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}