X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRotatableCanvas.java;h=32c4adc232bae8293503a87ec7102a68e70db549;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=5a963ec117663ac19ff07a286430a17e3db302f7;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 5a963ec..32c4adc 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -18,17 +18,14 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.*;
-
-import jalview.math.*;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-
-import java.util.*;
-
 import javax.swing.*;
 
+import jalview.datamodel.*;
+import jalview.math.*;
 
 /**
  * DOCUMENT ME!
@@ -36,736 +33,737 @@ import javax.swing.*;
  * @author $author$
  * @version $Revision$
  */
-public class RotatableCanvas extends JPanel implements MouseListener,
+public class RotatableCanvas
+    extends JPanel implements MouseListener,
     MouseMotionListener, KeyListener
 {
-    RotatableMatrix idmat = new RotatableMatrix(3, 3);
-    RotatableMatrix objmat = new RotatableMatrix(3, 3);
-    RotatableMatrix rotmat = new RotatableMatrix(3, 3);
-
-    //RubberbandRectangle rubberband;
-    boolean drawAxes = true;
-    int omx = 0;
-    int mx = 0;
-    int omy = 0;
-    int my = 0;
-    Image img;
-    Graphics ig;
-    Dimension prefsize;
-    float[] centre = new float[3];
-    float[] width = new float[3];
-    float[] max = new float[3];
-    float[] min = new float[3];
-    float maxwidth;
-    float scale;
-    int npoint;
-    Vector points;
-    float[][] orig;
-    float[][] axes;
-    int startx;
-    int starty;
-    int lastx;
-    int lasty;
-    int rectx1;
-    int recty1;
-    int rectx2;
-    int recty2;
-    float scalefactor = 1;
-    AlignViewport av;
-    AlignmentPanel ap;
-    boolean showLabels = false;
-    Color bgColour = Color.black;
-    boolean applyToAllViews = false;
-
-    //  Controller    controller;
-    public RotatableCanvas(AlignmentPanel ap)
+  RotatableMatrix idmat = new RotatableMatrix(3, 3);
+  RotatableMatrix objmat = new RotatableMatrix(3, 3);
+  RotatableMatrix rotmat = new RotatableMatrix(3, 3);
+
+  //RubberbandRectangle rubberband;
+  boolean drawAxes = true;
+  int omx = 0;
+  int mx = 0;
+  int omy = 0;
+  int my = 0;
+  Image img;
+  Graphics ig;
+  Dimension prefsize;
+  float[] centre = new float[3];
+  float[] width = new float[3];
+  float[] max = new float[3];
+  float[] min = new float[3];
+  float maxwidth;
+  float scale;
+  int npoint;
+  Vector points;
+  float[][] orig;
+  float[][] axes;
+  int startx;
+  int starty;
+  int lastx;
+  int lasty;
+  int rectx1;
+  int recty1;
+  int rectx2;
+  int recty2;
+  float scalefactor = 1;
+  AlignViewport av;
+  AlignmentPanel ap;
+  boolean showLabels = false;
+  Color bgColour = Color.black;
+  boolean applyToAllViews = false;
+
+  //  Controller    controller;
+  public RotatableCanvas(AlignmentPanel ap)
+  {
+    this.av = ap.av;
+    this.ap = ap;
+
+    addMouseWheelListener(new MouseWheelListener()
     {
-      this.av = ap.av;
-      this.ap = ap;
-
-      addMouseWheelListener(new MouseWheelListener()
+      public void mouseWheelMoved(MouseWheelEvent e)
       {
-        public void mouseWheelMoved(MouseWheelEvent e)
-        {
-          if (e.getWheelRotation() > 0)
-          {
-            scale = (float) (scale * 1.1);
-            repaint();
-          }
-
-          else
-          {
-            scale = (float) (scale * 0.9);
-            repaint();
-          }
-        }
-      });
-
-    }
-
-    public void showLabels(boolean b)
-    {
-      showLabels = b;
-      repaint();
-    }
-
-    public void setPoints(Vector points, int npoint)
-    {
-        this.points = points;
-        this.npoint = npoint;
-        ToolTipManager.sharedInstance().registerComponent(this);
-        ToolTipManager.sharedInstance().setInitialDelay(0);
-        ToolTipManager.sharedInstance().setDismissDelay(10000);
-
-        prefsize = getPreferredSize();
-        orig = new float[npoint][3];
-
-        for (int i = 0; i < npoint; i++)
+        if (e.getWheelRotation() > 0)
         {
-            SequencePoint sp = (SequencePoint) points.elementAt(i);
-
-            for (int j = 0; j < 3; j++)
-            {
-                orig[i][j] = sp.coord[j];
-            }
+          scale = (float) (scale * 1.1);
+          repaint();
         }
 
