X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRotatableCanvas.java;h=da48dd6e017f75d431a2fc802b2f1f48282b3b3a;hb=b6b044f8887234eb5ee0146064b906f5ca2a74a5;hp=6fabd95acb141cec0461cc83daa97a12ce5edc9b;hpb=0615edf610baff76b1675e2f174f22d855fd3fe4;p=jalview.git

diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 6fabd95..da48dd6 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -27,6 +27,7 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequencePoint;
 import jalview.math.RotatableMatrix;
 import jalview.math.RotatableMatrix.Axis;
+import jalview.util.ColorUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -45,7 +46,9 @@ 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 java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
 
 import javax.swing.JPanel;
 import javax.swing.ToolTipManager;
@@ -55,72 +58,81 @@ import javax.swing.ToolTipManager;
  * drawn, and rotated or zoomed with the mouse
  */
 public class RotatableCanvas extends JPanel implements MouseListener,
-        MouseMotionListener, KeyListener, RotatableCanvasI
+        MouseMotionListener, KeyListener, RotatableCanvasI,
+        MouseWheelListener
 {
+  private static final float ZOOM_OUT = 0.9f;
+
+  private static final float ZOOM_IN = 1.1f;
+
+  /*
+   * pixels distance within which tooltip shows sequence name
+   */
+  private static final int NEARBY = 3;
+
+  private static final List<String> AXES = Arrays.asList("x", "y", "z");
+
+  private static final Color AXIS_COLOUR = Color.yellow;
+
   private static final int DIMS = 3;
 
-  // RubberbandRectangle rubberband;
   boolean drawAxes = true;
 
-  int mouseX = 0;
+  int mouseX;
 
-  int mouseY = 0;
+  int mouseY;
 
   Image img;
 
   Graphics ig;
 
-  Dimension prefsize;
-
-  Point centre;
+  Dimension prefSize;
 
-  float[] width = new float[DIMS];
-
-  float[] max = new float[DIMS];
-
-  float[] min = new float[DIMS];
+  /*
+   * the min-max [x, y, z] values of sequence points when the points
+   * were set on the object, or when the view is reset; 
+   * x and y ranges are not recomputed as points are rotated, as this
+   * would make scaling (zoom) unstable, but z ranges are (for correct
+   * graduated colour brightness based on z-coordinate)
+   */
+  float[] seqMin;
 
-  float maxwidth;
+  float[] seqMax;
 
-  float scale;
+  /*
+   * a scale factor used in drawing; when equal to 1, the points span
+   * half the available width or height (whichever is less); increase this
+   * factor to zoom in, decrease it to zoom out
+   */
+  float scaleFactor;
 
   int npoint;
 
-  Vector<SequencePoint> points;
-
-  Point[] orig;
+  /*
+   * sequences and their (x, y, z) PCA dimension values
+   */
+  List<SequencePoint> sequencePoints;
 
+  /*
+   * x, y, z axis end points (PCA dimension values)
+   */
   Point[] axisEndPoints;
 
-  int startx;
-
-  int starty;
-
-  int lastx;
-
-  int lasty;
-
-  int rectx1;
-
-  int recty1;
-
-  int rectx2;
-
-  int recty2;
-
-  float scalefactor = 1;
+  // fields for 'select rectangle' (JAL-1124)
+  // int rectx1;
+  // int recty1;
+  // int rectx2;
+  // int recty2;
 
   AlignmentViewport av;
 
   AlignmentPanel ap;
 
-  boolean showLabels = false;
-
-  Color bgColour = Color.black;
+  boolean showLabels;
 
-  boolean applyToAllViews = false;
+  Color bgColour;
 
-  boolean first = true;
+  boolean applyToAllViews;
 
   /**
    * Constructor
@@ -132,79 +144,46 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     this.av = panel.av;
     this.ap = panel;
     axisEndPoints = new Point[DIMS];
+    showLabels = false;
+    applyToAllViews = false;
+    bgColour = Color.BLACK;
+    resetAxes();
 
