Package org.broad.igv.track

Examples of org.broad.igv.track.FeatureSource

43
44
45
46
47
48
49
50
51
52
53
54
     * @throws Exception
     */
    @Test
    public void loadBCF() throws Exception {
        String path = TestUtils.DATA_DIR + "bcf/ex2.bcf";
        FeatureSource source = TribbleFeatureSource.getFeatureSource(new ResourceLocator(path), genome);
        Iterator<Feature> features = source.getFeatures("chr20", 14000, 1300000);
        int count = 0;

        while (features.hasNext()) {
            features.next();
            count++;
View Full Code Here
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
     * @throws Exception
     */
    @Test
    public void compareBCFtoVCF() throws Exception {
        String BCF2path = TestUtils.DATA_DIR + "bcf/ex2.bcf";
        FeatureSource BCF2source = TribbleFeatureSource.getFeatureSource(new ResourceLocator(BCF2path), genome);
        Iterator<Feature> BCF2features = BCF2source.getFeatures("chr20", 14000, 1300000);
        List<VCFVariant> BCF2List = new ArrayList<VCFVariant>();

        String VCFpath = TestUtils.DATA_DIR + "vcf/ex2.vcf";
        TestUtils.createIndex(VCFpath);
        FeatureSource VCFsource = TribbleFeatureSource.getFeatureSource(new ResourceLocator(VCFpath), genome);
        Iterator<Feature> VCFfeatures = VCFsource.getFeatures("chr20", 14000, 1300000);
        List<VCFVariant> VCFList = new ArrayList<VCFVariant>();

        while (BCF2features.hasNext()) {
            VCFVariant bcfV = (VCFVariant) BCF2features.next();
            VCFVariant vcfV = (VCFVariant) VCFfeatures.next();
View Full Code Here
159
160
161
162
163
164
165
166
167
    @Test
    public void testIntersectBED() throws Exception {
        List<Feature> actFeatures = tstOperationBED3("intersect", 4);
        String expectedPath = TestUtils.DATA_DIR + "bed/isect_res.bed";
        TestUtils.createIndex(expectedPath);
        FeatureSource expFeatureSource = TribbleFeatureSource.getFeatureSource(new ResourceLocator(expectedPath), genome);
        Iterator<Feature> expFeatures = expFeatureSource.getFeatures("chr1", 0, (int) 1e6);
        TestUtils.assertFeatureListsEqual(expFeatures, actFeatures.iterator());
    }
View Full Code Here
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
            Track newTrack = null;
            switch (outputAttr.type) {
                case FEATURE_TRACK:
                    PluginFeatureSource featSource1 = new PluginFeatureSource(cmdList, argumentValues, outputAttr, specPath, this.forbidEmptyOutput);
                    //featSource1.setQueryTracker(queryTracker);
                    FeatureSource featSource = new CachingFeatureSource(featSource1);
                    newTrack = new FeatureTrack(UUID.randomUUID().toString(), name, featSource);
                    break;
                case DATA_SOURCE_TRACK:
                    PluginDataSource dataSource = new PluginDataSource(GenomeManager.getInstance().getCurrentGenome(), cmdList, argumentValues, outputAttr, specPath);
                    //dataSource.setQueryTracker(queryTracker);
                    newTrack = new DataSourceTrack(null, UUID.randomUUID().toString(), name, dataSource);
                    break;
                case VARIANT_TRACK:
                    PluginFeatureSource VfeatSource1 = new PluginFeatureSource(cmdList, argumentValues, outputAttr, specPath, this.forbidEmptyOutput);
                    FeatureSource VfeatSource = new CachingFeatureSource(VfeatSource1);
                    newTrack = new VariantTrack(name, VfeatSource);
                    break;
            }
            newTracks.add(newTrack);
        }
View Full Code Here
62
63
64
65
66
67
68
69
70
71
72
73
74
75
        String path = TestUtils.DATA_DIR + "gff/gffWithFasta.gff";
        final ResourceLocator locator = new ResourceLocator(path);

        TribbleFeatureSource tribbleFeatureSource = TribbleFeatureSource.getFeatureSource(locator, genome);
        FeatureSource source = new GFFFeatureSource(tribbleFeatureSource);

        int featureCount = 0;
        Iterator<Feature> iter = source.getFeatures("chr7", 0, Integer.MAX_VALUE);
        while (iter.hasNext()) {
            BasicFeature bf = (BasicFeature) iter.next();
            featureCount++;
        }
        assertEquals(2, featureCount);
View Full Code Here
TOP

Related Classes of org.broad.igv.track.FeatureSource

  • org.broad.igv.cli_plugin.BEDToolsPluginSourceTest
  • org.broad.igv.cli_plugin.ui.RunPlugin
  • org.broad.igv.feature.tribble.GFFCodecTest
  • org.broad.igv.variant.vcf.BCFReaderTest
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.