Mercurial > repos > iuc > recentrifuge
view test-data/centrifuge_test/test4_tsv.html @ 2:824497684a1f draft
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit e2468398e4a098eb781cc3e3935bb2c8e74c270a
| author | iuc |
|---|---|
| date | Mon, 31 Oct 2022 18:18:11 +0000 |
| parents | fe733f05c2f8 |
| children | 12f0968f171c |
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rel="stylesheet" href="https://fonts.googleapis.com/css?family=Ubuntu"><script id="notfound">window.onload=function(){document.body.innerHTML=""}</script><script language="javascript" type="text/javascript">{//---------------------------------------------------------------------------- // // PURPOSE // // Krona is a flexible tool for exploring the relative proportions of // hierarchical data, such as metagenomic classifications, using a // radial, space-filling display. It is implemented using HTML5 and // JavaScript, allowing charts to be explored locally or served over the // Internet, requiring only a current version of any major web // browser. Krona charts can be created using an Excel template or from // common bioinformatic formats using the provided conversion scripts. // // // COPYRIGHT LICENSE // // Copyright (c) 2011, Battelle National Biodefense Institute (BNBI); // all rights reserved. Authored by: Brian Ondov, Nicholas Bergman, and // Adam Phillippy // // This Software was prepared for the Department of Homeland Security // (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as // part of contract HSHQDC-07-C-00020 to manage and operate the National // Biodefense Analysis and Countermeasures Center (NBACC), a Federally // Funded Research and Development Center. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions and the following disclaimer. // // * 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. // // * Neither the name of the Battelle National Biodefense Institute nor // the names of its contributors may be used to endorse or promote // products derived from this software without specific prior written // permission. // // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS // "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 THE COPYRIGHT // HOLDER 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. // // // TRADEMARK LICENSE // // KRONA(TM) is a trademark of the Department of Homeland Security, and use // of the trademark is subject to the following conditions: // // * Distribution of the unchanged, official code/software using the // KRONA(TM) mark is hereby permitted by the Department of Homeland // Security, provided that the software is distributed without charge // and modification. // // * Distribution of altered source code/software using the KRONA(TM) mark // is not permitted unless written permission has been granted by the // Department of Homeland Security. // // // FOR MORE INFORMATION VISIT // // https://github.com/marbl/Krona/wiki/ // //---------------------------------------------------------------------------- // // Copyright (C) 2017-2022 Jose Manuel Martí Martínez, for the changes in // this file from the Krona Javascript 2.0 release. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the above copyright notice is // reproduced and all the above conditions are met. // // The KRONA(TM) mark has been substituted in the generated charts by // another logo in compliance with the above-stated conditions. // // FOR MORE INFORMATION VISIT // // https://github.com/khyox/recentrifuge/wiki/ // //---------------------------------------------------------------------------- } /////////////// // Variables // /////////////// var canvas; var canvasButtons = []; // Keep trace of CanvasButton objects var ChartEnum = Object.freeze({ TAXOMIC: 'taxonomic', GENOMIC: 'genomic' }) var chart = ChartEnum.TAXOMIC var context; var svg; // for snapshot mode var collapse = true; var collapseCheckBox; var collapseLast; var compress; var compressCheckBox; var maxAbsoluteDepthText; var maxAbsoluteDepthButtonDecrease; var maxAbsoluteDepthButtonIncrease; var fontSize = 12; var fontSizeText; var fontSizeButtonDecrease; var fontSizeButtonIncrease; var fontSizeLast; var bkgBright = "eeeeee"; var bkgBrightButtonDecrease; var bkgBrightButtonIncrease; var radiusButtonDecrease; var radiusButtonIncrease; var shorten; var shortenCheckBox; var maxAbsoluteDepth; var backButton; var upButton; var forwardButton; var snapshotButton; var snapshotMode = false; var details; var detailsName; var search; var searchResults; var nSearchResults; var useHueCheckBox; var useHueDiv; var sortByScoreCheckBox; var datasetDropDown; var datasetButtonLast; var datasetButtonPrev; var datasetButtonNext; var rankDropDown; var keyControl; var showKeys = true; var linkButton; var linkText; var frame; // Node references. Note that the meanings of 'selected' and 'focused' are // swapped in the docs. // var head; // the root of the entire tree var selectedNode = 0; // the root of the current view var focusNode = 0; // a node chosen for more info (single-click) var highlightedNode = 0; // mouse hover node var highlightingHidden = false; var nodes = new Array(); // Array with all the nodes var nodesIndex; // Index of nodes, points last using hue(score) buttons var currentNodeID = 0; // to iterate while loading var nodeHistory = new Array(); var nodeHistoryPosition = 0; var dataEnabled = false; // true when supplemental files are present // store non-Krona GET variables so they can be passed on to links // var getVariables = new Array(); // selectedNodeLast is separate from the history, since we need to check // properties of the last node viewed when browsing through the history // var selectedNodeLast = 0; var zoomOut = false; // temporary zoom-in while holding the mouse button on a wedge // var quickLook = false; // true when in quick look state var mouseDown = false; var mouseDownTime; // to detect mouse button hold var quickLookHoldLength = 200; var imageWidth; var imageHeight; var centerX; var centerY; var gRadius; var updateViewNeeded = false; // Determines the angle that the pie chart starts at. 90 degrees makes the // center label consistent with the children. // var rotationOffset = Math.PI / 2; var buffer; var bufferFactor = .1; // The maps are the small pie charts showing the current slice being viewed. // var mapBuffer = 10; var mapRadius = 0; var maxMapRadius = 25; var mapWidth = 150; var maxLabelOverhang = Math.PI * 4.18; // Keys are the labeled boxes for slices in the highest level that are too thin // to label. // var maxKeySizeFactor = 2; // will be multiplied by font size var keySize; var keys; var keyBuffer = 10; var currentKey; var keyMinTextLeft; var keyMinAngle; var minRingWidthFactor = 5; // will be multiplied by font size var maxPossibleDepth; // the theoretical max that can be displayed var maxDisplayDepth; // the actual depth that will be displayed var headerHeight = 0;//document.getElementById('options').clientHeight; var historySpacingFactor = 1.6; // will be multiplied by font size var historyAlphaDelta = .25; // appearance // var lineOpacity = 0.3; var saturation = 0.5; var lightnessBase = 0.6; var lightnessMax = .8; var thinLineWidth = .3; var highlightLineWidth = 1.5; var labelBoxBuffer = 6; var labelBoxRounding = 15; var labelWidthFudge = 1.05; // The width of unshortened labels are set slightly // longer than the name width so the animation // finishes faster. var fontNormal; var fontBold; var fontFamily = 'sans-serif'; //var fontFaceBold = 'bold Arial'; var nodeRadius; var angleFactor; var tickLength; var compressedRadii; // colors // var highlightFill = 'rgba(255, 255, 255, .3)'; var colorUnclassified = 'rgb(220,220,220)'; // label staggering // var labelOffsets; // will store the current offset at each depth // // This will store pointers to the last node that had a label in each offset // (or "track") of each depth. These will be used to shorten neighboring // labels that would overlap. The [nLabelNodes] index will store the last node // with a radial label. labelFirstNodes is the same, but to check for going all // the way around and overlapping the first labels. // var labelLastNodes; var labelFirstNodes; // var nLabelOffsets = 3; // the number of offsets to use var mouseX = -1; var mouseY = -1; var mouseXRel = -1; var mouseYRel = -1; // tweening // var progress = 0; // for tweening; goes from 0 to 1. var progressLast = 0; var tweenFactor = 0; // progress converted by a curve for a smoother effect. var tweenLength = 850; // in ms var tweenCurvature = 13; // // tweenMax is used to scale the sigmoid function so its range is [0,1] for the // domain [0,1] // var tweenMax = 1 / (1 + Math.exp(-tweenCurvature / 2)); // var tweenStartTime; // for framerate debug // var tweenFrames = 0; var fpsDisplay = document.getElementById('frameRate'); // Arrays to translate xml attribute names into displayable attribute names // var attributes = []; // var magnitudeIndex; // the index of attribute arrays used for magnitude var membersAssignedIndex; var membersSummaryIndex; // For defining gradients // var hueDisplayName; var hueStopPositions; var hueStopHues; var hueStopText; // multiple datasets // const DEFAULT_RANK = 'SUMMARY'; const NO_RANK = 'NONE'; var currentRank = DEFAULT_RANK; var currentDataset = 0; var lastDataset = 0; var datasets = 1; var datasetNames; const DATASET_MAX_SIZE = 20; // Max size in rows of the dataset selection list var datasetsVisible = 1; // Number of datasets not hidden var datasetAlpha = new Tween(0, 0); var datasetWidths = []; var datasetChanged; var datasetSelectWidth = 50; var numRawSamples; var stats; window.onload = load; var image; var hiddenPattern; var loadingImage; var logoImage; // Setup CSS-like style of tooltips for attributes // var csstring = '.CellWithTooltip{ position:relative; }\n' + '.Tooltip{ display:none;position:absolute;z-index:100;border:2px;' + 'background-color:white;border-style:solid;border-width:2px;' + 'border-color:red;padding:3px;color:red;top:20px;left:0px; }' + '.CellWithTooltip:hover span.Tooltip{ display:block; }'; var style = document.createElement('style'); if (style.styleSheet) { style.styleSheet.cssText = csstring; } else { style.appendChild(document.createTextNode(csstring)); } document.getElementsByTagName('head')[0].appendChild(style); /////////////// // Functions // /////////////// function backingScale() { if ('devicePixelRatio' in window) { if (window.devicePixelRatio > 1) { return window.devicePixelRatio; } } return 1; } function resize() { imageWidth = window.innerWidth; imageHeight = window.innerHeight; if (!snapshotMode) { context.canvas.width = imageWidth * backingScale(); context.canvas.height = imageHeight * backingScale(); context.canvas.style.width = imageWidth + "px" context.canvas.style.height = imageHeight + "px" context.scale(backingScale(), backingScale()); } if (datasetDropDown) { var ratio = (datasetDropDown.offsetTop + datasetDropDown.clientHeight) * 2 / imageHeight; if (ratio > 1) { ratio = 1; } ratio = Math.sqrt(ratio); datasetSelectWidth = (datasetDropDown.offsetLeft + datasetDropDown.clientWidth) * ratio; } var leftMargin = datasets > 1 ? datasetSelectWidth + 30 : 0; var minDimension = imageWidth - mapWidth - leftMargin > imageHeight ? imageHeight : imageWidth - mapWidth - leftMargin; maxMapRadius = minDimension * .03; buffer = minDimension * bufferFactor; margin = minDimension * .015; centerX = (imageWidth - mapWidth - leftMargin) / 2 + leftMargin; centerY = imageHeight / 2; gRadius = minDimension / 2 - buffer; //context.font = '11px sans-serif'; } function handleResize() { updateViewNeeded = true; } function Attribute() { } function SampleStats(sample, ictrl, sread, sclas, sfilt, scmin, scavg, scmax, lnmin, lnavg, lnmax, tclas, tfilt, tfold) { // Class to store the statistics of a sample this.sample = sample; this.is_ctrl = (ictrl === 'True'); this.sread = sread; this.sclas = sclas; this.sfilt = sfilt; this.scmin = scmin; this.scavg = scavg; this.scmax = scmax; this.lnmin = lnmin; this.lnavg = lnavg; this.lnmax = lnmax; this.tclas = tclas; this.tfilt = tfilt; this.tfold = tfold; } function CanvasButton(name, x, y, w, h, fill) { // Constructor for a button in the canvas this.name = name; this.x = x || 0; this.y = y || 0; this.w = w || 1; this.h = h || 1; this.fill = fill || '#000000'; // Draws the button to a given context this.draw = function (ctx) { var oldAlpha = ctx.globalAlpha ctx.globalAlpha = 1; ctx.strokeStyle = '#' + bkgBright; ctx.lineWidth = 3; ctx.strokeRect(this.x, this.y, this.w, this.h); ctx.fillStyle = this.fill; ctx.fillRect(this.x, this.y, this.w, this.h); ctx.strokeStyle = '#000000'; ctx.lineWidth = 0.5; ctx.strokeRect(this.x, this.y, this.w, this.h); // Draws symbols in buttons ctx.fillStyle = '#000000'; ctx.globalAlpha = 0.7; switch (this.name) { case 'mostScore': ctx.beginPath(); ctx.moveTo(this.x + 1 * this.w / 2, this.y + this.h / 8); ctx.lineTo(this.x + 1 * this.w / 6, this.y + this.h / 2); ctx.lineTo(this.x + 5 * this.w / 6, this.y + this.h / 2); ctx.fill(); case 'moreScore': ctx.beginPath(); ctx.moveTo(this.x + 1 * this.w / 2, this.y + 1 * this.h / 4); ctx.lineTo(this.x + 1 * this.w / 6, this.y + 3 * this.h / 4); ctx.lineTo(this.x + 5 * this.w / 6, this.y + 3 * this.h / 4); ctx.fill(); break; case 'lestScore': ctx.beginPath(); ctx.moveTo(this.x + 1 * this.w / 2, this.y + 7 * this.h / 8); ctx.lineTo(this.x + 1 * this.w / 6, this.y + 1 * this.h / 2); ctx.lineTo(this.x + 5 * this.w / 6, this.y + 1 * this.h / 2); ctx.fill(); case 'lessScore': ctx.beginPath(); ctx.moveTo(this.x + 1 * this.w / 2, this.y + 3 * this.h / 4); ctx.lineTo(this.x + 1 * this.w / 6, this.y + 1 * this.h / 4); ctx.lineTo(this.x + 5 * this.w / 6, this.y + 1 * this.h / 4); ctx.fill(); break; } ctx.globalAlpha = oldAlpha }; // Determine if a point is inside the button's bounds this.is_inside = function (mx, my) { // Check the Mouse X,Y fall in the button's area return (this.x <= mx) && (this.x + this.w >= mx) && (this.y <= my) && (this.y + this.h >= my); } } function Tween(start, end) { this.start = start; this.end = end; this.current = this.start; this.current = function () { if (progress == 1 || this.start == this.end) { return this.end; } else { return this.start + tweenFactor * (this.end - this.start); } }; this.setTarget = function (target) { this.start = this.current(); this.end = target; } } function Node() { this.id = currentNodeID; currentNodeID++; nodes[this.id] = this; this.angleStart = new Tween(Math.PI, 0); this.angleEnd = new Tween(Math.PI, 0); this.radiusInner = new Tween(1, 1); this.labelRadius = new Tween(1, 1); this.labelWidth = new Tween(0, 0); this.scale = new Tween(1, 1); // TEMP this.radiusOuter = new Tween(1, 1); this.r = new Tween(255, 255); this.g = new Tween(255, 255); this.b = new Tween(255, 255); this.alphaLabel = new Tween(0, 1); this.alphaLine = new Tween(0, 1); this.alphaArc = new Tween(0, 0); this.alphaWedge = new Tween(0, 1); this.alphaOther = new Tween(0, 1); this.alphaPattern = new Tween(0, 0); this.children = Array(); this.parent = 0; this.attributes = new Array(attributes.length); this.addChild = function (child) { this.children.push(child); }; this.addLabelNode = function (depth, labelOffset) { if (labelHeadNodes[depth][labelOffset] == 0) { // this will become the head node for this list labelHeadNodes[depth][labelOffset] = this; this.labelPrev = this; } var head = labelHeadNodes[depth][labelOffset]; this.labelNext = head; this.labelPrev = head.labelPrev; head.labelPrev.labelNext = this; head.labelPrev = this; } this.canDisplayDepth = function () { // whether this node is at a depth that can be displayed, according // to the max absolute depth return this.depth <= maxAbsoluteDepth; } this.canDisplayHistory = function () { var radiusInner; if (compress) { radiusInner = compressedRadii[0]; } else { radiusInner = nodeRadius; } return ( -this.labelRadius.end * gRadius + historySpacingFactor * fontSize / 2 < radiusInner * gRadius ); } this.canDisplayLabelCurrent = function () { return ( (this.angleEnd.current() - this.angleStart.current()) * (this.radiusInner.current() * gRadius + gRadius) >= minWidth()); } this.checkHighlight = function () { if (this.children.length == 0 && this == focusNode) { //return false; } if (this.hide) { return false; } if (this.radiusInner.end == 1) { // compressed to the outside; don't check return false; } var highlighted = false; var angleStartCurrent = this.angleStart.current() + rotationOffset; var angleEndCurrent = this.angleEnd.current() + rotationOffset; var radiusInner = this.radiusInner.current() * gRadius; for (var i = 0; i < this.children.length; i++) { highlighted = this.children[i].checkHighlight(); if (highlighted) { return true; } } if (this.radial) { var angleText = (angleStartCurrent + angleEndCurrent) / 2; var radiusText = (gRadius + radiusInner) / 2; context.rotate(angleText); context.beginPath(); context.moveTo(radiusText, -fontSize); context.lineTo(radiusText, fontSize); context.lineTo(radiusText + centerX, fontSize); context.lineTo(radiusText + centerX, -fontSize); context.closePath(); context.rotate(-angleText); if (context.isPointInPath(mouseXRel, mouseYRel)) { var label = String(this.getPercentage()) + '%' + ' ' + this.name; if (this.searchResultChildren()) { label += searchResultString(this.searchResultChildren()); } if ( Math.sqrt((mouseXRel) * (mouseXRel) + (mouseYRel) * (mouseYRel)) / backingScale() < radiusText + measureText(label) ) { highlighted = true; } } } else { for (var i = 0; i < this.hiddenLabels.length; i++) { var hiddenLabel = this.hiddenLabels[i]; context.rotate(hiddenLabel.angle); context.beginPath(); context.moveTo(gRadius, -fontSize); context.lineTo(gRadius, fontSize); context.lineTo(gRadius + centerX, fontSize); context.lineTo(gRadius + centerX, -fontSize); context.closePath(); context.rotate(-hiddenLabel.angle); if (context.isPointInPath(mouseXRel, mouseYRel)) { var label = String(hiddenLabel.value) + ' more'; if (hiddenLabel.search) { label += searchResultString(hiddenLabel.search); } if ( Math.sqrt((mouseXRel) * (mouseXRel) + (mouseYRel) * (mouseYRel)) / backingScale() < gRadius + fontSize + measureText(label) ) { highlighted = true; break; } } } } if (!highlighted && this != selectedNode && !this.getCollapse()) { context.beginPath(); context.arc(0, 0, radiusInner, angleStartCurrent, angleEndCurrent, false); context.arc(0, 0, gRadius, angleEndCurrent, angleStartCurrent, true); context.closePath(); if (context.isPointInPath(mouseXRel, mouseYRel)) { highlighted = true; } if ( !highlighted && (angleEndCurrent - angleStartCurrent) * (radiusInner + gRadius) < minWidth() && this.getDepth() == selectedNode.getDepth() + 1 ) { if (showKeys && this.checkHighlightKey()) { highlighted = true; } } } if (highlighted) { if (this != highlightedNode) { // document.body.style.cursor='pointer'; } highlightedNode = this; } return highlighted; } this.checkHighlightCenter = function () { if (!this.canDisplayHistory()) { return; } var cx = centerX; var cy = centerY - this.labelRadius.end * gRadius; //var dim = context.measureText(this.name); var width = this.nameWidth; if (this.searchResultChildren()) { var results = searchResultString(this.searchResultChildren()); var dim = context.measureText(results); width += dim.width; } if ( mouseX > cx - width / 2 && mouseX < cx + width / 2 && mouseY > cy - historySpacingFactor * fontSize / 2 && mouseY < cy + historySpacingFactor * fontSize / 2 ) { highlightedNode = this; return; } if (this.getParent()) { this.getParent().checkHighlightCenter(); } } this.checkHighlightKey = function () { var offset = keyOffset(); var xMin = imageWidth - keySize - margin - this.keyNameWidth - keyBuffer; var xMax = imageWidth - margin; var yMin = offset; var yMax = offset + keySize; currentKey++; return ( mouseX > xMin && mouseX < xMax && mouseY > yMin && mouseY < yMax); } this.checkHighlightMap = function () { if (this.parent) { this.parent.checkHighlightMap(); } if (this.getCollapse() || this == focusNode) { return; } var box = this.getMapPosition(); if ( mouseX > box.x - mapRadius && mouseX < box.x + mapRadius && mouseY > box.y - mapRadius && mouseY < box.y + mapRadius ) { highlightedNode = this; } } /* this.collapse = function() { for (var i = 0; i < this.children.length; i++ ) { this.children[i] = this.children[i].collapse(); } if ( this.children.length == 1 && this.children[0].magnitude == this.magnitude ) { this.children[0].parent = this.parent; this.children[0].getDepth() = this.parent.getDepth() + 1; return this.children[0]; } else { return this; } } */ this.draw = function (labelMode, selected, searchHighlighted) { var depth = this.getDepth() - selectedNode.getDepth() + 1; // var hidden = false; if (selectedNode == this) { selected = true; } var angleStartCurrent = this.angleStart.current() + rotationOffset; var angleEndCurrent = this.angleEnd.current() + rotationOffset; var radiusInner = this.radiusInner.current() * gRadius; var canDisplayLabelCurrent = this.canDisplayLabelCurrent(); var hiddenSearchResults = false; /* if ( ! this.hide ) { for ( var i = 0; i < this.children.length; i++ ) { if ( this.children[i].hide && this.children[i].searchResults ) { hiddenSearchResults = true; } } } */ var drawChildren = (!this.hide || !this.hidePrev && progress < 1) && (!this.hideAlone || !this.hideAlonePrev && progress < 1); // if ( this.alphaWedge.current() > 0 || this.alphaLabel.current() > 0 ) { var lastChildAngleEnd = angleStartCurrent; if (this.hasChildren())//canDisplayChildren ) { lastChildAngleEnd = this.children[this.children.length - 1].angleEnd.current() + rotationOffset; } if (labelMode) { var drawRadial = !