X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Fjws2%2FAAConClient.java;h=327864adb9a1d562c4029f764c985331244a8c50;hb=20a4d7ddb86ee996f2b6617a0470922b83354c35;hp=b025a8012a1f2868656a1a5b91ff15da12e712a4;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/src/jalview/ws/jws2/AAConClient.java b/src/jalview/ws/jws2/AAConClient.java
index b025a80..327864a 100644
--- a/src/jalview/ws/jws2/AAConClient.java
+++ b/src/jalview/ws/jws2/AAConClient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -48,10 +48,12 @@ public class AAConClient extends JabawsCalcWorker
     alignedSeqs = true;
     nucleotidesAllowed = false;
     proteinAllowed = true;
+    filterNonStandardResidues = true;
     gapMap = new boolean[0];
     initViewportParams();
   }
 
+  @Override
   public String getServiceActionText()
   {
     return "calculating Amino acid consensus using AACon service";
@@ -62,13 +64,14 @@ public class AAConClient extends JabawsCalcWorker
    * current visualization settings.
    */
 
+  @Override
   public void updateResultAnnotation(boolean immediate)
   {
     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
     {
       Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
       int alWidth = alignViewport.getAlignment().getWidth();
-      ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+      ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<>();
       for (String score : scoremap.keySet())
       {
         Set<Score> scores = scoremap.get(score);