-        //Initialize the matrices to identity
-        for (int i = 0; i < 3; i++)
+        else
         {
-            for (int j = 0; j < 3; j++)
-            {
-                if (i != j)
-                {
-                    idmat.addElement(i, j, 0);
-                    objmat.addElement(i, j, 0);
-                    rotmat.addElement(i, j, 0);
-                }
-                else
-                {
-                    idmat.addElement(i, j, 0);
-                    objmat.addElement(i, j, 0);
-                    rotmat.addElement(i, j, 0);
-                }
-            }
+          scale = (float) (scale * 0.9);
+          repaint();
         }
+      }
+    });
 
-        axes = new float[3][3];
-        initAxes();
+  }
 
-        findCentre();
-        findWidth();
+  public void showLabels(boolean b)
+  {
+    showLabels = b;
+    repaint();
+  }
 
-        scale = findScale();
+  public void setPoints(Vector points, int npoint)
+  {
+    this.points = points;
+    this.npoint = npoint;
+    ToolTipManager.sharedInstance().registerComponent(this);
+    ToolTipManager.sharedInstance().setInitialDelay(0);
+    ToolTipManager.sharedInstance().setDismissDelay(10000);
 
-        addMouseListener(this);
+    prefsize = getPreferredSize();
+    orig = new float[npoint][3];
 
-        addMouseMotionListener(this);
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
 
+      for (int j = 0; j < 3; j++)
+      {
+        orig[i][j] = sp.coord[j];
+      }
     }
 
-    public void initAxes()
+    //Initialize the matrices to identity
+    for (int i = 0; i < 3; i++)
     {
-        for (int i = 0; i < 3; i++)
+      for (int j = 0; j < 3; j++)
+      {
+        if (i != j)
         {
-            for (int j = 0; j < 3; j++)
-            {
-                if (i != j)
-                {
-                    axes[i][j] = 0;
-                }
-                else
-                {
-                    axes[i][j] = 1;
-                }
-            }
+          idmat.addElement(i, j, 0);
+          objmat.addElement(i, j, 0);
+          rotmat.addElement(i, j, 0);
         }
+        else
+        {
+          idmat.addElement(i, j, 0);
+          objmat.addElement(i, j, 0);
+          rotmat.addElement(i, j, 0);
+        }
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void findWidth()
-    {
-        max = new float[3];
-        min = new float[3];
+    axes = new float[3][3];
+    initAxes();
 
-        max[0] = (float) -1e30;
-        max[1] = (float) -1e30;
-        max[2] = (float) -1e30;
+    findCentre();
+    findWidth();
 
-        min[0] = (float) 1e30;
-        min[1] = (float) 1e30;
-        min[2] = (float) 1e30;
+    scale = findScale();
 
-        for (int i = 0; i < 3; i++)
-        {
-            for (int j = 0; j < npoint; j++)
-            {
-                SequencePoint sp = (SequencePoint) points.elementAt(j);
-
-                if (sp.coord[i] >= max[i])
-                {
-                    max[i] = sp.coord[i];
-                }
-
-                if (sp.coord[i] <= min[i])
-                {
-                    min[i] = sp.coord[i];
-                }
-            }
-        }
+    addMouseListener(this);
 
-        //    System.out.println("xmax " + max[0] + " min " + min[0]);
-        //System.out.println("ymax " + max[1] + " min " + min[1]);
-        //System.out.println("zmax " + max[2] + " min " + min[2]);
-        width[0] = Math.abs(max[0] - min[0]);
-        width[1] = Math.abs(max[1] - min[1]);
-        width[2] = Math.abs(max[2] - min[2]);
+    addMouseMotionListener(this);
 
