moss.java

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

/*----------------------------------------------------------------------
  File    : MoSS.java
  Contents: graphical user interface for the MoSS program
  Author  : Christian Borgelt
  History : 13.07.2006 file created from file PGView.java
            18.07.2006 first version completed
            09.08.2006 ignoring the atom type only in rings added
            12.08.2006 adapted to new Notation classes
            13.08.2006 atom types to exclude as seeds added
----------------------------------------------------------------------*/
package moss;

import java.awt.BorderLayout;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.EventQueue;
import java.awt.Font;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintStream;
import java.util.StringTokenizer;

import javax.swing.AbstractAction;
import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JSpinner;
import javax.swing.JTabbedPane;
import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.SpinnerNumberModel;
import javax.swing.Timer;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;

/*--------------------------------------------------------------------*/
public class MoSS extends JFrame implements Runnable, ChangeListener {
/*--------------------------------------------------------------------*/

  private static final String[] fmtnames = {
    "SMILES", "SLN" };

  private static final String[] extnames = {
    "maximum source", "rightmost path" };

  private static final String[] aromnames = {
    "extra type", "downgrade", "upgrade" };

  private static final String[] typenames = {
    "never", "in rings", "always" };

  private static final String[] pepnames = {
    "full", "partial", "none" };

  private static final String[] ringnames = {
    "none", "full", "filter", "merge" };

  /* --- fonts --- */
  private static final Font font  = new Font("Dialog", Font.BOLD,  12);
  private static final Font small = new Font("Dialog", Font.PLAIN, 10);

  /* --- files and format --- */
  private JComboBox   fmt_in;   /* input format for molecules */
  private JComboBox   fmt_out;  /* output format for substructures */
  private JComboBox   fmt_seed; /* seed format */
  private JTextField  fn_in;    /* name of input file */
  private JTextField  fn_sub;   /* name of substructure output file */
  private JTextField  fn_ids;   /* name of molecule identifier file */
  private JTextField  seed;     /* seed structure to start from */

  /* --- basic parameters --- */
  private JTextField  thresh;   /* threshold for split */
  private JCheckBox   invert;   /* whether to invert the split */
  private JTextField  minsupp;  /* minimal support in focus */
  private JTextField  maxsupp;  /* maximal support in complement */
  private JSpinner    minsize;  /* minimal size of a substructure */
  private JSpinner    maxsize;  /* maximal size of a substructure */

  /* --- matching --- */
  private JComboBox   bdarom;   /* treatment of aromatic bonds */
  private JComboBox   bdtype;   /* ignore the bond type */
  private JComboBox   attype;   /* ignore the atom type */
  private JCheckBox   charge;   /* match the atom charge */
  private JCheckBox   atarom;   /* match the atom aromaticity */
  private JTextField  excl;     /* excluded atom types */
  private JTextField  exseed;   /* excluded atom types for seeds */

  /* --- rings and chains --- */
  private JCheckBox   kekule;   /* convert Kekule representations */
  private JCheckBox   rings;    /* whether to mark rings */
  private JSpinner    minring;  /* minimal size of a ring */
  private JSpinner    maxring;  /* maximal size of a ring */
  private JComboBox   ringext;  /* type of ring extensions */
  private JCheckBox   chains;   /* variable length carbon chains */
  private JLabel[]    labels;   /* labels that can be disabled */

  /* --- miscellaneous --- */
  private JComboBox   exttype;  /* extension type */
  private JComboBox   perfect;  /* perfect extension pruning */
  private JCheckBox   equiv;    /* equivalent sibling pruning */
  private JCheckBox   canonic;  /* canonical form pruning */
  private JSpinner    maxemb;   /* maximal embeddings */
  private JCheckBox   normal;   /* normalize the output */
  private JCheckBox   verbose;  /* verbose message output */

  /* --- window and status line --- */
  private JTabbedPane tab;      /* pane for parameter tabs */
  private JButton     exec;     /* execute/abort button */
  private JTextField  stat;     /* status line */

  /* --- other variables --- */
  private Component    owner   = null;
  private boolean      isprog  = false;
  private JFileChooser chooser = null;
  private Thread       thread  = null;
  private Timer        timer   = null;
  private boolean      running = false;
  private boolean      stopped = true;
  private Miner        miner   = null;
  private long         start;

