public List<Pair<Rectangle, Feature2D>> findNearbyFeaturePairs(
MatrixZoomData zd, int chrIdx1, int chrIdx2, int x, int y, int n) {
double binOriginX = getXContext().getBinOrigin();
double binOriginY = getYContext().getBinOrigin();
double scale = getScaleFactor();
return feature2DHandler.findNearbyFeaturePairs(
zd, chrIdx1, chrIdx2, x, y, n, binOriginX, binOriginY, scale);
}
private void clearFeatures() {
trackManager.clearTracks();
feature2DHandler.clearLists();
}
public void removeLoadedAnnotation(String path) {
feature2DHandler.removeFeaturePath(path);
}
public void toggleFeatureOpacity(boolean status) {
feature2DHandler.toggleFeatureOpacity(status);
}
public void enlarge2DFeaturePlotting(boolean status) {
feature2DHandler.enlarge2DFeaturePlotting(status);
}
public void setSparseFeaturePlotting(boolean status) {
feature2DHandler.setSparseFeaturePlotting(status);
}
public List<Feature2D> getVisibleFeatures(int chrIdx1, int chrIdx2) {
return feature2DHandler.getVisibleFeatures(chrIdx1, chrIdx2);
}
public List<Feature2DList> getAllVisibleLoopLists() {
return feature2DHandler.getAllVisibleLoopLists();
}
public void loadLoopList(String path) {
feature2DHandler.loadLoopList(path, chromosomes);
}
public void setLoopsInvisible(String path) {
feature2DHandler.setLoopsInvisible(path);
}
public void setShowLoops(boolean showLoops) {
feature2DHandler.setShowLoops(showLoops);
}