Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 5070884..d625918 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -4484,8 +4484,8 @@ public class Jalview2XML
     }
 
     af.viewport.setGlobalColourScheme(cs);
-    af.viewport.getResidueShading().setThreshold(
-            view.getPidThreshold(), true);
+    af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
+            view.getIgnoreGapsinConsensus());
     af.viewport.getResidueShading().setConsensus(
             af.viewport.getSequenceConsensusHash());
     af.viewport.setColourAppliesToAllGroups(false);