public void moveTrack(HiCTrack track, boolean thisShouldBeMovedUp) {
if (thisShouldBeMovedUp) {
// move the track up
trackManager.moveTrackUp(track);
} else {
// move the track down
trackManager.moveTrackDown(track);
}
}
public void loadEigenvectorTrack() {
if (eigenvectorTrack == null) {
eigenvectorTrack = new EigenvectorTrack(eigString, eigString, this, false);
}
if (controlEigenvectorTrack == null && isControlLoaded()) {
controlEigenvectorTrack = new EigenvectorTrack(ctrlEigString, ctrlEigString, this, true);
}
trackManager.add(eigenvectorTrack);
if (controlEigenvectorTrack != null && isControlLoaded()) {
trackManager.add(controlEigenvectorTrack);
}
}
// TODO zgire - why iterate through tracksToRemove if you end up calling clearFeatures() at the
// end?
public void clearTracksForReloadState() {
ArrayList<HiCTrack> tracksToRemove = new ArrayList<HiCTrack>(trackManager.getLoadedTracks());
for (HiCTrack trackToRemove : tracksToRemove) {
if (trackToRemove.getName().equals(eigString)) {
eigenvectorTrack = null;
} else if (trackToRemove.getName().equals(ctrlEigString)) {
controlEigenvectorTrack = null;
} else {
trackManager.removeTrack(trackToRemove);
}
}
clearFeatures();
superAdapter.updateTrackPanel();
}
public List<HiCTrack> getLoadedTrackList() {
return trackManager.getLoadedTracks();
}
public void removeTrack(ResourceLocator locator) {
if (resourceTree != null) resourceTree.remove(locator);
if (encodeAction != null) encodeAction.remove(locator);
trackManager.removeTrack(locator);
}
public void removeTrack(HiCTrack track) {
if (resourceTree != null) resourceTree.remove(track.getLocator());
if (encodeAction != null) encodeAction.remove(track.getLocator());
trackManager.removeTrack(track);
}
public void loadCoverageTrack(NormalizationType no) {
trackManager.loadCoverageTrack(no);
}
public void loadTrack(String path) {
trackManager.loadTrack(path);
}
public void unsafeLoadHostedTracks(List<ResourceLocator> locators) {
trackManager.unsafeTrackLoad(locators);
}
public java.util.List<HiCTrack> getLoadedTracks() {
return trackManager == null ? new ArrayList<HiCTrack>() : trackManager.getLoadedTracks();
}
private void clearFeatures() {
trackManager.clearTracks();
feature2DHandler.clearLists();
}