org.biojava.bio.seq.db.biofetch

Class BioFetchSequenceDB

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.seq.db.biofetch.BioFetchSequenceDB

All Implemented Interfaces:

SequenceDBLite, Changeable

public class BioFetchSequenceDB
extends Unchangeable
implements SequenceDBLite

Simple SequenceDB implementation backed by a BioFetch (HTTP) server.

Since:

1.3

Author:

Thomas Down, Matthew Pocock, Greg Cox, Keith James

Field Summary

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

SEQUENCES

Constructor Summary

Constructors

Constructor and Description
BioFetchSequenceDB(String location, String dbName) Construct a BioFetchSequenceDB which connects to the specified BioFetch server.

Method Summary

Modifier and Type	Method and 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 class org.biojava.utils.Unchangeable

addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

BioFetchSequenceDB

public BioFetchSequenceDB(String location,
                          String dbName)

Construct a BioFetchSequenceDB which connects to the specified BioFetch server.

Parameters:

location - The base URL of the server.

dbName - The database name to use.

Method Detail

getName

public String getName()

Description copied from interface: SequenceDBLite

Get the name of this sequence database.

Specified by:

getName in interface SequenceDBLite

Returns:

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

addSequence

public void addSequence(Sequence seq)
                 throws ChangeVetoException

Description copied from interface: SequenceDBLite

Adds a sequence to the database.

Specified by:

addSequence in interface SequenceDBLite

Parameters:

seq - the Sequence to add

Throws:

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

removeSequence

public void removeSequence(String id)
                    throws ChangeVetoException

Description copied from interface: SequenceDBLite

Remove the sequence associated with an ID from the database.

Specified by:

removeSequence in interface SequenceDBLite

Parameters:

id - the ID of the sequence to remove

Throws:

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

getSequence

public Sequence getSequence(String id)
                     throws BioException,
                            IllegalIDException

Description copied from interface: SequenceDBLite

Retrieve a single sequence by its id.

Specified by:

getSequence in interface SequenceDBLite

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