Uses of Interface org.biojava.bio.seq.db.SequenceDBLite (BioJava-1.5-beta API)

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## 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 |
org.biojavax.bio.db.ncbi |

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` | `DummySequenceDBInstallation.getSequenceDB(String identifier)`
`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.

Methods in org.biojava.bio.seq.db with parameters of type SequenceDBLite
`void` | `DummySequenceDBInstallation.addSequenceDB(SequenceDBLite sequenceDB, Set otherIdentifiers)` As this is a dummy implementation adding a sequenceDB doesn't do anything
`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.

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.

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