Package htsjdk.tribble

Examples of htsjdk.tribble.Feature

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        addDisplayModeItems(tracks, featurePopupMenu);


        if (tracks.size() == 1) {
            Track t = tracks.iterator().next();
            Feature f = t.getFeatureAtMousePosition(te);
            if (f != null) {
                featurePopupMenu.addSeparator();

                // If we are over an exon, copy its sequence instead of the entire feature.
                if (f instanceof IGVFeature) {
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        String name = editing ? "Edit " + featDispName : "Add annotation to " + MongoFeatureTrack.this.getName();
        JMenuItem item = new JMenuItem(name);
        item.addActionListener(new ActionListener() {
            @Override
            public void actionPerformed(ActionEvent e) {
                Feature feat = editing ? selFeat.getDBFeature() : new BasicFeature(chr, start, end);
                FeatureAnnotDialog dialog = new FeatureAnnotDialog(IGV.getMainFrame(), getCollection(), feat);
                dialog.setVisible(true);
            }
        });
        return item;
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    public IGVPopupMenu getPopupMenu(TrackClickEvent te) {
        String title = getName();
        IGVPopupMenu menu = TrackMenuUtils.getPopupMenu(Arrays.<Track>asList(this), title, te);

        //Add annotation or edit existing one
        Feature feat = getFeatureAtMousePosition(te);
        JMenuItem item = createEditAnnotMenuEntry(te, (DBFeature.IGVFeat) feat);
        if(item != null) menu.add(item);

        return menu;
    }
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     * @param features List of features.
     * @return The feature whose start overlaps with position, or null.
     */
    private static Feature getFeatureAt(double position, List<? extends Feature> features) {
        int strt = (int) position;
        Feature key = new BasicFeature("", strt, strt + 1);

        int r = Collections.binarySearch(features, key, FEATURE_START_COMPARATOR);

        if (r >= 0) {
            return features.get(r);
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        List<Feature> returnList = null;

        double adjustedPosition = Math.max(0, position - maxLength);
        int startIdx = Math.max(0, getIndexBefore(adjustedPosition, features));
        for (int idx = startIdx; idx < features.size(); idx++) {
            Feature feature = features.get(idx);
            int start = feature.getStart() - (int) (minWidth / 2);

            if (start > position) {
                break;
            }

            int end = feature.getEnd() + (int) (minWidth / 2);

            if (position >= start && position <= end) {
                if (returnList == null) returnList = new ArrayList();
                returnList.add(feature);
            }
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                            "Exon navigation is only allowed when track is expanded and a single " +
                                    "feature row is selected.");
                    return;
                }
                List<Feature> featureList = ft.getFeaturesAtPositionInFeatureRow(center, ft.getSelectedFeatureRowIndex(), vc);
                Feature feature = featureList != null && featureList.size() > 0 ? featureList.get(0) : null;

                if (feature == null)
                    return;
                if (feature instanceof BasicFeature) {
                    BasicFeature bf = (BasicFeature) feature;
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                    //JOptionPane.showMessageDialog(IGV.getInstance(),
                    //        "Track panning is not enabled for data tracks.");
                    return;
                }

                Feature f = null;
                if (t instanceof FeatureTrack) {
                    f = ((FeatureTrack) t).nextFeature(frame.getChrName(), frame.getCenter(), forward, frame);
                } else if (t instanceof VariantTrack) {
                    f = ((VariantTrack) t).nextFeature(frame.getChrName(), frame.getCenter(), forward, frame);
                }

                if (f != null) {
                    String chr = GenomeManager.getInstance().getCurrentGenome().getChromosomeAlias(f.getChr());
                    double newCenter = f.getStart();
                    if (!chr.equals(frame.getChrName())) {
                        // Switch chromosomes.  We have to do some tricks to maintain the same resolution scale.
                        double range = frame.getEnd() - frame.getOrigin();
                        int newOrigin = (int) Math.max(newCenter - range / 2, 0);
                        int newEnd = (int) (newOrigin + range);
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                        } else if (nextLine.startsWith("#gffTags")) {
                            gffTags = true;
                        }
                    } else {
                        Feature feature = parseLine(nextLine);
                        if (feature != null) {
                            features.add(feature);
                        }
                    }
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                if (line.startsWith("#")) {
                    codec.readHeaderLine(line);
                } else {
                    try {
                        Feature f = codec.decode(line);
                        if (f != null) {
                            combiner.addFeature((BasicFeature) f);
                        }
                    } catch (Exception e) {
                        log.error("Error parsing: " + line, e);
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        try {

            iter = queryRaw(seq, start, end);

            while (iter != null && iter.hasNext()) {
                Feature record = iter.next();

                // Range of tile indices that this feature contributes to.
                int aStart = record.getStart();
                int aEnd = record.getEnd();
                int idx0 = 0;
                int idx1 = 0;
                if (binSize > 0) {
                    idx0 = Math.max(0, (aStart - start) / binSize);
                    idx1 = Math.min(tiles.size() - 1, (aEnd - start) / binSize);
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Related Classes of htsjdk.tribble.Feature

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  • org.broad.igv.cli_plugin.PluginSource
  • org.broad.igv.das.DASFeatureSource$DasReader
  • org.broad.igv.data.expression.GeneToLocusHelper
  • org.broad.igv.dev.db.SQLCodecSourceTest
  • org.broad.igv.dev.db.SQLInputStreamTest
  • org.broad.igv.dev.db.UCSC_SQL_Test
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