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 The biojavax packages contain a number of extensions to the core biojava interfaces.
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 and 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 and 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 and 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 and Description
Namespace The namespace of an entry in a database schema.

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

Class and 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 and 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 and 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.