(I===null||I>K)){R.fillRect(C,O-2,x_minus_scaled-C+1,2);C=-1}}if(I!==null&&I>H&&M<0){M=U}else{if(I!==null&&I<K&&C<0){C=U}}}R.restore()};var q=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};q.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(q.prototype,{get_required_height:function(D){var C=y_scale=this.get_row_height(),E=this.mode;if(E==="no_detail"||E==="Squish"||E==="Pack"){C=D*y_scale}return C+Math.max(Math.round(y_scale/2),5)},draw:function(O,F,N,K){var I=this.data,L=this.view_start,P=this.view_end;O.save();O.fillStyle=this.prefs.block_color;O.textAlign="right";var S=this.view_end-this.view_start,R=F/S,E=this.get_row_height();for(var H=0,J=I.length;H<J;H++){var Q=I[H],G=Q[0],C=Q[1],D=Q[2],M=(K&&K[G]!==undefined?K[G]:null);if((C<P&&D>L)&&(this.mode=="Dense"||M!==null)){this.draw_element(O,this.mode,Q,M,L,P,R,E,F)}}O.restore()}});var d=10,j=3,n=5,A=10,g=1,u=3,f=3,a=9,p=2,h="#ccc";var t=function(E,G,C,D,F){q.call(this,E,G,C,D,F)};extend(t.prototype,q.prototype,{get_row_height:function(){var D=this.mode,C;if(D==="Dense"){C=d}else{if(D==="no_detail"){C=j}else{if(D==="Squish"){C=n}else{C=A}}}return C},draw_element:function(O,H,W,J,Q,ag,ak,al,C){var T=W[0],ai=W[1],aa=W[2]-1,R=W[3],ab=Math.floor(Math.max(0,(ai-Q)*ak)),P=Math.ceil(Math.min(C,Math.max(0,(aa-Q)*ak))),Z=(H==="Dense"?0:(0+J))*al,N,ae,S=null,am=null,F=this.prefs.block_color,ad=this.prefs.label_color;if(H=="Dense"){J=1}if(H==="no_detail"){O.fillStyle=F;O.fillRect(ab,Z+5,P-ab,g)}else{var M=W[4],Y=W[5],ac=W[6],G=W[7];if(Y&&ac){S=Math.floor(Math.max(0,(Y-Q)*ak));am=Math.ceil(Math.min(C,Math.max(0,(ac-Q)*ak)))}var aj,U;if(H==="Squish"||H==="Dense"){aj=1;U=f}else{aj=5;U=a}if(!G){if(W.strand){if(W.strand==="+"){O.fillStyle=O.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){O.fillStyle=O.canvas.manager.get_pattern("left_strand_inv")}}}else{O.fillStyle=F}O.fillRect(ab,Z,P-ab,U)}else{var L,V;if(H==="Squish"||H==="Dense"){O.fillStyle=h;L=Z+Math.floor(f/2)+1;V=1}else{if(M){var L=Z;var V=U;if(M==="+"){O.fillStyle=O.canvas.manager.get_pattern("right_strand")}else{if(M==="-"){O.fillStyle=O.canvas.manager.get_pattern("left_strand")}}}else{O.fillStyle=h;L+=(f/2)+1;V=1}}O.fillRect(ab,L,P-ab,V);for(var ah=0,E=G.length;ah<E;ah++){var I=G[ah],D=Math.floor(Math.max(0,(I[0]-Q)*ak)),X=Math.ceil(Math.min(C,Math.max((I[1]-1-Q)*ak)));if(D>X){continue}O.fillStyle=F;O.fillRect(D,Z+(U-aj)/2+1,X-D,aj);if(S!==undefined&&ac>Y&&!(D>am||X<S)){var af=Math.max(D,S),K=Math.min(X,am);O.fillRect(af,Z+1,K-af,U);if(G.length==1&&H=="Pack"){if(M==="+"){O.fillStyle=O.canvas.manager.get_pattern("right_strand_inv")}else{if(M==="-"){O.fillStyle=O.canvas.manager.get_pattern("left_strand_inv")}}if(af+14<K){af+=2;K-=2}O.fillRect(af,Z+1,K-af,U)}}}}if(H==="Pack"&&ai>Q){O.fillStyle=ad;if(Q===0&&ab-O.measureText(R).width<0){O.textAlign="left";O.fillText(R,P+p,Z+8)}else{O.textAlign="right";O.fillText(R,ab-p,Z+8)}O.fillStyle=F}}}});var b=function(E,G,C,D,F){q.call(this,E,G,C,D,F)};extend(b.prototype,q.prototype,{draw_element:function(V,Q,K,G,Y,E,N,W,T){var K=data[i],M=K[0],U=K[1],F=K[2]-1,P=K[3],I=Math.floor(Math.max(0,(U-Y)*N)),L=Math.ceil(Math.min(T,Math.max(0,(F-Y)*N))),H=(Q==="Dense"?0:(0+G))*W,C,Z,D=null,O=null;if(no_label){V.fillStyle=block_color;V.fillRect(I+left_offset,H+5,L-I,1)}else{var X=K[4],S=K[5],J=K[6];C=9;Z=1;V.fillRect(I+left_offset,H,L-I,C);if(Q!=="Dense"&&P!