X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FScalePanel.java;h=8f49c6ce11342e657583914aa1d93fcc9ce09718;hb=961e285f3c6769a3d68152a7784d85f6e814cafb;hp=62cd3f139cfd8d56e6f9f8f97f4f2f08ed362dbc;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 62cd3f1..8f49c6c 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -21,20 +21,29 @@
 package jalview.gui;
 
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Color;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
+import java.awt.Point;
 import java.awt.RenderingHints;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
+import java.util.List;
 
 import javax.swing.JMenuItem;
 import javax.swing.JPanel;
@@ -43,17 +52,14 @@ import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * The panel containing the sequence ruler (when not in wrapped mode), and
+ * supports a range of mouse operations to select, hide or reveal columns.
  */
-public class ScalePanel extends JPanel implements MouseMotionListener,
-        MouseListener
+public class ScalePanel extends JPanel
+        implements MouseMotionListener, MouseListener, ViewportListenerI
 {
   protected int offy = 4;
 
-  /** DOCUMENT ME!! */
   public int width;
 
   protected AlignViewport av;
@@ -62,13 +68,26 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
   boolean stretchingGroup = false;
 
-  int min; // used by mouseDragged to see if user
+  /*
+   * min, max hold the extent of a mouse drag action
+   */
+  int min;
 
-  int max; // used by mouseDragged to see if user
+  int max;
 
   boolean mouseDragging = false;
 
-  // wants to delete columns
+  /*
+   * holds a hidden column range when the mouse is over an adjacent column
+   */
+  int[] reveal;
+
+  /**
+   * Constructor
+   * 
+   * @param av
+   * @param ap
+   */
   public ScalePanel(AlignViewport av, AlignmentPanel ap)
   {
     this.av = av;
@@ -76,6 +95,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     addMouseListener(this);
     addMouseMotionListener(this);
+
+    av.getRanges().addPropertyChangeListener(this);
   }
 
   /**
@@ -84,163 +105,210 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mousePressed(MouseEvent evt)
   {
-    int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int x = (evt.getX() / av.getCharWidth()) + av.getRanges().getStartRes();
     final int res;
 
     if (av.hasHiddenColumns())
     {
-      x = av.getColumnSelection().adjustForHiddenColumns(x);
+      x = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(x);
     }
+    res = Math.min(x, av.getAlignment().getWidth() - 1);
+
+    min = res;
+    max = res;
 
-    if (x >= av.getAlignment().getWidth())
+    if (evt.isPopupTrigger()) // Mac: mousePressed
+    {
+      rightMouseButtonPressed(evt, res);
+    }
+    else if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
     {
-      res = av.getAlignment().getWidth() - 1;
+      /*
+       * defer right-mouse click handling to mouse up on Windows
+       * (where isPopupTrigger() will answer true)
+       * but accept Cmd-click on Mac which passes isRightMouseButton
+       */
+      return;
     }
     else
     {
-      res = x;
+      leftMouseButtonPressed(evt, res);
     }
+  }
 
-    min = res;
-    max = res;
+  /**
+   * Handles right mouse button press. If pressed in a selected column, opens
+   * context menu for 'Hide Columns'. If pressed on a hidden columns marker,
+   * opens context menu for 'Reveal / Reveal All'. Else does nothing.
+   * 
+   * @param evt
+   * @param res
+   */
+  protected void rightMouseButtonPressed(MouseEvent evt, final int res)
+  {
+    JPopupMenu pop = buildPopupMenu(res);
+    if (pop.getSubElements().length > 0)
+    {
+      pop.show(this, evt.getX(), evt.getY());
+    }
+  }
 
