private void loadFromDBProfile(ResourceLocator profileLocator, List<Track> newTracks)
throws IOException {
DBProfile dbProfile = DBProfile.parseProfile(profileLocator.getPath());
for (DBProfile.DBTable table : dbProfile.getTableList()) {
SQLCodecSource source = SQLCodecSource.getFromTable(table);
if (source != null) {
CachingFeatureSource cachingReader = new CachingFeatureSource(source);
FeatureTrack track = new FeatureTrack(profileLocator, cachingReader);
track.setName(source.getTableName());
newTracks.add(track);
} else if (table.getFormat().equals("seg")) {
Genome genome = GenomeManager.getInstance().getCurrentGenome();
SegmentedAsciiDataSet ds =
(new SegmentedReader(table.getDbLocator(), genome)).loadFromDB(table);
loadSegTrack(table.getDbLocator(), newTracks, genome, ds);
} else if (table.getFormat().equals("sample.info")) {
// TODO sampleIdColumnLabel was previously hardcoded as "SAMPLE_ID_ARRAY"
// TODO Basically I'm shoehorning this information into a field usually used for something
// else. Only slightly better
String sampleIdColumnLabel = table.getBinColName();
if (sampleIdColumnLabel == null) {
throw new IllegalArgumentException(
"Profile must have binColName specifying the sample id column label");
}
(new SampleInfoSQLReader(table, sampleIdColumnLabel)).load();
}
}
}
private void loadSyntentyMapping(ResourceLocator locator, List<Track> newTracks) {
List<BlastMapping> mappings = (new BlastParser()).parse(locator.getPath());
List<htsjdk.tribble.Feature> features = new ArrayList<htsjdk.tribble.Feature>(mappings.size());
features.addAll(mappings);
Genome genome = GenomeManager.getInstance().getCurrentGenome();
FeatureTrack track = new FeatureTrack(locator, new FeatureCollectionSource(features, genome));
track.setName(locator.getTrackName());
// track.setRendererClass(AlignmentBlockRenderer.class);
newTracks.add(track);
}