X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=5c159fb89098216c251c0c7dc5d07b4dca63e271;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=afbc7e365e811e47664676c804005092d0d89237;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index afbc7e3..5c159fb 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -17,10 +17,15 @@
  */
 package jalview.appletgui;
 
-import java.awt.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
 
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
 
 public class SequenceRenderer implements jalview.api.SequenceRenderer
 {
@@ -82,7 +87,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   {
     if (cs != null)
     {
-      resBoxColour = cs.findColour(seq.getCharAt(i), i);
+      resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
     }
     else if (forOverview
             && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
@@ -223,7 +228,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         {
           // cheat - use this if we have a consensus for each group: s =
           // getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
-          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
+          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+                  '.');
         }
       }
       else
@@ -247,7 +253,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         if (av.getShowUnconserved())
         {
-          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
+          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+                  '.');
 
         }
       }