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); } } }