==undefined&&U>Y){V.fillStyle=label_color;if(Y===0&&I-V.measureText(P).width<0){V.textAlign="left";V.fillText(P,L+2+left_offset,H+8)}else{V.textAlign="right";V.fillText(P,I-2+left_offset,H+8)}V.fillStyle=block_color}var R=X+" / "+S;if(U>Y&&V.measureText(R).width<(L-I)){V.fillStyle="white";V.textAlign="center";V.fillText(R,left_offset+I+(L-I)/2,H+8);V.fillStyle=block_color}}}});var z=1001,m=1002,e=1003,y=1004,l=1005;var x=function(G,D){var I=G[0],H=G[1],F=D[0],E=D[1],C;if(I<F){if(H<F){C=z}else{if(H<=E){C=e}else{C=m}}}else{if(I>E){C=z}else{if(H<=E){C=l}else{C=y}}}return C};var v=function(F,H,C,E,G,D){q.call(this,F,H,C,E,G);this.ref_seq=D};v.prototype.default_prefs=extend({},q.prototype.default_prefs,{show_insertions:false});extend(v.prototype,q.prototype,{get_row_height:function(){var C,D=this.mode;if(D==="Dense"){C=d}else{if(D==="Squish"){C=n}else{C=A;if(this.prefs.show_insertions){C*=2}}}return C},draw_read:function(Z,U,P,ae,E,Y,M,J,I){Z.textAlign="center";var X=this,D=[ae,E],S=0,aa=0,W=0;ref_seq=this.ref_seq,char_width_px=Z.canvas.manager.char_width_px;var aj=[];if((U==="Pack"||this.mode==="Auto")&&J!==undefined&&P>char_width_px){W=Math.round(P/2)}if(!M){M=[[0,J.length]]}for(var Q=0,ac=M.length;Q<ac;Q++){var N=M[Q],F="MIDNSHP=X"[N[0]],R=N[1];if(F==="H"||F==="S"){S-=R}var K=Y+S,ai=Math.floor(Math.max(0,(K-ae)*P)),L=Math.floor(Math.max(0,(K+R-ae)*P));if(ai===L){L+=1}switch(F){case"H":break;case"S":case"M":case"=":var T=x([K,K+R],D);if(T!==z){var V=J.slice(aa,aa+R);if(W>0){Z.fillStyle=this.prefs.block_color;Z.fillRect(ai-W,I+1,L-ai,9);Z.fillStyle=h;for(var ag=0,C=V.length;ag<C;ag++){if(this.prefs.show_differences&&ref_seq){var O=ref_seq[K-ae+ag];if(!O||O.toLowerCase()===V[ag].toLowerCase()){continue}}if(K+ag>=ae&&K+ag<=E){var ah=Math.floor(Math.max(0,(K+ag-ae)*P));Z.fillText(V[ag],ah,I+9)}}}else{Z.fillStyle=this.prefs.block_color;Z.fillRect(ai,I+4,L-ai,f)}}aa+=R;S+=R;break;case"N":Z.fillStyle=h;Z.fillRect(ai-W,I+5,L-ai,1);S+=R;break;case"D":Z.fillStyle="red";Z.fillRect(ai-W,I+4,L-ai,3);S+=R;break;case"P":break;case"I":var T=x([K,K+R],D),ad=ai-W;if(T!==z){var V=J.slice(aa,aa+R);if(this.prefs.show_insertions){var H=ai-(L-ai)/2;if((U==="Pack"||this.mode==="Auto")&&J!==undefined&&P>char_width_px){Z.fillStyle="yellow";Z.fillRect(H-W,I-9,L-ai,9);aj[aj.length]={type:"triangle",data:[ad,I+4,5]};Z.fillStyle=h;switch(T){case (e):V=V.slice(ae-K);break;case (y):V=V.slice(0,K-E);break;case (l):break;case (m):V=V.slice(ae-K,K-E);break}for(var ag=0,C=V.length;ag<C;ag++){var ah=Math.floor(Math.max(0,(K+ag-ae)*P));Z.fillText(V[ag],ah-(L-ai)/2,I)}}else{Z.fillStyle="yellow";Z.fillRect(H,I+(this.mode!=="Dense"?2:5),L-ai,(U!=="Dense"?f:u))}}else{if((U==="Pack"||this.mode==="Auto")&&J!==undefined&&P>char_width_px){aj[aj.length]={type:"text",data:[V.length,ad,I+9]}}else{}}}aa+=R;break;case"X":aa+=R;break}}Z.fillStyle="yellow";var af,G,ak;for(var ab=0;ab<aj.length;ab++){af=aj[ab];G=af.type;ak=af.data;if(G==="text"){Z.save();Z.font="bold "+Z.font;Z.fillText(ak[0],ak[1],ak[2]);Z.restore()}else{if(G=="triangle"){s(Z,ak[0],ak[1],ak[2])}}}},draw_element:function(V,Q,I,F,Y,D,M,W,T){var L=I[0],U=I[1],E=I[2],N=I[3],H=Math.floor(Math.max(0,(U-Y)*M)),J=Math.ceil(Math.min(T,Math.max(0,(E-Y)*M))),G=(Q==="Dense"?0:(0+F))*W,Z=this.prefs.block_color,K=this.prefs.label_color,S=0;if((Q==="Pack"||this.mode==="Auto")&&M>V.canvas.manager.char_width_px){var S=Math.round(M/2)}V.fillStyle=Z;if(I[5] instanceof 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c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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