Uses of Package
org.biojavax

Packages that use org.biojavax

Package	Description
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio	Classes to represent biological entities and their relationships.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.db.ncbi	Interfaces to NCBI data.
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.
org.biojavax.ontology	Extensions to the biojava ontology model that represent BioSQL ontology.

Classes in org.biojavax used by org.biojavax

Class	Description
Comment	A simple ranked comment designed to be used for BioEntry comments in BioSQL.
CrossRef	Represents a cross reference to another database.
CrossReferenceResolutionException	An exception that indicates that an attempt to resolve a CrossRef has failed.
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.
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.

Classes in org.biojavax used by org.biojavax.bio

Class	Description
Comment	A simple ranked comment designed to be used for BioEntry comments in BioSQL.
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.

Classes in org.biojavax used by org.biojavax.bio.db.biosql

Class	Description
CrossRef	Represents a cross reference to another database.
CrossReferenceResolver	This interface returns symbols or sequence for a given cross-reference.
Note	Note is a generic class intended to hold a term describing the note, a value to associate with that term, and a rank.
RichObjectBuilder	This interface allows a class to generate Rich objects based on a class name and some parameters.

Classes in org.biojavax used by org.biojavax.bio.db.ncbi

Class	Description
Namespace	The namespace of an entry in a database schema.

Classes in org.biojavax used by org.biojavax.bio.seq

Class	Description
CrossRef	Represents a cross reference to another database.
CrossReferenceResolver	This interface returns symbols or sequence for a given cross-reference.
Namespace	The namespace of an entry in a database schema.
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.
RichAnnotatable	Annotatable objects that can have rich annotations.
RichAnnotation	An annotation collection which stores annotations as Note objects.

Classes in org.biojavax used by org.biojavax.bio.seq.io

Class	Description
Comment	A simple ranked comment designed to be used for BioEntry comments in BioSQL.
Namespace	The namespace of an entry in a database schema.
RankedCrossRef	Allows cross-references to other databases to be ranked.
RankedDocRef	Represents a documentary reference.

Classes in org.biojavax used by org.biojavax.ontology

Class	Description
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.