Package org.biojava.bio.seq.db

Class AbstractSequenceDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.db.AbstractSequenceDB

All Implemented Interfaces:

SequenceDB, SequenceDBLite, Changeable

Direct Known Subclasses:

AnnotatedSequenceDB, DistributedSequenceDB, DummySequenceDB, HashSequenceDB, IndexedSequenceDB, SequenceDBWrapper

public abstract class AbstractSequenceDB
extends AbstractChangeable
implements SequenceDB

An abstract implementation of SequenceDB that provides the sequenceIterator method.

Author:

Matthew Pocock, Thomas Down

Field Summary

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

SEQUENCES

Constructor Summary

Constructors

Constructor	Description
AbstractSequenceDB()

Method Summary

Modifier and Type	Method	Description
void	addSequence(Sequence seq)	Adds a sequence to the database.
FeatureHolder	filter(FeatureFilter ff)	Query features attached to all sequences in this database.
void	removeSequence(String id)	Remove the sequence associated with an ID from the database.
SequenceIterator	sequenceIterator()	Returns a SequenceIterator over all sequences in the database.

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.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

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

ids

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

getName, getSequence

Constructor Detail

AbstractSequenceDB

public AbstractSequenceDB()

Method Detail

sequenceIterator

public SequenceIterator sequenceIterator()

Description copied from interface: SequenceDB

Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined.

Specified by:

sequenceIterator in interface SequenceDB

Returns:

a SequenceIterator over all sequences

filter

public FeatureHolder filter(FeatureFilter ff)

Description copied from interface: SequenceDB

Query features attached to all sequences in this database. This is equivalent to applying filter to all sequences then merging the results.

Specified by:

filter in interface SequenceDB

Parameters:

ff - a FeatureFilter.

addSequence

public void addSequence(Sequence seq)
                 throws BioException,
                        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:

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

public void removeSequence(String id)
                    throws BioException,
                           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:

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