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 154bea4..862dd82 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -202,7 +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);
@@ -227,9 +227,7 @@ 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,
                   '.');
         }
       }
@@ -254,7 +252,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         if (av.getShowUnconserved())
         {
-          s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+          s = getDisplayChar(srep, i, s,
                   '.');
 
         }
@@ -287,10 +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)
     {