public EWigTrack(ResourceLocator locator, Genome genome) { super(locator); TDFReader reader = TDFReader.getReader(locator.getPath()); tdfSource = new TDFDataSource(reader, 4, "Pi", genome); setDataRange(new DataRange(0, 0, 10)); baseSources = new HashMap(); for (int i = 0; i < 4; i++) { TDFDataSource src = new TDFDataSource(reader, i, Character.toString(nucleotides[i]), genome); baseSources.put(nucleotides[i], src); } }
public void actionPerformed(ActionEvent e) { final IGVPreferences prefs = PreferencesManager.getPreferences(); File initDirectory = prefs.getLastTrackDirectory(); File file = FileDialogUtils.chooseFile("Select coverage file", initDirectory, FileDialog.LOAD); if (file != null) { prefs.setLastTrackDirectory(file.getParentFile()); String path = file.getAbsolutePath(); if (path.endsWith(".tdf") || path.endsWith(".tdf")) { TDFReader reader = TDFReader.getReader(file.getAbsolutePath()); TDFDataSource ds = new TDFDataSource(reader, 0, getName() + " coverage", genome); setDataSource(ds); IGV.getInstance().revalidateTrackPanels(); } else if (path.endsWith(".counts")) { CoverageDataSource ds = new GobyCountArchiveDataSource(file); setDataSource(ds); IGV.getInstance().revalidateTrackPanels(); } else { MessageUtils.showMessage("Coverage data must be in .tdf format"); } } } });
private float getCount(String filename, String chr, int zoom, int pos, Genome genome) { TDFReader reader = TDFReader.getReader(filename); TDFDataset ds = reader.getDataset(chr, zoom, WindowFunction.mean); TDFDataSource dataSource = new TDFDataSource(reader, 0, "test", genome); List<LocusScore> scores = dataSource.getSummaryScoresForRange(chr, pos - 1, pos + 1, zoom); return scores.get(0).getScore(); }
final DataSource dataSource = locator.getPath().endsWith(".counts") ? new GobyCountArchiveDataSource(locator) : new TDFDataSource(reader, trackNumber, heading, genome); DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, dataSource);
try { TDFReader reader = TDFReader.getReader(covPath); TDFDataSource ds = new TDFDataSource(reader, 0, dsName + " coverage", genome); covTrack.setDataSource(ds); } catch (Exception e) {
TDFDataSource ds = new TDFDataSource(reader, 0, "", genome);
TDFDataSource tdfSource = new TDFDataSource(tdfReader, 0, tdfPath, genome);