Package org.broad.igv.track

Examples of org.broad.igv.track.DataTrack

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    }

    private DataTrack updateTrackReference(DataTrack memberTrack, List<Track> allTracks){

        if(memberTrack.getName() == null && memberTrack.getResourceLocator() == null){
            DataTrack matchingTrack = (DataTrack) IGVSessionReader.getMatchingTrack(memberTrack.getId(), allTracks);
            if(matchingTrack == null) throw new IllegalStateException("Could not find track with ID " + memberTrack.getId());
            return matchingTrack;
        }else{
            return memberTrack;
        }
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            return dataTrack.getId();
        }

        @Override
        public DataTrack unmarshal(String trackId) throws Exception {
            DataTrack dataTrack = (DataTrack) IGVSessionReader.getMatchingTrack(trackId, null);
            if(dataTrack == null){
                dataTrack = new DataSourceTrack(null, trackId, null, null);
            }
            return dataTrack;
        }
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            for (NamedFeature locus : loci) {

                double regionScore;
                if (t instanceof DataTrack) {
                    DataTrack dataTrack = (DataTrack) t;
                    regionScore = dataTrack.getAverageScore(locus.getChr(), locus.getStart(), locus.getEnd(), zoom);
                    addToSampleData(sampleDataMap, sampleName, locus.getName(), t.getTrackType(), regionScore);
                }

                if(overlays != null) {
                    for (Track overlay : overlays) {
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Related Classes of org.broad.igv.track.DataTrack

  • org.broad.igv.data.CombinedDataSource
  • org.broad.igv.feature.Chromosome
  • org.broad.igv.feature.genome.Genome
  • org.broad.igv.feature.LocusScore
  • org.broad.igv.gitools.Gitools
  • org.broad.igv.session.SessionXmlAdapters$DataTrackIDAdapter
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