-    if (SwingUtilities.isRightMouseButton(evt))
+  /**
+   * Builds a popup menu with 'Hide' or 'Reveal' options, or both, or neither
+   * 
+   * @param res
+   *          column number (0..)
+   * @return
+   */
+  protected JPopupMenu buildPopupMenu(final int res)
+  {
+    JPopupMenu pop = new JPopupMenu();
+
+    /*
+     * logic here depends on 'reveal', set in mouseMoved;
+     * grab the hidden range in case mouseMoved nulls it later
+     */
+    final int[] hiddenRange = reveal;
+    if (hiddenRange != null)
     {
-      JPopupMenu pop = new JPopupMenu();
-      if (reveal != null)
+      JMenuItem item = new JMenuItem(
+              MessageManager.getString("label.reveal"));
+      item.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          av.showColumn(hiddenRange[0]);
+          reveal = null;
+          ap.updateLayout();
+          ap.paintAlignment(true, true);
+          av.sendSelection();
+        }
+      });
+      pop.add(item);
+
+      if (av.getAlignment().getHiddenColumns().hasMultiHiddenColumnRegions())
       {
-        JMenuItem item = new JMenuItem(
-                MessageManager.getString("label.reveal"));
+        item = new JMenuItem(MessageManager.getString("action.reveal_all"));
         item.addActionListener(new ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent e)
           {
-            av.showColumn(reveal[0]);
+            av.showAllHiddenColumns();
             reveal = null;
-            ap.paintAlignment(true);
-            if (ap.overviewPanel != null)
-            {
-              ap.overviewPanel.updateOverviewImage();
-            }
+            ap.updateLayout();
+            ap.paintAlignment(true, true);
+            av.sendSelection();
           }
         });
         pop.add(item);
-
-        if (av.getColumnSelection().hasHiddenColumns())
-        {
-          item = new JMenuItem(
-                  MessageManager.getString("action.reveal_all"));
-          item.addActionListener(new ActionListener()
-          {
-            public void actionPerformed(ActionEvent e)
-            {
-              av.showAllHiddenColumns();
-              reveal = null;
-              ap.paintAlignment(true);
-              if (ap.overviewPanel != null)
-              {
-                ap.overviewPanel.updateOverviewImage();
-              }
-            }
-          });
-          pop.add(item);
-        }
-        pop.show(this, evt.getX(), evt.getY());
       }
-      else if (av.getColumnSelection().contains(res))
+    }
+
+    if (av.getColumnSelection().contains(res))
+    {
+      JMenuItem item = new JMenuItem(
+              MessageManager.getString("label.hide_columns"));
+      item.addActionListener(new ActionListener()
       {
-        JMenuItem item = new JMenuItem(
-                MessageManager.getString("label.hide_columns"));
-        item.addActionListener(new ActionListener()
+        @Override
+        public void actionPerformed(ActionEvent e)
         {
-          public void actionPerformed(ActionEvent e)
+          av.hideColumns(res, res);
+          if (av.getSelectionGroup() != null && av.getSelectionGroup()
+                  .getSize() == av.getAlignment().getHeight())
           {
-            av.hideColumns(res, res);
-            if (av.getSelectionGroup() != null
-                    && av.getSelectionGroup().getSize() == av
-                            .getAlignment().getHeight())
-            {
-              av.setSelectionGroup(null);
-            }
-
-            ap.paintAlignment(true);
-            if (ap.overviewPanel != null)
-            {
-              ap.overviewPanel.updateOverviewImage();
-            }
+            av.setSelectionGroup(null);
           }
-        });
-        pop.add(item);
-        pop.show(this, evt.getX(), evt.getY());
-      }
+
+          ap.updateLayout();
+          ap.paintAlignment(true, true);
+          av.sendSelection();
+        }
+      });
+      pop.add(item);
     }
-    else
-    // LEFT MOUSE TO SELECT
+    return pop;
+  }
+
+  /**
+   * Handles left mouse button press
+   * 
+   * @param evt
+   * @param res
+   */
+  protected void leftMouseButtonPressed(MouseEvent evt, final int res)
+  {
+    /*
+     * Ctrl-click/Cmd-click adds to the selection
+     * Shift-click extends the selection
+     */
+    // TODO Problem: right-click on Windows not reported until mouseReleased?!?
+    if (!Platform.isControlDown(evt) && !evt.isShiftDown())
     {
-      if (!evt.isControlDown() && !evt.isShiftDown())
-      {
-        av.getColumnSelection().clear();
-      }
+      av.getColumnSelection().clear();
+    }
 
-      av.getColumnSelection().addElement(res);
-      SequenceGroup sg = new SequenceGroup();
-      // try to be as quick as possible
-      SequenceI[] iVec = av.getAlignment().getSequencesArray();
-      for (int i = 0; i < iVec.length; i++)
-      {
-        sg.addSequence(iVec[i], false);
-        iVec[i] = null;
-      }
-      iVec = null;
-      sg.setStartRes(res);
-      sg.setEndRes(res);
+    av.getColumnSelection().addElement(res);
+    SequenceGroup sg = new SequenceGroup(av.getAlignment().getSequences());
+    sg.setStartRes(res);
+    sg.setEndRes(res);
 
