X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FRotatableCanvas.java;h=617180f7ca209f19fe219d3381293e7e6b9d15e5;hb=2cc3a62e1ae63428db854af668e963f1b23af553;hp=91eb991451cb390306c5a11746a960071fdb0632;hpb=64238c060481db2d63a9f6d3e013bcca1693eba5;p=jalview.git

diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 91eb991..617180f 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -1,58 +1,70 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview 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 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
-import java.util.*;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
 import jalview.api.RotatableCanvasI;
-import jalview.datamodel.*;
-import jalview.math.*;
+import jalview.datamodel.Point;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
+import jalview.math.RotatableMatrix;
+import jalview.math.RotatableMatrix.Axis;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.RenderingHints;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.Vector;
+
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * Models a Panel on which a set of points, and optionally x/y/z axes, can be
+ * drawn, and rotated or zoomed with the mouse
  */
 public class RotatableCanvas extends JPanel implements MouseListener,
         MouseMotionListener, KeyListener, RotatableCanvasI
 {
-  RotatableMatrix idmat = new RotatableMatrix(3, 3);
-
-  RotatableMatrix objmat = new RotatableMatrix(3, 3);
-
-  RotatableMatrix rotmat = new RotatableMatrix(3, 3);
+  private static final int DIMS = 3;
 
   // RubberbandRectangle rubberband;
   boolean drawAxes = true;
 
-  int omx = 0;
-
-  int mx = 0;
+  int mouseX = 0;
 
-  int omy = 0;
-
-  int my = 0;
+  int mouseY = 0;
 
   Image img;
 
@@ -60,13 +72,13 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
   Dimension prefsize;
 
-  float[] centre = new float[3];
+  Point centre;
 
-  float[] width = new float[3];
+  float[] width = new float[DIMS];
 
-  float[] max = new float[3];
+  float[] max = new float[DIMS];
 
-  float[] min = new float[3];
+  float[] min = new float[DIMS];
 
   float maxwidth;
 
@@ -74,11 +86,11 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
   int npoint;
 
-  Vector points;
+  Vector<SequencePoint> points;
 
-  float[][] orig;
+  Point[] orig;
 
-  float[][] axes;
+  Point[] axisEndPoints;
 
   int startx;
 
@@ -98,7 +110,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
   float scalefactor = 1;
 
-  AlignViewport av;
+  AlignmentViewport av;
 
   AlignmentPanel ap;
 
@@ -108,24 +120,38 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
   boolean applyToAllViews = false;
 
-  // Controller controller;
-  public RotatableCanvas(AlignmentPanel ap)
+  boolean first = true;
+
+  /**
+   * Constructor
+   * 
+   * @param panel
+   */
+  public RotatableCanvas(AlignmentPanel panel)
   {
-    this.av = ap.av;
-    this.ap = ap;
+    this.av = panel.av;
+    this.ap = panel;
+    axisEndPoints = new Point[DIMS];
 
     addMouseWheelListener(new MouseWheelListener()
     {
+      @Override
       public void mouseWheelMoved(MouseWheelEvent e)
       {
-        if (e.getWheelRotation() > 0)
+        double wheelRotation = e.getPreciseWheelRotation();
+        if (wheelRotation > 0)
         {
+          /*
+           * zoom in
+           */
           scale = (float) (scale * 1.1);
           repaint();
         }
-
-        else
+        else if (wheelRotation < 0)
         {
+          /*
+           * zoom out
+           */
           scale = (float) (scale * 0.9);
           repaint();
         }
@@ -140,9 +166,8 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     repaint();
   }
 
-  boolean first = true;
-
-  public void setPoints(Vector points, int npoint)
+  @Override
+  public void setPoints(Vector<SequencePoint> points, int npoint)
   {
     this.points = points;
     this.npoint = npoint;
@@ -153,40 +178,15 @@ public class RotatableCanvas extends JPanel implements MouseListener,
       ToolTipManager.sharedInstance().setDismissDelay(10000);
     }
     prefsize = getPreferredSize();
-    orig = new float[npoint][3];
+    orig = new Point[npoint];
 
