Exemplo n.º 1
0
  public ExptLocatorTree(Genome g) {
    super();
    try {
      java.sql.Connection c = DatabaseFactory.getConnection(ExptLocator.dbRole);
      int species = g.getSpeciesDBID();
      int genome = g.getDBID();

      Statement s = c.createStatement();
      ResultSet rs = null;

      rs =
          s.executeQuery(
              "select e.name, e.version from experiment e, exptToGenome eg where e.active=1 and "
                  + "e.id=eg.experiment and eg.genome="
                  + genome);
      while (rs.next()) {
        String name = rs.getString(1);
        String version = rs.getString(2);
        ChipChipLocator loc = new ChipChipLocator(g, name, version);
        this.addElement(loc.getTreeAddr(), loc);
      }
      rs.close();

      rs =
          s.executeQuery(
              "select ra.name, ra.version from rosettaanalysis ra, rosettaToGenome rg where "
                  + "ra.id = rg.analysis and ra.active=1 and rg.genome="
                  + genome);
      while (rs.next()) {
        String name = rs.getString(1);
        String version = rs.getString(2);
        MSPLocator msp = new MSPLocator(g, name, version);
        this.addElement(msp.getTreeAddr(), msp);
      }
      rs.close();

      rs =
          s.executeQuery(
              "select ra.name, ra.version from bayesanalysis ra, bayesToGenome rg where "
                  + "ra.id = rg.analysis and ra.active=1 and rg.genome="
                  + genome);
      while (rs.next()) {
        String name2 = rs.getString(1);
        String version2 = rs.getString(2);
        ExptLocator loc2 = new BayesLocator(g, name2, version2);
        addElement(loc2.getTreeAddr(), loc2);
      }
      rs.close();
      s.close();

      DatabaseFactory.freeConnection(c);
    } catch (SQLException se) {
      se.printStackTrace(System.err);
      throw new RuntimeException(se);
    } catch (UnknownRoleException e) {
      e.printStackTrace();
    }
  }
Exemplo n.º 2
0
  public OrthologyPair(ResultSet rs, OrthologyLoader loader) throws NotFoundException {
    try {
      dbid = rs.getInt(1);
      int mappingID = rs.getInt(2);
      mapping = loader.loadMapping(mappingID);

      name1 = rs.getString(3);
      int gid1 = rs.getInt(4);

      name2 = rs.getString(5);
      int gid2 = rs.getInt(6);

      genome1 = Organism.findGenome(gid1);
      genome2 = Organism.findGenome(gid2);
    } catch (SQLException se) {
      throw new DatabaseException("Error: " + se.getMessage(), se);
    }
  }