-      if (evt.isShiftDown())
+    if (evt.isShiftDown())
+    {
+      int min = Math.min(av.getColumnSelection().getMin(), res);
+      int max = Math.max(av.getColumnSelection().getMax(), res);
+      for (int i = min; i < max; i++)
       {
-        int min = Math.min(av.getColumnSelection().getMin(), res);
-        int max = Math.max(av.getColumnSelection().getMax(), res);
-        for (int i = min; i < max; i++)
-        {
-          av.getColumnSelection().addElement(i);
-        }
-        sg.setStartRes(min);
-        sg.setEndRes(max);
+        av.getColumnSelection().addElement(i);
       }
-      av.setSelectionGroup(sg);
+      sg.setStartRes(min);
+      sg.setEndRes(max);
     }
-
-    ap.paintAlignment(false);
+    av.setSelectionGroup(sg);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on mouseUp is to set the limit of the current selection group (if
+   * there is one) and broadcast the selection
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
+    boolean wasDragging = mouseDragging;
     mouseDragging = false;
+    ap.getSeqPanel().stopScrolling();
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-
+    int xCords = Math.max(0, evt.getX()); // prevent negative X coordinates
+    ViewportRanges ranges = av.getRanges();
+    int res = (xCords / av.getCharWidth())
+            + ranges.getStartRes();
+    res = Math.min(res, ranges.getEndRes());
     if (av.hasHiddenColumns())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
-    }
-
-    if (res >= av.getAlignment().getWidth())
-    {
-      res = av.getAlignment().getWidth() - 1;
+      res = av.getAlignment().getHiddenColumns()
+              .visibleToAbsoluteColumn(res);
     }
+    res = Math.max(0, res);
 
     if (!stretchingGroup)
     {
-      ap.paintAlignment(false);
-
+      if (evt.isPopupTrigger()) // Windows: mouseReleased
+      {
+        rightMouseButtonPressed(evt, res);
+      }
+      else
+      {
+        ap.paintAlignment(false, false);
+      }
       return;
     }
 
@@ -256,151 +324,129 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       {
         sg.setStartRes(res);
       }
+      if (wasDragging)
+      {
+        min = Math.min(res, min);
+        max = Math.max(res, max);
+        av.getColumnSelection().stretchGroup(res, sg, min, max);
+      }
     }
     stretchingGroup = false;
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
+    av.isSelectionGroupChanged(true);
+    av.isColSelChanged(true);
     av.sendSelection();
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on dragging the mouse in the scale panel is to expand or shrink the
+   * selection group range (including any hidden columns that it spans). Note
+   * that the selection is only broadcast at the start of the drag (on
+   * mousePressed) and at the end (on mouseReleased), to avoid overload
+   * redrawing of other views.
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     mouseDragging = true;
+    ColumnSelection cs = av.getColumnSelection();
+    HiddenColumns hidden = av.getAlignment().getHiddenColumns();
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-    if (res < 0)
-    {
-      res = 0;
-    }
-
-    if (av.hasHiddenColumns())
-    {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
-    }
-
-    if (res >= av.getAlignment().getWidth())
-    {
-      res = av.getAlignment().getWidth() - 1;
-    }
-
-    if (res < min)
-    {
-      min = res;
-    }
-
-    if (res > max)
-    {
-      max = res;
-    }
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
+    res = Math.max(0, res);
+    res = hidden.visibleToAbsoluteColumn(res);
+    res = Math.min(res, av.getAlignment().getWidth() - 1);
+    min = Math.min(res, min);
+    max = Math.max(res, max);
 
     SequenceGroup sg = av.getSelectionGroup();
-
     if (sg != null)
     {
       stretchingGroup = true;
-
-      if (!av.getColumnSelection().contains(res))
-      {
-        av.getColumnSelection().addElement(res);
-      }
-
-      if (res > sg.getStartRes())
-      {
-        sg.setEndRes(res);
-      }
-      if (res < sg.getStartRes())
-      {
-        sg.setStartRes(res);
-      }
-
-      int col;
-      for (int i = min; i <= max; i++)
-      {
-        col = i; // av.getColumnSelection().adjustForHiddenColumns(i);
-
-        if ((col < sg.getStartRes()) || (col > sg.getEndRes()))
-        {
-          av.getColumnSelection().removeElement(col);
-        }
-        else
-        {
-          av.getColumnSelection().addElement(col);
-        }
-      }
-
-      ap.paintAlignment(false);
+      cs.stretchGroup(res, sg, min, max);
+      ap.paintAlignment(false, false);
     }
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
     if (mouseDragging)
     {
-      ap.getSeqPanel().scrollCanvas(null);
+      ap.getSeqPanel().stopScrolling();
     }
   }
 
