simpledp.java

Sequence alignement using different algorithms

package norman.baba.algorithms;

import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
import javax.swing.border.*;
import java.util.*;
import javax.swing.text.DefaultCaret;

import norman.baba.UI.*;
import norman.baba.grids.*;

/**
 * <p>Title: BABA</p>
 * <p>Description: Bioinformatique Research Project</p>
 * <p>Copyright: Copyright Norman Casagrande (c) 2003</p>
 * <p>Company: </p>
 * @author Norman Casagrande
 * @version 1.0
 */

public class SimpleDP
    implements CellInteractInterface {

   protected String m_defS1 = "";
   protected String m_defS2 = "";

   /**
    * **********************************************************************
    * User Interface Stuffs
    * **********************************************************************
    */

   /**
    * ****************** Useful things *********************************
    */
   protected Border m_defaultStringBorder = BorderFactory.createCompoundBorder(
       BorderFactory.
       createEtchedBorder(Color.white, new Color(165, 163, 151)),
       BorderFactory.createEmptyBorder(1, 2, 3, 2));

   protected Font m_resultAreaFont = new Font("Monospaced", 0, 11);

   /**
    * ************************* Panels *********************************
    */

   /** The main panel. Everything is attached here */
   protected JPanel m_mainPane = null;

   /**
    * The Scroll Area where the grid is painted.
    * NOTE: It is a ScrollPane and NOT a JScrollPane because this is way
    * faster. Double buffering is controlled by the grid class.
    */
   protected ScrollPane m_gridScrollArea = new ScrollPane();

   /** The grid class - CENTER */
   protected DPTable m_dpTable;

   /**
    * ********************** NORTH AREA *********************************
    */
   protected JTextField m_infoLabel = new JTextField(" Waiting..", 40);

   /**
    * ********************** SOUTH AREA *********************************
    */

   protected JTextArea m_bottomResultArea = new JTextArea(3, 50);

   /**
    * ********************** EAST AREA *********************************
    */

   protected JPanel m_clearPanel = new JPanel();
   protected JPanel m_currStatusPanel = new JPanel();
   protected JPanel m_stepsButtonPanel = new JPanel();

   protected JLabel m_gapOne_title = new JLabel("S1 Gap Penalty Array:");
   protected JLabel m_gapTwo_title = new JLabel("S2 Gap Penalty Array:");

   // These elements are public
   public JTextField m_StringOne = new JTextField(22);
   public JTextField m_StringTwo = new JTextField(22);

   public JTextField m_gapOne = new JTextField(22);
   public JTextField m_gapTwo = new JTextField(22);

   ////////
   public JButton m_btnSetOne = new JButton("Set");
   public JButton m_btnSetTwo = new JButton("Set");
   public JButton m_btnSetGapOne = new JButton("Set");
   public JButton m_btnSetGapTwo = new JButton("Set");

   ////////
   public JLabel m_lDEqual = new JLabel("D(S1,S2) = Min");

   public JLabel m_l1Choiche = new JLabel("D(S1-1, S2) + 1");
   public JLabel m_l2Choiche = new JLabel("D(S1, S2-1) + 1");
   public JLabel m_l3Choiche = new JLabel("D(S1 - 1, S2 - 1) + [1|0]");

   ////////
   public JButton m_btnBeginning = new JButton("|<");
   public JButton m_btnNext = new JButton(">");
   public JButton m_btnPrev = new JButton("<");
   public JButton m_btnEnd = new JButton(">|");

   ////////
   public JButton m_btnClear = new JButton("Clear");

   protected static String emptyStringMessage = "[Please Set String]";
   protected static String emptyGapMessage = "[Not Set]";

   /////////////////////////////////////////////////////////////////////

   /**
    * This class draws the three lines a the center of the right panel.
    * (From D(S1,S2) to the choiches.
    */
   protected class DrawablePanel
       extends JPanel {
      public void paintComponent(Graphics g) {
         //super.paintComponent(g);

         int startY;
         int width = this.getSize().width - 6;

         // /
         startY = this.getSize().height / 2 - 4;
         g.drawLine(4, startY, width, startY - 15);

         // --
         startY = this.getSize().height / 2;
         g.drawLine(4, startY, width, startY);

