Package org.biojavax.bio.db

Class AbstractRichSequenceDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.db.AbstractBioEntryDB

org.biojavax.bio.db.AbstractRichSequenceDB

All Implemented Interfaces:

SequenceDB, SequenceDBLite, Changeable, BioEntryDB, BioEntryDBLite, RichSequenceDB, RichSequenceDBLite

Direct Known Subclasses:

BioSQLRichSequenceDB, GenbankRichSequenceDB, GenpeptRichSequenceDB, HashRichSequenceDB

public abstract class AbstractRichSequenceDB
extends AbstractBioEntryDB
implements RichSequenceDB

An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.

Since:

1.5

Author:

Matthew Pocock, Thomas Down, Richard Holland

Field Summary

Fields inherited from interface org.biojavax.bio.db.BioEntryDBLite

BIOENTRYS

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

SEQUENCES

Constructor Summary

Constructors

Constructor	Description
AbstractRichSequenceDB()

Method Summary

Modifier and Type	Method	Description
void	addBioEntry(BioEntry seq)	Adds a sequence to the database.
void	addRichSequence(RichSequence seq)	Adds a sequence to the database.
void	addSequence(Sequence seq)	Adds a sequence to the database.
FeatureHolder	filter(FeatureFilter ff)	Query features attached to all sequences in this database.
BioEntry	getBioEntry(String id)	Retrieve a single BioEntry by its id.
BioEntryIterator	getBioEntryIterator()	Returns a BioEntryIterator over all BioEntrys in the database.
BioEntryDB	getBioEntrys(Set ids)	Retrieve multiple BioEntry by their ids.
BioEntryDB	getBioEntrys(Set ids, BioEntryDB db)	Retrieve multiple BioEntry into a specific sequence database.
RichSequenceIterator	getRichSequenceIterator()	Returns a RichSequenceIterator over all sequences in the database.
Sequence	getSequence(String id)	Retrieve a single sequence by its id.
void	removeBioEntry(String id)	Remove the BioEntry associated with an ID from the database.
void	removeRichSequence(String id)	Remove the RichSequence associated with an ID from the 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.biojavax.bio.db.BioEntryDB

ids

Methods inherited from interface org.biojavax.bio.db.BioEntryDBLite

getName

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojavax.bio.db.RichSequenceDBLite

getRichSequence, getRichSequences, getRichSequences

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

ids

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

getName

Constructor Detail

AbstractRichSequenceDB

public AbstractRichSequenceDB()

Method Detail

getSequence

public Sequence getSequence(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

getBioEntry

public BioEntry getBioEntry(String id)
                     throws BioException,
                            IllegalIDException

Description copied from interface: BioEntryDBLite

Retrieve a single BioEntry by its id.

Specified by:

getBioEntry in interface BioEntryDBLite

Parameters:

id - the id to retrieve by

Returns:

the BioEntry with that id

Throws:

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

BioException - if there was a failure in retrieving the BioEntry

getBioEntrys

public BioEntryDB getBioEntrys(Set ids)
                        throws BioException,
                               IllegalIDException

Description copied from interface: BioEntryDBLite

Retrieve multiple BioEntry by their ids.

Specified by:

getBioEntrys in interface BioEntryDBLite

Parameters:

ids - a set of ids to retrieve by

Returns:

the BioEntrys with those ids

Throws:

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

BioException

getBioEntrys

public BioEntryDB getBioEntrys(Set ids,
                               BioEntryDB db)
                        throws BioException,
                               IllegalIDException

Description copied from interface: BioEntryDBLite

Retrieve multiple BioEntry into a specific sequence database. If that database is null, a new HashBioEntryDB is used.

Specified by:

getBioEntrys in interface BioEntryDBLite

Parameters:

ids - a set of ids to retrieve by

db - a database to load the seqs into

Returns:

the BioEntrys with that id

Throws:

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

BioException

addSequence

public void addSequence(Sequence seq)
                 throws IllegalIDException,
                        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 IllegalIDException,
                           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

addBioEntry

public void addBioEntry(BioEntry seq)
                 throws IllegalIDException,
                        BioException,
                        ChangeVetoException

Description copied from interface: BioEntryDBLite

Adds a sequence to the database.

Specified by:

addBioEntry in interface BioEntryDBLite

Overrides:

addBioEntry in class AbstractBioEntryDB

Parameters:

seq - the BioEntry to add

Throws:

IllegalIDException - if a uniqe ID could not be generated for BioEntry

BioException - if something goes wrong with adding the BioEntry

ChangeVetoException - if either the database does not allow BioEntrys to be added or the modification was vetoed

removeBioEntry

public void removeBioEntry(String id)
                    throws IllegalIDException,
                           BioException,
                           ChangeVetoException

Description copied from interface: BioEntryDBLite

Remove the BioEntry associated with an ID from the database.

Specified by:

removeBioEntry in interface BioEntryDBLite

Overrides:

removeBioEntry in class AbstractBioEntryDB

Parameters:

id - the ID of the BioEntry to remove

Throws:

IllegalIDException - if there is no BioEntry for the ID

BioException - if something failed while removing the BioEntry for that ID

ChangeVetoException - if either the database does not allow BioEntrys to be removed or the modification was vetoed

addRichSequence

public void addRichSequence(RichSequence seq)
                     throws IllegalIDException,
                            BioException,
                            ChangeVetoException

Description copied from interface: RichSequenceDBLite

Adds a sequence to the database.

Specified by:

addRichSequence in interface RichSequenceDBLite

Parameters:

seq - the RichSequence to add

Throws:

IllegalIDException - if a uniqe ID could not be generated for RichSequence

BioException - if something goes wrong with adding the RichSequence

ChangeVetoException - if either the database does not allow RichSequences to be added or the modification was vetoed

removeRichSequence

public void removeRichSequence(String id)
                        throws IllegalIDException,
                               BioException,
                               ChangeVetoException

Description copied from interface: RichSequenceDBLite

Remove the RichSequence associated with an ID from the database.

Specified by:

removeRichSequence in interface RichSequenceDBLite

Parameters:

id - the ID of the RichSequence to remove

Throws:

IllegalIDException - if there is no RichSequence for the ID

BioException - if something failed while removing the RichSequence for that ID

ChangeVetoException - if either the database does not allow RichSequences to be removed or the modification was vetoed

sequenceIterator

public SequenceIterator sequenceIterator()

Description copied from interface: RichSequenceDB

Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined. Will always return an instance of RichSequenceIterator.

Specified by:

sequenceIterator in interface RichSequenceDB

Specified by:

sequenceIterator in interface SequenceDB

Returns:

a SequenceIterator over all sequences

getBioEntryIterator

public BioEntryIterator getBioEntryIterator()

Description copied from interface: BioEntryDB

Returns a BioEntryIterator over all BioEntrys in the database. The order of retrieval is undefined.

Specified by:

getBioEntryIterator in interface BioEntryDB

Overrides:

getBioEntryIterator in class AbstractBioEntryDB

Returns:

a BioEntryIterator over all BioEntrys

getRichSequenceIterator

public RichSequenceIterator getRichSequenceIterator()

Description copied from interface: RichSequenceDB

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

Specified by:

getRichSequenceIterator in interface RichSequenceDB

Returns:

a RichSequenceIterator 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.