/*
 *                    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.io;

import org.biojava.nbio.alignment.Alignments;
import org.biojava.nbio.alignment.Alignments.PairwiseSequenceAlignerType;
import org.biojava.nbio.alignment.SimpleGapPenalty;
import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
import org.biojava.nbio.alignment.template.GapPenalty;
import org.biojava.nbio.alignment.template.PairwiseSequenceAligner;
import org.biojava.nbio.core.alignment.template.SequencePair;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.DNASequence;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.RNASequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
import org.biojava.nbio.structure.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;

/**
 * Heuristical finding of Entities (called Compounds in legacy PDB format)
 * in a given Structure. Entities are the groups of sequence identical NCS-related polymer chains
 * in the Structure.
 *
 * This is related to {@link SeqRes2AtomAligner} but it is intended for raw PDB/mmCIF files where
 * possibly no SEQRES is given.
 *
 * @author Jose Duarte
 */
public class EntityFinder {

        private static final Logger logger = LoggerFactory.getLogger(EntityFinder.class);
        
        /**
         * Above this ratio of mismatching residue types for same residue numbers we
         * consider the 2 chains to have mismatching residue numbers and warn about it
         */
        public static final double RATIO_GAPS_FOR_MISMATCH = 0.50;

        /**
         * Identity value for 2 chains to be considered part of same entity
         */
        public static final double IDENTITY_THRESHOLD = 0.99999;

        /**
         * Gap coverage value (num gaps over length of sequence) for each chain of the match:
         * 2 chains with more gap coverage than this value will not be considered part of the same entity
         */
        public static final double GAP_COVERAGE_THRESHOLD = 0.3;

        
        
        
        /**
         * Utility method that employs some heuristics to find the {@link EntityInfo}s
         * for the polymeric chains given in constructor. 
         * To be used in case the information is missing in PDB/mmCIF file 
         * @return
         */
        public static List<EntityInfo> findPolyEntities(List<List<Chain>> polyModels) {
                TreeMap<String,EntityInfo> chainIds2entities = findEntitiesFromAlignment(polyModels);

                List<EntityInfo> entities = findUniqueEntities(chainIds2entities);

                return entities;
        }

        /**
         * Utility method to obtain a list of unique entities from the chainIds2entities map
         * @return
         */
        private static List<EntityInfo> findUniqueEntities(TreeMap<String,EntityInfo> chainIds2entities) {

                List<EntityInfo> list = new ArrayList<EntityInfo>();

                for (EntityInfo cluster:chainIds2entities.values()) {
                        boolean present = false;
                        for (EntityInfo cl:list) {
                                if (cl==cluster) {
                                        present = true;
                                        break;
                                }
                        }
                        if (!present) list.add(cluster);
                }
                return list;
        }

        /**
         * Given all chains of all models find entities for the nonpolymers and water chains within them,
         * assigning entity ids, types and descriptions to them. The result is written back to the passed entities List.
         * @param nonPolyModels
         * @param waterModels
         * @param entities
         */
        public static void createPurelyNonPolyEntities(List<List<Chain>> nonPolyModels, List<List<Chain>> waterModels, List<EntityInfo> entities) {

                if (nonPolyModels.isEmpty()) return;
                
                // let's find first the max entity id to assign entity ids to the newly found entities
                int maxMolId = 0;
                if (!entities.isEmpty()) {
                        maxMolId = Collections.max(entities, new Comparator<EntityInfo>() {
                                @Override
                                public int compare(EntityInfo o1, EntityInfo o2) {
                                        return new Integer(o1.getMolId()).compareTo(o2.getMolId());
                                }
                        }).getMolId();
                }
                // we go one over the max
                int molId = maxMolId + 1;
                                
                if (!nonPolyModels.get(0).isEmpty()) {
                        List<EntityInfo> nonPolyEntities = new ArrayList<>();
                        
                        for (List<Chain> model:nonPolyModels) {
                                for (Chain c: model) {
                                        // we assume there's only 1 group per non-poly chain
                                        String molecPdbName = c.getAtomGroup(0).getPDBName();

                                        EntityInfo nonPolyEntity = findNonPolyEntityWithDescription(molecPdbName, nonPolyEntities);
                                        if (nonPolyEntity == null) {
                                                nonPolyEntity = new EntityInfo();
                                                nonPolyEntity.setDescription(molecPdbName);
                                                nonPolyEntity.setType(EntityType.NONPOLYMER);
                                                nonPolyEntity.setMolId(molId++);
                                                nonPolyEntities.add(nonPolyEntity);