     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];
-      }
+      SequencePoint sp = points.elementAt(i);
+      orig[i] = sp.coord;
     }
 
-    // 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);
-        }
-      }
-    }
-
-    axes = new float[3][3];
-    initAxes();
+    resetAxes();
 
     findCentre();
     findWidth();
@@ -194,86 +194,56 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     scale = findScale();
     if (first)
     {
-
       addMouseListener(this);
-
       addMouseMotionListener(this);
     }
     first = false;
   }
 
-  public void initAxes()
+  /**
+   * Resets axes to the initial state: x-axis to the right, y-axis up, z-axis to
+   * back (so obscured in a 2-D display)
+   */
+  public void resetAxes()
   {
-    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;
-        }
-      }
-    }
+    axisEndPoints[0] = new Point(1f, 0f, 0f);
+    axisEndPoints[1] = new Point(0f, 1f, 0f);
+    axisEndPoints[2] = new Point(0f, 0f, 1f);
   }
 
   /**
-   * DOCUMENT ME!
+   * Computes and saves the maximum and minimum (x, y, z) positions of any
+   * sequence point, and also the min-max range (width) for each dimension, and
+   * the maximum width for all dimensions
    */
   public void findWidth()
   {
-    max = new float[3];
-    min = new float[3];
+    max = new float[DIMS];
+    min = new float[DIMS];
 
-    max[0] = (float) -1e30;
-    max[1] = (float) -1e30;
-    max[2] = (float) -1e30;
+    max[0] = Float.MIN_VALUE;
+    max[1] = Float.MIN_VALUE;
+    max[2] = Float.MIN_VALUE;
 
-    min[0] = (float) 1e30;
-    min[1] = (float) 1e30;
-    min[2] = (float) 1e30;
+    min[0] = Float.MAX_VALUE;
+    min[1] = Float.MAX_VALUE;
+    min[2] = Float.MAX_VALUE;
 
-    for (int i = 0; i < 3; i++)
+    for (SequencePoint sp : points)
     {
-      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];
-        }
-      }
+      max[0] = Math.max(max[0], sp.coord.x);
+      max[1] = Math.max(max[1], sp.coord.y);
+      max[2] = Math.max(max[2], sp.coord.z);
+      min[0] = Math.min(min[0], sp.coord.x);
+      min[1] = Math.min(min[1], sp.coord.y);
+      min[2] = Math.min(min[2], sp.coord.z);
     }
 
-    // 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]);
 
-    maxwidth = width[0];
-
-    if (width[1] > width[0])
-    {
-      maxwidth = width[1];
-    }
-
-    if (width[2] > width[1])
-    {
-      maxwidth = width[2];
-    }
-
-    // System.out.println("Maxwidth = " + maxwidth);
+    maxwidth = Math.max(width[0], Math.max(width[1], width[2]));
   }
 
   /**
@@ -284,47 +254,44 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   public float findScale()
   {
     int dim;
-    int width;
+    int w;
     int height;
 
     if (getWidth() != 0)
     {
-      width = getWidth();
+      w = getWidth();
       height = getHeight();
     }
     else
     {
-      width = prefsize.width;
+      w = prefsize.width;
       height = prefsize.height;
     }
 
-    if (width < height)
+    if (w < height)
     {
-      dim = width;
+      dim = w;
     }
     else
     {
       dim = height;
     }
 
-    return (float) ((dim * scalefactor) / (2 * maxwidth));
+    return (dim * scalefactor) / (2 * maxwidth);
   }
 
   /**
-   * DOCUMENT ME!
+   * Computes and saves the position of the centre of the view
    */
   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;
+    float x = (max[0] + min[0]) / 2;
+    float y = (max[1] + min[1]) / 2;
+    float z = (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]);
+    centre = new Point(x, y, z);
   }
 
