- galaxy-commits - lists.galaxyproject.org

galaxy-dist commit 78d2a72ee1d6: Add name/designation to hda name for new datasets created in collect_primary_datasets.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan(a)bx.psu.edu> # Date 1287756910 14400 # Node ID 78d2a72ee1d61099fc5958af953fb5976c544de6 # Parent 53d1fa98fa0573f84bbbd8c8264d15bfff0cb90f Add name/designation to hda name for new datasets created in collect_primary_datasets. --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1741,7 +1741,7 @@ class Tool: # Move data from temp location to dataset location shutil.move( filename, primary_data.file_name ) primary_data.set_size() - primary_data.name = outdata.name + primary_data.name = "%s (%s)" % ( outdata.name, designation ) primary_data.info = outdata.info primary_data.init_meta( copy_from=outdata ) primary_data.dbkey = dbkey

1 0

galaxy-dist commit 6ce4e430b6a0: Workflows now work in Internet Explorer again. IE does not implement Array.indexOf so we define it in galaxy.base. Update excanvas
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1287786227 14400 # Node ID 6ce4e430b6a0d69e6397ca96a01350401ae05d20 # Parent 070749f1a0f12cec2b8f20931a6224d8168a8c95 Workflows now work in Internet Explorer again. IE does not implement Array.indexOf so we define it in galaxy.base. 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The VML version of these look very // different from the canvas one. // * Clipping paths are not implemented. @@ -28,59 +28,107 @@ // (http://www.whatwg.org/specs/web-apps/current-work/#the-doctype) // or use Box Sizing Behavior from WebFX // (http://webfx.eae.net/dhtml/boxsizing/boxsizing.html) +// * Non uniform scaling does not correctly scale strokes. // * Optimize. There is always room for speed improvements. -//Known Issues: Silverlight version -// -// * Doing a transformation during a path (ie lineTo, transform, lineTo) will -// not work corerctly because the transform is done to the whole path (ie -// transform, lineTo, lineTo) -// * Patterns are not yet implemented. +// Only add this code if we do not already have a canvas implementation +if (!document.createElement('canvas').getContext) { +(function() { -// only add this code if we do not already have a canvas implementation -if (!window.CanvasRenderingContext2D) { + // alias some functions to make (compiled) code shorter + var m = Math; + var mr = m.round; + var ms = m.sin; + var mc = m.cos; + var abs = m.abs; + var sqrt = m.sqrt; -(function () { + // this is used for sub pixel precision + var Z = 10; + var Z2 = Z / 2; - var xamlId; + var IE_VERSION = +navigator.userAgent.match(/MSIE ([\d.]+)?/)[1]; + + /** + * This funtion is assigned to the <canvas> elements as element.getContext(). + * @this {HTMLElement} + * @return {CanvasRenderingContext2D_} + */ + function getContext() { + return this.context_ || + (this.context_ = new CanvasRenderingContext2D_(this)); + } + + var slice = Array.prototype.slice; + + /** + * Binds a function to an object. The returned function will always use the + * passed in {@code obj} as {@code this}. + * + * Example: + * + * g = bind(f, obj, a, b) + * g(c, d) // will do f.call(obj, a, b, c, d) + * + * @param {Function} f The function to bind the object to + * @param {Object} obj The object that should act as this when the function + * is called + * @param {*} var_args Rest arguments that will be used as the initial + * arguments when the function is called + * @return {Function} A new function that has bound this + */ + function bind(f, obj, var_args) { + var a = slice.call(arguments, 2); + return function() { + return f.apply(obj, a.concat(slice.call(arguments))); + }; + } + + function encodeHtmlAttribute(s) { + return String(s).replace(/&/g, '&').replace(/"/g, '"'); + } + + function addNamespace(doc, prefix, urn) { + if (!doc.namespaces[prefix]) { + doc.namespaces.add(prefix, urn, '#default#VML'); + } + } + + function addNamespacesAndStylesheet(doc) { + addNamespace(doc, 'g_vml_', 'urn:schemas-microsoft-com:vml'); + addNamespace(doc, 'g_o_', 'urn:schemas-microsoft-com:office:office'); + + // Setup default CSS. Only add one style sheet per document + if (!doc.styleSheets['ex_canvas_']) { + var ss = doc.createStyleSheet(); + ss.owningElement.id = 'ex_canvas_'; + ss.cssText = 'canvas{display:inline-block;overflow:hidden;' + + // default size is 300x150 in Gecko and Opera + 'text-align:left;width:300px;height:150px}'; + } + } + + // Add namespaces and stylesheet at startup. + addNamespacesAndStylesheet(document); var G_vmlCanvasManager_ = { - init: function (opt_doc) { + init: function(opt_doc) { var doc = opt_doc || document; // Create a dummy element so that IE will allow canvas elements to be // recognized. doc.createElement('canvas'); - if (/MSIE/.test(navigator.userAgent) && !window.opera) { - var self = this; - - createXamlScriptTag(); - - doc.attachEvent('onreadystatechange', function () { - self.init_(doc); - }); - } + doc.attachEvent('onreadystatechange', bind(this.init_, this, doc)); }, - init_: function (doc) { - // setup default css - var ss = doc.createStyleSheet(); - ss.cssText = 'canvas{display:inline-block;overflow:hidden;' + - // default size is 300x150 in Gecko and Opera - 'text-align:left;width:300px;height:150px}' + - 'canvas object{width:100%;height:100%;border:0;' + - 'background:transparen;margin:0}'; - + init_: function(doc) { // find all canvas elements var els = doc.getElementsByTagName('canvas'); for (var i = 0; i < els.length; i++) { - if (!els[i].getContext) { - this.initElement(els[i]); - } + this.initElement(els[i]); } }, - /** * Public initializes a canvas element so that it can be used as canvas * element from now on. This is called automatically before the page is @@ -89,35 +137,39 @@ if (!window.CanvasRenderingContext2D) { * @param {HTMLElement} el The canvas element to initialize. * @return {HTMLElement} the element that was created. */ - initElement: function (el) { - el.getContext = function () { - if (this.context_) { - return this.context_; + initElement: function(el) { + if (!el.getContext) { + el.getContext = getContext; + + // Add namespaces and stylesheet to document of the element. + addNamespacesAndStylesheet(el.ownerDocument); + + // Remove fallback content. There is no way to hide text nodes so we + // just remove all childNodes. We could hide all elements and remove + // text nodes but who really cares about the fallback content. + el.innerHTML = ''; + + // do not use inline function because that will leak memory + el.attachEvent('onpropertychange', onPropertyChange); + el.attachEvent('onresize', onResize); + + var attrs = el.attributes; + if (attrs.width && attrs.width.specified) { + // TODO: use runtimeStyle and coordsize + // el.getContext().setWidth_(attrs.width.nodeValue); + el.style.width = attrs.width.nodeValue + 'px'; + } else { + el.width = el.clientWidth; } - return this.context_ = new CanvasRenderingContext2D_(this); - }; - - var attrs = el.attributes; - if (attrs.width && attrs.width.specified) { - // TODO: use runtimeStyle and coordsize - // el.getContext().setWidth_(attrs.width.nodeValue); - el.style.width = attrs.width.nodeValue + 'px'; - } else { - el.width = el.clientWidth; + if (attrs.height && attrs.height.specified) { + // TODO: use runtimeStyle and coordsize + // el.getContext().setHeight_(attrs.height.nodeValue); + el.style.height = attrs.height.nodeValue + 'px'; + } else { + el.height = el.clientHeight; + } + //el.getContext().setCoordsize_() } - if (attrs.height && attrs.height.specified) { - // TODO: use runtimeStyle and coordsize - // el.getContext().setHeight_(attrs.height.nodeValue); - el.style.height = attrs.height.nodeValue + 'px'; - } else { - el.height = el.clientHeight; - } - - // insert object tag - el.innerHTML = getObjectHtml(); - - // do not use inline function because that will leak memory - el.attachEvent('onpropertychange', onPropertyChange); return el; } }; @@ -127,58 +179,34 @@ if (!window.CanvasRenderingContext2D) { switch (e.propertyName) { case 'width': + el.getContext().clearRect(); el.style.width = el.attributes.width.nodeValue + 'px'; - el.getContext().clearRect(); + // In IE8 this does not trigger onresize. + el.firstChild.style.width = el.clientWidth + 'px'; break; case 'height': + el.getContext().clearRect(); el.style.height = el.attributes.height.nodeValue + 'px'; - el.getContext().clearRect(); + el.firstChild.style.height = el.clientHeight + 'px'; break; } } + function onResize(e) { + var el = e.srcElement; + if (el.firstChild) { + el.firstChild.style.width = el.clientWidth + 'px'; + el.firstChild.style.height = el.clientHeight + 'px'; + } + } + G_vmlCanvasManager_.init(); - function createXamlScriptTag() { - // This script tag contains the boilerplate XAML. - document.write('<script type=text/xaml>' + - '<Canvas x:Name="root" ' + - 'xmlns="http://schemas.microsoft.com/client/2007" ' + - 'xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml" ' + - 'Width="300" ' + - 'Height="150" ' + - 'Background="Transparent"> ' + - '</Canvas>' + - '</script>'); - // Find the id of the writtenscript file. - var scripts = document.scripts; - var script = scripts[scripts.length - 1]; - xamlId = script.uniqueID; - script.id = xamlId; - } - - function getObjectHtml(fn) { - return '<object type="application/x-silverlight" >' + - '<param name="windowless" value="true">' + - '<param name="background" value="transparent">' + - '<param name="source" value="#' + xamlId + '">' + - '</object>'; - } - - function hasSilverlight() { - try { - new ActiveXObject('AgControl.AgControl'); - return true; - } catch(_) { - return false; - } - } - // precompute "00" to "FF" - var dec2hex = []; + var decToHex = []; for (var i = 0; i < 16; i++) { for (var j = 0; j < 16; j++) { - dec2hex[i * 16 + j] = i.toString(16) + j.toString(16); + decToHex[i * 16 + j] = i.toString(16) + j.toString(16); } } @@ -207,30 +235,6 @@ if (!window.CanvasRenderingContext2D) { return result; } - function doTransform(ctx) { - transformObject(ctx, getRoot(ctx), ctx.m_); - } - - function transformObject(ctx, obj, m) { - var transform = obj.renderTransform; - var matrix; - if (!transform) { - transform = create(ctx, '<MatrixTransform/>'); - matrix = create(ctx, '<Matrix/>'); - transform.matrix = matrix; - obj.renderTransform = transform; - } else { - matrix = transform.matrix; - } - - matrix.m11 = m[0][0]; - matrix.m12 = m[0][1]; - matrix.m21 = m[1][0]; - matrix.m22 = m[1][1]; - matrix.offsetX = m[2][0]; - matrix.offsetY = m[2][1]; - } - function copyState(o1, o2) { o2.fillStyle = o1.fillStyle; o2.lineCap = o1.lineCap; @@ -243,93 +247,327 @@ if (!window.CanvasRenderingContext2D) { o2.shadowOffsetY = o1.shadowOffsetY; o2.strokeStyle = o1.strokeStyle; o2.globalAlpha = o1.globalAlpha; + o2.font = o1.font; + o2.textAlign = o1.textAlign; + o2.textBaseline = o1.textBaseline; o2.arcScaleX_ = o1.arcScaleX_; o2.arcScaleY_ = o1.arcScaleY_; + o2.lineScale_ = o1.lineScale_; } - function translateColor(s) { - var rgbaMatch = /rgba$([^)]+)$/gi.exec(s); - if (rgbaMatch) { - var parts = rgbaMatch[1].split(','); - return '#' + dec2hex[Math.floor(Number(parts[3]) * 255)] + - dec2hex[Number(parts[0])] + - dec2hex[Number(parts[1])] + - dec2hex[Number(parts[2])]; + var colorData = { + aliceblue: '#F0F8FF', + antiquewhite: '#FAEBD7', + aquamarine: '#7FFFD4', + azure: '#F0FFFF', + beige: '#F5F5DC', + bisque: '#FFE4C4', + black: '#000000', + blanchedalmond: '#FFEBCD', + blueviolet: '#8A2BE2', + brown: '#A52A2A', + burlywood: '#DEB887', + cadetblue: '#5F9EA0', + chartreuse: '#7FFF00', + chocolate: '#D2691E', + coral: '#FF7F50', + cornflowerblue: '#6495ED', + cornsilk: '#FFF8DC', + crimson: '#DC143C', + cyan: '#00FFFF', + darkblue: '#00008B', + darkcyan: '#008B8B', + darkgoldenrod: '#B8860B', + darkgray: '#A9A9A9', + darkgreen: '#006400', + darkgrey: '#A9A9A9', + darkkhaki: '#BDB76B', + darkmagenta: '#8B008B', + darkolivegreen: '#556B2F', + darkorange: '#FF8C00', + darkorchid: '#9932CC', + darkred: '#8B0000', + darksalmon: '#E9967A', + darkseagreen: '#8FBC8F', + darkslateblue: '#483D8B', + darkslategray: '#2F4F4F', + darkslategrey: '#2F4F4F', + darkturquoise: '#00CED1', + darkviolet: '#9400D3', + deeppink: '#FF1493', + deepskyblue: '#00BFFF', + dimgray: '#696969', + dimgrey: '#696969', + dodgerblue: '#1E90FF', + firebrick: '#B22222', + floralwhite: '#FFFAF0', + forestgreen: '#228B22', + gainsboro: '#DCDCDC', + ghostwhite: '#F8F8FF', + gold: '#FFD700', + goldenrod: '#DAA520', + grey: '#808080', + greenyellow: '#ADFF2F', + honeydew: '#F0FFF0', + hotpink: '#FF69B4', + indianred: '#CD5C5C', + indigo: '#4B0082', + ivory: '#FFFFF0', + khaki: '#F0E68C', + lavender: '#E6E6FA', + lavenderblush: '#FFF0F5', + lawngreen: '#7CFC00', + lemonchiffon: '#FFFACD', + lightblue: '#ADD8E6', + lightcoral: '#F08080', + lightcyan: '#E0FFFF', + lightgoldenrodyellow: '#FAFAD2', + lightgreen: '#90EE90', + lightgrey: '#D3D3D3', + lightpink: '#FFB6C1', + lightsalmon: '#FFA07A', + lightseagreen: '#20B2AA', + lightskyblue: '#87CEFA', + lightslategray: '#778899', + lightslategrey: '#778899', + lightsteelblue: '#B0C4DE', + lightyellow: '#FFFFE0', + limegreen: '#32CD32', + linen: '#FAF0E6', + magenta: '#FF00FF', + mediumaquamarine: '#66CDAA', + mediumblue: '#0000CD', + mediumorchid: '#BA55D3', + mediumpurple: '#9370DB', + mediumseagreen: '#3CB371', + mediumslateblue: '#7B68EE', + mediumspringgreen: '#00FA9A', + mediumturquoise: '#48D1CC', + mediumvioletred: '#C71585', + midnightblue: '#191970', + mintcream: '#F5FFFA', + mistyrose: '#FFE4E1', + moccasin: '#FFE4B5', + navajowhite: '#FFDEAD', + oldlace: '#FDF5E6', + olivedrab: '#6B8E23', + orange: '#FFA500', + orangered: '#FF4500', + orchid: '#DA70D6', + palegoldenrod: '#EEE8AA', + palegreen: '#98FB98', + paleturquoise: '#AFEEEE', + palevioletred: '#DB7093', + papayawhip: '#FFEFD5', + peachpuff: '#FFDAB9', + peru: '#CD853F', + pink: '#FFC0CB', + plum: '#DDA0DD', + powderblue: '#B0E0E6', + rosybrown: '#BC8F8F', + royalblue: '#4169E1', + saddlebrown: '#8B4513', + salmon: '#FA8072', + sandybrown: '#F4A460', + seagreen: '#2E8B57', + seashell: '#FFF5EE', + sienna: '#A0522D', + skyblue: '#87CEEB', + slateblue: '#6A5ACD', + slategray: '#708090', + slategrey: '#708090', + snow: '#FFFAFA', + springgreen: '#00FF7F', + steelblue: '#4682B4', + tan: '#D2B48C', + thistle: '#D8BFD8', + tomato: '#FF6347', + turquoise: '#40E0D0', + violet: '#EE82EE', + wheat: '#F5DEB3', + whitesmoke: '#F5F5F5', + yellowgreen: '#9ACD32' + }; + + + function getRgbHslContent(styleString) { + var start = styleString.indexOf('(', 3); + var end = styleString.indexOf(')', start + 1); + var parts = styleString.substring(start + 1, end).split(','); + // add alpha if needed + if (parts.length != 4 || styleString.charAt(3) != 'a') { + parts[3] = 1; + } + return parts; + } + + function percent(s) { + return parseFloat(s) / 100; + } + + function clamp(v, min, max) { + return Math.min(max, Math.max(min, v)); + } + + function hslToRgb(parts){ + var r, g, b, h, s, l; + h = parseFloat(parts[0]) / 360 % 360; + if (h < 0) + h++; + s = clamp(percent(parts[1]), 0, 1); + l = clamp(percent(parts[2]), 0, 1); + if (s == 0) { + r = g = b = l; // achromatic + } else { + var q = l < 0.5 ? l * (1 + s) : l + s - l * s; + var p = 2 * l - q; + r = hueToRgb(p, q, h + 1 / 3); + g = hueToRgb(p, q, h); + b = hueToRgb(p, q, h - 1 / 3); } - var rgbMatch = /rgb$([^)]+)$/gi.exec(s); - if (rgbMatch) { - var parts = rgbMatch[1].split(','); - return '#FF' + dec2hex[Number(parts[0])] + - dec2hex[Number(parts[1])] + - dec2hex[Number(parts[2])]; + return '#' + decToHex[Math.floor(r * 255)] + + decToHex[Math.floor(g * 255)] + + decToHex[Math.floor(b * 255)]; + } + + function hueToRgb(m1, m2, h) { + if (h < 0) + h++; + if (h > 1) + h--; + + if (6 * h < 1) + return m1 + (m2 - m1) * 6 * h; + else if (2 * h < 1) + return m2; + else if (3 * h < 2) + return m1 + (m2 - m1) * (2 / 3 - h) * 6; + else + return m1; + } + + var processStyleCache = {}; + + function processStyle(styleString) { + if (styleString in processStyleCache) { + return processStyleCache[styleString]; } - return s; + var str, alpha = 1; + + styleString = String(styleString); + if (styleString.charAt(0) == '#') { + str = styleString; + } else if (/^rgb/.test(styleString)) { + var parts = getRgbHslContent(styleString); + var str = '#', n; + for (var i = 0; i < 3; i++) { + if (parts[i].indexOf('%') != -1) { + n = Math.floor(percent(parts[i]) * 255); + } else { + n = +parts[i]; + } + str += decToHex[clamp(n, 0, 255)]; + } + alpha = +parts[3]; + } else if (/^hsl/.test(styleString)) { + var parts = getRgbHslContent(styleString); + str = hslToRgb(parts); + alpha = parts[3]; + } else { + str = colorData[styleString] || styleString; + } + return processStyleCache[styleString] = {color: str, alpha: alpha}; } - function processLineCap(lineCap) { - switch (lineCap) { - case 'butt': - return 'flat'; - case 'round': - return 'round'; - case 'square': - default: - return 'square'; + var DEFAULT_STYLE = { + style: 'normal', + variant: 'normal', + weight: 'normal', + size: 10, + family: 'sans-serif' + }; + + // Internal text style cache + var fontStyleCache = {}; + + function processFontStyle(styleString) { + if (fontStyleCache[styleString]) { + return fontStyleCache[styleString]; } + + var el = document.createElement('div'); + var style = el.style; + try { + style.font = styleString; + } catch (ex) { + // Ignore failures to set to invalid font. + } + + return fontStyleCache[styleString] = { + style: style.fontStyle || DEFAULT_STYLE.style, + variant: style.fontVariant || DEFAULT_STYLE.variant, + weight: style.fontWeight || DEFAULT_STYLE.weight, + size: style.fontSize || DEFAULT_STYLE.size, + family: style.fontFamily || DEFAULT_STYLE.family + }; } - function getRoot(ctx) { - return ctx.canvas.firstChild.content.findName('root'); + function getComputedStyle(style, element) { + var computedStyle = {}; + + for (var p in style) { + computedStyle[p] = style[p]; + } + + // Compute the size + var canvasFontSize = parseFloat(element.currentStyle.fontSize), + fontSize = parseFloat(style.size); + + if (typeof style.size == 'number') { + computedStyle.size = style.size; + } else if (style.size.indexOf('px') != -1) { + computedStyle.size = fontSize; + } else if (style.size.indexOf('em') != -1) { + computedStyle.size = canvasFontSize * fontSize; + } else if(style.size.indexOf('%') != -1) { + computedStyle.size = (canvasFontSize / 100) * fontSize; + } else if (style.size.indexOf('pt') != -1) { + computedStyle.size = fontSize / .75; + } else { + computedStyle.size = canvasFontSize; + } + + // Different scaling between normal text and VML text. This was found using + // trial and error to get the same size as non VML text. + computedStyle.size *= 0.981; + + return computedStyle; } - function create(ctx, s, opt_args) { - if (opt_args) { - s = s.replace(/\%(\d+)/g, function(match, index) { - return opt_args[Number(index) - 1]; - }); - } - - try { - return ctx.canvas.firstChild.content.createFromXaml(s); - } catch (ex) { - throw Error('Could not create XAML from: ' + s); - } + function buildStyle(style) { + return style.style + ' ' + style.variant + ' ' + style.weight + ' ' + + style.size + 'px ' + style.family; } - function drawShape(ctx, s, opt_args) { - var canvas = ctx.lastCanvas_ || create(ctx, '<Canvas/>'); - var shape = create(ctx, s, opt_args); - canvas.children.add(shape); - transformObject(ctx, canvas, ctx.m_); - if (!ctx.lastCanvas_) { - getRoot(ctx).children.add(canvas); - ctx.lastCanvas_ = canvas; - } - return shape; - } + var lineCapMap = { + 'butt': 'flat', + 'round': 'round' + }; - function createBrushObject(ctx, value) { - if (value instanceof CanvasGradient_) { - return value.createBrush_(ctx); - } else if (value instanceof CanvasPattern_) { - throw Error('Not implemented'); - } else { - return create(ctx, '<SolidColorBrush Color="%1"/>', - [translateColor(value)]); - } + function processLineCap(lineCap) { + return lineCapMap[lineCap] || 'square'; } /** * This class implements CanvasRenderingContext2D interface as described by * the WHATWG. - * @param {HTMLElement} surfaceElement The element that the 2D context should - * be associated with + * @param {HTMLElement} canvasElement The element that the 2D context should + * be associated with */ - function CanvasRenderingContext2D_(surfaceElement) { + function CanvasRenderingContext2D_(canvasElement) { this.m_ = createMatrixIdentity(); - this.lastCanvas_ = null; this.mStack_ = []; this.aStack_ = []; @@ -342,100 +580,134 @@ if (!window.CanvasRenderingContext2D) { this.lineWidth = 1; this.lineJoin = 'miter'; this.lineCap = 'butt'; - this.miterLimit = 10; + this.miterLimit = Z * 1; this.globalAlpha = 1; - this.canvas = surfaceElement; - }; + this.font = '10px sans-serif'; + this.textAlign = 'left'; + this.textBaseline = 'alphabetic'; + this.canvas = canvasElement; + var cssText = 'width:' + canvasElement.clientWidth + 'px;height:' + + canvasElement.clientHeight + 'px;overflow:hidden;position:absolute'; + var el = canvasElement.ownerDocument.createElement('div'); + el.style.cssText = cssText; + canvasElement.appendChild(el); + + var overlayEl = el.cloneNode(false); + // Use a non transparent background. + overlayEl.style.backgroundColor = 'red'; + overlayEl.style.filter = 'alpha(opacity=0)'; + canvasElement.appendChild(overlayEl); + + this.element_ = el; + this.arcScaleX_ = 1; + this.arcScaleY_ = 1; + this.lineScale_ = 1; + } var contextPrototype = CanvasRenderingContext2D_.prototype; - contextPrototype.clearRect = function() { - var root = getRoot(this); - root.children.clear(); - - // TODO: Implement - this.currentPath_ = []; - this.lastCanvas_ = null; - + if (this.textMeasureEl_) { + this.textMeasureEl_.removeNode(true); + this.textMeasureEl_ = null; + } + this.element_.innerHTML = ''; }; contextPrototype.beginPath = function() { // TODO: Branch current matrix so that save/restore has no effect // as per safari docs. - this.currentPath_ = []; }; contextPrototype.moveTo = function(aX, aY) { - this.currentPath_.push('M' + aX + ',' + aY); + var p = getCoords(this, aX, aY); + this.currentPath_.push({type: 'moveTo', x: p.x, y: p.y}); + this.currentX_ = p.x; + this.currentY_ = p.y; }; contextPrototype.lineTo = function(aX, aY) { - if (this.currentPath_.length == 0) return; - this.currentPath_.push('L' + aX + ',' + aY); + var p = getCoords(this, aX, aY); + this.currentPath_.push({type: 'lineTo', x: p.x, y: p.y}); + + this.currentX_ = p.x; + this.currentY_ = p.y; }; contextPrototype.bezierCurveTo = function(aCP1x, aCP1y, aCP2x, aCP2y, aX, aY) { - if (this.currentPath_.length == 0) return; - this.currentPath_.push('C' + aCP1x + ',' + aCP1y + ' ' + - aCP2x + ',' + aCP2y + ' ' + - aX + ' ' + aY); + var p = getCoords(this, aX, aY); + var cp1 = getCoords(this, aCP1x, aCP1y); + var cp2 = getCoords(this, aCP2x, aCP2y); + bezierCurveTo(this, cp1, cp2, p); }; + // Helper function that takes the already fixed cordinates. + function bezierCurveTo(self, cp1, cp2, p) { + self.currentPath_.push({ + type: 'bezierCurveTo', + cp1x: cp1.x, + cp1y: cp1.y, + cp2x: cp2.x, + cp2y: cp2.y, + x: p.x, + y: p.y + }); + self.currentX_ = p.x; + self.currentY_ = p.y; + } + contextPrototype.quadraticCurveTo = function(aCPx, aCPy, aX, aY) { - if (this.currentPath_.length == 0) return; - this.currentPath_.push('Q' + aCPx + ',' + aCPy + ' ' + - aX + ',' + aY); - }; + // the following is lifted almost directly from + // http://developer.mozilla.org/en/docs/Canvas_tutorial:Drawing_shapes - contextPrototype.arcTo = function(x1, y1, x2, y2, radius) { - if (this.currentPath_.length == 0) return; - // TODO: Implement + var cp = getCoords(this, aCPx, aCPy); + var p = getCoords(this, aX, aY); + + var cp1 = { + x: this.currentX_ + 2.0 / 3.0 * (cp.x - this.currentX_), + y: this.currentY_ + 2.0 / 3.0 * (cp.y - this.currentY_) + }; + var cp2 = { + x: cp1.x + (p.x - this.currentX_) / 3.0, + y: cp1.y + (p.y - this.currentY_) / 3.0 + }; + + bezierCurveTo(this, cp1, cp2, p); }; contextPrototype.arc = function(aX, aY, aRadius, aStartAngle, aEndAngle, aClockwise) { - var deltaAngle = Math.abs(aStartAngle - aEndAngle); - // If start and stop are the same WebKit and Moz does nothing - if (aStartAngle == aEndAngle) { - // different browsers behave differently here so we do the easiest thing - return; + aRadius *= Z; + var arcType = aClockwise ? 'at' : 'wa'; + + var xStart = aX + mc(aStartAngle) * aRadius - Z2; + var yStart = aY + ms(aStartAngle) * aRadius - Z2; + + var xEnd = aX + mc(aEndAngle) * aRadius - Z2; + var yEnd = aY + ms(aEndAngle) * aRadius - Z2; + + // IE won't render arches drawn counter clockwise if xStart == xEnd. + if (xStart == xEnd && !aClockwise) { + xStart += 0.125; // Offset xStart by 1/80 of a pixel. Use something + // that can be represented in binary } - var endX = aX + aRadius * Math.cos(aEndAngle); - var endY = aY + aRadius * Math.sin(aEndAngle); + var p = getCoords(this, aX, aY); + var pStart = getCoords(this, xStart, yStart); + var pEnd = getCoords(this, xEnd, yEnd); - if (deltaAngle >= 2 * Math.PI) { - // if larger than 2PI - this.arc(aX, aY, aRadius, aStartAngle, aStartAngle + Math.PI, aClockwise); - this.arc(aX, aY, aRadius, aStartAngle + Math.PI, - aStartAngle + 2 * Math.PI, aClockwise); - // now move to end point - this.moveTo(endX, endY); - return; - } + this.currentPath_.push({type: arcType, + x: p.x, + y: p.y, + radius: aRadius, + xStart: pStart.x, + yStart: pStart.y, + xEnd: pEnd.x, + yEnd: pEnd.y}); - var startX = aX + aRadius * Math.cos(aStartAngle); - var startY = aY + aRadius * Math.sin(aStartAngle); - var rotationAngle = deltaAngle * 180 / Math.PI; // sign, abs? - var sweepDirection = aClockwise ? 0 : 1; - var isLargeArc = rotationAngle >= 180 == Boolean(aClockwise) ? 