Package org.biojavax.bio.db.biosql

Class BioSQLBioEntryDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.db.AbstractBioEntryDB

org.biojavax.bio.db.biosql.BioSQLBioEntryDB

All Implemented Interfaces:

Changeable, BioEntryDB, BioEntryDBLite

public class BioSQLBioEntryDB
extends AbstractBioEntryDB

Since:

1.5

Author:

Richard Holland, David Scott

Field Summary

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

BIOENTRYS

Constructor Summary

Constructors

Constructor	Description
BioSQLBioEntryDB(Object session)	Creates a new instance of BioSQLBioEntryDB
BioSQLBioEntryDB(String name, Object session)	Creates a new instance of BioSQLBioEntryDB

Method Summary

Modifier and Type	Method	Description
void	_addBioEntry(BioEntry seq)
void	addBioEntry(BioEntry seq)	Adds a sequence to the database.
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.
Object	getHibernateSession()
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

Constructor Detail

BioSQLBioEntryDB

public BioSQLBioEntryDB(Object session)

Creates a new instance of BioSQLBioEntryDB

BioSQLBioEntryDB

public BioSQLBioEntryDB(String name,
                        Object session)

Creates a new instance of BioSQLBioEntryDB

Method Detail

getName

public String getName()

Description copied from interface: BioEntryDBLite

Get the name of this sequence database.

Returns:

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

getHibernateSession

public Object getHibernateSession()

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.

Returns:

a Set of ids - at the moment, strings

getBioEntry

public BioEntry getBioEntry(String id)
                     throws IllegalIDException,
                            BioException

Description copied from interface: BioEntryDBLite

Retrieve a single BioEntry by its id.

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.

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.

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

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

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

_addBioEntry

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

Throws:

IllegalIDException

BioException

ChangeVetoException