moss.java

A program to find frequent molecular substructures and discriminative fragments in a database of mol

    g.setConstraints(bdtype, rc);      grid.add(bdtype);

    lbl = new JLabel("Ignore type of atoms:");
    g.setConstraints(lbl, lc);         grid.add(lbl);
    attype = new JComboBox(typenames);
    g.setConstraints(attype, rc);      grid.add(attype);

    lbl = new JLabel("Match charge of atoms:");
    g.setConstraints(lbl, lc);         grid.add(lbl);
    charge = new JCheckBox("", false);
    g.setConstraints(charge, rc);      grid.add(charge);

    lbl = new JLabel("Match aromaticity of atoms:");
    g.setConstraints(lbl, lc);         grid.add(lbl);
    atarom = new JCheckBox("", false);
    g.setConstraints(atarom, rc);      grid.add(atarom);

    help = new JTextArea(
       "An atom is aromatic if it is part of an aromatic ring.");
    help.setFont(small);
    help.setBackground(this.getBackground());
    g.setConstraints(help, rc); grid.add(help);

    help = new JTextArea((String)null);
    help.setFont(small); help.setBackground(this.getBackground());
    help.setPreferredSize(new Dimension(0,3));
    g.setConstraints(help, rc); grid.add(help);

    lbl = new JLabel("Atom types to exclude:");
    g.setConstraints(lbl, rc);          grid.add(lbl);
    excl = new JTextField("");          excl.setFont(font);
    g.setConstraints(excl, rc);         grid.add(excl);
 
    lbl = new JLabel("Atom types to exclude as seeds:");
    g.setConstraints(lbl, rc);          grid.add(lbl);
    exseed = new JTextField("");        exseed.setFont(font);
    g.setConstraints(exseed, rc);       grid.add(exseed);

    help = new JTextArea(
       "The former are generally excluded from the search, the latter\n"
      +"are not used as seeds, but may appear with other seeds.\n"
      +"Both have to be specified as a molecule, in seed format.");
    help.setFont(small);
    help.setBackground(this.getBackground());
    g.setConstraints(help, rc); grid.add(help);

    help = new JTextArea((String)null);
    help.setFont(small); help.setBackground(this.getBackground());
    help.setPreferredSize(new Dimension(0,0));
    rc.weighty = 1.0;
    g.setConstraints(help, rc); grid.add(help);
    rc.weighty = 0.0;

    /* --- rings and chains --- */
    grid = new JPanel(g);
    grid.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
    tab.addTab("Rings and Chains", null, grid, null);

    lbl = new JLabel("Convert Kekule representations:");
    g.setConstraints(lbl, lc);         grid.add(lbl);
    kekule = new JCheckBox("", true);
    g.setConstraints(kekule, rc);      grid.add(kekule);

    help = new JTextArea(
       "Aromatic rings may be coded as alternating single and double\n"
      +"bonds (so-called Kekule representation of an aromatic ring).\n"
      +"It is recommended to convert these "
      +"to actual aromatic bonds.");
    help.setFont(small);
    help.setBackground(this.getBackground());
    g.setConstraints(help, rc); grid.add(help);

    lbl = new JLabel("Distinguish ring bonds:");
    g.setConstraints(lbl, lc);         grid.add(lbl);
    rings = new JCheckBox("", false);
    g.setConstraints(rings, rc);       grid.add(rings);
    rings.addChangeListener(this);

    labels = new JLabel[3];
    labels[0] = lbl = new JLabel("Minimal ring size:");
    g.setConstraints(lbl, lc);         grid.add(lbl);
    minring = new JSpinner(new SpinnerNumberModel(5, 0, 256, 1));
    g.setConstraints(minring, rc);     grid.add(minring);

    labels[1] = lbl = new JLabel("Maximal ring size:");
    g.setConstraints(lbl, lc);         grid.add(lbl);
    maxring = new JSpinner(new SpinnerNumberModel(6, 0, 256, 1));
    g.setConstraints(maxring, rc);     grid.add(maxring);

    labels[2] = lbl = new JLabel("Ring extensions:");
    g.setConstraints(lbl, lc);         grid.add(lbl);
    ringext = new JComboBox(ringnames);
    g.setConstraints(ringext, rc);     grid.add(ringext);
    this.stateChanged(null);

    help = new JTextArea(
       "Ring extensions require that ring bonds are distinguished\n"
      +"and that a range of relevant ring sizes is specified.\n"
      +"It is recommended to use full ring extensions if any.");
    help.setFont(small);
    help.setBackground(this.getBackground());
    g.setConstraints(help, rc); grid.add(help);

    help = new JTextArea((String)null);
    help.setFont(small); help.setBackground(this.getBackground());
    help.setPreferredSize(new Dimension(0,10));
    g.setConstraints(help, rc); grid.add(help);