-    addMouseWheelListener(new MouseWheelListener()
-    {
-      @Override
-      public void mouseWheelMoved(MouseWheelEvent e)
-      {
-        double wheelRotation = e.getPreciseWheelRotation();
-        if (wheelRotation > 0)
-        {
-          /*
-           * zoom in
-           */
-          scale = (float) (scale * 1.1);
-          repaint();
-        }
-        else if (wheelRotation < 0)
-        {
-          /*
-           * zoom out
-           */
-          scale = (float) (scale * 0.9);
-          repaint();
-        }
-      }
-    });
+    ToolTipManager.sharedInstance().registerComponent(this);
 
+    addMouseListener(this);
+    addMouseMotionListener(this);
+    addMouseWheelListener(this);
   }
 
-  public void showLabels(boolean b)
+  /**
+   * Refreshes the display with labels shown (or not)
+   * 
+   * @param show
+   */
+  public void showLabels(boolean show)
   {
-    showLabels = b;
+    showLabels = show;
     repaint();
   }
 
   @Override
-  public void setPoints(Vector<SequencePoint> points, int npoint)
+  public void setPoints(List<SequencePoint> points, int np)
   {
-    this.points = points;
-    this.npoint = npoint;
-    if (first)
-    {
-      ToolTipManager.sharedInstance().registerComponent(this);
-      ToolTipManager.sharedInstance().setInitialDelay(0);
-      ToolTipManager.sharedInstance().setDismissDelay(10000);
-    }
-    prefsize = getPreferredSize();
-    orig = new Point[npoint];
-
-    for (int i = 0; i < npoint; i++)
-    {
-      SequencePoint sp = points.elementAt(i);
-      orig[i] = sp.coord;
-    }
+    this.sequencePoints = points;
+    this.npoint = np;
+    prefSize = getPreferredSize();
 
-    resetAxes();
-
-    findCentre();
-    findWidth();
+    findWidths();
 
-    scale = findScale();
-    if (first)
-    {
-      addMouseListener(this);
-      addMouseMotionListener(this);
-    }
-    first = false;
+    scaleFactor = 1f;
   }
 
   /**
    * 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()
+  protected void resetAxes()
   {
     axisEndPoints[0] = new Point(1f, 0f, 0f);
     axisEndPoints[1] = new Point(0f, 1f, 0f);
@@ -212,24 +191,23 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   }
 
   /**
-   * 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
+   * Computes and saves the min-max ranges of x/y/z positions of the sequence
+   * points
    */
-  public void findWidth()
+  protected void findWidths()
   {
-    max = new float[DIMS];
-    min = new float[DIMS];
-
-    max[0] = Float.MIN_VALUE;
-    max[1] = Float.MIN_VALUE;
-    max[2] = Float.MIN_VALUE;
-
+    float[] max = new float[DIMS];
+    float[] min = new float[DIMS];
+    
+    max[0] = -Float.MAX_VALUE;
+    max[1] = -Float.MAX_VALUE;
+    max[2] = -Float.MAX_VALUE;
+    
     min[0] = Float.MAX_VALUE;
     min[1] = Float.MAX_VALUE;
     min[2] = Float.MAX_VALUE;
-
-    for (SequencePoint sp : points)
+    
+    for (SequencePoint sp : sequencePoints)
     {
       max[0] = Math.max(max[0], sp.coord.x);
       max[1] = Math.max(max[1], sp.coord.y);
@@ -238,73 +216,22 @@ public class RotatableCanvas extends JPanel implements MouseListener,
       min[1] = Math.min(min[1], sp.coord.y);
       min[2] = Math.min(min[2], sp.coord.z);
     }
-
-    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 = Math.max(width[0], Math.max(width[1], width[2]));
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public float findScale()
-  {
-    int dim;
-    int w;
-    int height;
-
-    if (getWidth() != 0)
-    {
-      w = getWidth();
-      height = getHeight();
-    }
-    else
-    {
-      w = prefsize.width;
-      height = prefsize.height;
-    }
-
-    if (w < height)
-    {
-      dim = w;
-    }
-    else
-    {
-      dim = height;
-    }
-
-    return (dim * scalefactor) / (2 * maxwidth);
+    
+    seqMin = min;
+    seqMax = max;
   }
 