   /**
@@ -332,6 +299,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public Dimension getPreferredSize()
   {
     if (prefsize != null)
@@ -349,6 +317,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public Dimension getMinimumSize()
   {
     return getPreferredSize();
@@ -360,6 +329,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * @param g
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g1)
   {
 
@@ -370,7 +340,9 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     if (points == null)
     {
       g.setFont(new Font("Verdana", Font.PLAIN, 18));
-      g.drawString(MessageManager.getString("label.calculating_pca")+ "....", 20, getHeight() / 2);
+      g.drawString(
+              MessageManager.getString("label.calculating_pca") + "....",
+              20, getHeight() / 2);
     }
     else
     {
@@ -391,7 +363,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
       drawBackground(ig, bgColour);
       drawScene(ig);
 
-      if (drawAxes == true)
+      if (drawAxes)
       {
         drawAxes(ig);
       }
@@ -401,31 +373,37 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Resets the view to initial state (no rotation)
+   */
+  public void resetView()
+  {
+    img = null;
+    resetAxes();
+  }
+
+  /**
+   * Draws lines for the x, y, z axes
    * 
    * @param g
-   *          DOCUMENT ME!
    */
   public void drawAxes(Graphics g)
   {
 
     g.setColor(Color.yellow);
 
-    for (int i = 0; i < 3; i++)
+    for (int i = 0; i < DIMS; 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.drawLine(getWidth() / 2, getHeight() / 2,
+              (int) ((axisEndPoints[i].x * scale * max[0]) + (getWidth() / 2)),
+              (int) ((axisEndPoints[i].y * scale * max[1]) + (getHeight() / 2)));
     }
   }
 
   /**
-   * DOCUMENT ME!
+   * Fills the background with the specified colour
    * 
    * @param g
-   *          DOCUMENT ME!
    * @param col
-   *          DOCUMENT ME!
    */
   public void drawBackground(Graphics g, Color col)
   {
@@ -434,14 +412,16 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Draws points (6x6 squares) for the sequences of the PCA, and labels
+   * (sequence names) if configured to do so. The sequence points colours are
+   * taken from the sequence ids in the alignment (converting black to white).
+   * Sequences 'at the back' (z-coordinate is negative) are shaded slightly
+   * darker to help give a 3-D sensation.
    * 
    * @param g
-   *          DOCUMENT ME!
    */
   public void drawScene(Graphics g1)
   {
-
     Graphics2D g = (Graphics2D) g1;
 
     g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
@@ -452,25 +432,26 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
     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)
+      SequencePoint sp = points.elementAt(i);
+      int x = (int) ((sp.coord.x - centre.x) * scale) + halfwidth;
+      int y = (int) ((sp.coord.y - centre.y) * scale)
               + halfheight;
-      float z = sp.coord[1] - centre[2];
+      float z = sp.coord.y - centre.z; // todo sp.coord.z JAL-2963
 
-      if (av.getSequenceColour(sp.sequence) == Color.black)
+      SequenceI sequence = sp.getSequence();
+      if (av.getSequenceColour(sequence) == Color.black)
       {
         g.setColor(Color.white);
       }
       else
       {
-        g.setColor(av.getSequenceColour(sp.sequence));
+        g.setColor(av.getSequenceColour(sequence));
       }
 
       if (av.getSelectionGroup() != null)
       {
         if (av.getSelectionGroup().getSequences(null)
-                .contains(((SequencePoint) points.elementAt(i)).sequence))
+                .contains(sequence))
         {
           g.setColor(Color.gray);
         }
@@ -485,9 +466,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
       if (showLabels)
       {
         g.setColor(Color.red);
-        g.drawString(
-                ((SequencePoint) points.elementAt(i)).sequence.getName(),
-                x - 3, y - 4);
+        g.drawString(sequence.getName(), x - 3, y - 4);
       }
     }
 
@@ -499,52 +478,22 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     // }
   }
 
-  /**
-   * 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!
-   */
+  @Override
   public void keyTyped(KeyEvent evt)
   {
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
+  @Override
   public void keyReleased(KeyEvent evt)
   {
   }
 
