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.sequence.template.Compound;
027import org.biojava.nbio.core.sequence.template.Sequence;
028
029/**
030 * Defines a data structure for a view of sequence alignment.
031 *
032 * @author Mark Chapman
033 * @author Paolo Pavan
034 * @param <S> each element of the alignment {@link Profile} is of type S
035 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
036 */
037public interface ProfileView<S extends Sequence<C>, C extends Compound> extends Profile<S, C> {
038
039        /**
040         * Returns the column index of the viewed {@link Profile} corresponding to the final element in this view
041         *
042         * @return column index of this view's final element
043         */
044        int getEnd();
045
046        /**
047         * Returns the column index of the viewed {@link Profile} corresponding to the first element in this view
048         *
049         * @return column index of this view's first element
050         */
051        int getStart();
052
053        /**
054         * Returns the entire {@link Profile} being viewed
055         *
056         * @return the entire alignment profile
057         */
058        Profile<S, C> getViewedProfile();
059
060}