Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / src / jalview / ws / jws2 / AAConClient.java

diff --git a/src/jalview/ws/jws2/AAConClient.java b/src/jalview/ws/jws2/AAConClient.java
index 09fb6ae..327864a 100644 (file)
--- a/src/jalview/ws/jws2/AAConClient.java
+++ b/src/jalview/ws/jws2/AAConClient.java
@@ -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);
@@ -121,9 +123,9 @@ public class AAConClient extends JabawsCalcWorker
     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"));
   }
 }