X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=0eec840886106f86d93a69fdb3a3c9a54d3c4606;hb=d3bf4ae12b72df02dee34c95da750ab38a3816b9;hp=61099c3d4bdb96375afa5714d933ae8a92c388ae;hpb=a41b74d63832baaf00daac0a176118dc751c3b24;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 61099c3..0eec840 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -20,19 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
-import jalview.renderer.AwtRenderPanelI;
-import jalview.schemes.ResidueProperties;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
 import java.awt.AlphaComposite;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -57,13 +44,28 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
-import javax.swing.JColorChooser;
 import javax.swing.JMenuItem;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.Scrollable;
 import javax.swing.ToolTipManager;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
 /**
  * AnnotationPanel displays visible portion of annotation rows below unwrapped
  * alignment
@@ -75,6 +77,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         MouseListener, MouseWheelListener, MouseMotionListener,
         ActionListener, AdjustmentListener, Scrollable, ViewportListenerI
 {
+  enum DragMode
+  {
+    Select, Resize, Undefined
+  };
+
   String HELIX = MessageManager.getString("label.helix");
 
   String SHEET = MessageManager.getString("label.sheet");
@@ -107,7 +114,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   public volatile BufferedImage fadedImage;
 
-  Graphics2D gg;
+  // private Graphics2D gg;
 
   public FontMetrics fm;
 
@@ -118,11 +125,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   // Used For mouse Dragging and resizing graphs
   int graphStretch = -1;
 
-  int graphStretchY = -1;
+  int mouseDragLastX = -1;
 
-  int min; // used by mouseDragged to see if user
+  int mouseDragLastY = -1;
 
-  int max; // used by mouseDragged to see if user
+  DragMode dragMode = DragMode.Undefined;
 
   boolean mouseDragging = false;
 
@@ -143,6 +150,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    */
   public AnnotationPanel(AlignmentPanel ap)
   {
+    setName("AnnotationPanel");
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
     ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -175,11 +183,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     if (e.isShiftDown())
     {
       e.consume();
-      if (e.getWheelRotation() > 0)
+      double wheelRotation = e.getPreciseWheelRotation();
+      if (wheelRotation > 0)
       {
         av.getRanges().scrollRight(true);
       }
-      else
+      else if (wheelRotation < 0)
       {
         av.getRanges().scrollRight(false);
       }
@@ -205,7 +214,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public Dimension getPreferredScrollableViewportSize()
   {
-    return getPreferredSize();
+    Dimension ps = getPreferredSize();
+    return new Dimension(ps.width, adjustForAlignFrame(false, ps.height));
   }
 
   @Override
@@ -285,7 +295,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     if (anot.length < av.getColumnSelection().getMax())
     {
-      Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2];
+      Annotation[] temp = new Annotation[av.getColumnSelection().getMax()
+              + 2];
       System.arraycopy(anot, 0, temp, 0, anot.length);
       anot = temp;
       aa[activeRow].annotations = anot;
@@ -305,7 +316,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     else if (action.equals(LABEL))
     {
       String exMesg = collectAnnotVals(anot, LABEL);
-      String label = JvOptionPane.showInputDialog(this,
+      String label = JvOptionPane.showInputDialog(
               MessageManager.getString("label.enter_label"), exMesg);
 
