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.geometry; 022 023import javax.vecmath.Matrix4d; 024import javax.vecmath.Point3d; 025 026/** 027 * The SuperPositionAbstract contains common code shared by all SuperPosition 028 * algorithm implementations. 029 * 030 * @author Aleix Lafita 031 * @since 5.0.0 032 * 033 */ 034public abstract class SuperPositionAbstract implements SuperPosition { 035 036 protected boolean centered; 037 038 public SuperPositionAbstract(boolean centered) { 039 this.centered = centered; 040 } 041 042 @Override 043 public Matrix4d superposeAndTransform(Point3d[] fixed, Point3d[] moved) { 044 Matrix4d rotTrans = superpose(fixed, moved); 045 CalcPoint.transform(rotTrans, moved); 046 return rotTrans; 047 } 048 049 /** 050 * Check that the input to the superposition algorithms is valid. 051 * 052 * @param fixed 053 * @param moved 054 */ 055 protected void checkInput(Point3d[] fixed, Point3d[] moved) { 056 if (fixed.length != moved.length) 057 throw new IllegalArgumentException( 058 "Point arrays to superpose are of different lengths."); 059 } 060 061 /** 062 * @param centered 063 * true if the point arrays are centered at the origin (faster), 064 * false otherwise 065 */ 066 public void setCentered(boolean centered) { 067 this.centered = centered; 068 } 069 070}