   /**
-   * DOCUMENT ME!
+   * Responds to up or down arrow key by zooming in or out, respectively
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
+  @Override
   public void keyPressed(KeyEvent evt)
   {
     if (evt.getKeyCode() == KeyEvent.VK_UP)
@@ -559,8 +508,9 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     }
     else if (evt.getKeyChar() == 's')
     {
-      System.err.println("DEBUG: Rectangle selection"); // log.debug
-
+      // Cache.log.warn("DEBUG: Rectangle selection");
+      // todo not yet enabled as rectx2, recty2 are always -1
+      // need to set them in mouseDragged
       if ((rectx2 != -1) && (recty2 != -1))
       {
         rectSelect(rectx1, recty1, rectx2, recty2);
@@ -570,62 +520,40 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     repaint();
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
+   * If the mouse press is at (within 2 pixels of) a sequence point, toggles
+   * (adds or removes) the corresponding sequence as a member of the viewport
+   * selection group. This supports configuring a group in the alignment by
+   * clicking on points in the PCA display.
    */
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     int x = evt.getX();
     int y = evt.getY();
 
-    mx = x;
-    my = y;
-
-    omx = mx;
-    omy = my;
+    mouseX = x;
+    mouseY = y;
 
     startx = x;
     starty = y;
@@ -636,7 +564,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     rectx2 = -1;
     recty2 = -1;
 
-    SequenceI found = findPoint(x, y);
+    SequenceI found = findSequenceAtPoint(x, y);
 
     if (found != null)
     {
@@ -652,8 +580,8 @@ public class RotatableCanvas extends JPanel implements MouseListener,
         {
           aps[a].av.setSelectionGroup(new SequenceGroup());
           aps[a].av.getSelectionGroup().addOrRemove(found, true);
-          aps[a].av.getSelectionGroup().setEndRes(
-                  aps[a].av.getAlignment().getWidth() - 1);
+          aps[a].av.getSelectionGroup()
+                  .setEndRes(aps[a].av.getAlignment().getWidth() - 1);
         }
       }
       PaintRefresher.Refresh(this, av.getSequenceSetId());
@@ -664,34 +592,34 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     repaint();
   }
 
-  // private void fireSequenceSelectionEvent(Selection sel) {
-  // controller.handleSequenceSelectionEvent(new
-  // SequenceSelectionEvent(this,sel));
-  // }
+  /**
+   * Sets the tooltip to the name of the sequence within 2 pixels of the mouse
+   * position, or clears the tooltip if none found
+   */
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
-    SequenceI found = findPoint(evt.getX(), evt.getY());
+    SequenceI found = findSequenceAtPoint(evt.getX(), evt.getY());
 
-    if (found != null)
-    {
-      this.setToolTipText(found.getName());
-    }
-    else
-    {
-      this.setToolTipText(null);
-    }
+    this.setToolTipText(found == null ? null : found.getName());
   }
 
   /**
-   * DOCUMENT ME!
+   * Action handler for a mouse drag. Rotates the display around the X axis (for
+   * up/down mouse movement) and/or the Y axis (for left/right mouse movement).
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
-    mx = evt.getX();
-    my = evt.getY();
+    int xPos = evt.getX();
+    int yPos = evt.getY();
+
+    if (xPos == mouseX && yPos == mouseY)
+    {
+      return;
+    }
 
     // Check if this is a rectangle drawing drag
     if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
@@ -701,88 +629,105 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     }
     else
     {
-      rotmat.setIdentity();
+      /*
+       * get the identity transformation...
+       */
+      RotatableMatrix rotmat = new RotatableMatrix();
+
+      /*
+       * rotate around the X axis for change in Y
+       * (mouse movement up/down); note we are equating a
+       * number of pixels with degrees of rotation here!
+       */
+      if (yPos != mouseY)
+      {
+        rotmat.rotate(yPos - mouseY, Axis.X);
+      }
 
