Uses of Interface
org.biojava.bio.seq.db.SequenceDBLite

Packages that use SequenceDBLite

Package	Description
org.biojava.bio.seq.db	Collections of biological sequence data.
org.biojava.bio.seq.db.biofetch	Client for the OBDA BioFetch protocol.
org.biojava.bio.seq.db.biosql	General purpose Sequence storage in a relational database.
org.biojava.bio.seq.db.flat	Support for OBDA flatfile databases.
org.biojava.bio.seq.distributed	Sequences and SequenceDBs which are composed from data taken from a number of data sources.
org.biojava.directory	Open Bio Sequence Database Access (OBDA) registry support.
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 SequenceDBLite in org.biojava.bio.seq.db

Subinterfaces of SequenceDBLite in org.biojava.bio.seq.db

Modifier and Type	Interface and Description
interface	SequenceDB A database of sequences with accessible keys and iterators over all sequences.

Classes in org.biojava.bio.seq.db that implement SequenceDBLite

Modifier and Type	Class and Description
class	AbstractSequenceDB An abstract implementation of SequenceDB that provides the sequenceIterator method.
class	AnnotatedSequenceDB SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.
class	CachingSequenceDB SequenceDB implementation that caches the results of another SequenceDB.
class	DummySequenceDB DummySequenceDB is an implementation which contains only a DummySequence.
class	HashSequenceDB An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.
class	IndexedSequenceDB This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.
class	NCBISequenceDB
class	SequenceDBWrapper An abstract implementation of SequenceDB that wraps up another database.
class	SubSequenceDB
class	ViewingSequenceDB SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.
class	WebSequenceDB Functions for access to a web based database that returns sequences in a variety of formats.

Methods in org.biojava.bio.seq.db that return SequenceDBLite

Modifier and Type	Method and Description
SequenceDBLite	SimpleSequenceDBInstallation.getSequenceDB(String identifier) If the given identifier is known to this sequence db installation because it has been used in a call to addSequenceDB(), then this method returns the SequenceDB associated with this identifier.
SequenceDBLite	SequenceDBInstallation.getSequenceDB(String identifier) Return the SequenceDB for the given identifier.
SequenceDBLite	DummySequenceDBInstallation.getSequenceDB(String identifier)

Methods in org.biojava.bio.seq.db with parameters of type SequenceDBLite

Modifier and Type	Method and Description
void	SimpleSequenceDBInstallation.addSequenceDB(SequenceDBLite sequenceDB, Set otherIdentifiers) addSequenceDB adds a new SequenceDB which will be accessible via the name returned by its getName() method and via all other given identifiers.
void	SequenceDBInstallation.addSequenceDB(SequenceDBLite sequenceDB, Set otherIdentifiers) addSequenceDB adds a new SequenceDB under its own identifier which will additionally be recognised by the set of other identifiers.
void	DummySequenceDBInstallation.addSequenceDB(SequenceDBLite sequenceDB, Set otherIdentifiers) As this is a dummy implementation adding a sequenceDB doesn't do anything

Uses of SequenceDBLite in org.biojava.bio.seq.db.biofetch

Classes in org.biojava.bio.seq.db.biofetch that implement SequenceDBLite

Modifier and Type	Class and Description
class	BioFetchSequenceDB Simple SequenceDB implementation backed by a BioFetch (HTTP) server.

Methods in org.biojava.bio.seq.db.biofetch that return SequenceDBLite

Modifier and Type	Method and Description
SequenceDBLite	BioFetchSequenceDBProvider.getSequenceDB(Map config)

Uses of SequenceDBLite in org.biojava.bio.seq.db.biosql

Classes in org.biojava.bio.seq.db.biosql that implement SequenceDBLite

Modifier and Type	Class and Description
class	BioSQLSequenceDB Deprecated. Use hibernate and org.biojavax.bio.db.*

Methods in org.biojava.bio.seq.db.biosql that return SequenceDBLite

Modifier and Type	Method and Description
SequenceDBLite	BioSQLSequenceDBProvider.getSequenceDB(Map config) Deprecated.

Uses of SequenceDBLite in org.biojava.bio.seq.db.flat

Classes in org.biojava.bio.seq.db.flat that implement SequenceDBLite

Modifier and Type	Class and Description
class	FlatSequenceDB FlatSequenceDB is an OBDA flatfile sequence databank implementation.

Methods in org.biojava.bio.seq.db.flat that return SequenceDBLite

Modifier and Type	Method and Description
SequenceDBLite	FlatSequenceDBProvider.getSequenceDB(Map config)

Uses of SequenceDBLite in org.biojava.bio.seq.distributed

Classes in org.biojava.bio.seq.distributed that implement SequenceDBLite

Modifier and Type	Class and Description
class	DistributedSequenceDB Sequence database from the meta-DAS system.

Uses of SequenceDBLite in org.biojava.directory

Methods in org.biojava.directory that return SequenceDBLite

Modifier and Type	Method and Description
SequenceDBLite	Registry.getDatabase(String dbName) getDatabase retrieves a database instance known by a name String.
SequenceDBLite	SequenceDBProvider.getSequenceDB(Map config) Get a sequence database.

Uses of SequenceDBLite in org.biojavax.bio.db

Subinterfaces of SequenceDBLite in org.biojavax.bio.db

Modifier and Type	Interface and Description
interface	RichSequenceDB A database of RichSequences with accessible keys and iterators over all sequences.
interface	RichSequenceDBLite A database of RichSequences.

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

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.

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

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

Modifier and Type	Class and Description
class	BioSQLRichSequenceDB

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

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

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.