Merge remote-tracking branch 'origin/Tcoffee_JAL-1065' into develop conflicts due to refactoring according to JAL-972, JAL-968, JAL-968 Conflicts: .classpath examples/appletParameters.html src/jalview/appletgui/AlignFrame.java src/jalview/appletgui/AlignViewport.java src/jalview/datamodel/SequenceGroup.java src/jalview/gui/AlignFrame.java src/jalview/gui/AlignViewport.java src/jalview/jbgui/GAlignFrame.java