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; 024import org.biojava.nbio.structure.align.util.ConfigurationException; 025 026 027public class CeSideChainMain extends CeMain implements StructureAlignment { 028 029 public static final String algorithmName = "jCE-sidechain"; 030 031 /** 032 * version history: 033 * 2.4 - Added more parameters to the command line, including -maxOptRMSD 034 * 2.3 - Initial version 035 */ 036 private static final String version = "2.3"; 037 038 public CeSideChainMain(){ 039 super(); 040 041 if ( params == null) { 042 CeSideChainUserArgumentProcessor proc = new CeSideChainUserArgumentProcessor(); 043 params = (CeParameters) proc.getParameters(); 044 } 045 } 046 047 public static void main(String[] args) throws ConfigurationException { 048 CeSideChainUserArgumentProcessor processor = new CeSideChainUserArgumentProcessor(); 049 processor.process(args); 050 } 051 052 @Override 053 public String getAlgorithmName() { 054 055 return algorithmName; 056 } 057 058 @Override 059 public ConfigStrucAligParams getParameters() { 060 061 return params; 062 } 063 064 @Override 065 public void setParameters(ConfigStrucAligParams params){ 066 System.out.println("setting params : " + params); 067 if (! (params instanceof CeParameters )){ 068 throw new IllegalArgumentException("provided parameter object is not of type CeParameter"); 069 } 070 this.params = (CeParameters) params; 071 } 072 073 @Override 074 public String getVersion() { 075 return version; 076 } 077 078}