X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAAConClient.java;h=2c9b34a6b63dd0eec7c4d90bfba94fef6c1e3a66;hb=ad1f4306281b0894fa42394b9a68da834cf14af6;hp=ef810de9d544cf2daa8c4cb5694d0604e25c5b03;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/src/jalview/ws/jws2/AAConClient.java b/src/jalview/ws/jws2/AAConClient.java
index ef810de..2c9b34a 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 2.9.0b1)
- * 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);
@@ -113,7 +116,7 @@ public class AAConClient extends JabawsCalcWorker
     return CALC_ID;
   }
 
-  private static String CALC_ID = "jabaws2.AACon";
+  private final static String CALC_ID = "jabaws2.AACon";
 
   public static AlignAnalysisUIText getAlignAnalysisUITest()
   {