From 894a45573741b1b3a4a5d478499824ba653c3ae0 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 8 Aug 2017 11:18:12 +0100
Subject: [PATCH] JAL-2649 JAL-2650 wait for Conservation calc to complete
 before setting on new View coloured by Conservation

---
 src/jalview/viewmodel/AlignmentViewport.java |   14 ++++++++++++++
 test/jalview/gui/AlignFrameTest.java         |   14 +-------------
 2 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 5a7a27f..70f16d9 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -641,6 +641,20 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       if (getConservationSelected())
       {
+        int retry = 0;
+        synchronized (this)
+        {
+          while (isCalcInProgress() && retry < 10)
+          {
+            try
+            {
+              wait(50);
+              retry++;
+            } catch (InterruptedException e)
+            {
+            }
+          }
+        }
         residueShading.setConservation(hconservation);
       }
       residueShading.alignmentChanged(alignment, hiddenRepSequences);
diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index 1d8b240..af9c045 100644
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -26,7 +26,6 @@ import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
-import jalview.api.AlignCalcManagerI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.Alignment;
@@ -539,24 +538,13 @@ public class AlignFrameTest
             new String[] { "Background" }));
 
     /*
-     * make a new View, wait for Conservation thread to complete,
-     * verify alignment and group colour schemes
+     * make a new View, verify alignment and group colour schemes
      */
     af.newView_actionPerformed(null);
     assertEquals(af.alignPanel.getViewName(), "View 1");
     AlignViewport av2 = af.getViewport();
     assertNotSame(av, av2);
     assertSame(av2, af.alignPanel.av);
-    AlignCalcManagerI calcManager = av2.getCalcManager();
-    do
-    {
-      try
-      {
-        Thread.sleep(50);
-      } catch (InterruptedException x)
-      {
-      }
-    } while (calcManager.isWorking());
     rs = av2.getResidueShading();
     assertNotSame(av.getResidueShading(), rs);
     assertEquals(rs.getThreshold(), 10);
-- 
1.7.10.2