X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=fdf0cec085cb2c33a1e14f7242e78690da899d23;hb=f24dacb1da56fccf05d684e2f4899facec2aecf7;hp=8f94e97a6d6946f4a1e9c08d9aade46da18f7d66;hpb=133e5d7be0ca295fd4ac4ccfa6c82165c795ea80;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 8f94e97..fdf0cec 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -137,7 +137,7 @@ public class JPredClient
                              " Service location failed\nfor URL :" + WsURL +
                              "\n" +
                              ex.getMessage());
-      wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
 
       return false;
     }
@@ -172,9 +172,8 @@ public class JPredClient
       this.sequence.setSeq(AlignSeq.extractGaps("-. ",
                                                 msf[0].getSequence()));
 
-      jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();
       this.msa = new vamsas.objects.simple.Msfalignment();
-      msa.setMsf(mwrite.print(msf));
+      msa.setMsf(jalview.io.PileUpfile.print(msf));
     }
 
     public void run()
@@ -334,7 +333,7 @@ public class JPredClient
 
 
 
-    private void addFloatAnnotations(Alignment al, int[] gapmap,
+  /*  private void addFloatAnnotations(Alignment al, int[] gapmap,
                                      Vector values, String Symname,
                                      String Visname, float min,
                                      float max, int winLength)
@@ -350,7 +349,7 @@ public class JPredClient
 
       al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
                                                annotations, min, max, winLength));
-    }
+    }*/
 
     void parseResult()
     {
@@ -518,7 +517,7 @@ public class JPredClient
           i++;
         }
 
-        Hashtable scores = prediction.getScores();
+        //Hashtable scores = prediction.getScores();
 
         /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
                               "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);