/*
* 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/
*
* Created on Sep 9, 2009
* Author: Andreas Prlic
*
*/
package org.biojava.nbio.structure.align.xml;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Calc;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.jama.Matrix;
public class AFPChainFlipper {
/** Flip the position of name1 and name2 (as well as all underlying data) in an AFPChain.
* This is a utility function for AFPChainXMLParser.
* You will have to call AFPCHainXMLParser.rebuildAFPChain in order to get twisted groups...
*
* @param o ... the original AFPCHain that should be flipped
* @return a cloned AFPCHain which the positions of name1 and name2 flipped.
*/
public static AFPChain flipChain(AFPChain o) throws StructureException{
AFPChain n = new AFPChain(o.getAlgorithmName());
n.setVersion(o.getVersion());
n.setName2(o.getName1());
n.setName1(o.getName2());
n.setCa1Length(o.getCa2Length());
n.setCa2Length(o.getCa1Length());
int[] optLen = o.getOptLen();
n.setOptLen(optLen);
int blockNum = o.getBlockNum();
n.setBlockNum(blockNum);
n.setBlockSize(o.getBlockSize());
n.setBlockScore(o.getBlockScore());
n.setBlockRmsd(o.getBlockRmsd());
n.setBlockGap(o.getBlockGap());
int minLength = Math.min(n.getCa1Length(),n.getCa2Length());
int[][][] optAlnN = new int[blockNum][2][minLength];
int[][][] optAlnO = o.getOptAln();
String[][][] pdbAlnN = new String[blockNum][2][minLength];
String[][][] pdbAlnO = o.getPdbAln();
if ( ( optAlnO == null) && ( pdbAlnO == null) ){
System.err.println("Can't get either optAln or pdbAln data from original AFPChain. Not enough information to recreate alignment!");
}
for (int blockNr = 0 ; blockNr < blockNum ; blockNr++) {
for ( int eqrNr = 0 ; eqrNr < optLen[blockNr] ; eqrNr++ ) {
if ( optAlnO != null ){
optAlnN[blockNr][0][eqrNr] = optAlnO[blockNr][1][eqrNr];
optAlnN[blockNr][1][eqrNr] = optAlnO[blockNr][0][eqrNr];
}
if ( pdbAlnO != null) {
pdbAlnN[blockNr][0][eqrNr] = pdbAlnO[blockNr][1][eqrNr];
pdbAlnN[blockNr][1][eqrNr] = pdbAlnO[blockNr][0][eqrNr];
}
}
}
n.setOptAln(optAlnN);
if ( pdbAlnO != null) {
n.setPdbAln(pdbAlnN);
}
n.setAlnLength(o.getAlnLength());
n.setAlignScore(o.getAlignScore());
n.setAlignScoreUpdate(o.getAlignScoreUpdate());
n.setAfpSet(o.getAfpSet());
n.setChainRmsd(o.getChainRmsd());
n.setFocusRes1(o.getFocusRes2());
n.setFocusRes2(o.getFocusRes1());
n.setFocusResn(o.getFocusResn());
n.setGapLen(o.getGapLen());
n.setIdentity(o.getIdentity());
n.setNormAlignScore(o.getNormAlignScore());
n.setOptLength(o.getOptLength());
n.setProbability(o.getProbability());
n.setSimilarity(o.getSimilarity());
n.setTotalLenIni(o.getTotalLenIni());
n.setTotalRmsdIni(o.getTotalRmsdIni());
n.setTotalRmsdOpt(o.getTotalRmsdOpt());
n.setTMScore(o.getTMScore());
// change direction of the Matrix and shift!
//
Matrix[] maxO = o.getBlockRotationMatrix();
Matrix[] maxN = new Matrix[maxO.length];
int i = -1;
Atom[] shiftO = o.getBlockShiftVector();
Atom[] shiftN = new Atom[shiftO.length];
for (Matrix m : maxO){
i++;
if ( m == null) {
// alignment too short probably
continue;
}
Matrix mnew = m ;
Atom a = shiftO[i];
maxN[i] = mnew.transpose();
shiftN[i] = Calc.invert(a);
Calc.rotate(shiftN[i],maxN[i]);
}
n.setBlockRotationMatrix(maxN);
n.setBlockShiftVector(shiftN);
return n;
}
}