   /**
-   * Computes and saves the position of the centre of the view
-   */
-  public void findCentre()
-  {
-    findWidth();
-
-    float x = (max[0] + min[0]) / 2;
-    float y = (max[1] + min[1]) / 2;
-    float z = (max[2] + min[2]) / 2;
-
-    centre = new Point(x, y, z);
-  }
-
-  /**
-   * DOCUMENT ME!
+   * Answers the preferred size if it has been set, else 400 x 400
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   @Override
   public Dimension getPreferredSize()
   {
-    if (prefsize != null)
+    if (prefSize != null)
     {
-      return prefsize;
+      return prefSize;
     }
     else
     {
@@ -313,9 +240,10 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Answers the preferred size
    * 
-   * @return DOCUMENT ME!
+   * @return
+   * @see RotatableCanvas#getPreferredSize()
    */
   @Override
   public Dimension getMinimumSize()
@@ -324,10 +252,9 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Repaints the panel
    * 
    * @param g
-   *          DOCUMENT ME!
    */
   @Override
   public void paintComponent(Graphics g1)
@@ -337,7 +264,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
     g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
             RenderingHints.VALUE_ANTIALIAS_ON);
-    if (points == null)
+    if (sequencePoints == null)
     {
       g.setFont(new Font("Verdana", Font.PLAIN, 18));
       g.drawString(
@@ -346,16 +273,16 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     }
     else
     {
-      // Only create the image at the beginning -
-      if ((img == null) || (prefsize.width != getWidth())
-              || (prefsize.height != getHeight()))
+      /*
+       * create the image at the beginning or after a resize
+       */
+      boolean resized = prefSize.width != getWidth()
+              || prefSize.height != getHeight();
+      if (img == null || resized)
       {
-        prefsize.width = getWidth();
-        prefsize.height = getHeight();
-
-        scale = findScale();
+        prefSize.width = getWidth();
+        prefSize.height = getHeight();
 
-        // System.out.println("New scale = " + scale);
         img = createImage(getWidth(), getHeight());
         ig = img.getGraphics();
       }
@@ -373,12 +300,15 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   }
 
   /**
-   * Resets the view to initial state (no rotation)
+   * Resets the rotation and choice of axes to the initial state (without change
+   * of scale factor)
    */
   public void resetView()
   {
     img = null;
+    findWidths();
     resetAxes();
+    repaint();
   }
 
   /**
@@ -388,14 +318,20 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    */
   public void drawAxes(Graphics g)
   {
+    g.setColor(AXIS_COLOUR);
 
-    g.setColor(Color.yellow);
+    int midX = getWidth() / 2;
+    int midY = getHeight() / 2;
+    float maxWidth = Math.max(Math.abs(seqMax[0] - seqMin[0]),
+            Math.abs(seqMax[1] - seqMin[1]));
+    int pix = Math.min(getWidth(), getHeight());
+    float scaleBy = pix * scaleFactor / (2f * maxWidth);
 
     for (int i = 0; i < DIMS; i++)
     {
-      g.drawLine(getWidth() / 2, getHeight() / 2,
-              (int) ((axisEndPoints[i].x * scale * max[0]) + (getWidth() / 2)),
-              (int) ((axisEndPoints[i].y * scale * max[1]) + (getHeight() / 2)));
+      g.drawLine(midX, midY,
+              midX + (int) (axisEndPoints[i].x * scaleBy * seqMax[0]),
+              midY + (int) (axisEndPoints[i].y * scaleBy * seqMax[1]));
     }
   }
 
@@ -408,7 +344,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   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);
   }
 
   /**
@@ -426,6 +362,13 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
     g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
             RenderingHints.VALUE_ANTIALIAS_ON);
+    int pix = Math.min(getWidth(), getHeight());
+    float xWidth = Math.abs(seqMax[0] - seqMin[0]);
+    float yWidth = Math.abs(seqMax[1] - seqMin[1]);
+    float maxWidth = Math.max(xWidth, yWidth);
+    float scaleBy = pix * scaleFactor / (2f * maxWidth);
+
+    float[] centre = getCentre();
 
