private void loadIGVFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
if (locator.isLocal()) {
if (!checkSize(locator)) {
return;
}
}
String dsName = locator.getTrackName();
IGVDataset ds = new IGVDataset(locator, genome);
ds.setName(dsName);
TrackProperties trackProperties = ds.getTrackProperties();
String path = locator.getPath();
TrackType type = ds.getType();
for (String trackName : ds.getTrackNames()) {
DatasetDataSource dataSource = new DatasetDataSource(trackName, ds, genome);
String trackId = path + "_" + trackName;
DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, dataSource);
// track.setRendererClass(HeatmapRenderer.class);
track.setTrackType(ds.getType());
track.setProperties(trackProperties);
if (type == TrackType.ALLELE_FREQUENCY) {
track.setRendererClass(PointsRenderer.class);
track.setHeight(40);
}
newTracks.add(track);
}
}
/**
* Load a rnai gene score file and create a datasource and track.
*
* <p>
*
* @param locator
* @param newTracks
*/
private void loadRNAiGeneScoreFile(
ResourceLocator locator,
List<Track> newTracks,
RNAIGeneScoreParser.Type type,
Genome genome) {
RNAIGeneScoreParser parser = new RNAIGeneScoreParser(locator.getPath(), type, genome);
Collection<RNAIDataSource> dataSources = parser.parse();
String path = locator.getPath();
for (RNAIDataSource ds : dataSources) {
String name = ds.getName();
String trackId = path + "_" + name;
DataSourceTrack track = new DataSourceTrack(locator, trackId, name, ds);
// Set attributes. This "hack" is neccessary to register these attributes with the
// attribute manager to get displayed.
track.setAttributeValue("SCREEN", ds.getScreen());
if ((ds.getCondition() != null) && (ds.getCondition().length() > 0)) {
track.setAttributeValue("CONDITION", ds.getCondition());
}
track.setHeight(80);
// track.setDataRange(new DataRange(-3, 0, 3));
newTracks.add(track);
}
}
private void loadRnaiGctFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
RNAIGCTDatasetParser parser = new RNAIGCTDatasetParser(locator, genome);
Collection<RNAIDataSource> dataSources = parser.parse();
if (dataSources != null) {
String path = locator.getPath();
for (RNAIDataSource ds : dataSources) {
String trackId = path + "_" + ds.getName();
DataSourceTrack track = new DataSourceTrack(locator, trackId, ds.getName(), ds);
// Set attributes.
track.setAttributeValue("SCREEN", ds.getScreen());
track.setHeight(80);
newTracks.add(track);
}
}
}