Package org.broad.igv.util

Examples of org.broad.igv.util.ResourceLocator

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        String chr = "1";
        int start = 50542554; //557000;  //
        int end = 50542722; //558000; //

        AlignmentReader reader = AlignmentReaderFactory.getReader(new ResourceLocator(path));
        //reader.setValidationStringency(ValidationStringency.SILENT);
        //chr1:16,780,602-16,780,774
        //chr1:235675392
        CloseableIterator<Alignment> iter = reader.query("chr1", 50542554, 50542722, true);
        while (iter.hasNext()) {
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    @Deprecated
    private void loadFromDatabase(ResourceLocator locator, List<Track> newTracks, Genome genome) {

        //For backwards/forwards compatibility
        //We used to put path in the serverURL field
        ResourceLocator dbLocator = new ResourceLocator(locator.getDBUrl());
        if (".seg".equals(locator.getTypeString())) {
            //TODO Don't hardcode table name, this might note even be right for our target case
            SegmentedAsciiDataSet ds = (new SegmentedSQLReader(dbLocator, "CNV", genome)).load();
            loadSegTrack(locator, newTracks, genome, ds);
        } else {
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     */
    public FeatureIndex(String path) {

        InputStream is = null;
        try {
            is = ParsingUtils.openInputStreamGZ(new ResourceLocator(path));
            chrIndeces = new LinkedHashMap();
            read(is);
        } catch (IOException ex) {
            log.error("Error reading index", ex);
            throw new DataLoadException("Error reading index: " + ex.getMessage(), path);
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                BufferedReader reader = null;
                String path = rootDir + "/" + filename;
                try {
                    log.info("Loading " + path);
                    // Load features here
                    ResourceLocator loc = new ResourceLocator(path);

                    FeatureParser fp = AbstractFeatureParser.getInstanceFor(loc, genome);
                    reader = ParsingUtils.openBufferedReader(loc);
                    features = fp.loadFeatures(reader, genome);
                    featureCache.put(chr, features);
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            if (filter == null && filterURL != null && filterURL.trim().length() > 0) {
                Set<String> readGroups = new HashSet();
                AsciiLineReader reader = null;
                try {
                    reader = ParsingUtils.openAsciiReader(new ResourceLocator(filterURL));
                    String nextLine;
                    while ((nextLine = reader.readLine()) != null) {
                        readGroups.add(nextLine.trim());
                    }
                    filter = new ReadGroupFilter(readGroups);
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    static {
        SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
    }

    public static AlignmentReader getReader(String path, boolean requireIndex) throws IOException {
        return getReader(new ResourceLocator(path), requireIndex);
    }
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                        igv.doRestoreSession(url, locus, merge);
                    } catch (Exception ex) {
                        MessageUtils.showMessage("Error loading url: " + url + " (" + ex.toString() + ")");
                    }
                } else {
                    ResourceLocator rl = new ResourceLocator(url.trim());
                    igv.loadTracks(Arrays.asList(rl));

                }
            }
        } else if ((e.getActionCommand().equalsIgnoreCase(LOAD_FROM_DAS))) {
            String url = JOptionPane.showInputDialog(IGV.getMainFrame(), ta, "Enter DAS feature source URL",
                    JOptionPane.QUESTION_MESSAGE);
            if (url != null && url.trim().length() > 0) {
                ResourceLocator rl = new ResourceLocator(url.trim());
                rl.setType("das");
                igv.loadTracks(Arrays.asList(rl));
            }
        } else if ((e.getActionCommand().equalsIgnoreCase(LOAD_GENOME_FROM_URL))) {
            String url = JOptionPane.showInputDialog(IGV.getMainFrame(), ta, "Enter URL to .genome or FASTA file",
                    JOptionPane.QUESTION_MESSAGE);
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    @Test
    public void testLoadMultiAlleleFreqs() throws Exception {
        String filePath = TestUtils.DATA_DIR + "vcf/multi_allele_freqs.vcf";
        TestUtils.createIndex(filePath);

        Track newTrack = (new TrackLoader()).load(new ResourceLocator(filePath), genome).get(0);
        VariantTrack variantTrack = (VariantTrack) newTrack;

        List<Feature> featuresList = variantTrack.getFeatures("chr1", 542939 - 10, 543702 + 10);
        assertEquals(6, featuresList.size());
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        return new CombinedDataSource(trackA, trackB, operation);
    }

    private SegmentedAsciiDataSet getSegDataSet(String path){
        ResourceLocator locator = new ResourceLocator(path);
        SegmentFileParser parser = new SegmentFileParser(locator);
        return parser.loadSegments(locator, genome);
    }
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        if(maxDepth > 0){
            actMaxDepth = maxDepth;
        }

        try {
            ResourceLocator loc = new ResourceLocator(path);
            AlignmentReader reader = AlignmentReaderFactory.getReader(loc);
            AlignmentTileLoader loader = new AlignmentTileLoader(reader);

            AlignmentDataManager.DownsampleOptions downsampleOptions = new AlignmentDataManager.DownsampleOptions(true, 50, actMaxDepth);
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