Package org.broad.igv.feature

Examples of org.broad.igv.feature.Locus

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    /**
     * Return a locus from the gene (e.g. EGFR) or locus (e.g. chr1:1-100) string
     */
    Locus getLocus(String geneOrLocusString) {
        Locus locus = Locus.fromString(geneOrLocusString);
        if (locus != null && locus.isValid()) {
            return locus;
        } else {
            // Maybe its a gene or feature
            Feature gene = FeatureDB.getFeature(geneOrLocusString);
            if (gene != null) {
                return new Locus(gene.getChr(), gene.getStart(), gene.getEnd());
            }
        }
        return null;
    }
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                    try {
                        String chr = tokens[0];
                        int start = (int) Double.parseDouble(tokens[1]);
                        int end = (int) Double.parseDouble(tokens[2]);
                        String probe = tokens[3];
                        Locus locus = new Locus(chr, start, end);
                        probeLocusMap.put(probe, Arrays.asList(locus));
                    } catch (NumberFormatException e) {
                        log.info("Skipping line: " + nextLine);
                        errorCount++;
                        if (errorCount > maxErrors) {
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        Collection<Track> trackList = IGV.getInstance().getAllTracks();
        int flankingRegion = 1; //PreferenceManager.getInstance().getAsInt(PreferenceManager.FLANKING_REGION) + 1;
        String genomeId = GenomeManager.getInstance().getGenomeId();
        for (ReferenceFrame frame : FrameManager.getFrames()) {
            Locus locus = frame.getInitialLocus();
            if (locus != null) {
                for (Track track : trackList) {
                    if (track == null) continue;
                    if (track.isVisible()) {
                        if (track instanceof DataTrack) {
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                                    getAttribute((Element) childNode, SessionAttribute.START.getText()).replace(",", "");
                            final String endString =
                                    getAttribute((Element) childNode, SessionAttribute.END.getText()).replace(",", "");
                            int start = ParsingUtils.parseInt(startString);
                            int end = ParsingUtils.parseInt(endString);
                            org.broad.igv.feature.Locus locus = new Locus(chr, start, end);
                            f.jumpTo(locus);
                        } catch (NumberFormatException e) {
                            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                        }
                    }
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            int end = Integer.parseInt(param3);
            String desc = param4 != null ? param4 : "";
            roi = new RegionOfInterest(param1, start, end, desc);
        }
        if (param1 != null) {
            Locus locus = Locus.fromString(param1);
            if (locus != null) {
                int start = Math.max(0, locus.getStart() - 1);
                String desc = param2 != null ? param2 : "";
                roi = new RegionOfInterest(locus.getChr(), start, locus.getEnd(), desc);

            }
        }
        if (roi != null) {
            igv.addRegionOfInterest(roi);
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        RegionScoreType regionSortOption = getRegionSortOption(sortArg);
        String tag = "";
        if (regionSortOption != null) {
            RegionOfInterest roi = null;
            if (locusString != null) {
                Locus locus = Locus.fromString(locusString);
                if (locus != null) {
                    int start = Math.max(0, locus.getStart() - 1);
                    roi = new RegionOfInterest(locus.getChr(), start, locus.getEnd(), "");
                }
            }
            igv.sortByRegionScore(roi, regionSortOption, FrameManager.getDefaultFrame());

        } else {
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            //If we have what looks like a valid end position we keep it
            if (this.widthInPixels > 0 && this.initialLocus == null) {
                int start = (int) getOrigin();
                int end = (int) getEnd();
                if (start >= 0 && end >= 1) {
                    this.initialLocus = new Locus(getChrName(), start, end);
                }
            }

            this.widthInPixels = widthInPixels;
            computeLocationScale();
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     * @param chr
     * @param start
     * @param end
     */
    public void jumpTo(String chr, int start, int end) {
        Locus locus = new Locus(chr, start, end);
        this.jumpTo(locus);
    }
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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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