( this.parent && this.parent != selectedNode && angleEndCurrent == this.parent.angleEnd.current() + rotationOffset ); //if ( angleStartCurrent != angleEndCurrent ) { this.drawLines(angleStartCurrent, angleEndCurrent, radiusInner, drawRadial, selected); } var alphaOtherCurrent = this.alphaOther.current(); var childRadiusInner; if (this == selectedNode || alphaOtherCurrent) { childRadiusInner = this.children.length ? this.children[this.children.length - 1].radiusInner.current() * gRadius : radiusInner } if (this == selectedNode) { this.drawReferenceRings(childRadiusInner); } if ( selected && !searchHighlighted && this != selectedNode && ( this.isSearchResult || this.hideAlone && this.searchResultChildren() || false // this.hide && // this.containsSearchResult ) ) { context.globalAlpha = this.alphaWedge.current(); drawWedge ( angleStartCurrent, angleEndCurrent, radiusInner, gRadius, highlightFill, 0, true ); if ( this.keyed && !showKeys && this.searchResults && !searchHighlighted && this != highlightedNode && this != focusNode ) { var angle = (angleEndCurrent + angleStartCurrent) / 2; this.drawLabel(angle, true, false, true, true); } //this.drawHighlight(false); searchHighlighted = true; } if ( this == selectedNode || // true //(canDisplayLabelCurrent) && this != highlightedNode && this != focusNode ) { if (this.radial != this.radialPrev && this.alphaLabel.end == 1) { context.globalAlpha = tweenFactor; } else { context.globalAlpha = this.alphaLabel.current(); } this.drawLabel ( (angleStartCurrent + angleEndCurrent) / 2, this.hideAlone && this.searchResultChildren() || (this.isSearchResult || hiddenSearchResults) && selected, this == selectedNode && !this.radial, selected, this.radial ); if (this.radial != this.radialPrev && this.alphaLabel.start == 1 && progress < 1) { context.globalAlpha = 1 - tweenFactor; this.drawLabel ( (angleStartCurrent + angleEndCurrent) / 2, (this.isSearchResult || hiddenSearchResults) && selected, this == selectedNodeLast && !this.radialPrev, selected, this.radialPrev ); } } if ( alphaOtherCurrent && lastChildAngleEnd != null ) { if ( (angleEndCurrent - lastChildAngleEnd) * (childRadiusInner + gRadius) >= minWidth() ) { //context.font = fontNormal; context.globalAlpha = this.alphaOther.current(); drawTextPolar ( this.getUnclassifiedText(), this.getUnclassifiedPercentage(), (lastChildAngleEnd + angleEndCurrent) / 2, (childRadiusInner + gRadius) / 2, true, false, false, 0, 0 ); } } if (this == selectedNode && this.keyUnclassified && showKeys) { this.drawKey ( (lastChildAngleEnd + angleEndCurrent) / 2, false, false ); } } else { var alphaWedgeCurrent = this.alphaWedge.current(); if (alphaWedgeCurrent || this.alphaOther.current()) { var currentR = this.r.current(); var currentG = this.g.current(); var currentB = this.b.current(); var fill = rgbText(currentR, currentG, currentB); var radiusOuter; var lastChildAngle; var truncateWedge = ( (this.hasChildren() || this == selectedNode) && !this.keyed && (compress || depth < maxDisplayDepth) && drawChildren ); if (truncateWedge) { radiusOuter = this.children.length ? this.children[0].radiusInner.current() * gRadius : radiusInner; } else { radiusOuter = gRadius; } /* if ( this.hasChildren() ) { radiusOuter = this.children[0].getUncollapsed().radiusInner.current() * gRadius + 1; } else { // TEMP radiusOuter = radiusInner + nodeRadius * gRadius; if ( radiusOuter > gRadius ) { radiusOuter = gRadius; } } */ context.globalAlpha = alphaWedgeCurrent; if (radiusInner != radiusOuter || truncateWedge) { drawWedge ( angleStartCurrent, angleEndCurrent, radiusInner, radiusOuter,//this.radiusOuter.current() * gRadius, //'rgba(0, 200, 0, .1)', fill, this.alphaPattern.current() ); if (truncateWedge) { // fill in the extra space if the sum of our // childrens' magnitudes is less than ours if (lastChildAngleEnd < angleEndCurrent) //&& false) // TEMP { if (radiusOuter > 1) { // overlap slightly to hide the seam // radiusOuter -= 1; } if (alphaWedgeCurrent < 1) { context.globalAlpha = this.alphaOther.current(); drawWedge ( lastChildAngleEnd, angleEndCurrent, radiusOuter, gRadius, colorUnclassified, 0 ); context.globalAlpha = alphaWedgeCurrent; } drawWedge ( lastChildAngleEnd, angleEndCurrent, radiusOuter, gRadius, //this.radiusOuter.current() * gRadius, //'rgba(200, 0, 0, .1)', fill, this.alphaPattern.current() ); } } if (radiusOuter < gRadius) { // patch up the seam // context.beginPath(); context.arc(0, 0, radiusOuter, angleStartCurrent/*lastChildAngleEnd*/, angleEndCurrent, false); context.strokeStyle = fill; context.lineWidth = 1; context.stroke(); } } if (this.keyed && selected && showKeys) //&& progress == 1 ) { this.drawKey ( (angleStartCurrent + angleEndCurrent) / 2, ( this == highlightedNode || this == focusNode || this.searchResults ), this == highlightedNode || this == focusNode ); } } } } this.hiddenLabels = Array(); if (drawChildren) { // draw children // for (var i = 0; i < this.children.length; i++) { if (this.drawHiddenChildren(i, selected, labelMode, searchHighlighted)) { var childHiddenEnd = this.children[i].hiddenEnd; if (childHiddenEnd > i) { // Avoid infinite loop i = childHiddenEnd; } } else { this.children[i].draw(labelMode, selected, searchHighlighted); } } } }; this.drawHiddenChildren = function (firstHiddenChild, selected, labelMode, searchHighlighted) { var firstChild = this.children[firstHiddenChild]; if (firstChild.hiddenEnd == null || firstChild.radiusInner.current() == 1) { return false; } for (var i = firstHiddenChild; i < firstChild.hiddenEnd; i++) { if (!this.children[i].hide || !this.children[i].hidePrev && progress < 1) { return false; } } var angleStart = firstChild.angleStart.current() + rotationOffset; var lastChild = this.children[firstChild.hiddenEnd]; var angleEnd = lastChild.angleEnd.current() + rotationOffset; var radiusInner = gRadius * firstChild.radiusInner.current(); var hiddenChildren = firstChild.hiddenEnd - firstHiddenChild + 1; if (labelMode) { var hiddenSearchResults = 0; for (var i = firstHiddenChild; i <= firstChild.hiddenEnd; i++) { hiddenSearchResults += this.children[i].searchResults; if (this.children[i].magnitude == 0) { hiddenChildren--; } } if ( selected && (angleEnd - angleStart) * (gRadius + gRadius) >= minWidth() || this == highlightedNode && hiddenChildren || hiddenSearchResults ) { context.globalAlpha = this.alphaWedge.current(); this.drawHiddenLabel ( angleStart, angleEnd, hiddenChildren, hiddenSearchResults ); } } var drawWedges = true; for (var i = firstHiddenChild; i <= firstChild.hiddenEnd; i++) { // all hidden children must be completely hidden to draw together if (this.children[i].alphaPattern.current() != this.children[i].alphaWedge.current()) { drawWedges = false; break; } } if (labelMode) { if (drawWedges) { var drawRadial = (angleEnd < this.angleEnd.current() + rotationOffset); this.drawLines(angleStart, angleEnd, radiusInner, drawRadial); } if (hiddenSearchResults && !searchHighlighted) { drawWedge ( angleStart, angleEnd, radiusInner, gRadius,//this.radiusOuter.current() * gRadius, highlightFill, 0, true ); } } else if (drawWedges) { context.globalAlpha = this.alphaWedge.current(); var fill = rgbText ( firstChild.r.current(), firstChild.g.current(), firstChild.b.current() ); drawWedge ( angleStart, angleEnd, radiusInner, gRadius,//this.radiusOuter.current() * gRadius, fill, context.globalAlpha, false ); } return drawWedges; } this.drawHiddenLabel = function (angleStart, angleEnd, value, hiddenSearchResults) { var textAngle = (angleStart + angleEnd) / 2; var labelRadius = gRadius + fontSize;//(radiusInner + radius) / 2; var hiddenLabel = Array(); hiddenLabel.value = value; hiddenLabel.angle = textAngle; hiddenLabel.search = hiddenSearchResults; this.hiddenLabels.push(hiddenLabel); drawTick(gRadius - fontSize * .75, fontSize * 1.5, textAngle); drawTextPolar ( value.toString() + ' more', 0, // inner text textAngle, labelRadius, true, // radial hiddenSearchResults, // bubble this == highlightedNode || this == focusNode, // bold false, hiddenSearchResults ); } this.drawHighlight = function (bold) { var angleStartCurrent = this.angleStart.current() + rotationOffset; var angleEndCurrent = this.angleEnd.current() + rotationOffset; var radiusInner = this.radiusInner.current() * gRadius; //this.setHighlightStyle(); if (this == focusNode && this == highlightedNode && this.hasChildren()) { // context.fillStyle = "rgba(255, 255, 255, .3)"; arrow ( angleStartCurrent, angleEndCurrent, radiusInner ); } else { drawWedge ( angleStartCurrent, angleEndCurrent, radiusInner, gRadius, highlightFill, 0, true ); } // check if hidden children should be highlighted // for (var i = 0; i < this.children.length; i++) { if ( this.children[i].getDepth() - selectedNode.getDepth() + 1 <= maxDisplayDepth && this.children[i].hiddenEnd != null ) { var firstChild = this.children[i]; var lastChild = this.children[firstChild.hiddenEnd]; var hiddenAngleStart = firstChild.angleStart.current() + rotationOffset; var hiddenAngleEnd = lastChild.angleEnd.current() + rotationOffset; var hiddenRadiusInner = gRadius * firstChild.radiusInner.current(); drawWedge ( hiddenAngleStart, hiddenAngleEnd, hiddenRadiusInner, gRadius, 'rgba(255, 255, 255, .3)', 0, true ); if (false && !this.searchResults) { this.drawHiddenLabel ( hiddenAngleStart, hiddenAngleEnd, firstChild.hiddenEnd - i + 1 ); } i = firstChild.hiddenEnd; } } // context.strokeStyle = 'black'; context.fillStyle = 'black'; var highlight = !(progress < 1 && zoomOut && this == selectedNodeLast); var angle = (angleEndCurrent + angleStartCurrent) / 2; if (!(this.keyed && showKeys)) { this.drawLabel(angle, true, bold, true, this.radial); } } this.drawHighlightCenter = function () { if (!this.canDisplayHistory()) { return; } context.lineWidth = highlightLineWidth; context.strokeStyle = 'black'; context.fillStyle = "rgba(255, 255, 255, .6)"; context.fillStyle = 'black'; this.drawLabel(3 * Math.PI / 2, true, true, false); context.font = fontNormal; } this.drawKey = function (angle, highlight, bold) { var offset = keyOffset(); var color; var colorText = this.magnitude == 0 ? 'gray' : 'black'; var patternAlpha = this.alphaPattern.end; var boxLeft = imageWidth - keySize - margin; var textY = offset + keySize / 2; var label; var keyNameWidth; if (this == selectedNode) { color = colorUnclassified; label = this.getUnclassifiedText() + ' ' + this.getUnclassifiedPercentage(); keyNameWidth = measureText(label, false); } else { label = this.keyLabel; color = rgbText(this.r.end, this.g.end, this.b.end); if (highlight) { if (this.searchResultChildren()) { label = label + searchResultString(this.searchResultChildren()); } keyNameWidth = measureText(label, bold); } else { keyNameWidth = this.keyNameWidth; } } var textLeft = boxLeft - keyBuffer - keyNameWidth - fontSize / 2; var labelLeft = textLeft; if (labelLeft > keyMinTextLeft - fontSize / 2) { keyMinTextLeft -= fontSize / 2; if (keyMinTextLeft < centerX - gRadius + fontSize / 2) { keyMinTextLeft = centerX - gRadius + fontSize / 2; } labelLeft = keyMinTextLeft; } var lineX = new Array(); var lineY = new Array(); var bendRadius; var keyAngle = Math.atan((textY - centerY) / (labelLeft - centerX)); var arcAngle; if (keyAngle < 0) { keyAngle += Math.PI; } if (keyMinAngle == 0 || angle < keyMinAngle) { keyMinAngle = angle; } if (angle > Math.PI && keyMinAngle > Math.PI) { // allow lines to come underneath the chart angle -= Math.PI * 2; } lineX.push(Math.cos(angle) * gRadius); lineY.push(Math.sin(angle) * gRadius); if (angle < keyAngle && textY > centerY + Math.sin(angle) * (gRadius + buffer * (currentKey - 1) / (keys + 1) / 2 + buffer / 2)) { bendRadius = gRadius + buffer - buffer * currentKey / (keys + 1) / 2; } else { bendRadius = gRadius + buffer * currentKey / (keys + 1) / 2 + buffer / 2; } var outside = Math.sqrt ( Math.pow(labelLeft - centerX, 2) + Math.pow(textY - centerY, 2) ) > bendRadius; if (!outside) { arcAngle = Math.asin((textY - centerY) / bendRadius); keyMinTextLeft = min(keyMinTextLeft, centerX + bendRadius * Math.cos(arcAngle) - fontSize / 2); if (labelLeft < textLeft && textLeft > centerX + bendRadius * Math.cos(arcAngle)) { lineX.push(textLeft - centerX); lineY.push(textY - centerY); } } else { keyMinTextLeft = min(keyMinTextLeft, labelLeft - fontSize / 2); if (angle < keyAngle) { // flip everything over y = x // arcAngle = Math.PI / 2 - keyLineAngle ( Math.PI / 2 - angle, Math.PI / 2 - keyAngle, bendRadius, textY - centerY, labelLeft - centerX, lineY, lineX ); } else { arcAngle = keyLineAngle ( angle, keyAngle, bendRadius, labelLeft - centerX, textY - centerY, lineX, lineY ); } } if (labelLeft > centerX + bendRadius * Math.cos(arcAngle) || textY > centerY + bendRadius * Math.sin(arcAngle) + .01) // if ( outside || ) { lineX.push(labelLeft - centerX); lineY.push(textY - centerY); if (textLeft != labelLeft) { lineX.push(textLeft - centerX); lineY.push(textY - centerY); } } context.globalAlpha = this.alphaWedge.current(); if (snapshotMode) { var labelSVG; if (this == selectedNode) { labelSVG = this.getUnclassifiedText() + spacer() + this.getUnclassifiedPercentage(); } else { labelSVG = this.name + spacer() + this.getPercentage() + '%'; } svg += '<rect fill="' + color + '" ' + 'x="' + boxLeft + '" y="' + offset + '" width="' + keySize + '" height="' + keySize + '"/>'; if (patternAlpha) { svg += '<rect fill="url(#hiddenPattern)" style="stroke:none" ' + 'x="' + boxLeft + '" y="' + offset + '" width="' + keySize + '" height="' + keySize + '"/>'; } svg += '<path class="line' + (highlight ? ' highlight' : '') + '" d="M ' + (lineX[0] + centerX) + ',' + (lineY[0] + centerY); if (angle != arcAngle) { svg += ' L ' + (centerX + bendRadius * Math.cos(angle)) + ',' + (centerY + bendRadius * Math.sin(angle)) + ' A ' + bendRadius + ',' + bendRadius + ' 0 ' + '0,' + (angle > arcAngle ? '0' : '1') + ' ' + (centerX + bendRadius * Math.cos(arcAngle)) + ',' + (centerY + bendRadius * Math.sin(arcAngle)); } for (var i = 1; i < lineX.length; i++) { svg += ' L ' + (centerX + lineX[i]) + ',' + (centerY + lineY[i]); } svg += '"/>'; if (highlight) { if (this.searchResultChildren()) { labelSVG = labelSVG + searchResultString(this.searchResultChildren()); } drawBubbleSVG ( boxLeft - keyBuffer - keyNameWidth - fontSize / 2, textY - fontSize, keyNameWidth + fontSize, fontSize * 2, fontSize, 0 ); if (this.isSearchResult) { drawSearchHighlights ( label, boxLeft - keyBuffer - keyNameWidth, textY, 0 ) } } svg += svgText(labelSVG, boxLeft - keyBuffer, textY, 'end', bold, colorText); } else { context.fillStyle = color; context.translate(-centerX, -centerY); context.strokeStyle = 'black'; context.globalAlpha = 1;//this.alphaWedge.current(); context.fillRect(boxLeft, offset, keySize, keySize); if (patternAlpha) { context.globalAlpha = patternAlpha; context.fillStyle = hiddenPattern; // make clipping box for Firefox performance context.beginPath(); context.moveTo(boxLeft, offset); context.lineTo(boxLeft + keySize, offset); context.lineTo(boxLeft + keySize, offset + keySize); context.lineTo(boxLeft, offset + keySize); context.closePath(); context.save(); context.clip(); context.fillRect(boxLeft, offset, keySize, keySize); context.fillRect(boxLeft, offset, keySize, keySize); context.restore(); // remove clipping region } if (highlight) { this.setHighlightStyle(); context.fillRect(boxLeft, offset, keySize, keySize); } else { context.lineWidth = thinLineWidth; } context.strokeRect(boxLeft, offset, keySize, keySize); if (lineX.length) { context.beginPath(); context.moveTo(lineX[0] + centerX, lineY[0] + centerY); context.arc(centerX, centerY, bendRadius, angle, arcAngle, angle > arcAngle); for (var i = 1; i < lineX.length; i++) { context.lineTo(lineX[i] + centerX, lineY[i] + centerY); } context.globalAlpha = this == selectedNode ? this.children[0].alphaWedge.current() : this.alphaWedge.current(); context.lineWidth = highlight ? highlightLineWidth : thinLineWidth; context.stroke(); context.globalAlpha = 1; } if (highlight) { drawBubbleCanvas ( boxLeft - keyBuffer - keyNameWidth - fontSize / 2, textY - fontSize, keyNameWidth + fontSize, fontSize * 2, fontSize, 0 ); if (this.isSearchResult) { drawSearchHighlights ( label, boxLeft - keyBuffer - keyNameWidth, textY, 0 ) } } drawText(label, boxLeft - keyBuffer, offset + keySize / 2, 0, 'end', bold, colorText); context.translate(centerX, centerY); } currentKey++; } this.drawLabel = function (angle, bubble, bold, selected, radial) { if (context.globalAlpha == 0) { return; } var innerText; var label; var radius; if (radial) { radius = (this.radiusInner.current() + 1) * gRadius / 2; } else { radius = this.labelRadius.current() * gRadius; } if (radial && (selected || bubble)) { var percentage = this.getPercentage(); innerText = percentage + '%'; } if ( !radial && this != selectedNode && !bubble && (!zoomOut || this != selectedNodeLast) ) { label = this.shortenLabel(); } else { label = this.name; } var flipped = drawTextPolar ( label, innerText, angle, radius, radial, bubble, bold, // this.isSearchResult && this.shouldAddSearchResultsString() && (!selected || this == selectedNode || highlight), this.isSearchResult && (!selected || this == selectedNode || bubble), (this.hideAlone || !selected || this == selectedNode) ? this.searchResultChildren() : 0 ); var depth = this.getDepth() - selectedNode.getDepth() + 1; if ( !radial && !bubble && this != selectedNode && this.angleEnd.end != this.angleStart.end && nLabelOffsets[depth - 2] > 2 && this.labelWidth.current() > (this.angleEnd.end - this.angleStart.end) * Math.abs(radius) && !(zoomOut && this == selectedNodeLast) && this.labelRadius.end > 0 ) { // name extends beyond wedge; draw tick mark towards the central // radius for easier identification var radiusCenter = compress ? (compressedRadii[depth - 1] + compressedRadii[depth - 2]) / 2 : (depth - .5) * nodeRadius; if (this.labelRadius.end > radiusCenter) { if (flipped) { drawTick(radius - tickLength * 1.4, tickLength, angle); } else { drawTick(radius - tickLength * 1.7, tickLength, angle); } } else { if (flipped) { drawTick(radius + tickLength * .7, tickLength, angle); } else { drawTick(radius + tickLength * .4, tickLength, angle); } } } } this.drawLines = function (angleStart, angleEnd, radiusInner, drawRadial, selected) { if (snapshotMode) { if (this != selectedNode) { if (angleEnd == angleStart + Math.PI * 2) { // fudge to prevent overlap, which causes arc ambiguity // angleEnd -= .1 / gRadius; } var longArc = angleEnd - angleStart > Math.PI ? 1 : 0; var x1 = centerX + radiusInner * Math.cos(angleStart); var y1 = centerY + radiusInner * Math.sin(angleStart); var x2 = centerX + gRadius * Math.cos(angleStart); var y2 = centerY + gRadius * Math.sin(angleStart); var x3 = centerX + gRadius * Math.cos(angleEnd); var y3 = centerY + gRadius * Math.sin(angleEnd); var x4 = centerX + radiusInner * Math.cos(angleEnd); var y4 = centerY + radiusInner * Math.sin(angleEnd); if (this.alphaArc.end) { var dArray = [ " M ", x4, ",", y4, " A ", radiusInner, ",", radiusInner, " 0 ", longArc, " 0 ", x1, ",", y1 ]; svg += '<path class="line" d="' + dArray.join('') + '"/>'; } if (drawRadial && this.alphaLine.end) { svg += '<line x1="' + x3 + '" y1="' + y3 + '" x2="' + x4 + '" y2="' + y4 + '"/>'; } } } else { context.lineWidth = thinLineWidth; context.strokeStyle = 'black'; context.beginPath(); context.arc(0, 0, radiusInner, angleStart, angleEnd, false); context.globalAlpha = this.alphaArc.current(); context.stroke(); if (drawRadial) { var x1 = radiusInner * Math.cos(angleEnd); var y1 = radiusInner * Math.sin(angleEnd); var x2 = gRadius * Math.cos(angleEnd); var y2 = gRadius * Math.sin(angleEnd); context.beginPath(); context.moveTo(x1, y1); context.lineTo(x2, y2); // if ( this.getCollapse() )//( selected && this != selectedNode ) { context.globalAlpha = this.alphaLine.current(); } context.stroke(); } } } this.drawMap = function (child) { if (this.parent) { this.parent.drawMap(child); } if (this.getCollapse() && this != child || this == focusNode) { return; } var angleStart = (child.baseMagnitude - this.baseMagnitude) / this.magnitude * Math.PI * 2 + rotationOffset; var angleEnd = (child.baseMagnitude - this.baseMagnitude + child.magnitude) / this.magnitude * Math.PI * 2 + rotationOffset; var box = this.getMapPosition(); context.save(); context.fillStyle = 'black'; context.textAlign = 'end'; context.textBaseline = 'middle'; var textX = box.x - mapRadius - mapBuffer; var percentage = getPercentage(child.magnitude / this.magnitude); var highlight = this == selectedNode || this == highlightedNode; if (highlight) { context.font = fontBold; } else { context.font = fontNormal; } context.fillText(percentage + '% of', textX, box.y - mapRadius / 3); context.fillText(this.name, textX, box.y + mapRadius / 3); if (highlight) { context.font = fontNormal; } if (this == highlightedNode && this != selectedNode) { context.fillStyle = 'rgb(245, 245, 245)'; // context.fillStyle = 'rgb(200, 200, 200)'; } else { context.fillStyle = 'rgb(255, 255, 255)'; } context.beginPath(); context.arc(box.x, box.y, mapRadius, 0, Math.PI * 2, true); context.closePath(); context.fill(); if (this == selectedNode) { context.lineWidth = 1; context.fillStyle = 'rgb(100, 100, 100)'; } else { if (this == highlightedNode) { context.lineWidth = .2; context.fillStyle = 'rgb(190, 190, 190)'; } else { context.lineWidth = .2; context.fillStyle = 'rgb(200, 200, 200)'; } } var maxDepth = this.getMaxDepth(); if (!compress && maxDepth > maxPossibleDepth + this.getDepth() - 1) { maxDepth = maxPossibleDepth + this.getDepth() - 1; } if (this.getDepth() < selectedNode.getDepth()) { if (child.getDepth() - 1 >= maxDepth) { maxDepth = child.getDepth(); } } var radiusInner; if (compress) { radiusInner = 0; // Math.atan(child.getDepth() - this.getDepth()) / // Math.PI * 2 * .9; } else { radiusInner = (child.getDepth() - this.getDepth()) / (maxDepth - this.getDepth() + 1); } context.stroke(); context.beginPath(); if (radiusInner == 0) { context.moveTo(box.x, box.y); } else { context.arc(box.x, box.y, mapRadius * radiusInner, angleEnd, angleStart, true); } context.arc(box.x, box.y, mapRadius, angleStart, angleEnd, false); context.closePath(); context.fill(); if (this == highlightedNode && this != selectedNode) { context.lineWidth = 1; context.stroke(); } context.restore(); } this.drawReferenceRings = function (childRadiusInner) { if (snapshotMode) { svg += '<circle cx="' + centerX + '" cy="' + centerY + '" r="' + childRadiusInner + '"/>'; svg += '<circle cx="' + centerX + '" cy="' + centerY + '" r="' + gRadius + '"/>'; } else { context.globalAlpha = 1 - this.alphaLine.current();//this.getUncollapsed().alphaLine.current(); context.beginPath(); context.arc(0, 0, childRadiusInner, 0, Math.PI * 2, false); context.stroke(); context.beginPath(); context.arc(0, 0, gRadius, 0, Math.PI * 2, false); context.stroke(); } } this.getCollapse = function () { return ( collapse && this.collapse && this.depth != maxAbsoluteDepth ); } this.getDepth = function () { if (collapse) { return this.depthCollapsed; } else { return this.depth; } }; this.getHue = function () { return this.hues[currentDataset]; }; this.getMagnitude = function () { return this.attributes[magnitudeIndex][currentDataset]; }; this.getMapPosition = function () { return { x: (details.offsetLeft + details.clientWidth - mapRadius), y: ((focusNode.getDepth() - this.getDepth()) * (mapBuffer + mapRadius * 2) - mapRadius) + details.clientHeight + details.offsetTop }; } this.getMaxDepth = function (limit) { var max; if (collapse) { return this.maxDepthCollapsed; } else { if (this.maxDepth > maxAbsoluteDepth) { return maxAbsoluteDepth; } else { return this.maxDepth; } } } this.getData = function (index, summary) { var files = new Array(); if ( this.attributes[index] != null && this.attributes[index][currentDataset] != null && this.attributes[index][currentDataset] != '' ) { files.push ( document.location + '.files/' + this.attributes[index][currentDataset] ); } if (summary) { for (var i = 0; i < this.children.length; i++) { files = files.concat(this.children[i].getData(index, true)); } } return files; } this.getList = function (index, summary) { var list; if ( this.attributes[index] != null && this.attributes[index][currentDataset] != null ) { list = this.attributes[index][currentDataset]; } else { list = new Array(); } if (summary) { for (var i = 0; i < this.children.length; i++) { list = list.concat(this.children[i].getList(index, true)); } } return list; } this.getParent = function () { // returns parent, accounting for collapsing or 0 if doesn't exist var parent = this.parent; while (parent != 0 && parent.getCollapse()) { parent = parent.parent; } return parent; } this.getPercentage = function () { return getPercentage(this.magnitude / selectedNode.magnitude); } this.getUnclassifiedPercentage = function () { if (this.children.length) { var lastChild = this.children[this.children.length - 1]; return getPercentage ( ( this.baseMagnitude + this.magnitude - lastChild.magnitude - lastChild.baseMagnitude ) / this.magnitude ) + '%'; } else { return '100%'; } } this.getUnclassifiedText = function () { return '[other ' + this.name + ']'; } this.getUncollapsed = function () { // recurse through collapsed children until uncollapsed node is found if (this.getCollapse()) { return this.children[0].getUncollapsed(); } else { return this; } }; this.hasChildren = function () { return this.depth < maxAbsoluteDepth && this.magnitude && this.children.length; }; this.hasParent = function (parent) { if (this.parent) { if (this.parent === parent) { return true; } else { return this.parent.hasParent(parent); } } else { return false; } }; this.isLeaf = function (_recursing) { // Returns true/1 for a real leave, false/0 otherwise, counting the // non-empty leaves downstream and checking for positive counts. // Param _recursing is an internal auxiliar variable not to be used var leaves = 0; if (this.children.length) { // Node has children -> recurse for (var i = 0; i < this.children.length; i++) { leaves += this.children[i].isLeaf(true); } if (_recursing) { return leaves ? leaves : +!!this.magnitude; // If this has no leaves but has magnitude, this is a leaf. // NOTE: +!!num is 0 for num=0 and is 1 otherwise } else { return !!this.magnitude && !leaves; } } else { // Node has not children if (!this.magnitude) { return 0; // Fake leaf (empty) } else { return 1; // This is true leaf } } }; this.maxVisibleDepth = function (maxDepth) { var childInnerRadius; var depth = this.getDepth() - selectedNode.getDepth() + 1; var currentMaxDepth = depth; if (this.hasChildren() && depth < maxDepth) { var lastChild = this.children[this.children.length - 1]; if (lastChild.baseMagnitude + lastChild.magnitude < this.baseMagnitude + this.magnitude) { currentMaxDepth++; } if (compress) { childInnerRadius = compressedRadii[depth - 1]; } else { childInnerRadius = (depth) / maxDepth; } for (var i = 0; i < this.children.length; i++) { if (//true || this.children[i].magnitude * angleFactor * (childInnerRadius + 1) * gRadius >= minWidth() ) { var childMaxDepth = this.children[i].maxVisibleDepth(maxDepth); if (childMaxDepth > currentMaxDepth) { currentMaxDepth = childMaxDepth; } } } } return currentMaxDepth; } this.resetLabelWidth = function () { var nameWidthOld = this.nameWidth; if (true || !this.radial)//&& fontSize != fontSizeLast ) { var dim = context.measureText(this.name); this.nameWidth = dim.width; } if (fontSize != fontSizeLast && this.labelWidth.end == nameWidthOld * labelWidthFudge) { // font size changed; adjust start of tween to match this.labelWidth.start = this.nameWidth * labelWidthFudge; } else { this.labelWidth.start = this.labelWidth.current(); } this.labelWidth.end = this.nameWidth * labelWidthFudge; } this.restrictLabelWidth = function (width) { if (width < this.labelWidth.end) { this.labelWidth.end = width; } } this.search = function () { this.isSearchResult = false; this.searchResults = 0; if ( !this.getCollapse() && search.value !== '' && this.name.toLowerCase().indexOf(search.value.toLowerCase()) !== -1 ) { this.isSearchResult = true; this.searchResults = 1; nSearchResults++; } for (var i = 0; i < this.children.length; i++) { this.searchResults += this.children[i].search(); } return this.searchResults; } this.searchResultChildren = function () { if (this.isSearchResult) { return this.searchResults - 1; } else { return this.searchResults; } } this.setDepth = function (depth, depthCollapsed) { this.depth = depth; this.depthCollapsed = depthCollapsed; if ( this.children.length === 1 && // this.magnitude > 0 && this.children[0].magnitude === this.magnitude && (head.children.length > 1 || this.children[0].children.length) ) { this.collapse = true; } else { this.collapse = false; depthCollapsed++; } for (var i = 0; i < this.children.length; i++) { this.children[i].setDepth(depth + 1, depthCollapsed); } } this.setHighlightStyle = function () { context.lineWidth = highlightLineWidth; if (this.hasChildren() || this !== focusNode || this !== highlightedNode) { context.strokeStyle = 'black'; context.fillStyle = "rgba(255, 255, 255, .3)"; } else { context.strokeStyle = 'rgb(90,90,90)'; context.fillStyle = "rgba(155, 155, 155, .3)"; } } this.setLabelWidth = function (node) { if (!shorten || this.radial) { return; // don't need to set width } if (node.hide) { alert('wtf'); return; } var angle = (this.angleStart.end + this.angleEnd.end) / 2; var a; // angle difference if (node == selectedNode) { a = Math.abs(angle - node.angleOther); } else { a = Math.abs(angle - (node.angleStart.end + node.angleEnd.end) / 2); } if (a == 0) { return; } if (a > Math.PI) { a = 2 * Math.PI - a; } if (node.radial || node == selectedNode) { var nodeLabelRadius; if (node == selectedNode) { // radial 'other' label nodeLabelRadius = (node.children[0].radiusInner.end + 1) / 2; } else { nodeLabelRadius = (node.radiusInner.end + 1) / 2; } if (a < Math.PI / 2) { var r = this.labelRadius.end * gRadius + .5 * fontSize var hypotenuse = r / Math.cos(a); var opposite = r * Math.tan(a); var fontRadius = .8 * fontSize; if ( nodeLabelRadius * gRadius < hypotenuse && this.labelWidth.end / 2 + fontRadius > opposite ) { this.labelWidth.end = 2 * (opposite - fontRadius); } } } else if ( this.labelRadius.end == node.labelRadius.end && a < Math.PI / 4 ) { // same radius with small angle; use circumferential approximation var dist = a * this.labelRadius.end * gRadius - fontSize * (1 - a * 4 / Math.PI) * 1.3; if (this.labelWidth.end < dist) { node.restrictLabelWidth((dist - this.labelWidth.end / 2) * 2); } else if (node.labelWidth.end < dist) { this.restrictLabelWidth((dist - node.labelWidth.end / 2) * 2); } else { // both labels reach halfway point; restrict both this.labelWidth.end = dist; node.labelWidth.end = dist } } else { var r1 = this.labelRadius.end * gRadius; var r2 = node.labelRadius.end * gRadius; // first adjust the radii to account for the height of the font // by shifting them toward each other // var fontFudge = .35 * fontSize; // if (this.labelRadius.end < node.labelRadius.end) { r1 += fontFudge; r2 -= fontFudge; } else if (this.labelRadius.end > node.labelRadius.end) { r1 -= fontFudge; r2 += fontFudge; } else { r1 -= fontFudge; r2 -= fontFudge; } var r1s = r1 * r1; var r2s = r2 * r2; // distance between the centers of the two labels // var dist = Math.sqrt(r1s + r2s - 2 * r1 * r2 * Math.cos(a)); // angle at our label center between our radius and the line to the // other label center // var b = Math.acos((r1s + dist * dist - r2s) / (2 * r1 * dist)); // distance from our label center to the intersection of the // two tangents // var l1 = Math.sin(a + b - Math.PI / 2) * dist / Math.sin(Math.PI - a); // distance from other label center the the intersection of the // two tangents // var l2 = Math.sin(Math.PI / 2 - b) * dist / Math.sin(Math.PI - a); l1 = Math.abs(l1) - .4 * fontSize; l2 = Math.abs(l2) - .4 * fontSize; /* // amount to shorten the distances because of height of the font // var l3 = 0; var fontRadius = fontSize * .55; // if ( l1 < 0 || l2 < 0 ) { var l4 = fontRadius / Math.tan(a); l1 = Math.abs(l1); l2 = Math.abs(l2); l1 -= l4; l2 -= l4; } else { var c = Math.PI - a; l3 = fontRadius * Math.tan(c / 2); } */ if (this.labelWidth.end / 2 > l1 && node.labelWidth.end / 2 > l2) { // shorten the farthest one from the intersection if (l1 > l2) { this.restrictLabelWidth(2 * (l1));// - l3 - fontRadius)); } else { node.restrictLabelWidth(2 * (l2));// - l3 - fontRadius)); } } /* else if ( this.labelWidth.end / 2 > l1 + l3 && node.labelWidth.end / 2 > l2 - l3 ) { node.restrictLabelWidth(2 * (l2 - l3)); } else if ( this.labelWidth.end / 2 > l1 - l3 && node.labelWidth.end / 2 > l2 + l3 ) { this.restrictLabelWidth(2 * (l1 - l3)); }*/ } } this.setMagnitudes = function (baseMagnitude) { this.magnitude = this.getMagnitude(); this.baseMagnitude = baseMagnitude; for (var i = 0; i < this.children.length; i++) { this.children[i].setMagnitudes(baseMagnitude); baseMagnitude += this.children[i].magnitude; } this.maxChildMagnitude = baseMagnitude; } this.setMaxDepths = function () { this.maxDepth = this.depth; this.maxDepthCollapsed = this.depthCollapsed; for (i in this.children) { var child = this.children[i]; child.setMaxDepths(); if (child.maxDepth > this.maxDepth) { this.maxDepth = child.maxDepth; } if ( child.maxDepthCollapsed > this.maxDepthCollapsed && (child.depth <= maxAbsoluteDepth || maxAbsoluteDepth == 0) ) { this.maxDepthCollapsed = child.maxDepthCollapsed; } } } this.setTargetLabelRadius = function () { var depth = this.getDepth() - selectedNode.getDepth() + 1; var index = depth - 2; var labelOffset = labelOffsets[index]; if (this.radial) { //this.labelRadius.setTarget((this.radiusInner.end + 1) / 2); var max = depth == maxDisplayDepth ? 1 : compressedRadii[index + 1]; this.labelRadius.setTarget((compressedRadii[index] + max) / 2); } else { var radiusCenter; var width; if (compress) { if (nLabelOffsets[index] > 1) { this.labelRadius.setTarget ( lerp ( labelOffset + .75, 0, nLabelOffsets[index] + .5, compressedRadii[index], compressedRadii[index + 1] ) ); } else { this.labelRadius.setTarget((compressedRadii[index] + compressedRadii[index + 1]) / 2); } } else { radiusCenter = nodeRadius * (depth - 1) + nodeRadius / 2; width = nodeRadius; this.labelRadius.setTarget ( radiusCenter + width * ((labelOffset + 1) / (nLabelOffsets[index] + 1) - .5) ); } } if (!this.hide && !this.keyed && nLabelOffsets[index]) { // check last and first labels in each track for overlap for (var i = 0; i < maxDisplayDepth - 1; i++) { for (var j = 0; j <= nLabelOffsets[i]; j++) { var last = labelLastNodes[i][j]; var first = labelFirstNodes[i][j]; if (last) { if (j == nLabelOffsets[i]) { // last is radial this.setLabelWidth(last); } else { last.setLabelWidth(this); } } if (first) { if (j == nLabelOffsets[i]) { this.setLabelWidth(first); } else { first.setLabelWidth(this); } } } } if (selectedNode.canDisplayLabelOther) { // in case there is an 'other' label this.setLabelWidth(selectedNode); } if (this.radial) { // use the last 'track' of this depth for radial labelLastNodes[index][nLabelOffsets[index]] = this; if (labelFirstNodes[index][nLabelOffsets[index]] == 0) { labelFirstNodes[index][nLabelOffsets[index]] = this; } } else { labelLastNodes[index][labelOffset] = this; // update offset labelOffsets[index] += 1; if (labelOffsets[index] > nLabelOffsets[index]) { labelOffsets[index] -= nLabelOffsets[index]; if (!