X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRotatableCanvas.java;h=32c4adc232bae8293503a87ec7102a68e70db549;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=9dc57547e352fa8e220452d12e27df71e216f969;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git

diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 9dc5754..32c4adc 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -1,100 +1,149 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * 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.util.*;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
-import java.util.*;
 
+import jalview.datamodel.*;
+import jalview.math.*;
 
-public class RotatableCanvas extends JPanel implements MouseListener,
-                                                       MouseMotionListener,
-                                                       KeyListener
-                                                       //RubberbandListener,
-                                                       //SequenceSelectionListener
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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);
+  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[] 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;
-//  Controller    controller;
+  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()
+    {
+      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 RotatableCanvas(AlignViewport av,
-                          Vector points, int npoint) {
+  public void setPoints(Vector points, int npoint)
+  {
     this.points = points;
     this.npoint = npoint;
-    this.av = av;
     ToolTipManager.sharedInstance().registerComponent(this);
-    PaintRefresher.Register(this);
-//
+    ToolTipManager.sharedInstance().setInitialDelay(0);
+    ToolTipManager.sharedInstance().setDismissDelay(10000);
+
     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++) {
+    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);
+    //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);
         }
       }
     }
@@ -107,63 +156,59 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
     scale = findScale();
 
-    //    System.out.println("Scale factor = " + scale);
-
     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) {
+  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 {
+        }
+        else
+        {
           axes[i][j] = 1;
         }
       }
     }
   }
 
-  public void 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;
+    max[0] = (float) - 1e30;
+    max[1] = (float) - 1e30;
+    max[2] = (float) - 1e30;
+
+    min[0] = (float) 1e30;
+    min[1] = (float) 1e30;
+    min[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);
 
-    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]) {
+        if (sp.coord[i] >= max[i])
+        {
           max[i] = sp.coord[i];
         }
-        if (sp.coord[i] <= min[i]) {
+
+        if (sp.coord[i] <= min[i])
+        {
           min[i] = sp.coord[i];
         }
       }
@@ -172,7 +217,6 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     //    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]);
@@ -180,186 +224,348 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     maxwidth = width[0];
 
     if (width[1] > width[0])
+    {
       maxwidth = width[1];
+    }
+
     if (width[2] > width[1])
+    {
       maxwidth = width[2];
+    }
 
     //System.out.println("Maxwidth = " + maxwidth);
   }
 
-  public float findScale() {
-    int dim, width, height;
-    if (getWidth() != 0) {
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public float findScale()
+  {
+    int dim;
+    int width;
+    int height;
+
+    if (getWidth() != 0)
+    {
       width = getWidth();
       height = getHeight();
-    } else {
+    }
+    else
+    {
       width = prefsize.width;
       height = prefsize.height;
     }
 
-    if (width < height) {
+    if (width < height)
+    {
       dim = width;
-    } else {
+    }
+    else
+    {
       dim = height;
     }
 
-    return (float)(dim*scalefactor/(2*maxwidth));
+    return (float) ( (dim * scalefactor) / (2 * maxwidth));
   }
 
-  public void findCentre() {
+  /**
+   * 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;
+    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) {
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension getPreferredSize()
+  {
+    if (prefsize != null)
+    {
       return prefsize;
-    } else {
-      return new Dimension(400,400);
+    }
+    else
+    {
+      return new Dimension(400, 400);
     }
   }
 
-  public Dimension getMinimumSize() {
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  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();
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g1)
+  {
 
-      //      System.out.println("New scale = " + scale);
-      img = createImage(getWidth(),getHeight());
-      ig = img.getGraphics();
+    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()))
+      {
+        prefsize.width = getWidth();
+        prefsize.height = getHeight();
+
+        scale = findScale();
 
+        //      System.out.println("New scale = " + scale);
+        img = createImage(getWidth(), getHeight());
+        ig = img.getGraphics();
+      }
 
-      drawBackground(ig,Color.black);
+      drawBackground(ig, bgColour);
       drawScene(ig);
+
       if (drawAxes == true)
       {
         drawAxes(ig);
       }
 
-
-    g.drawImage(img,0,0,this);
+      g.drawImage(img, 0, 0, this);
+    }
   }
 
-  public void drawAxes(Graphics g) {
+  /**
+   * 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));
+
+    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)));
     }
   }
 
-  public void drawBackground(Graphics g, Color col) {
+  /**
+   * 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);
+    g.fillRect(0, 0, prefsize.width, prefsize.height);
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   */
+  public void drawScene(Graphics g1)
+  {
 
-  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];
+    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);
+      if (av.getSequenceColour(sp.sequence) == Color.black)
+      {
+        g.setColor(Color.white);
+      }
       else
-          g.setColor(sp.sequence.getColor());
-
+      {
+        g.setColor(av.getSequenceColour(sp.sequence));
+      }
 
       if (av.getSelectionGroup() != null)
       {
-        if (av.getSelectionGroup().sequences.contains(((SequencePoint)points.elementAt(i)).sequence))
+        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);
-      g.setColor(Color.red);
+      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);
-//    }
+
+    //    //Now the rectangle
+    //    if (rectx2 != -1 && recty2 != -1) {
+    //      g.setColor(Color.white);
+    //
+    //      g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
+    //    }
   }
 