                                        }
                                        nonPolyEntity.addChain(c);
                                        c.setEntityInfo(nonPolyEntity);                         
                                }
                        }
                        entities.addAll(nonPolyEntities);
                }
                
                if (!waterModels.get(0).isEmpty()) {
                        EntityInfo waterEntity = new EntityInfo();
                        waterEntity.setType(EntityType.WATER);
                        waterEntity.setDescription("water");
                        waterEntity.setMolId(molId);

                        for (List<Chain> model:waterModels) { 
                                for (Chain waterChain:model) {
                                        waterEntity.addChain(waterChain);
                                        waterChain.setEntityInfo(waterEntity);
                                }
                        }
                        entities.add(waterEntity);
                        
                }
                
                
        }
        
        private static EntityInfo findNonPolyEntityWithDescription(String description, List<EntityInfo> nonPolyEntities) {
                for (EntityInfo e:nonPolyEntities) {
                        if (e.getDescription().equals(description)) return e;
                }
                return null;
        }


        private static boolean areResNumbersAligned(Chain c1, Chain c2) {

                boolean isC1prot = c1.isProtein();
                boolean isC2prot = c2.isProtein();

                // different kind of chain: we won't try to align them
                if (isC1prot != isC2prot ) return false;

                List<Group> c1AtomGroups = null;
                if (isC1prot) {
                        c1AtomGroups = c1.getAtomGroups(GroupType.AMINOACID);
                }
                else {
                        c1AtomGroups = c1.getAtomGroups(GroupType.NUCLEOTIDE);
                }

                int countNonExisting = 0;

                for (Group g1:c1AtomGroups) {
                        try {
                                Group g2 = c2.getGroupByPDB(g1.getResidueNumber());
                                if (!g2.getPDBName().equals(g1.getPDBName())) {
                                        logger.debug("Mismatch of residues between chains {},{} for residue number {}: {} {}",
                                                        c1.getId(),c2.getId(),g1.getResidueNumber(), g1.getPDBName(), g2.getPDBName());
                                        return false;
                                }
                        } catch (StructureException e) {
                                // the group doesn't exist (no density) in the chain, go on
                                countNonExisting++;
                                continue;
                        }
                }

                if ((double)countNonExisting/(double)c1AtomGroups.size() > RATIO_GAPS_FOR_MISMATCH) {
                        logger.debug("More than {} of the residues ({} out of {}) are not present in chain {} when comparing by residue numbers to chain {}.",
                                        RATIO_GAPS_FOR_MISMATCH, countNonExisting, c1AtomGroups.size(), c2.getId(), c1.getId());
                        return false;
                }

                return true;
        }



        private static TreeMap<String,EntityInfo> findEntitiesFromAlignment(List<List<Chain>> polyModels) {



                TreeMap<String, EntityInfo> chainIds2entities = new TreeMap<String,EntityInfo>();

                if (polyModels.isEmpty()) return chainIds2entities;
                
                Set<Integer> polyChainIndices = new TreeSet<Integer>();
                for (int i=0;i<polyModels.get(0).size();i++) {
                        polyChainIndices.add(i);
                }

                
                int molId = 1;

                outer:
                        for (int i:polyChainIndices) {
                                for (int j:polyChainIndices) {

                                        if (j<=i) continue;

                                        Chain c1 = polyModels.get(0).get(i);
                                        Chain c2 = polyModels.get(0).get(j);

                                        Map<Integer,Integer> positionIndex1 = new HashMap<Integer, Integer>();
                                        Map<Integer,Integer> positionIndex2 = new HashMap<Integer, Integer>();
                                        // here we use false, which means that X will be used for unknown compounds
                                        String str1 = SeqRes2AtomAligner.getFullAtomSequence(c1.getAtomGroups(), positionIndex1, false);
                                        String str2 = SeqRes2AtomAligner.getFullAtomSequence(c2.getAtomGroups(), positionIndex2, false);

                                        int seq1Length = 0;
                                        int seq2Length = 0;

                                        SequencePair<?,?> pair = null;
                                        if (isProteinSequence(str1) && isProteinSequence(str2)) {
                                                ProteinSequence s1 = getProteinSequence(str1);
                                                ProteinSequence s2 = getProteinSequence(str2);
                                                seq1Length = s1.getLength();
                                                seq2Length = s2.getLength();

                                                pair = alignProtein(s1,s2);

