/* This class is based on the original FATCAT implementation by
 * <pre>
 * Yuzhen Ye & Adam Godzik (2003)
 * Flexible structure alignment by chaining aligned fragment pairs allowing twists.
 * Bioinformatics vol.19 suppl. 2. ii246-ii255.
 * https://www.ncbi.nlm.nih.gov/pubmed/14534198
 * </pre>
 *
 * Thanks to Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute this 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.
 *
 *
 * Created on Jun 17, 2009
 * Created by Andreas Prlic - RCSB PDB
 *
 */

package org.biojava.nbio.structure.align;

import org.biojava.nbio.structure.*;
import org.biojava.nbio.structure.align.model.AFP;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.jama.Matrix;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.util.ArrayList;
import java.util.List;

//import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;

public class AFPTwister
{
        private final static Logger logger = LoggerFactory.getLogger(AFPTwister.class);

//   private static final boolean showAlignmentSteps = false;

        /**
         * calculate the total rmsd of the blocks
         * output a merged pdb file for both proteins
          protein 1, in chain A
         protein 2 is twisted according to the twists detected, in chain B
         * @return  twisted Groups
         */
        public static Group[] twistPDB(AFPChain afpChain,Atom[] ca1, Atom[] ca2) throws StructureException {
                //--------------------------------------------------------

                if ( afpChain.isShortAlign())
                        return new Group[0];

                List<AFP> afpSet = afpChain.getAfpSet();

                int blockNum = afpChain.getBlockNum();

                int     i,  b2, e2;


                //superimposing according to the initial AFP-chaining
                Atom[] origCA      = StructureTools.cloneAtomArray(ca2);
                Atom[] iniTwistPdb = StructureTools.cloneAtomArray(ca2);

                int[] blockResSize = afpChain.getBlockResSize();

                int[][][] blockResList = afpChain.getBlockResList();

                int[] afpChainList    = afpChain.getAfpChainList();
                int[] block2Afp       = afpChain.getBlock2Afp();
                int[] blockSize       = afpChain.getBlockSize();
                int[] focusAfpList    = afpChain.getFocusAfpList();

                if ( focusAfpList == null){
                        focusAfpList = new int[afpChain.getMinLen()];
                        afpChain.setFocusAfpList(focusAfpList);
                }

                int  focusAfpn = 0;
                e2 = 0;
                b2 = 0;


                logger.debug("blockNUm at twister: ", blockNum);

                for(int bk = 0; bk < blockNum; bk ++)       {

                        // THIS IS TRANSFORMING THE ORIGINAL ca2 COORDINATES, NO CLONING...
                        // copies the atoms over to iniTwistPdb later on in modifyCod

                        transformOrigPDB(blockResSize[bk], blockResList[bk][0], blockResList[bk][1],  ca1, ca2, null,-1);

                        //transform pro2 according to comparison of pro1 and pro2 at give residues
                        if(bk > 0)      {
                                b2 = e2;
                        }

                        logger.debug("b2 is {} before  modifyCon", b2);

                        if(bk < (blockNum - 1))   {

                                //bend at the middle of two consecutive AFPs
                                int afpPos = afpChainList[block2Afp[bk] + blockSize[bk] - 1];
                                AFP a1 = afpSet.get(afpPos);
                                e2 = a1.getP2() ;

                                int afpPos2 = afpChainList[block2Afp[bk + 1]];
                                AFP a2 = afpSet.get(afpPos2);
                                e2 = (a2.getP2() - e2)/ 2 + e2;
                                logger.debug("e2 : {}", e2);
                        } else{
                                // last one is until the end...
                                e2 = ca2.length;
                        }

                        // this copies the coordinates over into iniTwistPdb
                        cloneAtomRange(iniTwistPdb, ca2, b2, e2);

                        //bound[bk] = e2;
                        for(i = 0; i < blockSize[bk]; i ++)     {
                                focusAfpList[focusAfpn] = afpChainList[block2Afp[bk] + i];
                                focusAfpn++;
                        }
                }


                int focusResn = afp2Res(afpChain, focusAfpn,  focusAfpList, 0);

                afpChain.setTotalLenIni(focusResn);

                logger.debug(String.format("calrmsdini for %d residues", focusResn));

                double totalRmsdIni = calCaRmsd(ca1,iniTwistPdb, focusResn, afpChain.getFocusRes1() , afpChain.getFocusRes2() );


                afpChain.setTotalRmsdIni(totalRmsdIni);
                logger.debug("got iniRMSD: {}", totalRmsdIni);
                if ( totalRmsdIni == 5.76611141613097) {
                        logger.debug("{}", afpChain.getAlnseq1());
                        logger.debug("{}", afpChain.getAlnsymb());
                        logger.debug("{}", afpChain.getAlnseq2());
                }

                afpChain.setFocusAfpList(focusAfpList);
                afpChain.setBlock2Afp(block2Afp);
                afpChain.setAfpChainList(afpChainList);

                return twistOptimized(afpChain,ca1,origCA);
        }

        /**       superimposing according to the optimized alignment
         *
         * @param afpChain
         * @param ca1
         * @param ca2
         * @return Group array twisted.
         * @throws StructureException
         */
        public static Group[] twistOptimized(AFPChain afpChain,Atom[] ca1, Atom[] ca2) throws StructureException {

