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 Jan 29, 2006
021 *
022 */
023package org.biojava.nbio.structure.align.pairwise;
024
025import org.biojava.nbio.structure.align.helper.AligMatEl;
026import org.biojava.nbio.structure.align.helper.IndexPair;
027
028public interface Alignable {
029        public int getRows();
030        public int getCols();
031        public AligMatEl[][] getAligMat();
032        public void setAligMat(AligMatEl[][] alignmentMatrix);
033        public float getGapExtCol();
034        public void setGapExtCol(float penalty);
035        public float getGapExtRow();
036        public void setGapExtRow(float penalty);
037        public float getGapOpenCol();
038        public void setGapOpenCol(float penalty);
039        public float getGapOpenRow();
040        public void setGapOpenRow(float penalty);
041        public void setScore(float score);
042        public float getScore();
043        public int getPathSize();
044        public void setPathSize(int pathSize);
045        public void setPath(IndexPair[] path);
046        public IndexPair[] getPath();
047}