org.biojavax.bio.db.biosql

Class BioSQLRichSequenceDB

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.db.AbstractBioEntryDB

org.biojavax.bio.db.AbstractRichSequenceDB

org.biojavax.bio.db.biosql.BioSQLRichSequenceDB

All Implemented Interfaces:

SequenceDB, SequenceDBLite, Changeable, BioEntryDB, BioEntryDBLite, RichSequenceDB, RichSequenceDBLite

public class BioSQLRichSequenceDB
extends AbstractRichSequenceDB

Since:

1.5

Author:

Richard Holland, David Scott

Field Summary

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

BIOENTRYS

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

SEQUENCES

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
void	addRichSequence(RichSequence seq) Adds a sequence to the database.
FeatureHolder	filter(FeatureFilter ff) Query features attached to all sequences in this database.
RichSequence	fullyLoadRichSequence(RichSequence id)
Object	getHibernateSession()
String	getName() Get the name of this sequence database.
RichSequence	getRichSequence(String id) Retrieve a single RichSequence by its id.
RichSequenceDB	getRichSequences(Set ids) Retrieve multiple RichSequence by its id.
RichSequenceDB	getRichSequences(Set ids, RichSequenceDB db) Retrieve multiple RichSequence into a specific sequence database.
Set	ids() Get an immutable set of all of the IDs in the database.
FeatureHolder	processFeatureFilter(FeatureFilter ff)
void	removeRichSequence(String id) Remove the RichSequence associated with an ID from the database.

Methods inherited from class org.biojavax.bio.db.AbstractRichSequenceDB

addBioEntry, addSequence, getBioEntry, getBioEntryIterator, getBioEntrys, getBioEntrys, getRichSequenceIterator, getSequence, removeBioEntry, removeSequence, sequenceIterator

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

BioSQLRichSequenceDB

public BioSQLRichSequenceDB(Object session)

Creates a new instance of BioSQLRichSequenceDB

BioSQLRichSequenceDB

public BioSQLRichSequenceDB(String name,
                            Object session)

Creates a new instance of BioSQLRichSequenceDB

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()

processFeatureFilter

public FeatureHolder processFeatureFilter(FeatureFilter ff)

filter

public FeatureHolder filter(FeatureFilter ff)

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

Overrides:

filter in class AbstractRichSequenceDB

Parameters:

ff - a FeatureFilter.

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

fullyLoadRichSequence

public RichSequence fullyLoadRichSequence(RichSequence id)
                                   throws IllegalIDException,
                                          BioException

Throws:

IllegalIDException

BioException

getRichSequence

public RichSequence getRichSequence(String id)
                             throws IllegalIDException,
                                    BioException

Description copied from interface: RichSequenceDBLite

Retrieve a single RichSequence by its id.

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

getRichSequences

public RichSequenceDB getRichSequences(Set ids)
                                throws BioException,
                                       IllegalIDException

Description copied from interface: RichSequenceDBLite

Retrieve multiple RichSequence by its id.

Parameters:

ids - a set of ids to retrieve by

Returns:

the RichSequences with that id

Throws:

IllegalIDException - if the database doesn't know about the id

BioException

getRichSequences

public RichSequenceDB getRichSequences(Set ids,
                                       RichSequenceDB db)
                                throws BioException,
                                       IllegalIDException

Description copied from interface: RichSequenceDBLite

Retrieve multiple RichSequence into a specific sequence database. If that database is null, a new HashRichSequenceDB is used.

Parameters:

ids - a set of ids to retrieve by

db - a database to load the seqs into

Returns:

the RichSequences with that id

Throws:

IllegalIDException - if the database doesn't know about the id

BioException

removeRichSequence

public void removeRichSequence(String id)
                        throws IllegalIDException,
                               BioException,
                               ChangeVetoException

Description copied from interface: RichSequenceDBLite

Remove the RichSequence associated with an ID from the database.

Specified by:

removeRichSequence in interface RichSequenceDBLite

Overrides:

removeRichSequence in class AbstractRichSequenceDB

Parameters:

id - the ID of the RichSequence to remove

Throws:

IllegalIDException - if there is no RichSequence for the ID

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

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

addRichSequence

public void addRichSequence(RichSequence seq)
                     throws IllegalIDException,
                            BioException,
                            ChangeVetoException

Description copied from interface: RichSequenceDBLite

Adds a sequence to the database.

Specified by:

addRichSequence in interface RichSequenceDBLite

Overrides:

addRichSequence in class AbstractRichSequenceDB

Parameters:

seq - the RichSequence to add

Throws:

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

BioException - if something goes wrong with adding the RichSequence

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