SequenceViewer.java

/* SequenceViewer.java
 *
 * created: Sat Dec 19 1998
 *
 * This file is part of Artemis
 *
 * Copyright (C) 1998,1999,2000  Genome Research Limited
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/SequenceViewer.java,v 1.1 2004-06-09 09:47:47 tjc Exp $
 */

package uk.ac.sanger.artemis.components;

import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.StringWriter;
import java.io.PrintWriter;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import javax.swing.ButtonGroup;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JRadioButtonMenuItem;
import javax.swing.text.Style;
import javax.swing.text.StyleConstants;
import javax.swing.text.StyledDocument;

/**
 *  This component provides a viewer for dna or amino acid sequences.  The
 *  units are numbered automatically, given a view like this:
 *  <pre>
 *  ATGATGATGATGATATGCATGATCG
 *           10        20
 *  </pre>
 *  @author Kim Rutherford
 *  @version $Id: SequenceViewer.java,v 1.1 2004-06-09 09:47:47 tjc Exp $
 **/

public class SequenceViewer extends FileViewer {
  /**
   *  Create a new SequenceViewer component.
   *  @param title The name to attach to the new JFrame.
   *  @param include_numbers If true then the sequence will be numbered
   *    (every second line of the display will be numbers rather than
   *    sequence).
   **/
  public SequenceViewer (final String title,
                         final boolean include_numbers) {
    super (title, true, false, true);
    this.include_numbers = include_numbers;
    initMenu();
  }
  
  private void initMenu()
  {
    final JMenuBar mBar = new JMenuBar();
    setJMenuBar(mBar);
    final JMenu viewMenu = new JMenu("View");
    mBar.add(viewMenu);
    
    final ButtonGroup group = new ButtonGroup();
    final JRadioButtonMenuItem none = new JRadioButtonMenuItem("No Colour");
    none.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent arg0)
      {
        if(none.isSelected())
          clearColour();
      }
    });
    viewMenu.add(none);
    group.add(none);
    
    final JRadioButtonMenuItem taylor = new JRadioButtonMenuItem("Taylor Colour");
    taylor.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent arg0)
      {
        if(taylor.isSelected())
          colourTaylor();
      }
    });
    viewMenu.add(taylor);
    group.add(taylor);
    
    final JRadioButtonMenuItem rasmol = new JRadioButtonMenuItem("Rasmol Colour");
    rasmol.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        colourRasmol();
      }  
    });
    viewMenu.add(rasmol);
    group.add(rasmol);
    
    final JRadioButtonMenuItem stops = new JRadioButtonMenuItem("Stop Codon Colour");
    stops.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        colourStops();
      }  
    });
    viewMenu.add(stops);
    group.add(stops);

    final JRadioButtonMenuItem nuc = new JRadioButtonMenuItem("Nucleotide Colour");
    nuc.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        colourNuc();
      }  
    });
    viewMenu.add(nuc);
    group.add(nuc);
    
    
    stops.setSelected(true);
    // add clear style
    final Style style = getTextPane().addStyle("clear", null);
    StyleConstants.setBackground(style, Color.white);
  }

  /**
   *  Set the sequence to display.
   *  @param comment_line A comment to put on the first line.  This may be
   *    null in which case there is no comment line.  This String should not
   *    be "\n" terminated.
   *  @param sequence The sequence to display.  This may be null in which case
   *    there is no comment line.  This String should not be "\n" terminated.
   **/
  public void setSequence (final String comment_line, final String sequence) {
    this.comment_line = comment_line;
    this.sequence = sequence;

    setView ();
  }

  /**
   *  Set the sequence to display with no comment line.
   *  @param sequence The sequence to display.  This may be null in which case
   *    there is no comment line.  This String should not be "\n" terminated.
   **/
  public void setSequence (final String sequence) {
    this.comment_line = null;
    this.sequence = sequence;

    setView ();
  }

  /**
   *  Write the sequence and comment_line in the view.
   **/
  private void setView () {
    final StringWriter string_writer = new StringWriter ();

    final PrintWriter writer = new PrintWriter (string_writer);

    if (comment_line != null) {
      writer.println (comment_line);
    }

    String rest_of_sequence = sequence;

