The Biojava extensions packages, classes that extend the core biojava functionality

The biojavax packages contain a number of extensions to the core biojava interfaces. These extensions are designed to very closely model the OBDA BioSQL database schema. Several new classes are introduced and their relationships are best explained by the BioSQL schema.

The interfaces of most interest to users will be the BioEntry and the RichSequence. The BioEntry holds key description information about a biological entity but no actual sequence. This allows consistent description of biological records that may or may not have sequence. The RichSequence interface is an extension of Sequence and BioEntry. Think of it as an old fashioned biojava Sequence with more accessors that let you get at the information with some funky relationship capabilities thrown in.

Where possible we have made extensive use of interfaces and multiple inheritance (via interfaces). Hence, RichSequence can be used whenever a Sequence is required. RichAnnotation can often be substituted for Annotation etc.

The basic implementations are also designed to work with Hibernate allowing easy persitence to a BioSQL db.