Mercurial > repos > pimarin > recentrifuge
changeset 5:62c6402dd50d draft
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 0bff76499478da0f47e93e02542414d6a2aa8077"
| author | pimarin |
|---|---|
| date | Wed, 18 May 2022 09:36:38 +0000 |
| parents | 512dc05a0e5a |
| children | ecc282b4fe01 |
| files | mylog.txt output.rcf.data.csv output.rcf.html output.rcf.stat.csv |
| diffstat | 4 files changed, 0 insertions(+), 6637 deletions(-) [+] |
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--- a/mylog.txt Wed May 18 09:28:48 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ - -=-= /home/pierre/anaconda3/envs/rcf/bin/rcf =-= v1.8.1 - Mar 2022 =-= by Jose Manuel Martí =-= - -[90mLoading NCBI nodes...[0m[92m OK! [0m -[90mLoading NCBI names...[0m[92m OK! [0m -[90mBuilding dict of parent to children taxa...[0m[92m OK! [0m -[90m -Please, wait, processing files in parallel... -[0m -[90mLoading output file test-data/kraken_test/kraken.out... [0m[92mOK! -[0m[90m Seqs read: [0m99 [90m[[0m52.81 knt[90m] -[0m[90m Seqs clas: [0m99 [90m([0m0.00%[90m unclassified) -[0m[90m Seqs pass: [0m99 [90m([0m0.00%[90m rejected) -[0m[90m Scores SHEL: min = [0m36.0,[90m max = [0m347.0,[90m avr = [0m99.9 -[90m Coverage(%): min = [0m0.2,[90m max = [0m88.1,[90m avr = [0m15.4 -[90m Read length: min = [0m198 nt,[90m max = [0m602 nt,[90m avr = [0m533 nt -[90m TaxIds: by classifier = [0m13[90m, by filter = [0m13 -[90mBuilding from raw data with mintaxa = [0m2[90m ... -[0m[90m Check for more seqs lost ([in/ex]clude affects)... [0m[94m - Info:[0m 65 [90madditional seqs discarded ([0m65.657% [90mof accepted) -[0m[93m - Warning![0m 9 orphan taxids[90m (rerun with --debug for details) -[0mtest-data/kraken_test/kraken[94m sample [0m[92mOK! -[0m[90mLoad elapsed time: [0m0.00243[90m sec -[0m -[90m -Building the taxonomy multiple tree... [0m[92mOK![0m -[90mGenerating interactive plot ([0m[95moutput.rcf.html[0m[90m)... [0m[92mOK![0m -[90mGenerating csv extra output ([0m[95m[output.rcf.]*.csv[0m[90m)... [0m[92mOK![0m -[90mTotal elapsed time:[0m 00:00:00
--- a/output.rcf.data.csv Wed May 18 09:28:48 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -Samples,test-data/kraken_test/kraken,test-data/kraken_test/kraken,test-data/kraken_test/kraken,Details,Details -Stats,count,unassigned,score,Rank,Name -Id,,,,, -1,34,0,26.826023135133102,no_rank,root -2,34,0,26.826023135133102,superkingdom,Bacteria -1224,34,0,26.826023135133102,phylum,Proteobacteria -1236,34,0,26.826023135133102,class,Gammaproteobacteria -91347,34,0,26.826023135133102,order,Unnamed -543,34,9,26.826023135133102,family,Enterobacteriaceae -547,25,25,31.582057972392526,genus,Enterobacter
--- a/output.rcf.html Wed May 18 09:28:48 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6581 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta charset="utf-8"><link rel="shortcut icon" 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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 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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="Kmer coverage (%)" tip="Averaged score of reads assigned to this and child taxa">score</attribute></attributes><datasets rawSamples="1"><dataset isctr="False" sread="99" sclas="99" sfilt="99" scmin="36" scavg="99.94949494949495" scmax="347" lnmin="198 nt" lnavg="533 nt" lnmax="602 nt" tclas="13" tfilt="13" tfold="2" sclim="None" totnt="52.81 knt">test-data/kraken_test/kraken</dataset></datasets><color attribute="score" hueStart="0" hueEnd="300" valueStart="26.8" valueEnd="31.6" default="true"> </color><node name="root" href="https://www.google.com/search?q=root"><count><val>34</val></count><unassigned><val></val></unassigned><tid><val href="1">1</val></tid><rank><val>no_rank</val></rank><score><val>26.8</val></score><node name="Bacteria" href="https://www.google.com/search?q=Bacteria"><count><val>34</val></count><unassigned><val></val></unassigned><tid><val href="2">2</val></tid><rank><val>superkingdom</val></rank><score><val>26.8</val></score><node name="Proteobacteria" href="https://www.google.com/search?q=Proteobacteria"><count><val>34</val></count><unassigned><val></val></unassigned><tid><val href="1224">1224</val></tid><rank><val>phylum</val></rank><score><val>26.8</val></score><node name="Gammaproteobacteria" href="https://www.google.com/search?q=Gammaproteobacteria"><count><val>34</val></count><unassigned><val></val></unassigned><tid><val href="1236">1236</val></tid><rank><val>class</val></rank><score><val>26.8</val></score><node name="Unnamed" href="https://www.google.com/search?q=Unnamed"><count><val>34</val></count><unassigned><val></val></unassigned><tid><val href="91347">91347</val></tid><rank><val>order</val></rank><score><val>26.8</val></score><node name="Enterobacteriaceae" href="https://www.google.com/search?q=Enterobacteriaceae"><count><val>34</val></count><unassigned><val>9</val></unassigned><tid><val href="543">543</val></tid><rank><val>family</val></rank><score><val>26.8</val></score><node name="Enterobacter" href="https://www.google.com/search?q=Enterobacter"><count><val>25</val></count><unassigned><val>25</val></unassigned><tid><val href="547">547</val></tid><rank><val>genus</val></rank><score><val>31.6</val></score></node></node></node></node></node></node></node></krona></div></body></html> \ No newline at end of file
--- a/output.rcf.stat.csv Wed May 18 09:28:48 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -,test-data/kraken_test/kraken -Seqs. read,99.0 -Seqs. unclass.,0.0 -Seqs. class.,99.0 -Seqs. filtered,99.0 -Score min,36.0 -Score mean,99.94949494949495 -Score max,347.0 -Length min,198.0 -Length mean,533.0 -Length max,602.0 -Total nt read,52814.0 -TIDs class.,13.0 -TIDs filtered,13.0 -TIDs folded,2.0 -Score limit,