Package org.biojavax

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.

Interface Summary

Interface	Description
Comment	A simple ranked comment designed to be used for BioEntry comments in BioSQL.
CrossRef	Represents a cross reference to another database.
CrossReferenceResolver	This interface returns symbols or sequence for a given cross-reference.
DocRef	Represents a documentary reference.
DocRefAuthor	Represents an author of a documentary reference.
Namespace	The namespace of an entry in a database schema.
Note	Note is a generic class intended to hold a term describing the note, a value to associate with that term, and a rank.
RankedCrossRef	Allows cross-references to other databases to be ranked.
RankedCrossRefable	Defines an object as being able to have ranked cross references associated with it.
RankedDocRef	Represents a documentary reference.
RichAnnotatable	Annotatable objects that can have rich annotations.
RichAnnotation	An annotation collection which stores annotations as Note objects.
RichObjectBuilder	This interface allows a class to generate Rich objects based on a class name and some parameters.

Class Summary

Class	Description
DocRefAuthor.Tools	Useful tools for working with authors.
DummyCrossReferenceResolver	A simple implementation of CrossReferenceResolver.
EmptyRichAnnotation	A place holder for a RichAnnotation that prevents null having to be used
RichObjectFactory	Runs a service that builds rich objects, and provides some default values for things like default ontology, default namespace, etc.
SimpleComment	An implementaion of Comment.
SimpleCrossRef	A basic CrossRef implementation.
SimpleDocRef	A basic DocRef implementation.
SimpleDocRefAuthor	Represents an author of a documentary reference.
SimpleNamespace	A basic Namespace implemenation.
SimpleNote	Simple implementation of Note.
SimpleRankedCrossRef	Simple implementation of RankedCrossRef.
SimpleRankedDocRef	Represents a documentary reference.
SimpleRichAnnotation	Simple annotation wrapper.
SimpleRichObjectBuilder	Creates objects and returns them, and stores them in an internal map of singletons for reference.

Exception Summary

Exception	Description
CrossReferenceResolutionException	An exception that indicates that an attempt to resolve a CrossRef has failed.