/**
* 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 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);
}
}
/**
* Add the provided SegmentedDataSet to the list of tracks, set other relevant properties
*
* @param locator
* @param newTracks
* @param genome
* @param ds
*/
private void loadSegTrack(
ResourceLocator locator, List<Track> newTracks, Genome genome, SegmentedDataSet ds) {
String path = locator.getPath();
TrackProperties props = null;
if (ds instanceof SegmentedAsciiDataSet) {
props = ((SegmentedAsciiDataSet) ds).getTrackProperties();
}
// The "freq" track. TODO - make this optional
if ((ds.getType() == TrackType.COPY_NUMBER || ds.getType() == TrackType.CNV)
&& ds.getSampleNames().size() > 1) {
FreqData fd = new FreqData(ds, genome);
String freqTrackId = path;
String freqTrackName = "CNV Summary";
CNFreqTrack freqTrack = new CNFreqTrack(locator, freqTrackId, freqTrackName, fd);
newTracks.add(freqTrack);
}
for (String trackName : ds.getSampleNames()) {
String trackId = path + "_" + trackName;
SegmentedDataSource dataSource = new SegmentedDataSource(trackName, ds);
DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, dataSource);
track.setRendererClass(HeatmapRenderer.class);
track.setTrackType(ds.getType());
if (props != null) {
track.setProperties(props);
}
newTracks.add(track);
}
}
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);
}
}
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);
}
}
}