Package org.broad.igv.track

Examples of org.broad.igv.track.TrackLoader.load()


//                                //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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        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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        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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        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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        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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            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());
        }
    }

    @Test
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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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        Function<String, Void> loadFileFunc = new Function<String, Void>() {
            @Override
            public Void apply(String input) {
                try {
                    List<Track> newTrack = loader.load(new ResourceLocator(path), genome);
                } catch (Exception e) {
                    e.printStackTrace()//To change body of catch statement use File | Settings | File Templates.
                }
                return null;
            }
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    public void testLoadGenePred() throws Exception {
        String file = TestUtils.DATA_DIR + "gene/EnsembleGenes_sample.genepred";
        TrackLoader loader = new TrackLoader();
        ResourceLocator locator = new ResourceLocator(file);
        Genome genome = TestUtils.loadGenome();
        List<Track> tracks = loader.load(locator, genome);

        assertEquals(1, tracks.size());

        FeatureCodec codec = CodecFactory.getCodec(locator, genome);
        AbstractFeatureReader<Feature, ?> bfs = AbstractFeatureReader.getFeatureReader(locator.getPath(), codec, false);
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    public void testLoadUCSC() throws Exception {
        String file = TestUtils.DATA_DIR + "gene/UCSCgenes_sample.gene";
        TrackLoader loader = new TrackLoader();
        ResourceLocator locator = new ResourceLocator(file);
        Genome genome = TestUtils.loadGenome();
        List<Track> tracks = loader.load(locator, genome);

        assertEquals(1, tracks.size());

        FeatureCodec codec = CodecFactory.getCodec(locator.getPath(), genome);
        AbstractFeatureReader<Feature, ?> bfs = AbstractFeatureReader.getFeatureReader(locator.getPath(), codec, false);
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