Package org.biojavax.bio.db

Class HashBioEntryDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.db.AbstractBioEntryDB

org.biojavax.bio.db.HashBioEntryDB

All Implemented Interfaces:

Changeable, BioEntryDB, BioEntryDBLite

public class HashBioEntryDB
extends AbstractBioEntryDB
implements BioEntryDB

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

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected void	addBioEntry(String id, BioEntry seq)
void	addBioEntry(BioEntry seq)	Add a BioEntry, the name of the BioEntry will be used as the ID
BioEntry	getBioEntry(String id)	Retrieve a single BioEntry by its id.
BioEntryDB	getBioEntrys(Set ids)	Retrieve multiple BioEntry by their ids.
BioEntryDB	getBioEntrys(Set ids, BioEntryDB db)	Retrieve multiple BioEntry into a specific sequence database.
String	getName()	Get the name of this sequence database.
Set	ids()	Get an immutable set of all of the IDs in the database.
void	removeBioEntry(String id)	Remove the BioEntry associated with an ID from the database.

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

getBioEntryIterator

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

Constructor Detail

HashBioEntryDB

public HashBioEntryDB()

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

HashBioEntryDB

public HashBioEntryDB(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

Method Detail

getName

public String getName()

Description copied from interface: BioEntryDBLite

Get the name of this sequence database.

Specified by:

getName in interface BioEntryDBLite

Returns:

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

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

ids

public Set ids()

Description copied from interface: BioEntryDB

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

Specified by:

ids in interface BioEntryDB

Returns:

a Set of ids - at the moment, strings

addBioEntry

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

Add a BioEntry, the name of the BioEntry will be used as the ID

Specified by:

addBioEntry in interface BioEntryDBLite

Overrides:

addBioEntry in class AbstractBioEntryDB

Parameters:

seq - the BioEntry to add

Throws:

ChangeVetoException - if this addition was vetoed

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

BioException - if something goes wrong with adding the BioEntry

addBioEntry

protected void addBioEntry(String id,
                           BioEntry seq)
                    throws IllegalIDException,
                           BioException,
                           ChangeVetoException

Throws:

IllegalIDException

BioException

ChangeVetoException

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