JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / ws / jws2 / JPred301Client.java

diff --git a/src/jalview/ws/jws2/JPred301Client.java b/src/jalview/ws/jws2/JPred301Client.java
index db70fa0..c15f256 100644 (file)
--- a/src/jalview/ws/jws2/JPred301Client.java
+++ b/src/jalview/ws/jws2/JPred301Client.java
@@ -20,7 +20,6 @@
  */
 package jalview.ws.jws2;
 
-import jalview.api.AlignCalcWorkerI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.gui.AlignFrame;
@@ -43,9 +42,7 @@ import compbio.data.sequence.JpredAlignment;
 import compbio.metadata.Argument;
 
 public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
-        implements AlignCalcWorkerI
 {
-
   /**
    * 
    * @return default args for this service when run as dynamic web service
@@ -87,6 +84,7 @@ public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
     return (seqs.size() > 1);
   }
 
+  @Override
   public String getServiceActionText()
   {
     return "calculating consensus secondary structure prediction using JPred service";
@@ -112,6 +110,7 @@ public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
    * update the consensus annotation from the sequence profile data using
    * current visualization settings.
    */
+  @Override
   public void updateResultAnnotation(boolean immediate)
   {
     if (immediate || !calcMan.isWorking(this) && msascoreset != null)
@@ -128,8 +127,7 @@ public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
           String[] k = jpredRowLabels.get(fsq.getId());
           if (k == null)
           {
-            k = new String[]
-            { fsq.getId(), "JNet Output" };
+            k = new String[] { fsq.getId(), "JNet Output" };
           }
           if (fsq.getId().startsWith("JNETSOL"))
           {
@@ -142,7 +140,8 @@ public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
               {
                 sol[spos] = '0';
               }
-              if (vseq[spos] == 'B' && (sol[spos]=='0' || sol[spos] < amnt))
+              if (vseq[spos] == 'B'
+                      && (sol[spos] == '0' || sol[spos] < amnt))
               {
                 sol[spos] = amnt;
               }
@@ -252,7 +251,7 @@ public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
         try
         {
           elm[i] = new Annotation("" + annot, "" + annot, annot,
-                  Integer.valueOf(""+annot));
+                  Integer.valueOf("" + annot));
         } catch (Exception x)
         {
           System.err.println("Expected numeric value in character '"