JAL-1807 explicit imports (jalview.ws.*)

[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 55ade66..bca8343 100644 (file)
--- a/src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/src/jalview/ws/jws2/RNAalifoldClient.java
@@ -24,7 +24,6 @@ import jalview.api.AlignCalcWorkerI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.gui.AlignFrame;
-import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.uimodel.AlignAnalysisUIText;
@@ -36,12 +35,13 @@ 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;
 import compbio.metadata.Argument;
+import compbio.ws.client.Services;
 
 /**
  * Client for the JABA RNA Alifold Service
@@ -85,8 +85,8 @@ public class RNAalifoldClient extends JabawsCalcWorker implements
   public static AlignAnalysisUIText getAlignAnalysisUITest()
   {
     return new AlignAnalysisUIText(
-            compbio.ws.client.Services.RNAalifoldWS.toString(),
-            jalview.ws.jws2.RNAalifoldClient.class,
+            Services.RNAalifoldWS.toString(),
+            RNAalifoldClient.class,
             CALC_ID,
             true,
             false,
@@ -185,11 +185,15 @@ 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());
@@ -269,7 +273,9 @@ 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) + "%  |  ";
@@ -349,7 +355,9 @@ 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()))
     {
@@ -386,7 +394,9 @@ 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;