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
023import org.biojava.nbio.structure.Atom;
024import org.biojava.nbio.structure.StructureException;
025import org.biojava.nbio.structure.align.ce.ConfigStrucAligParams;
026import org.biojava.nbio.structure.align.model.AFPChain;
027
028
029public interface StructureAlignment {
030
031        /** Run an alignment while specifying the atoms to be aligned. Will used default parameters for the algorithm.
032         *
033         * @param ca1
034         * @param ca2
035         * @return the afpChain object that contains the alignment.
036         * @throws StructureException
037         */
038        public AFPChain align(Atom[] ca1, Atom[] ca2) throws StructureException;
039
040        /** run an alignment and also send a bean containing the parameters.
041         *
042         * @param ca1
043         * @param ca2
044         * @param params
045         * @return the afpChain object that contains the alignment.
046         * @throws StructureException
047         */
048        public AFPChain align(Atom[] ca1, Atom[] ca2, Object params) throws StructureException;
049
050        /** Return the paramers for this algorithm.
051         *
052         * @return The returned object will be a Java bean.
053         */
054        public ConfigStrucAligParams getParameters();
055
056        /** Set the default parameters for this algorithm to use
057         *
058         * @param parameters
059         */
060        public void setParameters(ConfigStrucAligParams parameters);
061
062        /** Get the name of the Algorithm
063         *
064         * @return the name of the algorithm
065         */
066        public String getAlgorithmName();
067
068        /** Get the Version information for this Algorithm.
069         *
070         * @return the version of the algorithm
071         */
072        public String getVersion();
073}