X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJPred301Client.java;h=c15f256bf5f528a6577231cc3261bde6d6231eaa;hb=refs%2Fheads%2Ffeatures%2FJAL-2284_export-biojsmsa-via-cli;hp=7d7eb912391642c3d70eaca45dee1135481ceee6;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/ws/jws2/JPred301Client.java b/src/jalview/ws/jws2/JPred301Client.java
index 7d7eb91..c15f256 100644
--- a/src/jalview/ws/jws2/JPred301Client.java
+++ b/src/jalview/ws/jws2/JPred301Client.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,7 +20,6 @@
  */
 package jalview.ws.jws2;
 
-import jalview.api.AlignCalcWorkerI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.gui.AlignFrame;
@@ -35,15 +34,15 @@ import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
+import java.util.Set;
 
 import compbio.data.sequence.FastaSequence;
 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
@@ -85,20 +84,24 @@ public class JPred301Client extends JabawsMsaInterfaceAlignCalcWorker
     return (seqs.size() > 1);
   }
 
+  @Override
   public String getServiceActionText()
   {
     return "calculating consensus secondary structure prediction using JPred service";
   }
 
-  private static HashMap<String, String[]> jpredRowLabels = new HashMap<String, String[]>();
+  private static Map<String, String[]> jpredRowLabels = new HashMap<String, String[]>();
 
-  private static HashSet<String> jpredRes_graph, jpredRes_ssonly;
+  private static final Set<String> jpredRes_graph;
+
+  private static final Set<String> jpredRes_ssonly;
+  static
   {
-    jpredRes_ssonly = new HashSet();
+    jpredRes_ssonly = new HashSet<String>();
     jpredRes_ssonly.add("jnetpred".toLowerCase());
     jpredRes_ssonly.add("jnetpssm".toLowerCase());
     jpredRes_ssonly.add("jnethmm".toLowerCase());
-    jpredRes_graph = new HashSet();
+    jpredRes_graph = new HashSet<String>();
     jpredRes_graph.add("jnetconf".toLowerCase());
     jpredRes_graph.add("jnet burial".toLowerCase());
   }
@@ -107,6 +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)
@@ -123,8 +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"))
           {
@@ -137,7 +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;
               }
@@ -247,7 +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 '"