public void loadTDFFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
log.debug("Loading TDF file " + locator.getPath());
TDFReader reader = TDFReader.getReader(locator);
TrackType type = reader.getTrackType();
TrackProperties props = null;
String trackLine = reader.getTrackLine();
if (trackLine != null && trackLine.length() > 0) {
props = new TrackProperties();
ParsingUtils.parseTrackLine(trackLine, props);
}
// In case of conflict between the resource locator display name and the track properties name,
// use the resource locator
String name = locator.getName();
if (name != null && props != null) {
props.setName(name);
}
if (name == null) {
name = props == null ? locator.getTrackName() : props.getName();
}
int trackNumber = 0;
String path = locator.getPath();
boolean multiTrack = reader.getTrackNames().length > 1;
for (String heading : reader.getTrackNames()) {
String trackId = multiTrack ? path + "_" + heading : path;
String trackName = multiTrack ? heading : name;
final DataSource dataSource =
locator.getPath().endsWith(".counts")
? new GobyCountArchiveDataSource(locator)
: new TDFDataSource(reader, trackNumber, heading, genome);
DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, dataSource);
String displayName = (name == null || multiTrack) ? heading : name;
track.setName(displayName);
track.setTrackType(type);
if (props != null) {
track.setProperties(props);
}
newTracks.add(track);
trackNumber++;
}
}
private void loadWigFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
if (locator.isLocal()) {
if (!checkSize(locator)) {
return;
}
}
WiggleDataset ds = (new WiggleParser(locator, genome)).parse();
TrackProperties props = ds.getTrackProperties();
// In case of conflict between the resource locator display name and the track properties name,
// use the resource locator
String name = props == null ? null : props.getName();
String label = locator.getName();
if (name == null) {
name = locator.getFileName();
} else if (label != null) {
props.setName(label); // erase name rom track properties
}
String path = locator.getPath();
boolean multiTrack = ds.getTrackNames().length > 1;
for (String heading : ds.getTrackNames()) {
String trackId = multiTrack ? path + "_" + heading : path;
String trackName = multiTrack ? heading : name;
DatasetDataSource dataSource = new DatasetDataSource(trackId, ds, genome);
DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, dataSource);
String displayName = (label == null || multiTrack) ? heading : label;
track.setName(displayName);
track.setProperties(props);
track.setTrackType(ds.getType());
if (ds.getType() == TrackType.EXPR) {
track.setWindowFunction(WindowFunction.none);
}
newTracks.add(track);
}
}