    lbl = new JLabel("Variable length carbon chains:");
    g.setConstraints(lbl, lc);         grid.add(lbl);
    chains = new JCheckBox("", false);
    g.setConstraints(chains, rc);      grid.add(chains);

    help = new JTextArea(
       "A carbon chain consists only of carbon atoms connected by\n"
      +"single bonds, which are bridges in the molecule.");
    help.setFont(small);
    help.setBackground(this.getBackground());
    g.setConstraints(help, rc); grid.add(help);

    help = new JTextArea((String)null);
    help.setFont(small);
    help.setBackground(this.getBackground());
    rc.weighty = 1.0;
    g.setConstraints(help, rc); grid.add(help);
    rc.weighty = 0.0;

    /* --- miscellaneous --- */
    grid = new JPanel(g);
    grid.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
    tab.addTab("Miscellaneous", null, grid, null);

    lbl = new JLabel("Extension type:");
    g.setConstraints(lbl, lc);          grid.add(lbl);
    exttype = new JComboBox(extnames);  exttype.setFont(font);
    g.setConstraints(exttype, rc);      grid.add(exttype);
 
    help = new JTextArea(
       "Maximum source extension defines the MoSS/MoFa algorithm,\n"
      +"rightmost path extension the gSpan/CloseGraph algorithm.");
    help.setFont(small);
    help.setBackground(this.getBackground());
    g.setConstraints(help, rc); grid.add(help);

    lbl = new JLabel("Perfect extension pruning:");
    g.setConstraints(lbl, lc);         grid.add(lbl);
    perfect = new JComboBox(pepnames); perfect.setFont(font);
    g.setConstraints(perfect, rc);     grid.add(perfect);
 
    lbl = new JLabel("Equivalent sibling pruning:");
    g.setConstraints(lbl, lc);         grid.add(lbl);
    equiv = new JCheckBox("", false);
    g.setConstraints(equiv, rc);       grid.add(equiv);

    lbl = new JLabel("Canonical form pruning:");
    g.setConstraints(lbl, lc);         grid.add(lbl);
    canonic = new JCheckBox("", true);
    g.setConstraints(canonic, rc);     grid.add(canonic);

    lbl = new JLabel("Maximal embeddings:");
    g.setConstraints(lbl, lc);          grid.add(lbl);
    maxemb = new JSpinner(new SpinnerNumberModel(0, 0, 999999, 1));
    g.setConstraints(maxemb, rc);       grid.add(maxemb);

    help = new JTextArea(
       "Restricting the maximal number of embeddings that are kept\n"
      +"per molecule can reduce the amount of memory needed.");
    help.setFont(small);
    help.setBackground(this.getBackground());
    g.setConstraints(help, rc); grid.add(help);

    lbl = new JLabel("Normalize output:");
    g.setConstraints(lbl, lc);         grid.add(lbl);
    normal = new JCheckBox("", false);
    g.setConstraints(normal, rc);      grid.add(normal);

    help = new JTextArea(
       "Normalize the description of the found substructures,\n"
      +"so that they can be compared by a simple string comparison.");
    help.setFont(small);
    help.setBackground(this.getBackground());
    g.setConstraints(help, rc); grid.add(help);

    lbl = new JLabel("Verbose message output:");
    g.setConstraints(lbl, lc);         grid.add(lbl);
    verbose = new JCheckBox("", false);
    g.setConstraints(verbose, rc);      grid.add(verbose);

    help = new JTextArea(
      "Print the nodes of the search tree during the search.");
    help.setFont(small);
    help.setBackground(this.getBackground());
    g.setConstraints(help, rc); grid.add(help);

    help = new JTextArea((String)null);
    help.setFont(small); help.setBackground(this.getBackground());
    help.setPreferredSize(new Dimension(0,0));
    rc.weighty = 1.0;
    g.setConstraints(help, rc); grid.add(help);
    rc.weighty = 0.0;

    /* --- about --- */
    grid = new JPanel(g);
    grid.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
    tab.addTab("About", null, grid, null);

    help = new JTextArea(
       "MoSS - Molecular Substructure Miner");
    help.setFont(font); help.setBackground(this.getBackground());
    g.setConstraints(help, rc); grid.add(help);

