org.biojava.bio.seq.db

Interface SequenceDB

All Superinterfaces:

Changeable, SequenceDBLite

All Known Subinterfaces:

RichSequenceDB

All Known Implementing Classes:

AbstractRichSequenceDB, AbstractSequenceDB, AnnotatedSequenceDB, BioSQLRichSequenceDB, BioSQLSequenceDB, CachingSequenceDB, DistributedSequenceDB, DummySequenceDB, GenbankRichSequenceDB, GenpeptRichSequenceDB, HashRichSequenceDB, HashSequenceDB, IndexedSequenceDB, SequenceDBWrapper, SubSequenceDB, ViewingSequenceDB

public interface SequenceDB
extends SequenceDBLite

A database of sequences with accessible keys and iterators over all sequences.

This may have several implementations with rich behaviour, but basically most of the time you will just use the interface methods to do stuff. A sequence database contains a finite number of sequences stored under unique keys.

Author:

Matthew Pocock, Gerald Loeffler, Thomas Down

Field Summary

Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite

SEQUENCES

Method Summary

Modifier and Type	Method and Description
FeatureHolder	filter(FeatureFilter filter) Query features attached to all sequences in this database.
Set	ids() Get an immutable set of all of the IDs in the database.
SequenceIterator	sequenceIterator() Returns a SequenceIterator over all sequences in the database.

Methods inherited from interface org.biojava.bio.seq.db.SequenceDBLite

addSequence, getName, getSequence, removeSequence

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Method Detail

ids

Set ids()

Get an immutable set of all of the IDs in the database. The ids are legal arguments to getSequence.

Returns:

a Set of ids - at the moment, strings

sequenceIterator

SequenceIterator sequenceIterator()

Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined.

Returns:

a SequenceIterator over all sequences

filter

FeatureHolder filter(FeatureFilter filter)

Query features attached to all sequences in this database. This is equivalent to applying filter to all sequences then merging the results.

Parameters:

filter - a FeatureFilter.

Since:

1.3