X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=154bea4233300daa60daa757f684d0c83af54552;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=afbc7e365e811e47664676c804005092d0d89237;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index afbc7e3..154bea4 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,26 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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 +88,7 @@ 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 +229,8 @@ 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 +254,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         if (av.getShowUnconserved())
         {
-          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
+          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+                  '.');
 
         }
       }