001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021
022package org.biojava.bio.seq.db;
023
024import org.biojava.bio.BioException;
025import org.biojava.bio.seq.Sequence;
026import org.biojava.utils.ChangeType;
027import org.biojava.utils.ChangeVetoException;
028import org.biojava.utils.Changeable;
029
030/**
031 * A database of sequences. This may have several implementations with
032 * rich behaviour, but basically most of the time you will just use
033 * the interface methods to do stuff. A sequence database contains a
034 * finite number of sequences stored under unique keys.
035 *
036 * @author Matthew Pocock
037 * @author <A href="mailto:Gerald.Loeffler@vienna.at">Gerald Loeffler</A>
038 * @author Thomas Down
039 */
040public interface SequenceDBLite extends Changeable {
041  /**
042   * Signals that sequences are being added to or remove from the database.
043   * The sequences being removed should be listed in the previous field by
044   * id, either as a single String, an array or a Set. The sequences
045   * being added should be listed in the change field as either an array
046   * Object[] { id, seq}, or a Map of id->seq.
047   */
048  public static final ChangeType SEQUENCES = new ChangeType(
049    "Sequences have been added or removed from the database",
050    "org.biojava.bio.seq.db.SequenceDB",
051    "SEQUENCES"
052  );
053  
054  /**
055   * Get the name of this sequence database.
056   *
057   * @return the name of the sequence database, which may be null.
058   */
059  String getName();
060
061  /**
062   * Retrieve a single sequence by its id.
063   *
064   * @param id the id to retrieve by
065   * @return  the Sequence with that id
066   * @throws IllegalIDException if the database doesn't know about the id
067   * @throws BioException if there was a failure in retrieving the sequence
068   */
069  Sequence getSequence(String id) throws IllegalIDException, BioException;
070  
071  /**
072   * Adds a sequence to the database.
073   *
074   * @param seq the Sequence to add
075   * @throws IllegalIDException if a uniqe ID could not be generated for seq
076   * @throws BioException if something goes wrong with adding the sequence
077   * @throws ChangeVetoException  if either the database does not allow
078   *         sequences to be added or the modification was vetoed
079   */
080  void addSequence(Sequence seq)
081  throws IllegalIDException, BioException, ChangeVetoException;
082  
083  /**
084   * Remove the sequence associated with an ID from the database.
085   *
086   * @param id  the ID of the sequence to remove
087   * @throws  IllegalIDException if there is no sequence for the ID
088   * @throws  BioException if something failed while removing the sequence for
089   *          that ID
090   * @throws  ChangeVetoException  if either the database does not allow
091   *          sequences to be removed or the modification was vetoed
092   */
093  void removeSequence(String id)
094  throws IllegalIDException, BioException, ChangeVetoException;
095}