JAL-1269 is fixed by this merge
Conflicts:
.classpath
src/jalview/appletgui/AlignFrame.java
src/jalview/io/RnamlFile.java
src/jalview/io/StockholmFile.java
src/jalview/io/TCoffeeScoreFile.java
src/jalview/renderer/AnnotationRenderer.java
test/jalview/io/TCoffeeScoreFileTest.java