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var sizes = GenomePlot.chromosomes[ d.toString() ];
// the space between adjacent chroms
var space = GenomePlot.MAX_CHROMOSOME_BASE - sizes.chromSizeLeft - sizes.chromSizeRight;
return GenomePlot.linearGenomicToPaddedPixelScaleX( sizes.chromSizeLeft + space/2 ).toFixed(GenomePlot.FLOAT_PRECISION);
} )
.attr( "y1", function( d ) { return GenomePlot.linearWindowPixelToPaddedPixelScaleY( (d === 23 ? 12 : (d-1)) * GenomePlot.pixelsPerLine ).toFixed(GenomePlot.FLOAT_PRECISION); } )
.attr( "y2", function( d ) { return GenomePlot.linearWindowPixelToPaddedPixelScaleY( (d === 23 ? 13 : (d)) * GenomePlot.pixelsPerLine ).toFixed(GenomePlot.FLOAT_PRECISION); } )
;
divs.exit().remove();
}
var endTime = performance.now();
if( GenomePlot.debug ) console.info( sprintf( "%-20s duration: %.4f seconds", "drawVerticalDividers():", ((endTime-startTime)/1000) ) );
} // drawVerticalDividers
.done (function () {
GenomePlot.matepairDataStartTime = performance.now();
console.info( sprintf( "%-20s Started loading Mate Pair data file: %s at %.4fms", "initData():", GenomePlot.matepairDataFile, GenomePlot.matepairDataStartTime ) );
// load pipeline file, synchronously
GenomePlot.matepairData = $.ajaxJSONSync (GenomePlot.matepairDataFile);
var endTime = performance.now();
console.info( sprintf( "%-20s Finished loading Mate Pair data file: %s at %.4fms (duration: %.4f seconds)", "initData():", GenomePlot.matepairDataFile, endTime, ( ( endTime - GenomePlot.matepairDataStartTime ) / 1000 ) ) );
// initGUI should be initialized
if( GenomePlot.matepairData === undefined || GenomePlot.matepairData === null
|| GenomePlot.gui === undefined )
return;
// change the file paths to be relative to the directory the files were copied to
for( var record in GenomePlot.matepairData ) {
if( typeof GenomePlot.matepairData[record] !== "string" )
continue;
GenomePlot.matepairData[record] =
GenomePlot.prefixFile + "/" + GenomePlot.matepairData[record].basename();
}
GenomePlot.copyNumber30000DataFile = GenomePlot.matepairData["cnvBinned30KJson"];
.call( GenomePlot.axisY_R );
// fix the resulting text
yAxisNode_R.selectAll("text")
.style( {
"stroke": "none",
"fill": "black",
"cursor": "pointer",
} )
.each( vCenter( GenomePlot.scale * GenomePlot.pixelsPerLine ) )
.each( hCenter( GenomePlot.margin.right - 5, 1 ) )
;
}
var endTime = performance.now();
if( GenomePlot.debug ) console.info( sprintf( "%-20s duration: %.4f seconds", "drawAxis():", ((endTime-startTime)/1000) ) );
}; // drawAxis
console.error( sprintf( "%-20s Rejected loading Cytoband file: %s with %s at %.4fms (duration: %.4f seconds)", "initData():", GenomePlot.cytoBandFile, value, endTime, ( ( endTime - GenomePlot.cytoBandDataStartTime ) / 1000 ) ) );
},
function( error ) {
console.error( sprintf( "%-20s Failed to load Cytoband file: %s with %s", "initData():", GenomePlot.cytoBandFile, error ) );
}
);
} )
.fail (function () {
console.error( sprintf( "%-18s Failed to find Cytoband file: %s", "initData():", GenomePlot.cytoBandFile ) );
} );
}
// load alterations data
GenomePlot.alterationsData = undefined;
if( GenomePlot.alterationsDataFile === undefined ) {
console.error( sprintf( "%-18s Undefined Alterations file", "initData():" ) );
}
else {
$.ajaxFileExists (GenomePlot.alterationsDataFile)
.done (function () {
GenomePlot.alterationsDataStartTime = performance.now();
console.info( sprintf( "%-20s Started loading Alterations file: %s at %.4fms", "initData():", GenomePlot.alterationsDataFile, GenomePlot.alterationsDataStartTime ) );
GenomePlot.loadedResources++;
d3.text( GenomePlot.alterationsDataFile, "text/csv", function( data )
{
var endTime = performance.now();
console.info( sprintf( "%-20s Finished loading Alterations file: %s at %.4fms (duration: %.4f seconds)", "initData():", GenomePlot.alterationsDataFile, endTime, ( ( endTime - GenomePlot.alterationsDataStartTime ) / 1000 ) ) );
GenomePlot.loadedResources--;
GenomePlot.alterationsData = GenomePlot.processAlterationsData(data);
for( var j = 0; j < maskedIndicesRanges.length; j++ )
{
GenomePlot.copyNumber30000Data.toLegacy.wdnsMaskedPerChrom[ chrom_id ]
.push( GenomePlot.copyNumber30000Data.toLegacy.wdnsPerChrom[ chrom_id ][ maskedIndicesRanges[ j ] ] );