0 : 1; - - if (this.currentPath_.length != 0) { - // add line to start point - this.lineTo(startX, startY); - } else { - this.moveTo(startX, startY); - } - - this.currentPath_.push('A' + aRadius + ',' + aRadius + ' ' + - rotationAngle + ' ' + - isLargeArc + ' ' + - sweepDirection + ' ' + - endX + ',' + endY); }; contextPrototype.rect = function(aX, aY, aWidth, aHeight) { @@ -447,55 +719,85 @@ if (!window.CanvasRenderingContext2D) { }; contextPrototype.strokeRect = function(aX, aY, aWidth, aHeight) { - // Will destroy any existing path (same as FF behaviour) + var oldPath = this.currentPath_; this.beginPath(); + this.moveTo(aX, aY); this.lineTo(aX + aWidth, aY); this.lineTo(aX + aWidth, aY + aHeight); this.lineTo(aX, aY + aHeight); this.closePath(); this.stroke(); - this.currentPath_ = []; + + this.currentPath_ = oldPath; }; contextPrototype.fillRect = function(aX, aY, aWidth, aHeight) { - // Will destroy any existing path (same as FF behaviour) + var oldPath = this.currentPath_; this.beginPath(); + this.moveTo(aX, aY); this.lineTo(aX + aWidth, aY); this.lineTo(aX + aWidth, aY + aHeight); this.lineTo(aX, aY + aHeight); this.closePath(); this.fill(); - this.currentPath_ = []; + + this.currentPath_ = oldPath; }; contextPrototype.createLinearGradient = function(aX0, aY0, aX1, aY1) { - return new LinearCanvasGradient_(aX0, aY0, aX1, aY1); + var gradient = new CanvasGradient_('gradient'); + gradient.x0_ = aX0; + gradient.y0_ = aY0; + gradient.x1_ = aX1; + gradient.y1_ = aY1; + return gradient; }; - contextPrototype.createRadialGradient = function(x0, y0, - r0, x1, - y1, r1) { - return new RadialCanvasGradient_(x0, y0, r0, x1, y1, r1); + contextPrototype.createRadialGradient = function(aX0, aY0, aR0, + aX1, aY1, aR1) { + var gradient = new CanvasGradient_('gradientradial'); + gradient.x0_ = aX0; + gradient.y0_ = aY0; + gradient.r0_ = aR0; + gradient.x1_ = aX1; + gradient.y1_ = aY1; + gradient.r1_ = aR1; + return gradient; }; - contextPrototype.drawImage = function (image, var_args) { + contextPrototype.drawImage = function(image, var_args) { var dx, dy, dw, dh, sx, sy, sw, sh; - // For Silverlight we don't need to get the size of the image since - // Silverlight uses the image original dimension if not provided. + // to find the original width we overide the width and height + var oldRuntimeWidth = image.runtimeStyle.width; + var oldRuntimeHeight = image.runtimeStyle.height; + image.runtimeStyle.width = 'auto'; + image.runtimeStyle.height = 'auto'; + + // get the original size + var w = image.width; + var h = image.height; + + // and remove overides + image.runtimeStyle.width = oldRuntimeWidth; + image.runtimeStyle.height = oldRuntimeHeight; if (arguments.length == 3) { dx = arguments[1]; dy = arguments[2]; - // Keep sx, sy, sw, dw, sh and dh undefined + sx = sy = 0; + sw = dw = w; + sh = dh = h; } else if (arguments.length == 5) { dx = arguments[1]; dy = arguments[2]; dw = arguments[3]; dh = arguments[4]; - // Keep sx, sy, sw and sh undefined + sx = sy = 0; + sw = w; + sh = h; } else if (arguments.length == 9) { sx = arguments[1]; sy = arguments[2]; @@ -509,81 +811,298 @@ if (!window.CanvasRenderingContext2D) { throw Error('Invalid number of arguments'); } - var slImage; + var d = getCoords(this, dx, dy); - // If we have a source rect we need to clip the image. - if (arguments.length == 9) { - slImage = drawShape(this, '<Image Source="%1"/>', [image.src]); + var w2 = sw / 2; + var h2 = sh / 2; - var clipRect = create(this, - '<RectangleGeometry Rect="%1,%2,%3,%4"/>', [sx, sy, sw, sh]); - slImage.clip = clipRect; + var vmlStr = []; - var m = createMatrixIdentity(); + var W = 10; + var H = 10; - // translate to 0,0 - m[2][0] = -sx; - m[2][1] = -sy; + // For some reason that I've now forgotten, using divs didn't work + vmlStr.push(' <g_vml_:group', + ' coordsize="', Z * W, ',', Z * H, '"', + ' coordorigin="0,0"' , + ' style="width:', W, 'px;height:', H, 'px;position:absolute;'); - // scale - var m2 = createMatrixIdentity(); - m2[0][0] = dw / sw; - m2[1][1] = dh / sh; + // If filters are necessary (rotation exists), create them + // filters are bog-slow, so only create them if abbsolutely necessary + // The following check doesn't account for skews (which don't exist + // in the canvas spec (yet) anyway. - m = matrixMultiply(m, m2); + if (this.m_[0][0] != 1 || this.m_[0][1] || + this.m_[1][1] != 1 || this.m_[1][0]) { + var filter = []; - // translate to destination - m[2][0] += dx; - m[2][1] += dy; + // Note the 12/21 reversal + filter.push('M11=', this.m_[0][0], ',', + 'M12=', this.m_[1][0], ',', + 'M21=', this.m_[0][1], ',', + 'M22=', this.m_[1][1], ',', + 'Dx=', mr(d.x / Z), ',', + 'Dy=', mr(d.y / Z), ''); - transformObject(this, slImage, m); + // Bounding box calculation (need to minimize displayed area so that + // filters don't waste time on unused pixels. + var max = d; + var c2 = getCoords(this, dx + dw, dy); + var c3 = getCoords(this, dx, dy + dh); + var c4 = getCoords(this, dx + dw, dy + dh); + + max.x = m.max(max.x, c2.x, c3.x, c4.x); + max.y = m.max(max.y, c2.y, c3.y, c4.y); + + vmlStr.push('padding:0 ', mr(max.x / Z), 'px ', mr(max.y / Z), + 'px 0;filter:progid:DXImageTransform.Microsoft.Matrix(', + filter.join(''), ", sizingmethod='clip');"); } else { - slImage = drawShape(this, - '<Image Source="%1" Canvas.Left="%2" Canvas.Top="%3"/>', - [image.src, dx, dy]); - if (dw != undefined || dh != undefined) { - slImage.width = dw; - slImage.height = dh; - slImage.stretch = 'fill'; + vmlStr.push('top:', mr(d.y / Z), 'px;left:', mr(d.x / Z), 'px;'); + } + + vmlStr.push(' ">' , + '<g_vml_:image src="', image.src, '"', + ' style="width:', Z * dw, 'px;', + ' height:', Z * dh, 'px"', + ' cropleft="', sx / w, '"', + ' croptop="', sy / h, '"', + ' cropright="', (w - sx - sw) / w, '"', + ' cropbottom="', (h - sy - sh) / h, '"', + ' />', + '</g_vml_:group>'); + + this.element_.insertAdjacentHTML('BeforeEnd', vmlStr.join('')); + }; + + contextPrototype.stroke = function(aFill) { + var lineStr = []; + var lineOpen = false; + + var W = 10; + var H = 10; + + lineStr.push('<g_vml_:shape', + ' filled="', !!aFill, '"', + ' style="position:absolute;width:', W, 'px;height:', H, 'px;"', + ' coordorigin="0,0"', + ' coordsize="', Z * W, ',', Z * H, '"', + ' stroked="', !aFill, '"', + ' path="'); + + var newSeq = false; + var min = {x: null, y: null}; + var max = {x: null, y: null}; + + for (var i = 0; i < this.currentPath_.length; i++) { + var p = this.currentPath_[i]; + var c; + + switch (p.type) { + case 'moveTo': + c = p; + lineStr.push(' m ', mr(p.x), ',', mr(p.y)); + break; + case 'lineTo': + lineStr.push(' l ', mr(p.x), ',', mr(p.y)); + break; + case 'close': + lineStr.push(' x '); + p = null; + break; + case 'bezierCurveTo': + lineStr.push(' c ', + mr(p.cp1x), ',', mr(p.cp1y), ',', + mr(p.cp2x), ',', mr(p.cp2y), ',', + mr(p.x), ',', mr(p.y)); + break; + case 'at': + case 'wa': + lineStr.push(' ', p.type, ' ', + mr(p.x - this.arcScaleX_ * p.radius), ',', + mr(p.y - this.arcScaleY_ * p.radius), ' ', + mr(p.x + this.arcScaleX_ * p.radius), ',', + mr(p.y + this.arcScaleY_ * p.radius), ' ', + mr(p.xStart), ',', mr(p.yStart), ' ', + mr(p.xEnd), ',', mr(p.yEnd)); + break; + } + + + // TODO: Following is broken for curves due to + // move to proper paths. + + // Figure out dimensions so we can do gradient fills + // properly + if (p) { + if (min.x == null || p.x < min.x) { + min.x = p.x; + } + if (max.x == null || p.x > max.x) { + max.x = p.x; + } + if (min.y == null || p.y < min.y) { + min.y = p.y; + } + if (max.y == null || p.y > max.y) { + max.y = p.y; + } } } + lineStr.push(' ">'); + + if (!aFill) { + appendStroke(this, lineStr); + } else { + appendFill(this, lineStr, min, max); + } + + lineStr.push('</g_vml_:shape>'); + + this.element_.insertAdjacentHTML('beforeEnd', lineStr.join('')); }; - contextPrototype.stroke = function() { - if (this.currentPath_.length == 0) return; - var path = drawShape(this, '<Path Data="%1"/>', - [this.currentPath_.join(' ')]); - path.stroke = createBrushObject(this, this.strokeStyle); - path.opacity = this.globalAlpha; - path.strokeThickness = this.lineWidth; - path.strokeMiterLimit = this.miterLimit; - path.strokeLineJoin = this.lineJoin; - // Canvas does not differentiate start from end - path.strokeEndLineCap = path.strokeStartLineCap = - processLineCap(this.lineCap); - }; + function appendStroke(ctx, lineStr) { + var a = processStyle(ctx.strokeStyle); + var color = a.color; + var opacity = a.alpha * ctx.globalAlpha; + var lineWidth = ctx.lineScale_ * ctx.lineWidth; + + // VML cannot correctly render a line if the width is less than 1px. + // In that case, we dilute the color to make the line look thinner. + if (lineWidth < 1) { + opacity *= lineWidth; + } + + lineStr.push( + '<g_vml_:stroke', + ' opacity="', opacity, '"', + ' joinstyle="', ctx.lineJoin, '"', + ' miterlimit="', ctx.miterLimit, '"', + ' endcap="', processLineCap(ctx.lineCap), '"', + ' weight="', lineWidth, 'px"', + ' color="', color, '" />' + ); + } + + function appendFill(ctx, lineStr, min, max) { + var fillStyle = ctx.fillStyle; + var arcScaleX = ctx.arcScaleX_; + var arcScaleY = ctx.arcScaleY_; + var width = max.x - min.x; + var height = max.y - min.y; + if (fillStyle instanceof CanvasGradient_) { + // TODO: Gradients transformed with the transformation matrix. + var angle = 0; + var focus = {x: 0, y: 0}; + + // additional offset + var shift = 0; + // scale factor for offset + var expansion = 1; + + if (fillStyle.type_ == 'gradient') { + var x0 = fillStyle.x0_ / arcScaleX; + var y0 = fillStyle.y0_ / arcScaleY; + var x1 = fillStyle.x1_ / arcScaleX; + var y1 = fillStyle.y1_ / arcScaleY; + var p0 = getCoords(ctx, x0, y0); + var p1 = getCoords(ctx, x1, y1); + var dx = p1.x - p0.x; + var dy = p1.y - p0.y; + angle = Math.atan2(dx, dy) * 180 / Math.PI; + + // The angle should be a non-negative number. + if (angle < 0) { + angle += 360; + } + + // Very small angles produce an unexpected result because they are + // converted to a scientific notation string. + if (angle < 1e-6) { + angle = 0; + } + } else { + var p0 = getCoords(ctx, fillStyle.x0_, fillStyle.y0_); + focus = { + x: (p0.x - min.x) / width, + y: (p0.y - min.y) / height + }; + + width /= arcScaleX * Z; + height /= arcScaleY * Z; + var dimension = m.max(width, height); + shift = 2 * fillStyle.r0_ / dimension; + expansion = 2 * fillStyle.r1_ / dimension - shift; + } + + // We need to sort the color stops in ascending order by offset, + // otherwise IE won't interpret it correctly. + var stops = fillStyle.colors_; + stops.sort(function(cs1, cs2) { + return cs1.offset - cs2.offset; + }); + + var length = stops.length; + var color1 = stops[0].color; + var color2 = stops[length - 1].color; + var opacity1 = stops[0].alpha * ctx.globalAlpha; + var opacity2 = stops[length - 1].alpha * ctx.globalAlpha; + + var colors = []; + for (var i = 0; i < length; i++) { + var stop = stops[i]; + colors.push(stop.offset * expansion + shift + ' ' + stop.color); + } + + // When colors attribute is used, the meanings of opacity and o:opacity2 + // are reversed. + lineStr.push('<g_vml_:fill type="', fillStyle.type_, '"', + ' method="none" focus="100%"', + ' color="', color1, '"', + ' color2="', color2, '"', + ' colors="', colors.join(','), '"', + ' opacity="', opacity2, '"', + ' g_o_:opacity2="', opacity1, '"', + ' angle="', angle, '"', + ' focusposition="', focus.x, ',', focus.y, '" />'); + } else if (fillStyle instanceof CanvasPattern_) { + if (width && height) { + var deltaLeft = -min.x; + var deltaTop = -min.y; + lineStr.push('<g_vml_:fill', + ' position="', + deltaLeft / width * arcScaleX * arcScaleX, ',', + deltaTop / height * arcScaleY * arcScaleY, '"', + ' type="tile"', + // TODO: Figure out the correct size to fit the scale. + //' size="', w, 'px ', h, 'px"', + ' src="', fillStyle.src_, '" />'); + } + } else { + var a = processStyle(ctx.fillStyle); + var color = a.color; + var opacity = a.alpha * ctx.globalAlpha; + lineStr.push('<g_vml_:fill color="', color, '" opacity="', opacity, + '" />'); + } + } contextPrototype.fill = function() { - if (this.currentPath_.length == 0) return; - var path = drawShape(this, '<Path Data="%1"/>', - [this.currentPath_.join(' ')]); - // The spec says to use non zero but Silverlight uses EvenOdd by defaul - path.data.fillRule = 'NonZero'; - path.fill = createBrushObject(this, this.fillStyle); - // TODO: What about even-odd etc? + this.stroke(true); }; contextPrototype.closePath = function() { - this.currentPath_.push('z'); + this.currentPath_.push({type: 'close'}); }; - /** - * Sets the transformation matrix and marks things as dirty - */ - function setM(self, m) { - self.m_ = m; - self.lastCanvas_ = null; + function getCoords(ctx, aX, aY) { + var m = ctx.m_; + return { + x: Z * (aX * m[0][0] + aY * m[1][0] + m[2][0]) - Z2, + y: Z * (aX * m[0][1] + aY * m[1][1] + m[2][1]) - Z2 + }; }; contextPrototype.save = function() { @@ -591,14 +1110,38 @@ if (!window.CanvasRenderingContext2D) { copyState(this, o); this.aStack_.push(o); this.mStack_.push(this.m_); - setM(this, matrixMultiply(createMatrixIdentity(), this.m_)); + this.m_ = matrixMultiply(createMatrixIdentity(), this.m_); }; contextPrototype.restore = function() { - copyState(this.aStack_.pop(), this); - setM(this, this.mStack_.pop()); + if (this.aStack_.length) { + copyState(this.aStack_.pop(), this); + this.m_ = this.mStack_.pop(); + } }; + function matrixIsFinite(m) { + return isFinite(m[0][0]) && isFinite(m[0][1]) && + isFinite(m[1][0]) && isFinite(m[1][1]) && + isFinite(m[2][0]) && isFinite(m[2][1]); + } + + function setM(ctx, m, updateLineScale) { + if (!matrixIsFinite(m)) { + return; + } + ctx.m_ = m; + + if (updateLineScale) { + // Get the line scale. + // Determinant of this.m_ means how much the area is enlarged by the + // transformation. So its square root can be used as a scale factor + // for width. + var det = m[0][0] * m[1][1] - m[0][1] * m[1][0]; + ctx.lineScale_ = sqrt(abs(det)); + } + } + contextPrototype.translate = function(aX, aY) { var m1 = [ [1, 0, 0], @@ -606,12 +1149,12 @@ if (!window.CanvasRenderingContext2D) { [aX, aY, 1] ]; - setM(this, matrixMultiply(m1, this.m_)); + setM(this, matrixMultiply(m1, this.m_), false); }; contextPrototype.rotate = function(aRot) { - var c = Math.cos(aRot); - var s = Math.sin(aRot); + var c = mc(aRot); + var s = ms(aRot); var m1 = [ [c, s, 0], @@ -619,35 +1162,157 @@ if (!window.CanvasRenderingContext2D) { [0, 0, 1] ]; - setM(this, matrixMultiply(m1, this.m_)); + setM(this, matrixMultiply(m1, this.m_), false); }; contextPrototype.scale = function(aX, aY) { + this.arcScaleX_ *= aX; + this.arcScaleY_ *= aY; var m1 = [ [aX, 0, 0], [0, aY, 0], [0, 0, 1] ]; - setM(this, matrixMultiply(m1, this.m_)); + setM(this, matrixMultiply(m1, this.m_), true); }; contextPrototype.transform = function(m11, m12, m21, m22, dx, dy) { var m1 = [ [m11, m12, 0], [m21, m22, 0], - [ dx, dy, 1] + [dx, dy, 1] ]; - setM(this, matrixMultiply(m1, this.m_)); + setM(this, matrixMultiply(m1, this.m_), true); }; contextPrototype.setTransform = function(m11, m12, m21, m22, dx, dy) { - setM(this, [ + var m = [ [m11, m12, 0], [m21, m22, 0], - [ dx, dy, 1], - ]); + [dx, dy, 1] + ]; + + setM(this, m, true); + }; + + /** + * The text drawing function. + * The maxWidth argument isn't taken in account, since no browser supports + * it yet. + */ + contextPrototype.drawText_ = function(text, x, y, maxWidth, stroke) { + var m = this.m_, + delta = 1000, + left = 0, + right = delta, + offset = {x: 0, y: 0}, + lineStr = []; + + var fontStyle = getComputedStyle(processFontStyle(this.font), + this.element_); + + var fontStyleString = buildStyle(fontStyle); + + var elementStyle = this.element_.currentStyle; + var textAlign = this.textAlign.toLowerCase(); + switch (textAlign) { + case 'left': + case 'center': + case 'right': + break; + case 'end': + textAlign = elementStyle.direction == 'ltr' ? 'right' : 'left'; + break; + case 'start': + textAlign = elementStyle.direction == 'rtl' ? 'right' : 'left'; + break; + default: + textAlign = 'left'; + } + + // 1.75 is an arbitrary number, as there is no info about the text baseline + switch (this.textBaseline) { + case 'hanging': + case 'top': + offset.y = fontStyle.size / 1.75; + break; + case 'middle': + break; + default: + case null: + case 'alphabetic': + case 'ideographic': + case 'bottom': + offset.y = -fontStyle.size / 2.25; + break; + } + + switch(textAlign) { + case 'right': + left = delta; + right = 0.05; + break; + case 'center': + left = right = delta / 2; + break; + } + + var d = getCoords(this, x + offset.x, y + offset.y); + + lineStr.push('<g_vml_:line from="', -left ,' 0" to="', right ,' 0.05" ', + ' coordsize="100 100" coordorigin="0 0"', + ' filled="', !stroke, '" stroked="', !!stroke, + '" style="position:absolute;width:1px;height:1px;">'); + + if (stroke) { + appendStroke(this, lineStr); + } else { + // TODO: Fix the min and max params. + appendFill(this, lineStr, {x: -left, y: 0}, + {x: right, y: fontStyle.size}); + } + + var skewM = m[0][0].toFixed(3) + ',' + m[1][0].toFixed(3) + ',' + + m[0][1].toFixed(3) + ',' + m[1][1].toFixed(3) + ',0,0'; + + var skewOffset = mr(d.x / Z) + ',' + mr(d.y / Z); + + lineStr.push('<g_vml_:skew on="t" matrix="', skewM ,'" ', + ' offset="', skewOffset, '" origin="', left ,' 0" />', + '<g_vml_:path textpathok="true" />', + '<g_vml_:textpath on="true" string="', + encodeHtmlAttribute(text), + '" style="v-text-align:', textAlign, + ';font:', encodeHtmlAttribute(fontStyleString), + '" /></g_vml_:line>'); + + this.element_.insertAdjacentHTML('beforeEnd', lineStr.join('')); + }; + + contextPrototype.fillText = function(text, x, y, maxWidth) { + this.drawText_(text, x, y, maxWidth, false); + }; + + contextPrototype.strokeText = function(text, x, y, maxWidth) { + this.drawText_(text, x, y, maxWidth, true); + }; + + contextPrototype.measureText = function(text) { + if (!this.textMeasureEl_) { + var s = '<span style="position:absolute;' + + 'top:-20000px;left:0;padding:0;margin:0;border:none;' + + 'white-space:pre;"></span>'; + this.element_.insertAdjacentHTML('beforeEnd', s); + this.textMeasureEl_ = this.element_.lastChild; + } + var doc = this.element_.ownerDocument; + this.textMeasureEl_.innerHTML = ''; + this.textMeasureEl_.style.font = this.font; + // Don't use innerHTML or innerText because they allow markup/whitespace. + this.textMeasureEl_.appendChild(doc.createTextNode(text)); + return {width: this.textMeasureEl_.offsetWidth}; }; /******** STUBS ********/ @@ -655,116 +1320,97 @@ if (!window.CanvasRenderingContext2D) { // TODO: Implement }; - contextPrototype.createPattern = function() { - return new CanvasPattern_; + contextPrototype.arcTo = function() { + // TODO: Implement + }; + + contextPrototype.createPattern = function(image, repetition) { + return new CanvasPattern_(image, repetition); }; // Gradient / Pattern Stubs - function CanvasGradient_() { + function CanvasGradient_(aType) { + this.type_ = aType; + this.x0_ = 0; + this.y0_ = 0; + this.r0_ = 0; + this.x1_ = 0; + this.y1_ = 0; + this.r1_ = 0; this.colors_ = []; } CanvasGradient_.prototype.addColorStop = function(aOffset, aColor) { - aColor = translateColor(aColor); - this.colors_.push({offset: aOffset, color: aColor}); + aColor = processStyle(aColor); + this.colors_.push({offset: aOffset, + color: aColor.color, + alpha: aColor.alpha}); }; - CanvasGradient_.prototype.createStops_ = function(ctx, brushObj, colors) { - var gradientStopCollection = brushObj.gradientStops; - for (var i = 0, c; c = colors[i]; i++) { - var color = translateColor(c.color); - gradientStopCollection.add(create(ctx, - '<GradientStop Color="%1" Offset="%2"/>', [color, c.offset])); + function CanvasPattern_(image, repetition) { + assertImageIsValid(image); + switch (repetition) { + case 'repeat': + case null: + case '': + this.repetition_ = 'repeat'; + break + case 'repeat-x': + case 'repeat-y': + case 'no-repeat': + this.repetition_ = repetition; + break; + default: + throwException('SYNTAX_ERR'); } - }; - function LinearCanvasGradient_(x0, y0, x1, y1) { - CanvasGradient_.call(this); - this.x0_ = x0; - this.y0_ = y0; - this.x1_ = x1; - this.y1_ = y1; - } - LinearCanvasGradient_.prototype = new CanvasGradient_; - - LinearCanvasGradient_.prototype.createBrush_ = function(ctx) { - var brushObj = create(ctx, '<LinearGradientBrush MappingMode="Absolute" ' + - 'StartPoint="%1,%2" EndPoint="%3,%4"/>', - [this.x0_, this.y0_, this.x1_, this.y1_]); - this.createStops_(ctx, brushObj, this.colors_); - return brushObj; - }; - - function isNanOrInfinite(v) { - return isNaN(v) || !isFinite(v); + this.src_ = image.src; + this.width_ = image.width; + this.height_ = image.height; } - function RadialCanvasGradient_(x0, y0, r0, x1, y1, r1) { - if (r0 < 0 || r1 < 0 || isNanOrInfinite(x0) || isNanOrInfinite(y0) || - isNanOrInfinite(x1) || isNanOrInfinite(y1)) { - // IE does not support DOMException so this is as close as we get. - var error = Error('DOMException.INDEX_SIZE_ERR'); - error.code = 1; - throw error; + function throwException(s) { + throw new DOMException_(s); + } + + function assertImageIsValid(img) { + if (!img || img.nodeType != 1 || img.tagName != 'IMG') { + throwException('TYPE_MISMATCH_ERR'); } + if (img.readyState != 'complete') { + throwException('INVALID_STATE_ERR'); + } + } - CanvasGradient_.call(this); - this.x0_ = x0; - this.y0_ = y0; - this.r0_ = r0; - this.x1_ = x1; - this.y1_ = y1; - this.r1_ = r1; + function DOMException_(s) { + this.code = this[s]; + this.message = s +': DOM Exception ' + this.code; } - RadialCanvasGradient_.prototype = new CanvasGradient_; - - CanvasGradient_.prototype.createBrush_ = function(ctx) { - if (this.x0_ == this.x1_ && this.y0_ == this.y1_ && this.r0_ == this.r1_) { - return null; - } - - var radius = Math.max(this.r0_, this.r1_); - var minRadius = Math.min(this.r0_, this.r1_); - var brushObj = create(ctx, '<RadialGradientBrush MappingMode="Absolute" ' + - 'GradientOrigin="%1,%2" Center="%3,%4" ' + - 'RadiusX="%5" RadiusY="%5"/>', - [this.x0_, this.y0_, this.x1_, this.y1_, radius]); - - var colors = this.colors_.concat(); - - if (this.r1_ < this.r0_) { - // reverse color stop array - colors.reverse(); - for (var i = 0, c; c = colors[i]; i++) { - c.offset = 1 - c.offset; - } - } - - // sort the color stops - colors.sort(function(c1, c2) { - return c1.offset - c2.offset; - }); - - if (minRadius > 0) { - // We need to adjust the color stops since SL always have the inner radius - // at (0, 0) so we change the stops in case the min radius is not 0. - for (var i = 0, c; c = colors[i]; i++) { - c.offset = minRadius / radius + (radius - minRadius) / radius * c.offset; - } - } - - this.createStops_(ctx, brushObj, colors); - return brushObj; - }; - - function CanvasPattern_() {} + var p = DOMException_.prototype = new Error; + p.INDEX_SIZE_ERR = 1; + p.DOMSTRING_SIZE_ERR = 2; + p.HIERARCHY_REQUEST_ERR = 3; + p.WRONG_DOCUMENT_ERR = 4; + p.INVALID_CHARACTER_ERR = 5; + p.NO_DATA_ALLOWED_ERR = 6; + p.NO_MODIFICATION_ALLOWED_ERR = 7; + p.NOT_FOUND_ERR = 8; + p.NOT_SUPPORTED_ERR = 9; + p.INUSE_ATTRIBUTE_ERR = 10; + p.INVALID_STATE_ERR = 11; + p.SYNTAX_ERR = 12; + p.INVALID_MODIFICATION_ERR = 13; + p.NAMESPACE_ERR = 14; + p.INVALID_ACCESS_ERR = 15; + p.VALIDATION_ERR = 16; + p.TYPE_MISMATCH_ERR = 17; // set up externs G_vmlCanvasManager = G_vmlCanvasManager_; CanvasRenderingContext2D = CanvasRenderingContext2D_; CanvasGradient = CanvasGradient_; CanvasPattern = CanvasPattern_; - + DOMException = DOMException_; })(); } // if --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -1,3 +1,15 @@ +// IE doesn't implement Array.indexOf +if (!Array.indexOf) { + Array.prototype.indexOf = function(obj) { + for (var i = 0, len = this.length; i < len; i++) { + if (this[i] == obj) { + return i; + } + } + return -1; + } +} + // Returns the number of keys (elements) in an array/dictionary. function obj_length(obj) { if (obj.length !== undefined) { --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var 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async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).rem ove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!=""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStore.remove("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id;var h=$(this).children("div.historyItemBody");var i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){if(h.is (":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_state");if(k){delete k[j];$.jStore.store("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){var k=$.jStore.store("history_expand_state");if(k===undefined){k={}}k[j]=true;$.jStore.store("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStore.store("history_expand_state");if(h===undefined){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStore.store("history_expand_state",h)}).show()};if(a){b()}else{$.jStore.init("galaxy");$.jStore.engineReady(function(){b()})}}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c =$("#galaxy_tools").contents();if(c.length==0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.lo g_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(".trackster-add").live("click",function(){var b=this,a=$(this);$.ajax({url:a.attr("data-url"),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(c){var d=window.parent;d.show_modal("Add to Browser:",c,{Cancel:function(){d.hide_modal()},"Insert into selected":function(){$(d.document).find("input[name=id]:checked").each(function(){var e=$(this).val();d.location=a.attr("action-url")+"&id="+e})},"Insert into new browser":function(){d.location=a.attr("new-url")}})}})});$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c) ===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500)}); --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -22,8 +22,8 @@ ${parent.javascripts()} -  ${h.js( "jquery",