                                        } else if (isDNASequence(str1) && isDNASequence(str2)) {
                                                DNASequence s1 = getDNASequence(str1);
                                                DNASequence s2 = getDNASequence(str2);
                                                seq1Length = s1.getLength();
                                                seq2Length = s2.getLength();

                                                pair = alignDNA(s1,s2);

                                        } else if (isRNASequence(str1) && isRNASequence(str2)) {
                                                RNASequence s1 = getRNASequence(str1);
                                                RNASequence s2 = getRNASequence(str2);
                                                seq1Length = s1.getLength();
                                                seq2Length = s2.getLength();

                                                pair = alignRNA(s1,s2);

                                        } else {
                                                logger.debug("Chains {},{} are either different kind of polymers or could not be recognized as protein or nucleotide polymers");
                                                continue;
                                        }


                                        int numGaps = getNumGaps(pair);
                                        int numGaps1 = getNumGapsQuery(pair);
                                        int numGaps2 = getNumGapsTarget(pair);

                                        int nonGaps = pair.getLength() - numGaps;

                                        double identity = (double)pair.getNumIdenticals()/(double)nonGaps;
                                        double gapCov1 = (double) numGaps1 / (double) seq1Length;
                                        double gapCov2 = (double) numGaps2 / (double) seq2Length;

                                        logger.debug("Alignment for chain pair {},{}: identity: {}, gap coverage 1: {}, gap coverage 2: {}",
                                                        c1.getId(), c2.getId(), String.format("%4.2f",identity), String.format("%4.2f",gapCov1), String.format("%4.2f",gapCov2));
                                        logger.debug("\n"+pair.toString(100));

                                        if (identity > IDENTITY_THRESHOLD && gapCov1<GAP_COVERAGE_THRESHOLD && gapCov2<GAP_COVERAGE_THRESHOLD) {
                                                if (    !chainIds2entities.containsKey(c1.getId()) &&
                                                                !chainIds2entities.containsKey(c2.getId())) {
                                                        logger.debug("Creating Compound with chains {},{}",c1.getId(),c2.getId());

                                                        EntityInfo ent = new EntityInfo();
                                                        ent.addChain(c1);
                                                        ent.addChain(c2);
                                                        ent.setMolId(molId++);
                                                        ent.setType(EntityType.POLYMER);
                                                        c1.setEntityInfo(ent);
                                                        c2.setEntityInfo(ent);
                                                        chainIds2entities.put(c1.getId(), ent);
                                                        chainIds2entities.put(c2.getId(), ent);


                                                } else {
                                                        EntityInfo ent = chainIds2entities.get(c1.getId());

                                                        if (ent==null) {
                                                                logger.debug("Adding chain {} to entity {}",c1.getId(),c2.getId());
                                                                ent = chainIds2entities.get(c2.getId());
                                                                ent.addChain(c1);
                                                                c1.setEntityInfo(ent);
                                                                chainIds2entities.put(c1.getId(), ent);

                                                        } else {
                                                                logger.debug("Adding chain {} to entity {}",c2.getId(),c1.getId());
                                                                ent.addChain(c2);
                                                                c2.setEntityInfo(ent);
                                                                chainIds2entities.put(c2.getId(), ent);

                                                        }
                                                }
                                                if (!areResNumbersAligned(c1, c2)) {
                                                        logger.warn("Including 100% identical chains {},{} in same Compound, although they have misaligned residue numbers",
                                                                        c1.getId(),c2.getId());
                                                }
                                        }

                                        if (identity>1) {
                                                logger.warn("Identity for chains {},{} above 1. {} identicals out of {} non-gap-aligned residues (identity {})",
                                                                c1.getId(),c2.getId(),pair.getNumIdenticals(),nonGaps,identity);
                                                logger.warn("\n"+pair.toString(100));
                                        }

                                        if (chainIds2entities.size()==polyChainIndices.size()) // we've got all chains in entities
                                                break outer;
                                }
                        }

                // anything not in an Entity will be its own Entity
                for (int i:polyChainIndices) {
                        Chain c = polyModels.get(0).get(i);
                        if (!chainIds2entities.containsKey(c.getId())) {
                                logger.debug("Creating a 1-member Compound for chain {}",c.getId());

                                EntityInfo ent = new EntityInfo();
                                ent.addChain(c);
                                ent.setMolId(molId++);
                                c.setEntityInfo(ent); 

                                chainIds2entities.put(c.getId(),ent);
                        }
                }
                
