X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRotatableCanvas.java;h=724b9fbdda3c4f2c2659037fab782b860772cd55;hb=424a0faf266f649090f17dc65246cdfb4111217e;hp=b4af354b239dafe28f1b5a60f75e17df481a8374;hpb=577f505f54fe343e89f581461e780ea8308c20ec;p=jalview.git

diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index b4af354..724b9fb 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -1,520 +1,760 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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
+ * 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
-import jalview.math.*;
 import jalview.datamodel.*;
+
+import jalview.math.*;
+
 import jalview.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-import javax.swing.*;
+
 import java.util.*;
 
+import javax.swing.*;
+
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class RotatableCanvas extends JPanel implements MouseListener,
-                                                       MouseMotionListener,
-                                                       KeyListener
-                                                       //RubberbandListener,
-                                                       //SequenceSelectionListener
+    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;
+    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;
+    boolean showLabels = false;
+    Color bgColour = Color.black;
+
+    //  Controller    controller;
+    public RotatableCanvas(AlignViewport av)
+    {
+      this.av = av;
+    }
 
-  Vector points;
-  float[][] orig;
-  float[][] axes;
+    public void showLabels(boolean b)
+    {
+      showLabels = b;
+      repaint();
+    }
 
-  int startx;
-  int starty;
+    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);
+        PaintRefresher.Register(this, av.alignment);
+
+        prefsize = getPreferredSize();
+        orig = new float[npoint][3];
+
+        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];
+            }
+        }
 
-  int lastx;
-  int lasty;
+        //Initialize the matrices to identity
+        for (int i = 0; i < 3; i++)
+        {
+            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);
+                }
+            }
+        }
 
-  int rectx1;
-  int recty1;
-  int rectx2;
-  int recty2;
+        axes = new float[3][3];
+        initAxes();
 
-  float scalefactor = 1;
+        findCentre();
+        findWidth();
 
-  AlignViewport av;
-//  Controller    controller;
+        scale = findScale();
 
+        addMouseListener(this);
+        addKeyListener(this);
 
-  public RotatableCanvas(AlignViewport av,
-                          Vector points, int npoint) {
-    this.points = points;
-    this.npoint = npoint;
-    this.av = av;
-    ToolTipManager.sharedInstance().registerComponent(this);
-    PaintRefresher.Register(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];
-      }
     }
-    //Initialize the matrices to identity
-
-    for (int i = 0; i < 3; i++) {
-      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);
+
+    public void initAxes()
+    {
+        for (int i = 0; i < 3; i++)
+        {
+            for (int j = 0; j < 3; j++)
+            {
+                if (i != j)
+                {
+                    axes[i][j] = 0;
+                }
+                else
+                {
+                    axes[i][j] = 1;
+                }
+            }
         }
-      }
     }
 
-    axes = new float[3][3];
-    initAxes();
-
-    findCentre();
-    findWidth();
+    /**
+     * 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;
+
+        min[0] = (float) 1e30;
+        min[1] = (float) 1e30;
+        min[2] = (float) 1e30;
+
+        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];
+                }
+            }
+        }
 
-    scale = findScale();
+        //    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]);
 
-    //    System.out.println("Scale factor = " + scale);
+        maxwidth = width[0];
 
-    addMouseListener(this);
-    addKeyListener(this);
-   // if (getParent() != null) {
-   //   getParent().addKeyListener(this);
-    //}
-    addMouseMotionListener(this);
-
-    // Add rubberband
- //   rubberband  = new RubberbandRectangle(this);
-  //  rubberband.setActive(true);
- //   rubberband.addListener(this);
-  }
-
- /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {
-    redrawneeded = true;
-    repaint();
-    return true;
-  }
-
-  public void removeNotify() {
-    controller.removeListener(this);
-    super.removeNotify();
-  }*/
-
-  public void initAxes() {
-    for (int i = 0; i < 3; i++) {
-      for (int j=0; j < 3; j++) {
-        if (i != j) {
-          axes[i][j] = 0;
-        } else {
-          axes[i][j] = 1;
+        if (width[1] > width[0])
+        {
+            maxwidth = width[1];
         }
-      }
-    }
-  }
-
-  public void findWidth() {
-    max = new float[3];
-    min = new float[3];
 
-    max[0] = (float)-1e30;
-    max[1] = (float)-1e30;
-    max[2] = (float)-1e30;
+        if (width[2] > width[1])
+        {
+            maxwidth = width[2];
+        }
 