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galaxy-dist commit f72f73aa68da: Enable FormBuilder to accept and use parameter 'use_panels' in order to show panels. This enables forms built with FormBuilder to include Galaxy header. Use this new functionality to show headers for all workflow forms: create, rename, and import/upload.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287773333 14400 # Node ID f72f73aa68da51e0b5aebc063b11fa7f0b78a261 # Parent 8c1b6b3f706134b1e4ba21637f6a3b8ca5e00b67 Enable FormBuilder to accept and use parameter 'use_panels' in order to show panels. This enables forms built with FormBuilder to include Galaxy header. Use this new functionality to show headers for all workflow forms: create, rename, and import/upload. --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -391,7 +391,8 @@ class WorkflowController( BaseController #message = "Workflow renamed to '%s'." % new_name #return self.list_grid( trans, message=message, status='done' ) else: - return form( url_for( action='rename', id=trans.security.encode_id(stored.id) ), "Rename workflow", submit_text="Rename" ) \ + return form( url_for( action='rename', id=trans.security.encode_id(stored.id) ), + "Rename workflow", submit_text="Rename", use_panels=True ) \ .add_text( "new_name", "Workflow Name", value=to_unicode( stored.name ) ) @web.expose @@ -638,7 +639,7 @@ class WorkflowController( BaseController trans.set_message( "Workflow '%s' created" % stored_workflow.name ) return self.list( trans ) else: - return form( url_for(), "Create New Workflow", submit_text="Create" ) \ + return form( url_for(), "Create New Workflow", submit_text="Create", use_panels=True ) \ .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \ .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." ) @@ -1056,7 +1057,7 @@ class WorkflowController( BaseController @web.expose def import_workflow( self, trans, workflow_text=None, url=None ): if workflow_text is None and url is None: - return form( url_for(), "Import Workflow", submit_text="Import" ) \ + return form( url_for(), "Import Workflow", submit_text="Import", use_panels=True ) \ .add_text( "url", "URL to load workflow from", "" ) \ .add_input( "textarea", "Encoded workflow (as generated by export workflow)", "workflow_text", "" ) if url: --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -631,8 +631,9 @@ class GalaxyWebTransaction( base.Default """ Convenience method for displaying a simple page with a single HTML form. - """ - return self.fill_template( template, form=form, header=header, use_panels=use_panels, active_view=active_view ) + """ + return self.fill_template( template, form=form, header=header, use_panels=( form.use_panels or use_panels ), + active_view=active_view ) def fill_template(self, filename, **kwargs): """ Fill in a template, putting any keyword arguments on the context. @@ -725,12 +726,13 @@ class FormBuilder( object ): """ Simple class describing an HTML form """ - def __init__( self, action="", title="", name="form", submit_text="submit" ): + def __init__( self, action="", title="", name="form", submit_text="submit", use_panels=False ): self.title = title self.name = name self.action = action self.submit_text = submit_text self.inputs = [] + self.use_panels = use_panels def add_input( self, type, name, label, value=None, error=None, help=None, use_label=True ): self.inputs.append( FormInput( type, label, name, value, error, help, use_label ) ) return self

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galaxy-dist commit fc88085d47c3: Add some space between adjacent embedded items on Pages.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287780826 14400 # Node ID fc88085d47c384f34070952f84c22007e4a72721 # Parent 1d0eeaf2d06c7835d741fbfdab7120d366baca0b Add some space between adjacent embedded items on Pages. --- a/static/june_2007_style/embed_item.css.tmpl +++ b/static/june_2007_style/embed_item.css.tmpl @@ -1,5 +1,6 @@ .embedded-item { + margin-top: 0.5em margin-left:auto; margin-right:auto; width:90%; --- a/static/june_2007_style/blue/embed_item.css +++ b/static/june_2007_style/blue/embed_item.css @@ -1,4 +1,4 @@ -.embedded-item{margin-left:auto;margin-right:auto;width:90%;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;} +.embedded-item{margin-top:0.5em;margin-left:auto;margin-right:auto;width:90%;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em;} .embedded-item.display {padding: 0.5em;} .embedded-item.history{background-color:#C1C9E5} .embedded-item.history p{background:#C1C9E5 no-repeat 2px 2px;margin-top:0;margin-bottom:0;}

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galaxy-dist commit 070749f1a0f1: Graceful failure for ids with non-hex characters in URLs. Fix small typo with invalid history failure
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1287784895 14400 # Node ID 070749f1a0f12cec2b8f20931a6224d8168a8c95 # Parent fc88085d47c384f34070952f84c22007e4a72721 Graceful failure for ids with non-hex characters in URLs. Fix small typo with invalid history failure --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -143,8 +143,10 @@ class UsesVisualization( SharableItemSec def get_visualization( self, trans, id, check_ownership=True, check_accessible=False ): """ Get a Visualization from the database by id, verifying ownership. """ # Load workflow from database - id = trans.security.decode_id( id ) - visualization = trans.sa_session.query( trans.model.Visualization ).get( id ) + try: + visualization = trans.sa_session.query( trans.model.Visualization ).get( trans.security.decode_id( id ) ) + except TypeError: + visualization = None if not visualization: error( "Visualization not found" ) else: @@ -191,12 +193,14 @@ class UsesStoredWorkflow( SharableItemSe def get_stored_workflow( self, trans, id, check_ownership=True, check_accessible=False ): """ Get a StoredWorkflow from the database by id, verifying ownership. """ # Load workflow from database - id = trans.security.decode_id( id ) - stored = trans.sa_session.query( trans.model.StoredWorkflow ).get( id ) - if not stored: + try: + workflow = trans.sa_session.query( trans.model.StoredWorkflow ).get( trans.security.decode_id( id ) ) + except TypeError: + workflow = None + if not workflow: error( "Workflow not found" ) else: - return self.security_check( trans.get_user(), stored, check_ownership, check_accessible ) + return self.security_check( trans.get_user(), workflow, check_ownership, check_accessible ) def get_stored_workflow_steps( self, trans, stored_workflow ): """ Restores states for a stored workflow's steps. """ for step in stored_workflow.latest_workflow.steps: @@ -224,10 +228,12 @@ class UsesHistory( SharableItemSecurity def get_history( self, trans, id, check_ownership=True, check_accessible=False ): """Get a History from the database by id, verifying ownership.""" # Load history from database - id = trans.security.decode_id( id ) - history = trans.sa_session.query( trans.model.History ).get( id ) + try: + history = trans.sa_session.query( trans.model.History ).get( trans.security.decode_id( id ) ) + except TypeError: + history = None if not history: - err+msg( "History not found" ) + error( "History not found" ) else: return self.security_check( trans.get_user(), history, check_ownership, check_accessible ) def get_history_datasets( self, trans, history, show_deleted=False, show_hidden=False):

1 0

galaxy-dist commit 53d1fa98fa05: Add button that enables uploading or importing a workflow to Galaxy instance.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287691826 14400 # Node ID 53d1fa98fa0573f84bbbd8c8264d15bfff0cb90f # Parent 9d9f0de20f4f9da28d53be38411b1ee1075201a1 Add button that enables uploading or importing a workflow to Galaxy instance. --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1077,13 +1077,16 @@ class WorkflowController( BaseController # Create workflow. workflow = self._workflow_from_dict( trans, data, source="uploaded file" ).latest_workflow - # Provide user feedback. + # Provide user feedback and show workflow list. if workflow.has_errors: - return trans.show_warn_message( "Imported, but some steps in this workflow have validation errors" ) + trans.set_message( "Imported, but some steps in this workflow have validation errors", + type="warning" ) if workflow.has_cycles: - return trans.show_warn_message( "Imported, but this workflow contains cycles" ) + trans.set_message( "Imported, but this workflow contains cycles", + type="warning" ) else: - return trans.show_message( "Workflow '%s' imported" % workflow.name ) + trans.set_message( "Workflow '%s' imported" % workflow.name ) + return self.list( trans ) @web.json def get_datatypes( self, trans ): --- a/templates/workflow/list.mako +++ b/templates/workflow/list.mako @@ -17,12 +17,12 @@ %if message: <% try: - messagetype + status except: - messagetype = "done" + status = "done" %><p /> - <div class="${messagetype}message"> + <div class="${status}message"> ${h.to_unicode( message )} </div> %endif @@ -36,6 +36,12 @@ <span>Create new workflow</span></a></li> + <li> + <a class="action-button" href="${h.url_for( action='import_workflow' )}"> + <img src="${h.url_for('/static/images/fugue/arrow-090.png')}" /> + <span>Upload or import workflow</span> + </a> + </li></ul> %if workflows: Binary file static/images/fugue/arrow-090.png has changed --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -587,12 +587,14 @@ class GalaxyWebTransaction( base.Default rval = self.template_context[name] = FormData() rval.values.update( kwargs ) return rval - def set_message( self, message ): + def set_message( self, message, type=None ): """ - Convenience method for setting the 'message' element of the template - context. + Convenience method for setting the 'message' and 'message_type' + element of the template context. """ self.template_context['message'] = message + if type: + self.template_context['status'] = type def get_message( self ): """ Convenience method for getting the 'message' element of the template

1 0

galaxy-dist commit 8c1b6b3f7061: mutation viz tool UI fixes
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287761403 14400 # Node ID 8c1b6b3f706134b1e4ba21637f6a3b8ca5e00b67 # Parent 78d2a72ee1d61099fc5958af953fb5976c544de6 mutation viz tool UI fixes --- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -21,10 +21,11 @@ <repeat name="sample_chooser" title="Sample"><param name="name" type="text" label="Label" help="Optional" /><param name="a_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Base A Column" help="" /> - <param name="totals_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Totals Column" help="" /> + <param name="totals_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Coverage Column" help="" /></repeat><param name="zoom_value" type="select" label="Zoom"> + <option value="interactive">Interactive</option><option value="1">1x</option><option value="2">2x</option><option value="3">3x</option> @@ -35,7 +36,6 @@ <option value="8">8x</option><option value="9">9x</option><option value="10">10x</option> - <option value="interactive">Interactive</option></param></inputs>

1 0

galaxy-dist commit 1d0eeaf2d06c: Bug fix for displaying metadata items associated with library datasets that are lists of values.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1287775851 14400 # Node ID 1d0eeaf2d06c7835d741fbfdab7120d366baca0b # Parent f72f73aa68da51e0b5aebc063b11fa7f0b78a261 Bug fix for displaying metadata items associated with library datasets that are lists of values. --- a/templates/library/common/ldda_info.mako +++ b/templates/library/common/ldda_info.mako @@ -120,6 +120,8 @@ if isinstance( metadata_val, trans.model.MetadataFile ): metadata_val = metadata_val.file_name elif isinstance( metadata_val, list ): + # Make sure list items are strings + metadata_val = [ str( item ) for item in metadata_val ] metadata_val = ', '.join( metadata_val ) %> ${metadata_val}

1 0

galaxy-dist commit b3763f7ecec7: added more zoom levels for mutation viz tool
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287603271 14400 # Node ID b3763f7ecec7082e76a5ff407091fa7f0bffb7df # Parent e226033419a91100e657f6880562dc50ae01ef98 added more zoom levels for mutation viz tool --- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -30,6 +30,11 @@ <option value="3">3x</option><option value="4">4x</option><option value="5">5x</option> + <option value="6">6x</option> + <option value="7">7x</option> + <option value="8">8x</option> + <option value="9">9x</option> + <option value="10">10x</option><option value="interactive">Interactive</option></param> --- a/tools/mutation/visualize.py +++ b/tools/mutation/visualize.py @@ -263,8 +263,8 @@ def mainsvg(opts, args): # display legend for i, b in enumerate( bases ): bt = svg.SVG("tspan", b, style="font-family:Verdana;font-size:20%") - s.append(svg.SVG("text", bt, x=12+(i*10), y=4, stroke="none", fill="black")) - s.append(svg.SVG("rect", x=14+(i*10), y=1, width=4, height=3, + s.append(svg.SVG("text", bt, x=12+(i*10), y=3, stroke="none", fill="black")) + s.append(svg.SVG("rect", x=14+(i*10), y=0, width=4, height=3, stroke="none", fill=colors[b], fill_opacity=0.5)) reader = open(opts.input_file, 'U')

1 0

galaxy-dist commit 7afd79d131e4: Do not preserve table borders in Pages.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287607913 14400 # Node ID 7afd79d131e40f5f9a61125ec159552dc7c3fabd # Parent c375c4a8e4e42e5e29e996f3472aacdbdc3d22e0 Do not preserve table borders in Pages. --- a/templates/page/display.mako +++ b/templates/page/display.mako @@ -97,7 +97,6 @@ padding: 8px 5px 5px; min-width: 500px; border: none; - border-collapse: separate; } .page-body caption { text-align: left;

1 0

galaxy-dist commit 151d007da2f4: Stop redirecting output of the taxonomy2tree tool, since the binary has been updated to stop writing info messages to stderr.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1287681255 14400 # Node ID 151d007da2f4709ba546cd5cc76738e28b64e05d # Parent 8cc9544dd81d6c53e7c79a24b5fb30f58854e45b Stop redirecting output of the taxonomy2tree tool, since the binary has been updated to stop writing info messages to stderr. --- a/tools/taxonomy/t2t_report.xml +++ b/tools/taxonomy/t2t_report.xml @@ -3,7 +3,7 @@ <requirements><requirement type="package">taxonomy</requirement></requirements> - <command>taxonomy2tree $input 0 /dev/null $out_file1 0 &> /dev/null</command> + <command>taxonomy2tree $input 0 /dev/null $out_file1 0</command><inputs><param format="taxonomy" name="input" type="data" label="Summarize taxonomic representation for"/></inputs>

1 0

galaxy-dist commit 423e72ab1990: trackster: Don't index bottom level for summary_tree, greatly reducing computation time (>5x speedup) while not sacrificing usability
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1287612031 14400 # Node ID 423e72ab19901de8dc8f5e4e2d2e7524921380bc # Parent 5f9d6d9582e50f134c97e8523a015f210dd3af70 trackster: Don't index bottom level for summary_tree, greatly reducing computation time (>5x speedup) while not sacrificing usability --- a/lib/galaxy/visualization/tracks/summary.py +++ b/lib/galaxy/visualization/tracks/summary.py @@ -1,12 +1,15 @@ ''' 2010, Kanwei Li Summary tree data structure for aggregation + +10/20/2010: Changed version to 2 as we no longer look at bottom level, for better performance ''' import sys, os import cPickle -VERSION = 1 +VERSION = 2 +MIN_LEVEL = 2 class SummaryTree: def __init__(self, block_size, levels, draw_cutoff, detail_cutoff): @@ -27,11 +30,11 @@ class SummaryTree: else: blocks = self.chrom_blocks[chrom] = {} self.chrom_stats[chrom] = {} - for level in range(1, self.levels+1): + for level in range(MIN_LEVEL, self.levels+1): blocks[level] = {} - for level in range(1, self.levels+1): + for level in range(MIN_LEVEL, self.levels+1): block_level = blocks[level] starting_block = self.find_block(start, level) ending_block = self.find_block(end, level) @@ -45,7 +48,7 @@ class SummaryTree: ''' Checks for cutoff and only stores levels above it ''' for chrom, blocks in self.chrom_blocks.iteritems(): cur_best = 999 - for level in range(self.levels, 0, -1): + for level in range(self.levels, MIN_LEVEL-1, -1): max_val = max(blocks[level].values()) if max_val < self.draw_cutoff: if "draw_level" not in self.chrom_stats[chrom]:

1 0

galaxy-dist commit 8cc9544dd81d: Fix traceback encountered if you try to access the admin job management interface from a server with job running disabled.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1287678598 14400 # Node ID 8cc9544dd81d6c53e7c79a24b5fb30f58854e45b # Parent 423e72ab19901de8dc8f5e4e2d2e7524921380bc Fix traceback encountered if you try to access the admin job management interface from a server with job running disabled. --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1491,6 +1491,8 @@ class Admin( object ): deleted = [] msg = None status = None + if not trans.app.config.get_bool( "enable_job_running", True ): + return trans.show_error_message( 'This Galaxy instance is not configured to run jobs. If using multiple servers, please directly access the job running instance to manage jobs.' ) job_ids = util.listify( stop ) if job_ids and stop_msg in [ None, '' ]: msg = 'Please enter an error message to display to the user describing why the job was terminated'

1 0

galaxy-dist commit 5f9d6d9582e5: Read zipfiles in chunks when uncompressing in the upload tool. And I continue to wish zipfile was a lot more like tarfile...
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1287608406 14400 # Node ID 5f9d6d9582e50f134c97e8523a015f210dd3af70 # Parent 7afd79d131e40f5f9a61125ec159552dc7c3fabd Read zipfiles in chunks when uncompressing in the upload tool. And I continue to wish zipfile was a lot more like tarfile... --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -258,6 +258,9 @@ def add_file( dataset, registry, json_fi # See if we have a zip archive is_zipped = check_zip( dataset.path ) if is_zipped: + CHUNK_SIZE = 2**20 # 1Mb + uncompressed = None + uncompressed_name = None unzipped = False z = zipfile.ZipFile( dataset.path ) for name in z.namelist(): @@ -267,18 +270,28 @@ def add_file( dataset, registry, json_fi stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.' break fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_zip_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ), text=False ) - try: - outfile = open( uncompressed, 'wb' ) - outfile.write( z.read( name ) ) - outfile.close() - shutil.move( uncompressed, dataset.path ) - dataset.name = name - unzipped = True - except IOError: - os.close( fd ) - os.remove( uncompressed ) - file_err( 'Problem decompressing zipped data', dataset, json_file ) - return + zipped_file = z.open( name ) + while 1: + try: + chunk = zipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + file_err( 'Problem decompressing zipped data', dataset, json_file ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + zipped_file.close() + uncompressed_name = name + unzipped = True + z.close() + # Replace the zipped file with the decompressed file + if uncompressed is not None: + shutil.move( uncompressed, dataset.path ) + dataset.name = uncompressed_name + data_type = 'zip' if not data_type: if check_binary( dataset.path ): # We have a binary dataset, but it is not Bam, Sff or Pdf

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galaxy-dist commit c375c4a8e4e4: Fix more unicode issues when listing and running workflows.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287605437 14400 # Node ID c375c4a8e4e42e5e29e996f3472aacdbdc3d22e0 # Parent 647ca0049221bcadde31559d6a99a6ccf236d134 Fix more unicode issues when listing and running workflows. --- a/templates/workflow/list_for_run.mako +++ b/templates/workflow/list_for_run.mako @@ -36,7 +36,7 @@ %for i, workflow in enumerate( workflows ): <tr><td> - <a href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a> + <a href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">${h.to_unicode( workflow.name )}</a><a id="wf-${i}-popup" class="popup-arrow" style="display: none;">▼</a></td><td>${len(workflow.latest_workflow.steps)}</td> --- a/templates/workflow/run.mako +++ b/templates/workflow/run.mako @@ -119,7 +119,7 @@ from galaxy.jobs.actions.post import Act </div></%def> -<h2>Running workflow "${workflow.name}"</h2> +<h2>Running workflow "${h.to_unicode( workflow.name )}"</h2> %if has_upgrade_messages: <div class="warningmessage"> @@ -130,7 +130,7 @@ from galaxy.jobs.actions.post import Act %endif <form id="tool_form" name="tool_form" method="POST"> -## <input type="hidden" name="workflow_name" value="${workflow.name | h}" /> +## <input type="hidden" name="workflow_name" value="${h.to_unicode( workflow.name ) | h}" /> %for i, step in enumerate( steps ): %if step.type == 'tool' or step.type is None: <% tool = app.toolbox.tools_by_id[step.tool_id] %> @@ -153,7 +153,7 @@ from galaxy.jobs.actions.post import Act % if step.annotations: <hr/><div class='form-row'> - <label>Annotation:</label> ${step.annotations[0].annotation} + <label>Annotation:</label> ${h.to_unicode( step.annotations[0].annotation )} </div> % endif </div>

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galaxy-dist commit 647ca0049221: Enable display of unicode characters in history and workflow annotations.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287604356 14400 # Node ID 647ca0049221bcadde31559d6a99a6ccf236d134 # Parent b3763f7ecec7082e76a5ff407091fa7f0bffb7df Enable display of unicode characters in history and workflow annotations. --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -1038,7 +1038,7 @@ <label>Annotation / Notes:</label><div id="workflow-annotation" class="tooltip editable-text" original-title="Click to edit annotation"> %if annotation: - ${annotation | h} + ${h.to_unicode( annotation ) | h} %else: <em>Describe or add notes to workflow</em> %endif --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -378,7 +378,7 @@ div.form-row { <div id="history-annotation-container"><div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation"> %if annotation: - ${annotation | h} + ${h.to_unicode( annotation ) | h} %else: <em>Describe or add notes to history</em> %endif

1 0

galaxy-dist commit 9d9f0de20f4f: Make default initial value for Integer and Float parameters None.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan(a)bx.psu.edu> # Date 1287683139 14400 # Node ID 9d9f0de20f4f9da28d53be38411b1ee1075201a1 # Parent 151d007da2f4709ba546cd5cc76738e28b64e05d Make default initial value for Integer and Float parameters None. --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -212,7 +212,7 @@ class IntegerToolParameter( TextToolPara if self.value: return int( self.value ) else: - return 0 + return None class FloatToolParameter( TextToolParameter ): """ @@ -254,7 +254,7 @@ class FloatToolParameter( TextToolParame try: return float( self.value ) except: - return float( 0 ) + return None class BooleanToolParameter( ToolParameter ): """

