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Krona-Soils2_4_8_Protein_TaxonomyByFunction.html
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Krona-Soils2_4_8_Protein_TaxonomyByFunction.html
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{//-----------------------------------------------------------------------------
//
// 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/
//
//-----------------------------------------------------------------------------
}
var canvas;
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 = 11;
var fontSizeText;
var fontSizeButtonDecrease;
var fontSizeButtonIncrease;
var fontSizeLast;
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 datasetDropDown;
var datasetButtonLast;
var datasetButtonPrev;
var datasetButtonNext;
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();
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 a
// 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 = new Array();
//
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
//
var currentDataset = 0;
var lastDataset = 0;
var datasets = 1;
var datasetNames;
var datasetSelectSize = 30;
var datasetAlpha = new Tween(0, 0);
var datasetWidths = new Array();
var datasetChanged;
var datasetSelectWidth = 50;
window.onload = load;
var image;
var hiddenPattern;
var loadingImage;
var logoImage;
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 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;
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[this.children.length - 1].radiusInner.current() * gRadius;
}
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.keyed &&
(compress || depth < maxDisplayDepth) &&
drawChildren
);
if ( truncateWedge )
{
radiusOuter = this.children[0].radiusInner.current() * gRadius;
}
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 )
{
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 )
{