org.biojava.bio.seq.db
Interface SequenceDBLite

All Superinterfaces:
Changeable
All Known Subinterfaces:
RichSequenceDB, RichSequenceDBLite, SequenceDB
All Known Implementing Classes:
AbstractRichSequenceDB, AbstractSequenceDB, AnnotatedSequenceDB, BioFetchSequenceDB, BioSQLRichSequenceDB, BioSQLSequenceDB, CachingSequenceDB, DASSequenceDB, DistributedSequenceDB, DummySequenceDB, FlatSequenceDB, GenbankRichSequenceDB, GenpeptRichSequenceDB, HashRichSequenceDB, HashSequenceDB, IndexedSequenceDB, NCBISequenceDB, SequenceDBWrapper, SubSequenceDB, ViewingSequenceDB, WebSequenceDB

public interface SequenceDBLite
extends Changeable

A database of sequences. 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 sequence database contains a finite number of sequences stored under unique keys.

Author:
Matthew Pocock, Gerald Loeffler, Thomas Down

Field Summary
static ChangeType SEQUENCES
          Signals that sequences are being added to or remove from the database.
 
Method Summary
 void addSequence(Sequence seq)
          Adds a sequence to the database.
 java.lang.String getName()
          Get the name of this sequence database.
 Sequence getSequence(java.lang.String id)
          Retrieve a single sequence by its id.
 void removeSequence(java.lang.String id)
          Remove the sequence associated with an ID from the database.
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 

Field Detail

SEQUENCES

static final ChangeType SEQUENCES
Signals that sequences are being added to or remove from the database. The sequences being removed should be listed in the previous field by id, either as a single String, an array or a Set. The sequences being added should be listed in the change field as either an array Object[] { id, seq}, or a Map of id->seq.

Method Detail

getName

java.lang.String getName()
Get the name of this sequence database.

Returns:
the name of the sequence database, which may be null.

getSequence

Sequence getSequence(java.lang.String id)
                     throws IllegalIDException,
                            BioException
Retrieve a single sequence 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 - if there was a failure in retrieving the sequence

addSequence

void addSequence(Sequence seq)
                 throws IllegalIDException,
                        BioException,
                        ChangeVetoException
Adds a sequence to the database.

Parameters:
seq - the Sequence to add
Throws:
IllegalIDException - if a uniqe ID could not be generated for seq
BioException - if something goes wrong with adding the sequence
ChangeVetoException - if either the database does not allow sequences to be added or the modification was vetoed

removeSequence

void removeSequence(java.lang.String id)
                    throws IllegalIDException,
                           BioException,
                           ChangeVetoException
Remove the sequence associated with an ID from the database.

Parameters:
id - the ID of the sequence to remove
Throws:
IllegalIDException - if there is no sequence for the ID
BioException - if something failed while removing the sequence for that ID
ChangeVetoException - if either the database does not allow sequences to be removed or the modification was vetoed