-        maxwidth = width[0];
+  }
 
-        if (width[1] > width[0])
+  public void initAxes()
+  {
+    for (int i = 0; i < 3; i++)
+    {
+      for (int j = 0; j < 3; j++)
+      {
+        if (i != j)
         {
-            maxwidth = width[1];
+          axes[i][j] = 0;
         }
-
-        if (width[2] > width[1])
+        else
         {
-            maxwidth = width[2];
+          axes[i][j] = 1;
         }
-
-        //System.out.println("Maxwidth = " + maxwidth);
+      }
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void findWidth()
+  {
+    max = new float[3];
+    min = new float[3];
+
+    max[0] = (float) - 1e30;
+    max[1] = (float) - 1e30;
+    max[2] = (float) - 1e30;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public float findScale()
+    min[0] = (float) 1e30;
+    min[1] = (float) 1e30;
+    min[2] = (float) 1e30;
+
+    for (int i = 0; i < 3; i++)
     {
-        int dim;
-        int width;
-        int height;
+      for (int j = 0; j < npoint; j++)
+      {
+        SequencePoint sp = (SequencePoint) points.elementAt(j);
 
-        if (getWidth() != 0)
-        {
-            width = getWidth();
-            height = getHeight();
-        }
-        else
+        if (sp.coord[i] >= max[i])
         {
-            width = prefsize.width;
-            height = prefsize.height;
+          max[i] = sp.coord[i];
         }
 
-        if (width < height)
-        {
-            dim = width;
-        }
-        else
+        if (sp.coord[i] <= min[i])
         {
-            dim = height;
+          min[i] = sp.coord[i];
         }
-
-        return (float) ((dim * scalefactor) / (2 * maxwidth));
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void findCentre()
-    {
-        //Find centre coordinate
-        findWidth();
+    //    System.out.println("xmax " + max[0] + " min " + min[0]);
+    //System.out.println("ymax " + max[1] + " min " + min[1]);
+    //System.out.println("zmax " + max[2] + " min " + min[2]);
+    width[0] = Math.abs(max[0] - min[0]);
+    width[1] = Math.abs(max[1] - min[1]);
+    width[2] = Math.abs(max[2] - min[2]);
 
-        centre[0] = (max[0] + min[0]) / 2;
-        centre[1] = (max[1] + min[1]) / 2;
-        centre[2] = (max[2] + min[2]) / 2;
+    maxwidth = width[0];
 
-        //    System.out.println("Centre x " + centre[0]);
-        //System.out.println("Centre y " + centre[1]);
-        //System.out.println("Centre z " + centre[2]);
+    if (width[1] > width[0])
+    {
+      maxwidth = width[1];
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Dimension getPreferredSize()
+    if (width[2] > width[1])
     {
-        if (prefsize != null)
-        {
-            return prefsize;
-        }
-        else
-        {
-            return new Dimension(400, 400);
-        }
+      maxwidth = width[2];
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Dimension getMinimumSize()
+    //System.out.println("Maxwidth = " + maxwidth);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float findScale()
+  {
+    int dim;
+    int width;
+    int height;
+
+    if (getWidth() != 0)
     {
-        return getPreferredSize();
+      width = getWidth();
+      height = getHeight();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void paintComponent(Graphics g1)
+    else
     {
+      width = prefsize.width;
+      height = prefsize.height;
+    }
 
-      Graphics2D g = (Graphics2D) g1;
+    if (width < height)
+    {
+      dim = width;
+    }
+    else
+    {
+      dim = height;
+    }
 
-      g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                         RenderingHints.VALUE_ANTIALIAS_ON);
-      if(points==null)
-      {
-        g.setFont(new Font("Verdana", Font.PLAIN, 18));
-        g.drawString("Calculating PCA....", 20, getHeight()/2);
-      }
-      else
+    return (float) ( (dim * scalefactor) / (2 * maxwidth));
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void findCentre()
+  {
+    //Find centre coordinate
+    findWidth();
+
+    centre[0] = (max[0] + min[0]) / 2;
+    centre[1] = (max[1] + min[1]) / 2;
+    centre[2] = (max[2] + min[2]) / 2;
+
+    //    System.out.println("Centre x " + centre[0]);
+    //System.out.println("Centre y " + centre[1]);
+    //System.out.println("Centre z " + centre[2]);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension getPreferredSize()
+  {
+    if (prefsize != null)
+    {
+      return prefsize;
+    }
+    else
+    {
+      return new Dimension(400, 400);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension getMinimumSize()
+  {
+    return getPreferredSize();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g1)
+  {
+
+    Graphics2D g = (Graphics2D) g1;
+
+    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                       RenderingHints.VALUE_ANTIALIAS_ON);
+    if (points == null)
+    {
+      g.setFont(new Font("Verdana", Font.PLAIN, 18));
+      g.drawString("Calculating PCA....", 20, getHeight() / 2);
+    }
+    else
+    {
+      //Only create the image at the beginning -
+      if ( (img == null) || (prefsize.width != getWidth()) ||
+          (prefsize.height != getHeight()))
       {
-        //Only create the image at the beginning -
-        if ( (img == null) || (prefsize.width != getWidth()) ||
-            (prefsize.height != getHeight()))
-        {
-          prefsize.width = getWidth();
-          prefsize.height = getHeight();
-
-          scale = findScale();
-
-          //      System.out.println("New scale = " + scale);
-          img = createImage(getWidth(), getHeight());
-          ig = img.getGraphics();
-        }
+        prefsize.width = getWidth();
+        prefsize.height = getHeight();
 
