public int[] getCurrentRegionWindowGenomicPositions() {
// address int overflow or exceeding bound issues
int xEndEdge =
xContext.getGenomicPositionOrigin()
+ (int)
((double) getZoom().getBinSize()
* superAdapter.getHeatmapPanel().getWidth()
/ getScaleFactor());
if (xEndEdge < 0 || xEndEdge > xContext.getChromosome().getLength()) {
xEndEdge = xContext.getChromosome().getLength();
}
int yEndEdge =
yContext.getGenomicPositionOrigin()
+ (int)
((double) getZoom().getBinSize()
* superAdapter.getHeatmapPanel().getHeight()
/ getScaleFactor());
if (yEndEdge < 0 || yEndEdge > yContext.getChromosome().getLength()) {
yEndEdge = yContext.getChromosome().getLength();
}
return new int[] {
xContext.getGenomicPositionOrigin(), xEndEdge, yContext.getGenomicPositionOrigin(), yEndEdge
};
}
public Matrix getMatrix() {
if (dataset == null) {
// System.err.println("Dataset is null");
return null;
} else if (xContext == null) {
// System.err.println("xContext is null");
return null;
} else if (yContext == null) {
// System.err.println("yContext is null");
return null;
}
return dataset.getMatrix(xContext.getChromosome(), yContext.getChromosome());
}
public String getDefaultLocationDescription() {
String xChr = xContext.getChromosome().getName();
String yChr = yContext.getChromosome().getName();
if (!(xChr.toLowerCase().contains("chr"))) xChr = "chr" + xChr;
if (!(yChr.toLowerCase().contains("chr"))) yChr = "chr" + yChr;
return xChr
+ "@"
+ (long) (xContext.getBinOrigin() * currentZoom.getBinSize())
+ "_"
+ yChr
+ "@"
+ (long) (yContext.getBinOrigin() * currentZoom.getBinSize());
}
private void setChromosomesFromBroadcast(String chrXName, String chrYName) {
if (!chrXName.equals(xContext.getChromosome().getName())
|| !chrYName.equals(yContext.getChromosome().getName())) {
Chromosome chrX = HiCFileTools.getChromosomeNamed(chrXName, chromosomes);
Chromosome chrY = HiCFileTools.getChromosomeNamed(chrYName, chromosomes);
if (chrX == null || chrY == null) {
// log.info("Most probably origin is a different species saved location or sync/link between
// two different species maps.");
return;
}
this.xContext = new Context(chrX);
this.yContext = new Context(chrY);
superAdapter.setSelectedChromosomesNoRefresh(chrX, chrY);
refreshEigenvectorTrackIfExists();
}
}
public String getLocationDescription() {
String xChr = xContext.getChromosome().getName();
String yChr = yContext.getChromosome().getName();
if (!(xChr.toLowerCase().contains("chr"))) xChr = "chr" + xChr;
if (!(yChr.toLowerCase().contains("chr"))) yChr = "chr" + yChr;
return "setlocation "
+ xChr
+ " "
+ yChr
+ " "
+ currentZoom.getUnit().toString()
+ " "
+ currentZoom.getBinSize()
+ " "
+ xContext.getBinOrigin()
+ " "
+ yContext.getBinOrigin()
+ " "
+ getScaleFactor();
}
/**
* ************************************************************* Official Method for setting the
* zoom and location for heatmap DO NOT IMPLEMENT A NEW FUNCTION Make the necessary
* customizations, then call this function
* *************************************************************
*
* @param newZoom
* @param genomeX
* @param genomeY
* @param scaleFactor (pass -1 if scaleFactor should be calculated)
* @return
*/
public boolean unsafeActuallySetZoomAndLocation(
String chrXName,
String chrYName,
HiCZoom newZoom,
int genomeX,
int genomeY,
double scaleFactor,
boolean resetZoom,
ZoomCallType zoomCallType,
boolean allowLocationBroadcast) {
if (dataset == null) return false; // No data in view
// Check this zoom operation is possible, if not, fail it here:
// if (superAdapter.testNewZoom(newZoom))
// {
// return false;
// }
// String chr1OriginalName = xContext.getChromosome().getName();
// String chr2OriginalName = yContext.getChromosome().getName();
if (chrXName.length() > 0 && chrYName.length() > 0) {
setChromosomesFromBroadcast(chrXName, chrYName);
// We might end with All->All view, make sure normalization state is updates accordingly...
