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
Interface Summary Interface Description IDMakerInterface for objects that define how to make an ID for a sequence. IndexThis defines an index entry for an individual sequence within a set of indexed files. IndexStoreThis defines the objects that IndexedSequenceDB uses to store all of the database state, such as name, format, sequence builder and the actual file offsets. SequenceDBA database of sequences with accessible keys and iterators over all sequences. SequenceDBInstallationA 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. SequenceDBLiteA database of sequences.
Class Summary Class Description AbstractSequenceDBAn abstract implementation of SequenceDB that provides the sequenceIterator method. AnnotatedSequenceDBSequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB. BioIndexThe original object for indexing sequence files. CachingSequenceDBSequenceDB implementation that caches the results of another SequenceDB. DummySequenceDB
DummySequenceDBis an implementation which contains only a
DummySequenceDBInstallationis an implementation which returns the same
DummySequenceDBinstance regardless of the identifier used to retrieve a database.
EmblCDROMIndexStores implement a read-only
IndexStorebacked by EMBL CD-ROM format binary indices.
FetchURL GenbankSequenceDBThis class contains functions accessing DNA sequences in Genbank format. GenpeptSequenceDB HashSequenceDBAn implementation of SequenceDB that uses an underlying HashMap to store the sequence objects. IDMaker.ByName IDMaker.ByURN IndexedSequenceDBThis class implements SequenceDB on top of a set of sequence files and sequence offsets within these files. NCBISequenceDB SequenceDBWrapperAn abstract implementation of SequenceDB that wraps up another database. SimpleIndexThis is a no-frills implementation of the Index interface. SimpleSequenceDBInstallationThis class is an implementation of interface SequenceDBInstallation that manages a set of SequenceDB objects. SubSequenceDB SwissprotSequenceDBThis class contains functions accessing sequences in swiss-prot. TabIndexStoreImplements IndexStore as a serialized file for the java data and a tab-delimited file of offsets. ViewingSequenceDBSequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database. WebSequenceDBFunctions for access to a web based database that returns sequences in a variety of formats.
Exception Summary Exception Description IllegalIDException