         // \
         startY = this.getSize().height / 2 + 4;
         g.drawLine(4, startY, width, startY + 15);

      }
   }

   DrawablePanel m_dwPanel = new DrawablePanel();

   /**
    * **********************************************************************
    * Dynamic Programming Stuffs
    * **********************************************************************
    */
   protected String m_s1 = null;
   protected int m_s1_size = 0;
   protected String m_s2 = null;
   protected int m_s2_size = 0;

   protected String[] m_resLine = new String[3];

   public static final int STRING_ONE = 0; // VERTICAL string
   public static final int STRING_TWO = 1; // HORIZONTAL string

   protected boolean m_tableReady = false;

   protected int m_currentStep = 0;

   protected int m_gapPenaltyOne[];
   protected int m_gapPenaltyTwo[];

   protected static final int GAP_ONE = 0;
   protected static final int GAP_TWO = 1;

   /** In which state is the current calculus: phase calculating the grid */
   protected static final int PHASE_CALC_GRID = 0;
   /** In which state is the current calculus: phase backtracking the pointers */
   protected static final int PHASE_BACKTRACK = 1;

   /** The current calculating phase. At the beginning is calculating the grid */
   public int m_currentPhase = PHASE_CALC_GRID;

   // Linked list of the backtrack cells
   protected LinkedList m_backTrackList = new LinkedList();
   protected CellElement m_backtrackLastSel = null;
   protected int m_backtrackingPolicy = CellElement.
       POINTER_POLICY_COUNTERCLOCKWISE;

   /**
    * **********************************************************************
    * The class
    * **********************************************************************
    */

   /** Constructor */
   public SimpleDP(JPanel contentPane,
                   String defaultString1, String defaultString2) {

      m_mainPane = contentPane;
      m_mainPane.setLayout(new BorderLayout());

      m_defS1 = defaultString1;
      m_defS2 = defaultString2;

      try {
         jbInit();
      }
      catch (Exception e) {
         e.printStackTrace();
      }
   }

   public SimpleDP(JPanel contentPane) {
      this(contentPane, "", "");
   }

   public String getAlgorithmName() {
      return "Simple Dynamic Programming";
   }

   //Component initialization
   protected void jbInit() throws Exception {

      /**
       * ************************* Panels *********************************
       */

      /** The top panel - NORTH */
      JPanel topPanel = new JPanel();
      /** The bottom panel - SOUTH */
      JPanel bottomPanel = new JPanel();
      /** The right panel - EAST */
      JPanel rightPanel = new JPanel();

      /**
       * ********************** CENTER AREA *********************************
       */
      this.setCenter();
      /**
       * ********************** NORTH AREA ********************************
       */
      this.setNorth(topPanel);
      /**
       * ********************** SOUTH AREA ********************************
       */
      this.setSouth(bottomPanel);
      /**
       * ********************** EAST AREA *********************************
       */
      this.setEast(rightPanel);

      /////////////////////////////////////////////////////////////////////////
      /////////////////////////////////////////////////////////////////////////

      // Now adds everything to the main panel
      m_mainPane.add(topPanel, BorderLayout.NORTH);
      m_mainPane.add(m_gridScrollArea, BorderLayout.CENTER);
      m_mainPane.add(rightPanel, BorderLayout.EAST);
      m_mainPane.add(bottomPanel, BorderLayout.SOUTH);

   }

   /**
    * ********************** CENTER AREA *********************************
    */
   protected void setCenter() {
      m_dpTable = new DPTable(10, 6);
      m_dpTable.setCellListener(this);

      m_gridScrollArea.add(m_dpTable);
      // This is in the case of JScrollArea instead of ScrollArea
      //m_gridScrollArea.setDoubleBuffered(true);
      //m_gridScrollArea.getViewport().setView(m_dpTable);
   }

   /**
    * ********************** NORTH AREA *********************************
    */
   protected void setNorth(JPanel topPanel) {

//      JComboBox aliasingComboBox = new JComboBox(aliasingData);
      int i;
      String[] aliasingData = {
          "On", "Off"};
      Choice aliasingComboBox = new Choice();
      for (i = 0; i < aliasingData.length; ++i) {
         aliasingComboBox.add(aliasingData[i]);
      }