                // now that we've found the entities for first model, let's do the same for the rest of the models
                
                for (int i=1;i<polyModels.size();i++) {
                        for (Chain chain : polyModels.get(i)) {
                                EntityInfo e = chainIds2entities.get(chain.getId());
                                chain.setEntityInfo(e);
                                e.addChain(chain);
                        }
                }


                return chainIds2entities;
        }

        private static SequencePair<ProteinSequence, AminoAcidCompound> alignProtein(ProteinSequence s1, ProteinSequence s2) {
                SubstitutionMatrix<AminoAcidCompound> matrix = SubstitutionMatrixHelper.getIdentity();

                GapPenalty penalty = new SimpleGapPenalty(8, 1);

                PairwiseSequenceAligner<ProteinSequence, AminoAcidCompound> nw =
                                Alignments.getPairwiseAligner(s1, s2, PairwiseSequenceAlignerType.GLOBAL, penalty, matrix);

                return nw.getPair();
        }

        private static SequencePair<DNASequence, NucleotideCompound> alignDNA(DNASequence s1, DNASequence s2) {
                SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();

                GapPenalty penalty = new SimpleGapPenalty(8, 1);

                PairwiseSequenceAligner<DNASequence, NucleotideCompound> nw =
                                Alignments.getPairwiseAligner(s1, s2, PairwiseSequenceAlignerType.GLOBAL, penalty, matrix);

                return nw.getPair();
        }

        private static SequencePair<RNASequence, NucleotideCompound> alignRNA(RNASequence s1, RNASequence s2) {
                SubstitutionMatrix<NucleotideCompound> matrix = SubstitutionMatrixHelper.getNuc4_4();

                GapPenalty penalty = new SimpleGapPenalty(8, 1);

                PairwiseSequenceAligner<RNASequence, NucleotideCompound> nw =
                                Alignments.getPairwiseAligner(s1, s2, PairwiseSequenceAlignerType.GLOBAL, penalty, matrix);

                return nw.getPair();
        }



        private static int getNumGaps(SequencePair<?, ?> pair) {
                int numGaps = 0;
                for (int alignmentIndex=1;alignmentIndex<=pair.getLength();alignmentIndex++) {
                        if (pair.hasGap(alignmentIndex)) numGaps++;
                }
                return numGaps;
        }

        private static int getNumGapsQuery(SequencePair<?, ?> pair) {
                int numGaps = 0;
                for (int alignmentIndex=1;alignmentIndex<=pair.getLength();alignmentIndex++) {
                        if (pair.getCompoundInQueryAt(alignmentIndex).getShortName().equals("-")) {
                                numGaps++;
                        }
                }
                return numGaps;
        }

        private static int getNumGapsTarget(SequencePair<?, ?> pair) {
                int numGaps = 0;
                for (int alignmentIndex=1;alignmentIndex<=pair.getLength();alignmentIndex++) {
                        if (pair.getCompoundInTargetAt(alignmentIndex).getShortName().equals("-")) {
                                numGaps++;
                        }
                }
                return numGaps;
        }

        private static boolean isProteinSequence(String str) {
                try {
                        new ProteinSequence(str);
                } catch (CompoundNotFoundException e) {

                        return false;
                }
                return true;
        }

        private static boolean isDNASequence(String str) {
                try {
                        new DNASequence(str);
                } catch (CompoundNotFoundException e) {

                        return false;
                }
                return true;
        }

        private static boolean isRNASequence(String str) {
                try {
                        new RNASequence(str);
                } catch (CompoundNotFoundException e) {

                        return false;
                }
                return true;

        }

        /**
         * Returns the ProteinSequence or null if one can't be created
         * @param str
         * @return
         */
        private static ProteinSequence getProteinSequence(String str) {
                try {
                        ProteinSequence s = new ProteinSequence(str);
                        return s;
                } catch (CompoundNotFoundException e) {

                        logger.error("Unexpected error when creating ProteinSequence",e);
                }
                return null;
        }

        /**
         * Returns the DNASequence or null if one can't be created
         * @param str
         * @return
         */
        private static DNASequence getDNASequence(String str) {
                try {
                        DNASequence s = new DNASequence(str);
                        return s;
                } catch (CompoundNotFoundException e) {

                        logger.error("Unexpected error when creating DNASequence ",e);
                }
                return null;
        }

        /**
         * Returns the RNASequence or null if one can't be created
         * @param str
         * @return
         */
        private static RNASequence getRNASequence(String str) {
                try {
                        RNASequence s = new RNASequence(str);
                        return s;
                } catch (CompoundNotFoundException e) {

                        logger.error("Unexpected error when creating RNASequence ",e);
                }
                return null;
        }

}