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 CommentA simple ranked comment designed to be used for BioEntry comments in BioSQL. CrossRefRepresents a cross reference to another database. CrossReferenceResolverThis interface returns symbols or sequence for a given cross-reference. DocRefRepresents a documentary reference. DocRefAuthorRepresents an author of a documentary reference. NamespaceThe namespace of an entry in a database schema. NoteNote is a generic class intended to hold a term describing the note, a value to associate with that term, and a rank. RankedCrossRefAllows cross-references to other databases to be ranked. RankedCrossRefableDefines an object as being able to have ranked cross references associated with it. RankedDocRefRepresents a documentary reference. RichAnnotatableAnnotatable objects that can have rich annotations. RichAnnotationAn annotation collection which stores annotations as Note objects. RichObjectBuilderThis interface allows a class to generate Rich objects based on a class name and some parameters.
Class Summary Class Description DocRefAuthor.ToolsUseful tools for working with authors. DummyCrossReferenceResolverA simple implementation of CrossReferenceResolver. EmptyRichAnnotationA place holder for a RichAnnotation that prevents null having to be used RichObjectFactoryRuns a service that builds rich objects, and provides some default values for things like default ontology, default namespace, etc. SimpleCommentAn implementaion of Comment. SimpleCrossRefA basic CrossRef implementation. SimpleDocRefA basic DocRef implementation. SimpleDocRefAuthorRepresents an author of a documentary reference. SimpleNamespaceA basic Namespace implemenation. SimpleNoteSimple implementation of Note. SimpleRankedCrossRefSimple implementation of RankedCrossRef. SimpleRankedDocRefRepresents a documentary reference. SimpleRichAnnotationSimple annotation wrapper. SimpleRichObjectBuilderCreates objects and returns them, and stores them in an internal map of singletons for reference.
Exception Summary Exception Description CrossReferenceResolutionExceptionAn exception that indicates that an attempt to resolve a