avoid race condition by setting sequence logo flag directly rather than via accessor...

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 63695b6..eedc863 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -589,6 +589,7 @@ public class AlignViewport implements SelectionSource
 
     protected void updateAnnotation(boolean immediate)
     {
+      // TODO: make calls thread-safe, so if another thread calls this method, it will either return or wait until one calculation is finished.
       if (immediate
               || (!updatingConsensus && consensus != null && hconsensus != null))
       {

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 4b6879c..fd93d7f 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2877,11 +2877,11 @@ public class Jalview2XML
     }
     if (view.hasShowSequenceLogo())
     {
-      af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
+      af.viewport.showSequenceLogo = view.getShowSequenceLogo();
     }
     else
     {
-      af.viewport.setShowSequenceLogo(false);
+      af.viewport.showSequenceLogo = false;
     }
     if (view.hasShowDbRefTooltip())
     {