org.biojavax.bio.db

Interface BioEntryDB

All Superinterfaces:

BioEntryDBLite

All Known Subinterfaces:

RichSequenceDB

All Known Implementing Classes:

AbstractBioEntryDB, AbstractRichSequenceDB, BioSQLBioEntryDB, BioSQLRichSequenceDB, GenbankRichSequenceDB, GenpeptRichSequenceDB, HashBioEntryDB, HashRichSequenceDB

public interface BioEntryDB
extends BioEntryDBLite

. 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

Method Summary

Methods

Modifier and Type	Method and Description
BioEntryIterator	getBioEntryIterator() Returns a BioEntryIterator over all BioEntrys in the database.
Set	ids() Get an immutable set of all of the IDs in the database.

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

addBioEntry, getBioEntry, getBioEntrys, getBioEntrys, getName, removeBioEntry

Method Detail

ids

Set ids()

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

Returns:

a Set of ids - at the moment, strings

getBioEntryIterator

BioEntryIterator getBioEntryIterator()

Returns a BioEntryIterator over all BioEntrys in the database. The order of retrieval is undefined.

Returns:

a BioEntryIterator over all BioEntrys