Beispiel #1
0
  /**
   * Load a mutation file (".mut" or ".maf").
   *
   * @param locator
   * @param newTracks
   */
  private void loadMutFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
      throws IOException, TribbleIndexNotFoundException {

    MutationTrackLoader loader = new MutationTrackLoader();
    List<FeatureTrack> mutationTracks = loader.loadMutationTracks(locator, genome);
    for (FeatureTrack track : mutationTracks) {
      track.setTrackType(TrackType.MUTATION);
      track.setRendererClass(MutationRenderer.class);
      newTracks.add(track);
    }
  }
Beispiel #2
0
  /**
   * Load the input file as a feature, mutation, or maf (multiple alignment) file.
   *
   * @param locator
   * @param newTracks
   */
  private void loadTribbleFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
      throws IOException, TribbleIndexNotFoundException {

    String typeString = locator.getTypeString();

    // Mutation (mut, maf, vcf) files are handled special.  Check here, rather than depend on order
    // in giant case statement.
    if (MutationTrackLoader.isMutationAnnotationFile(locator)) {
      loadMutFile(locator, newTracks, genome); // Must be tried before generic "loadIndexed" below
    } else if (VariantTrack.isVCF(typeString)) {
      loadVCF(locator, newTracks, genome);
    } else {

      TribbleFeatureSource tribbleFeatureSource =
          TribbleFeatureSource.getFeatureSource(locator, genome);
      FeatureSource src =
          GFFFeatureSource.isGFF(locator.getPath())
              ? new GFFFeatureSource(tribbleFeatureSource)
              : tribbleFeatureSource;

      // Create feature source and track
      FeatureTrack t = new FeatureTrack(locator, src);
      t.setName(locator.getTrackName());
      // t.setRendererClass(BasicTribbleRenderer.class);

      // Set track properties from header
      Object header = tribbleFeatureSource.getHeader();
      if (header != null && header instanceof FeatureFileHeader) {
        FeatureFileHeader ffh = (FeatureFileHeader) header;
        if (ffh.getTrackType() != null) {
          t.setTrackType(ffh.getTrackType());
        }
        if (ffh.getTrackProperties() != null) {
          t.setProperties(ffh.getTrackProperties());
        }

        if (ffh.getTrackType() == TrackType.REPMASK) {
          t.setHeight(15);
        }
      }
      if (locator.getPath().contains(".narrowPeak")
          || locator.getPath().contains(".broadPeak")
          || locator.getPath().contains(".gappedPeak")) {
        t.setUseScore(true);
      }
      newTracks.add(t);
    }
  }