formatting

[jalview.git] / src / jalview / ws / jws2 / MsaWSThread.java

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 6ef07c6..9af205f 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -586,7 +586,7 @@ 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 +594,16 @@ 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 +647,7 @@ 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 +733,7 @@ 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 +744,45 @@ 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: "