+        scale = findScale();
 
-        drawBackground(ig, bgColour);
-        drawScene(ig);
+        //      System.out.println("New scale = " + scale);
+        img = createImage(getWidth(), getHeight());
+        ig = img.getGraphics();
+      }
 
-        if (drawAxes == true)
-        {
-          drawAxes(ig);
-        }
+      drawBackground(ig, bgColour);
+      drawScene(ig);
 
-        g.drawImage(img, 0, 0, this);
+      if (drawAxes == true)
+      {
+        drawAxes(ig);
       }
-    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void drawAxes(Graphics g)
-    {
+      g.drawImage(img, 0, 0, this);
+    }
+  }
 
-        g.setColor(Color.yellow);
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void drawAxes(Graphics g)
+  {
 
-        for (int i = 0; i < 3; i++)
-        {
-            g.drawLine(getWidth() / 2, getHeight() / 2,
-                (int) ((axes[i][0] * scale * max[0]) + (getWidth() / 2)),
-                (int) ((axes[i][1] * scale * max[1]) + (getHeight() / 2)));
-        }
-    }
+    g.setColor(Color.yellow);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     * @param col DOCUMENT ME!
-     */
-    public void drawBackground(Graphics g, Color col)
+    for (int i = 0; i < 3; i++)
     {
-        g.setColor(col);
-        g.fillRect(0, 0, prefsize.width, prefsize.height);
+      g.drawLine(getWidth() / 2, getHeight() / 2,
+                 (int) ( (axes[i][0] * scale * max[0]) + (getWidth() / 2)),
+                 (int) ( (axes[i][1] * scale * max[1]) + (getHeight() / 2)));
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param g DOCUMENT ME!
-     */
-    public void drawScene(Graphics g1)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   * @param col DOCUMENT ME!
+   */
+  public void drawBackground(Graphics g, Color col)
+  {
+    g.setColor(col);
+    g.fillRect(0, 0, prefsize.width, prefsize.height);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void drawScene(Graphics g1)
+  {
+
+    Graphics2D g = (Graphics2D) g1;
+
+    g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                       RenderingHints.VALUE_ANTIALIAS_ON);
+
+    int halfwidth = getWidth() / 2;
+    int halfheight = getHeight() / 2;
+
+    for (int i = 0; i < npoint; i++)
     {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      int x = (int) ( (float) (sp.coord[0] - centre[0]) * scale) +
+          halfwidth;
+      int y = (int) ( (float) (sp.coord[1] - centre[1]) * scale) +
+          halfheight;
+      float z = sp.coord[1] - centre[2];
+
+      if (av.getSequenceColour(sp.sequence) == Color.black)
+      {
+        g.setColor(Color.white);
+      }
+      else
+      {
+        g.setColor(av.getSequenceColour(sp.sequence));
+      }
 
