From 443f778768843153de0da7fd1ddbedd6e054f339 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 24 Feb 2006 11:35:52 +0000
Subject: [PATCH] If overview, residues are gray

---
 src/jalview/appletgui/SequenceRenderer.java |    6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 889df36..0fa8b2e 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -33,6 +33,7 @@ public class SequenceRenderer
   SequenceGroup[] allGroups = null;
   Color resBoxColour;
   Graphics graphics;
+  boolean forOverview = false;
 
   public SequenceRenderer(AlignViewport av)
   {
@@ -69,10 +70,15 @@ public class SequenceRenderer
     {
       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
     }
+    else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+    {
+        resBoxColour = Color.lightGray;
+    }
     else
     {
       resBoxColour = Color.white;
     }
+
   }
 
   public Color findSequenceColour(SequenceI seq, int i)
-- 
1.7.10.2