Esempio n. 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();
    }
  }
Esempio n. 2
0
 public static int[] getMSPIDs(MSPLocator loc, Connection c) throws SQLException {
   Statement s = c.createStatement();
   String name = loc.getNameVersion().name;
   String version = loc.getNameVersion().version;
   ResultSet rs =
       s.executeQuery(
           "select id from rosettaanalysis where name='"
               + name
               + "' and "
               + "version = '"
               + version
               + "'");
   Vector<Integer> values = new Vector<Integer>();
   while (rs.next()) {
     values.add(rs.getInt(1));
   }
   s.close();
   int[] array = new int[values.size()];
   for (int i = 0; i < values.size(); i++) {
     array[i] = values.get(i);
   }
   Arrays.sort(array);
   return array;
 }