Uses of Interface
org.biojavax.bio.db.RichSequenceDB

Packages that use RichSequenceDB

Package	Description
org.biojavax.bio.db	Interactions between biojavax objects and a DB.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.db.ncbi	Interfaces to NCBI data.

Uses of RichSequenceDB in org.biojavax.bio.db

Classes in org.biojavax.bio.db that implement RichSequenceDB

Modifier and Type	Class and Description
class	AbstractRichSequenceDB An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.
class	HashRichSequenceDB An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.

Methods in org.biojavax.bio.db that return RichSequenceDB

Modifier and Type	Method and Description
RichSequenceDB	RichSequenceDBLite.getRichSequences(Set ids) Retrieve multiple RichSequence by its id.
RichSequenceDB	HashRichSequenceDB.getRichSequences(Set ids)
RichSequenceDB	RichSequenceDBLite.getRichSequences(Set ids, RichSequenceDB db) Retrieve multiple RichSequence into a specific sequence database.
RichSequenceDB	HashRichSequenceDB.getRichSequences(Set ids, RichSequenceDB db)

Methods in org.biojavax.bio.db with parameters of type RichSequenceDB

Modifier and Type	Method and Description
RichSequenceDB	RichSequenceDBLite.getRichSequences(Set ids, RichSequenceDB db) Retrieve multiple RichSequence into a specific sequence database.
RichSequenceDB	HashRichSequenceDB.getRichSequences(Set ids, RichSequenceDB db)

Uses of RichSequenceDB in org.biojavax.bio.db.biosql

Classes in org.biojavax.bio.db.biosql that implement RichSequenceDB

Modifier and Type	Class and Description
class	BioSQLRichSequenceDB

Methods in org.biojavax.bio.db.biosql that return RichSequenceDB

Modifier and Type	Method and Description
RichSequenceDB	BioSQLRichSequenceDB.getRichSequences(Set ids)
RichSequenceDB	BioSQLRichSequenceDB.getRichSequences(Set ids, RichSequenceDB db)

Methods in org.biojavax.bio.db.biosql with parameters of type RichSequenceDB

Modifier and Type	Method and Description
RichSequenceDB	BioSQLRichSequenceDB.getRichSequences(Set ids, RichSequenceDB db)

Uses of RichSequenceDB in org.biojavax.bio.db.ncbi

Classes in org.biojavax.bio.db.ncbi that implement RichSequenceDB

Modifier and Type	Class and Description
class	GenbankRichSequenceDB This class contains functions accessing DNA sequences in Genbank format.
class	GenpeptRichSequenceDB This class contains functions accessing Peptide sequences in Genpept format.

Methods in org.biojavax.bio.db.ncbi that return RichSequenceDB

Modifier and Type	Method and Description
RichSequenceDB	GenpeptRichSequenceDB.getRichSequences(Set list) Retrieve rich sequences from a Genbank
RichSequenceDB	GenbankRichSequenceDB.getRichSequences(Set list) Retrieve rich sequences from a Genbank
RichSequenceDB	GenpeptRichSequenceDB.getRichSequences(Set list, RichSequenceDB database) Retrieve rich sequences from a Genbank
RichSequenceDB	GenbankRichSequenceDB.getRichSequences(Set list, RichSequenceDB database) Retrieve rich sequences from a Genbank

Methods in org.biojavax.bio.db.ncbi with parameters of type RichSequenceDB

Modifier and Type	Method and Description
RichSequenceDB	GenpeptRichSequenceDB.getRichSequences(Set list, RichSequenceDB database) Retrieve rich sequences from a Genbank
RichSequenceDB	GenbankRichSequenceDB.getRichSequences(Set list, RichSequenceDB database) Retrieve rich sequences from a Genbank