private void loadSMAPFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
List<Feature> features = SMAPParser.parseFeatures(locator, genome);
FeatureCollectionSource src = new FeatureCollectionSource(features, genome);
FeatureTrack track = new FeatureTrack(locator, locator.getName(), src);
track.setRendererClass(SMAPRenderer.class);
track.setDisplayMode(Track.DisplayMode.EXPANDED);
newTracks.add(track);
}
private void loadDASResource(ResourceLocator locator, List<Track> currentTracks)
throws DataLoadException {
// TODO Connect and get all the attributes of the DAS server, and run the appropriate load
// statements
// TODO Currently we are only going to be doing features
// TODO -- move the source creation to a factory
DASFeatureSource featureSource = null;
try {
featureSource = new DASFeatureSource(locator);
} catch (MalformedURLException e) {
log.error("Malformed URL", e);
throw new DataLoadException("Error: Malformed URL ");
}
FeatureTrack track = new FeatureTrack(locator, featureSource);
// Try to create a sensible name from the path
String name = locator.getName();
if (name == null || name.length() == 0) {
if (locator.getPath().contains("genome.ucsc.edu")) {
name = featureSource.getType();
} else {
name = featureSource.getPath().replace("/das/", "").replace("/features", "");
}
}
track.setName(name);
// A hack until we can notate this some other way
if (locator.getPath().contains("cosmic")) {
track.setRendererClass(CosmicFeatureRenderer.class);
track.setMinimumHeight(2);
track.setHeight(20);
track.setDisplayMode(Track.DisplayMode.EXPANDED);
} else {
track.setRendererClass(IGVFeatureRenderer.class);
track.setMinimumHeight(35);
track.setHeight(45);
}
currentTracks.add(track);
}
/**
* 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);
}
}