Merge branch 'patch/JAL-2663_filterAACons' into develop

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index d472ef8..ffbe6a1 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -4489,8 +4489,8 @@ 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);