-      Graphics2D g = (Graphics2D) g1;
-
-      g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                         RenderingHints.VALUE_ANTIALIAS_ON);
-
-
-        int halfwidth = getWidth() / 2;
-        int halfheight = getHeight() / 2;
-
-        for (int i = 0; i < npoint; i++)
+      if (av.getSelectionGroup() != null)
+      {
+        if (av.getSelectionGroup().getSequences(null).contains(
+            ( (SequencePoint) points.elementAt(i)).sequence))
         {
-            SequencePoint sp = (SequencePoint) points.elementAt(i);
-            int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) +
-                halfwidth;
-            int y = (int) ((float) (sp.coord[1] - centre[1]) * scale) +
-                halfheight;
-            float z = sp.coord[1] - centre[2];
-
-            if (av.getSequenceColour(sp.sequence) == Color.black)
-            {
-                g.setColor(Color.white);
-            }
-            else
-            {
-                g.setColor(av.getSequenceColour(sp.sequence));
-            }
-
-            if (av.getSelectionGroup() != null)
-            {
-                if (av.getSelectionGroup().getSequences(null).contains(
-                            ((SequencePoint) points.elementAt(i)).sequence))
-                {
-                    g.setColor(Color.gray);
-                }
-            }
-
-            if (z < 0)
-            {
-                g.setColor(g.getColor().darker());
-            }
-
-            g.fillRect(x - 3, y - 3, 6, 6);
-            if(showLabels)
-            {
-              g.setColor(Color.red);
-              g.drawString( ( (SequencePoint) points.elementAt(i)).sequence.
-                           getName(),
-                           x - 3, y - 4);
-            }
+          g.setColor(Color.gray);
         }
+      }
 
-        //    //Now the rectangle
-        //    if (rectx2 != -1 && recty2 != -1) {
-        //      g.setColor(Color.white);
-        //
-        //      g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
-        //    }
-    }
+      if (z < 0)
+      {
+        g.setColor(g.getColor().darker());
+      }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Dimension minimumsize()
-    {
-        return prefsize;
+      g.fillRect(x - 3, y - 3, 6, 6);
+      if (showLabels)
+      {
+        g.setColor(Color.red);
+        g.drawString( ( (SequencePoint) points.elementAt(i)).sequence.
+                     getName(),
+                     x - 3, y - 4);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Dimension preferredsize()
+    //    //Now the rectangle
+    //    if (rectx2 != -1 && recty2 != -1) {
+    //      g.setColor(Color.white);
+    //
+    //      g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
+    //    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension minimumsize()
+  {
+    return prefsize;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension preferredsize()
+  {
+    return prefsize;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void keyTyped(KeyEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void keyReleased(KeyEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void keyPressed(KeyEvent evt)
+  {
+    if (evt.getKeyCode() == KeyEvent.VK_UP)
     {
-        return prefsize;
+      scalefactor = (float) (scalefactor * 1.1);
+      scale = findScale();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void keyTyped(KeyEvent evt)
+    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
     {
+      scalefactor = (float) (scalefactor * 0.9);
+      scale = findScale();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void keyReleased(KeyEvent evt)
+    else if (evt.getKeyChar() == 's')
     {
+      System.err.println("DEBUG: Rectangle selection"); // log.debug
+
+      if ( (rectx2 != -1) && (recty2 != -1))
+      {
+        rectSelect(rectx1, recty1, rectx2, recty2);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void keyPressed(KeyEvent evt)
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseEntered(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseExited(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent evt)
+  {
+    int x = evt.getX();
+    int y = evt.getY();
+
+    mx = x;
+    my = y;
+
+    omx = mx;
+    omy = my;
+
+    startx = x;
+    starty = y;
+
+    rectx1 = x;
+    recty1 = y;
+
+    rectx2 = -1;
+    recty2 = -1;
+
+    SequenceI found = findPoint(x, y);
+
+    if (found != null)
     {
-        if (evt.getKeyCode() == KeyEvent.VK_UP)
-        {
-            scalefactor = (float) (scalefactor * 1.1);
-            scale = findScale();
-        }
-        else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+      AlignmentPanel[] aps = getAssociatedPanels();
+
+      for (int a = 0; a < aps.length; a++)
+      {
+        if (aps[a].av.getSelectionGroup() != null)
         {
-            scalefactor = (float) (scalefactor * 0.9);
-            scale = findScale();
+          aps[a].av.getSelectionGroup().addOrRemove(found, true);
         }
-        else if (evt.getKeyChar() == 's')
+        else
         {
-            System.err.println("DEBUG: Rectangle selection"); // log.debug
-
-            if ((rectx2 != -1) && (recty2 != -1))
-            {
-                rectSelect(rectx1, recty1, rectx2, recty2);
-            }
+          aps[a].av.setSelectionGroup(new SequenceGroup());
+          aps[a].av.getSelectionGroup().addOrRemove(found, true);
+          aps[a].av.getSelectionGroup().setEndRes(
+              aps[a].av.alignment.getWidth() - 1);
         }
+      }
 
