Package org.biojavax.bio.db

Interface RichSequenceDBLite

All Superinterfaces:

BioEntryDBLite, Changeable, SequenceDBLite

All Known Subinterfaces:

RichSequenceDB

All Known Implementing Classes:

AbstractRichSequenceDB, BioSQLRichSequenceDB, GenbankRichSequenceDB, GenpeptRichSequenceDB, HashRichSequenceDB

public interface RichSequenceDBLite
extends BioEntryDBLite, SequenceDBLite

A database of RichSequences. This may have several implementations with rich behaviour, but basically most of the time you will just use the interface methods to do stuff. A RichSequence database contains a finite number of RichSequences stored under unique keys.

Since:

1.5

Author:

Matthew Pocock, Gerald Loeffler, Thomas Down, Richard Holland

Field Summary

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

BIOENTRYS

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

SEQUENCES

Method Summary

Modifier and Type	Method	Description
void	addRichSequence(RichSequence seq)	Adds a sequence to the 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.
void	removeRichSequence(String id)	Remove the RichSequence associated with an ID from the database.

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

addBioEntry, getBioEntry, getBioEntrys, getBioEntrys, getName, removeBioEntry

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

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

addSequence, getName, getSequence, removeSequence

Method Detail

getRichSequence

RichSequence getRichSequence(String id)
                      throws BioException,
                             IllegalIDException

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

RichSequenceDB getRichSequences(Set ids)
                         throws BioException,
                                IllegalIDException

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

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

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

addRichSequence

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

Adds a sequence to the database.

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

removeRichSequence

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

Remove the RichSequence associated with an ID from the database.

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