JAL-2089 Merge branch releases/Release_2_10_Branch to master

[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 5d0df8a..a67029c 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 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,11 +20,10 @@
  */
 package jalview.ws.jws2;
 
-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;
@@ -36,6 +35,7 @@ import java.util.List;
 import java.util.TreeSet;
 import java.util.regex.Pattern;
 
+import compbio.data.sequence.FastaSequence;
 import compbio.data.sequence.RNAStructReader.AlifoldResult;
 import compbio.data.sequence.RNAStructScoreManager;
 import compbio.data.sequence.Range;
@@ -49,8 +49,7 @@ import compbio.metadata.Argument;
  * 
  */
 
-public class RNAalifoldClient extends JabawsAlignCalcWorker implements
-        AlignCalcWorkerI
+public class RNAalifoldClient extends JabawsCalcWorker
 {
 
   String methodName;
@@ -65,10 +64,6 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker 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;
@@ -78,6 +73,7 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
     initViewportParams();
   }
 
+  @Override
   public String getCalcId()
   {
     return CALC_ID;
@@ -89,16 +85,11 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker 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
@@ -109,6 +100,12 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
   }
 
   @Override
+  boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+  {
+    return (seqs.size() > 1);
+  }
+
+  @Override
   public void updateResultAnnotation(boolean immediate)
   {
 
@@ -182,11 +179,15 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker 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());
@@ -266,7 +267,9 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
           {
             float t = contacts.get(contact);
             if (t > prob)
+            {
               prob = t;
+            }
             description += Integer.toString(contact.from) + "->"
                     + Integer.toString(contact.to) + ": "
                     + Float.toString(t) + "%  |  ";
@@ -346,7 +349,9 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
                 score.getScores().get(0), score.getScores().get(1));
       }
       else
+      {
         description = "Stochastic Backtrack Structure";
+      }
     }
     else if (datatype.equals(AlifoldResult.MEAStucture.toString()))
     {
@@ -366,8 +371,7 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker 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
@@ -383,7 +387,9 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker 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;