//      JComboBox zoomComboBox = new JComboBox(zoomData);
      String[] zoomData = {
          "-2", "-1", "Normal", "+1", "+2", "+3"};
      Choice zoomComboBox = new Choice();
      for (i = 0; i < zoomData.length; ++i) {
         zoomComboBox.add(zoomData[i]);
      }

      /*      Dimension prevDim = zoomComboBox.getPreferredSize();
            prevDim.width += 2;
            zoomComboBox.setPreferredSize(prevDim);
       */
      zoomComboBox.select(2); // Selecting Normal Zoom

      m_infoLabel.setBorder(m_defaultStringBorder);
      m_infoLabel.setEditable(false);

      topPanel.add(new JLabel("AntiAliasing:"));
      topPanel.add(aliasingComboBox);

      topPanel.add(new JLabel("Zoom:"));
      topPanel.add(zoomComboBox);
      topPanel.add(new JLabel("Info:"));
      topPanel.add(m_infoLabel);

      // Listeners
      aliasingComboBox.addItemListener(new AliasingComboListener());
      zoomComboBox.addItemListener(new ZoomComboListener());

   }

   /**
    * ********************** SOUTH AREA *********************************
    */
   protected void setSouth(JPanel bottomPanel) {

      JTextArea bottomLabelArea = new JTextArea("S1:\n\nS2:", 3, 4);
      m_bottomResultArea.setFont(m_resultAreaFont);
      bottomLabelArea.setFont(m_resultAreaFont);

      m_bottomResultArea.setBorder(m_defaultStringBorder);
      bottomLabelArea.setBorder(m_defaultStringBorder);

      m_bottomResultArea.setEditable(false);
      bottomLabelArea.setEditable(false);

      bottomLabelArea.setBackground(UIManager.getColor("Label.background"));

      // Redefining height to be 3 rows: the default was not correct.
      FontMetrics fm = m_mainPane.getFontMetrics(m_resultAreaFont);
      int areasHeight = fm.getHeight() * 3 + fm.getDescent() * 3 - 2;

      m_bottomResultArea.setPreferredSize(new Dimension(400, areasHeight));
      bottomLabelArea.setPreferredSize(new Dimension(bottomLabelArea.
          getPreferredSize().width,
          areasHeight));

      bottomPanel.add(bottomLabelArea);
      bottomPanel.add(m_bottomResultArea);

   }

   /**
    * ********************** EAST AREA *********************************
    */
   protected void setEast(JPanel rightPanel) {

      /**
       * This panel is the only object in "rightPanel". I did this to
       * add some insets on every border.
       */
      JPanel rightInsPanel = new JPanel();
      rightInsPanel.setLayout(new GridBagLayout());

      /** In the "rightInsPanel" panel there is: */
      m_currStatusPanel.setLayout(new GridBagLayout());

      JLabel stringOne_title = new JLabel("String S1:");
      JLabel stringTwo_title = new JLabel("String S2:");

      ///////////////////////////////////////////////////////

      m_StringOne.setText(emptyStringMessage);
      m_StringTwo.setText(emptyStringMessage);
      m_gapOne.setText(emptyGapMessage);
      m_gapTwo.setText(emptyGapMessage);

      m_StringOne.setEditable(false);
      m_StringTwo.setEditable(false);
      m_gapOne.setEditable(false);
      m_gapTwo.setEditable(false);

      m_btnSetGapOne.setEnabled(false);
      m_btnSetGapTwo.setEnabled(false);

      m_StringOne.setBorder(m_defaultStringBorder);
      m_StringTwo.setBorder(m_defaultStringBorder);
      m_gapOne.setBorder(m_defaultStringBorder);
      m_gapTwo.setBorder(m_defaultStringBorder);

      ///////////////////////////////////////////////////////

      m_l1Choiche.setOpaque(true);
      m_l2Choiche.setOpaque(true);
      m_l3Choiche.setOpaque(true);

      ///////////////////////////////////////////////////////

      m_btnBeginning.setEnabled(false);
      m_btnBeginning.setMargin(new Insets(2, 8, 2, 8));

      m_btnNext.setEnabled(false);

      m_btnPrev.setEnabled(false);
      m_btnPrev.setMargin(new Insets(2, 8, 2, 8));

      m_btnEnd.setEnabled(false);
      m_btnEnd.setMargin(new Insets(2, 8, 2, 8));