-      rotmat.rotate((float) (my - omy), 'x');
-      rotmat.rotate((float) (mx - omx), 'y');
+      /*
+       * rotate around the Y axis for change in X
+       * (mouse movement left/right)
+       */
+      if (xPos != mouseX)
+      {
+        rotmat.rotate(xPos - mouseX, Axis.Y);
+      }
 
+      /*
+       * apply the composite transformation to sequence points
+       */
       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];
+        SequencePoint sp = points.elementAt(i);
+        sp.translateBack(centre);
 
         // 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];
+        sp.translate(centre);
       }
 
-      for (int i = 0; i < 3; i++)
+      /*
+       * rotate the x/y/z axis positions
+       */
+      for (int i = 0; i < DIMS; i++)
       {
-        axes[i] = rotmat.vectorMultiply(axes[i]);
+        axisEndPoints[i] = rotmat.vectorMultiply(axisEndPoints[i]);
       }
 
-      omx = mx;
-      omy = my;
+      mouseX = xPos;
+      mouseY = yPos;
 
       paint(this.getGraphics());
     }
   }
 
   /**
-   * DOCUMENT ME!
+   * Adds any sequences whose displayed points are within the given rectangle to
+   * the viewport's current selection. Intended for key 's' after dragging to
+   * select a region of the PCA.
    * 
    * @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));
+      SequencePoint sp = points.elementAt(i);
+      int tmp1 = (int) (((sp.coord.x - centre.x) * scale)
+              + (getWidth() / 2.0));
+      int tmp2 = (int) (((sp.coord.y - centre.y) * scale)
+              + (getHeight() / 2.0));
 
       if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
       {
         if (av != null)
         {
+          SequenceI sequence = sp.getSequence();
           if (!av.getSelectionGroup().getSequences(null)
-                  .contains(sp.sequence))
+                  .contains(sequence))
           {
-            av.getSelectionGroup().addSequence(sp.sequence, true);
+            av.getSelectionGroup().addSequence(sequence, true);
           }
         }
       }
     }
-
-    // if (changedSel) {
-    // fireSequenceSelectionEvent(av.getSelection());
-    // }
   }
 
   /**
-   * DOCUMENT ME!
+   * Answers the first sequence found whose point on the display is within 2
+   * pixels of the given coordinates, or null if none is found
    * 
    * @param x
-   *          DOCUMENT ME!
    * @param y
-   *          DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
-  public SequenceI findPoint(int x, int y)
+  public SequenceI findSequenceAtPoint(int x, int y)
   {
     int halfwidth = getWidth() / 2;
     int halfheight = getHeight() / 2;
@@ -791,21 +736,22 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int px = (int) ((float) (sp.coord[0] - centre[0]) * scale)
+      SequencePoint sp = points.elementAt(i);
+      int px = (int) ((sp.coord.x - centre.x) * scale)
               + halfwidth;
-      int py = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+      int py = (int) ((sp.coord.y - centre.y) * scale)
               + halfheight;
 
       if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
       {
         found = i;
+        break;
       }
     }
 
     if (found != -1)
     {
-      return ((SequencePoint) points.elementAt(found)).sequence;
+      return points.elementAt(found).getSequence();
     }
     else
     {
@@ -813,6 +759,12 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     }
   }
 
+  /**
+   * Answers the panel the PCA is associated with (all panels for this alignment
+   * if 'associate with all panels' is selected).
+   * 
+   * @return
+   */
   AlignmentPanel[] getAssociatedPanels()
   {
     if (applyToAllViews)
@@ -821,24 +773,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     }
     else
     {
-      return new AlignmentPanel[]
-      { ap };
+      return new AlignmentPanel[] { ap };
     }
   }
-
-  /**
-   * 
-   * @return x,y,z positions of point s (index into points) under current
-   *         transform.
-   */
-  public double[] getPointPosition(int s)
-  {
-    double pts[] = new double[3];
-    float[] p = ((SequencePoint) points.elementAt(s)).coord;
-    pts[0] = p[0];
-    pts[1] = p[1];
-    pts[2] = p[2];
-    return pts;
-  }
-
 }