Merge branch 'develop' into features/mchmmer

Conflicts:
	resources/lang/Messages.properties
	src/jalview/api/AlignViewportI.java
	src/jalview/datamodel/AlignmentAnnotation.java
	src/jalview/datamodel/Sequence.java
	src/jalview/datamodel/SequenceI.java
	src/jalview/gui/AlignFrame.java
	src/jalview/gui/AlignViewport.java
	src/jalview/gui/AnnotationLabels.java
	src/jalview/gui/PopupMenu.java
	src/jalview/gui/Preferences.java
	src/jalview/jbgui/GAlignFrame.java
	src/jalview/jbgui/GPreferences.java
	src/jalview/schemes/ResidueProperties.java
	src/jalview/viewmodel/AlignmentViewport.java