                Atom[] optTwistPdb = new Atom[ca2.length];

                int gPos = -1;
                for (Atom a : ca2){
                        gPos++;
                        optTwistPdb[gPos] = a;
                }

                int blockNum = afpChain.getBlockNum();

                int b2 =  0;
                int e2 =  0;
                int focusResn = 0;
                int[] focusRes1 = afpChain.getFocusRes1();
                int[] focusRes2 = afpChain.getFocusRes2();

                if(focusRes1 == null) {
                         focusRes1 = new int[afpChain.getCa1Length()];
                         afpChain.setFocusRes1(focusRes1);
                }
                if(focusRes2 == null) {
                         focusRes2 = new int[afpChain.getCa2Length()];
                         afpChain.setFocusRes2(focusRes2);
                }

                int[] optLen      = afpChain.getOptLen();
                int[][][] optAln  = afpChain.getOptAln();

                for(int bk = 0; bk < blockNum; bk ++)       {
                        //  THIS IS TRANSFORMING THE ORIGINAL ca2 COORDINATES, NO CLONING...
                        // copies the atoms over to iniTwistPdb later on in modifyCod
                        transformOrigPDB(optLen[bk], optAln[bk][0], optAln[bk][1], ca1, ca2,afpChain,bk);

                        //transform pro2 according to comparison of pro1 and pro2 at give residues
                        if(bk > 0)      { b2 = e2; }
                        if(bk < blockNum - 1)   { //bend at the middle of two consecutive blocks
                                e2 = optAln[bk][1][optLen[bk] - 1];
                                e2 = (optAln[bk + 1][1][0] - e2)/ 2 + e2;
                        }
                        else    { e2 = ca2.length; }
                        cloneAtomRange(optTwistPdb, ca2, b2, e2);
                        for(int i = 0; i < optLen[bk]; i ++)        {
                                focusRes1[focusResn] = optAln[bk][0][i];
                                focusRes2[focusResn] = optAln[bk][1][i];
                                focusResn ++;
                        }
                }
                int totalLenOpt = focusResn;
                logger.debug("calrmsdopt for {} residues", focusResn);
                double totalRmsdOpt = calCaRmsd(ca1, optTwistPdb, focusResn, focusRes1, focusRes2);
                logger.debug("got opt RMSD: {}", totalRmsdOpt);
                int optLength = afpChain.getOptLength();

                if(totalLenOpt != optLength)    {
                        logger.warn("Final alignment length is different {} {}", totalLenOpt, optLength);
                }
                logger.debug("final alignment length {}, rmsd {}", focusResn, totalRmsdOpt);

                afpChain.setTotalLenOpt(totalLenOpt);
                afpChain.setTotalRmsdOpt(totalRmsdOpt);

                return StructureTools.cloneGroups(optTwistPdb);

        }


        /**
         * transform the coordinates in the ca2 according to the superimposing of the given position pairs.
         * No Cloning, transforms input atoms.
         */
        // orig name: transPdb
        private static void transformOrigPDB(int n, int[] res1, int[] res2, Atom[] ca1, Atom[] ca2, AFPChain afpChain, int blockNr)
        throws StructureException
        {
                logger.debug("transforming original coordinates {} len1: {} res1: {} len2: {} res2: {}", n, ca1.length, res1.length, ca2.length, res2.length);

                Atom[] cod1 = getAtoms(ca1, res1, n,false);
                Atom[] cod2 = getAtoms(ca2, res2, n,false);

                //double  *cod1 = pro1->Cod4Res(n, res1);
                //double  *cod2 = pro2->Cod4Res(n, res2);

                Matrix r;
                Atom t;

                SVDSuperimposer svd = new SVDSuperimposer(cod1, cod2);

                r = svd.getRotation();
                t = svd.getTranslation();

                logger.debug("transPdb: transforming orig coordinates with matrix: {}", r);

                if ( afpChain != null ){
                        Matrix[] ms = afpChain.getBlockRotationMatrix();
                        if ( ms == null)
                                ms = new Matrix[afpChain.getBlockNum()];

                        ms[blockNr]= r;

