Examples of org.broad.igv.track.FeatureCollectionSource

org.broad.igv.track.FeatureCollectionSource
Implementation of FeatureSource that wraps a list or map of features for the entire genome. Instances are typically created by parsing a bed or gff file. This is a legacy implementation, and does not scale to large feature tracks.
User: jrobinso Date: Jan 31, 2010

            if (reader != null) {
                reader.close();
            }
        }


        FeatureTrack track = new FeatureTrack(locator, new FeatureCollectionSource(features, genome));
        track.setName(locator.getTrackName());
        track.setRendererClass(DRangerRenderer.class);
        tracks.add(track);


        return tracks;

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            List<htsjdk.tribble.Feature> features = loadFeatures(reader, genome);


            if (features.isEmpty()) {
                return null;
            } else {
                FeatureTrack track = new FeatureTrack(locator, new FeatureCollectionSource(features, genome));
                track.setName(locator.getTrackName());
                track.setMinimumHeight(35);
                track.setHeight(45);
                track.setRendererClass(GeneTrackRenderer.class);

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                    if (features.isEmpty()) {
                        MessageUtils.showMessage("No features found");
                    } else {


                        FeatureSource<PSLRecord> source = new FeatureCollectionSource(features, genome);
                        FeatureTrack newTrack = new FeatureTrack("Blat", "Blat", source);
                        newTrack.setUseScore(true);
                        newTrack.setDisplayMode(Track.DisplayMode.SQUISHED);
                        IGV.getInstance().getTrackPanel(IGV.FEATURE_PANEL_NAME).addTrack(newTrack);

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Related Classes of org.broad.igv.track.FeatureCollectionSource

org.broad.igv.data.DataTile

org.broad.igv.feature.BasicFeature

org.broad.igv.feature.dranger.DRangerParser

org.broad.igv.feature.EmblFeatureTableParser

org.broad.igv.feature.genome.Genome

org.broad.igv.feature.IGVFeature

org.broad.igv.feature.LocusScore

org.broad.igv.util.blat.BlatClient

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