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.ce;
022
023import org.biojava.nbio.structure.align.StructureAlignment;
024
025public class CeSideChainUserArgumentProcessor extends CeUserArgumentProcessor {
026
027        @Override
028        public StructureAlignment getAlgorithm() {
029                return new CeSideChainMain();
030        }
031
032        @Override
033        public Object getParameters() {
034
035                CeParameters params = new CeParameters();
036
037                params.setScoringStrategy(CeParameters.ScoringStrategy.SIDE_CHAIN_SCORING);
038                //params.setMaxGapSize(0);
039                return params;
040        }
041
042
043        @Override
044        public String getDbSearchLegend(){
045                String legend = "# name1\tname2\tscore\tz-score\trmsd\tlen1\tlen2\tsim1\tsim2\t " ;
046                return legend;
047        }
048
049}