/**
* Called from alt-drag zoom
*
* @param xBP0
* @param yBP0
* @param targetBinSize
*/
public void zoomToDrawnBox(final int xBP0, final int yBP0, final double targetBinSize) {
HiCZoom newZoom = currentZoom;
if (!isResolutionLocked()) {
List<HiCZoom> zoomList =
currentZoom.getUnit() == HiC.Unit.BP ? dataset.getBpZooms() : dataset.getFragZooms();
for (int i = zoomList.size() - 1; i >= 0; i--) {
if (zoomList.get(i).getBinSize() >= targetBinSize) {
newZoom = zoomList.get(i);
break;
}
}
// this addresses draw box to zoom when down from low res pearsons
// it can't zoom all the way in, but can zoom in a little more up to 500K
if (isInPearsonsMode() && newZoom.getBinSize() < HiCGlobals.MAX_PEARSON_ZOOM) {
for (int i = zoomList.size() - 1; i >= 0; i--) {
if (zoomList.get(i).getBinSize() >= HiCGlobals.MAX_PEARSON_ZOOM) {
newZoom = zoomList.get(i);
break;
}
}
}
}
safeActuallySetZoomAndLocation(
newZoom,
xBP0,
yBP0,
newZoom.getBinSize() / targetBinSize,
false,
ZoomCallType.DRAG,
"DragZoom",
true);
}
public double[] getEigenvector(final int chrIdx, final int n, boolean isControl) {
if (isControl) {
if (controlDataset == null) return null;
Chromosome chr = chromosomes.get(chrIdx);
return controlDataset.getEigenvector(chr, currentZoom, n, normalizationType);
} else {
if (dataset == null) return null;
Chromosome chr = chromosomes.get(chrIdx);
return dataset.getEigenvector(chr, currentZoom, n, normalizationType);
}
}
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());
}
}
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());
}
/**
* ************************************************************* 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 NormalizationVector getNormalizationVector(int chrIdx) {
if (dataset == null) return null;
return dataset.getNormalizationVector(chrIdx, currentZoom, normalizationType);
}
public ExpectedValueFunction getExpectedValues() {
if (dataset == null) return null;
return dataset.getExpectedValues(currentZoom, normalizationType);
}
public Matrix getControlMatrix() {
if (controlDataset == null || xContext == null || currentZoom == null) return null;
return controlDataset.getMatrix(xContext.getChromosome(), yContext.getChromosome());
}