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galaxy-dist commit 35b379691524: Add dynamic attribute filtering framework for trackster and enable dynamic filtering of VCF quality values and BED score values. Framework enables users to interactively filter a visualized dataset within trackster; for example, a BED file of peaks can be filtering so that only peaks with a score greater than 100 are shown.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287519951 14400 # Node ID 35b379691524c768ec84f86477f1ab49859afec2 # Parent 6372b67c9e370b3a80159bcc719e13d50ddc018f Add dynamic attribute filtering framework for trackster and enable dynamic filtering of VCF quality values and BED score values. Framework enables users to interactively filter a visualized dataset within trackster; for example, a BED file of peaks can be filtering so that only peaks with a score greater than 100 are shown. Individual changes include: (a) improvements to datatypes and data providers to support BED score filtering and VCF quality filtering; (b) addition of jQueryUI theme for slider; (c) modifications to trackster to show, update, and apply filters. --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -469,7 +469,7 @@ class Vcf( Tabular ): MetadataElement( name="columns", default=10, desc="Number of columns", readonly=True, visible=False ) MetadataElement( name="column_types", default=['str','int','str','str','str','int','str','list','str','str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) - MetadataElement( name="viz_filter_columns", default=[5] ) + MetadataElement( name="viz_filter_cols", default=[5], param=metadata.ColumnParameter, multiple=True ) def sniff( self, filename ): try: --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -function 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[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!=""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStore.remove("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id;var h=$(this).children("div.historyItemBody");var i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_s 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lass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false }$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(".trackster-add").live("click",function(){var b=this,a=$(this);$.ajax({url:a.attr("data-url"),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(c){var d=window.parent;d.show_modal("Add to Browser:",c,{Cancel:function(){d.hide_modal()},"Insert into selected":function(){$(d.document).find("input[name=id]:checked").each(function(){var e=$(this).val();d.location=a.attr("action-url")+"&id="+e})},"Insert into new browser":function(){d.location=a.attr("new-url")}})}})});$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(func tion(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500)}); Binary file static/june_2007_style/blue/overcast/images/ui-bg_inset-hard_75_999999_1x100.png has changed --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function() {RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this. min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);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_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);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_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<inp ut/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=d.chrom_info ;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(d){this.origin al_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a. low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.reset();c.redraw(true);for(var g i n c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.reset_overview();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this .tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=this.low/(this.max_high-this.max_low)*this.overview_viewport.width();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_locatio n(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);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 Track=function(b,a,c){this.name=b;this.parent_ element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<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=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name)}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("e rror");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined ){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}};b["Edit configuration"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},j=function(){d.update_options(d.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){j()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:l,OK :j})};b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};make_popupmenu(d.name_div,b)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){if(!c.initial_canvas){c.initial_ca nvas=$(tile_element).clone();var l=tile_element.get(0).getContext("2d");var j=c.initial_canvas.get(0).getContext("2d");var k=l.getImageData(0,0,l.canvas.width,l.canvas.height);j.putImageData(k,0,0);c.set_overview()}c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10 )))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey: this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,l,p){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),o=e.get(0).getContext("2d"),k=f+"_"+b;if(p>PX_PER_CHAR){if(this.data_cache.get(k)===undefined){this.get_data(f,b);return}var n=this.data_cache.get(k);if(n===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*p+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*p-this.left_offset});for(var h=0,m=n.length;h<m;h++){var a=Math.round(h*p),j=Math.round(p/2);o.fillText(n[h],a+this.left_offset+j,10)}l.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_ px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;a.container_div.find(".yaxislabel").remove();var e=$("<div />").addCl ass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,s,c,e){if(this.vertical_range===undefined){return}var t=s*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),w=p+"_"+s;if(this.data_cache.get(w)===undefined){this.get_data(p,s);return}v ar j=this.data_cache.get(w);if(j===null){return}b.css({position:"absolute",top:0,left:(t-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,u=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();o.fillStyle=this.prefs.color;if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var v,h;for(var q=0,r=data.length;q<r;q++){v=Math.round((data[q][0]-t)*e);h=data[q][1];if(h===null){if(k&&m==="Filled"){o.lineTo(v,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(d-(h-l)/n*d);o.fillRect(v,h,f,d-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(v,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(v,h)}else{k=true;if(m==="Filled"){o.moveTo(v,d);o.lineTo(v,h)}else{o.moveTo(v,h)}}}}}if(m==="Filled"){if(k){o.lineTo(v,d)}o.fill()}else {o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div />").addClass("form-row");var e="track_"+n+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+n+"_minval",m=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),l=$("<input></input>").attr("id",h).val(d),k="track_"+n+"_maxval",g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j);return a.append(m).append(l).append(g).append(f).append(b).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();color=$("#track_"+c+"_color").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value||color!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.prefs.color=color;this.vert ical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_colo r!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_ slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefine d&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(ad,n,r,aq){var M=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,L=ai-M;var ak=(!this.initial_canvas?"initial":M+"_"+ai);var H=this.data_cache.get(ak);var e;if(H===undefined||(this.mode!=="Auto"&&H.dataset_type==="summary_tree")){this.data_queue[[M,ai]]=true;this.get_data(M,ai);return}var a=Math.ceil(L*aq),R=$("<canvas class='tile'></canvas>"),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,w=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(H.extra_info==="no_detail")),V=this.left_offset,ap,C,ar;if(H.dataset_type==="summary_tree"){C=this.summary_draw_height}else{if(q==="Dense"){C=w;ar=10}else{ar=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var z=(aq<0.0001?1/view.zoom_res:aq);C=this.incremental_slots(z,H.data,ab,q)*ar+w;ap=this.inc_slots[z]}}R.css({position:"absolute",top:0,left:(M-this.view.low)*aq-V});R.get(0).width=a+V;R.get(0).height=C;r.parent().css("height",Math.max(this.height_px,C)+"px");var I=R.get(0).getContext("2d");I.fillStyle=h;I.font=this.default_font;I.textAlign="right";this.container_div.find(".yaxislabel").remove();if(H.dataset_type=="summary_tree"){var X=H.data,K=H.max,p=H.avg,b=Math.ceil(H.delta*aq);var o=$("<div />").addClass("yaxislabel").text(K);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,G=X.length;am<G;am++){var Z=Math.floor((X[am][0]-M)*aq);var Y=X[am][1];if(!Y){continue}var aj=Y/K*this.summary_draw_height;I.fillStyle="black";I.fillRect(Z+V,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&I.measureText(Y).width<b){I.fillStyle="#bbb";I.textAlign="center";I.fillText(Y,Z+V+(b/2),this.summary_draw_height-5)}}e="Summary";r.append (R);return R}if(H.message){R.css({border:"solid red","border-width":"2px 2px 2px 0px"});I.fillStyle="red";I.textAlign="left";I.fillText(H.message,100+V,ar)}var ao=H.data;var al=0;for(var am=0,G=ao.length;am<G;am++){var S=ao[am],Q=S[0],an=S[1],aa=S[2],N=S[3];if(an<=ai&&aa>=M){var ac=Math.floor(Math.max(0,(an-M)*aq)),J=Math.ceil(Math.min(a,Math.max(0,(aa-M)*aq))),W=(q==="Dense"?1:(1+ap[Q]))*ar;if(H.dataset_type==="bai"){var u=S[4];I.fillStyle=h;if(S[5] instanceof Array){var D=Math.floor(Math.max(0,(S[5][0]-M)*aq)),P=Math.ceil(Math.min(a,Math.max(0,(S[5][1]-M)*aq))),B=Math.floor(Math.max(0,(S[6][0]-M)*aq)),v=Math.ceil(Math.min(a,Math.max(0,(S[6][1]-M)*aq)));if(S[5][1]>=M&&S[5][0]<=ai){this.rect_or_text(I,aq,M,ai,S[5][0],S[5][2],D+V,P-D,W)}if(S[6][1]>=M&&S[6][0]<=ai){this.rect_or_text(I,aq,M,ai,S[6][0],S[6][2],B+V,v-B,W)}if(B>P){I.fillStyle="#999";I.fillRect(P+V,W+5,B-P,1)}}else{I.fillStyle=h;this.rect_or_text(I,aq,M,ai,an,N,ac+V,J-ac,W)}if(q!=="Dense"&&!ab&&an>M){I.fillStyle=th is.prefs.label_color;if(n===0&&ac-I.measureText(N).width<0){I.textAlign="left";I.fillText(Q,J+2+V,W+8)}else{I.textAlign="right";I.fillText(Q,ac-2+V,W+8)}I.fillStyle=h}}else{if(H.dataset_type==="interval_index"){if(ab){I.fillStyle=h;I.fillRect(ac+V,W+5,J-ac,1)}else{var F=S[4],U=S[5],ae=S[6],g=S[7];var E,ag,O=null,at=null;if(U&&ae){O=Math.floor(Math.max(0,(U-M)*aq));at=Math.ceil(Math.min(a,Math.max(0,(ae-M)*aq)))}if(q!=="Dense"&&N!==undefined&&an>M){I.fillStyle=af;if(n===0&&ac-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+V,W+8)}else{I.textAlign="right";I.fillText(N,ac-2+V,W+8)}I.fillStyle=h}if(g){if(F){if(F=="+"){I.fillStyle=RIGHT_STRAND}else{if(F=="-"){I.fillStyle=LEFT_STRAND}}I.fillRect(ac+V,W,J-ac,10);I.fillStyle=h}for(var ak=0,f=g.length;ak<f;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-M)*aq)),T=Math.ceil(Math.min(a,Math.max((t[1]-M)*aq)));if(d>T){continue}E=5;ag=3;I.fillRect(d+V,W+ag,T-d,E);if(O!==undefined&&!(d>at||T<O)){E=9;ag=1;var ah=Math.max(d,O) ,A=Math.min(T,at);I.fillRect(ah+V,W+ag,A-ah,E)}}}else{E=9;ag=1;I.fillRect(ac+V,W+ag,J-ac,E);if(S.strand){if(S.strand=="+"){I.fillStyle=RIGHT_STRAND_INV}else{if(S.strand=="-"){I.fillStyle=LEFT_STRAND_INV}}I.fillRect(ac+V,W,J-ac,10);I.fillStyle=h}}}}else{if(H.dataset_type==="vcf"){if(ab){I.fillStyle=h;I.fillRect(ac+V,W+5,J-ac,1)}else{var s=S[4],m=S[5],c=S[6];E=9;ag=1;I.fillRect(ac+V,W,J-ac,E);if(q!=="Dense"&&N!==undefined&&an>M){I.fillStyle=af;if(n===0&&ac-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+V,W+8)}else{I.textAlign="right";I.fillText(N,ac-2+V,W+8)}I.fillStyle=h}var l=s+" / "+m;if(an>M&&I.measureText(l).width<(J-ac)){I.fillStyle="white";I.textAlign="center";I.fillText(l,V+ac+(J-ac)/2,W+8);I.fillStyle=h}}}}}al++}}r.append(R);return R},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k ="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vert ical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";r ight_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_coun ter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Ove rview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack (a))}a.chrom_data=d.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("drag start",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.contai ner.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.rese t();c.redraw(true);for(var g in c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.reset_overview();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remo ve()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=this.low/(this.max_high-this.max_low)*this.overview_viewport.width();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a ,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);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 Filter=function( b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=Number.MIN_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=Number.MIN_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[th is.slider_min,this.slider_max])}}});var get_filters=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,d,c){this.name=b;this.view=a;this.parent_element=d;this.filters=(c!==undefined?get_filters(c):[]);this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<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=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.filtering_div=$("<div class='track-filters'>").appendTo(this.container_div);this.filte ring_div.hide();this.filtering_div.bind("drag",function(k){k.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);var c=this;for(var e=0;e<this.filters.length;e++){var a=this.filters[e];var f=$("<tr>").appendTo(b);var g=$("<th class='filter-info'>").appendTo(f);var j=$("<span class='name'>").appendTo(g);j.text(a.name+" ");var d=$("<span class='values'>").appendTo(g);d.text("[0-2]");var h=$("<td>").appendTo(f);a.control_element=$("<div id='"+a.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(h);a.control_element.slider({range:true,min:0,max:1,values:[0,1],slide:function(l,m){var k=m.values;d.text("["+k[0]+"-"+k[1]+"]");a.low=k[0];a.high=k[1];c.draw(true)},change:function(k,l){a.control_element.slider("option","slide").call(a.control_element,k,l)}});a.slider=a.control_element;a.slider_label=d}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},i nit_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div. addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}};b["Edit configurat ion"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},j=function(){d.update_options(d.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){j()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:l,OK:j})};if(d.filters.length>0){b["Show filters"]=function(){var j;if(!d.filtering_div.is(":visible")){j="Hide filters";d.filters_visible=true}else{j="Show filters";d.filters_visible=false}$("#"+d.name_div.attr("id")+"-menu").find("li").eq(2).text(j);d.filtering_div.toggle()}}b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};d.popup_menu=make_popupmenu(d.name_div,b);show_hide_popupmenu_options(d.popup_menu,"(Show|Hide) filters",false)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,h=g-m,f=this.view.res olution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h,k;this.content_div.append(p),this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=new Object();while((a*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+a;var e=this.tile_cache.get(n);if(!b&&e){var j=a*DENSITY*f;var d=(j-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(this,n,m,g,a,f,p,q,l)}a+=1}var c=this;var o=setInterval(function(){if(l.length!=0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var r=0;r<c.filters.length;r++){c.filters[r].update_ui_elt()}clearInterval(o)}},50)},delayed_draw:function(c,h,g,e,b,d,j,k,f){var a=setTimeout(function(){if(!(g>c.view.high||e<c.view.low)){tile_element=c.draw_tile(d,b,j,k);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var n=tile_element.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n. getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,tile_element);c.show_tile(tile_element,j)}}delete f.id},50);f.id=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a ,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_da ta:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,l,p){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),o=e.get(0).getContext("2d"),k=f+"_"+b;if(p>PX_PER_CHAR){if(this.data_cache.get(k)===undefined){this.get_data(f,b);return}var n=this.data_cache.get(k);if(n===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*p+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*p-this.left_offset});for(var h=0,m=n.length;h<m;h++){var a=Math.round(h*p),j=Math.round(p/2);o.fillText(n[h],a+this.left_offset+j,10)}l.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=func tion(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#trac k_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;a.container_div.find(".yaxislabel").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:func tion(p,s,c,e){if(this.vertical_range===undefined){return}var t=s*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),w=p+"_"+s;if(this.data_cache.get(w)===undefined){this.get_data(p,s);return}var j=this.data_cache.get(w);if(j===null){return}b.css({position:"absolute",top:0,left:(t-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,u=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();o.fillStyle=this.prefs.color;if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var v,h;for(var q=0,r=data.length;q<r;q++){v=Math.round((data[q][0]-t)*e);h=data[q][1];if(h===null){if(k&&m==="Filled"){o.lineTo(v,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(d-(h-l)/n*d);o.fillRect(v,h,f,d-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")"; o.fillRect(v,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(v,h)}else{k=true;if(m==="Filled"){o.moveTo(v,d);o.lineTo(v,h)}else{o.moveTo(v,h)}}}}}if(m==="Filled"){if(k){o.lineTo(v,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div />").addClass("form-row");var e="track_"+n+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+n+"_minval",m=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),l=$("<input></input>").attr("id",h).val(d),k="track_"+n+"_maxval",g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j);return a.append(m).append(l).append(g).append(f).append(b).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();color=$("#track_"+ c+"_color").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value||color!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.prefs.color=color;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container,e);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE );this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};th is.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e, f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(ah,o,s,aw){var N=o*DENSITY*ah,am=(o+1)*DENSITY*ah,M=am-N;var ao=(!this.initial_canvas?"initial":N+"_"+am);var I=this.data_cache.get(ao);var e;if(I===undefined||(this.mode!=="Auto"&&I.dataset_type==="summary_tree")){this.data_queue[[N,am]]=true;this.get_data(N,am);return}var a=Math.ceil(M*aw),S=$("<canvas class='tile'></canvas>"),aj=this.prefs.label_color,l=this.prefs.block_color,r=this.mode,z=25,af=(r==="Squish")||(r==="Dense")&&(r!=="Pack")||(r==="Auto"&&(I.extra_inf o==="no_detail")),X=this.left_offset,av,D,ax;if(I.dataset_type==="summary_tree"){D=this.summary_draw_height}else{if(r==="Dense"){D=z;ax=10}else{ax=(af?this.vertical_nodetail_px:this.vertical_detail_px);var A=(aw<0.0001?1/view.zoom_res:aw);D=this.incremental_slots(A,I.data,af,r)*ax+z;av=this.inc_slots[A]}}S.css({position:"absolute",top:0,left:(N-this.view.low)*aw-X});S.get(0).width=a+X;S.get(0).height=D;s.parent().css("height",Math.max(this.height_px,D)+"px");var J=S.get(0).getContext("2d");J.fillStyle=l;J.font=this.default_font;J.textAlign="right";this.container_div.find(".yaxislabel").remove();if(I.dataset_type=="summary_tree"){var Z=I.data,L=I.max,q=I.avg,b=Math.ceil(I.delta*aw);var p=$("<div />").addClass("yaxislabel").text(L);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var aq=0,H=Z.length;aq<H;aq++){var ab=Math.floor((Z[aq][0]-N)*aw);var aa=Z[aq][1];if(!aa){continue}var an=aa/L*this.summary_draw_height;J.fillStyle="black";J.fil lRect(ab+X,this.summary_draw_height-an,b,an);if(this.prefs.show_counts&&J.measureText(aa).width<b){J.fillStyle="#bbb";J.textAlign="center";J.fillText(aa,ab+X+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(S);return S}if(I.message){S.css({border:"solid red","border-width":"2px 2px 2px 0px"});J.fillStyle="red";J.textAlign="left";J.fillText(I.message,100+X,ax)}var ae=false;if(I.data.length!=0){ae=true;for(var at=0;at<this.filters.length;at++){if(!this.filters[at].applies_to(I.data[0])){ae=false}}}if(ae){S.addClass(FILTERABLE_CLASS)}var au=I.data;var ap=0;for(var aq=0,H=au.length;aq<H;aq++){var T=au[aq],R=T[0],ar=T[1],ad=T[2],O=T[3];var ac=false;var V;for(var at=0;at<this.filters.length;at++){V=this.filters[at];V.update_attrs(T);if(!V.keep(T)){ac=true;break}}if(ac){continue}if(ar<=am&&ad>=N){var ag=Math.floor(Math.max(0,(ar-N)*aw)),K=Math.ceil(Math.min(a,Math.max(0,(ad-N)*aw))),Y=(r==="Dense"?1:(1+av[R]))*ax;if(I.dataset_type==="bai"){var v=T[4];J.fillStyle=l;if(T[5] in stanceof Array){var E=Math.floor(Math.max(0,(T[5][0]-N)*aw)),Q=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-N)*aw))),C=Math.floor(Math.max(0,(T[6][0]-N)*aw)),w=Math.ceil(Math.min(a,Math.max(0,(T[6][1]-N)*aw)));if(T[5][1]>=N&&T[5][0]<=am){this.rect_or_text(J,aw,N,am,T[5][0],T[5][2],E+X,Q-E,Y)}if(T[6][1]>=N&&T[6][0]<=am){this.rect_or_text(J,aw,N,am,T[6][0],T[6][2],C+X,w-C,Y)}if(C>Q){J.fillStyle="#999";J.fillRect(Q+X,Y+5,C-Q,1)}}else{J.fillStyle=l;this.rect_or_text(J,aw,N,am,ar,O,ag+X,K-ag,Y)}if(r!=="Dense"&&!af&&ar>N){J.fillStyle=this.prefs.label_color;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(R,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(R,ag-2+X,Y+8)}J.fillStyle=l}}else{if(I.dataset_type==="interval_index"){if(af){J.fillStyle=l;J.fillRect(ag+X,Y+5,K-ag,1)}else{var G=T[4],W=T[5],ai=T[6],h=T[7];var F,ak,P=null,ay=null;if(W&&ai){P=Math.floor(Math.max(0,(W-N)*aw));ay=Math.ceil(Math.min(a,Math.max(0,(ai-N)*aw)))}if(r!=="Dense"&&O!==undefined&&ar>N){J.fil lStyle=aj;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(O,ag-2+X,Y+8)}J.fillStyle=l}if(h){if(G){if(G=="+"){J.fillStyle=RIGHT_STRAND}else{if(G=="-"){J.fillStyle=LEFT_STRAND}}J.fillRect(ag+X,Y,K-ag,10);J.fillStyle=l}for(var ao=0,g=h.length;ao<g;ao++){var u=h[ao],d=Math.floor(Math.max(0,(u[0]-N)*aw)),U=Math.ceil(Math.min(a,Math.max((u[1]-N)*aw)));if(d>U){continue}F=5;ak=3;J.fillRect(d+X,Y+ak,U-d,F);if(P!==undefined&&!(d>ay||U<P)){F=9;ak=1;var al=Math.max(d,P),B=Math.min(U,ay);J.fillRect(al+X,Y+ak,B-al,F)}}}else{F=9;ak=1;J.fillRect(ag+X,Y+ak,K-ag,F);if(T.strand){if(T.strand=="+"){J.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){J.fillStyle=LEFT_STRAND_INV}}J.fillRect(ag+X,Y,K-ag,10);J.fillStyle=l}}}}else{if(I.dataset_type==="vcf"){if(af){J.fillStyle=l;J.fillRect(ag+X,Y+5,K-ag,1)}else{var t=T[4],n=T[5],c=T[6];F=9;ak=1;J.fillRect(ag+X,Y,K-ag,F);if(r!=="Dense"&&O!==undefined&&ar>N){J.fillStyle=aj;if(o===0&&a g-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(O,ag-2+X,Y+8)}J.fillStyle=l}var m=t+" / "+n;if(ar>N&&J.measureText(m).width<(K-ag)){J.fillStyle="white";J.textAlign="center";J.fillText(m,X+ag+(K-ag)/2,Y+8);J.fillStyle=l}}}}}ap++}}return S},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_opti ons:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,e,c){FeatureTrack.call(this,d,b,a,e,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -10,6 +10,7 @@ var DENSITY = 200, DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Currently indexing... please wait", DATA_LOADING = "Loading data...", + FILTERABLE_CLASS = "filterable", CACHED_TILES_FEATURE = 10, CACHED_TILES_LINE = 30, CACHED_DATA = 5, @@ -448,10 +449,100 @@ var View = function( container, chrom, t } }); -var Track = function (name, view, parent_element) { +// Generic filter. +var Filter = function( name, index, value ) { this.name = name; + this.index = index; + this.value = value; +}; + +// Number filter for a track. +var NumberFilter = function( name, index ) { + this.name = name; + // Index into payload to filter. + this.index = index; + // Filter low/high. These values are used to filter elements. + this.low = Number.MIN_VALUE; + this.high = Number.MAX_VALUE; + // Slide min/max. These values are used to set/update slider. + this.slider_min = Number.MAX_VALUE; + this.slider_max = Number.MIN_VALUE; + // UI Slider element and label that is associated with filter. + this.slider = null; + this.slider_label = null; +}; +$.extend( NumberFilter.prototype, { + // Returns true if filter can be applied to element. + applies_to: function( element ) { + if ( element.length > this.index ) + return true; + return false; + }, + // Returns true iff element is in [low, high]; range is inclusive. + keep: function( element ) { + if ( !this.applies_to( element ) ) + // No element to filter on. + return true; + return ( element[this.index] >= this.low && element[this.index] <= this.high ); + }, + // Update filter's min and max values based on element's values. + update_attrs: function( element ) { + var updated = false; + if ( !this.applies_to( element ) ) { + return updated; + } + + // Update filter's min, max based on element values. + if ( element[this.index] < this.slider_min ) { + this.slider_min = element[this.index]; + updated = true; + } + if ( element[this.index] > this.slider_max ) { + this.slider_max = element[this.index]; + updated = false; + } + return updated; + }, + // Update filter's slider. + update_ui_elt: function () { + var + slider_min = this.slider.slider( "option", "min" ), + slider_max = this.slider.slider( "option", "max" ); + if (this.slider_min < slider_min || this.slider_max > slider_max) { + // Need to update slider. + this.slider.slider( "option", "min", this.slider_min ); + this.slider.slider( "option", "max", this.slider_max ); + // Refresh slider: + // TODO: do we want to keep current values or reset to min/max? + // Currently we reset values: + this.slider.slider( "option", "values", [ this.slider_min, this.slider_max ] ); + // To use the current values. + //var values = this.slider.slider( "option", "values" ); + //this.slider.slider( "option", "values", values ); + } + } +}); + +// Parse filters dict and return filters. +var get_filters = function( filters_dict ) { + var filters = [] + for (var i = 0; i < filters_dict.length; i++) { + var filter_dict = filters_dict[i]; + var name = filter_dict['name'], type = filter_dict['type'], index = filter_dict['index']; + if ( type == 'int' || type == 'float' ) { + filters[i] = new NumberFilter( name, index ); + } + else + filters[i] = new Filter( name, index, type ); + } + return filters; +}; + +var Track = function (name, view, parent_element, filters) { + this.name = name; + this.view = view; this.parent_element = parent_element; - this.view = view; + this.filters = (filters !== undefined ? get_filters( filters ) : []); this.init_global(); }; $.extend( Track.prototype, { @@ -462,7 +553,51 @@ var Track = function (name, view, parent 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() ); } + // Create track filtering div. + this.filtering_div = $("<div class='track-filters'>").appendTo(this.container_div); + this.filtering_div.hide(); + // Dragging is disabled on div so that actions on slider do not impact viz. + this.filtering_div.bind( "drag", function(e) { + e.stopPropagation(); + }); + var filters_table = $("<table class='filters'>").appendTo(this.filtering_div); + var track = this; + for (var i = 0; i < this.filters.length; i++) { + var filter = this.filters[i]; + var table_row = $("<tr>").appendTo(filters_table); + var filter_th = $("<th class='filter-info'>").appendTo(table_row); + var name_span = $("<span class='name'>").appendTo(filter_th); + name_span.text(filter.name + " "); // Extra spacing to separate name and values + var values_span = $("<span class='values'>").appendTo(filter_th); + values_span.text("[0-2]"); + // TODO: generate custom interaction elements based on filter type. + var table_data = $("<td>").appendTo(table_row); + filter.control_element = $("<div id='" + filter.name + "-filter-control' style='width: 200px; position: relative'>").appendTo(table_data); + filter.control_element.slider({ + range: true, + min: 0, + max: 1, + values: [0, 1], + slide: function( event, ui ) { + var values = ui.values; + // Set new values in UI. + values_span.text( "[" + values[0] + "-" + values[1] + "]" ); + // Set new values in filter. + filter.low = values[0]; + filter.high = values[1]; + // Redraw track. + track.draw( true ); + }, + change: function( event, ui ) { + filter.control_element.slider( "option", "slide" ).call( filter.control_element, event, ui ); + } + }); + filter.slider = filter.control_element; + filter.slider_label = values_span; + } + this.content_div = $("<div class='track-content'>").appendTo(this.container_div); this.parent_element.append(this.container_div); }, @@ -478,7 +613,7 @@ var Track = function (name, view, parent track.content_div.text(DATA_LOADING); } track.container_div.removeClass("nodata error pending"); - + if (track.view.chrom) { $.getJSON( data_url, params, function (result) { if (!result || result === "error" || result.kind === "error") { @@ -577,14 +712,30 @@ var TiledTrack = function() { "OK": ok_fn }); }; + if (track.filters.length > 0) { + track_dropdown["Show filters"] = function() { + // Set option text and toggle filtering div. + var menu_option_text; + if (!track.filtering_div.is(":visible")) { + menu_option_text = "Hide filters"; + track.filters_visible = true; + } + else { + menu_option_text = "Show filters"; + track.filters_visible = false; + } + $("#" + track.name_div.attr("id") + "-menu").find("li").eq(2).text(menu_option_text); + track.filtering_div.toggle(); + }; + } track_dropdown["Remove"] = function() { view.remove_track(track); if (view.num_tracks === 0) { $("#no-tracks").show(); } }; - make_popupmenu(track.name_div, track_dropdown); - + track.popup_menu = make_popupmenu(track.name_div, track_dropdown); + show_hide_popupmenu_options(track.popup_menu, "(Show|Hide) filters", false); /* if (track.overview_check_div === undefined) { track.overview_check_div = $("<div class='right-float' />").css("margin-top", "-3px").appendTo(track.header_div); @@ -604,7 +755,7 @@ var TiledTrack = function() { */ }; $.extend( TiledTrack.prototype, Track.prototype, { - draw: function() { + draw: function( force ) { var low = this.view.low, high = this.view.high, range = high - low, @@ -614,35 +765,54 @@ var TiledTrack = function() { w_scale = this.content_div.width() / range, tile_element; - this.content_div.children( ":first" ).remove(); this.content_div.append( parent_element ), this.max_height = 0; // Index of first tile that overlaps visible region var tile_index = Math.floor( low / resolution / DENSITY ); + // A list of setTimeout() ids used when drawing tiles. + var draw_tile_ids = new Object(); while ( ( tile_index * DENSITY * resolution ) < high ) { // Check in cache var key = this.content_div.width() + '_' + w_scale + '_' + tile_index; var cached = this.tile_cache.get(key); - if ( cached ) { - // console.log("cached tile " + tile_index); + if ( !force && cached ) { var tile_low = tile_index * DENSITY * resolution; var left = ( tile_low - low ) * w_scale; if (this.left_offset) { left -= this.left_offset; } cached.css({ left: left }); - // Our responsibility to move the element to the new parent - parent_element.append( cached ); - this.max_height = Math.max( this.max_height, cached.height() ); - this.content_div.css("height", this.max_height + "px"); + this.show_tile( cached, parent_element ); } else { - this.delayed_draw(this, key, low, high, tile_index, resolution, parent_element, w_scale); + this.delayed_draw(this, key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids); } tile_index += 1; } - }, delayed_draw: function(track, key, low, high, tile_index, resolution, parent_element, w_scale) { + + // + // Actions to take after new tiles have been loaded/drawn: + // (1) remove old tile(s); + // (2) update filtering UI elements. + // + var track = this; + var intervalId = setInterval(function() { + if ( draw_tile_ids.length != 0 ) { + // Add drawing has finished; if there is more than one child in the content div, + // remove the first one, which is the oldest. + if ( track.content_div.children().length > 1 ) { + track.content_div.children( ":first" ).remove(); + } + + // Update filtering UI. + for (var f = 0; f < track.filters.length; f++) + track.filters[f].update_ui_elt(); + // Method complete; do not call it again. + clearInterval(intervalId); + } + }, 50); + }, delayed_draw: function(track, key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids) { // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data - setTimeout(function() { + var id = setTimeout(function() { if ( !