Package org.broad.igv.ui.panel

Examples of org.broad.igv.ui.panel.ReferenceFrame

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        menuAction = new MenuAction("Scatter Plot ...") {
            @Override
            public void actionPerformed(ActionEvent e) {
                final ReferenceFrame defaultFrame = FrameManager.getDefaultFrame();
                String chr = defaultFrame.getChrName();
                int start = (int) defaultFrame.getOrigin();
                int end = (int) defaultFrame.getEnd();
                int zoom = defaultFrame.getZoom();
                ScatterPlotUtils.openPlot(chr, start, end, zoom);
            }
        };
        menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
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        return false;
    }

    public Feature getFeatureAtMousePosition(TrackClickEvent te) {
        MouseEvent e = te.getMouseEvent();
        final ReferenceFrame referenceFrame = te.getFrame();
        if (referenceFrame != null) {
            double location = referenceFrame.getChromosomePosition(e.getX());
            List<Feature> features = getAllFeatureAt(location, e.getY(), referenceFrame);
            return (features != null && features.size() > 0) ? features.get(0) : null;
        } else {
            return null;
        }
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        super.setDisplayMode(mode);
    }

    @Override
    public void load(RenderContext context) {
        ReferenceFrame frame = context.getReferenceFrame();
        PackedFeatures packedFeatures = packedFeaturesMap.get(frame.getName());
        String chr = context.getChr();
        int start = (int) context.getOrigin();
        int end = (int) context.getEndLocation();
        if (packedFeatures == null || !packedFeatures.containsInterval(chr, start, end)) {
            try {
                context.getReferenceFrame().getEventBus().unregister(FeatureTrack.this);
            } catch (IllegalArgumentException e) {
                //Don't care
            }
            loadFeatures(frame.getChrName(), (int) frame.getOrigin(), (int) frame.getEnd(), context);
        }
    }
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        // TODO -- do right thing if in geneListView
        if (FrameManager.isGeneListMode()) {
            MessageUtils.showMessage("To sort in gene list mode right-click the header of a gene panel.");
        } else {
            ReferenceFrame frame = FrameManager.getDefaultFrame();
            RegionOfInterest roi = new RegionOfInterest(frame.getChrName(), (int) frame.getOrigin(), (int) frame.getEnd(), "");
            IGV.getInstance().sortByRegionScore(roi, RegionScoreType.SCORE, frame);
        }
    }
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    void openTimeSeriesPlot(TrackClickEvent trackClickEvent) {

        if (trackClickEvent == null) return;

        ReferenceFrame referenceFrame = trackClickEvent.getFrame();
        if (referenceFrame == null) return;

        String chr = referenceFrame.getChrName();
        double position = trackClickEvent.getChromosomePosition();

        XYSeriesCollection data = new XYSeriesCollection();
        List<Color> colors = new ArrayList();
        for (SoftReference<PeakTrack> ref : PeakTrack.instances) {
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     * Rescale as necessary, and tell components to repaint
     * @param e
     */
    @Subscribe
    public void receiveDataLoaded(DataLoadedEvent e){
        ReferenceFrame frame = e.context.getReferenceFrame();
        rescale(frame);
        frame.getEventBus().post(new ViewChange.Result());
    }
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    @BeforeClass
    public static void setup() throws IOException {
        Map<String, List<Feature>> allFeatures = loadTestFeatures();

        frame = new ExomeReferenceFrame(new ReferenceFrame("test"), allFeatures);
        frame.jumpTo(new Locus("chr6", 1, 100));
    }
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        assertTrue("Did not check enough tracks", count > 2 * types.length);
    }

    private int tstSort(List<Track> tracks, RegionScoreType type) throws Exception {
        //Sort the "sortable" tracks
        ReferenceFrame frame = null;
        final int zoom = 0;
        final String chr = "chr20";
        final int start = Integer.parseInt("14104912") - 1;
        final int end = Integer.parseInt("36031032");
        RegionOfInterest roi = new RegionOfInterest(chr, start, end, "");
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        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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                }
                String resp = exec.execute("sort " + typeStr + " " + roi.getLocusString());
                assertEquals("OK", resp);

                tracks = igv.getAllTracks();
                ReferenceFrame frame = FrameManager.getDefaultFrame();
                IGVTestHeadless.checkIsSorted(tracks, roi, type, frame.getZoom(), frame);
                count++;
            }
        }
        deadlockChecker.cancel();
        deadlockChecker.purge();
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Related Classes of org.broad.igv.ui.panel.ReferenceFrame

  • com.google.common.eventbus.AsyncEventBus
  • org.broad.igv.batch.CommandExecutorTest
  • org.broad.igv.cbio.GeneNetwork
  • org.broad.igv.feature.Chromosome
  • org.broad.igv.feature.exome.ExomeUtilsTest
  • org.broad.igv.feature.genome.Genome
  • org.broad.igv.feature.Locus
  • org.broad.igv.feature.Range
  • org.broad.igv.peaks.PeakCommandBar
  • org.broad.igv.peaks.PeakTrackMenu
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