JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index e557614..2ef5256 100644 (file)
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -31,8 +31,8 @@ import jalview.gui.WebserviceInfo;
 import jalview.util.MessageManager;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 
-import java.util.LinkedHashSet;
-import java.util.Set;
+import java.util.ArrayList;
+import java.util.List;
 
 public abstract class AWSThread extends Thread
 {
@@ -60,7 +60,7 @@ public abstract class AWSThread extends Thread
   /**
    * dataset sequence relationships to be propagated onto new results
    */
-  protected Set<AlignedCodonFrame> codonframe = null;
+  protected List<AlignedCodonFrame> codonframe = null;
 
   /**
    * are there jobs still running in this thread.
@@ -98,6 +98,7 @@ public abstract class AWSThread extends Thread
   /**
    * generic web service job/subjob poll loop
    */
+  @Override
   public void run()
   {
     JobStateSummary jstate = null;
@@ -133,8 +134,8 @@ public abstract class AWSThread extends Thread
           {
             // Deal with Transaction exceptions
             wsInfo.appendProgressText(jobs[j].jobnum, MessageManager
-                    .formatMessage("info.server_exception", new Object[]
-                    { WebServiceName, ex.getMessage() }));
+                    .formatMessage("info.server_exception", new Object[] {
+                        WebServiceName, ex.getMessage() }));
             // always output the exception's stack trace to the log
             Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
                     + ") Server exception.");
@@ -199,7 +200,8 @@ public abstract class AWSThread extends Thread
       Cache.log
               .debug("WebServiceJob poll loop finished with no jobs created.");
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-      wsInfo.appendProgressText(MessageManager.getString("info.no_jobs_ran"));
+      wsInfo.appendProgressText(MessageManager
+              .getString("info.no_jobs_ran"));
       wsInfo.setFinishedNoResults();
     }
   }
@@ -377,11 +379,11 @@ public abstract class AWSThread extends Thread
     WsUrl = wsurl2;
     if (alframe != null)
     {
-      Set<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
+      List<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
               .getCodonFrames();
       if (cf != null)
       {
-        codonframe = new LinkedHashSet<AlignedCodonFrame>();
+        codonframe = new ArrayList<AlignedCodonFrame>();
         codonframe.addAll(cf);
       }
     }