-  public Dimension minimumsize() {
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension minimumsize()
+  {
     return prefsize;
   }
 
-  public Dimension preferredsize() {
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Dimension preferredsize()
+  {
     return prefsize;
   }
 
-  public void keyTyped(KeyEvent evt) { }
-  public void keyReleased(KeyEvent evt) { }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void keyTyped(KeyEvent evt)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void keyReleased(KeyEvent evt)
+  {
+  }
 
-  public void keyPressed(KeyEvent evt) {
-    requestFocus();
-    if (evt.getKeyCode() == KeyEvent.VK_UP) {
-      scalefactor = (float)(scalefactor * 1.1);
+  /**
+   * 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);
+    }
+    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+    {
+      scalefactor = (float) (scalefactor * 0.9);
       scale = findScale();
-    } else if (evt.getKeyChar() == 's') {
+    }
+    else if (evt.getKeyChar() == 's')
+    {
       System.err.println("DEBUG: Rectangle selection"); // log.debug
-      if (rectx2 != -1 && recty2 != -1) {
-        rectSelect(rectx1,recty1,rectx2,recty2);
 
+      if ( (rectx2 != -1) && (recty2 != -1))
+      {
+        rectSelect(rectx1, recty1, rectx2, recty2);
       }
     }
+
     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 mouseClicked(MouseEvent 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 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)
+  {
+  }
 
-  public void mousePressed(MouseEvent evt) {
+  /**
+   * DOCUMENT ME!
+   *
+   * @param evt DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent evt)
+  {
     int x = evt.getX();
     int y = evt.getY();
 
@@ -378,60 +584,82 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     rectx2 = -1;
     recty2 = -1;
 
-    SequenceI found = findPoint(x,y);
+    SequenceI found = findPoint(x, y);
 
     if (found != null)
     {
-      if (av.getSelectionGroup() != null)
+      AlignmentPanel[] aps = getAssociatedPanels();
+
+      for (int a = 0; a < aps.length; a++)
       {
-        av.getSelectionGroup().addOrRemove(found);
-        PaintRefresher.Refresh(this);
+        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);
+        }
       }
-      else
-      {
-          av.setSelectionGroup(new SequenceGroup());
-          av.getSelectionGroup().addOrRemove(found);
-          av.getSelectionGroup().setEndRes(av.alignment.getWidth());
 
-      }
+      PaintRefresher.Refresh(this, av.getSequenceSetId());
     }
+
     repaint();
   }
 
- // private void fireSequenceSelectionEvent(Selection sel) {
- //   controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
+  // 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) {
+    SequenceI found = findPoint(evt.getX(), evt.getY());
+
+    if (found != null)
+    {
+      this.setToolTipText(found.getName());
+    }
+    else
+    {
+      this.setToolTipText(null);
+    }
+  }
+
+  /**
+   * 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 {
+    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');
+      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);
+      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);
+        sp.coord = rotmat.vectorMultiply(sp.coord);
 
         //Now translate back again
         sp.coord[0] += centre[0];
@@ -439,82 +667,103 @@ public class RotatableCanvas extends JPanel implements MouseListener,
         sp.coord[2] += centre[2];
       }
 
-      for (int i=0; i < 3; i++) {
+      for (int i = 0; i < 3; i++)
+      {
         axes[i] = rotmat.vectorMultiply(axes[i]);
       }
+
       omx = mx;
       omy = my;
 
       paint(this.getGraphics());
     }
-
   }
 
-  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);
+  /**
+   * 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 (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2) {
-        if (av != null) {
-          if (!av.getSelectionGroup().sequences.contains(sp.sequence))
+      if ( (tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
+      {
+        if (av != null)
+        {
+          if (!av.getSelectionGroup().getSequences(null).contains(sp.sequence))
           {
-            changedSel = true;
-            av.getSelectionGroup().addSequence(sp.sequence);
+            av.getSelectionGroup().addSequence(sp.sequence, true);
           }
         }
       }
     }
-   // if (changedSel) {
-   //    fireSequenceSelectionEvent(av.getSelection());
-   // }
+
+    // if (changedSel) {
+    //    fireSequenceSelectionEvent(av.getSelection());
+    // }
   }
-  public SequenceI findPoint(int x, int y) {
 
-    int halfwidth = getWidth()/2;
-    int halfheight = getHeight()/2;
+  /**
+   * 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;
-
+    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 ) {
+      if ( (Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
+      {
         found = i;
       }
     }
-    if (found != -1) {
-      return ((SequencePoint)points.elementAt(found)).sequence;
-    } else {
+
+    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();
-
-    // Clear the current selection (instance variable)
-    //if ((rb.getModifiers() & Event.SHIFT_MASK) == 0) {
-    //   clearSelection();
-    //}
-
-    if (rb.getComponent() == this) {
-      Rectangle bounds = evt.getBounds();
-      rectSelect(bounds.x,bounds.y,bounds.x+bounds.width,bounds.y+bounds.height);
+  AlignmentPanel[] getAssociatedPanels()
+  {
+    if (applyToAllViews)
+    {
+      return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
     }
-
-    redrawneeded = true;
-    paint(this.getGraphics());
-
-    return true;
-  }*/
-
+    else
+    {
+      return new AlignmentPanel[]
+          {
+          ap};
+    }
+  }
 }