       if (label == null)
@@ -337,24 +348,31 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     }
     else if (action.equals(COLOUR))
     {
-      Color col = JColorChooser.showDialog(this,
-              MessageManager.getString("label.select_foreground_colour"),
-              Color.black);
-
-      for (int index : av.getColumnSelection().getSelected())
+      final Annotation[] fAnot = anot;
+      String title = MessageManager
+              .getString("label.select_foreground_colour");
+      ColourChooserListener listener = new ColourChooserListener()
       {
-        if (!av.getAlignment().getHiddenColumns().isVisible(index))
+        @Override
+        public void colourSelected(Color c)
         {
-          continue;
-        }
-
-        if (anot[index] == null)
-        {
-          anot[index] = new Annotation("", "", ' ', 0);
-        }
-
-        anot[index].colour = col;
-      }
+          HiddenColumns hiddenColumns = av.getAlignment()
+                  .getHiddenColumns();
+          for (int index : av.getColumnSelection().getSelected())
+          {
+            if (hiddenColumns.isVisible(index))
+            {
+              if (fAnot[index] == null)
+              {
+                fAnot[index] = new Annotation("", "", ' ', 0);
+              }
+              fAnot[index].colour = c;
+            }
+          }
+        };
+      };
+      JalviewColourChooser.showColourChooser(this, title, Color.black,
+              listener);
     }
     else
     // HELIX, SHEET or STEM
@@ -413,8 +431,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
           anot[index] = new Annotation(label, "", type, 0);
         }
 
-        anot[index].secondaryStructure = type != 'S' ? type : label
-                .length() == 0 ? ' ' : label.charAt(0);
+        anot[index].secondaryStructure = type != 'S' ? type
+                : label.length() == 0 ? ' ' : label.charAt(0);
         anot[index].displayCharacter = label;
 
       }
@@ -495,10 +513,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on right mouse pressed on Mac is to show a pop-up menu for the
+   * annotation. Action on left mouse pressed is to find which annotation is
+   * pressed and mark the start of a column selection or graph resize operation.
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mousePressed(MouseEvent evt)
@@ -509,7 +528,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       return;
     }
+    mouseDragLastX = evt.getX();
+    mouseDragLastY = evt.getY();
 
+    /*
+     * add visible annotation heights until we reach the y
+     * position, to find which annotation it is in
+     */
     int height = 0;
     activeRow = -1;
 
@@ -529,11 +554,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         }
         else if (aa[i].graph > 0)
         {
-          // Stretch Graph
+          /*
+           * we have clicked on a resizable graph annotation
+           */
           graphStretch = i;
-          graphStretchY = y;
         }
-
         break;
       }
     }
@@ -599,17 +624,20 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on mouse up is to clear mouse drag data and call mouseReleased on
+   * ScalePanel, to deal with defining the selection group (if any) defined by
+   * the mouse drag
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseReleased(MouseEvent evt)
   {
     graphStretch = -1;
-    graphStretchY = -1;
+    mouseDragLastX = -1;
+    mouseDragLastY = -1;
     mouseDragging = false;
+    dragMode = DragMode.Undefined;
     ap.getScalePanel().mouseReleased(evt);
 
     /*
@@ -632,14 +660,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseEntered(MouseEvent evt)
   {
+    this.mouseDragging = false;
     ap.getScalePanel().mouseEntered(evt);
   }
 
