X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=aca07b76b5d2a702666420b439419a43e7baa436;hb=aa91e8c4561c2dd0f18760e18fb0052979733bf8;hp=70acb7b89eeac12b9400924fd3f2ae7c9ba794e7;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 70acb7b..aca07b7 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -24,6 +24,7 @@ import jalview.api.FeatureRenderer;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.awt.FontMetrics;
@@ -150,7 +151,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
       resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
     }
     else if (forOverview
-            && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+            && !Comparison.isGap(seq.getCharAt(i)))
     {
       resBoxColour = Color.lightGray;
     }
@@ -323,12 +324,18 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     {
       boolean srep = av.isDisplayReferenceSeq();
       boolean getboxColour = false;
+      boolean isarep = av.getAlignment().getSeqrep() == seq;
+      boolean isgrep = currentSequenceGroup != null ? currentSequenceGroup
+              .getSeqrep() == seq : false;
+      char sr_c;
       for (int i = start; i <= end; i++)
       {
+
         graphics.setColor(av.getTextColour());
         getboxColour = false;
         s = seq.getCharAt(i);
-        if (!renderGaps && jalview.util.Comparison.isGap(s))
+
+        if (!renderGaps && Comparison.isGap(s))
         {
           continue;
         }
@@ -364,11 +371,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
           {
             graphics.setColor(currentSequenceGroup.textColour);
           }
-          if (currentSequenceGroup.getShowNonconserved()) // todo optimize
+          if (!isarep && !isgrep
+                  && currentSequenceGroup.getShowNonconserved()) // todo
+                                                                 // optimize
           {
             // todo - use sequence group consensus
-            s = getDisplayChar(srep, i, s,
-                    '.');
+            s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
 
           }
 
@@ -408,10 +416,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
               graphics.setColor(av.getTextColour2());
             }
           }
-          if (av.getShowUnconserved())
+          if (!isarep && av.getShowUnconserved())
           {
-            s = getDisplayChar(srep, i, s,
-                    '.');
+            s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
 
           }
 
@@ -438,12 +445,20 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    * @return
    */
   private char getDisplayChar(final boolean usesrep, int position,
-          char sequenceChar, char conservedChar)
+          char sequenceChar, char conservedChar, SequenceGroup currentGroup)
   {
     // TODO - use currentSequenceGroup rather than alignment
     // currentSequenceGroup.getConsensus()
-    char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
-            .charAt(0);
+    char conschar = (usesrep) ? (currentGroup == null ? av.getAlignment()
+            .getSeqrep().getCharAt(position)
+            : (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
+                    .getCharAt(position) : av.getAlignment().getSeqrep()
+                    .getCharAt(position)))
+            : (currentGroup != null && currentGroup.getConsensus() != null) ? currentGroup
+                    .getConsensus().annotations[position].displayCharacter
+                    .charAt(0)
+                    : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+                            .charAt(0);
     if (conschar != '-'
             && (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar))
     {