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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. |
LocusLinkParser | |
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 |
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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