Interface for objects that define how to make an ID for a sequence.
This defines an index entry for an individual sequence within a set of indexed files.
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.
A database of sequences with accessible keys and iterators over all sequences.
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.
A database of sequences.
An abstract implementation of SequenceDB that provides the sequenceIterator method.
SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.
The original object for indexing sequence files.
SequenceDB implementation that caches the results of another SequenceDB.
This class contains functions accessing DNA sequences in Genbank format.
An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.
This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.
An abstract implementation of SequenceDB that wraps up another database.
This is a no-frills implementation of the Index interface.
This class is an implementation of interface SequenceDBInstallation that manages a set of SequenceDB objects.
This class contains functions accessing sequences in swiss-prot.
Implements IndexStore as a serialized file for the java data and a tab-delimited file of offsets.
SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.
Functions for access to a web based database that returns sequences in a variety of formats.
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
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