     for (int i = 0; i < npoint; i++)
     {
@@ -433,41 +376,35 @@ public class RotatableCanvas extends JPanel implements MouseListener,
        * sequence point colour as sequence id, but
        * gray if sequence is currently selected
        */
-      SequencePoint sp = points.elementAt(i);
-      SequenceI sequence = sp.getSequence();
-      Color sequenceColour = av.getSequenceColour(sequence);
-      g.setColor(
-              sequenceColour == Color.black ? Color.white : sequenceColour);
-      if (av.getSelectionGroup() != null)
-      {
-        if (av.getSelectionGroup().getSequences(null)
-                .contains(sequence))
-        {
-          g.setColor(Color.gray);
-        }
-      }
-
-      /*
-       * dim sequence points 'at the back'
-       */
-      if (sp.coord.z < centre.z)
-      {
-        g.setColor(g.getColor().darker());
-      }
+      SequencePoint sp = sequencePoints.get(i);
+      Color sequenceColour = getSequencePointColour(sp);
+      g.setColor(sequenceColour);
 
       int halfwidth = getWidth() / 2;
       int halfheight = getHeight() / 2;
-      int x = (int) ((sp.coord.x - centre.x) * scale) + halfwidth;
-      int y = (int) ((sp.coord.y - centre.y) * scale) + halfheight;
+      int x = (int) ((sp.coord.x - centre[0]) * scaleBy) + halfwidth;
+      int y = (int) ((sp.coord.y - centre[1]) * scaleBy) + halfheight;
       g.fillRect(x - 3, y - 3, 6, 6);
 
       if (showLabels)
       {
         g.setColor(Color.red);
-        g.drawString(sequence.getName(), x - 3, y - 4);
+        g.drawString(sp.getSequence().getName(), x - 3, y - 4);
+      }
+    }
+    if (showLabels)
+    {
+      g.setColor(AXIS_COLOUR);
+      int midX = getWidth() / 2;
+      int midY = getHeight() / 2;
+      Iterator<String> axes = AXES.iterator();
+      for (Point p : axisEndPoints)
+      {
+        int x = midX + (int) (p.x * scaleBy * seqMax[0]);
+        int y = midY + (int) (p.y * scaleBy * seqMax[1]);
+        g.drawString(axes.next(), x - 3, y - 4);
       }
     }
-
     // //Now the rectangle
     // if (rectx2 != -1 && recty2 != -1) {
     // g.setColor(Color.white);
@@ -476,6 +413,49 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     // }
   }
 
+  /**
+   * Determines the colour to use when drawing a sequence point. The colour is
+   * taken from the sequence id, with black converted to white, and then
+   * graduated from darker (at the back) to brighter (at the front) based on the
+   * z-axis coordinate of the point.
+   * 
+   * @param sp
+   * @return
+   */
+  protected Color getSequencePointColour(SequencePoint sp)
+  {
+    SequenceI sequence = sp.getSequence();
+    Color sequenceColour = av.getSequenceColour(sequence);
+    if (sequenceColour == Color.black)
+    {
+      sequenceColour = Color.white;
+    }
+    if (av.getSelectionGroup() != null)
+    {
+      if (av.getSelectionGroup().getSequences(null).contains(sequence))
+      {
+        sequenceColour = Color.gray;
+      }
+    }
+
+    /*
+     * graduate brighter for point in front of centre, darker if behind centre
+     */
+    float zCentre = (seqMin[2] + seqMax[2]) / 2f;
+    if (sp.coord.z > zCentre)
+    {
+      sequenceColour = ColorUtils.getGraduatedColour(sp.coord.z, 0,
+              sequenceColour, seqMax[2], sequenceColour.brighter());
+    }
+    else if (sp.coord.z < zCentre)
+    {
+      sequenceColour = ColorUtils.getGraduatedColour(sp.coord.z, seqMin[2],
+              sequenceColour.darker(), 0, sequenceColour);
+    }
+
+    return sequenceColour;
+  }
+
   @Override
   public void keyTyped(KeyEvent evt)
   {
@@ -494,31 +474,40 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   @Override
   public void keyPressed(KeyEvent evt)
   {
-    if (evt.getKeyCode() == KeyEvent.VK_UP)
+    int keyCode = evt.getKeyCode();
+
+    if (keyCode == KeyEvent.VK_UP)
     {
-      scalefactor = (float) (scalefactor * 1.1);
-      scale = findScale();
+      zoom(ZOOM_IN);
     }
-    else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+    else if (keyCode == KeyEvent.VK_DOWN)
     {
-      scalefactor = (float) (scalefactor * 0.9);
-      scale = findScale();
+      zoom(ZOOM_OUT);
     }
     else if (evt.getKeyChar() == 's')
     {
       // 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);
-      }
+      // need to set them in mouseDragged; JAL-1124
+      // if ((rectx2 != -1) && (recty2 != -1))
+      // {
+      // rectSelect(rectx1, recty1, rectx2, recty2);
+      // }
     }
 
     repaint();
   }
 
   @Override
+  public void zoom(float factor)
+  {
+    if (factor > 0f)
+    {
+      scaleFactor *= factor;
+    }
+  }
+
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
@@ -553,14 +542,10 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     mouseX = x;
     mouseY = y;
 
