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 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.