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

  private JFileChooser createChooser ()
  {                             /* --- create a file chooser */
    JFileChooser fc = new JFileChooser();
    fc.setFileSelectionMode(JFileChooser.FILES_ONLY);
    fc.setCurrentDirectory(new File("."));
    fc.setFileHidingEnabled(true);
    fc.setAcceptAllFileFilterUsed(true);
    fc.setMultiSelectionEnabled(false);
    fc.setFileView(null);       /* create a standard file chooser */
    return fc;                  /* without customized filters */
  }  /* createChooser() */

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

  private static String readLine (BufferedReader rdr) throws IOException
  {                             /* --- read a line of config. file */
    String line = rdr.readLine();
    if (line == null) throw new IOException("premature end of file");
    return line;                /* read and check next line */
  }  /* readLine() */

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

  private static int getInt (StringTokenizer tok) throws IOException
  {                             /* --- get next integer value */
    if (!tok.hasMoreTokens())   /* check for another field */
      throw new IOException("too few fields in last line");
    try { return Integer.parseInt(tok.nextToken()); }
    catch (Exception e) { return 0; }
  }  /* getInt() */             /* decode and return the next field */

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

  private void loadConfig (File file)
  {                             /* --- load configuration */
    FileInputStream in;         /* the configuration file */
    BufferedReader  rdr;        /* reader for the configuration file */
    StringTokenizer tok;        /* tokenizer for the last line */

    try {                       /* open the configuration file */
      in  = new FileInputStream(file);
      rdr = new BufferedReader(new InputStreamReader(in));
      fn_in.setText  (MoSS.readLine(rdr));
      fn_sub.setText (MoSS.readLine(rdr));
      fn_ids.setText (MoSS.readLine(rdr));
      seed.setText   (MoSS.readLine(rdr));
      excl.setText   (MoSS.readLine(rdr));
      exseed.setText (MoSS.readLine(rdr));
      thresh.setText (MoSS.readLine(rdr));
      minsupp.setText(MoSS.readLine(rdr));
      maxsupp.setText(MoSS.readLine(rdr));
      tok = new StringTokenizer(MoSS.readLine(rdr), ",");
      minsize.setValue(new Integer(MoSS.getInt(tok)));
      maxsize.setValue(new Integer(MoSS.getInt(tok)));
      minring.setValue(new Integer(MoSS.getInt(tok)));
      maxring.setValue(new Integer(MoSS.getInt(tok)));
      maxemb.setValue (new Integer(MoSS.getInt(tok)));
      fmt_in.setSelectedIndex  (MoSS.getInt(tok));
      fmt_out.setSelectedIndex (MoSS.getInt(tok));
      fmt_seed.setSelectedIndex(MoSS.getInt(tok));
      bdarom.setSelectedIndex  (MoSS.getInt(tok));
      bdtype.setSelectedIndex  (MoSS.getInt(tok));
      attype.setSelectedIndex  (MoSS.getInt(tok));
      ringext.setSelectedIndex (MoSS.getInt(tok));
      exttype.setSelectedIndex (MoSS.getInt(tok));
      perfect.setSelectedIndex (MoSS.getInt(tok));
      rings.setSelected  (MoSS.getInt(tok) != 0);
      invert.setSelected (MoSS.getInt(tok) != 0);
      charge.setSelected (MoSS.getInt(tok) != 0);
      atarom.setSelected (MoSS.getInt(tok) != 0);
      kekule.setSelected (MoSS.getInt(tok) != 0);
      chains.setSelected (MoSS.getInt(tok) != 0);
      equiv.setSelected  (MoSS.getInt(tok) != 0);
      canonic.setSelected(MoSS.getInt(tok) != 0);
      normal.setSelected (MoSS.getInt(tok) != 0);
      verbose.setSelected(MoSS.getInt(tok) != 0);
      this.stat.setText("configuration loaded: " +file.getName()); }
    catch (IOException ioe) {   /* read the configuration values */
      JOptionPane.showMessageDialog(this,
        "Error reading configuration file:\n" +ioe.getMessage(),
        "Error", JOptionPane.ERROR_MESSAGE);
    }                           /* check for successful reading */
    this.stateChanged(null);    /* adapt state of rings tab */
  }  /* loadConfig() */

