/**
* Load a mutation file (".mut" or ".maf").
*
* @param locator
* @param newTracks
*/
private void loadMutFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException, TribbleIndexNotFoundException {
MutationTrackLoader loader = new MutationTrackLoader();
List<FeatureTrack> mutationTracks = loader.loadMutationTracks(locator, genome);
for (FeatureTrack track : mutationTracks) {
track.setTrackType(TrackType.MUTATION);
track.setRendererClass(MutationRenderer.class);
newTracks.add(track);
}
}
/**
* Load the input file as a feature, mutation, or maf (multiple alignment) file.
*
* @param locator
* @param newTracks
*/
private void loadTribbleFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException, TribbleIndexNotFoundException {
String typeString = locator.getTypeString();
// Mutation (mut, maf, vcf) files are handled special. Check here, rather than depend on order
// in giant case statement.
if (MutationTrackLoader.isMutationAnnotationFile(locator)) {
loadMutFile(locator, newTracks, genome); // Must be tried before generic "loadIndexed" below
} else if (VariantTrack.isVCF(typeString)) {
loadVCF(locator, newTracks, genome);
} else {
TribbleFeatureSource tribbleFeatureSource =
TribbleFeatureSource.getFeatureSource(locator, genome);
FeatureSource src =
GFFFeatureSource.isGFF(locator.getPath())
? new GFFFeatureSource(tribbleFeatureSource)
: tribbleFeatureSource;
// Create feature source and track
FeatureTrack t = new FeatureTrack(locator, src);
t.setName(locator.getTrackName());
// t.setRendererClass(BasicTribbleRenderer.class);
// Set track properties from header
Object header = tribbleFeatureSource.getHeader();
if (header != null && header instanceof FeatureFileHeader) {
FeatureFileHeader ffh = (FeatureFileHeader) header;
if (ffh.getTrackType() != null) {
t.setTrackType(ffh.getTrackType());
}
if (ffh.getTrackProperties() != null) {
t.setProperties(ffh.getTrackProperties());
}
if (ffh.getTrackType() == TrackType.REPMASK) {
t.setHeight(15);
}
}
if (locator.getPath().contains(".narrowPeak")
|| locator.getPath().contains(".broadPeak")
|| locator.getPath().contains(".gappedPeak")) {
t.setUseScore(true);
}
newTracks.add(t);
}
}