                        Atom[] shifts = afpChain.getBlockShiftVector();
                        if ( shifts == null)
                                shifts = new Atom[afpChain.getBlockNum()];
                        shifts[blockNr] = t;

                        afpChain.setBlockRotationMatrix(ms);
                        afpChain.setBlockShiftVector(shifts);
                }

                for (Atom a : ca2){
                        Calc.rotate(a.getGroup(),r);
                        Calc.shift(a.getGroup(),t);
                }


        }

        // like Cod4Res
        // most likely the clone flag is not needed
        private static Atom[] getAtoms(Atom[] ca, int[] positions, int length, boolean clone){

                List<Atom> atoms = new ArrayList<Atom>();
                for ( int i = 0 ; i < length ; i++){
                        int p = positions[i];
                        Atom a;
                        if ( clone ){
                                a = (Atom)ca[p].clone();
                                a.setGroup((Group)ca[p].getGroup().clone());
                        }
                        else {
                                a = ca[p];
                        }
                        atoms.add(a);
                }
                return atoms.toArray(new Atom[atoms.size()]);
        }



        /** Clones and copies the Atoms from p2 into p1 range is between r1 and r2
         *
         * @param p1
         * @param p2
         * @param r1
         * @param r2
         */
        // orig name: modifyCod
        private static void cloneAtomRange(Atom[] p1, Atom[] p2, int r1, int r2)
        throws StructureException
        {

                logger.debug("modifyCod from: {} to: {}", r1, r2);

                // special clone method, can;t use StructureTools.cloneCAArray, since we access the data
                // slightly differently here.
                List<Chain> model = new ArrayList<Chain>();
                for(int i = r1; i < r2; i ++) {

                        Group g = p2[i].getGroup();
                        Group newG = (Group)g.clone();

                        p1[i] = newG.getAtom(p2[i].getName());
                        Chain parentC = g.getChain();

                        Chain newChain = null;

                        for( Chain c: model){
                                if (c.getChainID().equals(parentC.getChainID())){
                                        newChain = c;
                                        break;
                                }
                        }

                        if ( newChain == null){
                                newChain = new ChainImpl();
                                newChain.setChainID(parentC.getChainID());
                                model.add(newChain);
                        }

                        newChain.addGroup(newG);


                } //modify caCod

        }



        /**
         * Return the rmsd of the CAs between the input pro and this protein, at given positions.
         * quite similar to transPdb but while that one transforms the whole ca2, this one only works on the res1 and res2 positions.
         *
         *  Modifies the coordinates in the second set of Atoms (pro).
         *
         * @return rmsd of CAs
         */
        private static double calCaRmsd(Atom[] ca1, Atom[] pro, int resn, int[] res1, int[] res2) throws StructureException
        {



                Atom[] cod1 = getAtoms(ca1,  res1,resn,false);
                Atom[] cod2 = getAtoms(pro,  res2,resn,false);

                Matrix r;
                Atom t;

                if ( cod1.length == 0  || cod2.length == 0){
                        logger.info("length of atoms  == 0!");
                        return 99;
                }
                SVDSuperimposer svd = new SVDSuperimposer(cod1, cod2);

                r = svd.getRotation();
                t = svd.getTranslation();

                for (Atom a : cod2){

                        Calc.rotate(a.getGroup(), r);
                        Calc.shift(a.getGroup(),  t);
                }

                return SVDSuperimposer.getRMS(cod1, cod2);
        }

        /**
         * Set the list of equivalent residues in the two proteins given a list of AFPs
         *
         * WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in afpChain!
         *
         * @param afpChain the AFPChain to store resuts
         * @param afpn nr of afp
         * @param afpPositions
         * @param listStart
         * @return nr of eq residues
         */

        public static int afp2Res(AFPChain afpChain, int afpn, int[] afpPositions , int listStart   )
        {
                int[] res1 = afpChain.getFocusRes1();
                int[] res2 = afpChain.getFocusRes2();
                int minLen = afpChain.getMinLen();

                int n = 0;

                List<AFP> afpSet =afpChain.getAfpSet();

                for(int i = listStart; i < listStart+afpn; i ++)      {
                        int a = afpPositions[i];
                        for(int j = 0; j < afpSet.get(a).getFragLen(); j ++)     {
                                if(n >= minLen) {
                                        throw new RuntimeException("Error: too many residues in AFPChainer.afp2Res!");
                                }
                                res1[n] = afpSet.get(a).getP1() + j;
                                res2[n] = afpSet.get(a).getP2() + j;
                                n ++;
                        }
                }

                afpChain.setFocusRes1(res1);
                afpChain.setFocusRes2(res2);
                afpChain.setFocusResn(n);

                if ( n == 0 ){
                        logger.warn("n=0!!! + " + afpn + " " + listStart + " " + afpPositions.length);
                }
                return n;
        }

}