ensure successive matches to a regex have distinct annotation name (indice suffix...

[jalview.git] / src / jalview / ws / JPredThread.java

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