   /**
-   * DOCUMENT ME!
+   * On leaving the panel, calls ScalePanel.mouseExited to deal with scrolling
+   * with column selection on a mouse drag
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseExited(MouseEvent evt)
@@ -656,21 +685,73 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseDragged(MouseEvent evt)
   {
-    if (graphStretch > -1)
+    /*
+     * todo: if dragMode is Undefined:
+     * - set to Select if dx > dy
+     * - set to Resize if dy > dx
+     * - do nothing if dx == dy
+     */
+    final int x = evt.getX();
+    final int y = evt.getY();
+    if (dragMode == DragMode.Undefined)
     {
-      av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
-              - evt.getY();
-      if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+      int dx = Math.abs(x - mouseDragLastX);
+      int dy = Math.abs(y - mouseDragLastY);
+      if (graphStretch == -1 || dx > dy)
+      {
+        /*
+         * mostly horizontal drag, or not a graph annotation
+         */
+        dragMode = DragMode.Select;
+      }
+      else if (dy > dx)
       {
-        av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+        /*
+         * mostly vertical drag
+         */
+        dragMode = DragMode.Resize;
       }
-      graphStretchY = evt.getY();
-      adjustPanelHeight();
-      ap.paintAlignment(true);
     }
-    else
+
+    if (dragMode == DragMode.Undefined)
+      {
+      /*
+       * drag is diagonal - defer deciding whether to
+       * treat as up/down or left/right
+       */
+        return;
+      }
+    try
+    {
+      if (dragMode == DragMode.Resize)
+      {
+        /*
+         * resize graph annotation if mouse was dragged up or down
+         */
+        int deltaY = mouseDragLastY - evt.getY();
+        if (deltaY != 0)
+        {
+          AlignmentAnnotation graphAnnotation = av.getAlignment()
+                  .getAlignmentAnnotation()[graphStretch];
+          int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY);
+          graphAnnotation.graphHeight = newHeight;
+          adjustPanelHeight();
+          setNoFastPaint();
+          ap.paintAlignment(false, false);
+        }
+      }
+      else
+      {
+        /*
+         * for mouse drag left or right, delegate to 
+         * ScalePanel to adjust the column selection
+         */
+        ap.getScalePanel().mouseDragged(evt);
+      }
+    } finally
     {
-      ap.getScalePanel().mouseDragged(evt);
+      mouseDragLastX = x;
+      mouseDragLastY = y;
     }
   }
 
@@ -683,30 +764,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseMoved(MouseEvent evt)
   {
+    int yPos = evt.getY();
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
 
-    if (aa == null)
-    {
-      this.setToolTipText(null);
-      return;
-    }
-
-    int row = -1;
-    int height = 0;
-
-    for (int i = 0; i < aa.length; i++)
-    {
-      if (aa[i].visible)
-      {
-        height += aa[i].height;
-      }
-
-      if (evt.getY() < height)
-      {
-        row = i;
-        break;
-      }
-    }
+    int row = getRowIndex(yPos, aa);
 
     if (row == -1)
     {
@@ -716,83 +777,121 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     int column = (evt.getX() / av.getCharWidth())
             + av.getRanges().getStartRes();
+    column = Math.min(column, av.getRanges().getEndRes());
 
     if (av.hasHiddenColumns())
     {
       column = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(column);
+              .visibleToAbsoluteColumn(column);
     }
 
     AlignmentAnnotation ann = aa[row];
     if (row > -1 && ann.annotations != null
             && column < ann.annotations.length)
     {
-      buildToolTip(ann, column, aa);
-      setStatusMessage(column, ann);
+      String toolTip = buildToolTip(ann, column, aa);
+      setToolTipText(toolTip == null ? null
+              : JvSwingUtils.wrapTooltip(true, toolTip));
+      String msg = getStatusMessage(av.getAlignment(), column, ann);
+      ap.alignFrame.setStatus(msg);
     }
     else
     {
       this.setToolTipText(null);
-      ap.alignFrame.statusBar.setText(" ");
+      ap.alignFrame.setStatus(" ");
     }
   }
 