-    startx = x;
-    starty = y;
-
-    rectx1 = x;
-    recty1 = y;
-
-    rectx2 = -1;
-    recty2 = -1;
+    // rectx1 = x;
+    // recty1 = y;
+    // rectx2 = -1;
+    // recty2 = -1;
 
     SequenceI found = findSequenceAtPoint(x, y);
 
@@ -619,6 +604,9 @@ public class RotatableCanvas extends JPanel implements MouseListener,
       return;
     }
 
+    int xDelta = xPos - mouseX;
+    int yDelta = yPos - mouseY;
+
     // Check if this is a rectangle drawing drag
     if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
     {
@@ -627,61 +615,101 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     }
     else
     {
-      /*
-       * get the identity transformation...
-       */
-      RotatableMatrix rotmat = new RotatableMatrix();
+      rotate(xDelta, yDelta);
 
-      /*
-       * 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);
-      }
+      mouseX = xPos;
+      mouseY = yPos;
 
-      /*
-       * rotate around the Y axis for change in X
-       * (mouse movement left/right)
-       */
-      if (xPos != mouseX)
-      {
-        rotmat.rotate(xPos - mouseX, Axis.Y);
-      }
+      // findWidths();
 
-      /*
-       * apply the composite transformation to sequence points
-       */
-      for (int i = 0; i < npoint; i++)
-      {
-        SequencePoint sp = points.elementAt(i);
-        sp.translateBack(centre);
+      repaint();
+    }
+  }
 
-        // Now apply the rotation matrix
-        sp.coord = rotmat.vectorMultiply(sp.coord);
+  @Override
+  public void rotate(float x, float y)
+  {
+    if (x == 0f && y == 0f)
+    {
+      return;
+    }
 
-        // Now translate back again
-        sp.translate(centre);
-      }
+    /*
+     * 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 (y != 0)
+    {
+      rotmat.rotate(y, Axis.X);
+    }
 
-      /*
-       * rotate the x/y/z axis positions
-       */
-      for (int i = 0; i < DIMS; i++)
-      {
-        axisEndPoints[i] = rotmat.vectorMultiply(axisEndPoints[i]);
-      }
+    /*
+     * rotate around the Y axis for change in X
+     * (mouse movement left/right)
+     */
+    if (x != 0)
+    {
+      rotmat.rotate(x, Axis.Y);
+    }
 
-      mouseX = xPos;
-      mouseY = yPos;
+    /*
+     * apply the composite transformation to sequence points;
+     * update z min-max range (affects colour graduation), but not
+     * x or y min-max (as this would affect axis scaling)
+     */
+    float[] centre = getCentre();
+    float zMin = Float.MAX_VALUE;
+    float zMax = -Float.MAX_VALUE;
+
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = sequencePoints.get(i);
+      sp.translate(-centre[0], -centre[1], -centre[2]);
+
+      // Now apply the rotation matrix
+      sp.coord = rotmat.vectorMultiply(sp.coord);
+
+      // Now translate back again
+      sp.translate(centre[0], centre[1], centre[2]);
+      
+      zMin = Math.min(zMin, sp.coord.z);
+      zMax = Math.max(zMax, sp.coord.z);
+    }
 
-      paint(this.getGraphics());
+    seqMin[2] = zMin;
+    seqMax[2] = zMax;
+
+    /*
+     * rotate the x/y/z axis positions
+     */
+    for (int i = 0; i < DIMS; i++)
+    {
+      axisEndPoints[i] = rotmat.vectorMultiply(axisEndPoints[i]);
     }
   }
 