(low > track.view.high || high < track.view.low) ) { tile_element = track.draw_tile( resolution, tile_index, parent_element, w_scale ); if (tile_element) { @@ -655,12 +825,36 @@ var TiledTrack = function() { tgt_ctx.putImageData(data, 0, 0); track.set_overview(); } + // Add tile to cache and show tile. track.tile_cache.set(key, tile_element); - track.max_height = Math.max( track.max_height, tile_element.height() ); - track.content_div.css("height", track.max_height + "px"); + track.show_tile( tile_element, parent_element ) } } + // Remove setTimeout id. + delete draw_tile_ids.id; }, 50); + draw_tile_ids.id = true; + }, + // Show track tile and perform associated actions. + show_tile: function( tile_element, parent_element ) { + // Readability. + var track = this; + + // Setup and show tile element. + parent_element.append( tile_element ); + track.max_height = Math.max( track.max_height, tile_element.height() ); + track.content_div.css("height", track.max_height + "px"); + + // Show/hide filters based on whether tile is filterable. + if ( tile_element.hasClass(FILTERABLE_CLASS) ) { + show_hide_popupmenu_options(track.popup_menu, "(Show|Hide) filters"); + if (track.filters_visible) + track.filtering_div.show(); + } + else { + show_hide_popupmenu_options(track.popup_menu, "(Show|Hide) filters", false); + track.filtering_div.hide(); + } }, set_overview: function() { var view = this.view; @@ -986,10 +1180,10 @@ var LineTrack = function ( name, view, d } }); -var FeatureTrack = function ( name, view, dataset_id, prefs ) { +var FeatureTrack = function ( name, view, dataset_id, filters, prefs ) { this.track_type = "FeatureTrack"; this.display_modes = ["Auto", "Dense", "Squish", "Pack"]; - Track.call( this, name, view, view.viewport_container ); + Track.call( this, name, view, view.viewport_container, filters ); TiledTrack.call( this ); this.height_px = 0; @@ -1245,6 +1439,24 @@ var FeatureTrack = function ( name, view ctx.fillText(result.message, 100 + left_offset, y_scale); } + // + // We're now working at the level of individual data points. + // + + // See if tile is filterable. If so, add class. + var filterable = false; + if ( result.data.length != 0 ) { + filterable = true; + for (var f = 0; f < this.filters.length; f++) + if ( !this.filters[f].applies_to( result.data[0] ) ) { + filterable = false; + } + } + if ( filterable ) { + new_canvas.addClass(FILTERABLE_CLASS); + } + + // Draw data points. var data = result.data; var j = 0; for (var i = 0, len = data.length; i < len; i++) { @@ -1254,6 +1466,20 @@ var FeatureTrack = function ( name, view feature_end = feature[2], feature_name = feature[3]; + // Apply filters to feature. + var hide_feature = false; + var filter; + for (var f = 0; f < this.filters.length; f++) { + filter = this.filters[f]; + filter.update_attrs( feature ); + if ( !filter.keep( feature ) ) { + hide_feature = true; + break; + } + } + if ( hide_feature ) + continue; + if (feature_start <= tile_high && feature_end >= tile_low) { var f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), @@ -1374,6 +1600,7 @@ var FeatureTrack = function ( name, view } } } else if (result.dataset_type === 'vcf') { + // VCF track. if (no_detail) { ctx.fillStyle = block_color; ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, 1); @@ -1414,7 +1641,6 @@ var FeatureTrack = function ( name, view j++; } } - parent_element.append(new_canvas); return new_canvas; }, gen_options: function(track_id) { var container = $("<div />").addClass("form-row"); @@ -1446,8 +1672,8 @@ var FeatureTrack = function ( name, view } }); -var ReadTrack = function ( name, view, dataset_id, prefs ) { - FeatureTrack.call( this, name, view, dataset_id, prefs ); +var ReadTrack = function ( name, view, dataset_id, filters, prefs ) { + FeatureTrack.call( this, name, view, dataset_id, filters, prefs ); this.track_type = "ReadTrack"; this.vertical_detail_px = 10; this.vertical_nodetail_px = 5; --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -90,6 +90,20 @@ function make_popupmenu( button_element, .appendTo( "body" ) .hide(); attach_popupmenu( button_element, wrapper ); + return menu_element; +} + +// Toggle popup menu options using regular expression on option names. +function show_hide_popupmenu_options( menu, option_name_re, show ) { + var show = (show === undefined ? true : show ); + var re = new RegExp(option_name_re); + $(menu).find("li").each( function() { + if ( re.exec( $(this).text() ) ) + if (show) + $(this).show(); + else + $(this).hide(); + }); } function make_popup_menus() { Binary file static/june_2007_style/blue/overcast/images/ui-bg_inset-soft_50_c9c9c9_1x100.png has changed --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -19,10 +19,13 @@ class TracksDataProvider( object ): """ Base class for tracks data providers. """ """ - Mapping from column name to index in data. This mapping is used to create - filters. + Mapping from column name to payload data; this mapping is used to create + filters. Key is column name, value is a dict with mandatory key 'index' and + optional key 'name'. E.g. this defines column 4 + + col_name_data_attr_mapping = {4 : { index: 5, name: 'Score' } } """ - col_name_data_index_mapping = {} + col_name_data_attr_mapping = {} def __init__( self, converted_dataset=None, original_dataset=None ): """ Create basic data provider. """ @@ -37,7 +40,7 @@ class TracksDataProvider( object ): def get_filters( self ): """ Returns filters for provider's data. Return value is a list of - filters; each filter is a dictionary with the keys 'name', 'index', 'value'. + filters; each filter is a dictionary with the keys 'name', 'index', 'type'. NOTE: This method uses the original dataset's datatype and metadata to create the filters. """ @@ -58,17 +61,17 @@ class TracksDataProvider( object ): # Create and return filters. filters = [] - if self.original_dataset.metadata.viz_filter_columns: - for viz_col_index in self.original_dataset.metadata.viz_filter_columns: + if self.original_dataset.metadata.viz_filter_cols: + for viz_col_index in self.original_dataset.metadata.viz_filter_cols: col_name = column_names[ viz_col_index ] # Make sure that column has a mapped index. If not, do not add filter. try: - index = self.col_name_data_index_mapping[ col_name ] + attrs = self.col_name_data_attr_mapping[ col_name ] except KeyError: continue filters.append( - { 'name' : col_name, 'value' : column_types[viz_col_index], \ - 'index' : index } ) + { 'name' : attrs[ 'name' ], 'type' : column_types[viz_col_index], \ + 'index' : attrs[ 'index' ] } ) return filters class SummaryTreeDataProvider( TracksDataProvider ): @@ -119,7 +122,7 @@ class VcfDataProvider( TracksDataProvide [ uid (offset), start, end, ID, reference base(s), alternate base(s), quality score] """ - col_name_data_index_mapping = { 'Qual' : 6 } + col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } def get_data( self, chrom, start, end, **kwargs ): """ Returns data in region defined by chrom, start, and end. """ @@ -153,7 +156,7 @@ class VcfDataProvider( TracksDataProvide # alternative base(s) feature[4], \ # phred quality score - feature[5] ] + int( feature[5] )] results.append(payload) return { 'data_type' : 'vcf', 'data': results, 'message': message } @@ -306,6 +309,9 @@ class IntervalIndexDataProvider( TracksD Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ + + col_name_data_attr_mapping = { 4 : { 'index': 8 , 'name' : 'Score' } } + def get_data( self, chrom, start, end, **kwargs ): start, end = int(start), int(end) source = open( self.original_dataset.file_name ) @@ -355,6 +361,9 @@ class IntervalIndexDataProvider( TracksD block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] blocks = zip(block_sizes, block_starts) payload.append( [ (start + block[1], start + block[1] + block[0]) for block in blocks] ) + + if length >= 5: + payload.append( int(feature[4]) ) # score results.append(payload) @@ -375,7 +384,7 @@ dataset_type_name_to_data_provider = { } dataset_type_to_data_provider = { - Vcf : VcfDataProvider + Vcf : VcfDataProvider, } def get_data_provider( name=None, original_dataset=None ): @@ -395,11 +404,16 @@ def get_data_provider( name=None, origin # Look for data provider in mapping. data_provider = dataset_type_to_data_provider.get( original_dataset.datatype.__class__, None ) if not data_provider: - # If get_track_type is available, then dataset can be added to trackster - # and hence has at least a generic data provider. + # Look up data provider from datatype's informaton. try: - original_dataset.datatype.get_track_type() - data_provider = TracksDataProvider + # Get data provider mapping and data provider for 'data'. If + # provider available, use it; otherwise use generic provider. + _ , data_provider_mapping = original_dataset.datatype.get_track_type() + data_provider_name = data_provider_mapping[ 'data' ] + if data_provider_name: + data_provider = get_data_provider( name=data_provider_name, original_dataset=original_dataset ) + else: + data_provider = TracksDataProvider except: pass return data_provider --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -12,7 +12,7 @@ <%def name="stylesheets()"> ${parent.stylesheets()} -${h.css( "history", "autocomplete_tagging", "trackster" )} +${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom" )} <style type="text/css"> #center { @@ -34,6 +34,17 @@ left: 0; bottom: 0; } + # Styles for filters. + .filter-name { + float: left; + } + table.filters { + border-collapse: separate; + border-spacing: 7px 0px; + } + .values { + padding-right: 1em; + } </style></%def> @@ -67,7 +78,7 @@ view.editor = true; %for track in config.get('tracks'): view.add_track( - new ${track["track_type"]}( "${track['name'] | h}", view, ${track['dataset_id']}, ${track['prefs']} ) + new ${track["track_type"]}( "${track['name'] | h}", view, ${track['dataset_id']}, ${track['filters']}, ${track['prefs']} ) ); %endfor init(); @@ -134,7 +145,7 @@ var add_async_success = function(track_data) { var td = track_data, track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack }, - new_track = new track_types[track_data.track_type]( track_data.name, view, track_data.dataset_id, track_data.prefs); + new_track = new track_types[track_data.track_type]( track_data.name, view, track_data.dataset_id, track_data.filters, track_data.prefs); view.add_track(new_track); view.has_changes = true; Binary file static/june_2007_style/blue/overcast/images/ui-bg_glass_35_dddddd_1x400.png has changed --- /dev/null +++ b/static/june_2007_style/blue/overcast/jquery-ui-1.8.5.custom.css @@ -0,0 +1,318 @@ +/* + * jQuery UI CSS Framework @VERSION + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Theming/API + */ + +/* Layout helpers +----------------------------------*/ +.ui-helper-hidden { display: none; } +.ui-helper-hidden-accessible { position: absolute; left: -99999999px; } +.ui-helper-reset { margin: 0; padding: 0; border: 0; outline: 0; line-height: 1.3; text-decoration: none; font-size: 100%; list-style: none; } +.ui-helper-clearfix:after { content: "."; display: block; height: 0; clear: both; visibility: hidden; } +.ui-helper-clearfix { display: inline-block; } +/* required comment for clearfix to work in Opera \*/ +* html .ui-helper-clearfix { height:1%; } +.ui-helper-clearfix { display:block; } +/* end clearfix */ +.ui-helper-zfix { width: 100%; height: 100%; top: 0; left: 0; position: absolute; opacity: 0; filter:Alpha(Opacity=0); } + + +/* Interaction Cues +----------------------------------*/ +.ui-state-disabled { cursor: default !important; } + + +/* Icons +----------------------------------*/ + +/* states and images */ +.ui-icon { display: block; text-indent: -99999px; overflow: hidden; background-repeat: no-repeat; } + + +/* Misc visuals +----------------------------------*/ + +/* Overlays */ +.ui-widget-overlay { position: absolute; top: 0; left: 0; width: 100%; height: 100%; } + + +/* + * jQuery UI CSS Framework @VERSION + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Theming/API + * + * To view and modify this theme, visit http://jqueryui.com/themeroller/?ffDefault=Trebuchet%20MS,%20Helvetica,%20A… Highlight=444444&iconColorHighlight=3383bb&bgColorError=c0402a&bgTextureError=01_flat.png&bgImgOpacityError=55&borderColorError=c0402a&fcError=ffffff&iconColorError=fbc856&bgColorOverlay=eeeeee&bgTextureOverlay=01_flat.png&bgImgOpacityOverlay=0&opacityOverlay=80&bgColorShadow=aaaaaa&bgTextureShadow=01_flat.png&bgImgOpacityShadow=0&opacityShadow=60&thicknessShadow=4px&offsetTopShadow=-4px&offsetLeftShadow=-4px&cornerRadiusShadow=0pxdow=0px + */ + + +/* Component containers +----------------------------------*/ +.ui-widget { font-family: Trebuchet MS, Helvetica, Arial, sans-serif; font-size: 1.1em; } +.ui-widget .ui-widget { font-size: 1em; } +.ui-widget input, .ui-widget select, .ui-widget textarea, .ui-widget button { font-family: Trebuchet MS, Helvetica, Arial, sans-serif; font-size: 1em; } +.ui-widget-content { border: 1px solid #aaaaaa; background: #c9c9c9 url(images/ui-bg_inset-soft_50_c9c9c9_1x100.png) 50% bottom repeat-x; color: #333333; } +.ui-widget-content a { color: #333333; } +.ui-widget-header { border: 1px solid #bbbbbb; background: #dddddd url(images/ui-bg_glass_35_dddddd_1x400.png) 50% 50% repeat-x; color: #444444; font-weight: bold; } +.ui-widget-header a { color: #444444; } + +/* Interaction states +----------------------------------*/ +.ui-state-default, .ui-widget-content .ui-state-default, .ui-widget-header .ui-state-default { border: 1px solid #cccccc; background: #eeeeee url(images/ui-bg_glass_60_eeeeee_1x400.png) 50% 50% repeat-x; font-weight: bold; color: #3383bb; } +.ui-state-default a, .ui-state-default a:link, .ui-state-default a:visited { color: #3383bb; text-decoration: none; } +.ui-state-hover, .ui-widget-content .ui-state-hover, .ui-widget-header .ui-state-hover, .ui-state-focus, .ui-widget-content .ui-state-focus, .ui-widget-header .ui-state-focus { border: 1px solid #bbbbbb; background: #f8f8f8 url(images/ui-bg_glass_100_f8f8f8_1x400.png) 50% 50% repeat-x; font-weight: bold; color: #599fcf; } +.ui-state-hover a, .ui-state-hover a:hover { color: #599fcf; text-decoration: none; } +.ui-state-active, .ui-widget-content .ui-state-active, .ui-widget-header .ui-state-active { border: 1px solid #999999; background: #999999 url(images/ui-bg_inset-hard_75_999999_1x100.png) 50% 50% repeat-x; font-weight: bold; color: #ffffff; } +.ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited { color: #ffffff; text-decoration: none; } +.ui-widget :active { outline: none; } + +/* Interaction Cues +----------------------------------*/ +.ui-state-highlight, .ui-widget-content .ui-state-highlight, .ui-widget-header .ui-state-highlight {border: 1px solid #ffffff; background: #eeeeee url(images/ui-bg_flat_55_eeeeee_40x100.png) 50% 50% repeat-x; color: #444444; } +.ui-state-highlight a, .ui-widget-content .ui-state-highlight a,.ui-widget-header .ui-state-highlight a { color: #444444; } +.ui-state-error, .ui-widget-content .ui-state-error, .ui-widget-header .ui-state-error {border: 1px solid #c0402a; background: #c0402a url(images/ui-bg_flat_55_c0402a_40x100.png) 50% 50% repeat-x; color: #ffffff; } +.ui-state-error a, .ui-widget-content .ui-state-error a, .ui-widget-header .ui-state-error a { color: #ffffff; } +.ui-state-error-text, .ui-widget-content .ui-state-error-text, .ui-widget-header .ui-state-error-text { color: #ffffff; } +.ui-priority-primary, .ui-widget-content .ui-priority-primary, .ui-widget-header .ui-priority-primary { font-weight: bold; } +.ui-priority-secondary, .ui-widget-content .ui-priority-secondary, .ui-widget-header .ui-priority-secondary { opacity: .7; filter:Alpha(Opacity=70); font-weight: normal; } +.ui-state-disabled, .ui-widget-content .ui-state-disabled, .ui-widget-header .ui-state-disabled { opacity: .35; filter:Alpha(Opacity=35); background-image: none; } + +/* Icons +----------------------------------*/ + +/* states and images */ +.ui-icon { width: 16px; height: 16px; background-image: url(images/ui-icons_999999_256x240.png); } +.ui-widget-content .ui-icon {background-image: url(images/ui-icons_999999_256x240.png); } +.ui-widget-header .ui-icon {background-image: url(images/ui-icons_999999_256x240.png); } +.ui-state-default .ui-icon { background-image: url(images/ui-icons_70b2e1_256x240.png); } +.ui-state-hover .ui-icon, .ui-state-focus .ui-icon {background-image: url(images/ui-icons_3383bb_256x240.png); } +.ui-state-active .ui-icon {background-image: url(images/ui-icons_454545_256x240.png); } +.ui-state-highlight .ui-icon {background-image: url(images/ui-icons_3383bb_256x240.png); } +.ui-state-error .ui-icon, .ui-state-error-text .ui-icon {background-image: url(images/ui-icons_fbc856_256x240.png); } + +/* positioning */ +.ui-icon-carat-1-n { background-position: 0 0; } +.ui-icon-carat-1-ne { background-position: -16px 0; } +.ui-icon-carat-1-e { background-position: -32px 0; } +.ui-icon-carat-1-se { background-position: -48px 0; } +.ui-icon-carat-1-s { background-position: -64px 0; } +.ui-icon-carat-1-sw { background-position: -80px 0; } +.ui-icon-carat-1-w { background-position: -96px 0; } +.ui-icon-carat-1-nw { background-position: -112px 0; } +.ui-icon-carat-2-n-s { background-position: -128px 0; } +.ui-icon-carat-2-e-w { background-position: -144px 0; } +.ui-icon-triangle-1-n { background-position: 0 -16px; } +.ui-icon-triangle-1-ne { background-position: -16px -16px; } +.ui-icon-triangle-1-e { background-position: -32px -16px; } +.ui-icon-triangle-1-se { background-position: -48px -16px; } +.ui-icon-triangle-1-s { background-position: -64px -16px; } +.ui-icon-triangle-1-sw { background-position: -80px -16px; } +.ui-icon-triangle-1-w { background-position: -96px -16px; } +.ui-icon-triangle-1-nw { background-position: -112px -16px; } +.ui-icon-triangle-2-n-s { background-position: -128px -16px; } +.ui-icon-triangle-2-e-w { background-position: -144px -16px; } +.ui-icon-arrow-1-n { background-position: 0 -32px; } +.ui-icon-arrow-1-ne { background-position: -16px -32px; } +.ui-icon-arrow-1-e { background-position: -32px -32px; } +.ui-icon-arrow-1-se { background-position: -48px -32px; } +.ui-icon-arrow-1-s { background-position: -64px -32px; } +.ui-icon-arrow-1-sw { background-position: -80px -32px; } +.ui-icon-arrow-1-w { background-position: -96px -32px; } +.ui-icon-arrow-1-nw { background-position: -112px -32px; } +.ui-icon-arrow-2-n-s { background-position: -128px -32px; } +.ui-icon-arrow-2-ne-sw { background-position: -144px -32px; } +.ui-icon-arrow-2-e-w { background-position: -160px -32px; } +.ui-icon-arrow-2-se-nw { background-position: -176px -32px; } +.ui-icon-arrowstop-1-n { background-position: -192px -32px; } +.ui-icon-arrowstop-1-e { background-position: -208px -32px; } +.ui-icon-arrowstop-1-s { background-position: -224px -32px; } +.ui-icon-arrowstop-1-w { background-position: -240px -32px; } +.ui-icon-arrowthick-1-n { background-position: 0 -48px; } +.ui-icon-arrowthick-1-ne { background-position: -16px -48px; } +.ui-icon-arrowthick-1-e { background-position: -32px -48px; } +.ui-icon-arrowthick-1-se { background-position: -48px -48px; } +.ui-icon-arrowthick-1-s { background-position: -64px -48px; } +.ui-icon-arrowthick-1-sw { background-position: -80px -48px; } +.ui-icon-arrowthick-1-w { background-position: -96px -48px; } +.ui-icon-arrowthick-1-nw { background-position: -112px -48px; } +.ui-icon-arrowthick-2-n-s { background-position: -128px -48px; } +.ui-icon-arrowthick-2-ne-sw { background-position: -144px -48px; } +.ui-icon-arrowthick-2-e-w { background-position: -160px -48px; } +.ui-icon-arrowthick-2-se-nw { background-position: -176px -48px; } +.ui-icon-arrowthickstop-1-n { background-position: -192px -48px; } +.ui-icon-arrowthickstop-1-e { background-position: -208px -48px; } +.ui-icon-arrowthickstop-1-s { background-position: -224px -48px; } +.ui-icon-arrowthickstop-1-w { background-position: -240px -48px; } +.ui-icon-arrowreturnthick-1-w { background-position: 0 -64px; } +.ui-icon-arrowreturnthick-1-n { background-position: -16px -64px; } +.ui-icon-arrowreturnthick-1-e { background-position: -32px -64px; } +.ui-icon-arrowreturnthick-1-s { background-position: -48px -64px; } +.ui-icon-arrowreturn-1-w { background-position: -64px -64px; } +.ui-icon-arrowreturn-1-n { background-position: -80px -64px; } +.ui-icon-arrowreturn-1-e { background-position: -96px -64px; } +.ui-icon-arrowreturn-1-s { background-position: -112px -64px; } +.ui-icon-arrowrefresh-1-w { background-position: -128px -64px; } +.ui-icon-arrowrefresh-1-n { background-position: -144px -64px; } +.ui-icon-arrowrefresh-1-e { background-position: -160px -64px; } +.ui-icon-arrowrefresh-1-s { background-position: -176px -64px; } +.ui-icon-arrow-4 { background-position: 0 -80px; } +.ui-icon-arrow-4-diag { background-position: -16px -80px; } +.ui-icon-extlink { background-position: -32px -80px; } +.ui-icon-newwin { background-position: -48px -80px; } +.ui-icon-refresh { background-position: -64px -80px; } +.ui-icon-shuffle { background-position: -80px -80px; } +.ui-icon-transfer-e-w { background-position: -96px -80px; } +.ui-icon-transferthick-e-w { background-position: -112px -80px; } +.ui-icon-folder-collapsed { background-position: 0 -96px; } +.ui-icon-folder-open { background-position: -16px -96px; } +.ui-icon-document { background-position: -32px -96px; } +.ui-icon-document-b { background-position: -48px -96px; } +.ui-icon-note { background-position: -64px -96px; } +.ui-icon-mail-closed { background-position: -80px -96px; } +.ui-icon-mail-open { background-position: -96px -96px; } +.ui-icon-suitcase { background-position: -112px -96px; } +.ui-icon-comment { background-position: -128px -96px; } +.ui-icon-person { background-position: -144px -96px; } +.ui-icon-print { background-position: -160px -96px; } +.ui-icon-trash { background-position: -176px -96px; } +.ui-icon-locked { background-position: -192px -96px; } +.ui-icon-unlocked { background-position: -208px -96px; } +.ui-icon-bookmark { background-position: -224px -96px; } +.ui-icon-tag { background-position: -240px -96px; } +.ui-icon-home { background-position: 0 -112px; } +.ui-icon-flag { background-position: -16px -112px; } +.ui-icon-calendar { background-position: -32px -112px; } +.ui-icon-cart { background-position: -48px -112px; } +.ui-icon-pencil { background-position: -64px -112px; } +.ui-icon-clock { background-position: -80px -112px; } +.ui-icon-disk { background-position: -96px -112px; } +.ui-icon-calculator { background-position: -112px -112px; } +.ui-icon-zoomin { background-position: -128px -112px; } +.ui-icon-zoomout { background-position: -144px -112px; } +.ui-icon-search { background-position: -160px -112px; } +.ui-icon-wrench { background-position: -176px -112px; } +.ui-icon-gear { background-position: -192px -112px; } +.ui-icon-heart { background-position: -208px -112px; } +.ui-icon-star { background-position: -224px -112px; } +.ui-icon-link { background-position: -240px -112px; } +.ui-icon-cancel { background-position: 0 -128px; } +.ui-icon-plus { background-position: -16px -128px; } +.ui-icon-plusthick { background-position: -32px -128px; } +.ui-icon-minus { background-position: -48px -128px; } +.ui-icon-minusthick { background-position: -64px -128px; } +.ui-icon-close { background-position: -80px -128px; } +.ui-icon-closethick { background-position: -96px -128px; } +.ui-icon-key { background-position: -112px -128px; } +.ui-icon-lightbulb { background-position: -128px -128px; } +.ui-icon-scissors { background-position: -144px -128px; } +.ui-icon-clipboard { background-position: -160px -128px; } +.ui-icon-copy { background-position: -176px -128px; } +.ui-icon-contact { background-position: -192px -128px; } +.ui-icon-image { background-position: -208px -128px; } +.ui-icon-video { background-position: -224px -128px; } +.ui-icon-script { background-position: -240px -128px; } +.ui-icon-alert { background-position: 0 -144px; } +.ui-icon-info { background-position: -16px -144px; } +.ui-icon-notice { background-position: -32px -144px; } +.ui-icon-help { background-position: -48px -144px; } +.ui-icon-check { background-position: -64px -144px; } +.ui-icon-bullet { background-position: -80px -144px; } +.ui-icon-radio-off { background-position: -96px -144px; } +.ui-icon-radio-on { background-position: -112px -144px; } +.ui-icon-pin-w { background-position: -128px -144px; } +.ui-icon-pin-s { background-position: -144px -144px; } +.ui-icon-play { background-position: 0 -160px; } +.ui-icon-pause { background-position: -16px -160px; } +.ui-icon-seek-next { background-position: -32px -160px; } +.ui-icon-seek-prev { background-position: -48px -160px; } +.ui-icon-seek-end { background-position: -64px -160px; } +.ui-icon-seek-start { background-position: -80px -160px; } +/* ui-icon-seek-first is deprecated, use ui-icon-seek-start instead */ +.ui-icon-seek-first { background-position: -80px -160px; } +.ui-icon-stop { background-position: -96px -160px; } +.ui-icon-eject { background-position: -112px -160px; } +.ui-icon-volume-off { background-position: -128px -160px; } +.ui-icon-volume-on { background-position: -144px -160px; } +.ui-icon-power { background-position: 0 -176px; } +.ui-icon-signal-diag { background-position: -16px -176px; } +.ui-icon-signal { background-position: -32px -176px; } +.ui-icon-battery-0 { background-position: -48px -176px; } +.ui-icon-battery-1 { background-position: -64px -176px; } +.ui-icon-battery-2 { background-position: -80px -176px; } +.ui-icon-battery-3 { background-position: -96px -176px; } +.ui-icon-circle-plus { background-position: 0 -192px; } +.ui-icon-circle-minus { background-position: -16px -192px; } +.ui-icon-circle-close { background-position: -32px -192px; } +.ui-icon-circle-triangle-e { background-position: -48px -192px; } +.ui-icon-circle-triangle-s { background-position: -64px -192px; } +.ui-icon-circle-triangle-w { background-position: -80px -192px; } +.ui-icon-circle-triangle-n { background-position: -96px -192px; } +.ui-icon-circle-arrow-e { background-position: -112px -192px; } +.ui-icon-circle-arrow-s { background-position: -128px -192px; } +.ui-icon-circle-arrow-w { background-position: -144px -192px; } +.ui-icon-circle-arrow-n { background-position: -160px -192px; } +.ui-icon-circle-zoomin { background-position: -176px -192px; } +.ui-icon-circle-zoomout { background-position: -192px -192px; } +.ui-icon-circle-check { background-position: -208px -192px; } +.ui-icon-circlesmall-plus { background-position: 0 -208px; } +.ui-icon-circlesmall-minus { background-position: -16px -208px; } +.ui-icon-circlesmall-close { background-position: -32px -208px; } +.ui-icon-squaresmall-plus { background-position: -48px -208px; } +.ui-icon-squaresmall-minus { background-position: -64px -208px; } +.ui-icon-squaresmall-close { background-position: -80px -208px; } +.ui-icon-grip-dotted-vertical { background-position: 0 -224px; } +.ui-icon-grip-dotted-horizontal { background-position: -16px -224px; } +.ui-icon-grip-solid-vertical { background-position: -32px -224px; } +.ui-icon-grip-solid-horizontal { background-position: -48px -224px; } +.ui-icon-gripsmall-diagonal-se { background-position: -64px -224px; } +.ui-icon-grip-diagonal-se { background-position: -80px -224px; } + + +/* Misc visuals +----------------------------------*/ + +/* Corner radius */ +.ui-corner-tl { -moz-border-radius-topleft: 6px; -webkit-border-top-left-radius: 6px; border-top-left-radius: 6px; } +.ui-corner-tr { -moz-border-radius-topright: 6px; -webkit-border-top-right-radius: 6px; border-top-right-radius: 6px; } +.ui-corner-bl { -moz-border-radius-bottomleft: 6px; -webkit-border-bottom-left-radius: 6px; border-bottom-left-radius: 6px; } +.ui-corner-br { -moz-border-radius-bottomright: 6px; -webkit-border-bottom-right-radius: 6px; border-bottom-right-radius: 6px; } +.ui-corner-top { -moz-border-radius-topleft: 6px; -webkit-border-top-left-radius: 6px; border-top-left-radius: 6px; -moz-border-radius-topright: 6px; -webkit-border-top-right-radius: 6px; border-top-right-radius: 6px; } +.ui-corner-bottom { -moz-border-radius-bottomleft: 6px; -webkit-border-bottom-left-radius: 6px; border-bottom-left-radius: 6px; -moz-border-radius-bottomright: 6px; -webkit-border-bottom-right-radius: 6px; border-bottom-right-radius: 6px; } +.ui-corner-right { -moz-border-radius-topright: 6px; -webkit-border-top-right-radius: 6px; border-top-right-radius: 6px; -moz-border-radius-bottomright: 6px; -webkit-border-bottom-right-radius: 6px; border-bottom-right-radius: 6px; } +.ui-corner-left { -moz-border-radius-topleft: 6px; -webkit-border-top-left-radius: 6px; border-top-left-radius: 6px; -moz-border-radius-bottomleft: 6px; -webkit-border-bottom-left-radius: 6px; border-bottom-left-radius: 6px; } +.ui-corner-all { -moz-border-radius: 6px; -webkit-border-radius: 6px; border-radius: 6px; } + +/* Overlays */ +.ui-widget-overlay { background: #eeeeee url(images/ui-bg_flat_0_eeeeee_40x100.png) 50% 50% repeat-x; opacity: .80;filter:Alpha(Opacity=80); } +.ui-widget-shadow { margin: -4px 0 0 -4px; padding: 4px; background: #aaaaaa url(images/ui-bg_flat_0_aaaaaa_40x100.png) 50% 50% repeat-x; opacity: .60;filter:Alpha(Opacity=60); -moz-border-radius: 0pxdow=0px; -webkit-border-radius: 0pxdow=0px; border-radius: 0pxdow=0px; }/* + * jQuery UI Slider @VERSION + * + * Copyright 2010, AUTHORS.txt (http://jqueryui.com/about) + * Dual licensed under the MIT or GPL Version 2 licenses. + * http://jquery.org/license + * + * http://docs.jquery.com/UI/Slider#theming + */ +.ui-slider { position: relative; text-align: left; } +.ui-slider .ui-slider-handle { position: absolute; z-index: 2; width: 1.2em; height: 1.2em; cursor: default; } +.ui-slider .ui-slider-range { position: absolute; z-index: 1; font-size: .7em; display: block; border: 0; background-position: 0 0; } + +.ui-slider-horizontal { height: .8em; } +.ui-slider-horizontal .ui-slider-handle { top: -.3em; margin-left: -.6em; } +.ui-slider-horizontal .ui-slider-range { top: 0; height: 100%; } +.ui-slider-horizontal .ui-slider-range-min { left: 0; } +.ui-slider-horizontal .ui-slider-range-max { right: 0; } + +.ui-slider-vertical { width: .8em; height: 100px; } +.ui-slider-vertical .ui-slider-handle { left: -.3em; margin-left: 0; margin-bottom: -.6em; } +.ui-slider-vertical .ui-slider-range { left: 0; width: 100%; } +.ui-slider-vertical .ui-slider-range-min { bottom: 0; } +.ui-slider-vertical .ui-slider-range-max { top: 0; } --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -406,6 +406,7 @@ class Bed( Interval ): MetadataElement( name="endCol", default=3, desc="End column", param=metadata.ColumnParameter ) MetadataElement( name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0 ) MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False ) + MetadataElement( name="viz_filter_cols", default=[4], param=metadata.ColumnParameter, multiple=True ) ###do we need to repeat these? they are the same as should be inherited from interval type def set_meta( self, dataset, overwrite = True, **kwd ): Binary file static/june_2007_style/blue/overcast/images/ui-bg_glass_100_f8f8f8_1x400.png has changed Binary file static/june_2007_style/blue/overcast/images/ui-bg_glass_60_eeeeee_1x400.png has changed