   /**
-   * Builds a tooltip for the annotation at the current mouse position.
+   * Answers the index in the annotations array of the visible annotation at the
+   * given y position. This is done by adding the heights of visible annotations
+   * until the y position has been exceeded. Answers -1 if no annotations are
+   * visible, or the y position is below all annotations.
+   * 
+   * @param yPos
+   * @param aa
+   * @return
+   */
+  static int getRowIndex(int yPos, AlignmentAnnotation[] aa)
+  {
+    if (aa == null)
+    {
+      return -1;
+    }
+    int row = -1;
+    int height = 0;
+
+    for (int i = 0; i < aa.length; i++)
+    {
+      if (aa[i].visible)
+      {
+        height += aa[i].height;
+      }
+
+      if (height > yPos)
+      {
+        row = i;
+        break;
+      }
+    }
+    return row;
+  }
+
+  /**
+   * Answers a tooltip for the annotation at the current mouse position, not
+   * wrapped in &lt;html&gt; tags (apply if wanted). Answers null if there is no
+   * tooltip to show.
    * 
    * @param ann
    * @param column
    * @param anns
    */
-  void buildToolTip(AlignmentAnnotation ann, int column,
+  static String buildToolTip(AlignmentAnnotation ann, int column,
           AlignmentAnnotation[] anns)
   {
+    String tooltip = null;
     if (ann.graphGroup > -1)
     {
       StringBuilder tip = new StringBuilder(32);
-      tip.append("<html>");
+      boolean first = true;
       for (int i = 0; i < anns.length; i++)
       {
         if (anns[i].graphGroup == ann.graphGroup
                 && anns[i].annotations[column] != null)
         {
+          if (!first)
+          {
+            tip.append("<br>");
+          }
+          first = false;
           tip.append(anns[i].label);
           String description = anns[i].annotations[column].description;
           if (description != null && description.length() > 0)
           {
             tip.append(" ").append(description);
           }
-          tip.append("<br>");
         }
       }
-      if (tip.length() != 6)
-      {
-        tip.setLength(tip.length() - 4);
-        this.setToolTipText(tip.toString() + "</html>");
-      }
+      tooltip = first ? null : tip.toString();
     }
-    else if (ann.annotations[column] != null)
+    else if (column < ann.annotations.length
+            && ann.annotations[column] != null)
     {
-      String description = ann.annotations[column].description;
-      if (description != null && description.length() > 0)
-      {
-        this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
-      }
-    }
-    else
-    {
-      // clear the tooltip.
-      this.setToolTipText(null);
+      tooltip = ann.annotations[column].description;
     }
+
+    return tooltip;
   }
 
   /**
-   * Constructs and displays the status bar message
+   * Constructs and returns the status bar message
    * 
+   * @param al
    * @param column
    * @param ann
    */
-  void setStatusMessage(int column, AlignmentAnnotation ann)
+  static String getStatusMessage(AlignmentI al, int column,
+          AlignmentAnnotation ann)
   {
     /*
      * show alignment column and annotation description if any
@@ -801,7 +900,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     text.append(MessageManager.getString("label.column")).append(" ")
             .append(column + 1);
 
-    if (ann.annotations[column] != null)
+    if (column < ann.annotations.length && ann.annotations[column] != null)
     {
       String description = ann.annotations[column].description;
       if (description != null && description.trim().length() > 0)
@@ -817,29 +916,29 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     SequenceI seqref = ann.sequenceRef;
     if (seqref != null)
     {
-      int seqIndex = av.getAlignment().findIndex(seqref);
+      int seqIndex = al.findIndex(seqref);
       if (seqIndex != -1)
       {
-        text.append(", ")
-                .append(MessageManager.getString("label.sequence"))
+        text.append(", ").append(MessageManager.getString("label.sequence"))
                 .append(" ").append(seqIndex + 1);
         char residue = seqref.getCharAt(column);
         if (!Comparison.isGap(residue))
         {
           text.append(" ");
           String name;
-          if (av.getAlignment().isNucleotide())
+          if (al.isNucleotide())
           {
-            name = ResidueProperties.nucleotideName.get(String
-                    .valueOf(residue));
-            text.append(" Nucleotide: ").append(
-                    name != null ? name : residue);
+            name = ResidueProperties.nucleotideName
+                    .get(String.valueOf(residue));
+            text.append(" Nucleotide: ")
+                    .append(name != null ? name : residue);
           }
           else
           {
-            name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
-                    : ResidueProperties.aa2Triplet.get(String
-                            .valueOf(residue)));
+            name = 'X' == residue ? "X"
+                    : ('*' == residue ? "STOP"
+                            : ResidueProperties.aa2Triplet
+                                    .get(String.valueOf(residue)));
             text.append(" Residue: ").append(name != null ? name : residue);
           }
           int residuePos = seqref.findPosition(column);
@@ -848,7 +947,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
     }
 
-    ap.alignFrame.statusBar.setText(text.toString());
+    return text.toString();
   }
 