(nLabelOffsets[index] & 1)) { labelOffsets[index]--; } } else if (labelOffsets[index] == nLabelOffsets[index]) { labelOffsets[index] -= nLabelOffsets[index]; if (false && !(nLabelOffsets[index] & 1)) { labelOffsets[index]++; } } if (labelFirstNodes[index][labelOffset] == 0) { labelFirstNodes[index][labelOffset] = this; } } } else if (this.hide) { this.labelWidth.end = 0; } } this.setTargets = function () { if (this == selectedNode) { this.setTargetsSelected ( 0, 1, lightnessBase, false, false ); return; } var depthRelative = this.getDepth() - selectedNode.getDepth(); var parentOfSelected = selectedNode.hasParent(this); /* ( // ! this.getCollapse() && this.baseMagnitude <= selectedNode.baseMagnitude && this.baseMagnitude + this.magnitude >= selectedNode.baseMagnitude + selectedNode.magnitude ); */ if (parentOfSelected) { this.resetLabelWidth(); } else { //context.font = fontNormal; var dim = context.measureText(this.name); this.nameWidth = dim.width; //this.labelWidth.setTarget(this.labelWidth.end); this.labelWidth.setTarget(0); } // set angles // if (this.baseMagnitude <= selectedNode.baseMagnitude) { this.angleStart.setTarget(0); } else { this.angleStart.setTarget(Math.PI * 2); } // if ( parentOfSelected || this.baseMagnitude + this.magnitude >= selectedNode.baseMagnitude + selectedNode.magnitude ) { this.angleEnd.setTarget(Math.PI * 2); } else { this.angleEnd.setTarget(0); } // children // for (var i = 0; i < this.children.length; i++) { this.children[i].setTargets(); } if (this.getDepth() <= selectedNode.getDepth()) { // collapse in this.radiusInner.setTarget(0); if (parentOfSelected) { this.labelRadius.setTarget ( (depthRelative) * historySpacingFactor * fontSize / gRadius ); //this.scale.setTarget(1 - (selectedNode.getDepth() // - this.getDepth()) / 18); // TEMP } else { this.labelRadius.setTarget(0); //this.scale.setTarget(1); // TEMP } } else if (depthRelative + 1 > maxDisplayDepth) { // collapse out this.radiusInner.setTarget(1); this.labelRadius.setTarget(1); //this.scale.setTarget(1); // TEMP } else { // don't collapse if (compress) { this.radiusInner.setTarget(compressedRadii[depthRelative - 1]); } else { this.radiusInner.setTarget(nodeRadius * (depthRelative)); } //this.scale.setTarget(1); // TEMP if (this == selectedNode) { this.labelRadius.setTarget(0); } else { if (compress) { this.labelRadius.setTarget ( (compressedRadii[depthRelative - 1] + compressedRadii[depthRelative]) / 2 ); } else { this.labelRadius.setTarget(nodeRadius * (depthRelative) + nodeRadius / 2); } } } // this.r.start = this.r.end; // this.g.start = this.g.end; // this.b.start = this.b.end; this.r.setTarget(255); this.g.setTarget(255); this.b.setTarget(255); this.alphaLine.setTarget(0); this.alphaArc.setTarget(0); this.alphaWedge.setTarget(0); this.alphaPattern.setTarget(0); this.alphaOther.setTarget(0); if (parentOfSelected && !this.getCollapse()) { var alpha = ( 1 - (selectedNode.getDepth() - this.getDepth()) / (Math.floor((compress ? compressedRadii[0] : nodeRadius) * gRadius / (historySpacingFactor * fontSize) - .5) + 1) ); if (alpha < 0) { alpha = 0; } this.alphaLabel.setTarget(alpha); this.radial = false; } else { this.alphaLabel.setTarget(0); } this.hideAlonePrev = this.hideAlone; this.hidePrev = this.hide; if (parentOfSelected) { this.hideAlone = false; this.hide = false; } if (this.getParent() == selectedNode.getParent()) { this.hiddenEnd = null; } this.radialPrev = this.radial; } this.setTargetsSelected = function (hueMin, hueMax, lightness, hide, nextSiblingHidden) { var collapse = this.getCollapse(); var depth = this.getDepth() - selectedNode.getDepth() + 1; var canDisplayChildLabels = false; var lastChild; if (this.hasChildren())//&& ! hide ) { lastChild = this.children[this.children.length - 1]; this.hideAlone = true; } else { this.hideAlone = false; } // set child wedges // for (var i = 0; i < this.children.length; i++) { this.children[i].setTargetWedge(); if ( !this.children[i].hide && (collapse || depth < maxDisplayDepth) && this.depth < maxAbsoluteDepth ) { canDisplayChildLabels = true; this.hideAlone = false; } } if (this == selectedNode || lastChild && lastChild.angleEnd.end < this.angleEnd.end - .01) { this.hideAlone = false; } if (this.hideAlonePrev == undefined) { this.hideAlonePrev = this.hideAlone; } if (this == selectedNode) { var otherArc = this.children.length ? angleFactor * ( this.baseMagnitude + this.magnitude - lastChild.baseMagnitude - lastChild.magnitude ) : this.baseMagnitude + this.magnitude; this.canDisplayLabelOther = this.children.length ? otherArc * (this.children[0].radiusInner.end + 1) * gRadius >= minWidth() : true; this.keyUnclassified = false; if (this.canDisplayLabelOther) { this.angleOther = Math.PI * 2 - otherArc / 2; } else if (otherArc > 0.0000000001) { this.keyUnclassified = true; keys++; } this.angleStart.setTarget(0); this.angleEnd.setTarget(Math.PI * 2); if (this.children.length) { this.radiusInner.setTarget(0); } else { this.radiusInner.setTarget(compressedRadii[0]); } this.hidePrev = this.hide; this.hide = false; this.hideAlonePrev = this.hideAlone; this.hideAlone = false; this.keyed = false; } if (hueMax - hueMin > 1 / 12) { hueMax = hueMin + 1 / 12; } // set lightness // if (!(hide || this.hideAlone)) { if (useHue()) { lightness = (lightnessBase + lightnessMax) / 2; } else { lightness = lightnessBase + (depth - 1) * lightnessFactor; if (lightness > lightnessMax) { lightness = lightnessMax; } } } if (hide) { this.hide = true; } if (this.hidePrev == undefined) { this.hidePrev = this.hide; } var hiddenStart = -1; var hiddenHueNumer = 0; var hiddenHueDenom = 0; if (!this.hide) { this.hiddenEnd = null; } for (var i = 0; true; i++) { if (!this.hideAlone && !hide && (i == this.children.length || !this.children[i].hide)) { // reached a non-hidden child or the end; set targets for // previous group of hidden children (if any) using their // average hue if (hiddenStart != -1) { var hiddenHue = hiddenHueDenom ? hiddenHueNumer / hiddenHueDenom : hueMin; for (var j = hiddenStart; j < i; j++) { this.children[j].setTargetsSelected ( hiddenHue, null, lightness, false, j < i - 1 ); this.children[j].hiddenEnd = null; } this.children[hiddenStart].hiddenEnd = i - 1; } } if (i == this.children.length) { break; } var child = this.children[i]; var childHueMin; var childHueMax; if (this.magnitude > 0 && !this.hide && !this.hideAlone) { if (useHue()) { childHueMin = child.hues[currentDataset]; } else if (this == selectedNode) { var min = 0.0; var max = 1.0; if (this.children.length > 6) { childHueMin = lerp((1 - Math.pow( 1 - i / this.children.length, 1.4)) * .95, 0, 1, min, max); childHueMax = lerp((1 - Math.pow( 1 - (i + .55) / this.children.length, 1.4)) * .95, 0, 1, min, max); } else { childHueMin = lerp(i / this.children.length, 0, 1, min, max); childHueMax = lerp((i + .55) / this.children.length, 0, 1, min, max); } } else { childHueMin = lerp ( child.baseMagnitude, this.baseMagnitude, this.baseMagnitude + this.magnitude, hueMin, hueMax ); childHueMax = lerp ( child.baseMagnitude + child.magnitude * .99, this.baseMagnitude, this.baseMagnitude + this.magnitude, hueMin, hueMax ); } } else { childHueMin = hueMin; childHueMax = hueMax; } if (!this.hideAlone && !hide && !this.hide && child.hide) { if (hiddenStart == -1) { hiddenStart = i; } if (useHue()) { hiddenHueNumer += childHueMin * child.magnitude; hiddenHueDenom += child.magnitude; } else { hiddenHueNumer += childHueMin; hiddenHueDenom++; } } else { hiddenStart = -1; this.children[i].setTargetsSelected ( childHueMin, childHueMax, lightness, hide || this.keyed || this.hideAlone || this.hide && !collapse, false ); } } if (this.hue && this.magnitude) { this.hue.setTarget(this.hues[currentDataset]); if (this.attributes[magnitudeIndex][lastDataset] == 0) { this.hue.start = this.hue.end; } } this.radialPrev = this.radial; if (this == selectedNode) { this.resetLabelWidth(); this.labelWidth.setTarget(this.nameWidth * labelWidthFudge); this.alphaWedge.setTarget(0); this.alphaLabel.setTarget(1); this.alphaOther.setTarget(1); this.alphaArc.setTarget(0); this.alphaLine.setTarget(0); this.alphaPattern.setTarget(0); this.r.setTarget(255); this.g.setTarget(255); this.b.setTarget(255); this.radial = false; this.labelRadius.setTarget(0); } else { var rgb = hslToRgb ( hueMin, saturation, lightness ); this.r.setTarget(rgb.r); this.g.setTarget(rgb.g); this.b.setTarget(rgb.b); this.alphaOther.setTarget(0); this.alphaWedge.setTarget(1); if (this.hide || this.hideAlone) { this.alphaPattern.setTarget(1); } else { this.alphaPattern.setTarget(0); } // set radial // if (!(hide || this.hide))//&& ! this.keyed ) { if (this.hideAlone) { this.radial = true; } else if (false && canDisplayChildLabels) { this.radial = false; } else { this.radial = true; if (this.hasChildren() && depth < maxDisplayDepth) { var lastChild = this.children[this.children.length - 1]; if ( lastChild.angleEnd.end == this.angleEnd.end || ( (this.angleStart.end + this.angleEnd.end) / 2 - lastChild.angleEnd.end ) * (this.radiusInner.end + 1) * gRadius * 2 < minWidth() ) { this.radial = false; } } } } // set alphaLabel // if ( collapse || hide || this.hide || this.keyed || depth > maxDisplayDepth || !this.canDisplayDepth() ) { this.alphaLabel.setTarget(0); } else { if ( (this.radial || nLabelOffsets[depth - 2]) ) { this.alphaLabel.setTarget(1); } else { this.alphaLabel.setTarget(0); if (this.radialPrev) { this.alphaLabel.start = 0; } } } // set alphaArc // if ( collapse || hide || depth > maxDisplayDepth || !this.canDisplayDepth() ) { this.alphaArc.setTarget(0); } else { this.alphaArc.setTarget(1); } // set alphaLine // if ( hide || this.hide && nextSiblingHidden || depth > maxDisplayDepth || !this.canDisplayDepth() ) { this.alphaLine.setTarget(0); } else { this.alphaLine.setTarget(1); } //if ( ! this.radial ) { this.resetLabelWidth(); } // set labelRadius target // if (collapse) { this.labelRadius.setTarget(this.radiusInner.end); } else { if (depth > maxDisplayDepth || !this.canDisplayDepth()) { this.labelRadius.setTarget(1); } else { this.setTargetLabelRadius(); } } } } this.setTargetWedge = function () { var depth = this.getDepth() - selectedNode.getDepth() + 1; // set angles // var baseMagnitudeRelative = this.baseMagnitude - selectedNode.baseMagnitude; // this.angleStart.setTarget(baseMagnitudeRelative * angleFactor); this.angleEnd.setTarget((baseMagnitudeRelative + this.magnitude) * angleFactor); // set radiusInner // if (depth > maxDisplayDepth || !this.canDisplayDepth()) { this.radiusInner.setTarget(1); } else { if (compress) { this.radiusInner.setTarget(compressedRadii[depth - 2]); } else { this.radiusInner.setTarget(nodeRadius * (depth - 1)); } } if (this.hide != undefined) { this.hidePrev = this.hide; } if (this.hideAlone != undefined) { this.hideAlonePrev = this.hideAlone; } // set hide // if ( (this.angleEnd.end - this.angleStart.end) * (this.radiusInner.end * gRadius + gRadius) < minWidth() ) { if (depth == 2 && !this.getCollapse() && this.depth <= maxAbsoluteDepth) { this.keyed = true; keys++; this.hide = false; var percentage = this.getPercentage(); this.keyLabel = this.name + ' ' + percentage + '%'; var dim = context.measureText(this.keyLabel); this.keyNameWidth = dim.width; } else { this.keyed = false; this.hide = depth > 2; } } else { this.keyed = false; this.hide = false; } } this.shortenLabel = function () { var label = this.name; var labelWidth = this.nameWidth; var maxWidth = this.labelWidth.current(); var minEndLength = 0; if (labelWidth > maxWidth && label.length > minEndLength * 2) { var endLength = Math.floor((label.length - 1) * maxWidth / labelWidth / 2); if (endLength < minEndLength) { endLength = minEndLength; } return ( label.substring(0, endLength) + '...' + label.substring(label.length - endLength)); } else { return label; } } /* this.shouldAddSearchResultsString = function() { if ( this.isSearchResult ) { return this.searchResults > 1; } else { return this.searchResults > 0; } } */ this.sort = function () { this.children.sort(function (a, b) { if (sortByScoreCheckBox.checked) { return b.getHue() - a.getHue() } else { return b.getMagnitude() - a.getMagnitude() } }); for (var i = 0; i < this.children.length; i++) { this.children[i].sort(); } } } var options; function addOptionElement(position, innerHTML, title, padding) { var div = document.createElement("div"); // div.style.position = 'absolute'; // div.style.top = position + 'px'; div.innerHTML = innerHTML; // div.style.display = 'block'; div.style.padding = padding || '2px'; if (title) { div.title = title; } options.appendChild(div); var height = 0;//div.clientHeight; return position + height; } function addOptionElements(hueName, hueDefault) { options = document.createElement('div'); options.style.position = 'absolute'; options.style.top = '0px'; options.addEventListener('mousedown', function (e) { mouseClick(e) }, false); // options.onmouseup = function(e) {mouseUp(e)} document.body.appendChild(options); if (chart === ChartEnum.TAXOMIC) { document.body.style.font = '11px Ubuntu'; } else { document.body.style.font = '12px Saira Semi Condensed'; } var position = 5; function logLoaded(fontFace) { console.log(fontFace.family, 'loaded successfully.'); } // Loading FontFaces via JavaScript is alternative to using CSS's @font-face rule. // var ubuntuMonoFontFace = new FontFace('Ubuntu Mono', 'url(https://fonts.gstatic.com/s/ubuntumono/v7/KFOjCneDtsqEr0keqCMhbCc6CsTYl4BO.woff2)'); // document.fonts.add(ubuntuMonoFontFace); // ubuntuMonoFontFace.loaded.then(logLoaded); // var oxygenFontFace = new FontFace('Oxygen', 'url(https://fonts.gstatic.com/s/oxygen/v5/qBSyz106i5ud7wkBU-FrPevvDin1pK8aKteLpeZ5c0A.woff2)'); // document.fonts.add(oxygenFontFace); // oxygenFontFace.loaded.then(logLoaded); var oxygenMonoFontFace = new FontFace('Oxygen Mono', 'url(https://fonts.gstatic.com/s/oxygenmono/v5/h0GsssGg9FxgDgCjLeAd7hjYx-6tPUUv.woff2)'); document.fonts.add(oxygenMonoFontFace); oxygenMonoFontFace.loaded.then(logLoaded); var sairaCondensedFontFace = new FontFace('Saira Condensed', 'url(https://fonts.gstatic.com/s/sairacondensed/v3/EJROQgErUN8XuHNEtX81i9TmEkrvoutF2o-Srg.woff2)'); document.fonts.add(sairaCondensedFontFace); sairaCondensedFontFace.loaded.then(logLoaded); var sairaSemiCondensedFontFace = new FontFace('Saira Semi Condensed', 'url(https://fonts.gstatic.com/s/sairasemicondensed/v3/U9MD6c-2-nnJkHxyCjRcnMHcWVWV1cWRRX8MaOY8q3T_.woff2)'); document.fonts.add(sairaSemiCondensedFontFace); sairaSemiCondensedFontFace.loaded.then(logLoaded); // The .ready promise resolves when all fonts that have been previously requested // are loaded and layout operations are complete. document.fonts.ready.then(function () { console.log('There are', document.fonts.size, 'FontFaces loaded.\n'); // document.fonts has a Set-like interface. Here, we're iterating over its values. for (var fontFace of document.fonts.values()) { console.log('FontFace:'); for (var property in fontFace) { console.log(' ' + property + ': ' + fontFace[property]); } console.log('\n'); } }); details = document.createElement('div'); details.style.position = 'absolute'; details.style.top = '1%'; details.style.right = '2%'; details.style.textAlign = 'right'; document.body.insertBefore(details, canvas); //<div id="details" style="position:absolute;top:1%;right:2%;text-align:right;"> details.innerHTML = '\ <span id="detailsName" style="font-weight:bold"></span> \ <input type="button" id="detailsExpand" onclick="expand(focusNode);"\ value="↔" title="Expand this wedge to become the new focus of the chart"/><br/>\ <div id="detailsInfo" style="float:right"></div>'; keyControl = document.createElement('input'); keyControl.type = 'button'; keyControl.value = showKeys ? 