X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=f0602c43812bbb138483609e92c956aeb91ad559;hb=1fe15a0bb2006a51a24f4757c89337d99db4ad26;hp=6ef07c60ec98ffdf2d597386d7dad3ee99a5281d;hpb=a883b8a87fe965a1d04f67b6f82c985b0b2c8605;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 6ef07c6..f0602c4 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -20,8 +20,6 @@ package jalview.ws.jws2;
 import java.util.*;
 
 import compbio.data.msa.MsaWS;
-import compbio.data.sequence.AlignmentMetadata;
-import compbio.data.sequence.Program;
 import compbio.metadata.Argument;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
@@ -586,7 +584,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
   {
     StringBuffer response = j.jobProgress;
     long lastchunk = j.getLastChunk();
-    boolean changed=false;
+    boolean changed = false;
     do
     {
       j.setLastChunk(lastchunk);
@@ -594,12 +592,16 @@ class MsaWSThread extends AWS2Thread implements WSClientI
               .pullExecStatistics(j.getJobId(), lastchunk);
       if (chunk != null)
       {
-        changed|=chunk.getChunk().length()>0;
+        changed |= chunk.getChunk().length() > 0;
         response.append(chunk.getChunk());
         lastchunk = chunk.getNextPosition();
-        try {
+        try
+        {
           Thread.sleep(50);
-        } catch (InterruptedException x){};
+        } catch (InterruptedException x)
+        {
+        }
+        ;
       }
       ;
     } while (lastchunk >= 0 && j.getLastChunk() != lastchunk);
@@ -643,7 +645,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       }
       else if (j.hasArguments())
       {
-        j.setJobId(server.customAlign(j.seqs,j.getJabaArguments()));
+        j.setJobId(server.customAlign(j.seqs, j.getJabaArguments()));
       }
       else
       {
@@ -729,7 +731,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
 
   public void parseResult()
   {
-    long progbar=System.currentTimeMillis();
+    long progbar = System.currentTimeMillis();
     wsInfo.setProgressBar("Collecting job results.", progbar);
     int results = 0; // number of result sets received
     JobStateSummary finalState = new JobStateSummary();
@@ -740,42 +742,45 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         MsaWSJob msjob = ((MsaWSJob) jobs[j]);
         if (jobs[j].isFinished() && msjob.alignment == null)
         {
-          int nunchanged=3,nexcept=3;
-          boolean jpchanged=false,jpex=false;
-          do {
+          int nunchanged = 3, nexcept = 3;
+          boolean jpchanged = false, jpex = false;
+          do
+          {
             try
             {
               jpchanged = updateJobProgress(msjob);
-              jpex=false;
-              if (jpchanged) {
-                nexcept=3;
+              jpex = false;
+              if (jpchanged)
+              {
+                nexcept = 3;
               }
             } catch (Exception e)
             {
-              
+
               Cache.log
                       .warn("Exception when retrieving remaining Job progress data for job "
                               + msjob.getJobId() + " on server " + WsUrl);
               e.printStackTrace();
               nexcept--;
-              nunchanged=3;
+              nunchanged = 3;
               // set flag remember that we've had an exception.
-              jpex=true;
-              jpchanged=false;
+              jpex = true;
+              jpchanged = false;
             }
             if (!jpchanged)
             {
               try
               {
-                Thread.sleep(jpex ? 2400 : 1200); // wait a bit longer if we experienced an exception.
+                Thread.sleep(jpex ? 2400 : 1200); // wait a bit longer if we
+                                                  // experienced an exception.
               } catch (Exception ex)
               {
               }
               ;
               nunchanged--;
-            } 
-          } while (nunchanged>0 && nexcept>0);
-          
+            }
+          } while (nunchanged > 0 && nexcept > 0);
+
           if (Cache.log.isDebugEnabled())
           {
             System.out.println("Job Execution file for job: "