   /**
@@ -891,6 +990,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   private volatile boolean imageFresh = false;
 
+  private Rectangle visibleRect = new Rectangle(),
+          clipBounds = new Rectangle();
+
   /**
    * DOCUMENT ME!
    * 
@@ -900,32 +1002,51 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void paintComponent(Graphics g)
   {
+
+    // BH: note that this method is generally recommended to
+    // call super.paintComponent(g). Otherwise, the children of this
+    // component will not be rendered. That is not needed here
+    // because AnnotationPanel does not have any children. It is
+    // just a JPanel contained in a JViewPort.
+
+    computeVisibleRect(visibleRect);
+
     g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
+    g.fillRect(0, 0, visibleRect.width, visibleRect.height);
 
-    if (image != null)
+    ViewportRanges ranges = av.getRanges();
+
+    if (allowFastPaint && image != null)
     {
-      if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
-              || (getVisibleRect().height != g.getClipBounds().height))
+      // BH 2018 optimizing generation of new Rectangle().
+      if (fastPaint
+              || (visibleRect.width != (clipBounds = g
+                      .getClipBounds(clipBounds)).width)
+              || (visibleRect.height != clipBounds.height))
       {
         g.drawImage(image, 0, 0, this);
         fastPaint = false;
         return;
       }
     }
-    imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() + 1)
+
+    imgWidth = (ranges.getEndRes() - ranges.getStartRes() + 1)
             * av.getCharWidth();
+
     if (imgWidth < 1)
     {
+      fastPaint = false;
       return;
     }
+    Graphics2D gg;
     if (image == null || imgWidth != image.getWidth(this)
             || image.getHeight(this) != getHeight())
     {
       try
       {
-        image = new BufferedImage(imgWidth, ap.getAnnotationPanel()
-                .getHeight(), BufferedImage.TYPE_INT_RGB);
+        image = new BufferedImage(imgWidth,
+                ap.getAnnotationPanel().getHeight(),
+                BufferedImage.TYPE_INT_RGB);
       } catch (OutOfMemoryError oom)
       {
         try
@@ -954,19 +1075,19 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       gg.fillRect(0, 0, imgWidth, image.getHeight());
       imageFresh = true;
     }
+    else
+    {
+      gg = (Graphics2D) image.getGraphics();
+
+    }
 
-    drawComponent(gg, av.getRanges().getStartRes(), av.getRanges()
-            .getEndRes() + 1);
+    drawComponent(gg, ranges.getStartRes(), av.getRanges().getEndRes() + 1);
+    gg.dispose();
     imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
 
   /**
-   * set true to enable redraw timing debug output on stderr
-   */
-  private final boolean debugRedraw = false;
-
-  /**
    * non-Thread safe repaint
    * 
    * @param horizontal
@@ -974,7 +1095,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    */
   public void fastPaint(int horizontal)
   {
-    if ((horizontal == 0) || gg == null
+    if ((horizontal == 0) || image == null
             || av.getAlignment().getAlignmentAnnotation() == null
             || av.getAlignment().getAlignmentAnnotation().length < 1
             || av.isCalcInProgress())
@@ -987,10 +1108,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     int er = av.getRanges().getEndRes() + 1;
     int transX = 0;
 
-    long stime = System.currentTimeMillis();
+    if (er == sr + 1)
+    {
+      fastPaint = false;
+      return;
+    }
+
+    Graphics2D gg = (Graphics2D) image.getGraphics();
+
     gg.copyArea(0, 0, imgWidth, getHeight(),
             -horizontal * av.getCharWidth(), 0);
-    long mtime = System.currentTimeMillis();
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
@@ -1007,17 +1134,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     drawComponent(gg, sr, er);
 
     gg.translate(-transX, 0);
-    long dtime = System.currentTimeMillis();
+
+    gg.dispose();
+
     fastPaint = true;
-    repaint();
-    long rtime = System.currentTimeMillis();
-    if (debugRedraw)
-    {
-      System.err.println("Scroll:\t" + horizontal + "\tCopyArea:\t"
-              + (mtime - stime) + "\tDraw component:\t" + (dtime - mtime)
-              + "\tRepaint call:\t" + (rtime - dtime));
-    }
 
