From 7e441a4a9594821ec56539b29cb3b8a13bfa3c65 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Mon, 16 Oct 2017 14:31:39 +0100
Subject: [PATCH] JAL-2775 added repaint clipping

---
 src/jalview/gui/OverviewCanvas.java |   22 ++++++++++++----------
 src/jalview/gui/OverviewPanel.java  |   18 +++++++++++++++++-
 2 files changed, 29 insertions(+), 11 deletions(-)

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 7371eb5..2991889 100644
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -183,6 +183,8 @@ public class OverviewCanvas extends JComponent
   @Override
   public void paintComponent(Graphics g)
   {
+    // super.paintComponent(g);
+
     if (restart)
     {
       if (lastMiniMe == null)
@@ -204,7 +206,8 @@ public class OverviewCanvas extends JComponent
               && ((getWidth() != od.getWidth())
                       || (getHeight() != od.getHeight())))
       {
-        // if there is annotation, scale the alignment and annotation separately
+        // if there is annotation, scale the alignment and annotation
+        // separately
         if (od.getGraphHeight() > 0)
         {
           BufferedImage topImage = lastMiniMe.getSubimage(0, 0,
@@ -235,25 +238,24 @@ public class OverviewCanvas extends JComponent
           od.setHeight(getHeight());
         }
 
-        // scale lastMiniMe to the new size
-        g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
-
         // make sure the box is in the right place
         od.setBoxPosition(av.getAlignment().getHiddenSequences(),
                 av.getAlignment().getHiddenColumns());
       }
-      else // not a resize
-      {
-        // fall back to normal behaviour
-        g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
-      }
+      // fall back to normal behaviour
+      g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
     }
-
+    else
+    {
+      g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
+    }
+    
     // draw the box
     g.setColor(Color.red);
     od.drawBox(g);
   }
 
+
   public void dispose()
   {
     dispose = true;
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 51d7a84..4145fbf 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -327,6 +327,22 @@ public class OverviewPanel extends JPanel
    * changed
    * 
    */
+  private void setBoxPositionOnly()
+  {
+    if (od != null)
+    {
+      int oldX = od.getBoxX();
+      int oldY = od.getBoxY();
+      int oldWidth = od.getBoxWidth();
+      int oldHeight = od.getBoxHeight();
+      od.setBoxPosition(av.getAlignment().getHiddenSequences(),
+              av.getAlignment().getHiddenColumns());
+      repaint(oldX - 1, oldY - 1, oldWidth + 2, oldHeight + 2);
+      repaint(od.getBoxX(), od.getBoxY(), od.getBoxWidth(),
+              od.getBoxHeight());
+    }
+  }
+
   private void setBoxPosition()
   {
     if (od != null)
@@ -340,7 +356,7 @@ public class OverviewPanel extends JPanel
   @Override
   public void propertyChange(PropertyChangeEvent evt)
   {
-    setBoxPosition();
+    setBoxPositionOnly();
   }
 
   /**
-- 
1.7.10.2