Annotation files extension with colour by annotation, threshold, and annotation visibility

Requested by Daron Handley via help and jalview-discuss. Should be able to store and recall colour by annotation settings for a group or for the background colouring on the alignment using the annotation file. Should also be able to set annotation visibility state using annotation file.


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This is a TODO for 2.5. Consider extending Applet api to add these capabilities dynamically.