+    // 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();
   }
 
   private volatile boolean lastImageGood = false;
@@ -1046,8 +1171,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       // and draw a faded image until the calculation
       // has completed
       if (lastImageGood
-              && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage
-                      .getHeight() != image.getHeight()))
+              && (fadedImage == null || fadedImage.getWidth() != imgWidth
+                      || fadedImage.getHeight() != image.getHeight()))
       {
         // System.err.println("redraw faded image ("+(fadedImage==null ?
         // "null image" : "") + " lastGood="+lastImageGood+")");
@@ -1059,8 +1184,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         fadedG.setColor(Color.white);
         fadedG.fillRect(0, 0, imgWidth, image.getHeight());
 
-        fadedG.setComposite(AlphaComposite.getInstance(
-                AlphaComposite.SRC_OVER, .3f));
+        fadedG.setComposite(
+                AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .3f));
         fadedG.drawImage(image, 0, 0, this);
 
       }
@@ -1101,8 +1226,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       return;
     }
-    lastImageGood = renderer.drawComponent(this, av, g, activeRow,
-            startRes, endRes);
+    lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes,
+            endRes);
     if (!lastImageGood && fadedImage == null)
     {
       fadedImage = oldFaded;
@@ -1129,6 +1254,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   private int[] bounds = new int[2];
 
+  private boolean allowFastPaint;
+
   @Override
   public int[] getVisibleVRange()
   {
@@ -1155,7 +1282,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     ap = null;
     image = null;
     fadedImage = null;
-    gg = null;
+    // gg = null;
     _mwl = null;
 
     /*
@@ -1180,5 +1307,69 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
     }
+    else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ))
+    {
+      fastPaint(((int[]) evt.getNewValue())[0]
+              - ((int[]) evt.getOldValue())[0]);
+    }
+    else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
+    {
+      repaint();
+    }
   }
+
+  /**
+   * computes the visible height of the annotation panel
+   * 
+   * @param adjustPanelHeight
+   *          - when false, just adjust existing height according to other
+   *          windows
+   * @param annotationHeight
+   * @return height to use for the ScrollerPreferredVisibleSize
+   */
+  public int adjustForAlignFrame(boolean adjustPanelHeight,
+          int annotationHeight)
+  {
+    /*
+     * Estimate available height in the AlignFrame for alignment +
+     * annotations. Deduct an estimate for title bar, menu bar, scale panel,
+     * hscroll, status bar, insets. 
+     */
+    int stuff = (ap.getViewName() != null ? 30 : 0)
+            + (Platform.isAMacAndNotJS() ? 120 : 140);
+    int availableHeight = ap.alignFrame.getHeight() - stuff;
+    int rowHeight = av.getCharHeight();
+
+    if (adjustPanelHeight)
+    {
+      int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+
+      /*
+       * If not enough vertical space, maximize annotation height while keeping
+       * at least two rows of alignment visible
+       */
+      if (annotationHeight + alignmentHeight > availableHeight)
+      {
+        annotationHeight = Math.min(annotationHeight,
+                availableHeight - 2 * rowHeight);
+      }
+    }
+    else
+    {
+      // maintain same window layout whilst updating sliders
+      annotationHeight = Math.min(ap.annotationScroller.getSize().height,
+              availableHeight - 2 * rowHeight);
+    }
+    return annotationHeight;
+  }
+  
+  /**
+   * Clears the flag that allows a 'fast paint' on the next repaint, so
+   * requiring a full repaint
+   */
+  public void setNoFastPaint()
+  {
+    allowFastPaint = false;
+  }
+
 }