JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index edb56a9..156bd84 100644 (file)
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -28,8 +28,11 @@ import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.WebserviceInfo;
-import jalview.gui.FeatureRenderer.FeatureRendererSettings;
 import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+
+import java.util.LinkedHashSet;
+import java.util.Set;
 
 public abstract class AWSThread extends Thread
 {
@@ -57,7 +60,7 @@ public abstract class AWSThread extends Thread
   /**
    * dataset sequence relationships to be propagated onto new results
    */
-  protected AlignedCodonFrame[] codonframe = null;
+  protected Set<AlignedCodonFrame> codonframe = null;
 
   /**
    * are there jobs still running in this thread.
@@ -87,6 +90,11 @@ public abstract class AWSThread extends Thread
    */
   protected String WsUrl = null;
 
+  /*
+   * The AlignFrame from which the service was requested.
+   */
+  private AlignFrame alignFrame;
+
   /**
    * generic web service job/subjob poll loop
    */
@@ -124,8 +132,9 @@ public abstract class AWSThread extends Thread
           } catch (Exception ex)
           {
             // Deal with Transaction exceptions
-            wsInfo.appendProgressText(jobs[j].jobnum, 
-                       MessageManager.formatMessage("info.server_exception", new String[]{WebServiceName,ex.getMessage()}));
+            wsInfo.appendProgressText(jobs[j].jobnum, MessageManager
+                    .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.");
@@ -189,8 +198,9 @@ public abstract class AWSThread extends Thread
     {
       Cache.log
               .debug("WebServiceJob poll loop finished with no jobs created.");
-      wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
-      wsInfo.appendProgressText(MessageManager.getString("info.no_jobs_ran"));
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+      wsInfo.appendProgressText(MessageManager
+              .getString("info.no_jobs_ran"));
       wsInfo.setFinishedNoResults();
     }
   }
@@ -295,13 +305,12 @@ public abstract class AWSThread extends Thread
       SequenceI[] alignment = al.getSequencesArray();
       for (int sq = 0; sq < alignment.length; sq++)
       {
-        for (int i = 0; i < codonframe.length; i++)
+        for (AlignedCodonFrame acf : codonframe)
         {
-          if (codonframe[i] != null
-                  && codonframe[i].involvesSequence(alignment[sq]))
+          final SequenceI seq = alignment[sq];
+          if (acf != null && acf.involvesSequence(seq))
           {
-            al.addCodonFrame(codonframe[i]);
-            codonframe[i] = null;
+            al.addCodonFrame(acf);
             break;
           }
         }
@@ -360,7 +369,7 @@ public abstract class AWSThread extends Thread
           AlignmentView alview, String wsurl2)
   {
     super();
-    // this.alignFrame = alframe;
+    this.alignFrame = alframe;
     currentView = alframe.getCurrentView().getAlignment();
     featureSettings = alframe.getFeatureRenderer().getSettings();
     defGapChar = alframe.getViewport().getGapCharacter();
@@ -369,13 +378,18 @@ public abstract class AWSThread extends Thread
     WsUrl = wsurl2;
     if (alframe != null)
     {
-      AlignedCodonFrame[] cf = alframe.getViewport().getAlignment()
+      Set<AlignedCodonFrame> cf = alframe.getViewport().getAlignment()
               .getCodonFrames();
       if (cf != null)
       {
-        codonframe = new AlignedCodonFrame[cf.length];
-        System.arraycopy(cf, 0, codonframe, 0, cf.length);
+        codonframe = new LinkedHashSet<AlignedCodonFrame>();
+        codonframe.addAll(cf);
       }
     }
   }
+
+  protected AlignFrame getRequestingAlignFrame()
+  {
+    return this.alignFrame;
+  }
 }