Merge branch 'JAL-1372_referenceseq' into feature_29/JAL-1372_referenceseq

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

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 177fc83..438ef00 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -319,6 +319,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     else
     {
+      boolean srep = av.isDisplayReferenceSeq();
       boolean getboxColour = false;
       for (int i = start; i <= end; i++)
       {
@@ -364,7 +365,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           if (currentSequenceGroup.getShowNonconserved()) // todo optimize
           {
             // todo - use sequence group consensus
-            s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+            s = getDisplayChar(srep, i, s,
                     '.');
 
           }
@@ -407,7 +408,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           }
           if (av.getShowUnconserved())
           {
-            s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
+            s = getDisplayChar(srep, i, s,
                     '.');
 
           }
@@ -422,10 +423,12 @@ 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)
     {