/**
* Add the provided SegmentedDataSet to the list of tracks, set other relevant properties
*
* @param locator
* @param newTracks
* @param genome
* @param ds
*/
private void loadSegTrack(
ResourceLocator locator, List<Track> newTracks, Genome genome, SegmentedDataSet ds) {
String path = locator.getPath();
TrackProperties props = null;
if (ds instanceof SegmentedAsciiDataSet) {
props = ((SegmentedAsciiDataSet) ds).getTrackProperties();
}
// The "freq" track. TODO - make this optional
if ((ds.getType() == TrackType.COPY_NUMBER || ds.getType() == TrackType.CNV)
&& ds.getSampleNames().size() > 1) {
FreqData fd = new FreqData(ds, genome);
String freqTrackId = path;
String freqTrackName = "CNV Summary";
CNFreqTrack freqTrack = new CNFreqTrack(locator, freqTrackId, freqTrackName, fd);
newTracks.add(freqTrack);
}
for (String trackName : ds.getSampleNames()) {
String trackId = path + "_" + trackName;
SegmentedDataSource dataSource = new SegmentedDataSource(trackName, ds);
DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, dataSource);
track.setRendererClass(HeatmapRenderer.class);
track.setTrackType(ds.getType());
if (props != null) {
track.setProperties(props);
}
newTracks.add(track);
}
}
private List<LocusScore> getSegments(String chr) {
return dataset.getSegments(trackIdentifier, chr);
}
public double getDataMin() {
return dataset.getDataMin(Globals.CHR_ALL);
}
public boolean isLogNormalized() {
return dataset.isLogNormalized();
}
public TrackType getTrackType() {
return dataset.getType();
}
public List<LocusScore> getWholeGenomeScores() {
return dataset.getWholeGenomeScores(trackIdentifier);
}
