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.gui; 022 023import java.util.List; 024 025import org.biojava.nbio.structure.Atom; 026import org.biojava.nbio.structure.Group; 027import org.biojava.nbio.structure.StructureException; 028import org.biojava.nbio.structure.StructureTools; 029import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol; 030import org.biojava.nbio.structure.align.model.AFPChain; 031import org.biojava.nbio.structure.align.util.AlignmentTools; 032 033public class StructureAlignmentDisplay { 034 035 /** Display an AFPChain alignment 036 * 037 * @param afpChain 038 * @param ca1 039 * @param ca2 040 * @return a StructureAlignmentJmol instance 041 * @throws StructureException 042 */ 043 public static StructureAlignmentJmol display(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException { 044 045 if ( ca1.length < 1 || ca2.length < 1){ 046 throw new StructureException("length of atoms arrays is too short! " + ca1.length + "," + ca2.length); 047 } 048 049 Group[] twistedGroups = AlignmentTools.prepareGroupsForDisplay(afpChain, ca1, ca2); 050 051 List<Group> hetatms = StructureTools.getUnalignedGroups(ca1); 052 List<Group> hetatms2 = StructureTools.getUnalignedGroups(ca2); 053 054 return DisplayAFP.display(afpChain, twistedGroups, ca1, ca2, hetatms, hetatms2); 055 056 } 057 058}