/*
 *                    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 22.01.2007
 *
 */
package org.biojava.nbio.structure;


import org.biojava.nbio.structure.io.FileParsingParameters;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;

/**
 * An object to contain the info from the PDB header for a Molecule.
 * In mmCIF dictionary, it is called an Entity. In the case of polymers it
 * is defined as each group of sequence identical NCS-related chains
 *
 * Now PDB file format 3.2 aware - contains the new TAX_ID fields for the
 * organism studied and the expression system.
 *
 * @author Jules Jacobsen
 * @author Jose Duarte
 * @author Anthony Bradley
 * @since 1.5
 */
public class EntityInfo implements Serializable {

        private final static Logger logger = LoggerFactory.getLogger(EntityInfo.class);


        // TODO We could drop a lot of the stuff here that is PDB-file related (actually many PDB files don't contain many of these fields) - JD 2016-03-25
        //     The only really essential part of a EntityInfo is the member chains and the entity_id/mol_id
        // See also issue https://github.com/biojava/biojava/issues/219

        private static final long serialVersionUID = 2991897825657586356L;

        /**
         * The list of chains that are described by this EntityInfo
         */
        private List<Chain> chains;

        /**
         * The Molecule identifier, called entity_id in mmCIF dictionary
         */
        private int molId;

        /**
         * A map to cache residue number mapping, between ResidueNumbers and index (1-based) in aligned sequences (SEQRES).
         * Initialised lazily upon call to {@link #getAlignedResIndex(Group, Chain)}
         * Keys are asym_ids of chains, values maps of residue numbers to indices.
         */
        private final Map<String, Map<ResidueNumber,Integer>> chains2pdbResNums2ResSerials;

        private String refChainId;
        private String description = null;
        private String title = null;
        /**
         * The type of entity (polymer, non-polymer, water)
         */
        private EntityType type = null;
        private List<String> synonyms = null;
        private List<String> ecNums = null;
        private String engineered = null;
        private String mutation = null;
        private String biologicalUnit = null;
        private String details = null;
        private String numRes = null;
        private String resNames = null;
        private String headerVars = null;
        private String synthetic = null;
        private String fragment = null;
        private String organismScientific = null;
        private String organismTaxId = null;
        private String organismCommon = null;
        private String strain = null;
        private String variant = null;
        private String cellLine = null;
        private String atcc = null;
        private String organ = null;
        private String tissue = null;
        private String cell = null;
        private String organelle = null;
        private String secretion = null;
        private String gene = null;
        private String cellularLocation = null;
        private String expressionSystem = null;
        private String expressionSystemTaxId = null;
        private String expressionSystemStrain = null;
        private String expressionSystemVariant = null;
        private String expressionSystemCellLine = null;
        private String expressionSystemAtccNumber = null;
        private String expressionSystemOrgan = null;
        private String expressionSystemTissue = null;
        private String expressionSystemCell = null;
        private String expressionSystemOrganelle = null;
        private String expressionSystemCellularLocation = null;
        private String expressionSystemVectorType = null;
        private String expressionSystemVector = null;
        private String expressionSystemPlasmid = null;
        private String expressionSystemGene = null;
        private String expressionSystemOtherDetails = null;

        private Long id;

        public EntityInfo () {
                chains = new ArrayList<>();
                chains2pdbResNums2ResSerials = new HashMap<>();
                molId = -1;
        }

        /**
         * Constructs a new EntityInfo copying all data from the given one
         * but not setting the Chains
         * @param c
         */
        public EntityInfo (EntityInfo c) {

            this.id = c.id;

                this.chains = new ArrayList<>();

                this.chains2pdbResNums2ResSerials = new HashMap<>();

                this.molId = c.molId;

                this.type = c.type;

                this.refChainId = c.refChainId;

                this.description = c.description;
                this.title = c.title;

                if (c.synonyms!=null) {
                        this.synonyms = new ArrayList<String>();
                        synonyms.addAll(c.synonyms);
                }
                if (c.ecNums!=null) {
                        this.ecNums = new ArrayList<String>();
                        ecNums.addAll(c.ecNums);
                }

                this.engineered = c.engineered;
                this.mutation = c.mutation;
                this.biologicalUnit = c.biologicalUnit;
                this.details = c.details;

                this.numRes = c.numRes;
                this.resNames = c.resNames;

                this.headerVars = c.headerVars;

