X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=d625918c56f8407b705a284391bf2f1b4d9a4d18;hb=d1bb7a31fc091606aedbc255a5766ac79e36fa91;hp=5070884c8264651c68c02f2361a2710c641db31b;hpb=29ac9aa26871544cbbd43f4ea313144a6bd8ae39;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 5070884..d625918 100644
--- 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);