1 0

galaxy-dist commit 73c4c66ff3dd: Add RNA-seq tools -- Tophat + Cufflinks suite -- to main.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287602065 14400 # Node ID 73c4c66ff3dd8101a0e6126077f4f8fc897c71fe # Parent 14fd007fc550092df7ea23f1019ab2d99ba03ce2 Add RNA-seq tools -- Tophat + Cufflinks suite -- to main. --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -288,7 +288,7 @@ <tool file="indels/indel_table.xml" />" <tool file="indels/indel_analysis.xml" /></section> - <section name="NGS: Expression Analysis" id="ngs-rna-tools"> + <section name="NGS: RNA Analysis" id="ngs-rna-tools"><label text="RNA-seq" id="rna_seq" /><tool file="ngs_rna/tophat_wrapper.xml" /><tool file="ngs_rna/cufflinks_wrapper.xml" /> --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -370,6 +370,15 @@ <tool file="genetrack/genetrack_indexer.xml" /><tool file="genetrack/genetrack_peak_prediction.xml" /></section> + <section name="NGS: RNA Analysis" id="ngs-rna-tools"> + <label text="RNA-seq" id="rna_seq" /> + <tool file="ngs_rna/tophat_wrapper.xml" /> + <tool file="ngs_rna/cufflinks_wrapper.xml" /> + <tool file="ngs_rna/cuffcompare_wrapper.xml" /> + <tool file="ngs_rna/cuffdiff_wrapper.xml" /> + <label text="Filtering" id="filtering" /> + <tool file="ngs_rna/filter_transcripts_via_tracking.xml" /> + </section><label text="RGENETICS" id="rgenetics" /><section name="SNP/WGA: Data; Filters" id="rgdat"><label text="Data: Import and upload" id="rgimport" />

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galaxy-dist commit e226033419a9: Update version numbers of Tophat and Cufflinks wrappers to reflect current tool installations on Galaxy main and test instances.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287602818 14400 # Node ID e226033419a91100e657f6880562dc50ae01ef98 # Parent 73c4c66ff3dd8101a0e6126077f4f8fc897c71fe Update version numbers of Tophat and Cufflinks wrappers to reflect current tool installations on Galaxy main and test instances. --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="cuffcompare" name="Cuffcompare" version="0.8.3"> +<tool id="cuffcompare" name="Cuffcompare" version="0.9.1"><description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description><requirements><requirement type="package">cufflinks</requirement> --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="cuffdiff" name="Cuffdiff" version="0.8.3"> +<tool id="cuffdiff" name="Cuffdiff" version="0.9.1"><description>find significant changes in transcript expression, splicing, and promoter use</description><requirements><requirement type="package">cufflinks</requirement> --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="cufflinks" name="Cufflinks" version="0.8.3"> +<tool id="cufflinks" name="Cufflinks" version="0.9.1"><description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description><requirements><requirement type="package">cufflinks</requirement> --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="tophat" name="Tophat" version="1.0.14"> +<tool id="tophat" name="Tophat" version="1.1.1"><description>Find splice junctions using RNA-seq data</description><requirements><requirement type="package">tophat</requirement>

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galaxy-dist commit 14fd007fc550: Fix setting of minimum and maximum values for tracker slider filters.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287549765 14400 # Node ID 14fd007fc550092df7ea23f1019ab2d99ba03ce2 # Parent 11031e92204b1590ff05119515673d37ae834188 Fix setting of minimum and maximum values for tracker slider filters. --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -462,11 +462,11 @@ var NumberFilter = function( name, index // Index into payload to filter. this.index = index; // Filter low/high. These values are used to filter elements. - this.low = Number.MIN_VALUE; + this.low = -Number.MAX_VALUE; this.high = Number.MAX_VALUE; // Slide min/max. These values are used to set/update slider. this.slider_min = Number.MAX_VALUE; - this.slider_max = Number.MIN_VALUE; + this.slider_max = -Number.MAX_VALUE; // UI Slider element and label that is associated with filter. this.slider = null; this.slider_label = null; @@ -571,15 +571,14 @@ var Track = function (name, view, parent var name_span = $("<span class='name'>").appendTo(filter_th); name_span.text(filter.name + " "); // Extra spacing to separate name and values var values_span = $("<span class='values'>").appendTo(filter_th); - values_span.text("[0-2]"); // TODO: generate custom interaction elements based on filter type. var table_data = $("<td>").appendTo(table_row); filter.control_element = $("<div id='" + filter.name + "-filter-control' style='width: 200px; position: relative'>").appendTo(table_data); filter.control_element.slider({ range: true, - min: 0, - max: 1, - values: [0, 1], + min: Number.MAX_VALUE, + max: -Number.MIN_VALUE, + values: [0, 0], slide: function( event, ui ) { var values = ui.values; // Set new values in UI. @@ -804,8 +803,9 @@ var TiledTrack = function() { } // Update filtering UI. - for (var f = 0; f < track.filters.length; f++) + for (var f = 0; f < track.filters.length; f++) { track.filters[f].update_ui_elt(); + } // Method complete; do not call it again. clearInterval(intervalId); } --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=50,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/st rand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,d,c,b){this.container=a;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_i d_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);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_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Clo se 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_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();r eturn false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new Referenc eTrack(a))}a.chrom_data=d.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind ("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a. container.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(!c.chrom){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.re set();c.redraw(true);for(var g in c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.reset_overview();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).re move()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=this.low/(this.max_high-this.max_low)*this.overview_viewport.width();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left :a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);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 Filter=functio n(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=Number.MIN_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=Number.MIN_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[ this.slider_min,this.slider_max])}}});var get_filters=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,d,c){this.name=b;this.view=a;this.parent_element=d;this.filters=(c!==undefined?get_filters(c):[]);this.init_global()};$.extend(Track.prototype,{init_global:function(){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.filtering_div=$("<div class='track-filters'>").appendTo(this.container_div);this.fil tering_div.hide();this.filtering_div.bind("drag",function(k){k.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);var c=this;for(var e=0;e<this.filters.length;e++){var a=this.filters[e];var f=$("<tr>").appendTo(b);var g=$("<th class='filter-info'>").appendTo(f);var j=$("<span class='name'>").appendTo(g);j.text(a.name+" ");var d=$("<span class='values'>").appendTo(g);d.text("[0-2]");var h=$("<td>").appendTo(f);a.control_element=$("<div id='"+a.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(h);a.control_element.slider({range:true,min:0,max:1,values:[0,1],slide:function(l,m){var k=m.values;d.text("["+k[0]+"-"+k[1]+"]");a.low=k[0];a.high=k[1];c.draw(true)},change:function(k,l){a.control_element.slider("option","slide").call(a.control_element,k,l)}});a.slider=a.control_element;a.slider_label=d}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)} ,init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_di v.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}};b["Edit configur ation"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},j=function(){d.update_options(d.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){j()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:l,OK:j})};if(d.filters.length>0){b["Show filters"]=function(){var j;if(!d.filtering_div.is(":visible")){j="Hide filters";d.filters_visible=true}else{j="Show filters";d.filters_visible=false}$("#"+d.name_div.attr("id")+"-menu").find("li").eq(2).text(j);d.filtering_div.toggle()}}b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};d.popup_menu=make_popupmenu(d.name_div,b);show_hide_popupmenu_options(d.popup_menu,"(Show|Hide) filters",false)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,h=g-m,f=this.view.r esolution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h,k;this.content_div.append(p),this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=new Object();while((a*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+a;var e=this.tile_cache.get(n);if(!b&&e){var j=a*DENSITY*f;var d=(j-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(this,n,m,g,a,f,p,q,l)}a+=1}var c=this;var o=setInterval(function(){if(l.length!=0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var r=0;r<c.filters.length;r++){c.filters[r].update_ui_elt()}clearInterval(o)}},50)},delayed_draw:function(c,h,g,e,b,d,j,k,f){var a=setTimeout(function(){if(!(g>c.view.high||e<c.view.low)){tile_element=c.draw_tile(d,b,j,k);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var n=tile_element.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m= n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,tile_element);c.show_tile(tile_element,j)}}delete f.id},50);f.id=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null ,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_ data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,l,p){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),o=e.get(0).getContext("2d"),k=f+"_"+b;if(p>PX_PER_CHAR){if(this.data_cache.get(k)===undefined){this.get_data(f,b);return}var n=this.data_cache.get(k);if(n===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*p+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*p-this.left_offset});for(var h=0,m=n.length;h<m;h++){var a=Math.round(h*p),j=Math.round(p/2);o.fillText(n[h],a+this.left_offset+j,10)}l.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=fu nction(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#tr ack_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;a.container_div.find(".yaxislabel").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:fu nction(p,s,c,e){if(this.vertical_range===undefined){return}var t=s*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),w=p+"_"+s;if(this.data_cache.get(w)===undefined){this.get_data(p,s);return}var j=this.data_cache.get(w);if(j===null){return}b.css({position:"absolute",top:0,left:(t-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,u=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();o.fillStyle=this.prefs.color;if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var v,h;for(var q=0,r=data.length;q<r;q++){v=Math.round((data[q][0]-t)*e);h=data[q][1];if(h===null){if(k&&m==="Filled"){o.lineTo(v,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(d-(h-l)/n*d);o.fillRect(v,h,f,d-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+") ";o.fillRect(v,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(v,h)}else{k=true;if(m==="Filled"){o.moveTo(v,d);o.lineTo(v,h)}else{o.moveTo(v,h)}}}}}if(m==="Filled"){if(k){o.lineTo(v,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div />").addClass("form-row");var e="track_"+n+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+n+"_minval",m=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),l=$("<input></input>").attr("id",h).val(d),k="track_"+n+"_maxval",g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j);return a.append(m).append(l).append(g).append(f).append(b).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();color=$("#track_ "+c+"_color").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value||color!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.prefs.color=color;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container,e);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATU RE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};t his.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(v<=MAX_FEATURE_DEPTH){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_ti le[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(r,m,s,b,q,f,h,e){r.textAlign="center";var l=0,p=Math.round(m/2);for(cig_id in h){var k=h[cig_id],d="MIDNSHP"[k[0]],n=k[1];if(d==="H"||d==="S"){l-=n}var g=q+l,v=Math.floor(Math.max(0,(g-s)*m)),j=Math.floor(Math.max(0,(g+n-s)*m));switch(d){case"S":case"H":case"M":var o=f.slice(l,n);if((this.mode==="Pack"||this.mode==="Auto")&&f!==undefined&&m>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(v+this.left_offset,e+1,j-v,9);r.fillStyle=CONNECTOR_COLOR;for(var t=0,a=o.length;t<a;t++){if(g+t>=s&&g+t<=b){var u=Math.floor(Math.max(0,(g+t-s)*m));r.fillText(o[t],u+this.left_offset+p,e+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(v+this.left_offset,e+4,j-v,3)}break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(v+this.left_offset,e+5,j-v,1);break;case"D":r.fillStyle="red";r.fillRect(v+this.left_offset,e+4,j-v,3);break;case"P":case"I":break}l+=n}},draw_tile:function( ah,o,s,aw){var N=o*DENSITY*ah,am=(o+1)*DENSITY*ah,M=am-N;var ao=(!this.initial_canvas?"initial":N+"_"+am);var I=this.data_cache.get(ao);var e;if(I===undefined||(this.mode!=="Auto"&&I.dataset_type==="summary_tree")){this.data_queue[[N,am]]=true;this.get_data(N,am);return}var a=Math.ceil(M*aw),S=$("<canvas class='tile'></canvas>"),aj=this.prefs.label_color,l=this.prefs.block_color,r=this.mode,z=25,af=(r==="Squish")||(r==="Dense")&&(r!=="Pack")||(r==="Auto"&&(I.extra_info==="no_detail")),X=this.left_offset,av,D,ax;if(I.dataset_type==="summary_tree"){D=this.summary_draw_height}else{if(r==="Dense"){D=z;ax=10}else{ax=(af?this.vertical_nodetail_px:this.vertical_detail_px);var A=(aw<0.0001?1/view.zoom_res:aw);D=this.incremental_slots(A,I.data,af,r)*ax+z;av=this.inc_slots[A]}}S.css({position:"absolute",top:0,left:(N-this.view.low)*aw-X});S.get(0).width=a+X;S.get(0).height=D;s.parent().css("height",Math.max(this.height_px,D)+"px");var J=S.get(0).getContext("2d");J.fillStyle=l;J.font=t his.default_font;J.textAlign="right";this.container_div.find(".yaxislabel").remove();if(I.dataset_type=="summary_tree"){var Z=I.data,L=I.max,q=I.avg,b=Math.ceil(I.delta*aw);var p=$("<div />").addClass("yaxislabel").text(L);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var aq=0,H=Z.length;aq<H;aq++){var ab=Math.floor((Z[aq][0]-N)*aw);var aa=Z[aq][1];if(!aa){continue}var an=aa/L*this.summary_draw_height;J.fillStyle="black";J.fillRect(ab+X,this.summary_draw_height-an,b,an);if(this.prefs.show_counts&&J.measureText(aa).width<b){J.fillStyle="#bbb";J.textAlign="center";J.fillText(aa,ab+X+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(S);return S}if(I.message){S.css({border:"solid red","border-width":"2px 2px 2px 0px"});J.fillStyle="red";J.textAlign="left";J.fillText(I.message,100+X,ax)}var ae=false;if(I.data.length!=0){ae=true;for(var at=0;at<this.filters.length;at++){if(!this.filters[at].applies_to(I.data[0])){ae=false}}}if(ae){S. addClass(FILTERABLE_CLASS)}var au=I.data;var ap=0;for(var aq=0,H=au.length;aq<H;aq++){var T=au[aq],R=T[0],ar=T[1],ad=T[2],O=T[3];if(av[R]===undefined){continue}var ac=false;var V;for(var at=0;at<this.filters.length;at++){V=this.filters[at];V.update_attrs(T);if(!V.keep(T)){ac=true;break}}if(ac){continue}if(ar<=am&&ad>=N){var ag=Math.floor(Math.max(0,(ar-N)*aw)),K=Math.ceil(Math.min(a,Math.max(0,(ad-N)*aw))),Y=(r==="Dense"?1:(1+av[R]))*ax;if(I.dataset_type==="bai"){var v=T[4];J.fillStyle=l;if(T[5] instanceof Array){var E=Math.floor(Math.max(0,(T[5][0]-N)*aw)),Q=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-N)*aw))),C=Math.floor(Math.max(0,(T[6][0]-N)*aw)),w=Math.ceil(Math.min(a,Math.max(0,(T[6][1]-N)*aw)));if(T[5][1]>=N&&T[5][0]<=am){this.rect_or_text(J,aw,N,am,T[5][0],T[5][2],v,Y)}if(T[6][1]>=N&&T[6][0]<=am){this.rect_or_text(J,aw,N,am,T[6][0],T[6][2],v,Y)}if(C>Q){J.fillStyle=CONNECTOR_COLOR;J.fillRect(Q+X,Y+5,C-Q,1)}}else{J.fillStyle=l;this.rect_or_text(J,aw,N,am,ar,O,v,Y)}if(r!= ="Dense"&&!af&&ar>N){J.fillStyle=this.prefs.label_color;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(R,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(R,ag-2+X,Y+8)}J.fillStyle=l}}else{if(I.dataset_type==="interval_index"){if(af){J.fillStyle=l;J.fillRect(ag+X,Y+5,K-ag,1)}else{var G=T[4],W=T[5],ai=T[6],h=T[7];var F,ak,P=null,ay=null;if(W&&ai){P=Math.floor(Math.max(0,(W-N)*aw));ay=Math.ceil(Math.min(a,Math.max(0,(ai-N)*aw)))}if(r!=="Dense"&&O!==undefined&&ar>N){J.fillStyle=aj;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(O,ag-2+X,Y+8)}J.fillStyle=l}if(h){if(G){if(G=="+"){J.fillStyle=RIGHT_STRAND}else{if(G=="-"){J.fillStyle=LEFT_STRAND}}J.fillRect(ag+X,Y,K-ag,10);J.fillStyle=l}for(var ao=0,g=h.length;ao<g;ao++){var u=h[ao],d=Math.floor(Math.max(0,(u[0]-N)*aw)),U=Math.ceil(Math.min(a,Math.max((u[1]-N)*aw)));if(d>U){continue}F=5;ak=3;J.fillRect(d+X,Y+ak,U-d,F);if(P!==undefined&&!(d>ay|| U<P)){F=9;ak=1;var al=Math.max(d,P),B=Math.min(U,ay);J.fillRect(al+X,Y+ak,B-al,F)}}}else{F=9;ak=1;J.fillRect(ag+X,Y+ak,K-ag,F);if(T.strand){if(T.strand=="+"){J.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){J.fillStyle=LEFT_STRAND_INV}}J.fillRect(ag+X,Y,K-ag,10);J.fillStyle=l}}}}else{if(I.dataset_type==="vcf"){if(af){J.fillStyle=l;J.fillRect(ag+X,Y+5,K-ag,1)}else{var t=T[4],n=T[5],c=T[6];F=9;ak=1;J.fillRect(ag+X,Y,K-ag,F);if(r!=="Dense"&&O!==undefined&&ar>N){J.fillStyle=aj;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(O,ag-2+X,Y+8)}J.fillStyle=l}var m=t+" / "+n;if(ar>N&&J.measureText(m).width<(K-ag)){J.fillStyle="white";J.textAlign="center";J.fillText(m,X+ag+(K-ag)/2,Y+8);J.fillStyle=l}}}}}ap++}}return S},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(th is.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,e,c){FeatureTrack.call(this,d,b,a,e,c);this.track_type="ReadTrack";this.vert ical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=50,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/st rand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,d,c,b){this.container=a;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_i d_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Clo se Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();r eturn false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new Referenc eTrack(a))}a.chrom_data=d.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind ("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a. container.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(!c.chrom){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.re set();c.redraw(true);for(var g in c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.reset_overview();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).re move()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=this.low/(this.max_high-this.max_low)*this.overview_viewport.width();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left :a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);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 Filter=functio n(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values" ,[this.slider_min,this.slider_max])}}});var get_filters=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,d,c){this.name=b;this.view=a;this.parent_element=d;this.filters=(c!==undefined?get_filters(c):[]);this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<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=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.filtering_div=$("<div class='track-filters'>").appendTo(this.container_div);this.f iltering_div.hide();this.filtering_div.bind("drag",function(k){k.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);var c=this;for(var e=0;e<this.filters.length;e++){var a=this.filters[e];var f=$("<tr>").appendTo(b);var g=$("<th class='filter-info'>").appendTo(f);var j=$("<span class='name'>").appendTo(g);j.text(a.name+" ");var d=$("<span class='values'>").appendTo(g);var h=$("<td>").appendTo(f);a.control_element=$("<div id='"+a.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(h);a.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(l,m){var k=m.values;d.text("["+k[0]+"-"+k[1]+"]");a.low=k[0];a.high=k[1];c.draw(true)},change:function(k,l){a.control_element.slider("option","slide").call(a.control_element,k,l)}});a.slider=a.control_element;a.slider_label=d}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(thi s.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending "){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}} ;b["Edit configuration"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},j=function(){d.update_options(d.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){j()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:l,OK:j})};if(d.filters.length>0){b["Show filters"]=function(){var j;if(!d.filtering_div.is(":visible")){j="Hide filters";d.filters_visible=true}else{j="Show filters";d.filters_visible=false}$("#"+d.name_div.attr("id")+"-menu").find("li").eq(2).text(j);d.filtering_div.toggle()}}b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};d.popup_menu=make_popupmenu(d.name_div,b);show_hide_popupmenu_options(d.popup_menu,"(Show|Hide) filters",false)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,h= g-m,f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h,k;this.content_div.append(p),this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=new Object();while((a*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+a;var e=this.tile_cache.get(n);if(!b&&e){var j=a*DENSITY*f;var d=(j-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(this,n,m,g,a,f,p,q,l)}a+=1}var c=this;var o=setInterval(function(){if(l.length!=0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var r=0;r<c.filters.length;r++){c.filters[r].update_ui_elt()}clearInterval(o)}},50)},delayed_draw:function(c,h,g,e,b,d,j,k,f){var a=setTimeout(function(){if(!(g>c.view.high||e<c.view.low)){tile_element=c.draw_tile(d,b,j,k);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var n=tile_element.get(0).getContext("2d");var l=c.initial_canvas.get(0).getCon text("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,tile_element);c.show_tile(tile_element,j)}}delete f.id},50);f.id=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Tra ck.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrac k.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,l,p){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),o=e.get(0).getContext("2d"),k=f+"_"+b;if(p>PX_PER_CHAR){if(this.data_cache.get(k)===undefined){this.get_data(f,b);return}var n=this.data_cache.get(k);if(n===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*p+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*p-this.left_offset});for(var h=0,m=n.length;h<m;h++){var a=Math.round(h*p),j=Math.round(p/2);o.fillText(n[h],a+this.left_offset+j,10)}l.append(e);return e}this.content_div.css("height","0px")}}) ;var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs. min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;a.container_div.find(".yaxislabel").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)} })}},draw_tile:function(p,s,c,e){if(this.vertical_range===undefined){return}var t=s*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),w=p+"_"+s;if(this.data_cache.get(w)===undefined){this.get_data(p,s);return}var j=this.data_cache.get(w);if(j===null){return}b.css({position:"absolute",top:0,left:(t-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,u=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();o.fillStyle=this.prefs.color;if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var v,h;for(var q=0,r=data.length;q<r;q++){v=Math.round((data[q][0]-t)*e);h=data[q][1];if(h===null){if(k&&m==="Filled"){o.lineTo(v,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(d-(h-l)/n*d);o.fillRect(v,h,f,d-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb(" +h+","+h+","+h+")";o.fillRect(v,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(v,h)}else{k=true;if(m==="Filled"){o.moveTo(v,d);o.lineTo(v,h)}else{o.moveTo(v,h)}}}}}if(m==="Filled"){if(k){o.lineTo(v,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div />").addClass("form-row");var e="track_"+n+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+n+"_minval",m=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),l=$("<input></input>").attr("id",h).val(d),k="track_"+n+"_maxval",g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j);return a.append(m).append(l).append(g).append(f).append(b).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val() ;color=$("#track_"+c+"_color").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value||color!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.prefs.color=color;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container,e);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(C ACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this. inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(v<=MAX_FEATURE_DEPTH){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]= []}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(r,m,s,b,q,f,h,e){r.textAlign="center";var l=0,p=Math.round(m/2);for(cig_id in h){var k=h[cig_id],d="MIDNSHP"[k[0]],n=k[1];if(d==="H"||d==="S"){l-=n}var g=q+l,v=Math.floor(Math.max(0,(g-s)*m)),j=Math.floor(Math.max(0,(g+n-s)*m));switch(d){case"S":case"H":case"M":var o=f.slice(l,n);if((this.mode==="Pack"||this.mode==="Auto")&&f!==undefined&&m>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(v+this.left_offset,e+1,j-v,9);r.fillStyle=CONNECTOR_COLOR;for(var t=0,a=o.length;t<a;t++){if(g+t>=s&&g+t<=b){var u=Math.floor(Math.max(0,(g+t-s)*m));r.fillText(o[t],u+this.left_offset+p,e+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(v+this.left_offset,e+4,j-v,3)}break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(v+this.left_offset,e+5,j-v,1);break;case"D":r.fillStyle="red";r.fillRect(v+this.left_offset,e+4,j-v,3);break;case"P":case"I":break}l+=n}},dr aw_tile:function(ah,o,s,aw){var N=o*DENSITY*ah,am=(o+1)*DENSITY*ah,M=am-N;var ao=(!this.initial_canvas?"initial":N+"_"+am);var I=this.data_cache.get(ao);var e;if(I===undefined||(this.mode!=="Auto"&&I.dataset_type==="summary_tree")){this.data_queue[[N,am]]=true;this.get_data(N,am);return}var a=Math.ceil(M*aw),S=$("<canvas class='tile'></canvas>"),aj=this.prefs.label_color,l=this.prefs.block_color,r=this.mode,z=25,af=(r==="Squish")||(r==="Dense")&&(r!=="Pack")||(r==="Auto"&&(I.extra_info==="no_detail")),X=this.left_offset,av,D,ax;if(I.dataset_type==="summary_tree"){D=this.summary_draw_height}else{if(r==="Dense"){D=z;ax=10}else{ax=(af?this.vertical_nodetail_px:this.vertical_detail_px);var A=(aw<0.0001?1/view.zoom_res:aw);D=this.incremental_slots(A,I.data,af,r)*ax+z;av=this.inc_slots[A]}}S.css({position:"absolute",top:0,left:(N-this.view.low)*aw-X});S.get(0).width=a+X;S.get(0).height=D;s.parent().css("height",Math.max(this.height_px,D)+"px");var J=S.get(0).getContext("2d");J.fil lStyle=l;J.font=this.default_font;J.textAlign="right";this.container_div.find(".yaxislabel").remove();if(I.dataset_type=="summary_tree"){var Z=I.data,L=I.max,q=I.avg,b=Math.ceil(I.delta*aw);var p=$("<div />").addClass("yaxislabel").text(L);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var aq=0,H=Z.length;aq<H;aq++){var ab=Math.floor((Z[aq][0]-N)*aw);var aa=Z[aq][1];if(!aa){continue}var an=aa/L*this.summary_draw_height;J.fillStyle="black";J.fillRect(ab+X,this.summary_draw_height-an,b,an);if(this.prefs.show_counts&&J.measureText(aa).width<b){J.fillStyle="#bbb";J.textAlign="center";J.fillText(aa,ab+X+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(S);return S}if(I.message){S.css({border:"solid red","border-width":"2px 2px 2px 0px"});J.fillStyle="red";J.textAlign="left";J.fillText(I.message,100+X,ax)}var ae=false;if(I.data.length!=0){ae=true;for(var at=0;at<this.filters.length;at++){if(!this.filters[at].applies_to(I.data[0])){ae= false}}}if(ae){S.addClass(FILTERABLE_CLASS)}var au=I.data;var ap=0;for(var aq=0,H=au.length;aq<H;aq++){var T=au[aq],R=T[0],ar=T[1],ad=T[2],O=T[3];if(av[R]===undefined){continue}var ac=false;var V;for(var at=0;at<this.filters.length;at++){V=this.filters[at];V.update_attrs(T);if(!V.keep(T)){ac=true;break}}if(ac){continue}if(ar<=am&&ad>=N){var ag=Math.floor(Math.max(0,(ar-N)*aw)),K=Math.ceil(Math.min(a,Math.max(0,(ad-N)*aw))),Y=(r==="Dense"?1:(1+av[R]))*ax;if(I.dataset_type==="bai"){var v=T[4];J.fillStyle=l;if(T[5] instanceof Array){var E=Math.floor(Math.max(0,(T[5][0]-N)*aw)),Q=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-N)*aw))),C=Math.floor(Math.max(0,(T[6][0]-N)*aw)),w=Math.ceil(Math.min(a,Math.max(0,(T[6][1]-N)*aw)));if(T[5][1]>=N&&T[5][0]<=am){this.rect_or_text(J,aw,N,am,T[5][0],T[5][2],v,Y)}if(T[6][1]>=N&&T[6][0]<=am){this.rect_or_text(J,aw,N,am,T[6][0],T[6][2],v,Y)}if(C>Q){J.fillStyle=CONNECTOR_COLOR;J.fillRect(Q+X,Y+5,C-Q,1)}}else{J.fillStyle=l;this.rect_or_text(J,aw,N,am ,ar,O,v,Y)}if(r!=="Dense"&&!af&&ar>N){J.fillStyle=this.prefs.label_color;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(R,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(R,ag-2+X,Y+8)}J.fillStyle=l}}else{if(I.dataset_type==="interval_index"){if(af){J.fillStyle=l;J.fillRect(ag+X,Y+5,K-ag,1)}else{var G=T[4],W=T[5],ai=T[6],h=T[7];var F,ak,P=null,ay=null;if(W&&ai){P=Math.floor(Math.max(0,(W-N)*aw));ay=Math.ceil(Math.min(a,Math.max(0,(ai-N)*aw)))}if(r!=="Dense"&&O!==undefined&&ar>N){J.fillStyle=aj;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(O,ag-2+X,Y+8)}J.fillStyle=l}if(h){if(G){if(G=="+"){J.fillStyle=RIGHT_STRAND}else{if(G=="-"){J.fillStyle=LEFT_STRAND}}J.fillRect(ag+X,Y,K-ag,10);J.fillStyle=l}for(var ao=0,g=h.length;ao<g;ao++){var u=h[ao],d=Math.floor(Math.max(0,(u[0]-N)*aw)),U=Math.ceil(Math.min(a,Math.max((u[1]-N)*aw)));if(d>U){continue}F=5;ak=3;J.fillRect(d+X,Y+ak,U-d,F);if(P!==un defined&&!(d>ay||U<P)){F=9;ak=1;var al=Math.max(d,P),B=Math.min(U,ay);J.fillRect(al+X,Y+ak,B-al,F)}}}else{F=9;ak=1;J.fillRect(ag+X,Y+ak,K-ag,F);if(T.strand){if(T.strand=="+"){J.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){J.fillStyle=LEFT_STRAND_INV}}J.fillRect(ag+X,Y,K-ag,10);J.fillStyle=l}}}}else{if(I.dataset_type==="vcf"){if(af){J.fillStyle=l;J.fillRect(ag+X,Y+5,K-ag,1)}else{var t=T[4],n=T[5],c=T[6];F=9;ak=1;J.fillRect(ag+X,Y,K-ag,F);if(r!=="Dense"&&O!==undefined&&ar>N){J.fillStyle=aj;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(O,ag-2+X,Y+8)}J.fillStyle=l}var m=t+" / "+n;if(ar>N&&J.measureText(m).width<(K-ag)){J.fillStyle="white";J.textAlign="center";J.fillText(m,X+ag+(K-ag)/2,Y+8);J.fillStyle=l}}}}}ap++}}return S},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr ("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,e,c){FeatureTrack.call(this,d,b,a,e,c);this.track_type="Rea dTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});

