Package org.broad.igv.track

Examples of org.broad.igv.track.FeatureTrack

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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();
        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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        rp.okButtonActionPerformed(null);

        int numTracksAfter = IGV.getInstance().getAllTracks().size();
        assertEquals(numTracksBefore + 1, numTracksAfter);

        FeatureTrack newTrack = (FeatureTrack) IGV.getInstance().getAllTracks().get(numTracksAfter - 1);
        List<Feature> features = newTrack.getFeatures("chr5", 1, 10000);
        assertNotNull(features);
        assertTrue(features.size() > 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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    private void tstSearchEGFR(List<Track> PosNegFeatureTracks){
        assertEquals(2, PosNegFeatureTracks.size());


        IGV.getInstance().goToLocus("EGFR");
        FeatureTrack posTrack = (FeatureTrack) PosNegFeatureTracks.get(0);
        FeatureTrack negTrack = (FeatureTrack) PosNegFeatureTracks.get(1);
        Feature expFeature = new Locus("chr7", 55054248, 55054301);

        ReferenceFrame frame = FrameManager.getDefaultFrame();
        List<Feature> posFeats = posTrack.getFeatures(frame.getChrName(), (int) frame.getOrigin(), (int) frame.getEnd());

        assertEquals(1, posFeats.size());
        TestUtils.assertFeaturesEqual(expFeature, posFeats.get(0));

        List<Feature> negFeats = negTrack.getFeatures(frame.getChrName(), (int) frame.getOrigin(), (int) frame.getEnd());

        assertEquals(0, negFeats.size());
    }
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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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            if (reader != null) {
                reader.close();
            }
        }

        FeatureTrack track = new FeatureTrack(locator, new FeatureCollectionSource(features, genome));
        track.setName(locator.getTrackName());
        track.setRendererClass(DRangerRenderer.class);
        tracks.add(track);

        return tracks;
    }
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            List<htsjdk.tribble.Feature> features = loadFeatures(reader, genome);

            if (features.isEmpty()) {
                return null;
            } else {
                FeatureTrack track = new FeatureTrack(locator, new FeatureCollectionSource(features, genome));
                track.setName(locator.getTrackName());
                track.setMinimumHeight(35);
                track.setHeight(45);
                track.setRendererClass(GeneTrackRenderer.class);

                List<FeatureTrack> newTracks = new ArrayList();

                newTracks.add(track);
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                    if (features.isEmpty()) {
                        MessageUtils.showMessage("No features found");
                    } else {

                        FeatureSource<PSLRecord> source = new FeatureCollectionSource(features, genome);
                        FeatureTrack newTrack = new FeatureTrack("Blat", "Blat", source);
                        newTrack.setUseScore(true);
                        newTrack.setDisplayMode(Track.DisplayMode.SQUISHED);
                        IGV.getInstance().getTrackPanel(IGV.FEATURE_PANEL_NAME).addTrack(newTrack);

                        BlatQueryWindow win = new BlatQueryWindow(userSeq, features);
                        win.setVisible(true);
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        if(track instanceof AlignmentTrack){
            List<Alignment> alignments = getAlignmentsForRange((AlignmentTrack) track, chr, start, end, zoom);
            return super.createTempFile(alignments, argument);
        }

        FeatureTrack fTrack = (FeatureTrack) track;
        List<Feature> features = fTrack.getFeatures(chr, start, end);
        //Workaround for BEDTools bug, github #88, it can't read an empty file
        if(features.size() == 0 && forbidEmptyOutput){
            features = Arrays.<Feature>asList(new Locus("XXXchr0XXX", 0, 1));
        }
        return super.createTempFile(features, argument);
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Related Classes of org.broad.igv.track.FeatureTrack

  • htsjdk.tribble.Feature
  • org.broad.igv.cli_plugin.Argument
  • org.broad.igv.cli_plugin.awkPluginTest
  • org.broad.igv.cli_plugin.BEDToolsPluginSourceTest
  • org.broad.igv.cli_plugin.PluginFeatureSource
  • org.broad.igv.cli_plugin.PluginFeatureSourceTest
  • org.broad.igv.cli_plugin.PluginSourceTest
  • org.broad.igv.cli_plugin.ui.MultiTrackArgument
  • org.broad.igv.cli_plugin.ui.RunPlugin
  • org.broad.igv.cli_plugin.ui.RunPluginTest
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