Package org.biojavax.bio.db

Class HashRichSequenceDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.db.AbstractBioEntryDB

org.biojavax.bio.db.AbstractRichSequenceDB

org.biojavax.bio.db.HashRichSequenceDB

All Implemented Interfaces:

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

public class HashRichSequenceDB
extends AbstractRichSequenceDB
implements RichSequenceDB

An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.

Since:

1.5

Author:

Matthew Pocock, Gerald Loeffler, 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
HashRichSequenceDB()	Generate a HashRichSequenceDB object that will use byName to generate ids for sequences and have a null name.
HashRichSequenceDB(String name)	Generate a HashRichSequenceDB object that will use byName to generate ids and will have the requested name.
HashRichSequenceDB(IDMaker idMaker)	Generate a HashRichSequenceDB object that will use idMaker to generate ids for sequences and have a null name.
HashRichSequenceDB(IDMaker idMaker, String name)	Generate a HashRichSequenceDB object that will use idMaker to generate ids for sequences and have the requested name.

Method Summary

Modifier and Type	Method	Description
protected void	addRichSequence(String id, RichSequence seq)
void	addRichSequence(RichSequence seq)	Add a sequence.
IDMaker	getIDMaker()	Retrieve the IDMaker associated with this database.
String	getName()	Get the name of this sequence database.
RichSequence	getRichSequence(String id)	Retrieve a single RichSequence by its id.
RichSequenceDB	getRichSequences(Set ids)	Retrieve multiple RichSequence by its id.
RichSequenceDB	getRichSequences(Set ids, RichSequenceDB db)	Retrieve multiple RichSequence into a specific sequence database.
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.

Methods inherited from class org.biojavax.bio.db.AbstractRichSequenceDB

addBioEntry, addSequence, filter, getBioEntry, getBioEntryIterator, getBioEntrys, getBioEntrys, getRichSequenceIterator, getSequence, removeBioEntry, removeRichSequence, sequenceIterator

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

getBioEntryIterator

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

addBioEntry, getBioEntry, getBioEntrys, getBioEntrys, removeBioEntry

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

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

getRichSequenceIterator, sequenceIterator

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

removeRichSequence

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

filter

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

addSequence, getSequence

Constructor Detail

HashRichSequenceDB

public HashRichSequenceDB()

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

HashRichSequenceDB

public HashRichSequenceDB(IDMaker idMaker)

Generate a HashRichSequenceDB 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

HashRichSequenceDB

public HashRichSequenceDB(String name)

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

Parameters:

name - the name for this database

HashRichSequenceDB

public HashRichSequenceDB(IDMaker idMaker,
                          String name)

Generate a HashRichSequenceDB 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 BioEntryDBLite

Specified by:

getName in interface SequenceDBLite

Returns:

the name of the sequence database, which may be null.

getIDMaker

public IDMaker getIDMaker()

Retrieve the IDMaker associated with this database.

Returns:

the current IDMaker object

getRichSequence

public RichSequence getRichSequence(String id)
                             throws BioException,
                                    IllegalIDException

Description copied from interface: RichSequenceDBLite

Retrieve a single RichSequence by its id.

Specified by:

getRichSequence in interface RichSequenceDBLite

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

getRichSequences

public RichSequenceDB getRichSequences(Set ids)
                                throws BioException,
                                       IllegalIDException

Description copied from interface: RichSequenceDBLite

Retrieve multiple RichSequence by its id.

Specified by:

getRichSequences in interface RichSequenceDBLite

Parameters:

ids - a set of ids to retrieve by

Returns:

the RichSequences with that id

Throws:

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

BioException

getRichSequences

public RichSequenceDB getRichSequences(Set ids,
                                       RichSequenceDB db)
                                throws BioException,
                                       IllegalIDException

Description copied from interface: RichSequenceDBLite

Retrieve multiple RichSequence into a specific sequence database. If that database is null, a new HashRichSequenceDB is used.

Specified by:

getRichSequences in interface RichSequenceDBLite

Parameters:

ids - a set of ids to retrieve by

db - a database to load the seqs into

Returns:

the RichSequences with that id

Throws:

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

BioException

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 BioEntryDB

Specified by:

ids in interface SequenceDB

Returns:

a Set of ids - at the moment, strings

addRichSequence

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

Add a sequence.

Specified by:

addRichSequence in interface RichSequenceDBLite

Overrides:

addRichSequence in class AbstractRichSequenceDB

Parameters:

seq - the RichSequence to add

Throws:

ChangeVetoException - if this addition was vetoed

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

BioException - if something goes wrong with adding the RichSequence

addRichSequence

protected void addRichSequence(String id,
                               RichSequence seq)
                        throws IllegalIDException,
                               BioException,
                               ChangeVetoException

Throws:

IllegalIDException

BioException

ChangeVetoException

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

Overrides:

removeSequence in class AbstractRichSequenceDB

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