Uses of Package
org.biojavax

Packages that use org.biojavax

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
org.biojavax.bio.db.ncbi
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

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

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.

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.

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

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

Namespace
The namespace of an entry in a database schema.

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

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.

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

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

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.