Package org.biojava.bio.seq.db

Class HashSequenceDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.db.AbstractSequenceDB

org.biojava.bio.seq.db.HashSequenceDB

All Implemented Interfaces:

Serializable, SequenceDB, SequenceDBLite, Changeable

public class HashSequenceDB
extends AbstractSequenceDB
implements SequenceDB, Serializable

An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.

Author:

Matthew Pocock, Gerald Loeffler, Matias Pilpari (LinkedHashMap)

See Also:

Serialized Form

Field Summary

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

SEQUENCES

Constructor Summary

Constructors

Constructor	Description
HashSequenceDB()	Generate a HashSequenceDB object that will use byName to generate ids for sequences and have a null name.
HashSequenceDB(String name)	Generate a HashSequenceDB object that will use byName to generate ids and will have the requested name.
HashSequenceDB(IDMaker idMaker)	Generate a HashSequenceDB object that will use idMaker to generate ids for sequences and have a null name.
HashSequenceDB(IDMaker idMaker, String name)	Generate a HashSequenceDB object that will use idMaker to generate ids for sequences and have the requested name.

Method Summary

Modifier and Type	Method	Description
void	addSequence(String id, Sequence seq)	Add a sequence under a particular id.
void	addSequence(Sequence seq)	Adds a sequence to the database.
IDMaker	getIDMaker()	Retrieve the IDMaker associated with this database.
String	getName()	Get the name of this sequence database.
Sequence	getSequence(String id)	Retrieve a single sequence by its id.
Set	ids()	Get an immutable set of all of the IDs in 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.bio.seq.db.AbstractSequenceDB

filter

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

filter

Constructor Detail

HashSequenceDB

public HashSequenceDB()

Generate a HashSequenceDB object that will use byName to generate ids for sequences and have a null name.

HashSequenceDB

public HashSequenceDB(IDMaker idMaker)

Generate a HashSequenceDB object that will use idMaker to generate ids for sequences and have a null name.

Parameters:

idMaker - the object that will work out the default id for a sequence

HashSequenceDB

public HashSequenceDB(String name)

Generate a HashSequenceDB object that will use byName to generate ids and will have the requested name.

Parameters:

name - the name for this database

HashSequenceDB

public HashSequenceDB(IDMaker idMaker,
                      String name)

Generate a HashSequenceDB object that will use idMaker to generate ids for sequences and have the requested name.

Parameters:

idMaker - the object that will work out the default id for a sequence

name - the name for this database

Method Detail

getName

public 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(String id)
                     throws 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

ids

public 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

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

Overrides:

sequenceIterator in class AbstractSequenceDB

Returns:

a SequenceIterator over all sequences

addSequence

public void addSequence(String id,
                        Sequence seq)
                 throws ChangeVetoException

Add a sequence under a particular id.

Parameters:

id - the id to use

seq - the Sequence to add

Throws:

ChangeVetoException - if this addition was vetoed

getIDMaker

public IDMaker getIDMaker()

Retrieve the IDMaker associated with this database.

Returns:

the current IDMaker object

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(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

Overrides:

removeSequence in class AbstractSequenceDB

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