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

  private void saveConfig (File file)
  {                             /* --- save configuration */
    PrintStream s = null;       /* to write the configuration file */

    try {                       /* open the configuration file */
      s = new PrintStream(new FileOutputStream(file));
      s.println(fn_in.getText());
      s.println(fn_sub.getText());
      s.println(fn_ids.getText());
      s.println(seed.getText());
      s.println(excl.getText());
      s.println(exseed.getText());
      s.println(thresh.getText());
      s.println(minsupp.getText());
      s.println(maxsupp.getText());
      s.print(((Integer)minsize.getValue()).intValue() +",");
      s.print(((Integer)maxsize.getValue()).intValue() +",");
      s.print(((Integer)minring.getValue()).intValue() +",");
      s.print(((Integer)maxring.getValue()).intValue() +",");
      s.print(((Integer)maxemb.getValue()).intValue() +",");
      s.print(fmt_in.getSelectedIndex() +",");
      s.print(fmt_out.getSelectedIndex() +",");
      s.print(fmt_seed.getSelectedIndex() +",");
      s.print(bdarom.getSelectedIndex() +",");
      s.print(bdtype.getSelectedIndex() +",");
      s.print(attype.getSelectedIndex() +",");
      s.print(ringext.getSelectedIndex() +",");
      s.print(exttype.getSelectedIndex() +",");
      s.print(perfect.getSelectedIndex() +",");
      s.print(rings.isSelected()   ? "1," : "0,");
      s.print(invert.isSelected()  ? "1," : "0,");
      s.print(charge.isSelected()  ? "1," : "0,");
      s.print(atarom.isSelected()  ? "1," : "0,");
      s.print(kekule.isSelected()  ? "1," : "0,");
      s.print(chains.isSelected()  ? "1," : "0,");
      s.print(equiv.isSelected()   ? "1," : "0,");
      s.print(canonic.isSelected() ? "1," : "0,");
      s.print(normal.isSelected()  ? "1," : "0,");
      s.println(verbose.isSelected() ? "1" : "0"); }
    catch (IOException ioe) {   /* write the configuration values */
      JOptionPane.showMessageDialog(this,
        "Error writing configuration file:\n" +ioe.getMessage(),
        "Error", JOptionPane.ERROR_MESSAGE);
    }                           /* check for successful writing */
    if (s != null) s.close();   /* close the configuration file */
    this.stat.setText("configuration saved: " +file.getName());
  }  /* saveConfig() */

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

  private void result ()
  {                             /* --- show result of computation */
    int   n;                    /* number of found substructures */
    float t;                    /* execution time */

    this.running = false;       /* thread is no longer running */
    this.exec.setText("Run");   /* reset the button text */
    if (this.stopped) {         /* if execution has been aborted */
      this.miner = null;        /* "delete" the miner */
      this.stat.setText("substructure search aborted.");
      JOptionPane.showMessageDialog(this,
        "Substructure search aborted.",
        "Information", JOptionPane.INFORMATION_MESSAGE);
      return;                   /* show an abortion dialog */
    }                           /* and abort the function */
    this.miner.stats();         /* show search statistics */
    n = this.miner.getCurrent();
    t = (System.currentTimeMillis() -this.start) / 1000.0F;
    this.stat.setText(n +" substructure(s), "
                     +"total search time: " +t +"s");
    JOptionPane.showMessageDialog(this,
      "Found " +n +" substructure(s).\nTotal search time: " +t +"s.\n"
     +"(See terminal for more information.)",
      "Information", JOptionPane.INFORMATION_MESSAGE);
    this.miner = null;          /* show a success message */
  }  /* result() */             /* and "delete" the miner */

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

  private void update ()
  {                             /* --- update the status text */
    if (!this.running) return;  /* check for a running search */
    this.stat.setText(" searching ... "
                     +this.miner.getCurrent() +" substructure(s)");
  }  /* update() */             /* display search statistics */

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

  public void execute ()
  {                             /* --- execute substructure search */
    int    mode;                /* search mode */
    String fmt;                 /* input/output format */
    float  spth = 0;            /* threshold for split */
    float  supp = 0, comp = 0;  /* support in focus and complement */
    int    matom, mbond;        /* atom and bond masks outside rings */
    int    mrgat, mrgbd;        /* atom and bond masks inside  rings */
    int    min,   max;          /* minimum and maximum fragment size */