Package org.broad.igv.tdf

Examples of org.broad.igv.tdf.TDFReader

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    }

    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) :
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    }

    private void loadEwigIBFFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {

        TDFReader reader = TDFReader.getReader(locator.getPath());
        TrackProperties props = null;
        String trackLine = reader.getTrackLine();
        if (trackLine != null && trackLine.length() > 0) {
            props = new TrackProperties();
            ParsingUtils.parseTrackLine(trackLine, props);
        }
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                }
                if (covPath != null) {
                    if (FileUtils.resourceExists(covPath)) {
                        log.debug("Loading TDF for coverage: " + covPath);
                        TDFReader reader = TDFReader.getReader(covPath);
                        TDFDataSource ds = new TDFDataSource(reader, 0, alignmentTrack.getName() + " coverage", genome);
                        covTrack.setDataSource(ds);
                    }

                }
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                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().repaintDataPanels();
                    } else if (path.endsWith(".counts")) {
                        CoverageDataSource ds = new GobyCountArchiveDataSource(file);
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            String input = "count " + opt + " " + inputFile + " " + fullout + " " + hg18id;
            String[] args = input.split("\\s+");
            igvTools.run(args);

            if (outputExt.equals("tdf")) {
                TDFReader reader = TDFReader.getReader(fullout);
                assertTrue(reader.getDatasetNames().size() > 0);
                if (query) {
                    for (String name : reader.getDatasetNames()) {
                        TDFDataset ds = reader.getDataset(name);
                        List<TDFTile> tiles = ds.getTiles();
                        for (TDFTile tile : tiles) {
                            assertTrue(tile.getTileStart() >= start);
                            assertTrue(tile.getTileStart() < end);
                        }
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            String fullout = outputFile + ind + ".tdf";
            String input = "count " + opt + " " + listArg + " " + fullout + " " + hg18id;
            String[] args = input.split("\\s+");
            igvTools.run(args);

            TDFReader reader = TDFReader.getReader(fullout);
            assertTrue(reader.getDatasetNames().size() > 0);
        }
    }
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        assertEquals(noDupCount, dupCount);

    }

    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();
    }
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        }
        wfs = wfs.substring(0, wfs.lastIndexOf(","));
        String[] cmd = {"count", "--windowFunctions", wfs, inputFile, outputFile, hg18id};
        igvTools.run(cmd);

        TDFReader reader = new TDFReader(new ResourceLocator(outputFile));
        for (WindowFunction wf : windowFunctions) {
            TDFDataset ds = reader.getDataset(chr, 0, wf);
            assertNotNull(ds);
        }
    }
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                            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);
                                    getCoverageTrack().setDataSource(ds);
                                    refresh();
                                } else if (path.endsWith(".counts")) {
                                    CoverageDataSource ds = new GobyCountArchiveDataSource(file);
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        return header;
    }

    private void initCoverageSource(String covPath) {
        if (ParsingUtils.pathExists(covPath)) {
            TDFReader reader = TDFReader.getReader(covPath);
            coverageSource = new TDFDataSource(reader, 0, "", genome);
        }
    }
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Related Classes of org.broad.igv.tdf.TDFReader

  • org.broad.igv.sam.AlignmentTrack$PopupMenu
  • org.broad.igv.sam.CoverageTrack
  • org.broad.igv.sam.EWigTrack
  • org.broad.igv.tools.IGVToolsCountTest
  • org.broad.igv.track.TrackLoader
  • org.broad.igv.track.TribbleFeatureSource
  • org.broad.igv.util.CompressionUtils
  • org.broad.igv.util.ResourceLocator
  • org.broad.igv.exceptions.DataLoadException
  • java.nio.ByteBuffer
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