'x' : '…'; keyControl.style.position = ''; keyControl.style.position = 'fixed'; keyControl.style.visibility = 'hidden'; document.body.insertBefore(keyControl, canvas); var logoElement = document.getElementById('logo'); if (logoElement) { logoImage = logoElement.src; } else { logoImage = 'https://raw.githubusercontent.com/khyox/recentrifuge/master/recentrifuge/img/logo-rcf-mini.uri'; } var placeholderTit; if (chart === ChartEnum.GENOMIC) { placeholderTit = "Complete or partial function, process, component..."; } else { placeholderTit = "Taxon scientific name, complete or partial name..."; } position = addOptionElement ( position, '<a style="margin:2px" target="_blank" href="http://www.recentrifuge.org"><img style="vertical-align:middle;width:136px;height:32px;padding:8px 10px 6px 10px" src="' + logoImage + '"/></a><input type="button" id="back" value="←" title="Go back (Shortcut: ←)"/>\ <input type="button" id="forward" value="→" title="Go forward (Shortcut: →)"/> \ Search: <input type="text" placeholder="' + placeholderTit + '" size="45" id="search"/>\ <input id="searchClear" type="button" value="x" onclick="clearSearch()"/> \ <span id="searchResults"></span>' ); if (datasets > 1) { var size = datasets < DATASET_MAX_SIZE ? datasets : DATASET_MAX_SIZE; var select = '<table style="border-collapse:collapse;margin-left:10px"><tr><td style="padding:0px">' + '<select id="datasets" style="min-width:100px" size="' + size + '" onchange="onDatasetChange()">'; for (var i = 0; i < datasetNames.length; i++) { select += '<option>' + datasetNames[i] + '</option>'; } select += '</select></td><td style="vertical-align:top;padding:2px;">' + '<input style="display:block" title="Previous dataset ' + '(Shortcut: ↑)" id="prevDataset" type="button"' + ' value="↑" onclick="prevDataset()" disabled="true"/>' + '<input title="Next dataset (Shortcut: ↓)" ' + 'id="nextDataset" type="button" value="↓" ' + 'onclick="nextDataset()"/><br/></td>' + '<td style="vertical-align:top;padding:2px;">' + '<input style="display:block" ' + 'title="Switch to the prior dataset that was viewed ' + '(Shortcut: TAB)" id="lastDataset" type="button" ' + 'style="font:11px Ubuntu" value="prior" ' + 'onclick="selectLastDataset()"/>' + '<select id="ranks" onchange="onRankChange()" ' + 'title="Filter samples by taxonomic rank">' + '<option value="SUMMARY">SUMMARY</option>' + '<option value="strain">strain</option>' + '<option value="species">species</option>' + '<option value="genus">genus</option>' + '<option value="family">family</option>' + '<option value="order">order</option>' + '<option value="class">class</option>' + '<option value="phylum">phylum</option>' + '<option value="kingdom">kingdom</option>' + '<option value="domain">domain</option>' + '<option value="ALL">ALL</option>' + '<option value="NONE">NONE</option>' + '</select></td></tr></table>'; position = addOptionElement(position + 5, select); datasetDropDown = document.getElementById('datasets'); datasetButtonLast = document.getElementById('lastDataset'); datasetButtonPrev = document.getElementById('prevDataset'); datasetButtonNext = document.getElementById('nextDataset'); rankDropDown = document.getElementById('ranks'); if (chart === ChartEnum.GENOMIC) { for (i = 1; i < 10; i++) { rankDropDown.remove(1); // Remove taxonomic ranks from options } datasetDropDown.style.color='#FFFFFF' datasetDropDown.style.backgroundColor='#555555' // #B20DFF22' } position += datasetDropDown.clientHeight; } position = addOptionElement ( position + 5, '<input type="button" id="maxAbsoluteDepthDecrease" style="margin:1px 4px 0 10px" value="-"/>\ <span id="maxAbsoluteDepth"></span>\ <input type="button" id="maxAbsoluteDepthIncrease" style="margin:2px 1px 0 2px" value="+"/> Max depth', 'Maximum depth to display, counted from the top level \ and including collapsed wedges.' ); position = addOptionElement ( position, '<input type="button" id="fontSizeDecrease" style="margin:0 4px 0 10px" value="-"/>\ <span id="fontSize"></span>\ <input type="button" id="fontSizeIncrease" style="margin:0 2px 0 2px" value="+"/> Font size' ); position = addOptionElement ( position, '<input type="button" id="radiusDecrease" style="margin:0 4px 0 10px" value="-"/>\ <input type="button" id="radiusIncrease" style="margin:0 2px 0 1px" value="+"/> Chart size' ); position = addOptionElement ( position, '<input type="button" id="bkgBrightDecrease" style="margin:0 4px 5px 10px" value="-"/>\ <input type="button" id="bkgBrightIncrease" style="margin:0 2px 5px 1px" value="+"/> Bkg bright' ); if (hueName) { hueDisplayName = attributes[attributeIndex(hueName)].displayName; position = addOptionElement ( position + 5, '<input type="checkbox" id="useHue" style="float:left; ' + 'margin:1px 4px 0 12px"/><div>Color by ' + hueDisplayName + '</div>' ); useHueCheckBox = document.getElementById('useHue'); useHueCheckBox.checked = hueDefault; useHueCheckBox.onclick = handleResize; useHueCheckBox.onmousedown = suppressEvent; position = addOptionElement ( position, '<input type="checkbox" id="sortByScore"/> Use to sort', 'Activates sorting the taxa by this magnitude', '0px 2px 2px 25px' ); sortByScoreCheckBox = document.getElementById('sortByScore'); sortByScoreCheckBox.onclick = onSortChange; sortByScoreCheckBox.onmousedown = suppressEvent; } position = addOptionElement ( position, '<input type="checkbox" id="collapse" style="margin:4px 4px 0 12px" ' + 'checked="checked"/>Collapse', 'Collapse wedges that are redundant (entirely composed of another ' + 'wedge). Also affects score navigation, restricting to lowest level.' ); /* position = addOptionElement ( position, ' <input type="checkbox" id="shorten" checked="checked" />Shorten labels</div>', 'Prevent labels from overlapping by shortening them' ); position = addOptionElement ( position, ' <input type="checkbox" id="compress" checked="checked" />Compress', 'Compress wedges if needed to show the entire depth' ); */ position = addOptionElement ( position, '<input type="button" id="snapshot" style="margin:5px 2px 0 10px"\ value="Snapshot" title="Render the current view as SVG (Scalable \ Vector Graphics), a vectorial publication-quality format that can be saved or \ printed as PDF"/> <input type="button" id="help" value="?"\ onclick="window.open(\'https://github.com/khyox/recentrifuge/wiki\',\ \'help\')" title="Help"/>'); position = addOptionElement ( position + 5, '<input type="button" id="linkButton" style="margin:5px 2px 0 10px" value="Link"/>\ <input type="text" size="30" id="linkText"/>', 'Show a link to this view that can be copied for bookmarking or sharing' ); } function arrow(angleStart, angleEnd, radiusInner) { if (context.globalAlpha == 0) { return; } var angleCenter = (angleStart + angleEnd) / 2; var radiusArrowInner = radiusInner - gRadius / 10;//nodeRadius * gRadius; var radiusArrowOuter = gRadius * 1.1;//(1 + nodeRadius); var radiusArrowCenter = (radiusArrowInner + radiusArrowOuter) / 2; var pointLength = (radiusArrowOuter - radiusArrowInner) / 5; context.fillStyle = highlightFill; context.lineWidth = highlightLineWidth; // First, mask out the first half of the arrow. This will prevent the tips // from superimposing if the arrow goes most of the way around the circle. // Masking is done by setting the clipping region to the inverse of the // half-arrow, which is defined by cutting the half-arrow out of a large // rectangle // context.beginPath(); context.arc(0, 0, radiusInner, angleCenter, angleEnd, false); context.lineTo ( radiusArrowInner * Math.cos(angleEnd), radiusArrowInner * Math.sin(angleEnd) ); context.lineTo ( radiusArrowCenter * Math.cos(angleEnd) - pointLength * Math.sin(angleEnd), radiusArrowCenter * Math.sin(angleEnd) + pointLength * Math.cos(angleEnd) ); context.lineTo ( radiusArrowOuter * Math.cos(angleEnd), radiusArrowOuter * Math.sin(angleEnd) ); context.arc(0, 0, gRadius, angleEnd, angleCenter, true); context.closePath(); context.moveTo(-imageWidth, -imageHeight); context.lineTo(imageWidth, -imageHeight); context.lineTo(imageWidth, imageHeight); context.lineTo(-imageWidth, imageHeight); context.closePath(); context.save(); context.clip(); // Next, draw the other half-arrow with the first half masked out // context.beginPath(); context.arc(0, 0, radiusInner, angleCenter, angleStart, true); context.lineTo ( radiusArrowInner * Math.cos(angleStart), radiusArrowInner * Math.sin(angleStart) ); context.lineTo ( radiusArrowCenter * Math.cos(angleStart) + pointLength * Math.sin(angleStart), radiusArrowCenter * Math.sin(angleStart) - pointLength * Math.cos(angleStart) ); context.lineTo ( radiusArrowOuter * Math.cos(angleStart), radiusArrowOuter * Math.sin(angleStart) ); context.arc(0, 0, gRadius, angleStart, angleCenter, false); context.fill(); context.stroke(); // Finally, remove the clipping region and draw the first half-arrow. This // half is extended slightly to fill the seam. // context.restore(); context.beginPath(); context.arc(0, 0, radiusInner, angleCenter - 2 / (2 * Math.PI * radiusInner), angleEnd, false); context.lineTo ( radiusArrowInner * Math.cos(angleEnd), radiusArrowInner * Math.sin(angleEnd) ); context.lineTo ( radiusArrowCenter * Math.cos(angleEnd) - pointLength * Math.sin(angleEnd), radiusArrowCenter * Math.sin(angleEnd) + pointLength * Math.cos(angleEnd) ); context.lineTo ( radiusArrowOuter * Math.cos(angleEnd), radiusArrowOuter * Math.sin(angleEnd) ); context.arc(0, 0, gRadius, angleEnd, angleCenter - 2 / (2 * Math.PI * gRadius), true); context.fill(); context.stroke(); } function attributeIndex(aname) { for (var i = 0; i < attributes.length; i++) { if (aname == attributes[i].name) { return i; } } return null; } function bkgBrightDecrease() { var bkgBrightInt = parseInt(bkgBright, 16) if (bkgBrightInt > parseInt('555555', 16)) { bkgBright = (bkgBrightInt - 0x111111).toString(16) document.body.style.backgroundColor = '#' + bkgBright updateViewNeeded = true; } } function bkgBrightIncrease() { var bkgBrightInt = parseInt(bkgBright, 16) if (bkgBrightInt < parseInt('ffffff', 16)) { bkgBright = (bkgBrightInt + 0x111111).toString(16) document.body.style.backgroundColor = '#' + bkgBright updateViewNeeded = true; } } function checkHighlight() { var lastHighlightedNode = highlightedNode; var lastHighlightingHidden = highlightingHidden; highlightedNode = selectedNode; resetKeyOffset(); if (progress == 1) { selectedNode.checkHighlight(); if (selectedNode.getParent()) { selectedNode.getParent().checkHighlightCenter(); } focusNode.checkHighlightMap(); } if (highlightedNode != selectedNode) { if (highlightedNode == focusNode) { // canvas.style.display='none'; // window.resizeBy(1,0); // canvas.style.cursor='ew-resize'; // window.resizeBy(-1,0); // canvas.style.display='inline'; } else { // canvas.style.cursor='pointer'; } } else { // canvas.style.cursor='auto'; } if ( ( true || highlightedNode != lastHighlightedNode || highlightingHidden != highlightingHiddenLast ) && progress == 1 ) { draw(); // TODO: handle in update() } } function checkSelectedCollapse() { var newNode = selectedNode; while (newNode.getCollapse()) { newNode = newNode.children[0]; } if (newNode.children.length == 0 && newNode.getParent()) { newNode = newNode.getParent(); } if (newNode != selectedNode) { selectNode(newNode); } } function clearSearch() { if (search.value != '') { search.value = ''; nodesIndex = undefined; onSearchChange(); } } function createSVG() { svgNS = "http://www.w3.org/2000/svg"; var SVG = {}; SVG.xlinkns = "http://www.w3.org/1999/xlink"; var newSVG = document.createElementNS(svgNS, "svg:svg"); newSVG.setAttribute("id", "canvas"); // How big is the canvas in pixels newSVG.setAttribute("width", '100%'); newSVG.setAttribute("height", '100%'); // Set the coordinates used by drawings in the canvas // newSVG.setAttribute("viewBox", "0 0 " + imageWidth + " " + imageHeight); // Define the XLink namespace that SVG uses newSVG.setAttributeNS ( "http://www.w3.org/2000/xmlns/", "xmlns:xlink", SVG.xlinkns ); return newSVG; } function degrees(radians) { return radians * 180 / Math.PI; } function draw() { tweenFrames++; //resize(); // context.fillRect(0, 0, imageWidth, imageHeight); context.clearRect(0, 0, imageWidth, imageHeight); context.font = fontNormal; context.textBaseline = 'middle'; //context.strokeStyle = 'rgba(0, 0, 0, 0.3)'; context.translate(centerX, centerY); resetKeyOffset(); head.draw(false, false); // draw pie slices head.draw(true, false); // draw labels var pathRoot = selectedNode; if (focusNode != 0 && focusNode != selectedNode) { context.globalAlpha = 1; focusNode.drawHighlight(true); pathRoot = focusNode; } if ( highlightedNode && highlightedNode.getDepth() >= selectedNode.getDepth() && highlightedNode != focusNode ) { if ( progress == 1 && highlightedNode != selectedNode && ( highlightedNode != focusNode || focusNode.children.length > 0 ) ) { context.globalAlpha = 1; highlightedNode.drawHighlight(true); } //pathRoot = highlightedNode; } else if ( progress == 1 && highlightedNode.getDepth() < selectedNode.getDepth() ) { context.globalAlpha = 1; highlightedNode.drawHighlightCenter(); } if (quickLook && false) // TEMP { context.globalAlpha = 1 - progress / 2; selectedNode.drawHighlight(true); } else if (progress < 1)//&& zoomOut() ) { if (!zoomOut)//() ) { context.globalAlpha = selectedNode.alphaLine.current(); selectedNode.drawHighlight(true); } else if (selectedNodeLast) { context.globalAlpha = 1 - 4 * Math.pow(progress - .5, 2); selectedNodeLast.drawHighlight(false); } } drawDatasetName(); //drawHistory(); context.translate(-centerX, -centerY); context.globalAlpha = 1; mapRadius = (imageHeight / 2 - details.clientHeight - details.offsetTop) / (pathRoot.getDepth() - 1) * 3 / 4 / 2; if (mapRadius > maxMapRadius) { mapRadius = maxMapRadius; } mapBuffer = mapRadius / 2; //context.font = fontNormal; pathRoot.drawMap(pathRoot); if (hueDisplayName && useHue()) { drawLegend(); } } function drawBubble(angle, radius, width, radial, flip) { var height = fontSize * 2; var x; var y; width = width + fontSize; if (radial) { y = -fontSize; if (flip) { x = radius - width + fontSize / 2; } else { x = radius - fontSize / 2; } } else { x = -width / 2; y = -radius - fontSize; } if (snapshotMode) { drawBubbleSVG(x + centerX, y + centerY, width, height, fontSize, angle); } else { drawBubbleCanvas(x, y, width, height, fontSize, angle); } } function drawBubbleCanvas(x, y, width, height, radius, rotation) { context.strokeStyle = 'black'; context.lineWidth = highlightLineWidth; context.fillStyle = 'rgba(255, 255, 255, .75)'; context.rotate(rotation); roundedRectangle(x, y, width, fontSize * 2, fontSize); context.fill(); context.stroke(); context.rotate(-rotation); } function drawBubbleSVG(x, y, width, height, radius, rotation) { svg += '<rect x="' + x + '" y="' + y + '" width="' + width + '" height="' + height + '" rx="' + radius + '" ry="' + radius + '" fill="rgba(255, 255, 255, .75)' + '" class="highlight" ' + 'transform="rotate(' + degrees(rotation) + ',' + centerX + ',' + centerY + ')"/>'; } function drawDatasetName() { var alpha = datasetAlpha.current(); if (alpha > 0) { var radius = gRadius * compressedRadii[0] / -2; if (alpha > 1) { alpha = 1; } context.globalAlpha = alpha; drawBubble(0, -radius, datasetWidths[currentDataset], false, false); drawText(datasetNames[currentDataset], 0, radius, 0, 'center', true); } } function drawHistory() { var alpha = 1; context.textAlign = 'center'; for (var i = 0; i < nodeHistoryPosition && alpha > 0; i++) { context.globalAlpha = alpha - historyAlphaDelta * tweenFactor; context.fillText ( nodeHistory[nodeHistoryPosition - i - 1].name, 0, (i + tweenFactor) * historySpacingFactor * fontSize - 1 ); if (alpha > 0) { alpha -= historyAlphaDelta; } } context.globalAlpha = 1; } function drawLegend() { var width = imageHeight * .0265; var side = width * 0.9 var left_buttons = imageWidth * .008; var left = left_buttons + side + fontSize; var height = imageHeight * .15; var top = imageHeight - fontSize * 3.5 - height; var textLeft = left + width + fontSize / 2; var delta = (height - side) / 3; canvasButtons = [] // Delete previous buttons var buttonMost = new CanvasButton('mostScore', left_buttons, top, side, side, '#c87cca'); var buttonLest = new CanvasButton('lestScore', left_buttons, top + 3 * delta, side, side, '#d38381'); canvasButtons.push(buttonMost, buttonLest); if (nodesIndex !== undefined) { var buttonMore = new CanvasButton('moreScore', left_buttons, top + delta, side, side, '#81c8d3'); var buttonLess = new CanvasButton('lessScore', left_buttons, top + 2 * delta, side, side, '#96d281'); canvasButtons.push(buttonMore, buttonLess) } canvasButtons.forEach(function (element) { element.draw(context); }); context.fillStyle = 'black'; context.textAlign = 'start'; context.font = fontNormal; context.fillText(hueDisplayName, left_buttons, imageHeight - fontSize * 1.5); var gradient = context.createLinearGradient(0, top + height, 0, top); for (var i = 0; i < hueStopPositions.length; i++) { gradient.addColorStop(hueStopPositions[i], hueStopHsl[i]); var textY = top + (1 - hueStopPositions[i]) * height; if ( i === 0 || i === hueStopPositions.length - 1 || textY > top + fontSize && textY < top + height - fontSize ) { context.fillText(hueStopText[i], textLeft, textY); } } context.fillStyle = gradient; context.fillRect(left, top, width, height); context.lineWidth = thinLineWidth; context.strokeRect(left, top, width, height); // Sample statistics if (currentDataset < numRawSamples) { var stat = stats[currentDataset]; // Define aux position variables var statsX = textLeft + 2 * width; var statsY = top; var rad = width; context.font = "Bold 11px Ubuntu"; var statLabelText; if (chart === ChartEnum.GENOMIC) { context.fillStyle = 'rgba(170, 20, 255, 1)'; statLabelText = 'Functional sample statistics'; } else if (stat.is_ctrl) { context.fillStyle = 'rgba(50, 50, 200, 1)'; statLabelText = 'Control statistics'; } else { context.fillStyle = 'rgba(200, 50, 50, 1)'; statLabelText = 'Sample statistics'; } context.fillText(statLabelText, statsX + width, imageHeight - fontSize * 1.5); // Get the set of strings var oldFont = context.font; context.font = "10.5px monospace"; // In case the next line fails context.font = "10.5px Oxygen Mono"; var readTit; var nodeTit; if (chart === ChartEnum.GENOMIC) { readTit = 'Annotations read: ' nodeTit = 'GOs' } else { readTit = 'Sequences read: ' nodeTit = 'TaxIDs' } var statsStrs = [ readTit + stat.sread, ' those classified: ' + ( stat.sclas / stat.sread * 100).toPrecision(3) + '%', ' those accepted: ' + (stat.sfilt / stat.sclas * 100).toPrecision(3) + '%', 'Score average: ' + parseFloat(stat.scavg).toFixed(1), ' min: ' + parseFloat(stat.scmin).toFixed(1) + ' max: ' + parseFloat(stat.scmax).toFixed(1), 'Length average: ' + stat.lnavg, ' min: ' + stat.lnmin + ' max: ' + stat.lnmax, nodeTit + ' by classifier: ' + stat.tclas, ' those accepted: ' + (stat.tfilt / stat.tclas * 100).toPrecision(3) + '%', ' final: ' + (stat.tfold / stat.tfilt * 100).toPrecision(3) + '% [' + stat.tfold + ']' ]; var maxTextWidth = Math.max.apply(null, statsStrs.map(function (text) { return context.measureText(text).width })); // Draw the rounded rectangle context.lineWidth = 3; if (chart === ChartEnum.GENOMIC) { context.strokeStyle = '#B20DFF'; context.fillStyle = 'rgba(180, 100, 255, 0.2)'; } else if (stat.is_ctrl) { context.strokeStyle = '#3333CC'; context.fillStyle = 'rgba(0, 255, 255, 0.2)'; } else { context.strokeStyle = '#CC3333'; context.fillStyle = 'rgba(255, 255, 0, 0.2)'; } var box = new roundedRectangle( statsX, statsY, 1.2 * maxTextWidth, height, {tr: rad, bl: rad}); context.stroke(); context.fill(); context.fillStyle = context.strokeStyle = '#222222'; // Write the stats inside var statsNum = statsStrs.length; var statsLeft = statsX + maxTextWidth * 0.1; var statsDelta = height / (statsNum + 1); for (i = 0; i < statsNum; i++) { context.fillText(statsStrs[i], statsLeft, top + i * statsDelta + fontSize); } // Restore font context.font = oldFont; } } function drawLegendSVG() { var left = imageWidth * .01; var width = imageHeight * .0265; var height = imageHeight * .15; var top = imageHeight - fontSize * 3.5 - height; var textLeft = left + width + fontSize / 2; var text = ''; text += svgText(hueDisplayName, left, imageHeight - fontSize * 1.5); var svgtest = '<linearGradient id="gradient" x1="0%" y1="100%" x2="0%" y2="0%">'; for (var i = 0; i < hueStopPositions.length; i++) { svgtest += '<stop offset="' + round(hueStopPositions[i] * 100) + '%" style="stop-color:' + hueStopHsl[i] + '"/>'; var textY = top + (1 - hueStopPositions[i]) * height; if ( i == 0 || i == hueStopPositions.length - 1 || textY > top + fontSize && textY < top + height - fontSize ) { text += svgText(hueStopText[i], textLeft, textY); } } svgtest += '</linearGradient>'; //alert(svgtest); svg += svgtest; svg += '<rect style="fill:url(#gradient)" x="' + left + '" y="' + top + '" width="' + width + '" height="' + height + '"/>'; svg += text; } function drawSearchHighlights(label, bubbleX, bubbleY, rotation, center) { var index = -1; var labelLength = label.length; bubbleX -= fontSize / 4; do { index = label.toLowerCase().indexOf(search.value.toLowerCase(), index + 1); if (index != -1 && index < labelLength) { var dim = context.measureText(label.substr(0, index)); var x = bubbleX + dim.width; dim = context.measureText(label.substr(index, search.value.length)); var y = bubbleY - fontSize * 3 / 4; var width = dim.width + fontSize / 2; var height = fontSize * 3 / 2; var radius = fontSize / 2; if (snapshotMode) { if (center) { x += centerX; y += centerY; } svg += '<rect x="' + x + '" y="' + y + '" width="' + width + '" height="' + height + '" rx="' + radius + '" ry="' + radius + '" class="searchHighlight' + '" transform="rotate(' + degrees(rotation) + ',' + centerX + ',' + centerY + ')"/>'; } else { context.fillStyle = 'rgb(255, 255, 100)'; context.rotate(rotation); roundedRectangle(x, y, width, height, radius); context.fill(); context.rotate(-rotation); } } } while (index != -1 && index < labelLength); } function drawText(text, x, y, angle, anchor, bold, color) { if (color == undefined) { color = 'black'; } if (snapshotMode) { svg += '<text x="' + (centerX + x) + '" y="' + (centerY + y) + '" text-anchor="' + anchor + '" style="font-color:' + color + ';font-weight:' + (bold ? 