alignjframe.java

emboss的linux版本的源代码

/***************************************************************
*
* 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.
*
*  @author: Copyright (C) Tim Carver
*
***************************************************************/

package org.emboss.jemboss.editor;

import javax.swing.*;
import java.awt.*;
import java.awt.event.*;
import java.util.*;
import java.io.File;
import javax.swing.border.*;
import java.net.URL;

import org.emboss.jemboss.gui.form.TextFieldInt;
import org.emboss.jemboss.gui.sequenceChooser.SequenceFilter;
import org.emboss.jemboss.gui.filetree.FileEditorDisplay;
import org.emboss.jemboss.gui.ScrollPanel;
import org.emboss.jemboss.gui.Browser;

/**
*  
* Displays a grapical representation of a collection of
* sequences.
*
*/
public class AlignJFrame extends JFrame
{

  private Vector graphicSequence;    // Vector containing graphical seqs
  protected JScrollPane jspSequence; // Sequence scrollpane
  protected static GraphicSequenceCollection gsc;
  private static Matrix mat;
  private PrettyPlotJFrame ppj = null;
  protected static JTextField statusField = new JTextField();
  private File sequenceFile = null;
  private Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
  private Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
  protected JCheckBoxMenuItem residueColor;
  protected Hashtable currentColour;
  protected boolean useExitMenu = false;  // whether to use 'Exit' or 'Close'
  protected JMenuBar menuBar;
 
  /**
  *
  * @param vseqs	vector containing Sequence objects
  *
  */ 
  public AlignJFrame(Vector vseqs)
  {
    this();
    if(vseqs != null && vseqs.size() > 0)
      openMethod(vseqs);
  }


  /**
  *
  * @param seqFile	sequence file
  *
  */
  public AlignJFrame(File seqFile)
  {
    this();

    SequenceReader sr = new SequenceReader(seqFile);
    sequenceFile = sr.getSequenceFile();
    openMethod(sr.getSequenceVector());
    setTitle("Jemboss Alignment Viewer    :: "+
              sequenceFile.getName());
  }


  /**
  *
  * @param seqString	formatted sequence string
  * @param name 	name of sequence set
  *
  */
  public AlignJFrame(String seqString, String name)
  {
    this();

    SequenceReader sr = new SequenceReader(seqString);
    sequenceFile = null;
    openMethod(sr.getSequenceVector());
    setTitle("Jemboss Alignment Viewer    :: "+name);
  }


  public AlignJFrame()
  {
    this(false);
  }


  /**
  *
  * @param useExitMenu	true if an exit menu is to be displayed
  *			otherwise a close menu is used
  *
  */
  public AlignJFrame(boolean useExitMenu)
  {
    super("Jemboss Alignment Editor");

    this.useExitMenu = useExitMenu;

    final Dimension dScreen = getToolkit().getScreenSize();
    int interval = 10;
//  Vector seqs = new Vector();
    mat = new Matrix("resources/resources.jar",
                     "EBLOSUM62");
    
    jspSequence = new JScrollPane();
    jspSequence.getViewport().setBackground(Color.white);

    final JButton leftbutt = new JButton("Lock");
    jspSequence.setCorner(JScrollPane.LOWER_LEFT_CORNER,
                                              leftbutt);
    leftbutt.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        if(leftbutt.getText().equals("Lock"))
        {
          gsc.setSequenceLock(true);
          leftbutt.setText("Unlock");
        }
        else
        {
          gsc.setSequenceLock(false);
          leftbutt.setText("Lock");
        }
      }
    });

    final JPanel mainPane = (JPanel)getContentPane();

// set up a menu bar
    menuBar = new JMenuBar();

// File menu
    JMenu fileMenu = new JMenu("File");
    fileMenu.setMnemonic(KeyEvent.VK_F);

// open sequence file
    final JMenuItem calculateCons = new JMenuItem("Consensus");
    final JMenuItem calculatePlotCon = new JMenuItem("Consensus plot");