-    min[0] = (float)1e30;
-    min[1] = (float)1e30;
-    min[2] = (float)1e30;
+        //System.out.println("Maxwidth = " + maxwidth);
+    }
 
-    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];
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public float findScale()
+    {
+        int dim;
+        int width;
+        int height;
+
+        if (getWidth() != 0)
+        {
+            width = getWidth();
+            height = getHeight();
         }
-        if (sp.coord[i] <= min[i]) {
-          min[i] = sp.coord[i];
+        else
+        {
+            width = prefsize.width;
+            height = prefsize.height;
         }
-      }
-    }
-
-    //    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]);
+        if (width < height)
+        {
+            dim = width;
+        }
+        else
+        {
+            dim = height;
+        }
 
-    maxwidth = width[0];
+        return (float) ((dim * scalefactor) / (2 * maxwidth));
+    }
 
-    if (width[1] > width[0])
-      maxwidth = width[1];
-    if (width[2] > width[1])
-      maxwidth = width[2];
+    /**
+     * DOCUMENT ME!
+     */
+    public void findCentre()
+    {
+        //Find centre coordinate
+        findWidth();
 
-    //System.out.println("Maxwidth = " + maxwidth);
-  }
+        centre[0] = (max[0] + min[0]) / 2;
+        centre[1] = (max[1] + min[1]) / 2;
+        centre[2] = (max[2] + min[2]) / 2;
 
-  public float findScale() {
-    int dim, width, height;
-    if (getWidth() != 0) {
-      width = getWidth();
-      height = getHeight();
-    } else {
-      width = prefsize.width;
-      height = prefsize.height;
+        //    System.out.println("Centre x " + centre[0]);
+        //System.out.println("Centre y " + centre[1]);
+        //System.out.println("Centre z " + centre[2]);
     }
 
-    if (width < height) {
-      dim = width;
-    } else {
-      dim = height;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Dimension getPreferredSize()
+    {
+        if (prefsize != null)
+        {
+            return prefsize;
+        }
+        else
+        {
+            return new Dimension(400, 400);
+        }
     }
 
-    return (float)(dim*scalefactor/(2*maxwidth));
-  }
-
-  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]);
-  }
-
-  public Dimension getPreferredSize() {
-    if (prefsize != null) {
-      return prefsize;
-    } else {
-      return new Dimension(400,400);
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Dimension getMinimumSize()
+    {
+        return getPreferredSize();
     }
-  }
-
-  public Dimension getMinimumSize() {
-    return getPreferredSize();
-  }
-
-  public void paintComponent(Graphics g) {
-    //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();
 
-    }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void paintComponent(Graphics g1)
+    {
 
+      Graphics2D g = (Graphics2D) g1;
 
-      drawBackground(ig,Color.black);
-      drawScene(ig);
-      if (drawAxes == true)
+      g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                         RenderingHints.VALUE_ANTIALIAS_ON);
+      if(points==null)
       {
-        drawAxes(ig);
+        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()))
+        {
+          prefsize.width = getWidth();
+          prefsize.height = getHeight();
+
+          scale = findScale();
+
+          //      System.out.println("New scale = " + scale);
+          img = createImage(getWidth(), getHeight());
+          ig = img.getGraphics();
+        }
 
 
-    g.drawImage(img,0,0,this);
-  }
+        drawBackground(ig, bgColour);
+        drawScene(ig);
 
-  public void drawAxes(Graphics g) {
+        if (drawAxes == true)
+        {
+          drawAxes(ig);
+        }
 
-    g.setColor(Color.yellow);
-    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.drawImage(img, 0, 0, this);
+      }
     }
-  }
-
-  public void drawBackground(Graphics g, Color col) {
-    g.setColor(col);
-    g.fillRect(0,0,prefsize.width,prefsize.height);
-  }
-
-
-  public void drawScene(Graphics g) {
-    boolean darker = false;
-
-    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];
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param g DOCUMENT ME!
+     */
+    public void drawAxes(Graphics g)
+    {
 
+        g.setColor(Color.yellow);
 
+        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)));
+        }
+    }
 
-      if (sp.sequence.getColor() == Color.black)
-          g.setColor(Color.white);
-      else
-          g.setColor(sp.sequence.getColor());
+    /**
+     * 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)
+    {
 
