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

Packages that use SequenceDBLite
org.biojava.bio.program.das: Development client for the Distributed Annotation System.
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.program.das

Classes in org.biojava.bio.program.das that implement SequenceDBLite
`class` `DASSequenceDB` Collection of sequences retrieved from the DAS network.

Methods in org.biojava.bio.program.das that return SequenceDBLite
`SequenceDBLite` `DASSequenceDB.allEntryPointsDB()`
`SequenceDBLite` `DASSequenceDBProvider.getSequenceDB(Map config)`

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

Subinterfaces of SequenceDBLite in org.biojava.bio.seq.db
`interface` `SequenceDB` A database of sequences with accessible keys and iterators over all sequences.

Classes in org.biojava.bio.seq.db that implement SequenceDBLite
`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
`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
`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
`class` `BioFetchSequenceDB` Simple SequenceDB implementation backed by a BioFetch (HTTP) server.

Methods in org.biojava.bio.seq.db.biofetch that return SequenceDBLite
`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
`class` `BioSQLSequenceDB` Deprecated. Use hibernate and org.biojavax.bio.db.*

Methods in org.biojava.bio.seq.db.biosql that return SequenceDBLite
`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
`class` `FlatSequenceDB` `FlatSequenceDB` is an OBDA flatfile sequence databank implementation.

Methods in org.biojava.bio.seq.db.flat that return SequenceDBLite
`SequenceDBLite` `FlatSequenceDBProvider.getSequenceDB(Map config)`

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

Classes in org.biojava.bio.seq.distributed that implement SequenceDBLite
`class` `DistributedSequenceDB` Sequence database from the meta-DAS system.

Uses of SequenceDBLite in org.biojava.directory

Methods in org.biojava.directory that return SequenceDBLite
`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
`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
`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
`class` `BioSQLRichSequenceDB`

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

Classes in org.biojavax.bio.db.ncbi that implement SequenceDBLite
`class` `GenbankRichSequenceDB` This class contains functions accessing DNA sequences in Genbank format.
`class` `GenpeptRichSequenceDB` This class contains functions accessing Peptide sequences in Genpept format.