## Package org.biojavax

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

See:
Description

Interface Summary
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
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
CrossReferenceResolutionException: An exception that indicates that an attempt to resolve a `CrossRef` has failed.

## Package org.biojavax Description

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.