+  /**
+   * Action on leaving the panel bounds with mouse drag in progress is to start
+   * scrolling the alignment in the direction of the mouse. To restrict
+   * scrolling to left-right (not up-down), the y-value of the mouse position is
+   * replaced with zero.
+   */
+  @Override
   public void mouseExited(MouseEvent evt)
   {
     if (mouseDragging)
     {
-      ap.getSeqPanel().scrollCanvas(evt);
+      ap.getSeqPanel().startScrolling(new Point(evt.getX(), 0));
     }
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  /**
+   * Creates a tooltip when the mouse is over a hidden columns marker
+   */
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
+    this.setToolTipText(null);
+    reveal = null;
     if (!av.hasHiddenColumns())
     {
       return;
     }
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
-    res = av.getColumnSelection().adjustForHiddenColumns(res);
+    reveal = av.getAlignment().getHiddenColumns()
+            .getRegionWithEdgeAtRes(res);
 
-    reveal = null;
-    if (av.getColumnSelection().getHiddenColumns() != null)
-    {
-      for (int[] region : av.getColumnSelection().getHiddenColumns())
-      {
-        if (res + 1 == region[0] || res - 1 == region[1])
-        {
-          reveal = region;
-          ToolTipManager.sharedInstance().registerComponent(this);
-          this.setToolTipText(MessageManager
-                  .getString("label.reveal_hidden_columns"));
-          break;
-        }
-        else
-        {
-          this.setToolTipText(null);
-        }
-      }
-    }
+    res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(res);
+
+    ToolTipManager.sharedInstance().registerComponent(this);
+    this.setToolTipText(
+            MessageManager.getString("label.reveal_hidden_columns"));
     repaint();
   }
 
-  int[] reveal;
-
   /**
    * DOCUMENT ME!
    * 
    * @param g
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g)
   {
-    drawScale(g, av.getStartRes(), av.getEndRes(), getWidth(), getHeight());
+    super.paintComponent(g);
+
+    /*
+     * shouldn't get called in wrapped mode as the scale above is
+     * drawn instead by SeqCanvas.drawNorthScale
+     */
+    if (!av.getWrapAlignment())
+    {
+      drawScale(g, av.getRanges().getStartRes(), av.getRanges().getEndRes(),
+              getWidth(), getHeight());
+    }
   }
 
   // scalewidth will normally be screenwidth,
@@ -423,21 +469,24 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     // Fill the selected columns
     ColumnSelection cs = av.getColumnSelection();
-    int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
+    HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+    int avCharWidth = av.getCharWidth();
+    int avCharHeight = av.getCharHeight();
 
-    int s;
     if (cs != null)
     {
       gg.setColor(new Color(220, 0, 0));
 
-      for (int i = 0; i < cs.size(); i++)
+      for (int sel : cs.getSelected())
       {
-        int sel = cs.columnAt(i);
+        // TODO: JAL-2001 - provide a fast method to list visible selected in a
+        // given range
+
         if (av.hasHiddenColumns())
         {
-          if (cs.isVisible(sel))
+          if (hidden.isVisible(sel))
           {
-            sel = cs.findColumnPosition(sel);
+            sel = hidden.absoluteToVisibleColumn(sel);
           }
           else
           {
@@ -452,80 +501,89 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
         }
       }
     }
-    // Draw the scale numbers
-    gg.setColor(Color.black);
 
-    int scalestartx = (startx / 10) * 10;
+    int widthx = 1 + endx - startx;
 
     FontMetrics fm = gg.getFontMetrics(av.getFont());
-    int y = avCharHeight - fm.getDescent();
-
-    if ((scalestartx % 10) == 0)
+    int y = avCharHeight;
+    int yOf = fm.getDescent();
+    y -= yOf;
+    if (av.hasHiddenColumns())
     {
-      scalestartx += 5;
-    }
-
-    String string;
-    int maxX = 0;
+      // draw any hidden column markers
+      gg.setColor(Color.blue);
+      int res;
 