    help = new JTextArea(
       "A simple graphical user interface for the MoSS program.\n\n"
      +"GUI version 1.3, Miner version 4.9 (2006.08.13)\n"
      +"written by Christian Borgelt\n"
      +"Intelligent Data Analysis and Graphical Models Research Unit\n"
      +"European Center for Soft Computing\n"
      +"c/ Gonzalo Gutierrez Quiros s/n, 33600 Mieres, Spain\n"
      +"e-mail: [e-mail]\n\n"
      +"This program is free software;\n"
      +"you can redistribute it and/or modify it under\n"
      +"the terms of the GNU Lesser General Public License\n"
      +"as published by the Free Software Foundation.\n\n"
      +"This program is distributed in the hope that\n"
      +"it will be useful, but WITHOUT ANY WARRANTY;\n"
      +"without even the implied warranty of MERCHANTABILITY\n"
      +"or FITNESS FOR A PARTICULAR PURPOSE. See the\n"
      +"GNU Lesser General Public License for more details.");
    help.setFont(small); help.setBackground(this.getBackground());
    g.setConstraints(help, rc); grid.add(help);

    /* --- buttons --- */
    lc.weightx = rc.weightx = 0.5;
    bbar = new JPanel(new GridLayout(1, 2, 5, 5));
    bbar.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
    this.exec = btn = new JButton("Run");
    g.setConstraints(btn, lc); bbar.add(btn);
    btn.addActionListener(new AbstractAction () {
      public void actionPerformed (ActionEvent e) {
        MoSS.this.execute(); } } );
    btn = new JButton("Load");
    g.setConstraints(btn, lc); bbar.add(btn);
    btn.addActionListener(new AbstractAction () {
      public void actionPerformed (ActionEvent e) {
        if (chooser == null) chooser = createChooser();
        chooser.setDialogType(JFileChooser.OPEN_DIALOG);
        chooser.setDialogTitle("Load Configuration");
        int r = chooser.showDialog(MoSS.this, null);
        if (r == JFileChooser.APPROVE_OPTION)
          MoSS.this.loadConfig(chooser.getSelectedFile());
      } } );
    btn = new JButton("Save");
    g.setConstraints(btn, lc); bbar.add(btn);
    btn.addActionListener(new AbstractAction () {
      public void actionPerformed (ActionEvent e) {
        if (chooser == null) chooser = createChooser();
        chooser.setDialogType(JFileChooser.SAVE_DIALOG);
        chooser.setDialogTitle("Save Configuration");
        int r = chooser.showDialog(MoSS.this, null);
        if (r == JFileChooser.APPROVE_OPTION)
          MoSS.this.saveConfig(chooser.getSelectedFile());
      } } );
    if (this.isprog) {          /* terminate the program */
      btn = new JButton("Quit");
      btn.addActionListener(new AbstractAction () {
        public void actionPerformed (ActionEvent e) {
          System.exit(0); } } );}
    else {                      /* only close the dialog box */
      btn = new JButton("Close");
      btn.addActionListener(new AbstractAction () {
        public void actionPerformed (ActionEvent e) {
          MoSS.this.setVisible(false); } } );
    }                           /* configure the button bar */
    g.setConstraints(btn, rc); bbar.add(btn);

    grid = new JPanel(new BorderLayout());
    grid.add(bbar, BorderLayout.NORTH);
    stat = new JTextField("MoSS - Molecular Substructure Miner");
    stat.setEditable(false);
    grid.add(stat, BorderLayout.SOUTH);

    this.getContentPane().add(tab,  BorderLayout.NORTH);
    this.getContentPane().add(grid, BorderLayout.SOUTH);
    this.setTitle("MoSS - Molecular Substructure Miner");
    this.setDefaultCloseOperation(this.isprog
      ? JFrame.EXIT_ON_CLOSE : JFrame.HIDE_ON_CLOSE);
    if (this.owner != null)
      this.setLocationRelativeTo(this.owner);
    this.setLocation(50, 50);
    this.pack();
  }  /* run() */

  /* Following the recommendations in the Java tutorial, the user   */
  /* interface is created in the "run" method, which is invoked     */
  /* from the event queue, in order to avoid problems with threads. */

  /*------------------------------------------------------------------*/

  public MoSS (Component owner, boolean isProg)
  { this.owner = owner; this.isprog = isProg;
    try { EventQueue.invokeAndWait(this); } catch (Exception e) {} }

  public MoSS (Component owner)
  { this.owner = owner; this.isprog = false;
    try { EventQueue.invokeAndWait(this); } catch (Exception e) {} }

  public MoSS ()
  { this.owner = null;  this.isprog = true;
    try { EventQueue.invokeAndWait(this); } catch (Exception e) {} }

  /*------------------------------------------------------------------*/

  public static void main (String args[])
  {                             /* --- main function */
    MoSS moss = new MoSS();     /* create a MoSS dialog */
    if (args.length > 0)        /* load configuration if necessary */
      moss.loadConfig(new File(args[0]));
    moss.setVisible(true);      /* make dialog visible */
  }  /* main() */

}  /* class MoSS */