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 Details
- 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 Details
- 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

Class BioSQLSequenceDB

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class org.biojava.utils.AbstractChangeable

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojava.utils.Changeable

Constructor Details

BioSQLSequenceDB

BioSQLSequenceDB

BioSQLSequenceDB

Method Details

createOntology

getOntology

addOntology

getName

createDummySequence

addSequence

getSequence

getSequence

removeSequence

ids

filter

sequenceIterator