-      if (av.getSelectionGroup() != null)
-      {
-        if (av.getSelectionGroup().sequences.contains(((SequencePoint)points.elementAt(i)).sequence))
-          g.setColor(Color.gray);
-      }
-      if (z < 0)
-        g.setColor(g.getColor().darker());
+      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 (sp.sequence.getColor() == Color.black)
+            {
+                g.setColor(Color.white);
+            }
+            else
+            {
+                g.setColor(sp.sequence.getColor());
+            }
+
+            if (av.getSelectionGroup() != null)
+            {
+                if (av.getSelectionGroup().sequences.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);
+            }
+        }
 
+        //    //Now the rectangle
+        //    if (rectx2 != -1 && recty2 != -1) {
+        //      g.setColor(Color.white);
+        //
+        //      g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
+        //    }
+    }
 
-      g.fillRect(x-3,y-3,6,6);
-      g.setColor(Color.red);
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Dimension minimumsize()
+    {
+        return prefsize;
     }
-//    //Now the rectangle
-//    if (rectx2 != -1 && recty2 != -1) {
-//      g.setColor(Color.white);
-//
-//      g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
-//    }
-  }
-
-  public Dimension minimumsize() {
-    return prefsize;
-  }
-
-  public Dimension preferredsize() {
-    return prefsize;
-  }
-
-  public void keyTyped(KeyEvent evt) { }
-  public void keyReleased(KeyEvent evt) { }
-
-  public void keyPressed(KeyEvent evt) {
-    requestFocus();
-    if (evt.getKeyCode() == KeyEvent.VK_UP) {
-      scalefactor = (float)(scalefactor * 1.1);
-      scale = findScale();
-    } else if (evt.getKeyCode() == KeyEvent.VK_DOWN) {
-      scalefactor = (float)(scalefactor * 0.9);
-      scale = findScale();
-    } else if (evt.getKeyChar() == 's') {
-      System.out.println("Rectangle selection");
-      if (rectx2 != -1 && recty2 != -1) {
-        rectSelect(rectx1,recty1,rectx2,recty2);
 
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Dimension preferredsize()
+    {
+        return prefsize;
     }
-    repaint();
-  }
-
-  public void printPoints() {
-    for (int i=0; i < npoint; i++) {
-      SequencePoint sp = (SequencePoint)points.elementAt(i);
-      Format.print(System.out,"%5d ", i);
-      for (int j=0; j < 3;j++) {
-        Format.print(System.out,"%13.3f  ",sp.coord[j]);
-      }
-      System.out.println();
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void keyTyped(KeyEvent evt)
+    {
     }
-  }
 
-  public void mouseClicked(MouseEvent evt) { }
-  public void mouseEntered(MouseEvent evt) { }
-  public void mouseExited(MouseEvent evt) { }
-  public void mouseReleased(MouseEvent evt) { }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void keyReleased(KeyEvent evt)
+    {
+    }
 
-  public void mousePressed(MouseEvent evt) {
-    int x = evt.getX();
-    int y = evt.getY();
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void keyPressed(KeyEvent evt)
+    {
+        if (evt.getKeyCode() == KeyEvent.VK_UP)
+        {
+            scalefactor = (float) (scalefactor * 1.1);
+            scale = findScale();
+        }
+        else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+        {
+            scalefactor = (float) (scalefactor * 0.9);
+            scale = findScale();
+        }
+        else if (evt.getKeyChar() == 's')
+        {
+            System.err.println("DEBUG: Rectangle selection"); // log.debug
+
+            if ((rectx2 != -1) && (recty2 != -1))
+            {
+                rectSelect(rectx1, recty1, rectx2, recty2);
+            }
+        }
 
-    mx = x;
-    my = y;
+        repaint();
+    }
 
-    omx = mx;
-    omy = my;
 
-    startx = x;
-    starty = y;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseClicked(MouseEvent evt)
+    {
+    }
 
-    rectx1 = x;
-    recty1 = y;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseEntered(MouseEvent evt)
+    {
+    }
 
-    rectx2 = -1;
-    recty2 = -1;
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseExited(MouseEvent evt)
+    {
+    }
 
-    SequenceI found = findPoint(x,y);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mouseReleased(MouseEvent evt)
+    {
+    }
 
