From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 14 Aug 2017 09:34:44 +0000 (+0100)
Subject: Merge branch 'patch/JAL-2663_filterAACons' into develop
X-Git-Tag: Release_2_10_2~3^2~6^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=17bd8a1b37531e1f2338e0b3fbdf9d0c8d753dc8;hp=fda3adcb9abc603b03188404f532a5bc8097dd55;p=jalview.git

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
--- 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);