Example #1
0
  private void loadSMAPFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
      throws IOException {

    List<Feature> features = SMAPParser.parseFeatures(locator, genome);
    FeatureCollectionSource src = new FeatureCollectionSource(features, genome);
    FeatureTrack track = new FeatureTrack(locator, locator.getName(), src);
    track.setRendererClass(SMAPRenderer.class);
    track.setDisplayMode(Track.DisplayMode.EXPANDED);
    newTracks.add(track);
  }
Example #2
0
  private void loadDASResource(ResourceLocator locator, List<Track> currentTracks)
      throws DataLoadException {

    // TODO Connect and get all the attributes of the DAS server, and run the appropriate load
    // statements
    // TODO Currently we are only going to be doing features
    // TODO -- move the source creation to a factory

    DASFeatureSource featureSource = null;
    try {
      featureSource = new DASFeatureSource(locator);
    } catch (MalformedURLException e) {
      log.error("Malformed URL", e);
      throw new DataLoadException("Error: Malformed URL ");
    }

    FeatureTrack track = new FeatureTrack(locator, featureSource);

    // Try to create a sensible name from the path
    String name = locator.getName();
    if (name == null || name.length() == 0) {
      if (locator.getPath().contains("genome.ucsc.edu")) {
        name = featureSource.getType();
      } else {
        name = featureSource.getPath().replace("/das/", "").replace("/features", "");
      }
    }
    track.setName(name);

    // A hack until we can notate this some other way
    if (locator.getPath().contains("cosmic")) {
      track.setRendererClass(CosmicFeatureRenderer.class);
      track.setMinimumHeight(2);
      track.setHeight(20);
      track.setDisplayMode(Track.DisplayMode.EXPANDED);
    } else {
      track.setRendererClass(IGVFeatureRenderer.class);
      track.setMinimumHeight(35);
      track.setHeight(45);
    }
    currentTracks.add(track);
  }
Example #3
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);
    }
  }