[Biojava-l] AGAVE IO in BioJava

[Brian King]

We'd like to add IO support for the AGAVE XML format
(http://www.agavexml.org) into the BioJava library.  Creating the output
code in a SequenceFormat seems straightforward, but I'm confused about
input.  AGAVE and BioJava have hierarchies of features and hierarchies of
sequences to represent assembly, but the SeqIOListener doesn't have
interfaces for sub-features and sub-sequences.  Do I ignore this for now or
is there a way to do it?  

Regards,
Brian