JAL-2738 copy to spikes/mungo

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

diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index b158448..80918f9 100644 (file)
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -31,9 +31,8 @@ import jalview.gui.WebserviceInfo;
 import jalview.util.MessageManager;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 
-import java.util.LinkedHashSet;
+import java.util.ArrayList;
 import java.util.List;
-import java.util.Set;
 
 public abstract class AWSThread extends Thread
 {
@@ -61,7 +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.
@@ -135,8 +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.");
@@ -170,8 +169,8 @@ public abstract class AWSThread extends Thread
                     WebserviceInfo.STATE_STOPPED_ERROR);
             Cache.log.error("Out of memory when retrieving Job " + j
                     + " id:" + WsUrl + "/" + jobs[j].jobId, er);
-            new jalview.gui.OOMWarning("retrieving result for "
-                    + WebServiceName, er);
+            new jalview.gui.OOMWarning(
+                    "retrieving result for " + WebServiceName, er);
             System.gc();
           }
         }
@@ -186,8 +185,8 @@ public abstract class AWSThread extends Thread
           Thread.sleep(5000);
         } catch (InterruptedException e)
         {
-          Cache.log
-                  .debug("Interrupted sleep waiting for next job poll.", e);
+          Cache.log.debug("Interrupted sleep waiting for next job poll.",
+                  e);
         }
         // System.out.println("I'm alive "+alTitle);
       }
@@ -198,11 +197,11 @@ public abstract class AWSThread extends Thread
     }
     else
     {
-      Cache.log
-              .debug("WebServiceJob poll loop finished with no jobs created.");
+      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();
     }
   }
@@ -384,7 +383,7 @@ public abstract class AWSThread extends Thread
               .getCodonFrames();
       if (cf != null)
       {
-        codonframe = new LinkedHashSet<AlignedCodonFrame>();
+        codonframe = new ArrayList<AlignedCodonFrame>();
         codonframe.addAll(cf);
       }
     }