X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAAConClient.java;h=2c9b34a6b63dd0eec7c4d90bfba94fef6c1e3a66;hb=ad1f4306281b0894fa42394b9a68da834cf14af6;hp=3f5fc6059f3e91451011ce37f5c7e9052c484641;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/ws/jws2/AAConClient.java b/src/jalview/ws/jws2/AAConClient.java
index 3f5fc60..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 2.8.2b1)
- * Copyright (C) 2014 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.
  * 
@@ -22,8 +22,7 @@ package jalview.ws.jws2;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignmentPanel;
-import jalview.ws.jws2.dm.AAConSettings;
+import jalview.util.MessageManager;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.uimodel.AlignAnalysisUIText;
@@ -49,10 +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";
@@ -63,13 +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);
@@ -114,16 +116,16 @@ 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()
   {
     return new AlignAnalysisUIText(
             compbio.ws.client.Services.AAConWS.toString(),
             jalview.ws.jws2.AAConClient.class, CALC_ID, false, true, true,
-            "AACon Calculations",
-            "When checked, AACon calculations are updated automatically.",
-            "Change AACon Settings...",
-            "Modify settings for AACon calculations.");
+            MessageManager.getString("label.aacon_calculations"),
+            MessageManager.getString("tooltip.aacon_calculations"),
+            MessageManager.getString("label.aacon_settings"),
+            MessageManager.getString("tooltip.aacon_settings"));
   }
 }