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 Jun 7, 2010
021 * Author: ap3
022 *
023 */
024
025package org.biojava.nbio.structure.align.seq;
026
027import org.biojava.nbio.structure.align.ce.ConfigStrucAligParams;
028
029import java.util.ArrayList;
030import java.util.List;
031
032public class SmithWaterman3DParameters implements ConfigStrucAligParams
033{
034
035
036        private short gapOpen ;
037        private short gapExtend ;
038
039        public SmithWaterman3DParameters(){
040                reset();
041        }
042
043
044
045        @Override
046        public List<String> getUserConfigHelp()
047        {
048                List<String> params =new ArrayList<String>();
049                params.add("The Gap open penalty");
050                params.add("The Gap Extension penalty");
051
052
053
054                // TODO Auto-generated method stub
055                return params;
056        }
057
058        @Override
059        public List<String> getUserConfigParameterNames()
060        {
061                List<String> params =new ArrayList<String>();
062                params.add("Gap Open");
063                params.add("Gap Extension");
064
065
066                return params;
067        }
068
069        @Override
070        public List<String> getUserConfigParameters()
071        {
072                List<String> params =new ArrayList<String>();
073                params.add("GapOpen");
074                params.add("GapExtend");
075
076                return params;
077        }
078
079        @Override
080        @SuppressWarnings("rawtypes")
081        public List<Class> getUserConfigTypes()
082        {
083                List<Class> params = new ArrayList<Class>();
084                params.add(Short.class);
085                params.add(Short.class);
086
087                return params;
088        }
089
090        @Override
091        public void reset()
092        {
093                gapOpen = (short) 8;
094                gapExtend = (short) 1;
095
096        }
097
098
099        public Short getGapExtend()
100        {
101                return gapExtend;
102        }
103
104
105
106        public void setGapExtend(Short gapExtend)
107        {
108                this.gapExtend = gapExtend;
109        }
110
111
112
113        public Short getGapOpen() {
114                return gapOpen;
115        }
116
117
118
119        public void setGapOpen(Short gapOpen) {
120                this.gapOpen = gapOpen;
121        }
122
123
124
125
126}