private void loadCufflinksFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
final String path = locator.getPath();
final String s = path.toLowerCase();
List<DataTrack> cuffTracks = new ArrayList<DataTrack>();
if (s.endsWith("fpkm_tracking")) {
FPKMTrackingCodec codec = new FPKMTrackingCodec(path);
List<FPKMValue> values = CufflinksParser.parse(codec, path);
for (int sampleIndex = 0; sampleIndex < codec.getNumSamples(); sampleIndex++) {
CufflinksDataSource ds = new CufflinksDataSource(sampleIndex, values, genome);
String supId = String.format("q%02d", sampleIndex);
DataTrack track =
new DataSourceTrack(
locator, locator.getPath() + " " + supId, locator.getTrackName() + " " + supId, ds);
cuffTracks.add(track);
}
} else if (s.endsWith("gene_exp.diff") || s.endsWith("cds_exp.diff")) {
AsciiFeatureCodec<ExpDiffValue> codec = new ExpDiffCodec(path);
List<ExpDiffValue> values = CufflinksParser.parse(codec, path);
CufflinksDataSource ds = new CufflinksDataSource(values, genome);
DataTrack track = new DataSourceTrack(locator, locator.getPath(), locator.getTrackName(), ds);
cuffTracks.add(track);
} else {
throw new RuntimeException("Unsupported file type: " + path);
}
for (DataTrack track : cuffTracks) {
track.setTrackType(TrackType.FPKM);
CufflinksTrack.setCufflinksScale(track);
newTracks.add(track);
}
}