}
// do the same for the end of the chrom. if the last point does not match the expected value it is masked
// add it directly to the array
if( GenomePlot.copyNumber30000Data.toLegacy.wdnsPerChrom[ chrom_id ][ GenomePlot.copyNumber30000Data.toLegacy.wdnsPerChrom[ chrom_id ].length - 1 ] !== (chromosomeEnds - chromosomeStarts) * GenomePlot.copyNumber30000Data.windowSize ) {
GenomePlot.copyNumber30000Data.toLegacy.wdnsMaskedPerChrom[ chrom_id ]
.push( GenomePlot.copyNumber30000Data.toLegacy.wdnsPerChrom[ chrom_id ][ GenomePlot.copyNumber30000Data.toLegacy.wdnsPerChrom[ chrom_id ].length - 1 ],
GenomePlot.chromosomes[ (chrom_id+1).toString() ].genomicSize ); // instead of pushing (chromosomeEnds - chromosomeStarts) * GenomePlot.copyNumber30000Data.windowSize push the actual chrom end since we now we are at the end of the chromosome
}
}
console.info( sprintf( "%-20s Total CNV elements to draw: %s", "initData():", frqCnt.toLocaleString() ) );
// for the garbage collector
GenomePlot.copyNumber30000Data.cnv = null;
GenomePlot.copyNumber30000Data.normalCnv = null;
GenomePlot.copyNumber30000Data.toLegacy.wdns = null;
GenomePlot.copyNumber30000Data.toLegacy.frq = null;
frqGreaterTwoPerChrom = null;
maskedIndicesArray = null;
maskedIndicesRanges = null;
}; // processCopyNumber30000Data
GenomePlot.computeChromosomeStartPositions = function ()
{
if( GenomePlot.graphTypeParams.graphType === "U-Shape" )
{
// initialize it every time the function runs; garbage collection will take care of the memory
GenomePlot.chromPixelStarts = new Array( GenomePlot.NUM_CHROMS );
GenomePlot.linesPerGraph = 13;
// height in pixels of one line holding one chromosome (or two)
GenomePlot.pixelsPerLine = GenomePlot.innerHeight / GenomePlot.linesPerGraph;
if (GenomePlot.debug) console.log (sprintf ("%-20s pixels/line: %f", "computeChromosomeStartPositions():", GenomePlot.pixelsPerLine));
// create the start pixels positions of the left chromosomes
for (var i = 0; i < 13; i++)
{
var chrom_id = i+1;
var cx = 0;
var cy = (i + 0.5) * GenomePlot.pixelsPerLine; // computed in the un-padded space
// x: genomic value; y: pixel value
if (chrom_id === 13)
GenomePlot.chromPixelStarts[24-2] = { x: cx, y: cy, adjust: 0 };
else
GenomePlot.chromPixelStarts[chrom_id-1] = { x: cx, y: cy, adjust: 0 };
}
GenomePlot.computeGraphSize = function ()
{
GenomePlot.viewportWidth = viewportSize.getWidth() -
parseFloat( $("#container").css( "margin-left" ).replace("px", "") ) -
parseFloat( $("#container").css( "margin-right" ).replace("px", "") );
GenomePlot.viewportHeight = viewportSize.getHeight();
if (GenomePlot.debug) console.log (sprintf ("%-20s viewport dims: %d x %d", "computeGraphSize():", GenomePlot.viewportWidth, GenomePlot.viewportHeight));
if( GenomePlot.viewportWidth <= 640
|| GenomePlot.viewportHeight <= 480 ) {
GenomePlot.noGUI = true;
hideElementDisplay( $(GenomePlot.gui.domElement) );
}
else {
GenomePlot.noGUI = false;
GenomePlot.viewportWidth -= GenomePlot.gui.adjustWidth;
}
GenomePlot.viewportUnitWidth = GenomePlot.viewportWidth / 100;
GenomePlot.viewportUnitHeight = GenomePlot.viewportHeight / 100;
function( error, data ) {
// fetchData( GenomePlot.cytoBandFile,
// function( data ) {
var endTime = performance.now();
console.info( sprintf( "%-20s Finished loading Cytoband file: %s at %.4fms (duration: %.4f seconds)", "initData():", GenomePlot.cytoBandFile, endTime, ( ( endTime - GenomePlot.cytoBandDataStartTime ) / 1000 ) ) );
GenomePlot.loadedResources--;
GenomePlot.cytoBandData = data;
console.info( sprintf( "%-20s Total Cytoband elements to draw: %s", "initData():", GenomePlot.cytoBandData.length.toLocaleString() ) );
},
function( value ) {
.done (function (data) {
var endTime = performance.now();
console.info( sprintf( "%-20s Finished loading CNV file of window size 30000: %s at %.4fms (duration: %.4f seconds)", "initData():", GenomePlot.copyNumber30000DataFile, endTime, ( ( endTime - GenomePlot.copyNumber30000DataStartTime ) / 1000 ) ) );
GenomePlot.loadedResources--;
GenomePlot.processCopyNumber30000Data(data);
} );
} )
function( error ) {
console.error( sprintf( "%-20s Failed to load Cytoband file: %s with %s", "initData():", GenomePlot.cytoBandFile, error ) );
}
);