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BaseCoverage.js
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BaseCoverage.js
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define( ['dojo/_base/declare',
'dojo/_base/array',
'JBrowse/View/Track/Wiggle',
'JBrowse/Util'
],
function( declare, array, Wiggle, Util ) {
// feature class for the features we make for the calculated coverage
// values
var CoverageFeature = Util.fastDeclare(
{
get: function(f) { return this[f]; },
tags: function() { return [ 'start', 'end', 'score' ]; },
score: 0,
constructor: function( args ) {
this.start = args.start;
this.end = args.end;
this.score = args.score;
}
});
return declare( Wiggle,
{
_defaultConfig: function() {
return Util.deepUpdate(
dojo.clone( this.inherited(arguments) ),
{
min_score: 0,
max_score: 100
}
);
},
getGlobalStats: function() {
return {};
},
getFeatures: function( query, featureCallback, finishCallback, errorCallback ) {
var leftBase = query.start;
var rightBase = query.end;
var scale = query.scale; // px/bp
var widthBp = rightBase-leftBase;
var widthPx = widthBp * ( query.scale || 1/query.basesPerSpan);
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 bpToBin = function( bp ) {
return Math.floor( (bp-leftBase) / binWidth );
};
this.store.getFeatures(
query,
dojo.hitch( this, function( feature ) {
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;
}
// 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;
default: alert("Unknown base encountered: " + SNPs[i].bases);
}
}
}
}),
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 nonSNP = (coverageBins[i] || 0) - (aCoverage[i] || 0) - (tCoverage[i] || 0) - (cCoverage[i] || 0) - (gCoverage[i] || 0);
var score = [nonSNP, aCoverage[i] || 0, tCoverage[i] || 0, cCoverage[i] || 0, gCoverage[i] || 0];
var bpOffset = leftBase+binWidth*i;
featureCallback( new CoverageFeature({
start: bpOffset,
end: bpOffset+binWidth,
score: score
}));
}
finishCallback();
}
);
},
/***********************************************************************************************************************
* Draw a set of features on the canvas.
* @private
*/
_drawFeatures: function( scale, leftBase, rightBase, block, canvas, features, featureRects, dataScale ) {
var context = canvas.getContext('2d');
var canvasHeight = canvas.height;
var toY = dojo.hitch( this, function( val ) {
return canvasHeight * ( 1-dataScale.normalize.call(this, val) );
});
var originY = toY( dataScale.origin );
var barColor = ['#777', 'green', 'red', 'blue', 'yellow'];
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');
for (var j = 0; j<5; j++) {
fRect.t = toY(score.slice(j,5).reduce(function(a,b){return a+b;})); // makes progressively shorter rectangles.
// 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 );
}
if( fRect.t <= canvasHeight ) { // if the rectangle is visible at all
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.');
}
}
}
}, this );
},
//*******************************************************************************************************************************
// a method blatently stolen from "Alignments.js" Perhaps it would be better just to include the file...
_mdToMismatches: function( feature, mdstring ) {
var mismatchRecords = [];
var curr = { start: 0, bases: '' };
var seq = feature.get('seq');
var nextRecord = function() {
mismatchRecords.push( curr );
curr = { start: curr.start + curr.bases.length, bases: ''};
};
array.forEach( mdstring.match(/(\d+|\^[a-z]+|[a-z])/ig), function( token ) {
if( token.match(/^\d/) ) { // matching bases
curr.start += parseInt( token );
}
else if( token.match(/^\^/) ) { // insertion in the template
var i = token.length-1;
while( i-- ) {
curr.bases += '*';
}
nextRecord();
}
else if( token.match(/^[a-z]/i) ) { // mismatch
curr.bases = seq.substr( curr.start, token.length );
nextRecord();
}
});
return mismatchRecords;
}
});
});