1 0

galaxy-dist commit 11031e92204b: trackster: Add proper CIGAR support to BAM display (properly displays matches, deletions, skipped bases, and clipping. Padding and insertions are skipped as of now as there is no good way to insert new space into the view.)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1287529137 14400 # Node ID 11031e92204b1590ff05119515673d37ae834188 # Parent ad9bb65d2d153af5db0ae497930eb35d17f63057 trackster: Add proper CIGAR support to BAM display (properly displays matches, deletions, skipped bases, and clipping. Padding and insertions are skipped as of now as there is no good way to insert new space into the view.) - Don't re-add new datasets when refreshing after using "Add into current viz" link - To prevent browser lockup, only display up to 50 lines of features by default (user-editable in future). TODO: add warning message when this occurs --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -4,8 +4,9 @@ var DENSITY = 200, FEATURE_LEVELS = 10, - MAX_FEATURE_DEPTH = 100, - DATA_ERROR = "There was an error in indexing this dataset. ", + MAX_FEATURE_DEPTH = 50, + CONNECTOR_COLOR = "#ccc", + DATA_ERROR = "There was an error in indexing this dataset.", DATA_NOCONVERTER = "A converter for this dataset is not installed. Please check your datatypes_conf.xml file.", DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Currently indexing... please wait", @@ -75,12 +76,11 @@ var Cache = function( num_elements ) { } }); -var View = function( container, chrom, title, vis_id, dbkey ) { +var View = function( container, title, vis_id, dbkey ) { this.container = container; this.vis_id = vis_id; this.dbkey = dbkey; this.title = title; - this.chrom = chrom; this.tracks = []; this.label_tracks = []; this.max_low = 0; @@ -271,7 +271,7 @@ var View = function( container, chrom, t } if (chrom !== view.chrom) { view.chrom = chrom; - if (view.chrom === "") { + if (!view.chrom) { // No chrom selected view.intro_div.show(); } else { @@ -1203,7 +1203,7 @@ var FeatureTrack = function ( name, view this.data_cache = new Cache(20); this.left_offset = 200; - this.prefs = { 'block_color': 'black', 'label_color': 'black', 'show_counts': true }; + this.prefs = { 'block_color': '#444', 'label_color': 'black', 'show_counts': true }; if (prefs.block_color !== undefined) { this.prefs.block_color = prefs.block_color; } if (prefs.label_color !== undefined) { this.prefs.label_color = prefs.label_color; } if (prefs.show_counts !== undefined) { this.prefs.show_counts = prefs.show_counts; } @@ -1294,7 +1294,7 @@ var FeatureTrack = function ( name, view var j = 0; // Try to fit the feature to the first slot that doesn't overlap any other features in that slot - while (true) { + while (j <= MAX_FEATURE_DEPTH) { var found = true; if (this.s_e_by_tile[level][j] !== undefined) { for (var k = 0, k_len = this.s_e_by_tile[level][j].length; k < k_len; k++) { @@ -1318,22 +1318,57 @@ var FeatureTrack = function ( name, view return highest_slot; }, - rect_or_text: function( ctx, w_scale, tile_low, tile_high, feature_start, name, x, x_len, y_center ) { + rect_or_text: function( ctx, w_scale, tile_low, tile_high, feature_start, orig_seq, cigar, y_center ) { ctx.textAlign = "center"; - var gap = Math.round(w_scale / 2); - if ( (this.mode === "Pack" || this.mode === "Auto") && name !== undefined && w_scale > PX_PER_CHAR) { - ctx.fillStyle = this.prefs.block_color; - ctx.fillRect(x, y_center + 1, x_len, 9); - ctx.fillStyle = "#eee"; - for (var c = 0, str_len = name.length; c < str_len; c++) { - if (feature_start + c >= tile_low && feature_start + c <= tile_high) { - var c_start = Math.floor( Math.max(0, (feature_start + c - tile_low) * w_scale) ); - ctx.fillText(name[c], c_start + this.left_offset + gap, y_center + 9); - } + var cur_offset = 0, + gap = Math.round(w_scale / 2); + + for (cig_id in cigar) { + var cig = cigar[cig_id], + cig_op = "MIDNSHP"[cig[0]], + cig_len = cig[1]; + + if (cig_op === "H" || cig_op === "S") { + // Go left if it clips + cur_offset -= cig_len; } - } else { - ctx.fillStyle = this.prefs.block_color; - ctx.fillRect(x, y_center + 4, x_len, 3); + var seq_start = feature_start + cur_offset, + s_start = Math.floor( Math.max(0, (seq_start - tile_low) * w_scale) ), + s_end = Math.floor( Math.max(0, (seq_start + cig_len - tile_low) * w_scale) ); + + switch (cig_op) { + case "S": // Soft clipping + case "H": // Hard clipping + case "M": // Match + var seq = orig_seq.slice(cur_offset, cig_len); + if ( (this.mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > PX_PER_CHAR) { + ctx.fillStyle = this.prefs.block_color; + ctx.fillRect(s_start + this.left_offset, y_center + 1, s_end - s_start, 9); + ctx.fillStyle = CONNECTOR_COLOR; + for (var c = 0, str_len = seq.length; c < str_len; c++) { + if (seq_start + c >= tile_low && seq_start + c <= tile_high) { + var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); + ctx.fillText(seq[c], c_start + this.left_offset + gap, y_center + 9); + } + } + } else { + ctx.fillStyle = this.prefs.block_color; + ctx.fillRect(s_start + this.left_offset, y_center + 4, s_end - s_start, 3); + } + break; + case "N": // Skipped bases + ctx.fillStyle = CONNECTOR_COLOR; + ctx.fillRect(s_start + this.left_offset, y_center + 5, s_end - s_start, 1); + break; + case "D": // Deletion + ctx.fillStyle = "red"; + ctx.fillRect(s_start + this.left_offset, y_center + 4, s_end - s_start, 3); + break; + case "P": // TODO: No good way to draw insertions/padding right now, so ignore + case "I": + break; + } + cur_offset += cig_len; } }, draw_tile: function( resolution, tile_index, parent_element, w_scale ) { @@ -1465,6 +1500,10 @@ var FeatureTrack = function ( name, view feature_start = feature[1], feature_end = feature[2], feature_name = feature[3]; + + if (slots[feature_uid] === undefined) { + continue; + } // Apply filters to feature. var hide_feature = false; @@ -1495,18 +1534,18 @@ var FeatureTrack = function ( name, view b2_end = Math.ceil( Math.min(width, Math.max(0, (feature[6][1] - tile_low) * w_scale)) ); if (feature[5][1] >= tile_low && feature[5][0] <= tile_high) { - this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], b1_start + left_offset, b1_end - b1_start, y_center); + this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], cigar, y_center); } if (feature[6][1] >= tile_low && feature[6][0] <= tile_high) { - this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[6][0], feature[6][2], b2_start + left_offset, b2_end - b2_start, y_center); + this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[6][0], feature[6][2], cigar, y_center); } if (b2_start > b1_end) { - ctx.fillStyle = "#999"; + ctx.fillStyle = CONNECTOR_COLOR; ctx.fillRect(b1_end + left_offset, y_center + 5, b2_start - b1_end, 1); } } else { ctx.fillStyle = block_color; - this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature_start, feature_name, f_start + left_offset, f_end - f_start, y_center); + this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature_start, feature_name, cigar, y_center); } if (mode !== "Dense" && !no_detail && feature_start > tile_low) { // Draw label --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -193,20 +193,17 @@ class BamDataProvider( TracksDataProvide message = "Only the first %s pairs are being displayed." % MAX_VALS break qname = read.qname - if no_detail: - seq = len(read.seq) - else: - seq = read.seq + seq = read.seq + read_len = sum( [cig[1] for cig in read.cigar] ) # Use cigar to determine length if read.is_proper_pair: if qname in paired_pending: # one in dict is always first pair = paired_pending[qname] - results.append( [ qname, pair['start'], read.pos + read.rlen, seq, read.cigar, [pair['start'], pair['end'], pair['seq']], [read.pos, read.pos + read.rlen, seq] ] ) - # results.append( [read.qname, pair['start'], read.pos + read.rlen, qname, [pair['start'], pair['end']], [read.pos, read.pos + read.rlen] ] ) + results.append( [ qname, pair['start'], read.pos + read_len, seq, read.cigar, [pair['start'], pair['end'], pair['seq']], [read.pos, read.pos + read_len, seq] ] ) del paired_pending[qname] else: - paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read.rlen, 'seq': seq, 'mate_start': read.mpos, 'rlen': read.rlen, 'cigar': read.cigar } + paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read_len, 'seq': seq, 'mate_start': read.mpos, 'rlen': read_len, 'cigar': read.cigar } else: - results.append( [qname, read.pos, read.pos + read.rlen, seq, read.cigar] ) + results.append( [qname, read.pos, read.pos + read_len, seq, read.cigar] ) # take care of reads whose mates are out of range for qname, read in paired_pending.iteritems(): if read['mate_start'] < read['start']: --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -159,9 +159,11 @@ class TracksController( BaseController, vis = session.query( model.Visualization ).get( decoded_id ) viz_config = self.get_visualization_config( trans, vis ) - # Set config chrom. - viz_config[ 'chrom' ] = chrom - return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=kwargs.get("dataset_id", None) ) + new_dataset = kwargs.get("dataset_id", None) + if new_dataset is not None: + if trans.security.decode_id(new_dataset) in [ d["dataset_id"] for d in viz_config.get("tracks") ]: + new_dataset = None # Already in browser, so don't add + return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset ) @web.json def chroms(self, trans, vis_id=None, dbkey=None ): --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -74,7 +74,7 @@ $(function() { %if config: - view = new View( $("#center"), "${config.get('chrom')}", "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); + view = new View( $("#center"), "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); view.editor = true; %for track in config.get('tracks'): view.add_track( @@ -84,7 +84,7 @@ init(); %else: var continue_fn = function() { - view = new View( $("#center"), undefined, $("#new-title").val(), undefined, $("#new-dbkey").val() ); + view = new View( $("#center"), $("#new-title").val(), undefined, $("#new-dbkey").val() ); view.editor = true; init(); hide_modal(); --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";r ight_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_coun ter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);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_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Ove rview</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_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack (a))}a.chrom_data=d.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("drag start",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.contai ner.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.rese t();c.redraw(true);for(var g in c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.reset_overview();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remo ve()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=this.low/(this.max_high-this.max_low)*this.overview_viewport.width();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a ,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);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 Filter=function( b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=Number.MIN_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=Number.MIN_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[th is.slider_min,this.slider_max])}}});var get_filters=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,d,c){this.name=b;this.view=a;this.parent_element=d;this.filters=(c!==undefined?get_filters(c):[]);this.init_global()};$.extend(Track.prototype,{init_global:function(){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.filtering_div=$("<div class='track-filters'>").appendTo(this.container_div);this.filte ring_div.hide();this.filtering_div.bind("drag",function(k){k.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);var c=this;for(var e=0;e<this.filters.length;e++){var a=this.filters[e];var f=$("<tr>").appendTo(b);var g=$("<th class='filter-info'>").appendTo(f);var j=$("<span class='name'>").appendTo(g);j.text(a.name+" ");var d=$("<span class='values'>").appendTo(g);d.text("[0-2]");var h=$("<td>").appendTo(f);a.control_element=$("<div id='"+a.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(h);a.control_element.slider({range:true,min:0,max:1,values:[0,1],slide:function(l,m){var k=m.values;d.text("["+k[0]+"-"+k[1]+"]");a.low=k[0];a.high=k[1];c.draw(true)},change:function(k,l){a.control_element.slider("option","slide").call(a.control_element,k,l)}});a.slider=a.control_element;a.slider_label=d}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},i nit_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div. addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}};b["Edit configurat ion"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},j=function(){d.update_options(d.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){j()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:l,OK:j})};if(d.filters.length>0){b["Show filters"]=function(){var j;if(!d.filtering_div.is(":visible")){j="Hide filters";d.filters_visible=true}else{j="Show filters";d.filters_visible=false}$("#"+d.name_div.attr("id")+"-menu").find("li").eq(2).text(j);d.filtering_div.toggle()}}b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};d.popup_menu=make_popupmenu(d.name_div,b);show_hide_popupmenu_options(d.popup_menu,"(Show|Hide) filters",false)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,h=g-m,f=this.view.res olution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h,k;this.content_div.append(p),this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=new Object();while((a*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+a;var e=this.tile_cache.get(n);if(!b&&e){var j=a*DENSITY*f;var d=(j-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(this,n,m,g,a,f,p,q,l)}a+=1}var c=this;var o=setInterval(function(){if(l.length!=0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var r=0;r<c.filters.length;r++){c.filters[r].update_ui_elt()}clearInterval(o)}},50)},delayed_draw:function(c,h,g,e,b,d,j,k,f){var a=setTimeout(function(){if(!(g>c.view.high||e<c.view.low)){tile_element=c.draw_tile(d,b,j,k);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var n=tile_element.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n. getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,tile_element);c.show_tile(tile_element,j)}}delete f.id},50);f.id=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a ,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_da ta:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,l,p){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),o=e.get(0).getContext("2d"),k=f+"_"+b;if(p>PX_PER_CHAR){if(this.data_cache.get(k)===undefined){this.get_data(f,b);return}var n=this.data_cache.get(k);if(n===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*p+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*p-this.left_offset});for(var h=0,m=n.length;h<m;h++){var a=Math.round(h*p),j=Math.round(p/2);o.fillText(n[h],a+this.left_offset+j,10)}l.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=func tion(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#trac k_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;a.container_div.find(".yaxislabel").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:func tion(p,s,c,e){if(this.vertical_range===undefined){return}var t=s*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),w=p+"_"+s;if(this.data_cache.get(w)===undefined){this.get_data(p,s);return}var j=this.data_cache.get(w);if(j===null){return}b.css({position:"absolute",top:0,left:(t-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,u=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();o.fillStyle=this.prefs.color;if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var v,h;for(var q=0,r=data.length;q<r;q++){v=Math.round((data[q][0]-t)*e);h=data[q][1];if(h===null){if(k&&m==="Filled"){o.lineTo(v,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(d-(h-l)/n*d);o.fillRect(v,h,f,d-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")"; o.fillRect(v,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(v,h)}else{k=true;if(m==="Filled"){o.moveTo(v,d);o.lineTo(v,h)}else{o.moveTo(v,h)}}}}}if(m==="Filled"){if(k){o.lineTo(v,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div />").addClass("form-row");var e="track_"+n+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+n+"_minval",m=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),l=$("<input></input>").attr("id",h).val(d),k="track_"+n+"_maxval",g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j);return a.append(m).append(l).append(g).append(f).append(b).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();color=$("#track_"+ c+"_color").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value||color!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.prefs.color=color;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container,e);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE );this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};th is.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e, f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(ah,o,s,aw){var N=o*DENSITY*ah,am=(o+1)*DENSITY*ah,M=am-N;var ao=(!this.initial_canvas?"initial":N+"_"+am);var I=this.data_cache.get(ao);var e;if(I===undefined||(this.mode!=="Auto"&&I.dataset_type==="summary_tree")){this.data_queue[[N,am]]=true;this.get_data(N,am);return}var a=Math.ceil(M*aw),S=$("<canvas class='tile'></canvas>"),aj=this.prefs.label_color,l=this.prefs.block_color,r=this.mode,z=25,af=(r==="Squish")||(r==="Dense")&&(r!=="Pack")||(r==="Auto"&&(I.extra_inf o==="no_detail")),X=this.left_offset,av,D,ax;if(I.dataset_type==="summary_tree"){D=this.summary_draw_height}else{if(r==="Dense"){D=z;ax=10}else{ax=(af?this.vertical_nodetail_px:this.vertical_detail_px);var A=(aw<0.0001?1/view.zoom_res:aw);D=this.incremental_slots(A,I.data,af,r)*ax+z;av=this.inc_slots[A]}}S.css({position:"absolute",top:0,left:(N-this.view.low)*aw-X});S.get(0).width=a+X;S.get(0).height=D;s.parent().css("height",Math.max(this.height_px,D)+"px");var J=S.get(0).getContext("2d");J.fillStyle=l;J.font=this.default_font;J.textAlign="right";this.container_div.find(".yaxislabel").remove();if(I.dataset_type=="summary_tree"){var Z=I.data,L=I.max,q=I.avg,b=Math.ceil(I.delta*aw);var p=$("<div />").addClass("yaxislabel").text(L);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var aq=0,H=Z.length;aq<H;aq++){var ab=Math.floor((Z[aq][0]-N)*aw);var aa=Z[aq][1];if(!aa){continue}var an=aa/L*this.summary_draw_height;J.fillStyle="black";J.fil lRect(ab+X,this.summary_draw_height-an,b,an);if(this.prefs.show_counts&&J.measureText(aa).width<b){J.fillStyle="#bbb";J.textAlign="center";J.fillText(aa,ab+X+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(S);return S}if(I.message){S.css({border:"solid red","border-width":"2px 2px 2px 0px"});J.fillStyle="red";J.textAlign="left";J.fillText(I.message,100+X,ax)}var ae=false;if(I.data.length!=0){ae=true;for(var at=0;at<this.filters.length;at++){if(!this.filters[at].applies_to(I.data[0])){ae=false}}}if(ae){S.addClass(FILTERABLE_CLASS)}var au=I.data;var ap=0;for(var aq=0,H=au.length;aq<H;aq++){var T=au[aq],R=T[0],ar=T[1],ad=T[2],O=T[3];var ac=false;var V;for(var at=0;at<this.filters.length;at++){V=this.filters[at];V.update_attrs(T);if(!V.keep(T)){ac=true;break}}if(ac){continue}if(ar<=am&&ad>=N){var ag=Math.floor(Math.max(0,(ar-N)*aw)),K=Math.ceil(Math.min(a,Math.max(0,(ad-N)*aw))),Y=(r==="Dense"?1:(1+av[R]))*ax;if(I.dataset_type==="bai"){var v=T[4];J.fillStyle=l;if(T[5] in stanceof Array){var E=Math.floor(Math.max(0,(T[5][0]-N)*aw)),Q=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-N)*aw))),C=Math.floor(Math.max(0,(T[6][0]-N)*aw)),w=Math.ceil(Math.min(a,Math.max(0,(T[6][1]-N)*aw)));if(T[5][1]>=N&&T[5][0]<=am){this.rect_or_text(J,aw,N,am,T[5][0],T[5][2],E+X,Q-E,Y)}if(T[6][1]>=N&&T[6][0]<=am){this.rect_or_text(J,aw,N,am,T[6][0],T[6][2],C+X,w-C,Y)}if(C>Q){J.fillStyle="#999";J.fillRect(Q+X,Y+5,C-Q,1)}}else{J.fillStyle=l;this.rect_or_text(J,aw,N,am,ar,O,ag+X,K-ag,Y)}if(r!=="Dense"&&!af&&ar>N){J.fillStyle=this.prefs.label_color;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(R,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(R,ag-2+X,Y+8)}J.fillStyle=l}}else{if(I.dataset_type==="interval_index"){if(af){J.fillStyle=l;J.fillRect(ag+X,Y+5,K-ag,1)}else{var G=T[4],W=T[5],ai=T[6],h=T[7];var F,ak,P=null,ay=null;if(W&&ai){P=Math.floor(Math.max(0,(W-N)*aw));ay=Math.ceil(Math.min(a,Math.max(0,(ai-N)*aw)))}if(r!=="Dense"&&O!==undefined&&ar>N){J.fil lStyle=aj;if(o===0&&ag-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(O,ag-2+X,Y+8)}J.fillStyle=l}if(h){if(G){if(G=="+"){J.fillStyle=RIGHT_STRAND}else{if(G=="-"){J.fillStyle=LEFT_STRAND}}J.fillRect(ag+X,Y,K-ag,10);J.fillStyle=l}for(var ao=0,g=h.length;ao<g;ao++){var u=h[ao],d=Math.floor(Math.max(0,(u[0]-N)*aw)),U=Math.ceil(Math.min(a,Math.max((u[1]-N)*aw)));if(d>U){continue}F=5;ak=3;J.fillRect(d+X,Y+ak,U-d,F);if(P!==undefined&&!(d>ay||U<P)){F=9;ak=1;var al=Math.max(d,P),B=Math.min(U,ay);J.fillRect(al+X,Y+ak,B-al,F)}}}else{F=9;ak=1;J.fillRect(ag+X,Y+ak,K-ag,F);if(T.strand){if(T.strand=="+"){J.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){J.fillStyle=LEFT_STRAND_INV}}J.fillRect(ag+X,Y,K-ag,10);J.fillStyle=l}}}}else{if(I.dataset_type==="vcf"){if(af){J.fillStyle=l;J.fillRect(ag+X,Y+5,K-ag,1)}else{var t=T[4],n=T[5],c=T[6];F=9;ak=1;J.fillRect(ag+X,Y,K-ag,F);if(r!=="Dense"&&O!==undefined&&ar>N){J.fillStyle=aj;if(o===0&&a g-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+X,Y+8)}else{J.textAlign="right";J.fillText(O,ag-2+X,Y+8)}J.fillStyle=l}var m=t+" / "+n;if(ar>N&&J.measureText(m).width<(K-ag)){J.fillStyle="white";J.textAlign="center";J.fillText(m,X+ag+(K-ag)/2,Y+8);J.fillStyle=l}}}}}ap++}}return S},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_opti ons:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,e,c){FeatureTrack.call(this,d,b,a,e,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=50,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/st rand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,d,c,b){this.container=a;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_i d_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Clo se Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();r eturn false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new Referenc eTrack(a))}a.chrom_data=d.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.overview_close.bind("click",function(){for(var d in a.tracks){a.tracks[d].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind ("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.enable_pan=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.enable_pan||this.in_reordering){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a. container.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(!c.chrom){c.intro_div.show()}else{c.intro_div.hide()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.re set();c.redraw(true);for(var g in c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.reset_overview();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).re move()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=this.low/(this.max_high-this.max_low)*this.overview_viewport.width();var e=(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width();var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left :a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);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 Filter=functio n(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=Number.MIN_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=Number.MIN_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[ this.slider_min,this.slider_max])}}});var get_filters=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,d,c){this.name=b;this.view=a;this.parent_element=d;this.filters=(c!==undefined?get_filters(c):[]);this.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<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=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.filtering_div=$("<div class='track-filters'>").appendTo(this.container_div);this.fil tering_div.hide();this.filtering_div.bind("drag",function(k){k.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);var c=this;for(var e=0;e<this.filters.length;e++){var a=this.filters[e];var f=$("<tr>").appendTo(b);var g=$("<th class='filter-info'>").appendTo(f);var j=$("<span class='name'>").appendTo(g);j.text(a.name+" ");var d=$("<span class='values'>").appendTo(g);d.text("[0-2]");var h=$("<td>").appendTo(f);a.control_element=$("<div id='"+a.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(h);a.control_element.slider({range:true,min:0,max:1,values:[0,1],slide:function(l,m){var k=m.values;d.text("["+k[0]+"-"+k[1]+"]");a.low=k[0];a.high=k[1];c.draw(true)},change:function(k,l){a.control_element.slider("option","slide").call(a.control_element,k,l)}});a.slider=a.control_element;a.slider_label=d}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)} ,init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_di v.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var d=this,c=d.view;if(d.hidden){return}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var h=d.display_modes[0];d.mode=h;d.mode_div.text(h);var a=function(j){d.mode_div.text(j);d.mode=j;d.tile_cache.clear();d.draw()};var f={};for(var e in d.display_modes){var g=d.display_modes[e];f[g]=function(j){return function(){a(j)}}(g)}make_popupmenu(d.mode_div,f)}else{d.mode_div.hide()}}var b={};b["Set as overview"]=function(){c.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var j in c.tracks){if(c.tracks[j]!==d){c.tracks[j].is_overview=false}}};b["Edit configur ation"]=function(){var l=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},j=function(){d.update_options(d.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},k=function(m){if((m.keyCode||m.which)===27){l()}else{if((m.keyCode||m.which)===13){j()}}};$(window).bind("keypress.check_enter_esc",k);show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:l,OK:j})};if(d.filters.length>0){b["Show filters"]=function(){var j;if(!d.filtering_div.is(":visible")){j="Hide filters";d.filters_visible=true}else{j="Show filters";d.filters_visible=false}$("#"+d.name_div.attr("id")+"-menu").find("li").eq(2).text(j);d.filtering_div.toggle()}}b.Remove=function(){c.remove_track(d);if(c.num_tracks===0){$("#no-tracks").show()}};d.popup_menu=make_popupmenu(d.name_div,b);show_hide_popupmenu_options(d.popup_menu,"(Show|Hide) filters",false)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(b){var m=this.view.low,g=this.view.high,h=g-m,f=this.view.r esolution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h,k;this.content_div.append(p),this.max_height=0;var a=Math.floor(m/f/DENSITY);var l=new Object();while((a*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+a;var e=this.tile_cache.get(n);if(!b&&e){var j=a*DENSITY*f;var d=(j-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(this,n,m,g,a,f,p,q,l)}a+=1}var c=this;var o=setInterval(function(){if(l.length!=0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var r=0;r<c.filters.length;r++){c.filters[r].update_ui_elt()}clearInterval(o)}},50)},delayed_draw:function(c,h,g,e,b,d,j,k,f){var a=setTimeout(function(){if(!(g>c.view.high||e<c.view.low)){tile_element=c.draw_tile(d,b,j,k);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var n=tile_element.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m= n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,tile_element);c.show_tile(tile_element,j)}}delete f.id},50);f.id=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null ,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_ data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,l,p){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),o=e.get(0).getContext("2d"),k=f+"_"+b;if(p>PX_PER_CHAR){if(this.data_cache.get(k)===undefined){this.get_data(f,b);return}var n=this.data_cache.get(k);if(n===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*p+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*p-this.left_offset});for(var h=0,m=n.length;h<m;h++){var a=Math.round(h*p),j=Math.round(p/2);o.fillText(n[h],a+this.left_offset+j,10)}l.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=fu nction(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#tr ack_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;a.container_div.find(".yaxislabel").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"22px",left:"10px"});d.prependTo(a.container_div);e.css({position:"absolute",top:a.height_px+11+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:fu nction(p,s,c,e){if(this.vertical_range===undefined){return}var t=s*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),w=p+"_"+s;if(this.data_cache.get(w)===undefined){this.get_data(p,s);return}var j=this.data_cache.get(w);if(j===null){return}b.css({position:"absolute",top:0,left:(t-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,u=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();o.fillStyle=this.prefs.color;if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var v,h;for(var q=0,r=data.length;q<r;q++){v=Math.round((data[q][0]-t)*e);h=data[q][1];if(h===null){if(k&&m==="Filled"){o.lineTo(v,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(d-(h-l)/n*d);o.fillRect(v,h,f,d-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+") ";o.fillRect(v,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(v,h)}else{k=true;if(m==="Filled"){o.moveTo(v,d);o.lineTo(v,h)}else{o.moveTo(v,h)}}}}}if(m==="Filled"){if(k){o.lineTo(v,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div />").addClass("form-row");var e="track_"+n+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+n+"_minval",m=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),l=$("<input></input>").attr("id",h).val(d),k="track_"+n+"_maxval",g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j);return a.append(m).append(l).append(g).append(f).append(b).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();color=$("#track_ "+c+"_color").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value||color!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.prefs.color=color;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,e,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container,e);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATU RE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};t his.inc_slots[a].w_scale=a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(v<=MAX_FEATURE_DEPTH){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_ti le[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(r,m,s,b,q,f,h,e){r.textAlign="center";var l=0,p=Math.round(m/2);for(cig_id in h){var k=h[cig_id],d="MIDNSHP"[k[0]],n=k[1];if(d==="H"||d==="S"){l-=n}var g=q+l,v=Math.floor(Math.max(0,(g-s)*m)),j=Math.floor(Math.max(0,(g+n-s)*m));switch(d){case"S":case"H":case"M":var o=f.slice(l,n);if((this.mode==="Pack"||this.mode==="Auto")&&f!==undefined&&m>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(v+this.left_offset,e+1,j-v,9);r.fillStyle=CONNECTOR_COLOR;for(var t=0,a=o.length;t<a;t++){if(g+t>=s&&g+t<=b){var u=Math.floor(Math.max(0,(g+t-s)*m));r.fillText(o[t],u+this.left_offset+p,e+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(v+this.left_offset,e+4,j-v,3)}break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(v+this.left_offset,e+5,j-v,1);break;case"D":r.fillStyle="red";r.fillRect(v+this.left_offset,e+4,j-v,3);break;case"P":case"I":break}l+=n}},draw_tile:function( ah,o,s,aw){var N=o*DENSITY*ah,am=(o+1)*DENSITY*ah,M=am-N;var ao=(!this.initial_canvas?"initial":N+"_"+am);var I=this.data_cache.get(ao);var e;if(I===undefined||(this.mode!=="Auto"&&I.dataset_type==="summary_tree")){this.data_queue[[N,am]]=true;this.get_data(N,am);return}var a=Math.ceil(M*aw),S=$("<canvas class='tile'></canvas>"),aj=this.prefs.label_color,l=this.prefs.block_color,r=this.mode,z=25,af=(r==="Squish")||(r==="Dense")&&(r!=="Pack")||(r==="Auto"&&(I.extra_info==="no_detail")),X=this.left_offset,av,D,ax;if(I.dataset_type==="summary_tree"){D=this.summary_draw_height}else{if(r==="Dense"){D=z;ax=10}else{ax=(af?this.vertical_nodetail_px:this.vertical_detail_px);var A=(aw<0.0001?1/view.zoom_res:aw);D=this.incremental_slots(A,I.data,af,r)*ax+z;av=this.inc_slots[A]}}S.css({position:"absolute",top:0,left:(N-this.view.low)*aw-X});S.get(0).width=a+X;S.get(0).height=D;s.parent().css("height",Math.max(this.height_px,D)+"px");var J=S.get(0).getContext("2d");J.fillStyle=l;J.font=t his.default_font;J.textAlign="right";this.container_div.find(".yaxislabel").remove();if(I.dataset_type=="summary_tree"){var Z=I.data,L=I.max,q=I.avg,b=Math.ceil(I.delta*aw);var p=$("<div />").addClass("yaxislabel").text(L);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var aq=0,H=Z.length;aq<H;aq++){var ab=Math.floor((Z[aq][0]-N)*aw);var aa=Z[aq][1];if(!aa){continue}var an=aa/L*this.summary_draw_height;J.fillStyle="black";J.fillRect(ab+X,this.summary_draw_height-an,b,an);if(this.prefs.show_counts&&J.measureText(aa).width<b){J.fillStyle="#bbb";J.textAlign="center";J.fillText(aa,ab+X+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(S);return S}if(I.message){S.css({border:"solid red","border-width":"2px 2px 2px 0px"});J.fillStyle="red";J.textAlign="left";J.fillText(I.message,100+X,ax)}var ae=false;if(I.data.length!=0){ae=true;for(var at=0;at<this.filters.length;at++){if(!this.filters[at].applies_to(I.data[0])){ae=false}}}if(ae){S. addClass(FILTERABLE_CLASS)}var au=I.data;var ap=0;for(var aq=0,H=au.length;aq<H;aq++){var T=au[aq],R=T[0],ar=T[1],ad=T[2],O=T[3];if(av[R]===undefined){continue}var ac=false;var V;for(var at=0;at<this.filters.length;at++){V=this.filters[at];V.update_attrs(T);if(!V.keep(T)){ac=true;break}}if(ac){continue}if(ar<=am&&ad>=N){var ag=Math.floor(Math.max(0,(ar-N)*aw)),K=Math.ceil(Math.min(a,Math.max(0,(ad-N)*aw))),Y=(r==="Dense"?1:(1+av[R]))*ax;if(I.dataset_type==="bai"){var v=T[4];J.fillStyle=l;if(T[5] instanceof Array){var E=Math.floor(Math.max(0,(T[5][0]-N)*aw)),Q=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-N)*aw))),C=Math.floor(Math.max(0,(T[6][0]-N)*aw)),w=Math.ceil(Math.min(a,Math.max(0,(T[6][1]-N)*aw)));if(T[5][1]>=N&&T[5][0]<=am){this.rect_or_text(J,aw,N,am,T[5][0],T[5][2],v,Y)}if(T[6][1]>=N&&T[6][0]<=am){this.rect_or_text(J,aw,N,am,T[6][0],T[6][2],v,Y)}if(C>Q){J.fillStyle=CONNECTOR_COLOR;J.fillRect(Q+X,Y+5,C-Q,1)}}else{J.fillStyle=l;this.rect_or_text(J,aw,N,am,ar,O,v,Y)}if(r!= 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is.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,e,c){FeatureTrack.call(this,d,b,a,e,c);this.track_type="ReadTrack";this.vert ical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});