-    if (found != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param evt DOCUMENT ME!
+     */
+    public void mousePressed(MouseEvent evt)
     {
-      if (av.getSelectionGroup() != null)
-      {
-        av.getSelectionGroup().addOrRemove(found);
-        PaintRefresher.Refresh(this);
-      }
-      else
-      {
-          av.setSelectionGroup(new SequenceGroup());
-          av.getSelectionGroup().addOrRemove(found);
-          av.getSelectionGroup().setEndRes(av.alignment.getWidth());
+        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 (av.getSelectionGroup() != null)
+            {
+                av.getSelectionGroup().addOrRemove(found, true);
+                PaintRefresher.Refresh(this, av.alignment);
+            }
+            else
+            {
+                av.setSelectionGroup(new SequenceGroup());
+                av.getSelectionGroup().addOrRemove(found, true);
+                av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);
+            }
+        }
 
-      }
+        repaint();
     }
-    repaint();
-  }
-
- // private void fireSequenceSelectionEvent(Selection sel) {
- //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
-  //}
-
-  public void mouseMoved(MouseEvent evt)
-  {
-   SequenceI found = findPoint(evt.getX(), evt.getY());
-   if (found != null)
-     this.setToolTipText(found.getName());
-   else
-     this.setToolTipText(null);
- }
-
-  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();
-    } 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;
+    // private void fireSequenceSelectionEvent(Selection sel) {
+    //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
+    //}
+    public void mouseMoved(MouseEvent evt)
+    {
+        SequenceI found = findPoint(evt.getX(), evt.getY());
 
-      paint(this.getGraphics());
+        if (found != null)
+        {
+            this.setToolTipText(found.getName());
+        }
+        else
+        {
+            this.setToolTipText(null);
+        }
     }
 
-  }
-
-  public void rectSelect(int x1, int y1, int x2, int y2) {
-    boolean changedSel = false;
-    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().sequences.contains(sp.sequence))
-          {
-            changedSel = true;
-            av.getSelectionGroup().addSequence(sp.sequence);
-          }
+    /**
+     * 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();
+        }
+        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());
         }
-      }
     }
-   // if (changedSel) {
-   //    fireSequenceSelectionEvent(av.getSelection());
-   // }
-  }
-  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++) {
+    /**
+     * 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)
+    {
+        boolean changedSel = false;
+
+        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().sequences.contains(sp.sequence))
+                    {
+                        changedSel = true;
+                        av.getSelectionGroup().addSequence(sp.sequence, true);
+                    }
+                }
+            }
+        }
 
-      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 (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++)
+        {
+            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 (Math.abs(px-x)<3 && Math.abs(py - y) < 3 ) {
-        found = i;
-      }
-    }
-    if (found != -1) {
-      return ((SequencePoint)points.elementAt(found)).sequence;
-    } else {
-      return null;
+        if (found != -1)
+        {
+            return ((SequencePoint) points.elementAt(found)).sequence;
+        }
+        else
+        {
+            return null;
+        }
     }
-  }
-/*  public boolean handleRubberbandEvent(RubberbandEvent evt) {
-    System.out.println("Rubberband handler called in RotatableCanvas with " +
-                       evt.getBounds());
 
-    Rubberband rb = (Rubberband)evt.getSource();
+    /*  public boolean handleRubberbandEvent(RubberbandEvent evt) {
+        System.out.println("Rubberband handler called in RotatableCanvas with " +
+                           evt.getBounds());
 
-    // Clear the current selection (instance variable)
-    //if ((rb.getModifiers() & Event.SHIFT_MASK) == 0) {
-    //   clearSelection();
-    //}
+        Rubberband rb = (Rubberband)evt.getSource();
 
-    if (rb.getComponent() == this) {
-      Rectangle bounds = evt.getBounds();
-      rectSelect(bounds.x,bounds.y,bounds.x+bounds.width,bounds.y+bounds.height);
-    }
+        // Clear the current selection (instance variable)
+        //if ((rb.getModifiers() & Event.SHIFT_MASK) == 0) {
+        //   clearSelection();
+        //}
 
-    redrawneeded = true;
-    paint(this.getGraphics());
+        if (rb.getComponent() == this) {
+          Rectangle bounds = evt.getBounds();
+     rectSelect(bounds.x,bounds.y,bounds.x+bounds.width,bounds.y+bounds.height);
+        }
 
-    return true;
-  }*/
+        redrawneeded = true;
+        paint(this.getGraphics());
 
+        return true;
+      }*/
 }