X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=98329b4920fef212710fe3c504bfdccfde4e0d95;hb=075b2506c45bf8ae70e7a3ce3bb29029a21824b1;hp=a3dd5a6d10249d88e8684b83cdd3371841f68823;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index a3dd5a6..98329b4 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -324,6 +324,12 @@ public class SequenceRenderer
           {
             graphics.setColor(currentSequenceGroup.textColour);
           }
+          if (currentSequenceGroup.getShowunconserved()) // todo optimize
+          {
+            // todo - use sequence group consensus
+            s = getDisplayChar(av.consensus, i, s, '.');                       
+   
+          }
 
         }
         else
@@ -361,6 +367,11 @@ public class SequenceRenderer
               graphics.setColor(av.textColour2);
             }
           }
+          if (av.showUnconserved)
+          {
+            s = getDisplayChar(av.consensus, i, s, '.');                       
+   
+          }
 
         }
 
@@ -371,6 +382,15 @@ public class SequenceRenderer
       }
     }
   }
+  private char getDisplayChar(AlignmentAnnotation consensus, int position, char s, char c)
+  {
+    char conschar = consensus.annotations[position].displayCharacter.charAt(0);
+    if (conschar!='-' && s==conschar)
+    {
+      s= c;
+    }
+    return s;
+  }
 
   /**
    * DOCUMENT ME!