Package org.biojava.bio.seq.db

Interface SequenceDBLite

All Superinterfaces:

Changeable

All Known Subinterfaces:

RichSequenceDB, RichSequenceDBLite, SequenceDB

All Known Implementing Classes:

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

public interface SequenceDBLite
extends Changeable

A database of 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

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

Method Summary

Modifier and Type	Method	Description
void	addSequence(Sequence seq)	Adds a sequence to the database.
String	getName()	Get the name of this sequence database.
Sequence	getSequence(String id)	Retrieve a single sequence by its id.
void	removeSequence(String id)	Remove the sequence associated with an ID from the database.

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

SEQUENCES

static final ChangeType SEQUENCES

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.

getSequence

Sequence getSequence(String id)
              throws IllegalIDException,
                     BioException

Retrieve a single sequence by its id.

Parameters:

id - the id to retrieve by

Returns:

the Sequence with that id

Throws:

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

BioException - if there was a failure in retrieving the sequence

addSequence

void addSequence(Sequence seq)
          throws IllegalIDException,
                 BioException,
                 ChangeVetoException

Adds a sequence to the database.

Parameters:

seq - the Sequence to add

Throws:

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

BioException - if something goes wrong with adding the sequence

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

removeSequence

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

Remove the sequence associated with an ID from the database.

Parameters:

id - the ID of the sequence to remove

Throws:

IllegalIDException - if there is no sequence for the ID

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

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