Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure...

Merge branch 'develop' into feature/JAL-4386_calculate_tree_using_secondary_structure_annotation

# Conflicts:
#	src/jalview/analysis/AAFrequency.java
#	src/jalview/analysis/AlignmentUtils.java
#	src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java
#	src/jalview/api/AlignViewportI.java
#	src/jalview/datamodel/Profile.java
#	src/jalview/datamodel/SequenceGroup.java
#	src/jalview/gui/AlignFrame.java
#	src/jalview/gui/AlignViewport.java
#	src/jalview/gui/PopupMenu.java
#	src/jalview/jbgui/GAlignFrame.java
#	src/jalview/project/Jalview2XML.java
#	src/jalview/renderer/AnnotationRenderer.java
#	src/jalview/renderer/ResidueShader.java
#	src/jalview/renderer/ResidueShaderI.java
#	src/jalview/util/Constants.java
#	src/jalview/viewmodel/AlignmentViewport.java
#	src/jalview/workers/SecondaryStructureConsensusThread.java
#	test/jalview/analysis/AlignmentUtilsTests.java