From 63059e2e3f0f36f329c2c1fea59362cdd4391c72 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 7 Jun 2017 09:14:37 +0100
Subject: [PATCH] JAL-2591 Overview window update interrupts

---
 src/jalview/gui/OverviewCanvas.java        |    8 +++++++-
 src/jalview/renderer/OverviewRenderer.java |   29 ++++++++++++++++++++++++++--
 2 files changed, 34 insertions(+), 3 deletions(-)

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 6f9fbbf..27f9c3f 100644
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -53,6 +53,8 @@ public class OverviewCanvas extends JComponent
 
   private OverviewDimensions od;
 
+  private OverviewRenderer or = null;
+
   private AlignViewportI av;
 
   public OverviewCanvas(OverviewDimensions overviewDims,
@@ -89,6 +91,10 @@ public class OverviewCanvas extends JComponent
       if (updaterunning)
       {
         restart = true;
+        if (or != null)
+        {
+          or.setRedraw(true);
+        }
       }
       else
       {
@@ -120,7 +126,7 @@ public class OverviewCanvas extends JComponent
 
     setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
-    OverviewRenderer or = new OverviewRenderer(sr, fr, od);
+    or = new OverviewRenderer(sr, fr, od);
     miniMe = or.draw(od.getRows(av.getAlignment()),
             od.getColumns(av.getAlignment()));
 
diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java
index 9291ca6..913c870 100644
--- a/src/jalview/renderer/OverviewRenderer.java
+++ b/src/jalview/renderer/OverviewRenderer.java
@@ -48,12 +48,14 @@ public class OverviewRenderer
   // raw number of pixels to allocate to each row
   private float pixelsPerSeq;
 
+  // flag to indicate whether to halt drawing
+  private boolean redraw = false;
+
   public OverviewRenderer(jalview.api.SequenceRenderer seqRenderer,
           FeatureRenderer fr, OverviewDimensions od)
-  // FeatureColourFinder colfinder, OverviewDimensions od)
   {
     sr = seqRenderer;
-    finder = new FeatureColourFinder(fr); // colfinder;
+    finder = new FeatureColourFinder(fr);
 
     pixelsPerCol = od.getPixelsPerCol();
     pixelsPerSeq = od.getPixelsPerSeq();
@@ -76,8 +78,14 @@ public class OverviewRenderer
     int rgbcolor = Color.white.getRGB();
     int seqIndex = 0;
     int pixelRow = 0;
+
     for (int alignmentRow : rows)
     {
+      if (redraw)
+      {
+        break;
+      }
+
       // get details of this alignment row
       boolean hidden = rows.isHidden(alignmentRow);
       SequenceI seq = rows.getSequence(alignmentRow);
@@ -90,6 +98,11 @@ public class OverviewRenderer
       int pixelCol = 0;
       for (int alignmentCol : cols)
       {
+        if (redraw)
+        {
+          break;
+        }
+
         // calculate where this column extends to in pixels
         int endCol = Math.min(
                 Math.round((colIndex + 1) * pixelsPerCol) - 1,
@@ -171,6 +184,10 @@ public class OverviewRenderer
     int pixelCol = 0;
     for (int alignmentCol : cols)
     {
+      if (redraw)
+      {
+        break;
+      }
       if (alignmentCol >= annotations.length)
       {
         break; // no more annotations to draw here
@@ -205,4 +222,12 @@ public class OverviewRenderer
       }
     }
   }
+
+  public void setRedraw(boolean b)
+  {
+    synchronized (this)
+    {
+      redraw = b;
+    }
+  }
 }
-- 
1.7.10.2