/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.structure.align.gui;
import java.util.List;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.AtomImpl;
import org.biojava.nbio.structure.Calc;
import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.AFPTwister;
import org.biojava.nbio.structure.align.fatcat.FatCatFlexible;
import org.biojava.nbio.structure.align.fatcat.FatCatRigid;
import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.util.AlignmentTools;
import org.biojava.nbio.structure.jama.Matrix;
public class StructureAlignmentDisplay {
/** Display an AFPChain alignment
*
* @param afpChain
* @param ca1
* @param ca2
* @return a StructureAlignmentJmol instance
* @throws StructureException
*/
public static StructureAlignmentJmol display(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException {
if ( ca1.length < 1 || ca2.length < 1){
throw new StructureException("length of atoms arrays is too short! " + ca1.length + "," + ca2.length);
}
Group[] twistedGroups = AlignmentTools.prepareGroupsForDisplay(afpChain, ca1, ca2);
List<Group> hetatms = StructureTools.getUnalignedGroups(ca1);
List<Group> hetatms2 = StructureTools.getUnalignedGroups(ca2);
return DisplayAFP.display(afpChain, twistedGroups, ca1, ca2, hetatms, hetatms2);
}
}