Merge branch 'develop' into merge/JAL-3127

Conflicts:
	src/jalview/viewmodel/AlignmentViewport.java

diff --cc src/jalview/project/Jalview2XML.java
Simple merge

diff --cc src/jalview/viewmodel/AlignmentViewport.java
index 850c68e,0ea31d7..148ea16
--- 1/src/jalview/viewmodel/AlignmentViewport.java
--- 2/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,

diff --cc test/jalview/project/Jalview2xmlTests.java
Simple merge