Uses of Interface
org.biojava.bio.seq.db.SequenceDBLite
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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 databasesorg.biojavax.bio.db.ncbi Interfaces to NCBI data. -
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Uses of SequenceDBLite in org.biojava.bio.seq.db
Subinterfaces of SequenceDBLite in org.biojava.bio.seq.db Modifier and Type Interface 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 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 aDummySequence
.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 Description SequenceDBLite
DummySequenceDBInstallation. getSequenceDB(String identifier)
SequenceDBLite
SequenceDBInstallation. getSequenceDB(String identifier)
Return the SequenceDB for the given 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.Methods in org.biojava.bio.seq.db with parameters of type SequenceDBLite Modifier and Type Method Description void
DummySequenceDBInstallation. addSequenceDB(SequenceDBLite sequenceDB, Set otherIdentifiers)
As this is a dummy implementation adding a sequenceDB doesn't do anythingvoid
SequenceDBInstallation. addSequenceDB(SequenceDBLite sequenceDB, Set otherIdentifiers)
addSequenceDB
adds a newSequenceDB
under its own identifier which will additionally be recognised by the set of other identifiers.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. -
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 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 Description SequenceDBLite
BioFetchSequenceDBProvider. getSequenceDB(Map config)
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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 Description class
BioSQLSequenceDB
Deprecated.Use hibernate and org.biojavax.bio.dbMethods in org.biojava.bio.seq.db.biosql that return SequenceDBLite Modifier and Type Method 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 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 Description SequenceDBLite
FlatSequenceDBProvider. getSequenceDB(Map config)
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Uses of SequenceDBLite in org.biojava.bio.seq.distributed
Classes in org.biojava.bio.seq.distributed that implement SequenceDBLite Modifier and Type Class 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 Description SequenceDBLite
Registry. getDatabase(String dbName)
getDatabase
retrieves a database instance known by a nameString
.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 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 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 Description class
BioSQLRichSequenceDB
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Uses of SequenceDBLite in org.biojavax.bio.db.ncbi
Classes in org.biojavax.bio.db.ncbi that implement SequenceDBLite Modifier and Type Class 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.
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