X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredThread.java;h=106bb530fea08188369dbd4fc898d2fe6ee60c1b;hb=f683f4d6c8af43be0ffeb96513b52572619efed5;hp=0cac70911b5f2a038bcc7723b1eb8b8d27532d84;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/ws/JPredThread.java b/src/jalview/ws/JPredThread.java
index 0cac709..106bb53 100644
--- a/src/jalview/ws/JPredThread.java
+++ b/src/jalview/ws/JPredThread.java
@@ -88,7 +88,7 @@ class JPredThread
           if (predMap != null)
           {
             Object[] alandcolsel = input.getAlignmentAndColumnSelection(
-                alignFrame.getViewport().getGapCharacter());
+                getGapChar());
             sqs = (SequenceI[]) alandcolsel[0];
             al = new Alignment(sqs);
             alcsel = (ColumnSelection) alandcolsel[1];
@@ -131,7 +131,7 @@ class JPredThread
         FirstSeq = prediction.getQuerySeqPosition();
         if (predMap != null)
         {
-          char gc = alignFrame.getViewport().getGapCharacter();
+          char gc = getGapChar();
           SequenceI[] sqs = (SequenceI[]) ( (java.lang.Object[]) input.
                                            getAlignmentAndColumnSelection(gc))[
               0];
@@ -146,8 +146,7 @@ class JPredThread
           new jalview.commands.RemoveGapsCommand("Remove Gaps",
                                                  new SequenceI[]
                                                  {sqs[msaIndex]},
-                                                 alignFrame.getCurrentView().
-                                                 getAlignment());
+                                                 currentView);
 
           SequenceI profileseq = al.getSequenceAt(FirstSeq);
           profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
@@ -350,13 +349,9 @@ class JPredThread
   JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server,
               String wsurl, AlignmentView alview, AlignFrame alframe)
   {
-    super();
+    super(alframe, wsinfo, alview, wsurl);
     this.altitle = altitle;
     this.server = server;
-    this.wsInfo = wsinfo;
-    this.input = alview;
-    this.alignFrame = alframe;
-    WsUrl = wsurl;
   }
 
   JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server,
@@ -418,6 +413,7 @@ class JPredThread
           job.result = (vamsas.objects.simple.Result)new JpredResult();
           job.result.setInvalid(true);
           job.result.setStatus("Submission " + job.jobId);
+          throw new Exception(job.jobId); 
         }
         else
         {
@@ -433,6 +429,8 @@ class JPredThread
     }
     catch (Exception e)
     {
+      // kill the whole job.
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
       if (e.getMessage().indexOf("Exception") > -1)
       {
         wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);