'bold' : 'normal') + '" transform="rotate(' + degrees(angle) + ',' + centerX + ',' + centerY + ')">' + text + '</text>'; } else { context.fillStyle = color; context.textAlign = anchor; context.font = bold ? fontBold : fontNormal; context.rotate(angle); context.fillText(text, x, y); context.rotate(-angle); } } function drawTextPolar (text, innerText, angle, radius, radial, bubble, bold, searchResult, searchResults) { var anchor; var textX; var textY; var spacer; var totalText = text; var flip; if (snapshotMode) { spacer = '   '; } else { spacer = ' '; } if (radial) { flip = angle < 3 * Math.PI / 2; if (flip) { angle -= Math.PI; radius = -radius; anchor = 'end'; if (innerText) { totalText = text + spacer + innerText; } } else { anchor = 'start'; if (innerText) { totalText = innerText + spacer + text; } } textX = radius; textY = 0; } else { flip = angle < Math.PI || angle > 2 * Math.PI; var label; anchor = snapshotMode ? 'middle' : 'center'; if (flip) { angle -= Math.PI; radius = -radius; } angle += Math.PI / 2; textX = 0; textY = -radius; } if (bubble) { var textActual = totalText; if (innerText && snapshotMode) { if (flip) { textActual = text + ' ' + innerText; } else { textActual = innerText + ' ' + text; } } if (searchResults) { textActual = textActual + searchResultString(searchResults); } var textWidth = measureText(textActual, bold); var x = textX; if (anchor == 'end') { x -= textWidth; } else if (anchor != 'start') { // centered x -= textWidth / 2; } drawBubble(angle, radius, textWidth, radial, flip); if (searchResult) { drawSearchHighlights ( textActual, x, textY, angle, true ) } } if (searchResults) { totalText = totalText + searchResultString(searchResults); } drawText(totalText, textX, textY, angle, anchor, bold); return flip; } function drawTick(start, length, angle) { if (snapshotMode) { svg += '<line x1="' + (centerX + start) + '" y1="' + centerY + '" x2="' + (centerX + start + length) + '" y2="' + centerY + '" class="tick" transform="rotate(' + degrees(angle) + ',' + centerX + ',' + centerY + ')"/>'; } else { context.rotate(angle); context.beginPath(); context.moveTo(start, 0); context.lineTo(start + length, 0); context.lineWidth = thinLineWidth * 2; context.stroke(); context.rotate(-angle); } } function drawWedge (angleStart, angleEnd, radiusInner, radiusOuter, color, patternAlpha, highlight) { if (context.globalAlpha == 0) { return; } if (snapshotMode) { if (angleEnd == angleStart + Math.PI * 2) { // fudge to prevent overlap, which causes arc ambiguity // angleEnd -= .1 / gRadius; } var longArc = angleEnd - angleStart > Math.PI ? 1 : 0; var x1 = centerX + radiusInner * Math.cos(angleStart); var y1 = centerY + radiusInner * Math.sin(angleStart); var x2 = centerX + gRadius * Math.cos(angleStart); var y2 = centerY + gRadius * Math.sin(angleStart); var x3 = centerX + gRadius * Math.cos(angleEnd); var y3 = centerY + gRadius * Math.sin(angleEnd); var x4 = centerX + radiusInner * Math.cos(angleEnd); var y4 = centerY + radiusInner * Math.sin(angleEnd); var dArray = [ " M ", x1, ",", y1, " L ", x2, ",", y2, " A ", gRadius, ",", gRadius, " 0 ", longArc, ",1 ", x3 , ",", y3, " L ", x4, ",", y4, " A ", radiusInner, ",", radiusInner, " 0 ", longArc, " 0 ", x1, ",", y1, " Z " ]; svg += '<path class="' + (highlight ? 'highlight' : 'wedge') + '" fill="' + color + '" d="' + dArray.join('') + '"/>'; if (patternAlpha > 0) { svg += '<path class="wedge" fill="url(#hiddenPattern)" d="' + dArray.join('') + '"/>'; } } else { // fudge to prevent seams during animation // angleEnd += 1 / gRadius; context.fillStyle = color; context.beginPath(); context.arc(0, 0, radiusInner, angleStart, angleEnd, false); context.arc(0, 0, radiusOuter, angleEnd, angleStart, true); context.closePath(); context.fill(); if (patternAlpha > 0) { context.save(); context.clip(); context.globalAlpha = patternAlpha; context.fillStyle = hiddenPattern; context.fill(); context.restore(); } if (highlight) { context.lineWidth = highlight ? highlightLineWidth : thinLineWidth; context.strokeStyle = 'black'; context.stroke(); } } } function expand(node) { selectNode(node); updateView(); } function focusLost() { mouseX = -1; mouseY = -1; checkHighlight(); document.body.style.cursor = 'auto'; } function fontSizeDecrease() { if (fontSize > 1) { fontSize--; updateViewNeeded = true; } } function fontSizeIncrease() { fontSize++; updateViewNeeded = true; } function getGetString(name, value, bool) { return name + '=' + (bool ? value ? 'true' : 'false' : value); } function hideLink() { hide(linkText); show(linkButton); } function show(object) { object.style.display = 'inline'; } function hide(object) { object.style.display = 'none'; } function showLink() { var urlHalves = String(document.location).split('?'); var newGetVariables = new Array(); newGetVariables.push ( getGetString('dataset', currentDataset, false), getGetString('node', selectedNode.id, false), getGetString('collapse', collapse, true), getGetString('color', useHue(), true), getGetString('depth', maxAbsoluteDepth - 1, false), getGetString('font', fontSize, false), getGetString('key', showKeys, true) ); hide(linkButton); show(linkText); linkText.value = urlHalves[0] + '?' + getVariables.concat(newGetVariables).join('&'); //linkText.disabled = false; linkText.focus(); linkText.select(); //linkText.disabled = true; // document.location = urlHalves[0] + '?' + getVariables.join('&'); } function getFirstChild(element) { element = element.firstChild; if (element && element.nodeType != 1) { element = getNextSibling(element); } return element; } function getNextSibling(element) { do { element = element.nextSibling; } while (element && element.nodeType != 1); return element; } function getPercentage(fraction) { return round(fraction * 100); } function hslText(hue) { if (1 || snapshotMode) { // Safari doesn't seem to allow hsl() in SVG var rgb = hslToRgb(hue, saturation, (lightnessBase + lightnessMax) / 2); return rgbText(rgb.r, rgb.g, rgb.b); } else { var hslArray = [ 'hsl(', Math.floor(hue * 360), ',', Math.floor(saturation * 100), '%,', Math.floor((lightnessBase + lightnessMax) * 50), '%)' ]; return hslArray.join(''); } } function hslToRgb(h, s, l) { var m1, m2; var r, g, b; if (s == 0) { r = g = b = Math.floor((l * 255)); } else { if (l <= 0.5) { m2 = l * (s + 1); } else { m2 = l + s - l * s; } m1 = l * 2 - m2; r = Math.floor(hueToRgb(m1, m2, h + 1 / 3)); g = Math.floor(hueToRgb(m1, m2, h)); b = Math.floor(hueToRgb(m1, m2, h - 1 / 3)); } return {r: r, g: g, b: b}; } function hueToRgb(m1, m2, hue) { var v; while (hue < 0) { hue += 1; } while (hue > 1) { hue -= 1; } if (6 * hue < 1) v = m1 + (m2 - m1) * hue * 6; else if (2 * hue < 1) v = m2; else if (3 * hue < 2) v = m1 + (m2 - m1) * (2 / 3 - hue) * 6; else v = m1; return 255 * v; } function interpolateHue(hueStart, hueEnd, valueStart, valueEnd) { // since the gradient will be RGB based, we need to add stops to hit all the // colors in the hue spectrum function selective_round(value){ // Selective round depending on the hue scale width if(valueEnd - valueStart < 10){ return(value.toFixed(1)) } else { return(round(value)) } } hueStopPositions = new Array(); hueStopHsl = new Array(); hueStopText = new Array(); hueStopPositions.push(0); hueStopHsl.push(hslText(hueStart)); hueStopText.push(selective_round(valueStart)); for ( var i = (hueStart > hueEnd ? 5 / 6 : 1 / 6); (hueStart > hueEnd ? i > 0 : i < 1); i += (hueStart > hueEnd ? -1 : 1) / 6 ) { if ( hueStart > hueEnd ? i > hueEnd && i < hueStart : i > hueStart && i < hueEnd ) { hueStopPositions.push(lerp(i, hueStart, hueEnd, 0, 1)); hueStopHsl.push(hslText(i)); hueStopText.push(selective_round(lerp( i, hueStart, hueEnd, valueStart, valueEnd))); } } hueStopPositions.push(1); hueStopHsl.push(hslText(hueEnd)); hueStopText.push(selective_round(valueEnd)); } function keyLineAngle(angle, keyAngle, bendRadius, keyX, keyY, pointsX, pointsY) { if (angle < Math.PI / 2 && keyY < bendRadius * Math.sin(angle) || angle > Math.PI / 2 && keyY < bendRadius) { return Math.asin(keyY / bendRadius); } else { // find the angle of the normal to a tangent line that goes to // the label var textDist = Math.sqrt ( Math.pow(keyX, 2) + Math.pow(keyY, 2) ); var tanAngle = Math.acos(bendRadius / textDist) + keyAngle; if (angle < tanAngle || angle < Math.PI / 2)//|| labelLeft < centerX ) { // angle doesn't reach far enough for tangent; collapse and // connect directly to label if (keyY / Math.tan(angle) > 0) { pointsX.push(keyY / Math.tan(angle)); pointsY.push(keyY); } else { pointsX.push(bendRadius * Math.cos(angle)); pointsY.push(bendRadius * Math.sin(angle)); } return angle; } else { return tanAngle; } } } function keyOffset() { return imageHeight - (keys - currentKey + 1) * (keySize + keyBuffer) + keyBuffer - margin; } function lerp(value, fromStart, fromEnd, toStart, toEnd) { // Rescale value from source scale [fromStart, fromEnd] // to target scale [toStart, toEnd] return (value - fromStart) * (toEnd - toStart) / (fromEnd - fromStart) + toStart; } function createCanvas() { canvas = document.createElement('canvas'); document.body.appendChild(canvas); context = canvas.getContext('2d'); } function load() { document.body.style.overflow = "hidden"; document.body.style.margin = 0; document.body.style.backgroundColor = '#' + bkgBright; createCanvas(); if (context == undefined) { document.body.innerHTML = '\ <br/>Recentrifuge: Sorry, this browser does not support HTML5 (please see \ <a href="https://github.com/khyox/recentrifuge/wiki/Browser-support">Browser support</a>).\ '; return; } if (typeof context.fillText != 'function') { document.body.innerHTML = '\ <br/>Recentrifuge: Sorry, this browser does not support HTML5 canvas text (please see \ <a href="https://github.com/khyox/recentrifuge/wiki/Browser-support">Browser support</a>).\ '; return; } resize(); var kronaElement = document.getElementsByTagName('krona')[0]; var magnitudeName; var hueName; var hueDefault; var hueStart; var hueEnd; var valueStart; var valueEnd; if (kronaElement.getAttribute('collapse') !== undefined) { collapse = kronaElement.getAttribute('collapse') === 'true'; } if (kronaElement.getAttribute('key') !== undefined) { showKeys = kronaElement.getAttribute('key') === 'true'; } if (kronaElement.getAttribute('chart') !== undefined) { switch (kronaElement.getAttribute('chart')) { case 'TAXOMIC': chart = ChartEnum.TAXOMIC; fontFamily = 'Ubuntu' fontSize = 11 break; case 'GENOMIC': chart = ChartEnum.GENOMIC; fontFamily = 'Saira Condensed' fontSize = 12 break; } } for ( var element = getFirstChild(kronaElement); element; element = getNextSibling(element) ) { switch (element.tagName.toLowerCase()) { case 'attributes': magnitudeName = element.getAttribute('magnitude'); // for ( var attributeElement = getFirstChild(element); attributeElement; attributeElement = getNextSibling(attributeElement) ) { var tag = attributeElement.tagName.toLowerCase(); if (tag == 'attribute') { var attribute = new Attribute(); attribute.name = attributeElement.firstChild.nodeValue.toLowerCase(); attribute.displayName = attributeElement.getAttribute('display'); if (attributeElement.getAttribute('tip')) { attribute.tip = attributeElement.getAttribute('tip'); } if (attributeElement.getAttribute('hrefBase')) { attribute.hrefBase = attributeElement.getAttribute('hrefBase'); } if (attributeElement.getAttribute('target')) { attribute.target = attributeElement.getAttribute('target'); } if (attribute.name === magnitudeName) { magnitudeIndex = attributes.length; } if (attributeElement.getAttribute('listAll')) { attribute.listAll = attributeElement.getAttribute('listAll').toLowerCase(); } else if (attributeElement.getAttribute('listNode')) { attribute.listNode = attributeElement.getAttribute('listNode').toLowerCase(); } else if (attributeElement.getAttribute('dataAll')) { attribute.dataAll = attributeElement.getAttribute('dataAll').toLowerCase(); } else if (attributeElement.getAttribute('dataNode')) { attribute.dataNode = attributeElement.getAttribute('dataNode').toLowerCase(); } if (attributeElement.getAttribute('postUrl')) { attribute.postUrl = attributeElement.getAttribute('postUrl'); } if (attributeElement.getAttribute('postVar')) { attribute.postVar = attributeElement.getAttribute('postVar'); } if (attributeElement.getAttribute('mono')) { attribute.mono = true; } attributes.push(attribute); } else if (tag == 'list') { var attribute = new Attribute(); attribute.name = attributeElement.firstChild.nodeValue; attribute.list = true; attributes.push(attribute); } else if (tag == 'data') { var attribute = new Attribute(); attribute.name = attributeElement.firstChild.nodeValue; attribute.data = true; attributes.push(attribute); var enableScript = document.createElement('script'); var date = new Date(); enableScript.src = attributeElement.getAttribute('enable') + '?' + date.getTime(); document.body.appendChild(enableScript); } } break; case 'color': hueName = element.getAttribute('attribute'); hueStart = Number(element.getAttribute('hueStart')) / 360; hueEnd = Number(element.getAttribute('hueEnd')) / 360; valueStart = Number(element.getAttribute('valueStart')); valueEnd = Number(element.getAttribute('valueEnd')); // interpolateHue(hueStart, hueEnd, valueStart, valueEnd); // if (element.getAttribute('default') == 'true') { hueDefault = true; } break; case 'datasets': datasetNames = []; stats = []; numRawSamples = element.getAttribute('rawSamples'); var i = 0; for (var j = getFirstChild(element); j; j = getNextSibling(j)) { var datasetName = j.firstChild.nodeValue; datasetNames.push(datasetName); if (i < numRawSamples) { // Get stats of raw samples var stat = new SampleStats( datasetName, j.getAttribute('isctr'), j.getAttribute('sread'), j.getAttribute('sclas'), j.getAttribute('sfilt'), j.getAttribute('scmin'), j.getAttribute('scavg'), j.getAttribute('scmax'), j.getAttribute('lnmin'), j.getAttribute('lnavg'), j.getAttribute('lnmax'), j.getAttribute('tclas'), j.getAttribute('tfilt'), j.getAttribute('tfold') ); stats.push(stat) } } datasets = datasetNames.length; break; case 'node': head = loadTreeDOM ( element, magnitudeName, hueName, hueStart, hueEnd, valueStart, valueEnd ); break; } } // get GET options // var urlHalves = String(document.location).split('?'); var datasetDefault = 0; var maxDepthDefault; var nodeDefault = 0; // if (urlHalves[1]) { var vars = urlHalves[1].split('&'); for (i = 0; i < vars.length; i++) { var pair = vars[i].split('='); switch (pair[0]) { case 'collapse': collapse = pair[1] == 'true'; break; case 'color': hueDefault = pair[1] == 'true'; break; case 'dataset': datasetDefault = Number(pair[1]); break; case 'depth': maxDepthDefault = Number(pair[1]) + 1; break; case 'key': showKeys = pair[1] == 'true'; break; case 'font': fontSize = Number(pair[1]); break; case 'node': nodeDefault = Number(pair[1]); break; default: getVariables.push(pair[0] + '=' + pair[1]); break; } } } addOptionElements(hueName, hueDefault); if (datasets > 1) { if (datasets > numRawSamples) { // Check for cross-analysis samples selectRank(DEFAULT_RANK); } else { selectRank(NO_RANK); } } setCallBacks(); head.sort(); maxAbsoluteDepth = 0; selectDataset(datasetDefault); if (maxDepthDefault && maxDepthDefault < head.maxDepth) { maxAbsoluteDepth = maxDepthDefault; } else { maxAbsoluteDepth = head.maxDepth; } selectNode(nodes[nodeDefault]); setInterval(update, 20); window.onresize = handleResize; updateMaxAbsoluteDepth(); updateViewNeeded = true; } function loadTreeDOM (domNode, magnitudeName, hueName, hueStart, hueEnd, valueStart, valueEnd) { var newNode = new Node(); newNode.name = domNode.getAttribute('name'); if (domNode.getAttribute('href')) { newNode.href = domNode.getAttribute('href'); } if (hueName) { newNode.hues = new Array(); } for (var i = getFirstChild(domNode); i; i = getNextSibling(i)) { switch (i.tagName.toLowerCase()) { case 'node': var newChild = loadTreeDOM ( i, magnitudeName, hueName, hueStart, hueEnd, valueStart, valueEnd ); newChild.parent = newNode; newNode.children.push(newChild); break; default: var attributeName = i.tagName.toLowerCase(); var index = attributeIndex(attributeName); // newNode.attributes[index] = new Array(); // for (var j = getFirstChild(i); j; j = getNextSibling(j)) { if (attributes[index] == undefined) { var x = 5; } if (attributes[index].list) { newNode.attributes[index].push(new Array()); for (var k = getFirstChild(j); k; k = getNextSibling(k)) { newNode.attributes[index][ newNode.attributes[ index].length - 1].push( k.firstChild.nodeValue); } } else { var value = j.firstChild ? j.firstChild.nodeValue : ''; if (j.getAttribute('href')) { var target; if (attributes[index].target) { target = ' target="' + attributes[index].target + '"'; } value = '<a href="' + attributes[index].hrefBase + j.getAttribute('href') + '"' + target + '>' + value + '</a>'; } newNode.attributes[index].push(value); } } // if (attributeName == magnitudeName || attributeName == hueName) { for (j = 0; j < datasets; j++) { // j is the dataset index (goes from 0 to datasets-1) var value = newNode.attributes[index][j] == undefined ? 