Beispiel #1
0
 private void parseGenePositionText() {
   String genomeID = hic.getDataset().getGenomeId();
   // Currently only human and mouse, not worrying about small differences in location between
   // genomes
   if (genomeID.equals("b37")) genomeID = "hg19";
   if (geneLocationHashMap == null || !genomeID.equals(this.genomeID)) {
     initializeGeneHashMap(genomeID);
   } else {
     extractGeneLocation();
   }
 }
Beispiel #2
0
  private void unsafeInitializeGeneHashMap(String genomeID) {
    // Custom format parsed from ref Gene file.
    // Name1 Name2 chromosome position (where position is midpoint of transcription start and end)
    String path = "http://hicfiles.s3.amazonaws.com/internal/" + genomeID + "_refGene.txt";
    BufferedReader reader;
    try {
      SeekableHTTPStream stream = new SeekableHTTPStream(new URL(path));

      reader = new BufferedReader(new InputStreamReader(stream), HiCGlobals.bufferSize);
      MessageUtils.showMessage(
          "Loading gene database for " + genomeID + ".\nIt might take a minute or so. ");
    } catch (Exception error) {
      MessageUtils.showErrorMessage("Failed to read gene database", error);
      positionChrTop.setBackground(Color.yellow);
      geneLocationHashMap = null;
      return;
    }

    geneLocationHashMap = new HashMap<String, GeneLocation>();
    String nextLine;

    try {
      while ((nextLine = reader.readLine()) != null) {
        String[] values = nextLine.split(" ");
        GeneLocation location =
            new GeneLocation(values[2].trim(), Integer.valueOf(values[3].trim()));
        geneLocationHashMap.put(values[0].trim().toLowerCase(), location);
        geneLocationHashMap.put(values[1].trim().toLowerCase(), location);
      }
    } catch (Exception error) {
      MessageUtils.showErrorMessage("Failed to parse gene database", error);
      positionChrTop.setBackground(Color.yellow);
      geneLocationHashMap = null;
    }
    if (geneLocationHashMap != null) this.genomeID = genomeID;
    extractGeneLocation();
  }