From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 30 Nov 2005 15:07:38 +0000 (+0000)
Subject: GetResidueBoxColour needs no colourscheme
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=62387bf69fd0fb3fccb599213f7bd477d8bf383e;p=jalview.git

GetResidueBoxColour needs no colourscheme
---

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 217a67d..c68e85c 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -44,11 +44,24 @@ public class SequenceRenderer
     renderGaps = b;
   }
 
-  public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+  public Color getResidueBoxColour(SequenceI seq, int i)
   {
-    getBoxColour(cs, seq, i);
+    allGroups = av.alignment.findAllGroups(seq);
+
+    if (inCurrentSequenceGroup(i))
+    {
+      if (currentSequenceGroup.getDisplayBoxes())
+      {
+        getBoxColour(currentSequenceGroup.cs, seq, i);
+      }
+    }
+    else if (av.getShowBoxes())
+    {
+        getBoxColour(av.globalColourScheme, seq, i);
+    }
+
     return resBoxColour;
-  }
+    }
 
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {