Package org.biojavax.bio.db

Class AbstractBioEntryDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.db.AbstractBioEntryDB

All Implemented Interfaces:

Changeable, BioEntryDB, BioEntryDBLite

Direct Known Subclasses:

AbstractRichSequenceDB, BioSQLBioEntryDB, HashBioEntryDB

public abstract class AbstractBioEntryDB
extends AbstractChangeable
implements BioEntryDB

An abstract implementation of BioEntryDB that provides the getBioEntryIterator method.

Since:

1.5

Author:

Matthew Pocock, Thomas Down, Richard Holland

Field Summary

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

BIOENTRYS

Constructor Summary

Constructors

Constructor	Description
AbstractBioEntryDB()

Method Summary

Modifier and Type	Method	Description
void	addBioEntry(BioEntry seq)	Adds a sequence to the database.
BioEntryIterator	getBioEntryIterator()	Returns a BioEntryIterator over all BioEntrys in the database.
void	removeBioEntry(String id)	Remove the BioEntry associated with an ID from 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

getBioEntry, getBioEntrys, getBioEntrys, getName

Constructor Detail

AbstractBioEntryDB

public AbstractBioEntryDB()

Method Detail

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

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

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

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

Returns:

a BioEntryIterator over all BioEntrys