Package org.biojava.bio.seq.db.biosql

Class BioSQLSequenceDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.seq.db.biosql.BioSQLSequenceDB

All Implemented Interfaces:

SequenceDB, SequenceDBLite, Changeable

public class BioSQLSequenceDB
extends AbstractChangeable
implements SequenceDB

Deprecated.

Use hibernate and org.biojavax.bio.db.*

SequenceDB keyed off a BioSQL database. This is an almost-complete implementation of the BioJava Sequence, SequenceDB, and Feature interfaces, and can be used in a wide range of applications. Note: It now uses BioSQL schema version 1.0 (Post Singapore) All previous versions are no longer supported.

Since:

1.3

Author:

Thomas Down, Matthew Pocock, Simon Foote, Len Trigg, Mark Schreiber, Richard Holland

Field Summary

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

SEQUENCES

Constructor Summary

Constructors

Constructor	Description
BioSQLSequenceDB(String dbURL, String dbUser, String dbPass, String biodatabase, boolean create)	Deprecated. Connect to a BioSQL database.
BioSQLSequenceDB(String dbDriver, String dbURL, String dbUser, String dbPass, String biodatabase, boolean create)	Deprecated. Connect to a BioSQL database.
BioSQLSequenceDB(DataSource ds, String biodatabase, boolean create)	Deprecated.

Method Summary

Modifier and Type	Method	Description
Ontology	addOntology(Ontology onto)	Deprecated.
void	addSequence(Sequence seq)	Deprecated. Adds a sequence to the database.
void	createDummySequence(String id, Alphabet alphabet, int length)	Deprecated.
Ontology	createOntology(String name, String description)	Deprecated.
FeatureHolder	filter(FeatureFilter ff)	Deprecated. Query features attached to all sequences in this database.
String	getName()	Deprecated. Get the name of this sequence database.
Ontology	getOntology(String name)	Deprecated.
Sequence	getSequence(int bioentry_id)	Deprecated.
Sequence	getSequence(String id)	Deprecated. Retrieve a single sequence by its id.
Set	ids()	Deprecated. Get an immutable set of all of the IDs in the database.
void	removeSequence(String id)	Deprecated. Remove the sequence associated with an ID from the database.
SequenceIterator	sequenceIterator()	Deprecated. Returns a SequenceIterator over all sequences in 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.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

BioSQLSequenceDB

public BioSQLSequenceDB(String dbDriver,
                        String dbURL,
                        String dbUser,
                        String dbPass,
                        String biodatabase,
                        boolean create)
                 throws BioException

Deprecated.

Connect to a BioSQL database.

Parameters:

dbDriver - A JDBC database driver. For example, com.jdbc.mysql.Driver

dbURL - A JDBC database URL. For example, jdbc:postgresql://localhost/thomasd_biosql

dbUser - The username to use when connecting to the database (or an empty string).

dbPass - The password to use when connecting to the database (or an empty string).

biodatabase - The identifier of a namespace within the physical BioSQL database.

create - If the requested namespace doesn't exist, and this flag is true, a new namespace will be created.

Throws:

BioException - if an error occurs communicating with the database

BioSQLSequenceDB

public BioSQLSequenceDB(String dbURL,
                        String dbUser,
                        String dbPass,
                        String biodatabase,
                        boolean create)
                 throws BioException

Deprecated.

Connect to a BioSQL database.

Parameters:

dbURL - A JDBC database URL. For example, jdbc:postgresql://localhost/thomasd_biosql

dbUser - The username to use when connecting to the database (or an empty string).

dbPass - The password to use when connecting to the database (or an empty string).

biodatabase - The identifier of a namespace within the physical BioSQL database.

create - If the requested namespace doesn't exist, and this flag is true, a new namespace will be created.

Throws:

BioException - if an error occurs communicating with the database

BioSQLSequenceDB

public BioSQLSequenceDB(DataSource ds,
                        String biodatabase,
                        boolean create)
                 throws BioException

Deprecated.

Throws:

BioException

Method Detail

createOntology

public Ontology createOntology(String name,
                               String description)
                        throws Exception

Deprecated.

Throws:

Exception

getOntology

public Ontology getOntology(String name)
                     throws Exception

Deprecated.

Throws:

Exception

addOntology

public Ontology addOntology(Ontology onto)
                     throws Exception

Deprecated.

Throws:

Exception

getName

public String getName()

Deprecated.

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.

createDummySequence

public void createDummySequence(String id,
                                Alphabet alphabet,
                                int length)
                         throws ChangeVetoException,
                                BioException

Deprecated.

Throws:

ChangeVetoException

BioException

addSequence

public void addSequence(Sequence seq)
                 throws ChangeVetoException,
                        BioException

Deprecated.

Description copied from interface: SequenceDBLite

Adds a sequence to the database.

Specified by:

addSequence in interface SequenceDBLite

Parameters:

seq - the Sequence to add

Throws:

ChangeVetoException - if either the database does not allow sequences to be added or the modification was vetoed

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

BioException - if something goes wrong with adding the sequence

getSequence

public Sequence getSequence(String id)
                     throws BioException

Deprecated.

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

BioException - if there was a failure in retrieving the sequence

getSequence

public Sequence getSequence(int bioentry_id)
                     throws BioException

Deprecated.

Throws:

BioException

removeSequence

public void removeSequence(String id)
                    throws ChangeVetoException,
                           BioException

Deprecated.

Description copied from interface: SequenceDBLite

Remove the sequence associated with an ID from the database.

Specified by:

removeSequence in interface SequenceDBLite

Parameters:

id - the ID of the sequence to remove

Throws:

ChangeVetoException - if either the database does not allow sequences to be removed or the modification was vetoed

IllegalIDException - if there is no sequence for the ID

BioException - if something failed while removing the sequence for that ID

ids

public Set ids()

Deprecated.

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

filter

public FeatureHolder filter(FeatureFilter ff)

Deprecated.

Description copied from interface: SequenceDB

Query features attached to all sequences in this database. This is equivalent to applying filter to all sequences then merging the results.

Specified by:

filter in interface SequenceDB

Parameters:

ff - a FeatureFilter.

sequenceIterator

public SequenceIterator sequenceIterator()

Deprecated.

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

Returns:

a SequenceIterator over all sequences