Classes for converting between AGAVE XML and BioJava objects. Use AGAVEHandler with a SAX parser to parse AGAVE XML into BioJava Sequences, and use AgaveWriter to write BioJava Sequences into AGAVE format. When writing BioJava to AGAVE we need to specify how the data in BioJava stored. Two conversion filters are implemented. The Agave2AgaveAnnotFilter helps write data that was parsed from AGAVE, and Embl2AgaveAnnotFilter helps write data that was parsed from EMBL. This package uses a modified version of the BioJava StAX parser architecture that supports nested features.