org.biojava.bio.seq.db

Class WebSequenceDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.db.WebSequenceDB

All Implemented Interfaces:

SequenceDBLite, Changeable

Direct Known Subclasses:

NCBISequenceDB

public abstract class WebSequenceDB
extends AbstractChangeable
implements SequenceDBLite

Functions for access to a web based database that returns sequences in a variety of formats.

Author:

Jason Stajich, Matthew Pocock, Mark Schreiber, Richard Holland

Field Summary

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

SEQUENCES

Constructor Summary

Constructors

Constructor and Description
WebSequenceDB()

Method Summary

Methods

Modifier and Type	Method and Description
void	addSequence(Sequence seq) Not supported, You can't add sequences to a WebDB!
protected abstract URL	getAddress(String id)
protected abstract Alphabet	getAlphabet()
Sequence	getSequence(String id) Gets a sequence using its unique ID (eg for GenBank this would be the GI number)
protected abstract SequenceFormat	getSequenceFormat()
void	removeSequence(String id) Not supported, you can't remove a sequence from a WebDB!

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

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

getName

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

WebSequenceDB

public WebSequenceDB()

Method Detail

getSequenceFormat

protected abstract SequenceFormat getSequenceFormat()

getAddress

protected abstract URL getAddress(String id)
                           throws MalformedURLException

Throws:

MalformedURLException

getAlphabet

protected abstract Alphabet getAlphabet()

getSequence

public Sequence getSequence(String id)
                     throws BioException

Gets a sequence using its unique ID (eg for GenBank this would be the GI number)

Specified by:

getSequence in interface SequenceDBLite

Parameters:

id - the unique ID

Returns:

the matching sequence

Throws:

BioException - if the ID is invalid

BioException - if the io operation times out or has problems connecting. Can also indicate an invalid URL has been constructed.

addSequence

public void addSequence(Sequence seq)
                 throws ChangeVetoException

Not supported, You can't add sequences to a WebDB!

Specified by:

addSequence in interface SequenceDBLite

Parameters:

seq - the sequence you tried to add

Throws:

ChangeVetoException - always!

removeSequence

public void removeSequence(String id)
                    throws ChangeVetoException

Not supported, you can't remove a sequence from a WebDB!

Specified by:

removeSequence in interface SequenceDBLite

Parameters:

id - the sequence you tried to change.

Throws:

ChangeVetoException - always!