private void loadGctFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
if (locator.isLocal()) {
if (!checkSize(locator)) {
return;
}
}
ExpressionFileParser parser = null;
ExpressionDataset ds = null;
parser = new ExpressionFileParser(locator, null, genome);
ds = parser.createDataset();
if (ds.isEmpty()) {
String message =
"The probes in the file <br> "
+ locator.getPath()
+ "<br>"
+ "could not be mapped to genomic positions. This can be corrected by specify a probe mapping<br>"
+ "file from the Preferences window (Probes tab), or by specifing the genomic positions in the<br>"
+ "expression data file. Please see the user guide for more details.";
MessageUtils.showMessage(message);
} else {
ds.setName(locator.getTrackName());
ds.setNormalized(true);
ds.setLogValues(true);
/*
* File outputFile = new File(IGV.DEFAULT_USER_DIRECTORY, file.getName() + ".h5");
* OverlappingProcessor proc = new OverlappingProcessor(ds);
* proc.setZoomMax(0);
* proc.process(outputFile.getAbsolutePath());
* loadH5File(outputFile, messages, attributeList, group);
*/
// Counter for generating ID
TrackProperties trackProperties = ds.getTrackProperties();
String path = locator.getPath();
for (String trackName : ds.getTrackNames()) {
DatasetDataSource dataSource = new DatasetDataSource(trackName, ds, genome);
String trackId = path + "_" + trackName;
Track track = new DataSourceTrack(locator, trackId, trackName, dataSource);
track.setRendererClass(HeatmapRenderer.class);
track.setProperties(trackProperties);
newTracks.add(track);
}
}
}
