Uses of Interface
org.biojava.bio.seq.db.SequenceDBLite
Packages that use SequenceDBLite
Package
Description
Collections of biological sequence data.
Client for the OBDA BioFetch protocol.
General purpose Sequence storage in a relational database.
Support for OBDA flatfile databases.
Sequences and SequenceDBs which are composed from data taken
from a number of data sources.
Open Bio Sequence Database Access (OBDA) registry support.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
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.dbModifier and TypeInterfaceDescriptioninterface
A database of sequences with accessible keys and iterators over all sequences.Classes in org.biojava.bio.seq.db that implement SequenceDBLiteModifier and TypeClassDescriptionclass
An abstract implementation of SequenceDB that provides the sequenceIterator method.class
SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.class
SequenceDB implementation that caches the results of another SequenceDB.class
DummySequenceDB
is an implementation which contains only aDummySequence
.class
An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.final class
This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.class
class
An abstract implementation of SequenceDB that wraps up another database.class
class
SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.class
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 SequenceDBLiteModifier and TypeMethodDescriptionDummySequenceDBInstallation.getSequenceDB
(String identifier) SequenceDBInstallation.getSequenceDB
(String identifier) Return the SequenceDB for the given identifier.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 SequenceDBLiteModifier and TypeMethodDescriptionvoid
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 SequenceDBLiteModifier and TypeClassDescriptionclass
Simple SequenceDB implementation backed by a BioFetch (HTTP) server.Methods in org.biojava.bio.seq.db.biofetch that return SequenceDBLite -
Uses of SequenceDBLite in org.biojava.bio.seq.db.biosql
Classes in org.biojava.bio.seq.db.biosql that implement SequenceDBLiteModifier and TypeClassDescriptionclass
Deprecated.Use hibernate and org.biojavax.bio.dbMethods in org.biojava.bio.seq.db.biosql that return SequenceDBLite -
Uses of SequenceDBLite in org.biojava.bio.seq.db.flat
Classes in org.biojava.bio.seq.db.flat that implement SequenceDBLiteModifier and TypeClassDescriptionclass
FlatSequenceDB
is an OBDA flatfile sequence databank implementation.Methods in org.biojava.bio.seq.db.flat that return SequenceDBLite -
Uses of SequenceDBLite in org.biojava.bio.seq.distributed
Classes in org.biojava.bio.seq.distributed that implement SequenceDBLiteModifier and TypeClassDescriptionclass
Sequence database from the meta-DAS system. -
Uses of SequenceDBLite in org.biojava.directory
Methods in org.biojava.directory that return SequenceDBLiteModifier and TypeMethodDescriptionRegistry.getDatabase
(String dbName) getDatabase
retrieves a database instance known by a nameString
.SequenceDBProvider.getSequenceDB
(Map config) Get a sequence database. -
Uses of SequenceDBLite in org.biojavax.bio.db
Subinterfaces of SequenceDBLite in org.biojavax.bio.dbModifier and TypeInterfaceDescriptioninterface
A database of RichSequences with accessible keys and iterators over all sequences.interface
A database of RichSequences.Classes in org.biojavax.bio.db that implement SequenceDBLiteModifier and TypeClassDescriptionclass
An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.class
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 -
Uses of SequenceDBLite in org.biojavax.bio.db.ncbi
Classes in org.biojavax.bio.db.ncbi that implement SequenceDBLiteModifier and TypeClassDescriptionclass
This class contains functions accessing DNA sequences in Genbank format.class
This class contains functions accessing Peptide sequences in Genpept format.