org.biojavax.bio.db

Interface BioEntryDBLite

All Known Subinterfaces:

BioEntryDB, RichSequenceDB, RichSequenceDBLite

All Known Implementing Classes:

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

public interface BioEntryDBLite

A database of BioEntrys. 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 BioEntry database contains a finite number of BioEntrys stored under unique keys.

Since:

1.5

Author:

Matthew Pocock, Gerald Loeffler, Thomas Down, Richard Holland

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	BIOENTRYS Signals that sequences are being added to or remove from the database.

Method Summary

Methods

Modifier and Type	Method and Description
void	addBioEntry(BioEntry seq) Adds a sequence to the database.
BioEntry	getBioEntry(String id) Retrieve a single BioEntry by its id.
BioEntryDB	getBioEntrys(Set ids) Retrieve multiple BioEntry by their ids.
BioEntryDB	getBioEntrys(Set ids, BioEntryDB db) Retrieve multiple BioEntry into a specific sequence database.
String	getName() Get the name of this sequence database.
void	removeBioEntry(String id) Remove the BioEntry associated with an ID from the database.

Field Detail

BIOENTRYS

static final ChangeType BIOENTRYS

Signals that sequences are being added to or remove from the database. The sequences being removed should be listed in the previous field by id, either as a single String, an array or a Set. The sequences being added should be listed in the change field as either an array Object[] { id, seq}, or a Map of id->seq.

Method Detail

getName

String getName()

Get the name of this sequence database.

Returns:

the name of the sequence database, which may be null.

getBioEntry

BioEntry getBioEntry(String id)
                     throws IllegalIDException,
                            BioException

Retrieve a single BioEntry by its id.

Parameters:

id - the id to retrieve by

Returns:

the BioEntry with that id

Throws:

IllegalIDException - if the database doesn't know about the id

BioException - if there was a failure in retrieving the BioEntry

getBioEntrys

BioEntryDB getBioEntrys(Set ids)
                        throws BioException,
                               IllegalIDException

Retrieve multiple BioEntry by their ids.

Parameters:

ids - a set of ids to retrieve by

Returns:

the BioEntrys with those ids

Throws:

IllegalIDException - if the database doesn't know about the id

BioException

getBioEntrys

BioEntryDB getBioEntrys(Set ids,
                      BioEntryDB db)
                        throws BioException,
                               IllegalIDException

Retrieve multiple BioEntry into a specific sequence database. If that database is null, a new HashBioEntryDB is used.

Parameters:

ids - a set of ids to retrieve by

db - a database to load the seqs into

Returns:

the BioEntrys with that id

Throws:

IllegalIDException - if the database doesn't know about the id

BioException

addBioEntry

void addBioEntry(BioEntry seq)
                 throws IllegalIDException,
                        BioException,
                        ChangeVetoException

Adds a sequence to the database.

Parameters:

seq - the BioEntry to add

Throws:

IllegalIDException - if a uniqe ID could not be generated for BioEntry

BioException - if something goes wrong with adding the BioEntry

ChangeVetoException - if either the database does not allow BioEntrys to be added or the modification was vetoed

removeBioEntry

void removeBioEntry(String id)
                    throws IllegalIDException,
                           BioException,
                           ChangeVetoException

Remove the BioEntry associated with an ID from the database.

Parameters:

id - the ID of the BioEntry to remove

Throws:

IllegalIDException - if there is no BioEntry for the ID

BioException - if something failed while removing the BioEntry for that ID

ChangeVetoException - if either the database does not allow BioEntrys to be removed or the modification was vetoed