Examples of TDFDataSource

org.broad.igv.tdf.TDFDataSource
@author jrobinso

Examples of org.broad.igv.tdf.TDFDataSource


            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);

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Examples of org.broad.igv.tdf.TDFDataSource

                }
                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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Examples of org.broad.igv.tdf.TDFDataSource

        if (timeSignalSources == null) {
            if (timeSignalPaths != null && timeSignalPaths.length > 0) {
                timeSignalSources = new WrappedDataSource[timeSignalPaths.length];
                for (int i = 0; i < timeSignalPaths.length; i++) {
                    try {
                        timeSignalSources[i] = new WrappedDataSource(new TDFDataSource(TDFReader.getReader(timeSignalPaths[i]), 0, "", genome));
                        timeSignalSources[i].setNormalizeCounts(true, 1.0e9f);
                    } catch (Exception e) {
                        timeSignalSources[i] = null;
                        e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                    }

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Examples of org.broad.igv.tdf.TDFDataSource

    WrappedDataSource getSignalSource(final String chr, final int contextStart, final int contextEnd, final int zoom) {
        if (signalSource == null && signalPath != null && !signalSourceLoading) {
            signalSourceLoading = true;
            NamedRunnable runnable = new NamedRunnable() {
                public void run() {
                    signalSource = new WrappedDataSource(new TDFDataSource(TDFReader.getReader(signalPath), 0, "", genome));
                    signalSource.setNormalizeCounts(true, 1.0e9f);
                    signalSource.getSummaryScoresForRange(chr, contextStart, contextEnd, zoom);
                }


                public String getName() {

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Examples of org.broad.igv.tdf.TDFDataSource

                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);
                        setDataSource(ds);

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Examples of org.broad.igv.tdf.TDFDataSource

    }


    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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Examples of org.broad.igv.tdf.TDFDataSource

                            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);
                                    getCoverageTrack().setDataSource(ds);

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Examples of org.broad.igv.tdf.TDFDataSource

    }


    private void initCoverageSource(String covPath) {
        if (ParsingUtils.pathExists(covPath)) {
            TDFReader reader = TDFReader.getReader(covPath);
            coverageSource = new TDFDataSource(reader, 0, "", genome);
        }
    }

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Examples of org.broad.igv.tdf.TDFDataSource


    public EWigTrack(ResourceLocator locator, Genome genome) {
        super(locator);


        TDFReader reader = TDFReader.getReader(locator.getPath());
        scoreSource = 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);
        }
    }

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