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; 022 023 024import org.biojava.nbio.structure.Atom; 025import org.biojava.nbio.structure.StructureException; 026import org.biojava.nbio.structure.align.ce.ConfigStrucAligParams; 027import org.biojava.nbio.structure.align.model.AFPChain; 028 029public abstract class AbstractStructureAlignment implements StructureAlignment{ 030 031 public static String newline = System.getProperty("line.separator"); 032 033 @Override 034 abstract public AFPChain align(Atom[] ca1, Atom[] ca2) 035 throws StructureException; 036 037 @Override 038 abstract public AFPChain align(Atom[] ca1, Atom[] ca2, Object params) 039 throws StructureException; 040 041 @Override 042 abstract public String getAlgorithmName() ; 043 044 @Override 045 abstract public ConfigStrucAligParams getParameters() ; 046 047 @Override 048 abstract public String getVersion() ; 049 050 @Override 051 abstract public void setParameters(ConfigStrucAligParams parameters); 052 053}