    JMenuItem openSequence = new JMenuItem("Open...");
    openSequence.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        SequenceReader sr = new SequenceReader();

        if(sr.isReading())
        {
          sequenceFile = sr.getSequenceFile();
          openMethod(sr.getSequenceVector());
          calculateCons.setText("Calculate consensus");
          calculatePlotCon.setText("Calculate consensus plot");
          setTitle("Jemboss Alignment Viewer    :: "+
                    sequenceFile.getName());
        }
      }
    });
    fileMenu.add(openSequence);

// save 
    JMenuItem saveAsMenu = new JMenuItem("Save As...");
    saveAsMenu.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        new SequenceSaver(gsc.getSequenceCollection(),sequenceFile);
      }
    });
    fileMenu.add(saveAsMenu);

    JMenuItem saveConsMenu = new JMenuItem("Save Consensus");
    saveConsMenu.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      { 
        Vector v = new Vector();
        v.add(gsc.getConsensusSequence());
        new SequenceSaver(v);
      }
    });
    fileMenu.add(saveConsMenu);

  
// print
    JMenu printMenu = new JMenu("Print");
    fileMenu.add(printMenu);

    JMenuItem print = new JMenuItem("Print Postscript...");
    print.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        new PrintAlignment(gsc);
      }
    });
    printMenu.add(print);

//
    JMenuItem printImage = new JMenuItem("Print Image Files (png/jpeg)...");
    printImage.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        PrintAlignmentImage pai = new PrintAlignmentImage(gsc);
        pai.print();
      }
    });
    printMenu.add(printImage);
 
    JMenuItem printOneImage = new JMenuItem("Print to Single Image File...");
    printOneImage.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {   
        PrintAlignmentImage pai = new PrintAlignmentImage(gsc);
        String fsave = pai.showOptions();
        if(fsave == null)
          return;

        pai.print(fsave,0.,0.,0.,0.);
      }
    });
    printMenu.add(printOneImage);

// print preview
    JMenu printPreviewMenu = new JMenu("Print Preview");
    fileMenu.add(printPreviewMenu);

    JMenuItem printPreview = new JMenuItem("Multiple Pages...");
    printPreview.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        PrintAlignmentImage pai = new PrintAlignmentImage(gsc);
        pai.printPreview();
      }
    });
    printPreviewMenu.add(printPreview);

    JMenuItem printSinglePreview = new JMenuItem("Single Page...");
    printSinglePreview.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {  
        PrintAlignmentImage pai = new PrintAlignmentImage(gsc);
        String type = pai.showPrintPreviewOptions();
        pai.printSinglePagePreview();
      }
    });
    printPreviewMenu.add(printSinglePreview);

// close
    fileMenu.add(new JSeparator());
    if(!useExitMenu)
    {
      JMenuItem close = new JMenuItem("Close");
      close.setAccelerator(KeyStroke.getKeyStroke(
              KeyEvent.VK_E, ActionEvent.CTRL_MASK));

      close.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e)
        {
          dispose();
        }
      });
      fileMenu.add(close);
    }
    else         // exit
    {
      JMenuItem fileMenuExit = new JMenuItem("Exit");
      fileMenuExit.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e)
        {
          System.exit(0);
        }
      });
      fileMenu.add(fileMenuExit);
    }
    menuBar.add(fileMenu);
  
// Edit menu
    JMenu editMenu = new JMenu("Edit");
    menuBar.add(editMenu);

