/**
* 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 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());
}
public void unsafeSetLocation(
String chrXName,
String chrYName,
String unitName,
int binSize,
double xOrigin,
double yOrigin,
double scaleFactor,
ZoomCallType zoomCallType,
boolean allowLocationBroadcast) {
HiCZoom newZoom = currentZoom;
if (currentZoom.getBinSize() != binSize) {
newZoom = new HiCZoom(HiC.valueOfUnit(unitName), binSize);
}
unsafeActuallySetZoomAndLocation(
chrXName,
chrYName,
newZoom,
(int) xOrigin,
(int) yOrigin,
scaleFactor,
true,
zoomCallType,
allowLocationBroadcast);
}
public void generateTrackFromLocation(int mousePos, boolean isHorizontal) {
if (!MatrixType.isObservedOrControl(displayOption)) {
MessageUtils.showMessage("This feature is only available for Observed or Control views");
return;
}
// extract the starting position
int binStartPosition = (int) (getXContext().getBinOrigin() + mousePos / getScaleFactor());
if (isHorizontal)
binStartPosition = (int) (getYContext().getBinOrigin() + mousePos / getScaleFactor());
// Initialize default file name
String filename = displayOption == MatrixType.OBSERVED ? "obs" : "ctrl";
filename += isHorizontal ? "_horz" : "_vert";
filename += "_bin" + binStartPosition + "_res" + currentZoom.getBinSize();
filename = cleanUpNumbersInName(filename);
// allow user to customize or change the name
filename = MessageUtils.showInputDialog("Enter a name for the resulting .wig file", filename);
if (filename == null || filename.equalsIgnoreCase("null")) return;
File outputWigFile = new File(DirectoryManager.getHiCDirectory(), filename + ".wig");
MessageUtils.showMessage("Data will be saved to " + outputWigFile.getAbsolutePath());
Chromosome chromosomeForPosition = getXContext().getChromosome();
if (isHorizontal) chromosomeForPosition = getYContext().getChromosome();
safeSave1DTrackToWigFile(chromosomeForPosition, outputWigFile, binStartPosition);
}
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();
}
public boolean isResolutionLocked() {
return superAdapter.isResolutionLocked()
||
// pearson can't zoom in
(isInPearsonsMode() && currentZoom.getBinSize() == HiCGlobals.MAX_PEARSON_ZOOM);
}
public boolean isPearsonEdgeCaseEncountered(HiCZoom zoom) {
return isInPearsonsMode() && zoom.getBinSize() < HiCGlobals.MAX_PEARSON_ZOOM;
}