Merge branch 'Release_2_8_1_Branch' into JAL-1372_referenceseq

[jalview.git] / src / jalview / appletgui / SequenceRenderer.java

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index afbc7e3..862dd82 100755 (executable)
--- 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)))
@@ -196,7 +202,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
 
     char s = ' ';
-
+    boolean srep = av.isDisplayReferenceSeq();
     for (int i = start; i <= end; i++)
     {
       graphics.setColor(Color.black);
@@ -221,9 +227,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         if (currentSequenceGroup.getShowNonconserved())
         {
-          // 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(srep, i, s,
+                  '.');
         }
       }
       else
@@ -247,7 +252,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         if (av.getShowUnconserved())
         {
-          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s, '.');
+          s = getDisplayChar(srep, i, s,
+                  '.');
 
         }
       }
@@ -279,10 +285,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
   }
 
-  private char getDisplayChar(AlignmentAnnotation consensus, int position,
+  private char getDisplayChar(final boolean usesrep, int position,
           char s, char c)
   {
-    char conschar = consensus.annotations[position].displayCharacter
+    // TODO - use currentSequenceGroup rather than alignemnt 
+    // currentSequenceGroup.getConsensus()
+    char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
             .charAt(0);
     if (conschar != '-' && s == conschar)
     {