Examples of Locus

mondrian.server.Locus
Point of execution from which a service is invoked.
org.broad.igv.feature.Locus
@author jrobinso
org.broad.igv.feature.tribble.Locus
A minimal representation of a Feature.
org.mizartools.dli.Locus

Examples of org.broad.igv.feature.Locus

        assertConsistent();
    }


    @Test
    public void testJumpTo_00() throws Exception{
        Locus locus = new Locus("chr1", 1000, 2000);
        frame.jumpTo(locus);


        assertEquals(locus.getChr(), frame.getChrName());
        assertEquals(locus.getStart(), frame.getOrigin(), 1.0);
        assertEquals(locus.getEnd(), frame.getEnd(), 1.0);
        assertConsistent();
    }

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Examples of org.broad.igv.feature.Locus

        assertConsistent();
    }


    @Test
    public void testJumpTo_01() throws Exception{
        Locus locus = new Locus("chr1", 1000, 2000);
        frame.jumpTo(locus);
        double oldLocScale = frame.getScale();
        int oldZoom = frame.getZoom();
        int oldMidPoint = frame.getMidpoint();
        double oldCenter = frame.getCenter();


        int delta = 12344;
        frame.jumpTo(locus.getChr(), locus.getStart() + delta, locus.getEnd() + delta);


        assertEquals(oldLocScale, frame.getScale());
        assertEquals(oldZoom, frame.getZoom());
        assertEquals(oldMidPoint, frame.getMidpoint());

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Examples of org.broad.igv.feature.Locus


        for(int ii=0; ii < loci.size(); ii++){
            ReferenceFrame frame = frameList.get(ii);
            ReferenceFrameTest.assertConsistent(frame);


            Locus locus = Locus.fromString(loci.get(ii));


            assertEquals(locus.getChr(), frame.getChrName());
            assertEquals(locus.getStart() - 1, frame.getOrigin(), 0.5);
            assertEquals(locus.getEnd(), frame.getEnd(), 0.5);
        }
    }

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Examples of org.broad.igv.feature.Locus




        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());

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Examples of org.broad.igv.feature.Locus


        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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Examples of org.broad.igv.feature.Locus

        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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Examples of org.broad.igv.feature.Locus

        assertEquals(startingNumTracks + 2, tracks.size());


        String startLocString = "chr1:151666494-151666594";


        String midLocString = "chr1:153148479-153148579";
        Locus midLocus = Locus.fromString(midLocString);


        String destLocString = "chr1:155232055-155232155";
        Locus destLocus = Locus.fromString(destLocString);




        AlignmentTrack alTrack = (AlignmentTrack) tracks.get(1);
        AlignmentDataManager dataManager = (alTrack).getDataManager();

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Examples of org.broad.igv.feature.Locus

    public void goToLociList(List<String> loci) {


        List<ReferenceFrame> frames = FrameManager.getFrames();
        if (frames.size() == loci.size()) {
            for (int i = 0; i < loci.size(); i++) {
                frames.get(i).jumpTo(new Locus(loci.get(i)));
            }
            repaint();
        } else {
            GeneList geneList = new GeneList("", loci, false);
            getSession().setCurrentGeneList(geneList);

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Examples of org.broad.igv.feature.Locus


        if (exomeTrack == null) return false;


        ExomeReferenceFrame exomeFrame = new ExomeReferenceFrame(defaultFrame, exomeTrack);


        Locus locus = new Locus(defaultFrame.getChrName(), (int) defaultFrame.getOrigin(), (int) defaultFrame.getEnd());
        exomeFrame.jumpTo(locus);
        defaultFrame = exomeFrame;
        frames.clear();
        frames.add(defaultFrame);
        exomeMode = true;

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Examples of org.broad.igv.feature.Locus

    }


    private static boolean switchToGenomeMode() {
        ReferenceFrame refFrame = new ReferenceFrame(defaultFrame);


        Locus locus = new Locus(defaultFrame.getChrName(), (int) defaultFrame.getOrigin(), (int) defaultFrame.getEnd());
        refFrame.jumpTo(locus);
        defaultFrame = refFrame;
        frames.clear();
        frames.add(defaultFrame);
        exomeMode = false;

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