Package org.biojava.bio.seq.db

Collections of biological sequence data. This package contains SequenceDB, a simple interface for objects which allow sequences to be retrieved by name, and several useful SequenceDB implementations.

Interface Summary

Interface	Description
IDMaker	Interface for objects that define how to make an ID for a sequence.
Index	This defines an index entry for an individual sequence within a set of indexed files.
IndexStore	This defines the objects that IndexedSequenceDB uses to store all of the database state, such as name, format, sequence builder and the actual file offsets.
SequenceDB	A database of sequences with accessible keys and iterators over all sequences.
SequenceDBInstallation	A SequenceDBInstallation has the functionality of a factory for SequenceDB objects and additionally manages the SequenceDB objects created by itself such that the minimum number of SequenceDB objects is created by a particular SequenceDBInstallation object.
SequenceDBLite	A database of sequences.

Class Summary

Class	Description
AbstractSequenceDB	An abstract implementation of SequenceDB that provides the sequenceIterator method.
AnnotatedSequenceDB	SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.
BioIndex	The original object for indexing sequence files.
CachingSequenceDB	SequenceDB implementation that caches the results of another SequenceDB.
DummySequenceDB	DummySequenceDB is an implementation which contains only a DummySequence.
DummySequenceDBInstallation	DummySequenceDBInstallation is an implementation which returns the same DummySequenceDB instance regardless of the identifier used to retrieve a database.
EmblCDROMIndexStore	EmblCDROMIndexStores implement a read-only IndexStore backed by EMBL CD-ROM format binary indices.
FetchURL
GenbankSequenceDB	This class contains functions accessing DNA sequences in Genbank format.
GenpeptSequenceDB
HashSequenceDB	An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.
IDMaker.ByName
IDMaker.ByURN
IndexedSequenceDB	This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.
NCBISequenceDB
SequenceDBWrapper	An abstract implementation of SequenceDB that wraps up another database.
SimpleIndex	This is a no-frills implementation of the Index interface.
SimpleSequenceDBInstallation	This class is an implementation of interface SequenceDBInstallation that manages a set of SequenceDB objects.
SubSequenceDB
SwissprotSequenceDB	This class contains functions accessing sequences in swiss-prot.
TabIndexStore	Implements IndexStore as a serialized file for the java data and a tab-delimited file of offsets.
ViewingSequenceDB	SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.
WebSequenceDB	Functions for access to a web based database that returns sequences in a variety of formats.

Exception Summary

Exception	Description
IllegalIDException