X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=a06fed5f3dc5d8059e57b3521c8e3553cf68f335;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=a1b8e7ac32eb64b229724a37ba6437f6b642a5c3;hpb=4f77328104498504339216829abf5ea87e2791ec;p=jalview.git

diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index a1b8e7a..a06fed5 100644
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -53,48 +53,22 @@ public class AADisorderClient extends JabawsCalcWorker
 
   private static final String RANGE = "RANGE";
 
-  String typeName;
+  private String typeName;
 
-  String methodName;
+  private String methodName;
 
-  String groupName;
+  // private String groupName;
 
   AlignFrame af;
 
-  public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
-          WsParamSetI thePreset, List<Argument> paramset)
-  {
-    super(sh, alignFrame, thePreset, paramset);
-    af = alignFrame;
-    typeName = sh.action;
-    methodName = sh.serviceType;
+  private final static Map<String, Map<String, String[]>> featureMap;
 
-    submitGaps = false;
-    alignedSeqs = false;
-    nucleotidesAllowed = false;
-    proteinAllowed = true;
-    bySequence = true;
-  }
+  private final static Map<String, Map<String, Map<String, Object>>> annotMap;
 
-  @Override
-  public String getServiceActionText()
-  {
-    return "Submitting amino acid sequences for disorder prediction.";
-  }
+  private final static String DONTCOMBINE = "DONTCOMBINE";
 
-  @Override
-  boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
-  {
-    return (seqs.size() > 0);
-  }
-
-  private static Map<String, Map<String, String[]>> featureMap;
+  private final static String INVISIBLE = "INVISIBLE";
 
-  private static Map<String, Map<String, Map<String, Object>>> annotMap;
-
-  private static String DONTCOMBINE = "DONTCOMBINE";
-
-  private static String INVISIBLE = "INVISIBLE";
   static
   {
     // TODO: turn this into some kind of configuration file that's a bit easier
@@ -162,6 +136,33 @@ public class AADisorderClient extends JabawsCalcWorker
     amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
   }
 
+  public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
+          WsParamSetI thePreset, List<Argument> paramset)
+  {
+    super(sh, alignFrame, thePreset, paramset);
+    af = alignFrame;
+    typeName = sh.action;
+    methodName = sh.serviceType;
+
+    submitGaps = false;
+    alignedSeqs = false;
+    nucleotidesAllowed = false;
+    proteinAllowed = true;
+    bySequence = true;
+  }
+
+  @Override
+  public String getServiceActionText()
+  {
+    return "Submitting amino acid sequences for disorder prediction.";
+  }
+
+  @Override
+  boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+  {
+    return (seqs.size() > 0);
+  }
+
   @Override
   public void updateResultAnnotation(boolean immediate)
   {
@@ -239,13 +240,13 @@ public class AADisorderClient extends JabawsCalcWorker
                 if (vals.hasNext())
                 {
                   val = vals.next().floatValue();
-                  sf = new SequenceFeature(type[0], type[1],
-                          base + rn.from, base + rn.to, val, methodName);
+                  sf = new SequenceFeature(type[0], type[1], base + rn.from,
+                          base + rn.to, val, methodName);
                 }
                 else
                 {
-                  sf = new SequenceFeature(type[0], type[1],
-                          base + rn.from, base + rn.to, methodName);
+                  sf = new SequenceFeature(type[0], type[1], base + rn.from,
+                          base + rn.to, methodName);
                 }
                 dseq.addSequenceFeature(sf);
                 if (last != val && !Float.isNaN(last))