Package org.broad.igv.track

Examples of org.broad.igv.track.FeatureTrack

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    private int getMinSizeFromTracks(Iterable tracks) {
        int featureWindowSize = Integer.MAX_VALUE;
        for (Object val : tracks) {
            int tmpSize = Integer.MAX_VALUE;
            if (val instanceof FeatureTrack) {
                FeatureTrack track = ((FeatureTrack) val);
                tmpSize = track.getFeatureWindowSize();
            } else if (val instanceof List) {
                featureWindowSize = getMinSizeFromTracks((List) val);
            }
            featureWindowSize = Math.min(featureWindowSize, tmpSize);
        }
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            switch (outputAttr.type) {
                case FEATURE_TRACK:
                    PluginFeatureSource featSource1 = new PluginFeatureSource(cmdList, argumentValues, outputAttr, specPath, this.forbidEmptyOutput);
                    //featSource1.setQueryTracker(queryTracker);
                    FeatureSource featSource = new CachingFeatureSource(featSource1);
                    newTrack = new FeatureTrack(UUID.randomUUID().toString(), name, featSource);
                    break;
                case DATA_SOURCE_TRACK:
                    PluginDataSource dataSource = new PluginDataSource(GenomeManager.getInstance().getCurrentGenome(), cmdList, argumentValues, outputAttr, specPath);
                    //dataSource.setQueryTracker(queryTracker);
                    newTrack = new DataSourceTrack(null, UUID.randomUUID().toString(), name, dataSource);
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    @Override
    public List<FeatureTrack> getValue() {
        Object[] rawRet = trackCheckBoxList.getCheckBoxListSelectedValues();
        List<FeatureTrack> trackList = new ArrayList<FeatureTrack>(rawRet.length);
        for (Object obj : rawRet) {
            FeatureTrack track = (FeatureTrack) ((TrackWrapper) obj).getTrack();
            trackList.add(track);
        }
        return trackList;
    }
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                    if(tName == null) continue;

                    MotifFinderSource src = new MotifFinderSource(pattern, strands[ci], GenomeManager.getInstance().getCurrentGenome());
                    CachingFeatureSource cachingSrc= new CachingFeatureSource(src);

                    FeatureTrack track = new FeatureTrack(tName, tName, cachingSrc);
                    if(colors[ci] != null) track.setColor(colors[ci]);

                    track.setDisplayMode(Track.DisplayMode.SQUISHED);
                    trackList.add(track);
                }
            }

        }
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                return value instanceof FeatureTrack;
            case MULTI_FEATURE_TRACK:
                if (!(value instanceof List)) return false;
                try {
                    List<FeatureTrack> lVal = (List<FeatureTrack>) value;
                    FeatureTrack fVal = lVal.get(0);
                    return true;
                } catch (Exception e) {
                    return false;
                }
            default:
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        DBCollection collection = MongoCollabPlugin.getCollection(locator);
        //TODO Make this more flexible
        collection.setObjectClass(DBFeature.class);
        MongoFeatureSource source = new MongoFeatureSource(collection, locator.buildLocusIndex);
        FeatureTrack track = new MongoFeatureTrack(collection.getFullName(), collection.getName(), source);
        SearchCommand.registerNamedFeatureSearcher(source);
        newTracks.add(track);
        track.setMargin(0);
        return track;
    }
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            }

            Exon e = null;
            if (t instanceof FeatureTrack) {
                int center = (int) vc.getCenter();
                FeatureTrack ft = (FeatureTrack) t;
                if (ft.getDisplayMode() == Track.DisplayMode.COLLAPSED ||
                        ft.getSelectedFeatureRowIndex() == FeatureTrack.NO_FEATURE_ROW_SELECTED) {
                    MessageUtils.showMessage(
                            "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) {
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  • org.broad.igv.cli_plugin.BEDToolsPluginSourceTest
  • org.broad.igv.cli_plugin.PluginFeatureSource
  • org.broad.igv.cli_plugin.PluginFeatureSourceTest
  • org.broad.igv.cli_plugin.PluginSourceTest
  • org.broad.igv.cli_plugin.ui.MultiTrackArgument
  • org.broad.igv.cli_plugin.ui.RunPlugin
  • org.broad.igv.cli_plugin.ui.RunPluginTest
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