                this.synthetic = c.synthetic;
                this.fragment = c.fragment;
                this.organismScientific = c.organismScientific;
                this.organismTaxId = c.organismTaxId;
                this.organismCommon = c.organismCommon;
                this.strain = c.strain;
                this.variant = c.variant;
                this.cellLine = c.cellLine;
                this.atcc = c.atcc;
                this.organ = c.organ;
                this.tissue = c.tissue;
                this.cell = c.cell;
                this.organelle = c.organelle;
                this.secretion = c.secretion;
                this.gene = c.gene;
                this.cellularLocation = c.cellularLocation;
                this.expressionSystem = c.expressionSystem;
                this.expressionSystemTaxId = c.expressionSystemTaxId;
                this.expressionSystemStrain = c.expressionSystemStrain;
                this.expressionSystemVariant = c.expressionSystemVariant;
                this.expressionSystemCellLine = c.expressionSystemCellLine;
                this.expressionSystemAtccNumber = c.expressionSystemAtccNumber;
                this.expressionSystemOrgan = c.expressionSystemOrgan;
                this.expressionSystemTissue = c.expressionSystemTissue;
                this.expressionSystemCell = c.expressionSystemCell;
                this.expressionSystemOrganelle = c.expressionSystemOrganelle;
                this.expressionSystemCellularLocation = c.expressionSystemCellularLocation;
                this.expressionSystemVectorType = c.expressionSystemVectorType;
                this.expressionSystemVector = c.expressionSystemVector;
                this.expressionSystemPlasmid = c.expressionSystemPlasmid;
                this.expressionSystemGene = c.expressionSystemGene;
                this.expressionSystemOtherDetails = c.expressionSystemOtherDetails;


        }

        @Override
        public String toString(){
                StringBuilder buf = new StringBuilder();
                buf.append("EntityInfo: ").append(molId).append(" ");
                buf.append(description==null?"(no name)":"("+description+")");
                buf.append(" asymIds: ");
                if (chains!=null) {
                        for (int i=0;i<chains.size();i++) {
                                buf.append(chains.get(i).getId());
                                if (i!=chains.size()-1) buf.append(",");
                        }
                } else {
                        buf.append("no chains");
                }
                return buf.toString();
        }

        /**
         * Get the representative Chain for this EntityInfo.
         * We choose the Chain with the first asym_id chain identifier after
         * lexicographical sorting (case insensitive),
         * e.g. chain A if EntityInfo is composed of chains A,B,C,D,E
         * @return
         */
        public Chain getRepresentative() {

                List<String> chainIds = new ArrayList<>();
                for (Chain chain:chains) {
                        chainIds.add(chain.getId());
                }

                Collections.sort(chainIds, String.CASE_INSENSITIVE_ORDER);

                for (Chain chain:chains) {
                        if (chain.getId().equals(chainIds.get(0))) {
                                return chain;
                        }
                }

                logger.error("Could not find a representative chain for EntityInfo '{}'", this.toString());

                return null;
        }

        /** get the ID used by Hibernate
         *
         * @return the ID used by Hibernate
         */
        public Long getId() {
                return id;
        }

        /** set the ID used by Hibernate
         *
         * @param id
         */
        public void setId(Long id) {
                this.id = id;
        }

        /**
         * Return the list of member chain ids (asym ids) that are described by this EntityInfo,
         * only unique chain IDs are contained in the list.
         * Note that in the case of multimodel structures this will return just the unique
         * chain identifiers whilst {@link #getChains()} will return a corresponding chain
         * per model.
         * @return the list of unique ChainIDs that are described by this EnityInfo
         * @see #setChains(List)
         * @see #getChains()
         */
        public List<String> getChainIds() {

                Set<String> uniqChainIds = new TreeSet<>();
                for (int i=0;i<getChains().size();i++) {
                        uniqChainIds.add(getChains().get(i).getId());
                }

                return new ArrayList<>(uniqChainIds);
        }

        /**
         * Given a Group g of Chain c (member of this EntityInfo) return the corresponding position in the
         * alignment of all member sequences (1-based numbering), i.e. the index (1-based) in the SEQRES sequence.
         * This allows for comparisons of residues belonging to different chains of the same EntityInfo (entity).
         * <p>
         * Note this method should only be used for entities of type {@link EntityType#POLYMER}
         * <p>
         * If {@link FileParsingParameters#setAlignSeqRes(boolean)} is not used or SEQRES not present, a mapping
         * will not be available and this method will return {@link ResidueNumber#getSeqNum()} for all residues, which
         * in some cases will be correctly aligned indices (when no insertion codes are
         * used and when all chains within the entity are numbered in the same way), but
         * in general they will be neither unique (because of insertion codes) nor aligned.
         * </p>
         * @param g the group
         * @param c the chain
         * @return the aligned residue index (1 to n), if no SEQRES groups are available at all then {@link ResidueNumber#getSeqNum()}
         * is returned as a fall-back, if the group is not found in the SEQRES groups then -1 is returned
         * for the given group and chain
         * @throws IllegalArgumentException if the given Chain is not a member of this EntityInfo
         * @see Chain#getSeqResGroup(int)
         */
        public int getAlignedResIndex(Group g, Chain c) {