   /**
+   * Answers the x/y/z coordinates that are midway between the maximum and
+   * minimum sequence point values
+   * 
+   * @return
+   */
+  private float[] getCentre()
+  {
+    float xCentre = (seqMin[0] + seqMax[0]) / 2f;
+    float yCentre = (seqMin[1] + seqMax[1]) / 2f;
+    float zCentre = (seqMin[2] + seqMax[2]) / 2f;
+
+    return new float[] { xCentre, yCentre, zCentre };
+  }
+
+  /**
    * 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.
@@ -691,14 +719,16 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * @param x2
    * @param y2
    */
-  public void rectSelect(int x1, int y1, int x2, int y2)
+  protected void rectSelect(int x1, int y1, int x2, int y2)
   {
+    float[] centre = getCentre();
+
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = points.elementAt(i);
-      int tmp1 = (int) (((sp.coord.x - centre.x) * scale)
+      SequencePoint sp = sequencePoints.get(i);
+      int tmp1 = (int) (((sp.coord.x - centre[0]) * scaleFactor)
               + (getWidth() / 2.0));
-      int tmp2 = (int) (((sp.coord.y - centre.y) * scale)
+      int tmp2 = (int) (((sp.coord.y - centre[1]) * scaleFactor)
               + (getHeight() / 2.0));
 
       if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
@@ -725,22 +755,29 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * 
    * @return
    */
-  public SequenceI findSequenceAtPoint(int x, int y)
+  protected SequenceI findSequenceAtPoint(int x, int y)
   {
     int halfwidth = getWidth() / 2;
     int halfheight = getHeight() / 2;
 
     int found = -1;
+    int pix = Math.min(getWidth(), getHeight());
+    float xWidth = Math.abs(seqMax[0] - seqMin[0]);
+    float yWidth = Math.abs(seqMax[1] - seqMin[1]);
+    float maxWidth = Math.max(xWidth, yWidth);
+    float scaleBy = pix * scaleFactor / (2f * maxWidth);
+
+    float[] centre = getCentre();
 
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = points.elementAt(i);
-      int px = (int) ((sp.coord.x - centre.x) * scale)
+      SequencePoint sp = sequencePoints.get(i);
+      int px = (int) ((sp.coord.x - centre[0]) * scaleBy)
               + halfwidth;
-      int py = (int) ((sp.coord.y - centre.y) * scale)
+      int py = (int) ((sp.coord.y - centre[1]) * scaleBy)
               + halfheight;
 
-      if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
+      if ((Math.abs(px - x) < NEARBY) && (Math.abs(py - y) < NEARBY))
       {
         found = i;
         break;
@@ -749,7 +786,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
     if (found != -1)
     {
-      return points.elementAt(found).getSequence();
+      return sequencePoints.get(found).getSequence();
     }
     else
     {
@@ -774,4 +811,65 @@ public class RotatableCanvas extends JPanel implements MouseListener,
       return new AlignmentPanel[] { ap };
     }
   }
+
+  public Color getBackgroundColour()
+  {
+    return bgColour;
+  }
+
+  /**
+   * Zooms in or out in response to mouse wheel movement
+   */
+  @Override
+  public void mouseWheelMoved(MouseWheelEvent e)
+  {
+    double wheelRotation = e.getPreciseWheelRotation();
+    if (wheelRotation > 0)
+    {
+      zoom(ZOOM_IN);
+      repaint();
+    }
+    else if (wheelRotation < 0)
+    {
+      zoom(ZOOM_OUT);
+      repaint();
+    }
+  }
+
+  /**
+   * Answers the sequence point minimum [x, y, z] values. Note these are derived
+   * when sequence points are set, but x and y values are not updated on
+   * rotation (because this would result in changes to scaling).
+   * 
+   * @return
+   */
+  public float[] getSeqMin()
+  {
+    return seqMin;
+  }
+
+  /**
+   * Answers the sequence point maximum [x, y, z] values. Note these are derived
+   * when sequence points are set, but x and y values are not updated on
+   * rotation (because this would result in changes to scaling).
+   * 
+   * @return
+   */
+  public float[] getSeqMax()
+  {
+    return seqMax;
+  }
+
+  /**
+   * Sets the minimum and maximum [x, y, z] positions for sequence points. For
+   * use when restoring a saved PCA from state data.
+   * 
+   * @param min
+   * @param max
+   */
+  public void setSeqMinMax(float[] min, float[] max)
+  {
+    seqMin = min;
+    seqMax = max;
+  }
 }