The package sbc.orthoxml.io contains the OrthoXMLReader class for reading OrthoXML and the OrthoXMLWriter for writing. The data structures are defined in the package sbc.orthoxml and mostly resemble the tag types of OrthoXML. The most important class is the Group class which in contrast to the OrthoXML format contains the genes directly. The IO classes transparently hides the global definition and local referencing and allows stream parsing and writing of ortholog groups. The genes are encapsulated into Membership objects to allow scoring of the genes but connivence methods exist to access the genes directly. For more details see the API documentation.

Simple examples for reading and writing OrthoXML with Java: