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 */
021package org.biojava.nbio.structure.align;
022
023
024import org.biojava.nbio.structure.Atom;
025import org.biojava.nbio.structure.StructureException;
026import org.biojava.nbio.structure.align.ce.ConfigStrucAligParams;
027import org.biojava.nbio.structure.align.model.AFPChain;
028
029public abstract class AbstractStructureAlignment implements StructureAlignment{
030
031        public static String newline = System.getProperty("line.separator");
032
033        @Override
034        abstract public  AFPChain align(Atom[] ca1, Atom[] ca2)
035                        throws StructureException;
036
037        @Override
038        abstract public AFPChain align(Atom[] ca1, Atom[] ca2, Object params)
039                        throws StructureException;
040
041        @Override
042        abstract public String getAlgorithmName() ;
043
044        @Override
045        abstract public ConfigStrucAligParams getParameters() ;
046
047        @Override
048        abstract public String getVersion() ;
049
050        @Override
051        abstract public void setParameters(ConfigStrucAligParams parameters);
052
053}