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 * Created on June 7, 2010
021 * Author: Mark Chapman
022 */
023
024package org.biojava.nbio.core.alignment.template;
025
026import org.biojava.nbio.core.alignment.template.Profile;
027import org.biojava.nbio.core.alignment.template.AlignedSequence;
028import org.biojava.nbio.core.sequence.template.Compound;
029import org.biojava.nbio.core.sequence.template.Sequence;
030
031import java.util.List;
032
033/**
034 * Defines a mutable (editable) data structure for a {@link Profile}.  Returned {@link List}s are modifiable.
035 *
036 * @author Mark Chapman
037 * @author Paolo Pavan
038 * @param <S> each element of the alignment {@link Profile} is of type S
039 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
040 */
041public interface MutableProfile<S extends Sequence<C>, C extends Compound> extends Profile<S, C> {
042
043        /**
044         * Sets entirely new set of {@link AlignedSequence}s.
045         *
046         * @param sequences new set of sequences
047         * @throws IllegalArgumentException if sequences have different lengths
048         */
049        void setSequences(List<AlignedSequence<S, C>> sequences);
050
051        // TODO? - make compatible with core.sequence.MultipleSequenceAlignment
052}