org.biojavax.package.html Maven / Gradle / Ivy
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.