                boolean contained = false;
                for (Chain member:getChains()) {
                        if (c.getId().equals(member.getId())) {
                                contained = true;
                                break;
                        }
                }
                if (!contained)
                        throw new IllegalArgumentException("Given chain with asym_id "+c.getId()+" is not a member of this entity: "+getChainIds().toString());

                if (!chains2pdbResNums2ResSerials.containsKey(c.getId())) {
                        // we do lazy initialisation of the map
                        initResSerialsMap(c);
                }
                // if no seqres groups are available at all the map will be null
                Map<ResidueNumber,Integer> map = chains2pdbResNums2ResSerials.get(c.getId());
                int serial;
                if (map!=null) {

                        ResidueNumber resNum = g.getResidueNumber();
                        // the resNum will be null for groups that are SEQRES only and not in ATOM,
                        // still it can happen that a group is in ATOM in one chain but not in other of the same entity.
                        // This is what we try to find out here (analogously to what we do in initResSerialsMap() ):
                        if (resNum==null && c.getSeqResGroups()!=null && !c.getSeqResGroups().isEmpty()) {

                                int index = c.getSeqResGroups().indexOf(g);

                                resNum = findResNumInOtherChains(index, c);

                        }

                        if (resNum == null) {
                                // still null, we really can't map
                                serial = -1;
                        }
                        else {

                                Integer alignedSerial = map.get(resNum);

                                if (alignedSerial==null) {
                                        // the map doesn't contain this group, something's wrong: return -1
                                        serial = -1;
                                } else {
                                        serial = alignedSerial;
                                }
                        }

                } else {
                        // no seqres groups available we resort to using the pdb residue numbers are given
                        serial = g.getResidueNumber().getSeqNum();
                }
                return serial;
        }

        private void initResSerialsMap(Chain c) {
                if (c.getSeqResGroups()==null || c.getSeqResGroups().isEmpty()) {
                        logger.warn("No SEQRES groups found in chain with asym_id {}, will use residue numbers as given (no insertion codes, not necessarily aligned). "
                                        + "Make sure your structure has SEQRES records and that you use FileParsingParameters.setAlignSeqRes(true)",
                                        c.getId());
                        // we add a explicit null to the map so that we flag it as unavailable for this chain
                        chains2pdbResNums2ResSerials.put(c.getId(), null);
                        return;
                }

                Map<ResidueNumber,Integer> resNums2ResSerials = new HashMap<ResidueNumber, Integer>();
                chains2pdbResNums2ResSerials.put(c.getId(), resNums2ResSerials);

                for (int i=0;i<c.getSeqResGroups().size();i++) {

                        // The seqres group will have a null residue number whenever its corresponding atom group doesn't exist
                        // because it is missing in the electron density.
                        // However, it can be observed in the density in other chains of the same entity,
                        // to be complete we go and look for the residue number in other chains, so that we have a
                        // seqres to atom mapping as complete as possible (with all known atom groups of any chain of this entity)

                        ResidueNumber resNum = c.getSeqResGroup(i).getResidueNumber();

                        if (resNum==null) {
                                resNum = findResNumInOtherChains(i,c);
                        }

                        // NOTE that resNum will still be null here for cases where the residue
                        // is missing in atom groups (not observed in density) in all chains
                        // Thus the mapping will not be possible for residues that are only in SEQRES groups
                        resNums2ResSerials.put(resNum, i+1);
                }
        }

        private ResidueNumber findResNumInOtherChains(int i, Chain chain) {

                // note that getChains contains all chains from all models, we'll just use first model found and skip the others
                for (Chain c: getFirstModelChains()) {

                        if (c == chain) continue;

                        Group seqResGroup = c.getSeqResGroup(i);

                        if (seqResGroup==null) {
                                logger.warn("The SEQRES group is null for index {} in chain with asym_id {}, whilst it wasn't null in chain with asym_id {}",
                                                 i, c.getId(), chain.getId());
                                continue;
                        }

                        if (seqResGroup.getResidueNumber()!=null) return seqResGroup.getResidueNumber();

                }

                return null;
        }

        /**
         * Return the ref chain id value.
         * @return the RefChainID
         * @see #setRefChainId(String)
         */
        public String getRefChainId() {
                return refChainId;
        }

        /**
         * Return the ref chain id value.
         * @param refChainId the RefChainID
         * @see #getRefChainId()
         */
        public void setRefChainId(String refChainId) {
                this.refChainId = refChainId;
        }

