org.biojava.bio.seq.db (BioJava-1.5-beta API)
Keywords: org.biojava.bio.seq.db package

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## Package org.biojava.bio.seq.db

Collections of biological sequence data.

See:
Description

Interface Summary
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
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 | `EmblCDROMIndexStore`s 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
IllegalIDException |

## Package org.biojava.bio.seq.db Description

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.

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