org.biojavax.bio.db

Interface RichSequenceDB

All Superinterfaces:

BioEntryDB, BioEntryDBLite, Changeable, RichSequenceDBLite, SequenceDB, SequenceDBLite

All Known Implementing Classes:

AbstractRichSequenceDB, BioSQLRichSequenceDB, GenbankRichSequenceDB, GenpeptRichSequenceDB, HashRichSequenceDB

public interface RichSequenceDB
extends SequenceDB, BioEntryDB, RichSequenceDBLite

A database of RichSequences 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.

Since:

1.5

Author:

Matthew Pocock, Gerald Loeffler, Thomas Down, Richard Holland

Field Summary

Fields inherited from interface org.biojavax.bio.db.BioEntryDBLite

BIOENTRYS

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

SEQUENCES

Method Summary

Modifier and Type	Method and Description
RichSequenceIterator	getRichSequenceIterator() Returns a RichSequenceIterator over all sequences in the database.
SequenceIterator	sequenceIterator() Returns a SequenceIterator over all sequences in the database.

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

filter, ids

Methods inherited from interface org.biojavax.bio.db.BioEntryDB

getBioEntryIterator, ids

Methods inherited from interface org.biojavax.bio.db.RichSequenceDBLite

addRichSequence, getRichSequence, getRichSequences, getRichSequences, removeRichSequence

Methods inherited from interface org.biojavax.bio.db.BioEntryDBLite

addBioEntry, getBioEntry, getBioEntrys, getBioEntrys, getName, removeBioEntry

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

sequenceIterator

SequenceIterator sequenceIterator()

Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined. Will always return an instance of RichSequenceIterator.

Specified by:

sequenceIterator in interface SequenceDB

Returns:

a SequenceIterator over all sequences

getRichSequenceIterator

RichSequenceIterator getRichSequenceIterator()

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

Returns:

a RichSequenceIterator over all sequences