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Removed hard-coded elements
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@jsmirob
jsmirob committed Jan 17, 2013
1 parent 7c60754 commit 59c6a30
Showing 1 changed file with 66 additions and 49 deletions.
115 changes: 66 additions & 49 deletions src/JBrowse/View/Track/BaseCoverage.js
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Expand Up @@ -45,12 +45,7 @@ return declare( Wiggle,

var binWidth = Math.ceil( query.basesPerSpan ); // in bp

var arraySize = Math.ceil( widthBp/binWidth );
var coverageBins = new Array( arraySize );
var aCoverage = new Array( arraySize );
var tCoverage = new Array( arraySize );
var cCoverage = new Array( arraySize );
var gCoverage = new Array( arraySize );
var coverageBins = {};
var bpToBin = function( bp ) {
return Math.floor( (bp-leftBase) / binWidth );
};
Expand All @@ -61,45 +56,48 @@ return declare( Wiggle,
var startBin = bpToBin( feature.get('start') );
var endBin = bpToBin( feature.get('end')-1 );
for( var i = startBin; i <= endBin; i++ ) {
coverageBins[i] = (coverageBins[i] || 0) + 1;
if ( coverageBins[i] ) {
coverageBins[i]['matchCoverage']++;
}
else {
coverageBins[i] = {};
coverageBins[i]['matchCoverage'] = 1;
}
}
// Calculate SNP coverage
var mdTag = feature.get('MD');
if(mdTag) {
var SNPs = this._mdToMismatches(feature, mdTag);
// loops through mismatches and updates coverage variables accordingly.
for (var i = 0; i<SNPs.length; i++) {
var pos = feature.get('start') + SNPs[i].start - leftBase;
switch (SNPs[i].bases) {
case "A": aCoverage[pos] = (aCoverage[pos] || 0) + 1; break;
case "T": tCoverage[pos] = (tCoverage[pos] || 0) + 1; break;
case "C": cCoverage[pos] = (cCoverage[pos] || 0) + 1; break;
case "G": gCoverage[pos] = (gCoverage[pos] || 0) + 1; break;
case "*": break; // unknown base. current version ignores these.
default: alert("Unknown base encountered: " + SNPs[i].bases);
var pos = bpToBin( feature.get('start') + SNPs[i].start );
// Note: we reduce matchCoverage so the sum is the total coverage
coverageBins[pos]['matchCoverage']--;
if ( coverageBins[pos][SNPs[i].bases] ) {
coverageBins[pos][SNPs[i].bases]++;
}
else {
coverageBins[pos][SNPs[i].bases] = 1;
}
}
}
}),
function () {
// make fake features from the coverage
for( var i = 0; i < coverageBins.length; i++ ) {
// score contains [non-SNP coverage, a SNPs, t SNPs, c SNPs, g SNPs]
var score = [0, aCoverage[i] || 0, tCoverage[i] || 0, cCoverage[i] || 0, gCoverage[i] || 0];
score[0] = coverageBins[i] - score.reduce(function(a,b){return a+b;});
for( var i = 0; i < Math.ceil( widthBp/binWidth ); i++ ) {
var bpOffset = leftBase+binWidth*i;
featureCallback( new CoverageFeature({
start: bpOffset,
end: bpOffset+binWidth,
score: score
score: coverageBins[i] || {'matchCoverage': 0}
}));
}
finishCallback();
}
);
},

/***********************************************************************************************************************
/*
* Draw a set of features on the canvas.
* @private
*/
Expand All @@ -111,48 +109,67 @@ return declare( Wiggle,
});
var originY = toY( dataScale.origin );

var barColor = ['#999', 'green', 'red', 'blue', 'yellow'];
var barColor = {'matchCoverage':'#999', 'A':'#00BF00', 'T':'red', 'C':'#4747ff', 'G':'#d5bb04'}; // base colors from "main.css"
var negColor = this.config.style.neg_color;
var clipColor = this.config.style.clip_marker_color;
var bgColor = this.config.style.bg_color;
var disableClipMarkers = this.config.disable_clip_markers;

dojo.forEach( features, function(f,i) {

var fRect = featureRects[i];

var score = f.get('score');
var drawRectangle = function(ID, yPos, height, fRect) {
// draw the background color if we are configured to do so
if( bgColor && yPos >= 0 ) {
context.fillStyle = bgColor;
context.fillRect( fRect.l, 0, fRect.w, canvasHeight );
}

for (var j = 0; j<5; j++) {
if( yPos <= canvasHeight ) { // if the rectangle is visible at all

fRect.t = toY(score.slice(j,5).reduce(function(a,b){return a+b;})); // makes progressively shorter rectangles.
if( yPos <= originY ) {
// bar goes upward
context.fillStyle = barColor[ID] || 'black';
context.fillRect( fRect.l, yPos, fRect.w, height);
if( !disableClipMarkers && yPos < 0 ) { // draw clip marker if necessary
context.fillStyle = clipColor || negColor;
context.fillRect( fRect.l, 0, fRect.w, 2 );
}
}
else {
// bar goes downward (Should not be reached)
context.fillStyle = negColor;
context.fillRect( fRect.l, originY, fRect.w, height );
if( !disableClipMarkers && yPos >= canvasHeight ) { // draw clip marker if necessary
context.fillStyle = clipColor || barColor[0];
context.fillRect( fRect.l, canvasHeight-3, fRect.w, 2 );
}
}
}
};

// draw the background color if we are configured to do so
if( bgColor && fRect.t >= 0 ) {
context.fillStyle = bgColor;
context.fillRect( fRect.l, 0, fRect.w, canvasHeight );
dojo.forEach( features, function(f,i) {
var fRect = featureRects[i];
var score = f.get('score');
var totalHeight = 0;
for (counts in score) {
if (score.hasOwnProperty(counts)) {
totalHeight += score[counts];
}
}

if( fRect.t <= canvasHeight ) { // if the rectangle is visible at all
// Note: 'matchCoverage' is done first to ensure the grey part of the graph is on top
drawRectangle('matchCoverage', toY(totalHeight), originY-toY( score['matchCoverage'] )+1, fRect);
totalHeight -= score['matchCoverage'];

if( fRect.t <= originY ) {
// bar goes upward
context.fillStyle = barColor[j];
context.fillRect( fRect.l, fRect.t, fRect.w, originY-fRect.t+1);
if( !disableClipMarkers && fRect.t < 0 ) { // draw clip marker if necessary
context.fillStyle = clipColor || negColor;
context.fillRect( fRect.l, 0, fRect.w, 2 );
}
}
else {
alert('Invalid data used. Negative values are not possible.');
}
for (counts in score) {
if (score.hasOwnProperty(counts) && counts != 'matchCoverage') {
drawRectangle( counts, toY(totalHeight), originY-toY( score[counts] )+1, fRect);
totalHeight -= score[counts];
}
}
}, this );

}, this );
},
//*******************************************************************************************************************************

// a method blatently stolen from "Alignments.js" Perhaps it would be better just to include the file...
// a method from "Alignments.js" Perhaps it would be better just to include the file...
_mdToMismatches: function( feature, mdstring ) {
var mismatchRecords = [];
var curr = { start: 0, bases: '' };
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