-    for (int i = scalestartx; i < endx; i += 5)
-    {
-      if ((i % 10) == 0)
+      if (av.getShowHiddenMarkers())
       {
-        string = String.valueOf(av.getColumnSelection()
-                .adjustForHiddenColumns(i));
-        if ((i - startx - 1) * avCharWidth > maxX)
+        Iterator<Integer> it = hidden.getStartRegionIterator(startx,
+                startx + widthx + 1);
+        while (it.hasNext())
         {
-          gg.drawString(string, (i - startx - 1) * avCharWidth, y);
-          maxX = (i - startx + 1) * avCharWidth + fm.stringWidth(string);
+          res = it.next() - startx;
+
+          gg.fillPolygon(
+                  new int[]
+          { -1 + res * avCharWidth - avCharHeight / 4,
+              -1 + res * avCharWidth + avCharHeight / 4,
+              -1 + res * avCharWidth }, new int[]
+          { y, y, y + 2 * yOf }, 3);
         }
-
-        gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2),
-                y + 2,
-                ((i - startx - 1) * avCharWidth) + (avCharWidth / 2), y
-                        + (fm.getDescent() * 2));
-      }
-      else
-      {
-        gg.drawLine(((i - startx - 1) * avCharWidth) + (avCharWidth / 2), y
-                + fm.getDescent(), ((i - startx - 1) * avCharWidth)
-                + (avCharWidth / 2), y + (fm.getDescent() * 2));
       }
     }
+    // Draw the scale numbers
+    gg.setColor(Color.black);
 
-    if (av.hasHiddenColumns())
+    int maxX = 0;
+    List<ScaleMark> marks = new ScaleRenderer().calculateMarks(av, startx,
+            endx);
+
+    for (ScaleMark mark : marks)
     {
-      gg.setColor(Color.blue);
-      int res;
-      if (av.getShowHiddenMarkers()
-              && av.getColumnSelection().getHiddenColumns() != null)
+      boolean major = mark.major;
+      int mpos = mark.column; // (i - startx - 1)
+      String mstring = mark.text;
+      if (mstring != null)
       {
-        for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
-                .size(); i++)
+        if (mpos * avCharWidth > maxX)
         {
-
-          res = av.getColumnSelection().findHiddenRegionPosition(i)
-                  - startx;
-
-          if (res < 0 || res > endx - scalestartx)
-          {
-            continue;
-          }
-
-          gg.fillPolygon(new int[] { res * avCharWidth - avCharHeight / 4,
-              res * avCharWidth + avCharHeight / 4, res * avCharWidth },
-                  new int[] { y - avCharHeight / 2, y - avCharHeight / 2,
-                      y + 8 }, 3);
-
+          gg.drawString(mstring, mpos * avCharWidth, y);
+          maxX = (mpos + 2) * avCharWidth + fm.stringWidth(mstring);
         }
       }
-
-      if (reveal != null && reveal[0] > startx && reveal[0] < endx)
+      if (major)
+      {
+        gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + 2,
+                (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
+      }
+      else
       {
-        gg.drawString(MessageManager.getString("label.reveal_columns"),
-                reveal[0] * avCharWidth, 0);
+        gg.drawLine((mpos * avCharWidth) + (avCharWidth / 2), y + yOf,
+                (mpos * avCharWidth) + (avCharWidth / 2), y + (yOf * 2));
       }
     }
+  }
 
+  @Override
+  public void propertyChange(PropertyChangeEvent evt)
+  {
+    // Respond to viewport change events (e.g. alignment panel was scrolled)
+    // Both scrolling and resizing change viewport ranges: scrolling changes
+    // both start and end points, but resize only changes end values.
+    // Here we only want to fastpaint on a scroll, with resize using a normal
+    // paint, so scroll events are identified as changes to the horizontal or
+    // vertical start value.
+    if (evt.getPropertyName().equals(ViewportRanges.STARTRES)
+            || evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ)
+            || evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
+    {
+      // scroll event, repaint panel
+    	
+  	// Call repaint on alignment panel so that repaints from other alignment
+    // panel components can be aggregated. Otherwise performance of the overview
+    // window and others may be adversely affected.
+      av.getAlignPanel().repaint();
+    }
   }
+
 }