From 7bd8dd38f8ba6cbec54343bc4ac04ee21b8de776 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 8 Aug 2017 16:44:45 +0100
Subject: [PATCH] JAL-2560 alternative fix (reinstate lost line of code)

---
 src/jalview/viewmodel/AlignmentViewport.java |   19 +++++--------------
 1 file changed, 5 insertions(+), 14 deletions(-)

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 70f16d9..2881e81 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -641,22 +641,13 @@ 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);
       }
+      /*
+       * reset conservation flag in case just set to false if
+       * Conservation was null (calculation still in progress)
+       */
+      residueShading.setConservationApplied(getConservationSelected());
       residueShading.alignmentChanged(alignment, hiddenRepSequences);
     }
 
-- 
1.7.10.2