Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index b158448..2e3dddd 100644 (file)
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -20,7 +20,7 @@
  */
 package jalview.ws;
 
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -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.
@@ -128,17 +127,16 @@ public abstract class AWSThread extends Thread
               throw (new Exception(
                       "Timed out when communicating with server\nTry again later.\n"));
             }
-            jalview.bin.Cache.log.debug("Job " + j + " Result state "
-                    + jobs[j].getState() + "(ServerError="
-                    + jobs[j].isServerError() + ")");
+            Console.debug("Job " + j + " Result state " + jobs[j].getState()
+                    + "(ServerError=" + jobs[j].isServerError() + ")");
           } catch (Exception ex)
           {
             // 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
+            Console.warn(WebServiceName + " job(" + jobs[j].jobnum
                     + ") Server exception.");
             // todo: could limit trace to cause if this is a SOAPFaultException.
             ex.printStackTrace();
@@ -146,7 +144,7 @@ public abstract class AWSThread extends Thread
             if (jobs[j].allowedServerExceptions > 0)
             {
               jobs[j].allowedServerExceptions--;
-              Cache.log.debug("Sleeping after a server exception.");
+              Console.debug("Sleeping after a server exception.");
               try
               {
                 Thread.sleep(5000);
@@ -156,7 +154,7 @@ public abstract class AWSThread extends Thread
             }
             else
             {
-              Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+              Console.warn("Dropping job " + j + " " + jobs[j].jobId);
               jobs[j].subjobComplete = true;
               wsInfo.setStatus(jobs[j].jobnum,
                       WebserviceInfo.STATE_STOPPED_SERVERERROR);
@@ -168,10 +166,10 @@ public abstract class AWSThread extends Thread
             jobs[j].clearResponse(); // may contain out of date result data
             wsInfo.setStatus(jobs[j].jobnum,
                     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);
+            Console.error("Out of memory when retrieving Job " + j + " id:"
+                    + WsUrl + "/" + jobs[j].jobId, er);
+            new jalview.gui.OOMWarning(
+                    "retrieving result for " + WebServiceName, er);
             System.gc();
           }
         }
@@ -186,10 +184,9 @@ public abstract class AWSThread extends Thread
           Thread.sleep(5000);
         } catch (InterruptedException e)
         {
-          Cache.log
-                  .debug("Interrupted sleep waiting for next job poll.", e);
+          Console.debug("Interrupted sleep waiting for next job poll.", e);
         }
-        // System.out.println("I'm alive "+alTitle);
+        // jalview.bin.Console.outPrintln("I'm alive "+alTitle);
       }
     }
     if (jobComplete && jobs != null)
@@ -198,11 +195,11 @@ public abstract class AWSThread extends Thread
     }
     else
     {
-      Cache.log
-              .debug("WebServiceJob poll loop finished with no jobs created.");
+      Console.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 +381,7 @@ public abstract class AWSThread extends Thread
               .getCodonFrames();
       if (cf != null)
       {
-        codonframe = new LinkedHashSet<AlignedCodonFrame>();
+        codonframe = new ArrayList<AlignedCodonFrame>();
         codonframe.addAll(cf);
       }
     }