use webservice info

diff --git a/src/jalview/io/JPredClient.java b/src/jalview/io/JPredClient.java
index c403730..3ebc1f0 100755 (executable)
--- a/src/jalview/io/JPredClient.java
+++ b/src/jalview/io/JPredClient.java
@@ -14,103 +14,56 @@ import ext.vamsas.*;
 \r
 public class JPredClient\r
 {\r
-\r
-  JInternalFrame outputFrame = new JInternalFrame();\r
-  CutAndPasteTransfer output = new CutAndPasteTransfer(false);\r
   int jobsRunning = 0;\r
   ext.vamsas.JpredSoapBindingStub server;\r
+  WebserviceInfo wsInfo;\r
 \r
   public JPredClient(SequenceI[] msf)\r
   {\r
-    SequenceI seq = msf[0];\r
-    output.formatForOutput();\r
-    outputFrame.setContentPane(output);\r
+    wsInfo = new WebserviceInfo("JNet secondary structure prediction job",\r
+          "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\".");\r
 \r
-    output.setText("Job details for MSA based prediction on sequence :\nName : "\r
+    SequenceI seq = msf[0];\r
+    wsInfo.setProgressText("Job details for MSA based prediction on sequence :\nName : "\r
                    + seq.getName() + "\nSequence : "\r
                    + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");\r
-    Desktop.addInternalFrame(outputFrame,\r
-                             "JNet secondary structure prediction job", 800,\r
-                             300);\r
+\r
 \r
     JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
     try {\r
       this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties\r
     }\r
     catch (Exception ex) {\r
-      output.setText("Serious! JPred Service location failed\nfor URL :"\r
+      wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :"\r
                      +loc.getjpredAddress()+"\n"+ex.getMessage());\r
     }\r
 \r
     JPredThread jthread = new JPredThread(msf);\r
     jthread.start();\r
-    ImageTwirler thread = new ImageTwirler();\r
-    thread.start();\r
   }\r
 \r
   public JPredClient(SequenceI seq)\r
   {\r
-    output.formatForOutput();\r
-    outputFrame.setContentPane(output);\r
+    wsInfo = new WebserviceInfo("JNet secondary structure prediction job",\r
+                                "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\".");\r
 \r
-    output.setText("Job details for prediction on sequence :\nName : "\r
+\r
+    wsInfo.setProgressText("Job details for prediction on sequence :\nName : "\r
                    + seq.getName() + "\nSequence : " + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");\r
-    Desktop.addInternalFrame(outputFrame,\r
-                             "JNet secondary structure prediction job", 800,\r
-                             300);\r
 \r
     JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
     try {\r
       this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties\r
     }\r
     catch (Exception ex) {\r
-      output.setText("Serious! JPred Service location failed\nfor URL :"\r
+      wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :"\r
                      +loc.getjpredAddress()+"\n"+ex.getMessage());\r
     }\r
 \r
     JPredThread jthread = new JPredThread(seq);\r
     jthread.start();\r
-    ImageTwirler thread = new ImageTwirler();\r
-    thread.start();\r
   }\r
 \r
-  class ImageTwirler\r
-      extends Thread\r
-  {\r
-    ImageIcon[] imageIcon;\r
-    int imageIndex = 0;\r
-    public ImageTwirler()\r
-    {\r
-      imageIcon = new ImageIcon[9];\r
-      for (int i = 0; i < 9; i++)\r
-      {\r
-        java.net.URL url = getClass().getResource("/images/dna" + (i + 1) +\r
-                                                  ".gif");\r
-        if (url != null)\r
-          imageIcon[i] = new ImageIcon(url);\r
-      }\r
-    }\r
-\r
-    public void run()\r
-    {\r
-      while (jobsRunning > 0)\r
-      {\r
-        try\r
-        {\r
-          Thread.sleep(100);\r
-          imageIndex++;\r
-          imageIndex %= 9;\r
-          outputFrame.setFrameIcon(imageIcon[imageIndex]);\r
-          outputFrame.setTitle("JNet Secondary Structure Prediction : " +\r
-                               jobsRunning + " jobs running.");\r
-\r
-        }\r
-        catch (Exception ex)\r
-        {}\r
-\r
-      }\r
-    }\r
-  }\r
 \r
   class JPredThread\r
       extends Thread\r
@@ -124,7 +77,7 @@ public class JPredClient
     int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
     JPredThread(SequenceI seq)\r
     {\r
-      OutputHeader = output.getText();\r
+      OutputHeader = wsInfo.getProgressText();\r
       this.sequence = new ext.vamsas.Sequence();\r
       this.sequence.setId(seq.getName());\r
       this.sequence.setSeq(AlignSeq.extractGaps("-. ",seq.getSequence()));\r
@@ -132,7 +85,7 @@ public class JPredClient
 \r
     JPredThread(SequenceI[] msf)\r
     {\r
-      OutputHeader = output.getText();\r
+      OutputHeader = wsInfo.getProgressText();\r
       this.sequence = new ext.vamsas.Sequence();\r
       this.sequence.setId(msf[0].getName());\r
       this.sequence.setSeq(AlignSeq.extractGaps("-. ",msf[0].getSequence()));\r
@@ -147,13 +100,17 @@ public class JPredClient
 \r
       StartJob();\r
 \r
-      while (!jobComplete\r
-             && (allowedServerExceptions > 0))\r
+      while (!jobComplete && (allowedServerExceptions > 0))\r
       {\r
         try\r
         {\r
           result = server.getresult(jobId);\r
 \r
+         if( result.isRunning() )\r
+           wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
+         else if( result.isQueued() )\r
+           wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
+\r
           if (result.isFinished())\r
           {\r
             parseResult();\r
@@ -162,21 +119,25 @@ public class JPredClient
           }\r
           else\r
           {\r
-            output.setText(OutputHeader + "\n" + result.getStatus());\r
+            wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());\r
             if (! (result.isJobFailed() || result.isServerError()))\r
             {\r
               Thread.sleep(5000);\r
-              //      System.out.println("I'm alive "+seqid+" "+jobid);\r
+              //  System.out.println("I'm alive "+seqid+" "+jobid);\r
             }\r
           }\r
         }\r
         catch (Exception ex)\r
         {\r
           allowedServerExceptions--;\r
-          String msg = output.getText();\r
-          output.setText(msg + "\nJPredWS Server exception!\n" + ex.getMessage());\r
+          wsInfo.appendProgressText("\nJPredWS Server exception!\n" + ex.getMessage());\r
         }\r
       }\r
+\r
+      if (! (result.isJobFailed() || result.isServerError()))\r
+        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
+      else\r
+        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
     }\r
 \r
     void StartJob()\r
@@ -225,7 +186,7 @@ public class JPredClient
       if (result.getAligfile()!=null) {\r
         OutputHeader += "\n"+result.getAligfile();\r
       }\r
-      output.setText(OutputHeader);\r
+      wsInfo.setProgressText(OutputHeader);\r
       try {\r
         // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
         jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.getPredfile(), "Paste");\r