superAdapter.getMainViewPanel().setNormalizationDisplayState(superAdapter.getHiC());
}
if (newZoom == null) {
System.err.println("Invalid zoom " + newZoom);
}
Chromosome chr1 = xContext.getChromosome();
Chromosome chr2 = yContext.getChromosome();
final Matrix matrix = dataset.getMatrix(chr1, chr2);
if (matrix == null) {
superAdapter.launchGenericMessageDialog(
"Sorry, this region is not available", "Matrix unavailable", JOptionPane.WARNING_MESSAGE);
return false;
}
MatrixZoomData newZD = matrix.getZoomData(newZoom);
if (HiCFileTools.isAllChromosome(chr1)) {
newZD = matrix.getFirstZoomData(Unit.BP);
}
if (newZD == null) {
superAdapter.launchGenericMessageDialog(
"Sorry, this zoom is not available", "Zoom unavailable", JOptionPane.WARNING_MESSAGE);
return false;
}
/* TODO Undo Zoom implementation mss2 _UZI
if(currentZoom != null) {
tempZoomState = new ZoomState(chr1OriginalName, chr2OriginalName, currentZoom.clone(), (int) xContext.getBinOrigin(),
(int) yContext.getBinOrigin(), getScaleFactor(), resetZoom, ZoomCallType.GOTO);
}
*/
currentZoom = newZoom;
xContext.setZoom(currentZoom);
yContext.setZoom(currentZoom);
if (scaleFactor > 0) {
setScaleFactor(scaleFactor);
} else {
int maxBinCount =
Math.max(newZD.getXGridAxis().getBinCount(), newZD.getYGridAxis().getBinCount());
double defaultScaleFactor =
Math.max(
1.0, (double) superAdapter.getHeatmapPanel().getMinimumDimension() / maxBinCount);
setScaleFactor(defaultScaleFactor);
}
int binX = newZD.getXGridAxis().getBinNumberForGenomicPosition(genomeX);
int binY = newZD.getYGridAxis().getBinNumberForGenomicPosition(genomeY);
switch (zoomCallType) {
case INITIAL:
case STANDARD:
center(binX, binY);
break;
case DRAG:
xContext.setBinOrigin(binX);
yContext.setBinOrigin(binY);
break;
case DIRECT:
xContext.setBinOrigin(genomeX);
yContext.setBinOrigin(genomeY);
break;
}
// Notify HeatmapPanel render that zoom has changed. Render should update zoom slider once with
// previous range values
setZoomChanged();
if (resetZoom) {
superAdapter.updateAndResetZoom(newZoom);
} else {
superAdapter.updateZoom(newZoom);
}
superAdapter.refresh();
if (linkedMode && allowLocationBroadcast) {
broadcastLocation();
}
/*
TODO Undo Zoom implementation mss2 _UZI
if(zoomCallType == ZoomCallType.INITIAL || tempZoomState == null || chrXName.equals(Globals.CHR_ALL) || chrYName.equals(Globals.CHR_ALL)
|| tempZoomState.chr1Name.equals(Globals.CHR_ALL) || tempZoomState.chr2Name.equals(Globals.CHR_ALL)){
canRedoZoomChange = false;
canUndoZoomChange = false;
}
else {
// defauts for a normal zoom operation
canRedoZoomChange = false;
canUndoZoomChange = true;
previousZoomState = tempZoomState;
}
*/
return true;
}
public boolean isWholeGenome() {
return xContext != null && HiCFileTools.isAllChromosome(xContext.getChromosome());
}
public Matrix getControlMatrix() {
if (controlDataset == null || xContext == null || currentZoom == null) return null;
return controlDataset.getMatrix(xContext.getChromosome(), yContext.getChromosome());
}