JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java
index fac0857..769100e 100644 (file)
--- a/src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/src/jalview/ws/jws2/RNAalifoldClient.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 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -24,7 +24,7 @@ import jalview.api.AlignCalcWorkerI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.gui.AlignFrame;
-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;
@@ -36,8 +36,8 @@ import java.util.List;
 import java.util.TreeSet;
 import java.util.regex.Pattern;
 
-import compbio.data.sequence.RNAStructReader.AlifoldResult;
 import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.RNAStructReader.AlifoldResult;
 import compbio.data.sequence.RNAStructScoreManager;
 import compbio.data.sequence.Range;
 import compbio.data.sequence.Score;
@@ -66,10 +66,6 @@ public class RNAalifoldClient extends JabawsCalcWorker implements
           WsParamSetI preset, List<Argument> paramset)
   {
     super(sh, alignFrame, preset, paramset);
-
-    // if (arguments == null)
-    // arguments = new ArrayList<Argument>();
-
     af = alignFrame;
     methodName = sh.serviceType;
     alignedSeqs = true;
@@ -90,16 +86,11 @@ public class RNAalifoldClient extends JabawsCalcWorker implements
   {
     return new AlignAnalysisUIText(
             compbio.ws.client.Services.RNAalifoldWS.toString(),
-            jalview.ws.jws2.RNAalifoldClient.class,
-            CALC_ID,
-            true,
-            false,
-            true,
-            "RNAAliFold Prediction",
-            "When checked, RNA secondary structure predictions will be calculated for the alignment, and updated when edits are made.",
-            "Change RNAAliFold settings...",
-            "Modify settings for the RNAAliFold prediction. Use this to hide or show different results of the RNA calculation, and change RNA folding parameters");
-
+            jalview.ws.jws2.RNAalifoldClient.class, CALC_ID, true, false,
+            true, MessageManager.getString("label.rnalifold_calculations"),
+            MessageManager.getString("tooltip.rnalifold_calculations"),
+            MessageManager.getString("label.rnalifold_settings"),
+            MessageManager.getString("tooltip.rnalifold_settings"));
   }
 
   @Override
@@ -189,11 +180,15 @@ public class RNAalifoldClient extends JabawsCalcWorker implements
      * same data object as was overwritten with the contact probabilites data.
      */
     if (data == null)
+    {
       data = compbio.data.sequence.RNAStructReader
               .newEmptyScore(AlifoldResult.consensusAlignment);
+    }
 
     if (descriptionData == null)
+    {
       descriptionData = data;
+    }
 
     String[] typenameAndDescription = constructTypenameAndDescription(descriptionData
             .first());
@@ -273,7 +268,9 @@ public class RNAalifoldClient extends JabawsCalcWorker implements
           {
             float t = contacts.get(contact);
             if (t > prob)
+            {
               prob = t;
+            }
             description += Integer.toString(contact.from) + "->"
                     + Integer.toString(contact.to) + ": "
                     + Float.toString(t) + "%  |  ";
@@ -353,7 +350,9 @@ public class RNAalifoldClient extends JabawsCalcWorker implements
                 score.getScores().get(0), score.getScores().get(1));
       }
       else
+      {
         description = "Stochastic Backtrack Structure";
+      }
     }
     else if (datatype.equals(AlifoldResult.MEAStucture.toString()))
     {
@@ -373,8 +372,7 @@ public class RNAalifoldClient extends JabawsCalcWorker implements
       description = typename;
     }
 
-    return new String[]
-    { typename, description };
+    return new String[] { typename, description };
   }
 
   // Check whether, at position i there is a base contact and return all the
@@ -390,7 +388,9 @@ public class RNAalifoldClient extends JabawsCalcWorker implements
       // ordering of the Scores TreeSet in ScoreManager which is, descending
       // probability
       if (contact.from == i || contact.to == i)
+      {
         contacts.put(contact, basePairs.get(contact));
+      }
     }
 
     return contacts;