-        repaint();
+      PaintRefresher.Refresh(this, av.getSequenceSetId());
     }
 
+    repaint();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseClicked(MouseEvent evt)
-    {
-    }
+  // private void fireSequenceSelectionEvent(Selection sel) {
+  //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
+  //}
+  public void mouseMoved(MouseEvent evt)
+  {
+    SequenceI found = findPoint(evt.getX(), evt.getY());
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseEntered(MouseEvent evt)
+    if (found != null)
     {
+      this.setToolTipText(found.getName());
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseExited(MouseEvent evt)
+    else
     {
+      this.setToolTipText(null);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseReleased(MouseEvent evt)
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mouseDragged(MouseEvent evt)
+  {
+    mx = evt.getX();
+    my = evt.getY();
+
+    //Check if this is a rectangle drawing drag
+    if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
     {
+      //      rectx2 = evt.getX();
+      //      recty2 = evt.getY();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mousePressed(MouseEvent evt)
+    else
     {
-        int x = evt.getX();
-        int y = evt.getY();
-
-        mx = x;
-        my = y;
+      rotmat.setIdentity();
 
-        omx = mx;
-        omy = my;
+      rotmat.rotate( (float) (my - omy), 'x');
+      rotmat.rotate( (float) (mx - omx), 'y');
 
-        startx = x;
-        starty = y;
+      for (int i = 0; i < npoint; i++)
+      {
+        SequencePoint sp = (SequencePoint) points.elementAt(i);
+        sp.coord[0] -= centre[0];
+        sp.coord[1] -= centre[1];
+        sp.coord[2] -= centre[2];
+
+        //Now apply the rotation matrix
+        sp.coord = rotmat.vectorMultiply(sp.coord);
+
+        //Now translate back again
+        sp.coord[0] += centre[0];
+        sp.coord[1] += centre[1];
+        sp.coord[2] += centre[2];
+      }
 
-        rectx1 = x;
-        recty1 = y;
+      for (int i = 0; i < 3; i++)
+      {
+        axes[i] = rotmat.vectorMultiply(axes[i]);
+      }
 
-        rectx2 = -1;
-        recty2 = -1;
+      omx = mx;
+      omy = my;
 
-        SequenceI found = findPoint(x, y);
+      paint(this.getGraphics());
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param x1 DOCUMENT ME!
+   * @param y1 DOCUMENT ME!
+   * @param x2 DOCUMENT ME!
+   * @param y2 DOCUMENT ME!
+   */
+  public void rectSelect(int x1, int y1, int x2, int y2)
+  {
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      int tmp1 = (int) ( ( (sp.coord[0] - centre[0]) * scale) +
+                        ( (float) getWidth() / 2.0));
+      int tmp2 = (int) ( ( (sp.coord[1] - centre[1]) * scale) +
+                        ( (float) getHeight() / 2.0));
 
-        if (found != null)
+      if ( (tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
+      {
+        if (av != null)
         {
-          AlignmentPanel[] aps = getAssociatedPanels();
-
-          for (int a = 0; a < aps.length; a++)
+          if (!av.getSelectionGroup().getSequences(null).contains(sp.sequence))
           {
-            if (aps[a].av.getSelectionGroup() != null)
-            {
-              aps[a].av.getSelectionGroup().addOrRemove(found, true);
-            }
-            else
-            {
-              aps[a].av.setSelectionGroup(new SequenceGroup());
-              aps[a].av.getSelectionGroup().addOrRemove(found, true);
-              aps[a].av.getSelectionGroup().setEndRes(
-                  aps[a].av.alignment.getWidth() - 1);
-            }
+            av.getSelectionGroup().addSequence(sp.sequence, true);
           }
-
-          PaintRefresher.Refresh(this, av.getSequenceSetId());
         }
-
-        repaint();
+      }
     }
 