0 : Number(newNode.attributes[index][j]); newNode.attributes[index][j] = value; if (attributeName == hueName) { var hue = lerp ( value, valueStart, valueEnd, hueStart, hueEnd ); if (hue < hueStart == hueStart < hueEnd) { hue = hueStart; } else if (hue > hueEnd == hueStart < hueEnd) { hue = hueEnd; } newNode.hues[j] = hue; } } if (attributeName == hueName) { newNode.hue = new Tween(newNode.hues[0], newNode.hues[0]); } } break; } } return newNode; } function maxAbsoluteDepthDecrease() { if (maxAbsoluteDepth > 2) { maxAbsoluteDepth--; head.setMaxDepths(); handleResize(); } } function maxAbsoluteDepthIncrease() { if (maxAbsoluteDepth < head.maxDepth) { maxAbsoluteDepth++; head.setMaxDepths(); handleResize(); } } function measureText(text, bold) { context.font = bold ? fontBold : fontNormal; var dim = context.measureText(text); return dim.width; } function min(a, b) { return a < b ? a : b; } function minWidth() { // Min wedge width (at center) for displaying a node (or for displaying a // label if it's at the highest level being viewed, multiplied by 2 to make // further calculations simpler return (fontSize * 2.3); } function mouseMove(e) { mouseX = e.pageX; mouseY = e.pageY - headerHeight; mouseXRel = (mouseX - centerX) * backingScale() mouseYRel = (mouseY - centerY) * backingScale() if (head && !quickLook) { checkHighlight(); } } function mouseClick(e) { // Event listener function for mouse click on CANVAS if (highlightedNode == focusNode && focusNode != selectedNode || selectedNode.hasParent(highlightedNode)) { if (highlightedNode.hasChildren()) { expand(highlightedNode); } } else if (progress == 1)//( highlightedNode != selectedNode ) { setFocus(highlightedNode); // document.body.style.cursor='ew-resize'; draw(); checkHighlight(); var date = new Date(); mouseDownTime = date.getTime(); mouseDown = true; var button = undefined; for (var i = 0; i < canvasButtons.length; i++) { if (canvasButtons[i].is_inside(e.pageX, e.pageY)) { context.strokeStyle = '#CC0000'; context.lineWidth = 2; button = canvasButtons[i]; context.strokeRect(button.x, button.y, button.w, button.h); } } if (button) { // Reorder the array of nodes only when needed if (nodesIndex === undefined || !nodes.reduce( function (acc, current, index) { // Calculate deviation from id == index for every node return acc + Math.abs(current.id - index) }, 0)) { nodes.sort(function (a, b) { return b.getHue() - a.getHue() }); } function lookForLeaf(testIndex, reverse) { // Look for nodes without children but with counts for (; testIndex >= 0 && testIndex <= nodes.length - 1 && !nodes[testIndex].isLeaf(); reverse ? testIndex-- : testIndex++) { } if (testIndex >= 0 && testIndex <= nodes.length - 1 && nodes[testIndex].isLeaf()) nodesIndex = testIndex; } function lookForNode(testIndex, reverse) { // Look for nodes with counts for (; testIndex >= 0 && testIndex <= nodes.length - 1 && nodes[testIndex].getHue() <= 0; reverse ? testIndex-- : testIndex++) { } if (testIndex >= 0 && testIndex <= nodes.length - 1 && nodes[testIndex].getHue() > 0) nodesIndex = testIndex; } switch (button.name) { case 'mostScore': nodesIndex = 0; if (collapseCheckBox.checked) { lookForLeaf(nodesIndex, false); } else { lookForNode(nodesIndex, false); } break; case 'moreScore': if (collapseCheckBox.checked) { lookForLeaf(nodesIndex - 1, true); } else { lookForNode(nodesIndex - 1, true); } break; case 'lessScore': if (collapseCheckBox.checked) { lookForLeaf(nodesIndex + 1, false); } else { lookForNode(nodesIndex + 1, false); } break; case 'lestScore': nodesIndex = nodes.length - 1; if (collapseCheckBox.checked) { lookForLeaf(nodesIndex, true); } else { lookForNode(nodesIndex, true); } break; default: alert('ERROR! Unknown button in canvas. Ignoring!') } search.value = nodes[nodesIndex].name; onSearchChange(); context.strokeStyle = '#CC0000'; context.lineWidth = 2; context.strokeRect(button.x, button.y, button.w, button.h); setTimeout(function () { drawLegend() }, 700) } } } function mouseUp(e) { if (quickLook) { navigateBack(); quickLook = false; } mouseDown = false; } function navigateBack() { if (nodeHistoryPosition > 0) { nodeHistory[nodeHistoryPosition] = selectedNode; nodeHistoryPosition--; if (nodeHistory[nodeHistoryPosition].collapse) { collapseCheckBox.checked = collapse = false; } setSelectedNode(nodeHistory[nodeHistoryPosition]); updateDatasetButtons(); updateView(); } } function navigateUp() { if (selectedNode.getParent()) { selectNode(selectedNode.getParent()); updateView(); } } function navigateForward() { if (nodeHistoryPosition < nodeHistory.length - 1) { nodeHistoryPosition++; var newNode = nodeHistory[nodeHistoryPosition]; if (newNode.collapse) { collapseCheckBox.checked = collapse = false; } if (nodeHistoryPosition == nodeHistory.length - 1) { // this will ensure the forward button is disabled nodeHistory.length = nodeHistoryPosition; } setSelectedNode(newNode); updateDatasetButtons(); updateView(); } } function nextDataset() { var newDataset = currentDataset; do { if (newDataset === datasets - 1) { newDataset = 0; } else { newDataset++; } } while (datasetDropDown.options[newDataset].disabled || datasetDropDown.options[newDataset].hidden) selectDataset(newDataset); } function onDatasetChange() { selectDataset(datasetDropDown.selectedIndex); nodesIndex = undefined; } function onKeyDown(event) { if ( event.keyCode == 37 && document.activeElement.id != 'search' && document.activeElement.id != 'linkText' ) { navigateBack(); event.preventDefault(); } else if ( event.keyCode == 39 && document.activeElement.id != 'search' && document.activeElement.id != 'linkText' ) { navigateForward(); event.preventDefault(); } else if (event.keyCode == 38 && datasets > 1) { prevDataset(); //if ( document.activeElement.id == 'datasets' ) { event.preventDefault(); } } else if (event.keyCode == 40 && datasets > 1) { nextDataset(); //if ( document.activeElement.id == 'datasets' ) { event.preventDefault(); } } else if (event.keyCode == 9 && datasets > 1) { selectLastDataset(); event.preventDefault(); } else if (event.keyCode == 83) { progress += .2; } else if (event.keyCode == 66) { progress -= .2; } else if (event.keyCode == 70) { progress = 1; } } function onKeyPress(event) { if (event.keyCode == 38 && datasets > 1) { // prevDataset(); //if ( document.activeElement.id == 'datasets' ) { event.preventDefault(); } } else if (event.keyCode == 40 && datasets > 1) { // nextDataset(); //if ( document.activeElement.id == 'datasets' ) { event.preventDefault(); } } } function onKeyUp(event) { if (event.keyCode == 27 && document.activeElement.id == 'search') { search.value = ''; onSearchChange(); } else if (event.keyCode == 38 && datasets > 1) { // prevDataset(); //if ( document.activeElement.id == 'datasets' ) { event.preventDefault(); } } else if (event.keyCode == 40 && datasets > 1) { // nextDataset(); //if ( document.activeElement.id == 'datasets' ) { event.preventDefault(); } } } function onRankChange() { selectRank(rankDropDown.value); } function onSearchChange() { nSearchResults = 0; head.search(); if (search.value == '') { searchResults.innerHTML = ''; } else { searchResults.innerHTML = nSearchResults + ' results'; } setFocus(selectedNode); draw(); } function onSortChange() { head.sort(); head.setMagnitudes(0); handleResize(); } function post(url, variable, value, postWindow) { var form = document.createElement('form'); var input = document.createElement('input'); var inputDataset = document.createElement('input'); form.appendChild(input); form.appendChild(inputDataset); form.method = "POST"; form.action = url; if (postWindow == undefined) { form.target = '_blank'; postWindow = window; } input.type = 'hidden'; input.name = variable; input.value = value; inputDataset.type = 'hidden'; inputDataset.name = 'dataset'; inputDataset.value = currentDataset; postWindow.document.body.appendChild(form); form.submit(); } function prevDataset() { var newDataset = currentDataset; do { if (newDataset == 0) { newDataset = datasets - 1; } else { newDataset--; } } while (datasetDropDown.options[newDataset].disabled || datasetDropDown.options[newDataset].hidden); selectDataset(newDataset); } function radiusDecrease() { if (bufferFactor < .309) { bufferFactor += .03; updateViewNeeded = true; } } function radiusIncrease() { if (bufferFactor > .041) { bufferFactor -= .03; updateViewNeeded = true; } } function resetKeyOffset() { currentKey = 1; keyMinTextLeft = centerX + gRadius + buffer - buffer / (keys + 1) / 2 + fontSize / 2; keyMinAngle = 0; } function rgbText(r, g, b) { var rgbArray = [ "rgb(", Math.floor(r), ",", Math.floor(g), ",", Math.floor(b), ")" ]; return rgbArray.join(''); } function round(number) { if (number >= 1 || number <= -1) { return number.toFixed(0); } else { return number.toPrecision(1); } } function roundedRectangle(x, y, width, height, radius, fill, stroke) { // Optionals: radius, stroke, fill if (typeof stroke === 'undefined') { stroke = true; } if (typeof radius === 'undefined') { radius = 5; } else if (typeof radius === 'number') { if (radius * 2 > width) { radius = width / 2; } if (radius * 2 > height) { radius = height / 2; } radius = {tl: radius, tr: radius, br: radius, bl: radius}; } else { var defaultRadius = {tl: 0, tr: 0, br: 0, bl: 0}; for (var side in defaultRadius) { radius[side] = radius[side] || defaultRadius[side]; } } context.beginPath(); context.arc(x + radius.tl, y + radius.tl, radius.tl, Math.PI, Math.PI * 3 / 2, false); context.lineTo(x + width - radius.tr, y); context.arc(x + width - radius.tr, y + radius.tr, radius.tr, Math.PI * 3 / 2, Math.PI * 2, false); context.lineTo(x + width, y + height - radius.br); context.arc(x + width - radius.br, y + height - radius.br, radius.br, 0, Math.PI / 2, false); context.lineTo(x + radius.bl, y + height); context.arc(x + radius.bl, y + height - radius.bl, radius.bl, Math.PI / 2, Math.PI, false); context.lineTo(x, y + radius.tl); if (fill) { context.fill(); } if (stroke) { context.stroke(); } } function passClick(e) { mouseClick(e); } function searchResultString(results) { var searchResults = this.searchResults; if (this.isSearchResult) { // don't count ourselves searchResults--; } return ' - ' + results + (results > 1 ? ' results' : ' result'); } function setCallBacks() { canvas.onselectstart = function () { return false; } // prevent unwanted highlighting options.onselectstart = function () { return false; } // prevent unwanted highlighting document.onmousemove = mouseMove; window.onblur = focusLost; window.onmouseout = focusLost; document.onkeyup = onKeyUp; document.onkeydown = onKeyDown; canvas.onmousedown = mouseClick; document.onmouseup = mouseUp; keyControl.onclick = toggleKeys; collapseCheckBox = document.getElementById('collapse'); collapseCheckBox.checked = collapse; collapseCheckBox.onclick = handleResize; collapseCheckBox.onmousedown = suppressEvent; maxAbsoluteDepthText = document.getElementById('maxAbsoluteDepth'); maxAbsoluteDepthButtonDecrease = document.getElementById('maxAbsoluteDepthDecrease'); maxAbsoluteDepthButtonIncrease = document.getElementById('maxAbsoluteDepthIncrease'); maxAbsoluteDepthButtonDecrease.onclick = maxAbsoluteDepthDecrease; maxAbsoluteDepthButtonIncrease.onclick = maxAbsoluteDepthIncrease; maxAbsoluteDepthButtonDecrease.onmousedown = suppressEvent; maxAbsoluteDepthButtonIncrease.onmousedown = suppressEvent; fontSizeText = document.getElementById('fontSize'); fontSizeButtonDecrease = document.getElementById('fontSizeDecrease'); fontSizeButtonIncrease = document.getElementById('fontSizeIncrease'); fontSizeButtonDecrease.onclick = fontSizeDecrease; fontSizeButtonIncrease.onclick = fontSizeIncrease; fontSizeButtonDecrease.onmousedown = suppressEvent; fontSizeButtonIncrease.onmousedown = suppressEvent; bkgBrightButtonDecrease = document.getElementById('bkgBrightDecrease'); bkgBrightButtonIncrease = document.getElementById('bkgBrightIncrease'); bkgBrightButtonDecrease.onclick = bkgBrightDecrease; bkgBrightButtonIncrease.onclick = bkgBrightIncrease; bkgBrightButtonDecrease.onmousedown = suppressEvent; bkgBrightButtonIncrease.onmousedown = suppressEvent; radiusButtonDecrease = document.getElementById('radiusDecrease'); radiusButtonIncrease = document.getElementById('radiusIncrease'); radiusButtonDecrease.onclick = radiusDecrease; radiusButtonIncrease.onclick = radiusIncrease; radiusButtonDecrease.onmousedown = suppressEvent; radiusButtonIncrease.onmousedown = suppressEvent; maxAbsoluteDepth = 0; backButton = document.getElementById('back'); backButton.onclick = navigateBack; backButton.onmousedown = suppressEvent; forwardButton = document.getElementById('forward'); forwardButton.onclick = navigateForward; forwardButton.onmousedown = suppressEvent; snapshotButton = document.getElementById('snapshot'); snapshotButton.onclick = snapshot; snapshotButton.onmousedown = suppressEvent; detailsName = document.getElementById('detailsName'); detailsExpand = document.getElementById('detailsExpand'); detailsInfo = document.getElementById('detailsInfo'); search = document.getElementById('search'); search.onkeyup = onSearchChange; search.onmousedown = suppressEvent; searchResults = document.getElementById('searchResults'); useHueDiv = document.getElementById('useHueDiv'); linkButton = document.getElementById('linkButton'); linkButton.onclick = showLink; linkButton.onmousedown = suppressEvent; linkText = document.getElementById('linkText'); linkText.onblur = hideLink; linkText.onmousedown = suppressEvent; hide(linkText); var helpButton = document.getElementById('help'); helpButton.onmousedown = suppressEvent; var searchClear = document.getElementById('searchClear'); searchClear.onmousedown = suppressEvent; if (datasets > 1) { datasetDropDown.onmousedown = suppressEvent; var prevDatasetButton = document.getElementById('prevDataset'); prevDatasetButton.onmousedown = suppressEvent; var nextDatasetButton = document.getElementById('nextDataset'); nextDatasetButton.onmousedown = suppressEvent; var lastDatasetButton = document.getElementById('lastDataset'); lastDatasetButton.onmousedown = suppressEvent; } image = document.getElementById('hiddenImage'); if (image.complete) { hiddenPattern = context.createPattern(image, 'repeat'); } else { image.onload = function () { hiddenPattern = context.createPattern(image, 'repeat'); } } var loadingImageElement = document.getElementById('loadingImage'); if (loadingImageElement) { loadingImage = loadingImageElement.src; } } function selectDataset(newDataset) { lastDataset = currentDataset; currentDataset = newDataset if (datasets > 1) { datasetDropDown.selectedIndex = currentDataset; updateDatasetButtons(); datasetAlpha.start = 1.5; datasetChanged = true; } head.setMagnitudes(0); head.setDepth(1, 1); head.setMaxDepths(); handleResize(); } function selectLastDataset() { selectDataset(lastDataset); } function selectNode(newNode) { if (selectedNode != newNode) { // truncate history at current location to create a new branch // nodeHistory.length = nodeHistoryPosition; if (selectedNode != 0) { nodeHistory.push(selectedNode); nodeHistoryPosition++; } setSelectedNode(newNode); //updateView(); } updateDatasetButtons(); } function selectRank(rank) { rankDropDown.value = rank; currentRank = rank; datasetsVisible = 0; for (var i = 0; i < datasets; i++) { if (currentRank === 'ALL' || i < numRawSamples || (currentRank !== NO_RANK && ( datasetNames[i].endsWith('EXCLUSIVE_' + currentRank) || datasetNames[i].endsWith('SHARED_' + currentRank) || datasetNames[i].endsWith('CONTROL_SHARED' + currentRank) || datasetNames[i].endsWith('CTRL_' + currentRank)))) { datasetDropDown.options[i].hidden = false; datasetsVisible++; } else { datasetDropDown.options[i].hidden = true; } } if (datasetDropDown.options[currentDataset].hidden === true) { selectDataset(0); } else { selectDataset(currentDataset); } datasetDropDown.size = (datasetsVisible < DATASET_MAX_SIZE ? datasetsVisible : DATASET_MAX_SIZE); } function setFocus(node) { if (node == focusNode) { // return; } focusNode = node; if (node.href) { detailsName.innerHTML = '<a target="_blank" href="' + node.href + '">' + node.name + '</a>'; } else { detailsName.innerHTML = node.name; } var table = '<table>'; table += '<tr><td></td></tr>'; for (var i = 0; i < node.attributes.length; i++) { if (attributes[i].displayName && node.attributes[i] != undefined) { var index = node.attributes[i].length == 1 && attributes[i].mono ? 0 : currentDataset; if (typeof node.attributes[i][currentDataset] == 'number' || node.attributes[i][index] != undefined && node.attributes[i][currentDataset] != '') { var value = node.attributes[i][index]; if (attributes[i].listNode != undefined) { value = '<a href="" onclick="showList(' + attributeIndex(attributes[i].listNode) + ',' + i + ',false);return false;" title="Show list">' + value + '</a>'; } else if (attributes[i].listAll != undefined) { value = '<a href="" onclick="showList(' + attributeIndex(attributes[i].listAll) + ',' + i + ',true);return false;" title="Show list">' + value + '</a>'; } else if (attributes[i].dataNode != undefined && dataEnabled) { value = '<a href="" onclick="showData(' + attributeIndex(attributes[i].dataNode) + ',' + i + ',false);return false;" title="Show data">' + value + '</a>'; } else if (attributes[i].dataAll != undefined && dataEnabled) { value = '<a href="" onclick="showData(' + attributeIndex(attributes[i].dataAll) + ',' + i + ',true);return false;" title="Show data">' + value + '</a>'; } table += '<tr><td class="CellWithTooltip">' + '<strong>' + attributes[i].displayName + ':</strong>' + '<span class="Tooltip">' + attributes[i].tip + '</span>' + '</td><td>' + value + '</td></tr>'; } } } table += '</table>'; detailsInfo.innerHTML = table; detailsExpand.disabled = !focusNode.hasChildren() || focusNode == selectedNode; } function setSelectedNode(newNode) { if (selectedNode && selectedNode.hasParent(newNode)) { zoomOut = true; } else { zoomOut = false; } selectedNodeLast = selectedNode; selectedNode = newNode; //if ( focusNode != selectedNode ) { setFocus(selectedNode); } } function waitForData(dataWindow, target, title, time, postUrl, postVar) { if (nodeData.length == target) { if (postUrl != undefined) { for (var i = 0; i < nodeData.length; i++) { nodeData[i] = nodeData[i].replace(/\n/g, ','); } var postString = nodeData.join(''); postString = postString.slice(0, -1); dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); document.body.removeChild(document.getElementById('data')); post(postUrl, postVar, postString, dataWindow); } else { //dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); //document.body.removeChild(document.getElementById('data')); dataWindow.document.open(); dataWindow.document.write('<pre>' + nodeData.join('') + '</pre>'); dataWindow.document.close(); } dataWindow.document.title = title; // replace after document.write() } else { var date = new Date(); if (date.getTime() - time > 10000) { dataWindow.document.body.removeChild(dataWindow.document.getElementById('loading')); document.body.removeChild(document.getElementById('data')); dataWindow.document.body.innerHTML = 'Timed out loading supplemental files for:<br/>' + document.location; } else { setTimeout(function () { waitForData(dataWindow, target, title, time, postUrl, postVar); }, 100); } } } function data(newData) { nodeData.push(newData); } function enableData() { dataEnabled = true; } function showData(indexData, indexAttribute, summary) { var dataWindow = window.open('', '_blank'); var title = 'Re@ - ' + attributes[indexAttribute].displayName + ' - ' + focusNode.name; dataWindow.document.title = title; nodeData = new Array(); if (dataWindow && dataWindow.document && dataWindow.document.body != null) { //var loadImage = document.createElement('img'); //loadImage.src = "file://localhost/Users/ondovb/Krona/KronaTools/img/loading.gif"; //loadImage.id = "loading"; //loadImage.alt = "Loading..."; //dataWindow.document.body.appendChild(loadImage); dataWindow.document.body.innerHTML = '<img id="loading" src="' + loadingImage + '" alt="Loading..."