Merge branch 'Jalview-JS/develop_j2s_v3_2_9_j11' into Jalview-JS/develop

[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 ce9e334..327864a 100644 (file)
--- 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 2.8.2)
- * 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;
@@ -34,10 +33,11 @@ import java.util.Map;
 import java.util.Set;
 import java.util.TreeSet;
 
+import compbio.data.sequence.FastaSequence;
 import compbio.data.sequence.Score;
 import compbio.metadata.Argument;
 
-public class AAConClient extends JabawsAlignCalcWorker
+public class AAConClient extends JabawsCalcWorker
 {
 
   public AAConClient(Jws2Instance service, AlignFrame alignFrame,
@@ -48,10 +48,12 @@ public class AAConClient extends JabawsAlignCalcWorker
     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 JabawsAlignCalcWorker
    * 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);
@@ -102,20 +105,27 @@ public class AAConClient extends JabawsAlignCalcWorker
   }
 
   @Override
+  boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+  {
+    return (seqs.size() > 1);
+  }
+
+  @Override
   public String getCalcId()
   {
     return CALC_ID;
   }
-  private static String CALC_ID="jabaws2.AACon";
+
+  private 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"));
   }
 }