-    // private void fireSequenceSelectionEvent(Selection sel) {
-    //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
-    //}
-    public void mouseMoved(MouseEvent evt)
+    // if (changedSel) {
+    //    fireSequenceSelectionEvent(av.getSelection());
+    // }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param x DOCUMENT ME!
+   * @param y DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceI findPoint(int x, int y)
+  {
+    int halfwidth = getWidth() / 2;
+    int halfheight = getHeight() / 2;
+
+    int found = -1;
+
+    for (int i = 0; i < npoint; i++)
     {
-        SequenceI found = findPoint(evt.getX(), evt.getY());
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      int px = (int) ( (float) (sp.coord[0] - centre[0]) * scale) +
+          halfwidth;
+      int py = (int) ( (float) (sp.coord[1] - centre[1]) * scale) +
+          halfheight;
 
-        if (found != null)
-        {
-            this.setToolTipText(found.getName());
-        }
-        else
-        {
-            this.setToolTipText(null);
-        }
+      if ( (Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
+      {
+        found = i;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param evt DOCUMENT ME!
-     */
-    public void mouseDragged(MouseEvent evt)
+    if (found != -1)
     {
-        mx = evt.getX();
-        my = evt.getY();
-
-        //Check if this is a rectangle drawing drag
-        if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
-        {
-            //      rectx2 = evt.getX();
-            //      recty2 = evt.getY();
-        }
-        else
-        {
-            rotmat.setIdentity();
-
-            rotmat.rotate((float) (my - omy), 'x');
-            rotmat.rotate((float) (mx - omx), 'y');
-
-            for (int i = 0; i < npoint; i++)
-            {
-                SequencePoint sp = (SequencePoint) points.elementAt(i);
-                sp.coord[0] -= centre[0];
-                sp.coord[1] -= centre[1];
-                sp.coord[2] -= centre[2];
-
-                //Now apply the rotation matrix
-                sp.coord = rotmat.vectorMultiply(sp.coord);
-
-                //Now translate back again
-                sp.coord[0] += centre[0];
-                sp.coord[1] += centre[1];
-                sp.coord[2] += centre[2];
-            }
-
-            for (int i = 0; i < 3; i++)
-            {
-                axes[i] = rotmat.vectorMultiply(axes[i]);
-            }
-
-            omx = mx;
-            omy = my;
-
-            paint(this.getGraphics());
-        }
+      return ( (SequencePoint) points.elementAt(found)).sequence;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param x1 DOCUMENT ME!
-     * @param y1 DOCUMENT ME!
-     * @param x2 DOCUMENT ME!
-     * @param y2 DOCUMENT ME!
-     */
-    public void rectSelect(int x1, int y1, int x2, int y2)
+    else
     {
-        for (int i = 0; i < npoint; i++)
-        {
-            SequencePoint sp = (SequencePoint) points.elementAt(i);
-            int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale) +
-                ((float) getWidth() / 2.0));
-            int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale) +
-                ((float) getHeight() / 2.0));
-
-            if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
-            {
-                if (av != null)
-                {
-                    if (!av.getSelectionGroup().getSequences(null).contains(sp.sequence))
-                    {
-                        av.getSelectionGroup().addSequence(sp.sequence, true);
-                    }
-                }
-            }
-        }
-
-        // if (changedSel) {
-        //    fireSequenceSelectionEvent(av.getSelection());
-        // }
+      return null;
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param x DOCUMENT ME!
-     * @param y DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceI findPoint(int x, int y)
+  AlignmentPanel[] getAssociatedPanels()
+  {
+    if (applyToAllViews)
     {
-        int halfwidth = getWidth() / 2;
-        int halfheight = getHeight() / 2;
-
-        int found = -1;
-
-        for (int i = 0; i < npoint; i++)
-        {
-            SequencePoint sp = (SequencePoint) points.elementAt(i);
-            int px = (int) ((float) (sp.coord[0] - centre[0]) * scale) +
-                halfwidth;
-            int py = (int) ((float) (sp.coord[1] - centre[1]) * scale) +
-                halfheight;
-
-            if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
-            {
-                found = i;
-            }
-        }
-
-        if (found != -1)
-        {
-            return ((SequencePoint) points.elementAt(found)).sequence;
-        }
-        else
-        {
-            return null;
-        }
+      return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
     }
-
-    AlignmentPanel[] getAssociatedPanels()
+    else
     {
-      if (applyToAllViews)
-      {
-        return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
-      }
-      else
-        return new AlignmentPanel[]
-            { ap };
+      return new AlignmentPanel[]
+          {
+          ap};
     }
+  }
 }