org.biojava.bio.seq.distributed
Class DistributedSequenceDB

java.lang.Object
  |
  +--org.biojava.utils.AbstractChangeable
        |
        +--org.biojava.bio.seq.db.AbstractSequenceDB
              |
              +--org.biojava.bio.seq.distributed.DistributedSequenceDB

All Implemented Interfaces:

Changeable, SequenceDB, SequenceDBLite

public class DistributedSequenceDB

extends AbstractSequenceDB

implements SequenceDB

Sequence database from the meta-DAS system.

Since:

1.2

Author:

Thomas Down, Matthew Pocock

For general use:

Once you've made one of these and populated it with a few DistDataSource instances, you should be able to prety much forget about it and use it directly as a normal SequenceDB implementation.

For advanced users:

DataSources can be added and removed while the object is live.

Field Summary

static ChangeType	DATASOURCE
static ChangeType	DATASOURCE_SELECTION

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

SEQUENCES

Constructor Summary

DistributedSequenceDB()

Method Summary

void	addDataSource(DistDataSource dds)
void	addSequence(Sequence seq) Adds a sequence to the database.
FeatureHolder	filter(FeatureFilter ff) Query features attached to all sequences in this database.
protected ChangeSupport	getChangeSupport()
java.util.Set	getDataSources()
java.lang.String	getName() Get the name of this sequence database.
Sequence	getSequence(java.lang.String id) Retrieve a single sequence by its id.
protected boolean	hasChangeSupport()
java.util.Set	ids() Get an immutable set of all of the IDs in the database.
void	removeDataSource(DistDataSource dds)
void	removeSequence(java.lang.String id) Remove the sequence associated with an ID from the database.

Methods inherited from class org.biojava.bio.seq.db.AbstractSequenceDB

sequenceIterator

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, 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.SequenceDB

sequenceIterator

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

DATASOURCE

public static final ChangeType DATASOURCE

DATASOURCE_SELECTION

public static final ChangeType DATASOURCE_SELECTION

Constructor Detail

DistributedSequenceDB

public DistributedSequenceDB()

Method Detail

hasChangeSupport

protected boolean hasChangeSupport()

getChangeSupport

protected ChangeSupport getChangeSupport()

getDataSources

public java.util.Set getDataSources()

addDataSource

public void addDataSource(DistDataSource dds)
                   throws ChangeVetoException

ChangeVetoException

removeDataSource

public void removeDataSource(DistDataSource dds)
                      throws ChangeVetoException

ChangeVetoException

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.

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

Overrides:

addSequence in class AbstractSequenceDB

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(java.lang.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

Overrides:

removeSequence in class AbstractSequenceDB

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(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

Returns:

the Sequence with that id

Throws:

BioException - if there was a failure in retrieving the sequence

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

ids

public java.util.Set ids()

Description copied from interface: SequenceDB

Get an immutable set of all of the IDs in the database. The ids are legal arguments to getSequence.

Specified by:

ids in interface SequenceDB

Returns:

a Set of ids - at the moment, strings

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

Overrides:

filter in class AbstractSequenceDB

Parameters:

ff - a FeatureFilter.