Example #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();
    }
  }
  private void execute() {

    gResult.clear();

    String sCmd = null;

    if (4096 <= ifHuge.length()) {
      sCmd = ifHuge;
    } else {
      sCmd = txtCommand.getText();
    }

    if (sCmd.startsWith("-->>>TEST<<<--")) {
      testPerformance();

      return;
    }

    String g[] = new String[1];

    try {
      lTime = System.currentTimeMillis();

      sStatement.execute(sCmd);

      int r = sStatement.getUpdateCount();

      if (r == -1) {
        formatResultSet(sStatement.getResultSet());
      } else {
        g[0] = "update count";

        gResult.setHead(g);

        g[0] = "" + r;

        gResult.addRow(g);
      }

      lTime = System.currentTimeMillis() - lTime;

      addToRecent(txtCommand.getText());
      gResult.fireTableChanged(null);
    } catch (SQLException e) {
      lTime = System.currentTimeMillis() - lTime;
      g[0] = "SQL Error";

      gResult.setHead(g);

      String s = e.getMessage();

      s += " / Error Code: " + e.getErrorCode();
      s += " / State: " + e.getSQLState();
      g[0] = s;

      gResult.addRow(g);
      gResult.fireTableChanged(null);
    }

    updateResult();
    System.gc();
  }
  public void actionPerformed(ActionEvent ev) {

    String s = ev.getActionCommand();

    if (s == null) {
      if (ev.getSource() instanceof JMenuItem) {
        JMenuItem i;

        s = ((JMenuItem) ev.getSource()).getText();
      }
    }

    /*
    // button replace by toolbar
            if (s.equals("Execute")) {
                execute();
            } else
    */
    if (s.equals("Exit")) {
      windowClosing(null);
    } else if (s.equals("Transfer")) {
      Transfer.work(null);
    } else if (s.equals("Dump")) {
      Transfer.work(new String[] {"-d"});
    } else if (s.equals("Restore")) {
      Transfer.work(new String[] {"-r"});
    } else if (s.equals("Logging on")) {
      javaSystem.setLogToSystem(true);
    } else if (s.equals("Logging off")) {
      javaSystem.setLogToSystem(false);
    } else if (s.equals("Refresh Tree")) {
      refreshTree();
    } else if (s.startsWith("#")) {
      int i = Integer.parseInt(s.substring(1));

      txtCommand.setText(sRecent[i]);
    } else if (s.equals("Connect...")) {
      connect(ConnectionDialogSwing.createConnection(fMain, "Connect"));
      refreshTree();
    } else if (s.equals("Results in Grid")) {
      iResult = 0;

      pResult.removeAll();
      pResult.add(gScrollPane, BorderLayout.CENTER);
      pResult.doLayout();
      gResult.fireTableChanged(null);
      pResult.repaint();
    } else if (s.equals("Open Script...")) {
      JFileChooser f = new JFileChooser(".");

      f.setDialogTitle("Open Script...");

      // (ulrivo): set default directory if set from command line
      if (defDirectory != null) {
        f.setCurrentDirectory(new File(defDirectory));
      }

      int option = f.showOpenDialog(fMain);

      if (option == JFileChooser.APPROVE_OPTION) {
        File file = f.getSelectedFile();

        if (file != null) {
          StringBuffer buf = new StringBuffer();

          ifHuge = DatabaseManagerCommon.readFile(file.getAbsolutePath());

          if (4096 <= ifHuge.length()) {
            buf.append("This huge file cannot be edited. Please execute\n");
            txtCommand.setText(buf.toString());
          } else {
            txtCommand.setText(ifHuge);
          }
        }
      }
    } else if (s.equals("Save Script...")) {
      JFileChooser f = new JFileChooser(".");

      f.setDialogTitle("Save Script");

      // (ulrivo): set default directory if set from command line
      if (defDirectory != null) {
        f.setCurrentDirectory(new File(defDirectory));
      }

      int option = f.showSaveDialog(fMain);

      if (option == JFileChooser.APPROVE_OPTION) {
        File file = f.getSelectedFile();

        if (file != null) {
          DatabaseManagerCommon.writeFile(file.getAbsolutePath(), txtCommand.getText());
        }
      }
    } else if (s.equals("Save Result...")) {
      JFileChooser f = new JFileChooser(".");

      f.setDialogTitle("Save Result...");

      // (ulrivo): set default directory if set from command line
      if (defDirectory != null) {
        f.setCurrentDirectory(new File(defDirectory));
      }

      int option = f.showSaveDialog(fMain);

      if (option == JFileChooser.APPROVE_OPTION) {
        File file = f.getSelectedFile();

        if (file != null) {
          showResultInText();
          DatabaseManagerCommon.writeFile(file.getAbsolutePath(), txtResult.getText());
        }
      }
    } else if (s.equals("Results in Text")) {
      iResult = 1;

      pResult.removeAll();
      pResult.add(txtResultScroll, BorderLayout.CENTER);
      pResult.doLayout();
      showResultInText();
      pResult.repaint();
    } else if (s.equals("AutoCommit on")) {
      try {
        cConn.setAutoCommit(true);
      } catch (SQLException e) {
      }
    } else if (s.equals("AutoCommit off")) {
      try {
        cConn.setAutoCommit(false);
      } catch (SQLException e) {
      }
    } else if (s.equals("Commit")) {
      try {
        cConn.commit();
      } catch (SQLException e) {
      }
    } else if (s.equals("Insert test data")) {
      insertTestData();
    } else if (s.equals("Rollback")) {
      try {
        cConn.rollback();
      } catch (SQLException e) {
      }
    } else if (s.equals("Disable MaxRows")) {
      try {
        sStatement.setMaxRows(0);
      } catch (SQLException e) {
      }
    } else if (s.equals("Set MaxRows to 100")) {
      try {
        sStatement.setMaxRows(100);
      } catch (SQLException e) {
      }
    } else if (s.equals("SELECT")) {
      showHelp(DatabaseManagerCommon.selectHelp);
    } else if (s.equals("INSERT")) {
      showHelp(DatabaseManagerCommon.insertHelp);
    } else if (s.equals("UPDATE")) {
      showHelp(DatabaseManagerCommon.updateHelp);
    } else if (s.equals("DELETE")) {
      showHelp(DatabaseManagerCommon.deleteHelp);
    } else if (s.equals("CREATE TABLE")) {
      showHelp(DatabaseManagerCommon.createTableHelp);
    } else if (s.equals("DROP TABLE")) {
      showHelp(DatabaseManagerCommon.dropTableHelp);
    } else if (s.equals("CREATE INDEX")) {
      showHelp(DatabaseManagerCommon.createIndexHelp);
    } else if (s.equals("DROP INDEX")) {
      showHelp(DatabaseManagerCommon.dropIndexHelp);
    } else if (s.equals("CHECKPOINT")) {
      showHelp(DatabaseManagerCommon.checkpointHelp);
    } else if (s.equals("SCRIPT")) {
      showHelp(DatabaseManagerCommon.scriptHelp);
    } else if (s.equals("SHUTDOWN")) {
      showHelp(DatabaseManagerCommon.shutdownHelp);
    } else if (s.equals("SET")) {
      showHelp(DatabaseManagerCommon.setHelp);
    } else if (s.equals("Test Script")) {
      showHelp(DatabaseManagerCommon.testHelp);
    }
  }