From 9829b31986b83957217a6b9086665ef7be9b1c8c Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 10 May 2012 17:24:09 +0100
Subject: [PATCH] JAL-1085 - ensure sequence fetching client waits around
 until feature retrieval has finished before returning
 sequences for display.

---
 src/jalview/ws/DasSequenceFeatureFetcher.java              |   12 ++++++++++--
 .../ws/dbsources/das/datamodel/DasSequenceSource.java      |   10 ++++++++++
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index 2a5476b..bef6425 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -221,6 +221,7 @@ public class DasSequenceFeatureFetcher
   }
   private void _startFetching()
   {
+    running=true;
     new Thread(new FetchSeqFeatures()).start();
   }
   class FetchSeqFeatures implements Runnable
@@ -235,6 +236,7 @@ public class DasSequenceFeatureFetcher
   {
     public void run()
     {
+      running=true;
       new DBRefFetcher(sequences, af).fetchDBRefs(true);
       startFetching();
       setGuiFetchComplete();
@@ -246,6 +248,7 @@ public class DasSequenceFeatureFetcher
    */
   void startFetching()
   {
+    running=true;
     cancelled = false;
     startTime = System.currentTimeMillis();
     if (af != null)
@@ -546,10 +549,10 @@ public class DasSequenceFeatureFetcher
   }
 
   int sourcesRemaining = 0;
-
+  private boolean running=false;
   private void setGuiFetchComplete()
   {
-
+    running=false;
     if (!cancelled && af != null)
     {
       // only update the progress bar if we've completed the fetch normally
@@ -879,4 +882,9 @@ public class DasSequenceFeatureFetcher
     return type.getContent();
   }
 
+  public boolean isRunning()
+  {
+    return running;
+  }
+
 }
diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index 4f053aa..5f18331 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -275,6 +275,16 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
         {
           jalview.ws.DasSequenceFeatureFetcher dssf=new jalview.ws.DasSequenceFeatureFetcher(sqs, null, srcs, false,
                   false, multiple);
+          while (dssf.isRunning())
+          {
+            try {
+              Thread.sleep(200);
+            } catch (InterruptedException x)
+            {
+              
+            }
+          }
+          
         } catch (Exception x)
         {
           Cache.log
-- 
1.7.10.2