1 0

galaxy-dist commit 6372b67c9e37: mutation viz tool test data files
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287517282 14400 # Node ID 6372b67c9e370b3a80159bcc719e13d50ddc018f # Parent e029c860e71710d69f725e5c136b7e55fa529a42 mutation viz tool test data files --- /dev/null +++ b/test-data/mutation_data1_zoom3x.svg @@ -0,0 +1,639 @@ +<?xml version="1.0" standalone="no"?> +<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"> + +<svg style="stroke-linejoin:round; stroke:black; stroke-width:0.5pt; text-anchor:middle; fill:none" xmlns="http://www.w3.org/2000/svg" font-family="Helvetica, Arial, FreeSans, Sans, sans, sans-serif" height="1980px" width="208px" version="1.1" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 116 496"> + +<g id="viewport"> + +<text y="4" x="12" stroke="none" fill="black"><tspan style="font-family:Verdana;font-size:20%">A</tspan></text> + +<rect fill-opacity="0.5" height="3" width="4" 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wheel) + * - Object dargging + * + * Known issues: + * + * - Zooming (while panning) on Safari has still some issues + * + * Releases: + * + * 1.2, Sat Mar 20 08:42:50 GMT 2010, Zeng Xiaohui + * Fixed a bug with browser mouse handler interaction + * + * 1.1, Wed Feb 3 17:39:33 GMT 2010, Zeng Xiaohui + * Updated the zoom code to support the mouse wheel on Safari/Chrome + * + * 1.0, Andrea Leofreddi + * First release + * + * This code is licensed under the following BSD license: + * + * Copyright 2009-2010 Andrea Leofreddi (a.leofreddi(a)itcharm.com) All rights reserved. + * + * Redistribution and use in source and binary forms, with or without modification, are + * permitted provided that the following conditions are met: + * + * 1. Redistributions of source code must retain the above copyright notice, this list of + * conditions and the following disclaimer. + * + * 2. Redistributions in binary form must reproduce the above copyright notice, this list + * of conditions and the following disclaimer in the documentation and/or other materials + * provided with the distribution. + * + * THIS SOFTWARE IS PROVIDED BY Andrea Leofreddi ``AS IS'' AND ANY EXPRESS OR IMPLIED + * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND + * FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL Andrea Leofreddi OR + * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR + * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON + * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING + * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF + * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * The views and conclusions contained in the software and documentation are those of the + * authors and should not be interpreted as representing official policies, either expressed + * or implied, of Andrea Leofreddi. + */ + +var root = document.documentElement; + +var state = 'none', stateTarget, stateOrigin, stateTf; + +setupHandlers(root); + +/** + * Register handlers + */ +function setupHandlers(root){ + setAttributes(root, { + "onmouseup" : "add(evt)", + "onmousedown" : "handleMouseDown(evt)", + "onmousemove" : "handleMouseMove(evt)", + "onmouseup" : "handleMouseUp(evt)", + //"onmouseout" : "handleMouseUp(evt)", // Decomment this to stop the pan functionality when dragging out of the SVG element + }); + + if(navigator.userAgent.toLowerCase().indexOf('webkit') >= 0) + window.addEventListener('mousewheel', handleMouseWheel, false); // Chrome/Safari + else + window.addEventListener('DOMMouseScroll', handleMouseWheel, false); // Others +} + +/** + * Instance an SVGPoint object with given event coordinates. + */ +function getEventPoint(evt) { + var p = root.createSVGPoint(); + + p.x = evt.clientX; + p.y = evt.clientY; + + return p; +} + +/** + * Sets the current transform matrix of an element. + */ +function setCTM(element, matrix) { + var s = "matrix(" + matrix.a + "," + matrix.b + "," + matrix.c + "," + matrix.d + "," + matrix.e + "," + matrix.f + ")"; + + element.setAttribute("transform", s); +} + +/** + * Dumps a matrix to a string (useful for debug). + */ +function dumpMatrix(matrix) { + var s = "[ " + matrix.a + ", " + matrix.c + ", " + matrix.e + "\n " + matrix.b + ", " + matrix.d + ", " + matrix.f + "\n 0, 0, 1 ]"; + + return s; +} + +/** + * Sets attributes of an element. + */ +function setAttributes(element, attributes){ + for (i in attributes) + element.setAttributeNS(null, i, attributes[i]); +} + +/** + * Handle mouse move event. + */ +function handleMouseWheel(evt) { + if(evt.preventDefault) + evt.preventDefault(); + + evt.returnValue = false; + + var svgDoc = evt.target.ownerDocument; + + var delta; + + if(evt.wheelDelta) + delta = evt.wheelDelta / 3600; // Chrome/Safari + else + delta = evt.detail / -90; // Mozilla + + var z = 1 + delta; // Zoom factor: 0.9/1.1 + + var g = svgDoc.getElementById("viewport"); + + var p = getEventPoint(evt); + + p = p.matrixTransform(g.getCTM().inverse()); + + // Compute new scale matrix in current mouse position + var k = root.createSVGMatrix().translate(p.x, p.y).scale(z).translate(-p.x, -p.y); + + setCTM(g, g.getCTM().multiply(k)); + + stateTf = stateTf.multiply(k.inverse()); +} + +/** + * Handle mouse move event. + */ +function handleMouseMove(evt) { + if(evt.preventDefault) + evt.preventDefault(); + + evt.returnValue = false; + + var svgDoc = evt.target.ownerDocument; + + var g = svgDoc.getElementById("viewport"); + + if(state == 'pan') { + // Pan mode + var p = getEventPoint(evt).matrixTransform(stateTf); + + setCTM(g, stateTf.inverse().translate(p.x - stateOrigin.x, p.y - stateOrigin.y)); + } else if(state == 'move') { + // Move mode + var p = getEventPoint(evt).matrixTransform(g.getCTM().inverse()); + + setCTM(stateTarget, root.createSVGMatrix().translate(p.x - stateOrigin.x, p.y - stateOrigin.y).multiply(g.getCTM().inverse()).multiply(stateTarget.getCTM())); + + stateOrigin = p; + } +} + +/** + * Handle click event. + */ +function handleMouseDown(evt) { + if(evt.preventDefault) + evt.preventDefault(); + + evt.returnValue = false; + 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1 0

galaxy-dist commit ad9bb65d2d15: mutation viz tool help cleanup
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287520820 14400 # Node ID ad9bb65d2d153af5db0ae497930eb35d17f63057 # Parent 35b379691524c768ec84f86477f1ab49859afec2 mutation viz tool help cleanup --- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -20,7 +20,7 @@ <repeat name="sample_chooser" title="Sample"><param name="name" type="text" label="Label" help="Optional" /> - <param name="a_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="A Column" help="" /> + <param name="a_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Base A Column" help="" /><param name="totals_col" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Totals Column" help="" /></repeat> @@ -60,27 +60,42 @@ </test></tests><help> - -**Example** +**What it does** This tool allows you to visualize mutations described in a tabular input file. It generates an SVG image which can be viewed in any web browser. +You will need to specify the position and reference columns in the input file. Then click on the 'Add new Sample' to add samples in the input file that you would like to visualize. For each sample you select, specify the column for base 'A', the totals column and enter a name. +This tool assumes the columns specifying bases A, C, G, T are placed consecutively and in that order in an input file. + +Interactivity: If interactive zoom option is selected, then the resultant image can be zoomed in or out using the scroll mouse wheel and can be panned by dragging the image using left mouse button. + +----- + +**General Example** + Given the input file:: - gm blood gm cheek chrM 72 73 G 26394 4 49 0 26447 26398 1 23389 3 45 0 23437 23392 1 chrM 149 150 T 11 50422 2 96 50531 50435 1 4 45417 1 65 45487 45422 1 -You will need to specify the position and reference columns in the input file. Then click on the 'Add new Sample' to add samples in the input file that you would like to visualize. For each sample you select, specify the column for base 'A' and the totals column. -This tool assumes the columns specifying bases A, C, G, T are placed consecutively and in that order in an input file. +To visualize the two samples in the input file, the following parameters are selected before running the tool:: + + Position column: 2 + Reference Base column: 4 + Sample 1 Label: gm blood + Sample 1 Base A column: 5 + Sample 1 Totals column: 9 + Sample 2 Label: gm cheek + Sample 2 Base A column: 12 + Sample 2 Totals column: 16 -Visualization: +Visualization output: .. image:: ../static/images/mutation_visualization_example.png :width: 150 -Interactivity:: - If interactive zoom option is selected, then the resultant image can be zoomed in or out using the scroll mouse wheel and can be panned by dragging the image using left mouse button. +Here the left-most column represents the position and the background color is the reference base color. Each column on its right describe each sample. +In the output above, the blue bar is the longest, which means that base A is maximum in position 72 for both the samples. </help></tool>

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galaxy-dist commit d4b85e30e56d: sample tracking
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287147090 14400 # Node ID d4b85e30e56d605edc2236ccba5cde41bda1510a # Parent fb2a31820ccff6f02bb24a0632f214bfef0a8b0a sample tracking - create request search+select box bug fixed. - sample datasets grid operations fixed --- a/templates/requests/common/sample_datasets.mako +++ b/templates/requests/common/sample_datasets.mako @@ -1,5 +1,5 @@ <%def name="render_sample_datasets( sample )"> - ${len( sample.transferred_dataset_files )}/${len( sample.datasets )} + ${len( sample.transferred_dataset_files )} / ${len( sample.datasets )} </%def> ${render_sample_datasets( sample )} --- a/templates/requests/common/create_request.mako +++ b/templates/requests/common/create_request.mako @@ -21,7 +21,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Create a new request</div> + <div class="toolFormTitle">Create a new sequencing request</div> %if len( request_type_select_field.options ) == 1: There are no sequencer configurations available for ${trans.user.email} to create sequencing requests. %else: --- a/templates/admin/requests/get_data.mako +++ b/templates/admin/requests/get_data.mako @@ -104,7 +104,9 @@ <option value="${f}">${f}</option> %endfor </select> - <br/> + </div> + <div class="form-row"> + <div id="file_details" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div></div><div class="form-row"><input type="submit" name="select_show_datasets_button" value="Select & show datasets"/> --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -140,9 +140,20 @@ class RequestsCommon( BaseController, Us request_type = None # user_id will not be 'none' if an admin user is submitting this request on behalf of another user # and they selected that user's id from the user_id SelectField. + user_id_encoded = True user_id = params.get( 'user_id', 'none' ) if user_id != 'none': - user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) + try: + user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) + except TypeError, e: + # We must have an email address rather than an encoded user id + # This is because the galaxy.base.js creates a search+select box + # when there are more than 20 items in a selectfield + user = trans.sa_session.query( trans.model.User ) \ + .filter( trans.model.User.table.c.email==util.restore_text( user_id ) ) \ + .first() + user_id_encoded = False + elif not is_admin: user = trans.user else: @@ -152,6 +163,9 @@ class RequestsCommon( BaseController, Us if is_admin and user_id == 'none': message = 'Select the user on behalf of whom you are submitting this request.' status = 'error' + elif user is None: + message = 'Invalid user ID (%s)' % str(user_id) + status = 'error' elif not name: message = 'Enter the name of the request.' status = 'error' @@ -170,10 +184,6 @@ class RequestsCommon( BaseController, Us widgets = [] if request_type is not None or status == 'error': # Either the user selected a request_type or an error exists on the form. - if is_admin: - widgets.append( dict( label='Select user', - widget=self.__build_user_id_select_field( trans, selected_value=user_id ), - helptext='Submit the request on behalf of the selected user (Required)')) widgets.append( dict( label='Name of the Experiment', widget=TextField( 'name', 40, util.restore_text( params.get( 'name', '' ) ) ), helptext='(Required)') ) @@ -182,9 +192,20 @@ class RequestsCommon( BaseController, Us helptext='(Optional)') ) if request_type is not None: widgets += request_type.request_form.get_widgets( user, **kwd ) - # In case there is an error on the form, make sure to populate widget fields with anything the user - # may have already entered. - self.populate_widgets_from_kwd( trans, widgets, **kwd ) + # In case there is an error on the form, make sure to populate widget fields with anything the user + # may have already entered. + self.populate_widgets_from_kwd( trans, widgets, **kwd ) + if request_type is not None or status == 'error': + # Either the user selected a request_type or an error exists on the form. + if is_admin: + if not user_id_encoded: + selected_user_id = trans.security.encode_id( user.id ) + else: + selected_user_id = user_id + user_widget = dict( label='Select user', + widget=self.__build_user_id_select_field( trans, selected_value=selected_user_id ), + helptext='Submit the request on behalf of the selected user (Required)') + widgets = [ user_widget ] + widgets return trans.fill_template( '/requests/common/create_request.mako', cntrller=cntrller, request_type_select_field=request_type_select_field, @@ -873,7 +894,7 @@ class RequestsCommon( BaseController, Us # Build the library_select_field and folder_select_field for the new sample being added. library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans, user=request.user, - sample_index=sample_index, + sample_index=len( current_samples ), libraries=libraries, sample=None, library_id=library_id, --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -184,23 +184,6 @@ class RequestsAdmin( BaseController, Use **kwd ) ) # Render the list view return self.request_grid( trans, **kwd ) - @web.json - def get_file_details( self, trans, id, folder_path ): - def print_ticks( d ): - # pexpect timeout method - pass - # Avoid caching - trans.response.headers['Pragma'] = 'no-cache' - trans.response.headers['Expires'] = '0' - request = trans.sa_session.query( trans.model.Request ).get( int( id ) ) - datatx_info = request.type.datatx_info - cmd = 'ssh %s@%s "ls -oghp \'%s\'"' % ( datatx_info['username'], - datatx_info['host'], - folder_path ) - output = pexpect.run( cmd, - events={ '.ssword:*' : datatx_info[ 'password'] + '\r\n', pexpect.TIMEOUT : print_ticks }, - timeout=10 ) - return unicode( output.replace( '\n', '<br/>' ) ) @web.expose @web.require_admin def reject( self, trans, **kwd ): @@ -244,11 +227,6 @@ class RequestsAdmin( BaseController, Use params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - sample_id = params.get( 'sample_id', None ) - try: - sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id ( sample_id ) ) - except: - return invalid_id_redirect( trans, 'requests_admin', sample_id ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() sample_dataset_id = params.get( 'id', None ) @@ -268,7 +246,9 @@ class RequestsAdmin( BaseController, Use not_deleted = [] for sample_dataset in selected_sample_datasets: # Make sure the dataset has been transferred before deleting it. - if sample_dataset in sample.untransferred_dataset_files: + if sample_dataset in sample_dataset.sample.untransferred_dataset_files: + # save the sample to which these datasets belong to + sample = sample_dataset.sample trans.sa_session.delete( sample_dataset ) trans.sa_session.flush() else: @@ -279,7 +259,7 @@ class RequestsAdmin( BaseController, Use message = message + ' %s could not be deleted because their transfer status is not "Not Started". ' % str( not_deleted ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', - sample_id=sample_id, + sample_id=trans.security.encode_id( sample.id ), status=status, message=message ) ) elif operation == "rename": @@ -288,7 +268,7 @@ class RequestsAdmin( BaseController, Use # has not yet been transferred. no_datasets_transferred = True for selected_sample_dataset in selected_sample_datasets: - if selected_sample_dataset in sample.untransferred_dataset_files: + if selected_sample_dataset in selected_sample_dataset.sample.untransferred_dataset_files: no_datasets_transferred = False break if no_datasets_transferred: @@ -296,15 +276,20 @@ class RequestsAdmin( BaseController, Use message = 'A dataset can be renamed only if it is in the "Not Started" state.' return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', - sample_id=sample_id, + sample_id=trans.security.encode_id( selected_sample_datasets[0].sample.id ), status=status, message=message ) ) return trans.fill_template( '/admin/requests/rename_datasets.mako', - sample=sample, + sample=selected_sample_datasets[0].sample, id_list=id_list ) elif operation == "start transfer": - self.__start_datatx( trans, sample, selected_sample_datasets ) + self.__start_datatx( trans, selected_sample_datasets[0].sample, selected_sample_datasets ) # Render the grid view + sample_id = params.get( 'sample_id', None ) + try: + sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id ( sample_id ) ) + except: + return invalid_id_redirect( trans, 'requests_admin', sample_id ) request_id = trans.security.encode_id( sample.request.id ) library_id = trans.security.encode_id( sample.library.id ) self.datatx_grid.title = 'Datasets of sample "%s"' % sample.name @@ -395,6 +380,10 @@ class RequestsAdmin( BaseController, Use if folder_path[-1] == os.sep: folder_path = os.path.dirname( folder_path[:-1] ) folder_path = self.__check_path( folder_path ) + elif params.get( 'open_folder', False ): + if len(selected_files) == 1: + folder_path = os.path.join(folder_path, selected_files[0]) + folder_path = self.__check_path( folder_path ) elif params.get( 'select_show_datasets_button', False ) or params.get( 'select_more_button', False ): # get the sample these datasets are associated with try: @@ -443,8 +432,26 @@ class RequestsAdmin( BaseController, Use status=status, message=message ) @web.json + def get_file_details( self, trans, id, folder_path ): + def print_ticks( d ): + # pexpect timeout method + pass + # Avoid caching + trans.response.headers['Pragma'] = 'no-cache' + trans.response.headers['Expires'] = '0' + request = trans.sa_session.query( trans.model.Request ).get( int( id ) ) + datatx_info = request.type.datatx_info + cmd = 'ssh %s@%s "ls -oghp \'%s\'"' % ( datatx_info['username'], + datatx_info['host'], + folder_path ) + output = pexpect.run( cmd, + events={ '.ssword:*' : datatx_info[ 'password'] + '\r\n', pexpect.TIMEOUT : print_ticks }, + timeout=10 ) + return unicode( output.replace( '\n', '<br/>' ) ) + @web.json def open_folder( self, trans, id, folder_path ): def print_ticks( d ): + # pexpect timeout method pass # Avoid caching trans.response.headers['Pragma'] = 'no-cache' --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -340,8 +340,7 @@ class UsesFormDefinitionWidgets: widget_dict[ 'widget' ] = widget else: # An existing address object was selected - address_obj = trans.sa_session.query( trans.app.model.UserAddress ).get( int( value ) ) - widget_dict[ 'widget' ] = address_obj + widget_dict[ 'widget' ] = widget # Populate the AddressField params with the form field contents widget_params_dict = {} for field_name, label, help_text in widget.fields():

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