org.biojava.bio.seq.db.flat

Class FlatSequenceDB

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.seq.db.flat.FlatSequenceDB

All Implemented Interfaces:

SequenceDBLite, Changeable

public class FlatSequenceDB
extends Unchangeable
implements SequenceDBLite

FlatSequenceDB is an OBDA flatfile sequence databank implementation. It is backed by an index created using the org.biojava.bio.program.indexdb package.

Author:

Keith James

Field Summary

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

SEQUENCES

Constructor Summary

Constructors

Constructor and Description
FlatSequenceDB(java.lang.String location, java.lang.String dbName)

Method Summary

Methods

Modifier and Type	Method and Description
void	addSequence(Sequence sequence) addSequence always throws a ChangeVetoException as this implementation is immutable.
java.lang.String	getName() Get the name of this sequence database.
Sequence	getSequence(java.lang.String id) Retrieve a single sequence by its id.
void	removeSequence(java.lang.String id) removeSequence always throws a ChangeVetoException as this implementation is immutable.

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

FlatSequenceDB

public FlatSequenceDB(java.lang.String location,
              java.lang.String dbName)
               throws java.io.IOException,
                      BioException

Throws:

java.io.IOException

BioException

Method Detail

getName

public java.lang.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.

getSequence

public Sequence getSequence(java.lang.String id)
                     throws IllegalIDException,
                            BioException

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

addSequence

public void addSequence(Sequence sequence)
                 throws ChangeVetoException

addSequence always throws a ChangeVetoException as this implementation is immutable.

Specified by:

addSequence in interface SequenceDBLite

Parameters:

sequence - a Sequence.

Throws:

ChangeVetoException

removeSequence

public void removeSequence(java.lang.String id)
                    throws ChangeVetoException

removeSequence always throws a ChangeVetoException as this implementation is immutable.

Specified by:

removeSequence in interface SequenceDBLite

Parameters:

id - a String.

Throws:

ChangeVetoException