Package org.broad.igv.ui.panel

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

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        final int halfwidth = 1000;
        final int end = start + 2 * halfwidth;

        //Load separate intervals, check they don't merge
        AlignmentDataManager manager = getManager171();
        ReferenceFrame frame = new ReferenceFrame(frameName);
        AlignmentTrack.RenderOptions renderOptions = new AlignmentTrack.RenderOptions();
        frame.setBounds(0, end - start);

        RenderContextImpl context = new RenderContextImpl(null, null, frame, null);

        int lastStart = genome.getChromosome(chr).getLength() - 4 * halfwidth;
        int[] starts = new int[]{500, 5000, 15000, start, 500000, lastStart};
        int[] ends = new int[]{600, 10000, 20000, end, 600000, lastStart + 2 * halfwidth};
        for (int ii = 0; ii < starts.length; ii++) {
            frame.jumpTo(new Locus(chr, starts[ii], ends[ii]));
            int actEnd = (int) frame.getEnd();

            manager.load(context, renderOptions, false);

            assertManagerHasInterval(manager, chr, starts[ii], actEnd);
        }
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        AlignmentDataManager manager = getManager171();

        int shift = 0;

        ReferenceFrame frame = new ReferenceFrame(frameName);
        AlignmentTrack.RenderOptions renderOptions = new AlignmentTrack.RenderOptions();
        frame.setBounds(0, end - start);
        RenderContextImpl context = new RenderContextImpl(null, null, frame, null);

        for (int pp = 0; pp < numPans; pp++) {
            shift = pp * panInterval;
            Locus locus = new Locus(chr, start + shift, end + shift);
            frame.jumpTo(locus);

            manager.load(context, renderOptions, false);

            assertManagerHasInterval(manager, chr, locus.getStart(), locus.getEnd());
        }

        return manager.getLoadedInterval(frame.getCurrentRange());

    }
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    @Ignore //Never seems to work on our testrunner for reasons unrelated to the code
    @Test
    public void testHome() throws Exception {
        IGV igv = IGV.getInstance();
        ReferenceFrame frame = FrameManager.getDefaultFrame();
        String chr = "chr1";
        int start = 5;
        int end = 5000;
        int limit = 2;

        frame.jumpTo(chr, start, end);

        Assert.assertEquals(chr, frame.getChrName());
        assertTrue(Math.abs(frame.getCurrentRange().getStart() - start) < limit);
        assertTrue(Math.abs(frame.getCurrentRange().getEnd() - end) < limit);


        FrameFixture frameFixture = new FrameFixture(IGV.getMainFrame());
        //Make sure frame has focus, or else homeButton won't work
        JButtonFixture homeButton = frameFixture.button("homeButton");

        homeButton.focus();
        homeButton.click();

        homeButton.focus();
        homeButton.click();

        igv.waitForNotify(500);

        Assert.assertEquals(Globals.CHR_ALL, frame.getChrName());

        //In all genome view these should be the same
        assertEquals(frame.getChromosomeLength(), frame.getCurrentRange().getEnd());
        Assert.assertEquals(0.0, frame.getOrigin());
    }
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    public double[] getDividerFractions() {
        return dividerFractions;
    }

    public void recordHistory() {
        final ReferenceFrame defaultFrame = FrameManager.getDefaultFrame();
        history.push(defaultFrame.getFormattedLocusString(), defaultFrame.getZoom());
    }
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        List<NamedFeature> features = FeatureDB.getFeaturesList(name, Integer.MAX_VALUE);

        //If we are viewing a gene list, use the frame
        List<ReferenceFrame> frames = Globals.isHeadless() ? null : FrameManager.getFrames();
        ReferenceFrame frame = Globals.isHeadless() ? null : FrameManager.getDefaultFrame();
        if (frames != null) {
            for (ReferenceFrame frm : frames) {
                if (frm.getName().equalsIgnoreCase(name)) {
                    frame = frm;
                }
            }
        }
        String frameName = frame != null ? frame.getName() : null;

        ScoreData<String, Float> results = new ScoreData(RegionScoreType.values().length);

        int initCapacity = tracks.size() / 10;
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        private void addConsensusSequence(TrackClickEvent e) {
            //Export consensus sequence
            JMenuItem item = new JMenuItem("Copy consensus sequence");


            final ReferenceFrame frame;
            if (e.getFrame() == null && FrameManager.getFrames().size() == 1) {
                frame = FrameManager.getFrames().get(0);
            } else {
                frame = e.getFrame();
            }

            item.setEnabled(frame != null);
            add(item);

            item.addActionListener(new ActionListener() {
                @Override
                public void actionPerformed(ActionEvent ae) {
                    //This shouldn't ever be true, but just in case it's more user-friendly
                    if (frame == null) {
                        MessageUtils.showMessage("Unknown region bounds, cannot export consensus");
                        return;
                    }
                    final int start = (int) frame.getOrigin();
                    final int end = (int) frame.getEnd();
                    if ((end - start) > 1000000) {
                        MessageUtils.showMessage("Cannot export region more than 1 Megabase");
                        return;
                    }
                    AlignmentInterval interval = dataManager.getLoadedInterval(frame.getCurrentRange());
                    AlignmentCounts counts = interval.getCounts();
                    String text = PFMExporter.createPFMText(counts, frame.getChrName(), start, end);
                    StringUtils.copyTextToClipboard(text);
                }
            });

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        }
        return false;
    }

    protected boolean openTooltipWindow(TrackClickEvent e) {
        ReferenceFrame frame = e.getFrame();
        final MouseEvent me = e.getMouseEvent();
        String popupText = getValueStringAt(frame.getChrName(), e.getChromosomePosition(), e.getMouseEvent().getY(), frame);

        if (popupText != null) {

            final TooltipTextFrame tf = new TooltipTextFrame(getName(), popupText);
            Point p = me.getComponent().getLocationOnScreen();
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        public void addCopyToClipboardItem(final TrackClickEvent te) {

            final MouseEvent me = te.getMouseEvent();
            JMenuItem item = new JMenuItem("Copy read details to clipboard");

            final ReferenceFrame frame = te.getFrame();
            if (frame == null) {
                item.setEnabled(false);
            } else {
                final double location = frame.getChromosomePosition(me.getX());
                final Alignment alignment = getAlignmentAt(location, me.getY(), frame);

                // Change track height by attribute
                item.addActionListener(new ActionListener() {
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        }

        public void addCopyFlowSignalDistributionToClipboardItem(final TrackClickEvent te) {
            final MouseEvent me = te.getMouseEvent();
            JMenuItem item = new JMenuItem("Copy the flow signal distrubtion for this base to the clipboard");
            final ReferenceFrame frame = te.getFrame();
            if (frame == null) {
                item.setEnabled(false);
            } else {
                final int location = (int) (frame.getChromosomePosition(me.getX()));

                // Change track height by attribute
                item.addActionListener(new ActionListener() {

                    public void actionPerformed(ActionEvent aEvt) {
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        public void addGoToMate(final TrackClickEvent te) {
            // Change track height by attribute
            JMenuItem item = new JMenuItem("Go to mate");
            MouseEvent e = te.getMouseEvent();

            final ReferenceFrame frame = te.getFrame();
            if (frame == null) {
                item.setEnabled(false);
            } else {
                double location = frame.getChromosomePosition(e.getX());
                final Alignment alignment = getAlignmentAt(location, e.getY(), frame);
                item.addActionListener(new ActionListener() {

                    public void actionPerformed(ActionEvent aEvt) {
                        gotoMate(te, alignment);
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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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