From cb0513773f8588e6b8c4ae0e53af66e7b43b998b Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 14 Jun 2012 11:45:28 +0100
Subject: [PATCH] JAL-1003 visual delay when running a sequence or alignment
 annotation job

---
 src/jalview/ws/jws2/JabawsAlignCalcWorker.java |   16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
index 1f5250a..eb898b3 100644
--- a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
@@ -8,6 +8,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.IProgressIndicator;
 import jalview.workers.AlignCalcWorker;
 import jalview.ws.jws2.dm.JabaWsParamSet;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -47,10 +48,13 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
     super(alignViewport, alignPanel);
   }
 
+  IProgressIndicator guiProgress;
+
   public JabawsAlignCalcWorker(Jws2Instance service, AlignFrame alignFrame,
           WsParamSetI preset, List<Argument> paramset)
   {
     this(alignFrame.getCurrentView(), alignFrame.alignPanel);
+    this.guiProgress = alignFrame;
     this.preset = preset;
     this.arguments = paramset;
     aaservice = (SequenceAnnotation) service.service;
@@ -132,6 +136,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
     {
       return;
     }
+    long progressId = -1;
 
     String rslt = "JOB NOT DEFINED";
 
@@ -152,7 +157,11 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
 
       AlignmentAnnotation[] aa = alignViewport.getAlignment()
               .getAlignmentAnnotation();
-
+      if (guiProgress != null)
+      {
+        guiProgress.setProgressBar("JABA " + getServiceActionText(),
+                progressId = System.currentTimeMillis());
+      }
       if (preset == null)
       {
         rslt = aaservice.analize(seqs);
@@ -268,6 +277,11 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
       calcMan.workerComplete(this);
       if (ap != null)
       {
+        calcMan.workerComplete(this);
+        if (guiProgress != null)
+        {
+          guiProgress.setProgressBar("", progressId);
+        }
         ap.paintAlignment(true);
       }
     }
-- 
1.7.10.2