Package org.broad.igv.track

Examples of org.broad.igv.track.TrackLoader

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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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    private void doTestAnnotation(GeneNetwork network) throws Exception {

        //Load some tracks
        String dataPath = TestUtils.DATA_DIR + "seg/Broad.080528.subtypes.seg.gz";
        ResourceLocator locator = new ResourceLocator(dataPath);
        List<Track> tracks = new TrackLoader().load(locator, genome);
        network.annotateAll(tracks);
    }
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            //and not use too much disk space
            GenomeManager.getInstance().clearGenomeCache();

            String genomeURL = LoadFromServerAction.getGenomeDataURL(genomeItem.getId());

            TrackLoader loader = new TrackLoader();
            Genome curGenome = null;
            try {
                curGenome = GenomeManager.getInstance().loadGenome(genomeItem.getLocation(), null);
            } catch (IOException e) {
                recordError(new ResourceLocator(genomeItem.getLocation()), e, failedFiles);
                continue;
            }

            errorWriter.println("Genome: " + curGenome.getId());

            try {
                nodeURLs = LoadFromServerAction.getNodeURLs(genomeURL);
                if (nodeURLs == null) {
                    errorWriter.println("Warning: No Data found for " + genomeURL);
                    continue;
                }
            } catch (Exception e) {
                recordError(genomeURL, e, failedFiles);
                continue;
            }

            for (String nodeURL : nodeURLs) {

                errorWriter.println("NodeURL: " + nodeURL);

                try {
                    Document xmlDocument = LoadFromServerAction.createMasterDocument(Arrays.asList(nodeURL));
                    DefaultMutableTreeNode treeNode = new DefaultMutableTreeNode("HostedDataTest");
                    ResourceTree.buildLocatorTree(treeNode, xmlDocument.getDocumentElement(),
                            Collections.<ResourceLocator>emptySet(), null);

                    Enumeration enumeration = treeNode.depthFirstEnumeration();

                    while (enumeration.hasMoreElements()) {
                        Object nextEl = enumeration.nextElement();
                        DefaultMutableTreeNode node = (DefaultMutableTreeNode) nextEl;

                        Object userObject = node.getUserObject();
                        //Get resource locator from tree
                        //don't load resources we've already tried (same file can be listed multiple times)
                        ResourceTree.CheckableResource checkableResource;
                        ResourceLocator locator;
                        if (userObject instanceof ResourceTree.CheckableResource) {
                            checkableResource = (ResourceTree.CheckableResource) userObject;
                            locator = checkableResource.getResourceLocator();
                            if (locator.getPath() == null || loadedResources.contains(locator)) {
                                continue;
                            } else {
                                loadedResources.add(locator);
                            }
                        } else {
                            continue;
                        }

//                        int childCount = node.getChildCount();
//                        if(childCount > 0){
//                            System.out.println(node.getUserObject()  + " Children: " + childCount);
//                            if(childCount > maxChildCount){
//                                maxChildCount = childCount;
//                                maxNode = node;
//                            }
//                        }

                        FeatureDB.clearFeatures();

                        try {
//                            if(locator.getServerURL() != null){
//                                //System.out.println("server url " + locator.getServerURL());
//                                //System.out.println("path " + locator.getPath());
//                            }else{
//                                continue;
//                            }
//                            errorWriter.println("Loading " + locator);
                            loader.load(locator, curGenome);
                        } catch (Exception e) {
                            recordError(locator, e, failedFiles);
                        }

                        counter = (counter + 1) % clearInterval;
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            arguments.put(argument, value);
        }


        List<FeatureTrack> trackList = new ArrayList<FeatureTrack>(paths.length);
        TrackLoader loader = new TrackLoader();
        for (String path : paths) {
            TestUtils.createIndex(path);
            FeatureTrack track = (FeatureTrack) loader.load(new ResourceLocator(path), genome).get(0);
            trackList.add(track);
        }

        if (cmd.equals("multiinter")) {
            arguments.put(argumentList.get(argnum++), trackList);
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        List<Track> tracks = new ArrayList<Track>();
        InputStream cbioStream = ParsingUtils.openInputStream(sessionPath);
        Document document = Utilities.createDOMDocumentFromXmlStream(cbioStream);
        NodeList nodeTracks = document.getElementsByTagName("Resource");

        TrackLoader loader = new TrackLoader();

        for (int nt = 0; nt < nodeTracks.getLength(); nt++) {
            Node node = nodeTracks.item(nt);
            ResourceLocator locator = new ResourceLocator(node.getAttributes().getNamedItem("path").getTextContent());
            tracks.addAll(loader.load(locator, genome));
        }

        RegionScoreType[] types = RegionScoreType.values();
        int count = 0;
        for (RegionScoreType type : types) {
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        LinkedHashMap<Argument, Object> arguments = new LinkedHashMap<Argument, Object>(argumentList.size());

        int argnum = 0;
        arguments.put(argumentList.get(argnum++), "");

        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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    @Test
    public void testLoadFiles() throws Exception{

        GSDirectoryListing dirListing = DMUtils.getDirectoryListing(personaldirectoryURL);

        TrackLoader loader = new TrackLoader();
        Map<String, Exception> exceptions = new HashMap<String, Exception>();

        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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        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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    }

    @Test
    public void testLoadGWAS() throws Exception{
        ResourceLocator locator = new ResourceLocator(TestUtils.DATA_DIR + "gwas/smallp.gwas");
        List<Track> tracks = (new TrackLoader()).load(locator, genome);
        GWASTrack track = (GWASTrack) tracks.get(0);
        String desc = track.getDescription("chr6", 1);

        String[] lines = desc.split("<br>");
        String[] expTokens = new String[]{"rs29228", "6", "29623739", "0.931148124684"};
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            Element element = (Element) elements.item(el);
            sessionReader.processResource(session, element, new HashMap(), sessionPath);
        }
        assertEquals(elements.getLength(), sessionReader.dataFiles.size());

        TrackLoader loader = new TrackLoader();
        for (ResourceLocator locator : sessionReader.dataFiles) {
            File file = new File(locator.getPath());
            assertTrue(file.isAbsolute());
            assertTrue(file.canRead());

            File testDataDir = new File(TestUtils.DATA_DIR);
            assertTrue(file.getAbsolutePath().contains(testDataDir.getAbsolutePath()));

            List<Track> testTrack = loader.load(locator, genome);
            assertEquals(1, testTrack.size());
        }
    }
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Related Classes of org.broad.igv.track.TrackLoader

  • htsjdk.variant.vcf.VCFHeader
  • org.broad.igv.bbfile.BBFileReader
  • org.broad.igv.bigwig.BigWigDataSource
  • org.broad.igv.cbio.GeneNetworkTest
  • org.broad.igv.cli_plugin.awkPluginTest
  • org.broad.igv.cli_plugin.BEDToolsPluginSourceTest
  • org.broad.igv.cli_plugin.PluginFeatureSourceTest
  • org.broad.igv.cli_plugin.PluginSourceTest
  • org.broad.igv.cli_plugin.VCFEncoderTest
  • org.broad.igv.das.DASFeatureSource
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