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());
}
}
/**
* Chromosome "0" is whole genome
*
* @param chromosomes list of chromosomes
*/
void setChromosomes(List<Chromosome> chromosomes) {
int[] chromosomeBoundaries = new int[chromosomes.size() - 1];
long bound = 0;
for (int i = 1; i < chromosomes.size(); i++) {
Chromosome c = chromosomes.get(i);
bound += (c.getLength() / 1000);
chromosomeBoundaries[i - 1] = (int) bound;
}
heatmapPanel.setChromosomeBoundaries(chromosomeBoundaries);
chrBox1.setModel(
new DefaultComboBoxModel<Chromosome>(
chromosomes.toArray(new Chromosome[chromosomes.size()])));
chrBox2.setModel(
new DefaultComboBoxModel<Chromosome>(
chromosomes.toArray(new Chromosome[chromosomes.size()])));
}