## 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

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

    public class BioSQLSequenceDB

extends AbstractChangeable
implements SequenceDB

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
`BioSQLSequenceDB(DataSource ds, String biodatabase, boolean create)` Deprecated.
`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.

Method Summary
`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