public void setSelectedChromosomesNoRefresh(
Chromosome xChrom, Chromosome yChrom, Context xContext, Context yContext) {
chrBox1.setSelectedIndex(yChrom.getIndex());
chrBox2.setSelectedIndex(xChrom.getIndex());
rulerPanelX.setContext(xContext, HiCRulerPanel.Orientation.HORIZONTAL);
rulerPanelY.setContext(yContext, HiCRulerPanel.Orientation.VERTICAL);
resolutionSlider.setEnabled(!xChrom.getName().equals(Globals.CHR_ALL));
}
public void unsafeRefreshChromosomes(SuperAdapter superAdapter) {
if (chrBox1.getSelectedIndex() == 0 || chrBox2.getSelectedIndex() == 0) {
chrBox1.setSelectedIndex(0);
chrBox2.setSelectedIndex(0);
}
Chromosome chr1 = (Chromosome) chrBox1.getSelectedItem();
Chromosome chr2 = (Chromosome) chrBox2.getSelectedItem();
Chromosome chrX = chr1.getIndex() < chr2.getIndex() ? chr1 : chr2;
Chromosome chrY = chr1.getIndex() < chr2.getIndex() ? chr2 : chr1;
setNormalizationDisplayState(superAdapter.getHiC());
superAdapter.unsafeUpdateHiCChromosomes(chrX, chrY);
updateThumbnail(superAdapter.getHiC());
}
private void unsafeSave1DTrackToWigFile(
Chromosome chromosomeForPosition, PrintWriter printWriter, int binStartPosition)
throws IOException {
int resolution = getZoom().getBinSize();
for (Chromosome chromosome : chromosomes) {
if (chromosome.getName().equals(Globals.CHR_ALL)) continue;
Matrix matrix = null;
if (displayOption == MatrixType.OBSERVED) {
matrix = dataset.getMatrix(chromosomeForPosition, chromosome);
} else if (displayOption == MatrixType.CONTROL) {
matrix = controlDataset.getMatrix(chromosomeForPosition, chromosome);
}
if (matrix == null) continue;
MatrixZoomData zd = matrix.getZoomData(currentZoom);
printWriter.println(
"fixedStep chrom=chr"
+ chromosome.getName().replace("chr", "")
+ " start=1 step="
+ resolution
+ " span="
+ resolution);
int[] regionIndices;
if (chromosomeForPosition.getIndex() < chromosome.getIndex()) {
regionIndices = new int[] {binStartPosition, binStartPosition, 0, chromosome.getLength()};
} else {
regionIndices = new int[] {0, chromosome.getLength(), binStartPosition, binStartPosition};
}
zd.dump1DTrackFromCrossHairAsWig(
printWriter,
chromosomeForPosition,
binStartPosition,
chromosomeForPosition.getIndex() == chromosome.getIndex(),
regionIndices,
normalizationType,
displayOption,
getExpectedValues());
}
}
private boolean isIntraChromosomal() {
Chromosome chr1 = (Chromosome) chrBox1.getSelectedItem();
Chromosome chr2 = (Chromosome) chrBox2.getSelectedItem();
return chr1.getIndex() != chr2.getIndex();
}
/*
* Only accessed from within another unsafe method in Heatmap Panel class,
* which in turn is encapsulated (i.e. made safe)
*/
public void unsafeSetSelectedChromosomes(
SuperAdapter superAdapter, Chromosome xChrom, Chromosome yChrom) {
chrBox1.setSelectedIndex(yChrom.getIndex());
chrBox2.setSelectedIndex(xChrom.getIndex());
unsafeRefreshChromosomes(superAdapter);
}