regenerated Jpred stubs and tidied client thread.

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

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index c7508df..04a6101 100755 (executable)
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -30,7 +30,7 @@ import jalview.gui.*;
 public class JPredClient\r
     extends WSClient\r
 {\r
-  ext.vamsas.JPredWS server;\r
+  ext.vamsas.Jpred server;\r
   String altitle = "";\r
   java.util.Hashtable SequenceInfo = null;\r
   public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq) {\r
@@ -115,7 +115,7 @@ public class JPredClient
 \r
   private boolean locateWebService()\r
   {\r
-    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
+    ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default\r
 \r
     try\r
     {\r
@@ -146,9 +146,9 @@ public class JPredClient
       extends Thread\r
   {\r
     String OutputHeader;\r
-    ext.vamsas.JpredResult result;\r
-    ext.vamsas.Sequence sequence;\r
-    ext.vamsas.Msfalignment msa;\r
+    vamsas.objects.simple.JpredResult result;\r
+    vamsas.objects.simple.Sequence sequence;\r
+    vamsas.objects.simple.Msfalignment msa;\r
     String jobId;\r
     boolean jobComplete = false;\r
     int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
@@ -156,7 +156,7 @@ public class JPredClient
     JPredThread(SequenceI seq)\r
     {\r
       OutputHeader = wsInfo.getProgressText();\r
-      this.sequence = new ext.vamsas.Sequence();\r
+      this.sequence = new vamsas.objects.simple.Sequence();\r
       this.sequence.setId(seq.getName());\r
       this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));\r
     }\r
@@ -164,13 +164,13 @@ public class JPredClient
     JPredThread(SequenceI[] msf)\r
     {\r
       OutputHeader = wsInfo.getProgressText();\r
-      this.sequence = new ext.vamsas.Sequence();\r
+      this.sequence = new vamsas.objects.simple.Sequence();\r
       this.sequence.setId(msf[0].getName());\r
       this.sequence.setSeq(AlignSeq.extractGaps("-. ",\r
                                                 msf[0].getSequence()));\r
 \r
       jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();\r
-      this.msa = new ext.vamsas.Msfalignment();\r
+      this.msa = new vamsas.objects.simple.Msfalignment();\r
       msa.setMsf(mwrite.print(msf));\r
     }\r
 \r
@@ -187,27 +187,28 @@ public class JPredClient
             throw (new Exception(\r
                 "Timed out when communicating with server\nTry again later.\n"));\r
           }\r
-\r
+          if (result.getState()==0)\r
+            jalview.bin.Jalview.log.debug("Finished "+jobId);\r
           if (result.isRunning())\r
           {\r
             wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
           }\r
-          else if (result.isQueued())\r
+          if (result.isQueued())\r
           {\r
             wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
           }\r
 \r
+          wsInfo.setProgressText(OutputHeader + "\n" +\r
+                                 result.getStatus());\r
+\r
           if (result.isFinished())\r
           {\r
+\r
             parseResult();\r
             jobComplete = true;\r
             jobsRunning--;\r
-          }\r
-          else\r
-          {\r
-            wsInfo.setProgressText(OutputHeader + "\n" +\r
-                                   result.getStatus());\r
-\r
+          } else {\r
+            // catch exceptions\r
             if (! (result.isJobFailed() || result.isServerError()))\r
             {\r
               try\r
@@ -223,6 +224,8 @@ public class JPredClient
             else\r
             {\r
               wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+              jobsRunning--;\r
+              jobComplete = true;\r
             }\r
           }\r
         }\r
@@ -298,7 +301,7 @@ public class JPredClient
             "JPredWS Client: Failed to submit the prediction (Probably a server error - see below)\n" +\r
             e.toString() + "\n");\r
 \r
-        // e.printStackTrace(); TODO: JBPNote DEBUG\r
+        jalview.bin.Jalview.log.debug("Failed Submission",e);\r
       }\r
     }\r
 \r
@@ -494,7 +497,8 @@ public class JPredClient
       }\r
       catch (Exception ex)\r
       {\r
-        ex.printStackTrace();\r
+        jalview.bin.Jalview.log.warn("Exception whilst parsing JNet style secondary structure prediction.");\r
+        jalview.bin.Jalview.log.debug(ex);\r
       }\r
     }\r
   }\r