From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 11 Mar 2019 15:07:39 +0000 (+0000)
Subject: Merge branch 'develop' into merge/JAL-3127
X-Git-Tag: Release_2_11_0~17^2~49
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8aa94d348698138bb5c30715ef0aa15349f47fbb;p=jalview.git

Merge branch 'develop' into merge/JAL-3127

Conflicts:
	src/jalview/viewmodel/AlignmentViewport.java
---

8aa94d348698138bb5c30715ef0aa15349f47fbb
diff --cc src/jalview/viewmodel/AlignmentViewport.java
index 850c68e,0ea31d7..148ea16
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@@ -662,7 -662,8 +662,8 @@@ public abstract class AlignmentViewpor
           * retain any colour thresholds per group while
           * changing choice of colour scheme (JAL-2386)
           */
-         sg.setColourScheme(cs.getInstance(this, sg));
+         sg.setColourScheme(
 -                cs == null ? null : cs.getInstance(sg, hiddenRepSequences));
++                cs == null ? null : cs.getInstance(this, sg));
          if (cs != null)
          {
            sg.getGroupColourScheme().alignmentChanged(sg,