></img>'; } var scripts = document.createElement('div'); scripts.id = 'data'; document.body.appendChild(scripts); var files = focusNode.getData(indexData, summary); var date = new Date(); var time = date.getTime(); for (var i = 0; i < files.length; i++) { var script = document.createElement('script'); script.src = files[i] + '?' + time; scripts.appendChild(script); } waitForData(dataWindow, files.length, title, time, attributes[indexAttribute].postUrl, attributes[indexAttribute].postVar); return false; } function showList(indexList, indexAttribute, summary) { var list = focusNode.getList(indexList, summary); if (attributes[indexAttribute].postUrl != undefined) { post(attributes[indexAttribute].postUrl, attributes[indexAttribute].postVar, list.join(',')); } else { var dataWindow = window.open('', '_blank'); if (true || navigator.appName == 'Microsoft Internet Explorer') // :( { dataWindow.document.open(); dataWindow.document.write('<pre>' + list.join('\n') + '</pre>'); dataWindow.document.close(); } else { var pre = document.createElement('pre'); dataWindow.document.body.appendChild(pre); pre.innerHTML = list; } dataWindow.document.title = 'Re@ - ' + attributes[indexAttribute].displayName + ' - ' + focusNode.name; } } function snapshot() { svg = svgHeader(); resetKeyOffset(); snapshotMode = true; selectedNode.draw(false, true); selectedNode.draw(true, true); if (focusNode != 0 && focusNode != selectedNode) { context.globalAlpha = 1; focusNode.drawHighlight(true); } if (hueDisplayName && useHue()) { drawLegendSVG(); } snapshotMode = false; svg += svgFooter(); var snapshotWindow = window.open('', '_blank', '', 'replace=false'); snapshotWindow.document.write('<html><body>' + '<button title="Download Rec@ntrifuge snapshot as SVG file" ' + 'onclick="document.getElementById(\'link\').click()">' + 'Download</button><a id="link" href="data:image/svg+xml,' + encodeURIComponent(svg) + '" download="Recfg_snapshot.svg" hidden>' + 'Download</a><br></html></body>'); snapshotWindow.document.title = 'Re@ [snapshot] ' + location.href.split("/").slice(-1)[0].split(".html")[0]; snapshotWindow.document.write(svg); } function save() { alert(document.body.innerHTML); } function spacer() { if (snapshotMode) { return '   '; } else { return ' '; } } function suppressEvent(e) { e.cancelBubble = true; if (e.stopPropagation) e.stopPropagation(); } function svgFooter() { return '</svg>'; } function svgHeader() { var patternWidth = fontSize * .6;//radius / 50; return '\ <?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 width="' + imageWidth + '" height="' + imageHeight + '" version="1.1"\ xmlns="http://www.w3.org/2000/svg">\ <title>Rec@ntrifuge (snapshot) - ' + (datasets > 1 ? datasetNames[currentDataset] + ' - ' : '') + selectedNode.name + '</title>\ <defs>\ <style type="text/css">\ @import url("https://fonts.googleapis.com/css?family=' + fontFamily + '");\ text {font-size: ' + fontSize + 'px; font-family: ' + fontFamily + '; dominant-baseline:central}\ path {stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ path.wedge {stroke:none}\ path.line {fill:none;stroke:black;}\ line {stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ line.tick {stroke-width:' + thinLineWidth * fontSize / 6 + ';}\ line.pattern {stroke-width:' + thinLineWidth * fontSize / 18 + ';}\ circle {fill:none;stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ rect {stroke:black;stroke-width:' + thinLineWidth * fontSize / 12 + ';}\ .highlight {stroke:black;stroke-width:' + highlightLineWidth * fontSize / 12 + ';}\ .searchHighlight {fill:rgb(255, 255, 100);stroke:none;}\ </style>\ <pattern id="hiddenPattern" patternUnits="userSpaceOnUse" \ x="0" y="0" width="' + patternWidth + '" height="' + patternWidth + '">\ <line class="pattern" x1="0" y1="0" x2="' + patternWidth / 2 + '" y2="' + patternWidth / 2 + '"/>\ <line class="pattern" x1="' + patternWidth / 2 + '" y1="' + patternWidth + '" x2="' + patternWidth + '" y2="' + patternWidth / 2 + '"/>\ </pattern>\ </defs>\ '; } function svgText(text, x, y, anchor, bold, color) { if (typeof(anchor) == 'undefined') { anchor = 'start'; } if (color == undefined) { color = 'black'; } return '<text x="' + x + '" y="' + y + '" style="font-color:' + color + ';font-weight:' + (bold ? 'bold' : 'normal') + '" text-anchor="' + anchor + '">' + text + '</text>'; } function toggleKeys() { if (showKeys) { keyControl.value = '…'; showKeys = false; } else { keyControl.value = 'x'; showKeys = true; } updateKeyControl(); if (progress == 1) { draw(); } } function update() { if (!head) { return; } if (mouseDown && focusNode != selectedNode) { var date = new Date(); if (date.getTime() - mouseDownTime > quickLookHoldLength) { if (focusNode.hasChildren()) { expand(focusNode); quickLook = true; } } } if (updateViewNeeded) { resize(); mouseX = -1; mouseY = -1; collapse = collapseCheckBox.checked; compress = true;//compressCheckBox.checked; shorten = true;//shortenCheckBox.checked; checkSelectedCollapse(); updateMaxAbsoluteDepth(); if (focusNode.getCollapse() || focusNode.depth > maxAbsoluteDepth) { setFocus(selectedNode); } else { setFocus(focusNode); } updateView(); updateViewNeeded = false; } var date = new Date(); progress = (date.getTime() - tweenStartTime) / tweenLength; // progress += .01; if (progress >= 1) { progress = 1; } if (progress != progressLast) { tweenFactor =// progress; (1 / (1 + Math.exp(-tweenCurvature * (progress - .5))) - .5) / (tweenMax - .5) / 2 + .5; if (progress == 1) { snapshotButton.disabled = false; zoomOut = false; //updateKeyControl(); if (!quickLook) { //checkHighlight(); } if (fpsDisplay) { fpsDisplay.innerHTML = 'fps: ' + Math.round(tweenFrames * 1000 / tweenLength); } } draw(); } progressLast = progress; } function updateDatasetButtons() { if (datasets == 1) { return; } var node = selectedNode ? selectedNode : head; datasetButtonLast.disabled = node.attributes[magnitudeIndex][lastDataset] == 0; datasetButtonPrev.disabled = true; datasetButtonNext.disabled = true; for (var i = 0; i < datasets; i++) { var disable = node.attributes[magnitudeIndex][i] == 0; datasetDropDown.options[i].disabled = disable; if (!disable) { if (i != currentDataset) { datasetButtonPrev.disabled = false; datasetButtonNext.disabled = false; } } } } function updateDatasetWidths() { if (datasets > 1) { for (var i = 0; i < datasets; i++) { context.font = fontBold; var dim = context.measureText(datasetNames[i]); datasetWidths[i] = dim.width; } } } function updateKeyControl() { if (keys == 0)//|| progress != 1 ) { keyControl.style.visibility = 'hidden'; } else { keyControl.style.visibility = 'visible'; keyControl.style.right = margin + 'px'; if (showKeys) { keyControl.style.top = imageHeight - ( keys * (keySize + keyBuffer) - keyBuffer + margin + keyControl.clientHeight * 1.5 ) + 'px'; } else { keyControl.style.top = (imageHeight - margin - keyControl.clientHeight) + 'px'; } } } function updateView() { if (selectedNode.depth > maxAbsoluteDepth - 1) { maxAbsoluteDepth = selectedNode.depth + 1; } highlightedNode = selectedNode; angleFactor = 2 * Math.PI / (selectedNode.magnitude); maxPossibleDepth = Math.floor(gRadius / (fontSize * minRingWidthFactor)); if (maxPossibleDepth < 4) { maxPossibleDepth = 4; } var minRadiusInner = fontSize * 8 / gRadius; var minRadiusFirst = fontSize * 6 / gRadius; var minRadiusOuter = fontSize * 5 / gRadius; if (.25 < minRadiusInner) { minRadiusInner = .25; } if (.15 < minRadiusFirst) { minRadiusFirst = .15; } if (.15 < minRadiusOuter) { minRadiusOuter = .15; } // visibility of nodes depends on the depth they are displayed at, // so we need to set the max depth assuming they can all be displayed // and iterate it down based on the deepest child node we can display // var maxDepth; var newMaxDepth = selectedNode.getMaxDepth() - selectedNode.getDepth() + 1; // do { maxDepth = newMaxDepth; if (!compress && maxDepth > maxPossibleDepth) { maxDepth = maxPossibleDepth; } if (compress) { compressedRadii = new Array(maxDepth); compressedRadii[0] = minRadiusInner; var offset = 0; while ( lerp ( Math.atan(offset + 2), Math.atan(offset + 1), Math.atan(maxDepth + offset - 1), minRadiusInner, 1 - minRadiusOuter ) - minRadiusInner > minRadiusFirst && offset < 10 ) { offset++; } offset--; for (var i = 1; i < maxDepth; i++) { compressedRadii[i] = lerp ( Math.atan(i + offset), Math.atan(offset), Math.atan(maxDepth + offset - 1), minRadiusInner, 1 - minRadiusOuter ) } } else { nodeRadius = 1 / maxDepth; } newMaxDepth = selectedNode.maxVisibleDepth(maxDepth); if (compress) { if (newMaxDepth <= maxPossibleDepth) { // compress } } else { if (newMaxDepth > maxPossibleDepth) { newMaxDepth = maxPossibleDepth; } } } while (newMaxDepth < maxDepth); maxDisplayDepth = maxDepth; lightnessFactor = (lightnessMax - lightnessBase) / (maxDepth > 8 ? 8 : maxDepth); keys = 0; nLabelOffsets = new Array(maxDisplayDepth - 1); labelOffsets = new Array(maxDisplayDepth - 1); labelLastNodes = new Array(maxDisplayDepth - 1); labelFirstNodes = new Array(maxDisplayDepth - 1); for (var i = 0; i < maxDisplayDepth - 1; i++) { if (compress) { if (i == maxDisplayDepth - 1) { nLabelOffsets[i] = 0; } else { var width = (compressedRadii[i + 1] - compressedRadii[i]) * gRadius; nLabelOffsets[i] = Math.floor(width / fontSize / 1.2); if (nLabelOffsets[i] > 2) { nLabelOffsets[i] = min ( Math.floor(width / fontSize / 1.75), 5 ); } } } else { nLabelOffsets[i] = Math.max ( Math.floor(Math.sqrt((nodeRadius * gRadius / fontSize)) * 1.5), 3 ); } labelOffsets[i] = Math.floor((nLabelOffsets[i] - 1) / 2); labelLastNodes[i] = new Array(nLabelOffsets[i] + 1); labelFirstNodes[i] = new Array(nLabelOffsets[i] + 1); for (var j = 0; j <= nLabelOffsets[i]; j++) { // these arrays will allow nodes with neighboring labels to link to // each other to determine max label length labelLastNodes[i][j] = 0; labelFirstNodes[i][j] = 0; } } fontSizeText.innerHTML = fontSize; fontNormal = fontSize + 'px ' + fontFamily; context.font = fontNormal; fontBold = 'bold ' + fontSize + 'px ' + fontFamily; tickLength = fontSize * .7; head.setTargets(0); keySize = ((imageHeight - margin * 3) * 1 / 2) / keys * 3 / 4; if (keySize > fontSize * maxKeySizeFactor) { keySize = fontSize * maxKeySizeFactor; } keyBuffer = keySize / 3; fontSizeLast = fontSize; if (datasetChanged) { datasetChanged = false; } else { datasetAlpha.start = 0; } var date = new Date(); tweenStartTime = date.getTime(); progress = 0; tweenFrames = 0; updateKeyControl(); updateDatasetWidths(); document.title = ('Re@ - ' + location.href.split("/").slice(-1)[0].split(".html")[0]); updateNavigationButtons(); snapshotButton.disabled = true; maxAbsoluteDepthText.innerHTML = maxAbsoluteDepth - 1; maxAbsoluteDepthButtonDecrease.disabled = (maxAbsoluteDepth == 2); maxAbsoluteDepthButtonIncrease.disabled = (maxAbsoluteDepth == head.maxDepth); bkgBrightButtonDecrease.disabled = (bkgBright == '555555'); bkgBrightButtonIncrease.disabled = (bkgBright == 'ffffff'); if (collapse != collapseLast && search.value != '') { onSearchChange(); collapseLast = collapse; } } function updateMaxAbsoluteDepth() { while (maxAbsoluteDepth > 1 && selectedNode.depth > maxAbsoluteDepth - 1) { selectedNode = selectedNode.getParent(); } } function updateNavigationButtons() { backButton.disabled = (nodeHistoryPosition == 0); // upButton.disabled = (selectedNode.getParent() == 0); forwardButton.disabled = (nodeHistoryPosition == nodeHistory.length); } function useHue() { return useHueCheckBox && useHueCheckBox.checked; } /* function zoomOut() { return ( selectedNodeLast != 0 && selectedNodeLast.getDepth() < selectedNode.getDepth()); } */</script></head><body><img id="hiddenImage" 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" style="display:none"><noscript>Javascript must be enabled to view this page.</noscript><div style="display:none"><krona collapse="true" key="true" chart="TAXOMIC"><attributes magnitude="count"><attribute display="Count" dataAll="members" tip="Number of reads assigned to this and child taxa">count</attribute><attribute display="Unassigned" dataNode="members" tip="Number of reads assigned specifically to this taxon">unassigned</attribute><attribute display="TaxID" mono="true" hrefBase="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" tip="Taxonomic identifier">tid</attribute><attribute display="Rank" mono="true" tip="Taxonomic rank/level">rank</attribute><attribute display="Read length (avg)" tip="Averaged score of reads assigned to this and child taxa">score</attribute></attributes><datasets rawSamples="3"><dataset isctr="False" sread="10999" sclas="10354" sfilt="10354" scmin="23.0" scavg="190.73954464627033" scmax="400.1051804377604" lnmin="70 nt" lnavg="387 nt" lnmax="602 nt" tclas="215" tfilt="215" tfold="5" sclim="None" totnt="4.22 Mnt">input_dir/centrifuge_1_out</dataset><dataset isctr="False" sread="10999" sclas="10354" sfilt="10354" scmin="23.0" scavg="190.73954464627033" scmax="400.1051804377604" lnmin="70 nt" lnavg="387 nt" lnmax="602 nt" tclas="215" tfilt="215" tfold="5" sclim="None" totnt="4.22 Mnt">input_dir/centrifuge_2_out</dataset><dataset isctr="False" sread="10999" sclas="10354" sfilt="10354" scmin="23.0" scavg="190.73954464627033" scmax="400.1051804377604" lnmin="70 nt" lnavg="387 nt" lnmax="602 nt" tclas="215" tfilt="215" tfold="5" sclim="None" totnt="4.22 Mnt">input_dir/centrifuge_out</dataset><dataset>SHARED_species</dataset><dataset>SHARED_genus</dataset><dataset>SHARED_family</dataset><dataset>SHARED_order</dataset><dataset>SHARED_class</dataset><dataset>SHARED_phylum</dataset><dataset>SHARED_SUMMARY</dataset></datasets><color attribute="score" hueStart="0" hueEnd="300" valueStart="390.6" valueEnd="494.0" default="true"> </color><node name="root" href="https://www.google.com/search?q=root"><count><val>75</val><val>75</val><val>75</val><val>31</val><val>35</val><val>67</val><val>73</val><val>75</val><val>75</val><val>75</val></count><unassigned><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val></unassigned><tid><val href="1">1</val></tid><rank><val>no_rank</val></rank><score><val>392.6</val><val>392.6</val><val>392.6</val><val>488.4</val><val>489.0</val><val>446.7</val><val>442.0</val><val>440.7</val><val>440.7</val><val>440.7</val></score><node name="Bacteria" href="https://www.google.com/search?q=Bacteria"><count><val>75</val><val>75</val><val>75</val><val>31</val><val>35</val><val>67</val><val>73</val><val>75</val><val>75</val><val>75</val></count><unassigned><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val></unassigned><tid><val href="2">2</val></tid><rank><val>superkingdom</val></rank><score><val>392.6</val><val>392.6</val><val>392.6</val><val>488.4</val><val>489.0</val><val>446.7</val><val>442.0</val><val>440.7</val><val>440.7</val><val>440.7</val></score><node name="Proteobacteria" href="https://www.google.com/search?q=Proteobacteria"><count><val>75</val><val>75</val><val>75</val><val>31</val><val>35</val><val>67</val><val>73</val><val>75</val><val>75</val><val>75</val></count><unassigned><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val></val><val>75</val><val></val></unassigned><tid><val href="1224">1224</val></tid><rank><val>phylum</val></rank><score><val>392.6</val><val>392.6</val><val>392.6</val><val>488.4</val><val>489.0</val><val>446.7</val><val>442.0</val><val>440.7</val><val>440.7</val><val>440.7</val></score><node name="Gammaproteobacteria" href="https://www.google.com/search?q=Gammaproteobacteria"><count><val>75</val><val>75</val><val>75</val><val>31</val><val>35</val><val>67</val><val>73</val><val>75</val><val></val><val>75</val></count><unassigned><val>2</val><val>2</val><val>2</val><val></val><val></val><val></val><val></val><val>75</val><val></val><val>2</val></unassigned><tid><val href="1236">1236</val></tid><rank><val>class</val></rank><score><val>392.6</val><val>392.6</val><val>392.6</val><val>488.4</val><val>489.0</val><val>446.7</val><val>442.0</val><val>440.7</val><val>0</val><val>440.7</val></score><node name="Enterobacteriales" href="https://www.google.com/search?q=Enterobacteriales"><count><val>73</val><val>73</val><val>73</val><val>31</val><val>35</val><val>67</val><val>73</val><val></val><val></val><val>73</val></count><unassigned><val>6</val><val>6</val><val>6</val><val></val><val></val><val></val><val>73</val><val></val><val></val><val>6</val></unassigned><tid><val href="91347">91347</val></tid><rank><val>order</val></rank><score><val>390.6</val><val>390.6</val><val>390.6</val><val>488.4</val><val>489.0</val><val>446.7</val><val>442.0</val><val>0</val><val>0</val><val>442.0</val></score><node name="Enterobacteriaceae" href="https://www.google.com/search?q=Enterobacteriaceae"><count><val>67</val><val>67</val><val>67</val><val>31</val><val>35</val><val>67</val><val></val><val></val><val></val><val>67</val></count><unassigned><val>32</val><val>32</val><val>32</val><val></val><val></val><val>67</val><val></val><val></val><val></val><val>32</val></unassigned><tid><val href="543">543</val></tid><rank><val>family</val></rank><score><val>400.3</val><val>400.3</val><val>400.3</val><val>488.4</val><val>489.0</val><val>446.7</val><val>0</val><val>0</val><val>0</val><val>446.7</val></score><node name="Escherichia" href="https://www.google.com/search?q=Escherichia"><count><val>35</val><val>35</val><val>35</val><val>31</val><val>35</val><val></val><val></val><val></val><val></val><val>35</val></count><unassigned><val>4</val><val>4</val><val>4</val><val></val><val>35</val><val></val><val></val><val></val><val></val><val>4</val></unassigned><tid><val href="561">561</val></tid><rank><val>genus</val></rank><score><val>494.0</val><val>494.0</val><val>494.0</val><val>488.4</val><val>489.0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>489.0</val></score><node name="Escherichia coli" href="https://www.google.com/search?q=Escherichia coli"><count><val>31</val><val>31</val><val>31</val><val>31</val><val></val><val></val><val></val><val></val><val></val><val>31</val></count><unassigned><val>31</val><val>31</val><val>31</val><val>31</val><val></val><val></val><val></val><val></val><val></val><val>31</val></unassigned><tid><val href="562">562</val></tid><rank><val>species</val></rank><score><val>488.4</val><val>488.4</val><val>488.4</val><val>488.4</val><val>0</val><val>0</val><val>0</val><val>0</val><val>0</val><val>488.4</val></score></node></node></node></node></node></node></node></node></krona></div></body></html>