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}