    final int UNITS_PER_LINE = 60;

    int line_count = 0;

    while (rest_of_sequence != null) {
      final String this_line;

      if (rest_of_sequence.length () < UNITS_PER_LINE) {
        this_line = rest_of_sequence;
        rest_of_sequence = null;
      } else {
        this_line = rest_of_sequence.substring (0, UNITS_PER_LINE);
        rest_of_sequence = rest_of_sequence.substring (UNITS_PER_LINE);
      }


      writer.println (this_line);

      if (include_numbers) {
        final int COUNT_INTERVAL = 10;

        for (int i = 1 ;
             i <= this_line.length () / COUNT_INTERVAL;
             ++i) {
          final int this_unit_count =
            i * COUNT_INTERVAL + line_count * UNITS_PER_LINE;

          final int number_of_spaces =
            COUNT_INTERVAL - String.valueOf (this_unit_count).length ();

          for (int space_index = 0 ;
               space_index < number_of_spaces ;
               ++space_index) {
            writer.print (' ');
          }

          writer.print (this_unit_count);
        }

        writer.println ();
      }

      ++line_count;
    }

    writer.flush ();

    setText (string_writer.toString ());
    
    colourStops();
  }
  
  private void colourStops()
  {
    clearColour();
    final StyledDocument doc = getTextPane().getStyledDocument();
    final Style style = getTextPane().addStyle("Red", null);
    StyleConstants.setBackground(style, Color.red);
    
    final Matcher matcher = STOP_CODON_PATTERN.matcher(getText());
    while( matcher.find() )
    {
      doc.setCharacterAttributes(matcher.start(), matcher.end()-matcher.start(), 
          getTextPane().getStyle("Red"), true);
    } 
  }
  
  /**
   * Use Taylor colour scheme
   * W.R.Taylor Protein Eng. vol.10 no. 7 pp743-746, 1997
   */
  private void colourTaylor()
  {
    clearColour();
    applyColourScheme(org.emboss.jemboss.editor.SequenceProperties.taylorColor);
  }
  
  /**
   * Use Rasmol colour scheme
   */
  private void colourRasmol()
  {
    clearColour();
    applyColourScheme(org.emboss.jemboss.editor.SequenceProperties.rasmolColor);
  }
  
  /**
   * Use Rasmol colour scheme
   */
  private void colourNuc()
  {
    clearColour();
    applyColourScheme(org.emboss.jemboss.editor.SequenceProperties.baseColor);
  }
  
  
  private void applyColourScheme(final Hashtable<String, Color> colourHash)
  {
    final Enumeration<String> keys = colourHash.keys();
    final StyledDocument doc = getTextPane().getStyledDocument();
    
    while(keys.hasMoreElements())
    {
      final String aa = keys.nextElement();
      Style style = getTextPane().addStyle(aa, null);
      StyleConstants.setBackground(style, colourHash.get(aa));
    }
    
    final String seq = getText();
    int seqStart = 0;
    if(seq.startsWith(">"))
    {
      final Matcher matcher = EOL_PATTERN.matcher(getText());
      if(matcher.find())
        seqStart = matcher.start();
      if(seqStart < 0)
        seqStart = 0;
    }

    for(int i=seqStart; i<seq.length(); i++)
    {
      String c = Character.toString( seq.charAt(i) );
      if(getTextPane().getStyle(c) != null)
        doc.setCharacterAttributes(i, 1, getTextPane().getStyle(c), true);
    }
  }
  
  private void clearColour()
  {
    final StyledDocument doc = getTextPane().getStyledDocument();
    doc.setCharacterAttributes(0, getText().length(), getTextPane().getStyle("clear"), true);
  }
  

  /** Pattern for locating stop codons */
  private static Pattern STOP_CODON_PATTERN = Pattern.compile("[\\*#+]");
  private static Pattern EOL_PATTERN = Pattern.compile("[\r\n]");
  
  /** The sequence to display. */
  private String sequence = "";

  /** A comment to put on the first line.  If null don't display any comment. */
  private String comment_line = null;

  /** If true then the amino acids will be numbered (every second line of the
      display will be numbers rather than sequence). */
  private final boolean include_numbers;
}