Package org.broad.igv.util

Examples of org.broad.igv.util.ResourceLocator

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        TrackLoader loader = new TrackLoader();
        String[] paths = new String[]{TestUtils.DATA_DIR + "bed/test.bed", TestUtils.DATA_DIR + "bed/testAlternateColor.bed"};
        for (String path : paths) {
            TestUtils.createIndex(path);
            FeatureTrack track = (FeatureTrack) loader.load(new ResourceLocator(path), genome).get(0);
            arguments.put(argumentList.get(argnum++), track);
        }


        List<String> cmd = Arrays.asList(reader.getToolPath(tool), command.cmd);
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        assertFalse(PreferenceManager.getInstance().getAsBoolean(showSC));

        //Load a data file which has a soft clipped block
        String path = TestUtils.DATA_DIR + "sam/hardSoftClip.sam";
        TestUtils.createIndex(path);
        List<Track> tracks = IGV.getInstance().load(new ResourceLocator(path));
        AlignmentTrack alTrack = (AlignmentTrack) tracks.get(1);

        //NPE happens when event is broadcast, clutters up stacktrace
        alTrack.getDataManager().getEventBus().unregister(tracks.get(0));
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     * Should be read if available, not cause error if wrong format
     */
    @Test
    public void testFlowSignalTags() throws Exception {
        String inpath = TestUtils.DATA_DIR + "sam/zf_tags.sam";
        AlignmentReader reader = AlignmentReaderFactory.getReader(new ResourceLocator(inpath));
        Iterator<Alignment> iter = reader.iterator();

        int[] expFlowStarts = new int[]{-1, 5, -1};
        int row = 0;
        while (iter.hasNext()) {
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        for(GSFileMetadata md: dirListing.getContents()){
            String mdurl = md.getUrl();
            if(!md.isDirectory() && (mdurl.endsWith(".bed") || mdurl.endsWith(".bam"))){
                System.out.println("Loading file " + mdurl);
                try{
                    List<Track> tracks = loader.load(new ResourceLocator(mdurl), genome);
                    assertNotNull(tracks);
                    assertNotSame(0, tracks.size());
                }catch(Exception e){
                    exceptions.put(mdurl, e);
                }
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    int end = start + 1000;
    boolean contained = false;


    private AlignmentInterval getAlignmentInterval() throws Exception {
        ResourceLocator rl = new ResourceLocator(path);
        AlignmentReader samReader = AlignmentReaderFactory.getReader(rl);
        CloseableIterator<Alignment> iter = samReader.query(chr, start, end, contained);
        List<Alignment> list = new ArrayList<Alignment>();
        while(iter.hasNext()){
            list.add(iter.next());
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     * @return The transcripts.gtf file cufflinks calculated
     */
    private List<Object> basicRunCufflinks(String chr, int start, int end, File inFile) throws Exception{

        //Load some alignment data
        ResourceLocator locator = new ResourceLocator(inFile.getAbsolutePath());
        AlignmentDataManager dataManager = new AlignmentDataManager(locator, genome);
        AlignmentTrack alignmentTrack = new AlignmentTrack(locator, dataManager, genome);
        dataManager.loadAlignments(chr, start, end, null, null);

        PluginSpecReader.Command command = tool.commandList.get(0);
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        List<PluginSpecReader.Output> outputAttrs = command.outputList;
        PluginSpecReader.Output outputAttr = outputAttrs.get(0);

        String testFile = TestUtils.DATA_DIR + "bed/Unigene.sample.bed";
        FeatureTrack track = (FeatureTrack) (new TrackLoader()).load(new ResourceLocator(testFile), genome).get(0);

        List<Argument> argumentList = command.argumentList;
        LinkedHashMap<Argument, Object> arguments = new LinkedHashMap<Argument, Object>(argumentList.size());
        int argnum = 0;
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     * @throws Exception
     */
    @Test
    public void testIterateMergedBam() throws Exception {
        String listPath = TestUtils.DATA_DIR + "bam/test.unindexed.bam.list";
        AlignmentReader reader = AlignmentReaderFactory.getReader(new ResourceLocator(listPath), false);

        Set<String> visitedChromosomes = new HashSet();
        String lastChr = null;
        int lastStart = -1;

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        String input = "formatexp " + inputFile + " " + outputFile;
        igvTools.run(input.split("\\s+"));
        Genome genome = TestUtils.loadGenome();

        ExpressionFileParser parser = new ExpressionFileParser(new ResourceLocator(outputFile), null, genome);
        Dataset ds = parser.createDataset();
        assertEquals(10, ds.getChromosomes().length);
    }
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    public void testDescriptionMapping() throws IOException {
        String gctFile = TestUtils.DATA_DIR + "gct/igv_test2.gct";
        File igvFile = new File(TestUtils.DATA_DIR + "gct/igv_test2.gct.igv");
        igvFile.deleteOnExit();

        ResourceLocator locator = new ResourceLocator(gctFile);
        GCTtoIGVConverter.convert(locator, igvFile, null, 50000, null, genome);
    }
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Related Classes of org.broad.igv.util.ResourceLocator

  • org.broad.igv.batch.CommandExecutorTest
  • org.broad.igv.cli_plugin.awkPluginTest
  • org.broad.igv.cli_plugin.BEDToolsPluginSourceTest
  • org.broad.igv.cli_plugin.CufflinksPluginTest
  • org.broad.igv.cli_plugin.PluginFeatureSourceTest
  • org.broad.igv.cli_plugin.PluginSourceTest
  • org.broad.igv.cli_plugin.VCFEncoderTest
  • org.broad.igv.cursor.CursorUtils
  • org.broad.igv.data.AbstractDataSourceTest
  • org.broad.igv.data.CombinedDataSourceTest
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