    JMenuItem insertAnn = new JMenuItem("Insert Annotation Sequence");
    editMenu.add(insertAnn);
    insertAnn.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        ScrollPanel pane = new ScrollPanel(new BorderLayout());
        Box bacross = Box.createVerticalBox();
        JRadioButton openFile = new JRadioButton("Read from File");
        JRadioButton cut      = new JRadioButton("Cut and Paste");
        ButtonGroup group = new ButtonGroup();
        group.add(openFile);
        group.add(cut);
        cut.setSelected(true);
        bacross.add(openFile);
        bacross.add(cut);
        pane.add(bacross,BorderLayout.CENTER);
        int selectedValue = JOptionPane.showConfirmDialog(null,
                          pane, "Cut and Paste/Read from File",
                          JOptionPane.OK_CANCEL_OPTION,
                          JOptionPane.QUESTION_MESSAGE);
        if(selectedValue == JOptionPane.OK_OPTION)
        {
          SequenceReader sr = null;
          if(openFile.isSelected())
            sr = new SequenceReader();
          else
          {
            Paste pastePane = new Paste();
            selectedValue = JOptionPane.showConfirmDialog(null,
                          pastePane, "Cut and Paste",
                          JOptionPane.OK_CANCEL_OPTION,
                          JOptionPane.QUESTION_MESSAGE);
            if(selectedValue == JOptionPane.OK_OPTION)
              sr = new SequenceReader(pastePane.getSequence());
          }
          if(sr != null && sr.isReading())
          {
            sequenceFile = sr.getSequenceFile();
            gsc.addAnnotationSequence(sr.getSequence(0));
            Dimension dpane = gsc.getPanelSize();
            gsc.setPreferredSize(dpane);
            gsc.setNamePanelWidth(gsc.getNameWidth());
            jspSequence.setViewportView(gsc);
          }
        }
      }
    });

    JMenuItem trimMenu = new JMenuItem("Trim Sequences");
    editMenu.add(trimMenu);
    trimMenu.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        ScrollPanel pane = new ScrollPanel(new BorderLayout());
        Box bacross = Box.createHorizontalBox();
        TextFieldInt start = new TextFieldInt();
        start.setValue(1);
        TextFieldInt end   = new TextFieldInt();  
        end.setValue(gsc.getMaxSeqLength());
        bacross.add(start);
        bacross.add(new JLabel(" start "));
        bacross.add(end);
        bacross.add(new JLabel(" end"));
        pane.add(bacross,BorderLayout.CENTER);
        int selectedValue = JOptionPane.showConfirmDialog(null,
                          pane, "Select Sequence Range to Use",
                          JOptionPane.OK_CANCEL_OPTION,      
                          JOptionPane.QUESTION_MESSAGE);
        if(selectedValue == JOptionPane.OK_OPTION)
        {
          Vector vseq = gsc.getSequenceCollection();
          Enumeration enumer = vseq.elements();
          while(enumer.hasMoreElements())
          {
            Sequence s = (Sequence)enumer.nextElement();
            s.trim(start.getValue(),end.getValue());  
          }
          gsc.setMaxSeqLength();
          gsc.repaint();
        }
      }
    });

    JMenuItem unlock = new JMenuItem("Unlock All Sequences");
    editMenu.add(unlock);
    unlock.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.setSequenceLock(false);
      }
    });

// View menu
    JMenu viewMenu = new JMenu("View");
    viewMenu.setMnemonic(KeyEvent.VK_V);

// find pattern
    JMenuItem findMenu = new JMenuItem("Find pattern");
    viewMenu.add(findMenu);
    final PatternJFrame patFrame = new PatternJFrame();
    findMenu.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        Point pos = getLocationOnScreen();
        pos.y = pos.y - patFrame.getHeight();
        if(pos.y+patFrame.getHeight() > dScreen.getHeight())
          pos.x = (int)(dScreen.getWidth()-patFrame.getHeight());
        
        patFrame.setLocation(pos);
        patFrame.setGraphic(gsc);
        patFrame.setVisible(true);
        patFrame.toFront();
      }
    });
    viewMenu.add(new JSeparator());

// matrix display
    JMenuItem showMatrix = new JMenuItem("Matrix Display");
    viewMenu.add(showMatrix);
    final MatrixJFrame matFrame = new MatrixJFrame(mat,statusField,
                                                   this);
    showMatrix.addActionListener(new ActionListener()
    {