Package org.broad.igv.feature

Examples of org.broad.igv.feature.Locus

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        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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    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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        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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    }

    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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    public static void setToDefaultFrame(String searchString) {
        frames.clear();
        if (searchString != null) {
            Locus locus = getLocus(searchString, 0);
            if (locus != null) {
                getDefaultFrame().jumpTo(locus);
            }
        }
        frames.add(getDefaultFrame());
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        getDefaultFrame().recordHistory();
    }

    private static boolean addNewFrame(String searchString){
        boolean locusAdded = false;
        Locus locus = getLocus(searchString);
        if (locus != null) {
            ReferenceFrame referenceFrame = new ReferenceFrame(searchString);
            referenceFrame.jumpTo(locus);
            locusAdded = frames.add(referenceFrame);
        }
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            frames.add(getDefaultFrame());
        } else {
            List<String> lociNotFound = new ArrayList();
            List<String> loci = gl.getLoci();
            if (loci.size() == 1) {
                Locus locus = getLocus(loci.get(0));
                if (locus == null) {
                    lociNotFound.add(loci.get(0));
                } else {
                    IGV.getInstance().getSession().setCurrentGeneList(null);
                    getDefaultFrame().jumpTo(locus.getChr(), locus.getStart(), locus.getEnd());
                }
            } else {
                for (String searchString : gl.getLoci()) {
                    if(!addNewFrame(searchString)){
                        lociNotFound.add(searchString);
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     * @return The found locus, null if not found
     */
    public static Locus getLocus(String searchString, int flankingRegion) {
        SearchCommand cmd = new SearchCommand(getDefaultFrame(), searchString);
        List<SearchCommand.SearchResult> results = cmd.runSearch(searchString);
        Locus locus = null;
        for (SearchCommand.SearchResult result : results) {
            if (result.getType() != SearchCommand.ResultType.ERROR) {
                int delta = 0;

                if (result.getType() != SearchCommand.ResultType.LOCUS) {
                    if (flankingRegion < 0) {
                        delta = (-flankingRegion * (result.getEnd() - result.getStart())) / 100;
                    } else {
                        delta = flankingRegion;
                    }
                }

                int start = result.getStart() - delta;
                //Don't allow flanking region to extend past origin
                //There are some circumstances in which we render before origin (e.g. soft-clips)
                //so we are conservative
                if (start < 0 && result.getStart() >= -1) {
                    start = 0;
                }
                locus = new Locus(
                        result.getChr(),
                        start,
                        result.getEnd() + delta);
                //We just take the first result
                break;
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        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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            if (locusStrings != null) {

                List<Locus> loci = new ArrayList(locusStrings.length);
                for (String ls : locusStrings) {
                    ls = ls.trim();
                    Locus locus = getLocus(ls);
                    if ((locus != null) && locus.isValid()) {
                        loci.add(locus);
                    }
                }
                return loci;
            }
        }

        // Search for locus from the probe name itself.
        Locus locus = getLocus(probeId);
        if ((locus != null) && locus.isValid()) {
            return Arrays.asList(locus);
        }


        // See if the probes can be mapped to genes
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Related Classes of org.broad.igv.feature.Locus

  • org.broad.igv.batch.CommandExecutor
  • org.broad.igv.cli_plugin.PluginFeatureSource
  • org.broad.igv.data.cufflinks.ExpDiffCodec
  • org.broad.igv.data.cufflinks.FPKMTrackingCodec
  • org.broad.igv.data.expression.GeneToLocusHelper
  • org.broad.igv.feature.exome.ExomeUtilsTest
  • org.broad.igv.lists.Preloader
  • org.broad.igv.sam.AlignmentDataManagerTest
  • org.broad.igv.sam.CoverageTrackTest
  • org.broad.igv.session.IGVSessionReader
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