Beispiel #1
0
  public static int close() {
    int count = 0;

    Iterator iterator = m_notUsedConnection.iterator();
    while (iterator.hasNext()) {
      try {
        ((ConnectionWrapper) iterator.next()).close();
        count++;
      } catch (Exception e) {
      }
    }
    m_notUsedConnection.clear();

    iterator = m_usedUsedConnection.iterator();
    while (iterator.hasNext()) {
      try {
        ConnectionWrapper wrapper = (ConnectionWrapper) iterator.next();
        wrapper.close();
        if (DEBUG) {
          wrapper.debugInfo.printStackTrace();
        }
        count++;
      } catch (Exception e) {
      }
    }
    m_usedUsedConnection.clear();

    return count;
  }
Beispiel #2
0
  public void parseInputFile(File inputFile) throws IOException {
    geneFeatures.clear();
    otherRecords.clear();

    try {
      GFFEntrySet gffEntries = GFFTools.readGFF(inputFile);

      Iterator itr = gffEntries.lineIterator();
      int count = 0;
      int intronFeatures = 0;
      LinkedList<GFFRecord> cdsRecs = new LinkedList<GFFRecord>();

      while (itr.hasNext()) {
        Object val = itr.next();
        if (val instanceof GFFRecord) {
          GFFRecord rec = (GFFRecord) val;
          count += 1;

          if (rec.getFeature().endsWith("gene")) {
            GeneFeatures gf = new GeneFeatures(rec);
            geneFeatures.put(gf.id, gf);
          } else if (rec.getFeature().equals("CDS")) {
            cdsRecs.addLast(rec);
          } else {
            otherRecords.add(rec);
          }
        }
      }

      for (GFFRecord rec : cdsRecs) {
        Map<String, List<String>> attrs = decodeAttrMap(rec);
        if (geneFeatures.containsKey(attrs.get("Parent").get(0))) {
          geneFeatures.get(attrs.get("Parent").get(0)).addCDS(rec, attrs);
        } else {
          System.err.println("Unknown CDS Parent: " + attrs.get("Parent").get(0));
        }
      }

      for (String k : geneFeatures.keySet()) {
        GeneFeatures gf = geneFeatures.get(k);
        if (gf.cds != null && gf.cds.size() > 1) {
          intronFeatures++;
        }
      }

      System.err.println("# GFF Records: " + count);
      System.err.println("# Gene Feature Sets: " + geneFeatures.size());
      System.err.println("\t# Intron-Features: " + intronFeatures);

    } catch (ParserException e) {
      e.printStackTrace();
    } catch (BioException e) {
      e.printStackTrace();
    }
  }
Beispiel #3
0
  public static synchronized Connection getConnection() {
    clearClosedConnection();
    while (m_notUsedConnection.size() > 0) {
      try {
        ConnectionWrapper wrapper = (ConnectionWrapper) m_notUsedConnection.removeFirst();
        if (wrapper.connection.isClosed()) {
          continue;
        }
        m_usedUsedConnection.add(wrapper);
        if (DEBUG) {
          wrapper.debugInfo = new Throwable("Connection initial statement");
        }
        return wrapper.connection;
      } catch (Exception e) {
      }
    }
    int newCount = getIncreasingConnectionCount();
    LinkedList list = new LinkedList();
    ConnectionWrapper wrapper = null;
    for (int i = 0; i < newCount; i++) {
      wrapper = getNewConnection();
      if (wrapper != null) {
        list.add(wrapper);
      }
    }
    if (list.size() == 0) {
      return null;
    }
    wrapper = (ConnectionWrapper) list.removeFirst();
    m_usedUsedConnection.add(wrapper);

    m_notUsedConnection.addAll(list);
    list.clear();

    return wrapper.connection;
  }