Package org.biojava.bio.program.das

Class DASSequenceDB

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.program.das.DASSequenceDB

All Implemented Interfaces:

SequenceDB, SequenceDBLite, Changeable

public class DASSequenceDB
extends Unchangeable
implements SequenceDB

Collection of sequences retrieved from the DAS network.

The DAS-specific parts of this API are still subject to change.

Since:

1.1

Author:

Thomas Down

Field Summary

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

SEQUENCES

Constructor Summary

Constructors

Constructor	Description
DASSequenceDB(java.net.URL dataSourceURL)

Method Summary

Modifier and Type	Method	Description
void	addSequence(Sequence seq)	Adds a sequence to the database.
SequenceDBLite	allEntryPointsDB()
FeatureHolder	filter(FeatureFilter ff)	Query features attached to all sequences in this database.
java.lang.String	getName()	Get the name of this sequence database.
Sequence	getSequence(java.lang.String id)	Retrieve a single sequence by its id.
java.net.URL	getURL()	Return the URL of the reference server for this database.
java.util.Set	ids()	Get an immutable set of all of the IDs in the database.
void	removeSequence(java.lang.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.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

DASSequenceDB

public DASSequenceDB(java.net.URL dataSourceURL)
              throws BioException

Throws:

BioException

Method Detail

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.

allEntryPointsDB

public SequenceDBLite allEntryPointsDB()

getURL

public java.net.URL getURL()

Return the URL of the reference server for this database.

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 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

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

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(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

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

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