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));
}
/**
* 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()])));
}
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 void parsePositionText() {
// Expected format 1: <chr>:<start>-<end>:<resolution>
// Expected format 2: <chr>:<midpt>:<resolution>
String delimiters = "\\s+|:\\s*|\\-\\s*";
String dashDelimiters = "\\s+|\\-\\s*";
String[] leftChrTokens = positionChrLeft.getText().split(delimiters);
String[] topChrTokens = positionChrTop.getText().split(delimiters);
String[] leftDashChrTokens = positionChrLeft.getText().split(dashDelimiters);
String[] topDashChrTokens = positionChrTop.getText().split(dashDelimiters);
if (topChrTokens.length == 1 || leftChrTokens.length == 1) {
parseGenePositionText();
return;
}
// Read Chromosomes:
HashMap<String, Chromosome> chromosomeMap = new HashMap<String, Chromosome>();
for (Chromosome c : hic.getDataset().getChromosomes()) {
chromosomeMap.put(c.getName().toLowerCase(), c);
chromosomeMap.put("chr" + c.getName().toLowerCase(), c);
if (c.getName().equals("MT")) chromosomeMap.put("chrm", c);
}
Chromosome topChr = chromosomeMap.get(topChrTokens[0].toLowerCase());
if (topChr == null) {
positionChrTop.setBackground(Color.yellow);
log.error("Cannot find " + topChrTokens[0] + " in dataset's chromosome list");
return;
}
Chromosome leftChr = chromosomeMap.get(leftChrTokens[0].toLowerCase());
if (leftChr == null) {
positionChrLeft.setBackground(Color.yellow);
log.error("Cannot find " + leftChrTokens[0] + " in dataset's chromosome list");
return;
}
// chrPositions {start, end, outBin, estimatedOutBinSize}
int[] topChrPositions;
try {
topChrPositions = extractParametersFromTokens(topChrTokens, topDashChrTokens, positionChrTop);
} catch (Exception e) {
return;
}
int[] leftChrPositions;
try {
leftChrPositions =
extractParametersFromTokens(leftChrTokens, leftDashChrTokens, positionChrLeft);
} catch (Exception e) {
return;
}
// Read resolution:
int outBinSize = 0;
HiC.Unit resolutionUnits = HiC.Unit.BP;
int estimatedOutBinSize = Math.max(topChrPositions[3], leftChrPositions[3]);
if (topChrTokens.length > 3 || (topDashChrTokens.length == 1 && topChrTokens.length > 2)) {
try {
int[] resolutionParameters =
extractResolutionParametersFromTokens(topChrTokens, topDashChrTokens, positionChrTop);
outBinSize = resolutionParameters[0];
if (resolutionParameters[1] < 0) {
resolutionUnits = HiC.Unit.FRAG;
}
} catch (Exception e) {
return;
}
} else if (leftChrTokens.length > 3
|| (leftDashChrTokens.length == 1 && leftChrTokens.length > 2)) {
try {
int[] resolutionParameters =
extractResolutionParametersFromTokens(
leftChrTokens, leftDashChrTokens, positionChrLeft);
outBinSize = resolutionParameters[0];
if (resolutionParameters[1] < 0) {
resolutionUnits = HiC.Unit.FRAG;
}
} catch (Exception e) {
return;
}
} else if (estimatedOutBinSize > 0) {
outBinSize = estimatedOutBinSize;
} else if (hic.getZoom().getBinSize()
!= 0) { // no resolution specified, not at whole genome view
outBinSize = hic.validateBinSize(String.valueOf(hic.getZoom().getBinSize()));
if (outBinSize != Integer.MIN_VALUE) {
resolutionUnits = hic.getZoom().getUnit();
}
}
positionChrTop.setBackground(Color.white);
positionChrLeft.setBackground(Color.white);
if (outBinSize == Integer.MIN_VALUE) {
outBinSize = 250000; // If bin size is not valid, set to max bin size
}
hic.setLocation(
topChr.getName(),
leftChr.getName(),
resolutionUnits,
outBinSize,
Math.max(topChrPositions[2], 0),
Math.max(leftChrPositions[2], 0),
hic.getScaleFactor(),
HiC.ZoomCallType.STANDARD,
"Goto",
true);
}
private boolean isWholeGenome() {
Chromosome chr1 = (Chromosome) chrBox1.getSelectedItem();
Chromosome chr2 = (Chromosome) chrBox2.getSelectedItem();
return chr1.getName().equals("All") || chr2.getName().equals("All");
}
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);
}