X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FRNAalifoldClient.java;h=5d0df8a86875f9b271cbb9789d9ed4f09787b16b;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=126266bafdcbebdd7bc9b97fbca6e129f72130a6;hpb=1889827c44c51f6353fe8619e5d44b421158af23;p=jalview.git

diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java
index 126266b..5d0df8a 100644
--- a/src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/src/jalview/ws/jws2/RNAalifoldClient.java
@@ -44,8 +44,9 @@ import compbio.metadata.Argument;
 
 /**
  * Client for the JABA RNA Alifold Service
+ * 
  * @author daluke - Daniel Barton
- *
+ * 
  */
 
 public class RNAalifoldClient extends JabawsAlignCalcWorker implements
@@ -65,23 +66,24 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
   {
     super(sh, alignFrame, preset, paramset);
 
-    //if (arguments == null)
-    //  arguments = new ArrayList<Argument>();
+    // if (arguments == null)
+    // arguments = new ArrayList<Argument>();
 
     af = alignFrame;
     methodName = sh.serviceType;
-    alignedSeqs=true;
-    submitGaps=true;
+    alignedSeqs = true;
+    submitGaps = true;
     nucleotidesAllowed = true;
     proteinAllowed = false;
     initViewportParams();
   }
-  
+
   public String getCalcId()
   {
     return CALC_ID;
   }
-  private static String CALC_ID="jalview.ws.jws2.RNAalifoldClient";
+
+  private static String CALC_ID = "jalview.ws.jws2.RNAalifoldClient";
 
   public static AlignAnalysisUIText getAlignAnalysisUITest()
   {
@@ -218,7 +220,8 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
   private AlignmentAnnotation constructAnnotationFromScoreHolder(
           AlignmentAnnotation annotation, String struct, TreeSet<Score> data)
   {
-    Annotation[] anns = new Annotation[gapMap!= null ? gapMap.length+1 : struct.length()];
+    Annotation[] anns = new Annotation[gapMap != null ? gapMap.length + 1
+            : struct.length()];
 
     if (data != null
             && data.size() > 1
@@ -236,10 +239,10 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
         basePairs.put(score.getRanges().first(), new Float(score
                 .getScores().get(0)));
       }
-      
-      for (int i = 0,ri=0,iEnd=struct.length();i<iEnd; i++,ri++)
+
+      for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
       {
-        if (gapMap!=null)
+        if (gapMap != null)
         {
           // skip any gapped columns in the input data
           while (!gapMap[ri])
@@ -276,16 +279,16 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
     }
     else if (data == null || data.size() == 1)
     {
-      for (int i = 0,ri=0,iEnd=struct.length();i<iEnd; i++,ri++)
+      for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)
       {
-        if (gapMap!=null)
+        if (gapMap != null)
         {
           // skip any gapped columns in the input data
-          while (!gapMap[ri] && ri<gapMap.length)
+          while (!gapMap[ri] && ri < gapMap.length)
           {
             ri++;
           }
-          if (ri==gapMap.length)
+          if (ri == gapMap.length)
           {
             break;
           }