        /**
         * Return the molecule identifier, called entity_id in mmCIF dictionary.
         * @return the molecule id
         * @see #setMolId(int)
         */
        public int getMolId() {
                return molId;
        }

        /**
         * Set the molecule identifier, called entity_id in mmCIF dictionary.
         * @param molId the molecule id
         * @see #getMolId()
         */
        public void setMolId(int molId) {
                this.molId = molId;
        }

        public String getDescription() {
                return description;
        }

        public void setDescription(String molName) {
                this.description = molName;
        }

        public String getTitle() {
                return title;
        }

        public void setTitle(String title) {
                this.title = title;
        }

        public List<String> getSynonyms() {
                return synonyms;
        }

        public void setSynonyms(List<String> synonyms) {
                this.synonyms = synonyms;
        }

        public List<String> getEcNums() {
                return ecNums;
        }

        public void setEcNums(List<String> ecNums) {
                this.ecNums = ecNums;
        }

        public String getEngineered() {
                return engineered;
        }

        public void setEngineered(String engineered) {
                this.engineered = engineered;
        }

        public String getMutation() {
                return mutation;
        }

        public void setMutation(String mutation) {
                this.mutation = mutation;
        }

        public String getBiologicalUnit() {
                return biologicalUnit;
        }

        public void setBiologicalUnit(String biologicalUnit) {
                this.biologicalUnit = biologicalUnit;
        }

        public String getDetails() {
                return details;
        }

        public void setDetails(String details) {
                this.details = details;
        }

        public String getNumRes() {
                return numRes;
        }

        public void setNumRes(String numRes) {
                this.numRes = numRes;
        }

        public String getResNames() {
                return resNames;
        }

        public void setResNames(String resNames) {
                this.resNames = resNames;
        }

        public String getHeaderVars() {
                return headerVars;
        }

        public void setHeaderVars(String headerVars) {
                this.headerVars = headerVars;
        }

        public String getSynthetic() {
                return synthetic;
        }

        public void setSynthetic(String synthetic) {
                this.synthetic = synthetic;
        }

        public String getFragment() {
                return fragment;
        }

        public void setFragment(String fragment) {
                this.fragment = fragment;
        }

        public String getOrganismScientific() {
                return organismScientific;
        }

        public void setOrganismScientific(String organismScientific) {
                this.organismScientific = organismScientific;
        }

        public String getOrganismTaxId() {
                return organismTaxId;
        }

        public void setOrganismTaxId(String organismTaxId) {
                this.organismTaxId = organismTaxId;
        }

        public String getOrganismCommon() {
                return organismCommon;
        }

        public void setOrganismCommon(String organismCommon) {
                this.organismCommon = organismCommon;
        }

        public String getStrain() {
                return strain;
        }

        public void setStrain(String strain) {
                this.strain = strain;
        }

        public String getVariant() {
                return variant;
        }

        public void setVariant(String variant) {
                this.variant = variant;
        }

        public String getCellLine() {
                return cellLine;
        }

        public void setCellLine(String cellLine) {
                this.cellLine = cellLine;
        }

        public String getAtcc() {
                return atcc;
        }

        public void setAtcc(String atcc) {
                this.atcc = atcc;
        }

        public String getOrgan() {
                return organ;
        }

        public void setOrgan(String organ) {
                this.organ = organ;
        }

        public String getTissue() {
                return tissue;
        }

        public void setTissue(String tissue) {
                this.tissue = tissue;
        }

        public String getCell() {
                return cell;
        }

        public void setCell(String cell) {
                this.cell = cell;
        }

        public String getOrganelle() {
                return organelle;
        }

        public void setOrganelle(String organelle) {
                this.organelle = organelle;
        }

        public String getSecretion() {
                return secretion;
        }

        public void setSecretion(String secretion) {
                this.secretion = secretion;
        }

        public String getGene() {
                return gene;
        }

        public void setGene(String gene) {
                this.gene = gene;
        }

        public String getCellularLocation() {
                return cellularLocation;
        }

        public void setCellularLocation(String cellularLocation) {
                this.cellularLocation = cellularLocation;
        }

        public String getExpressionSystem() {
                return expressionSystem;
        }

        public String getExpressionSystemTaxId() {
                return expressionSystemTaxId;
        }

        public void setExpressionSystemTaxId(String expressionSystemTaxId) {
                this.expressionSystemTaxId = expressionSystemTaxId;
        }

        public void setExpressionSystem(String expressionSystem) {
                this.expressionSystem = expressionSystem;
        }

        public String getExpressionSystemStrain() {
                return expressionSystemStrain;
        }

        public void setExpressionSystemStrain(String expressionSystemStrain) {
                this.expressionSystemStrain = expressionSystemStrain;
        }

        public String getExpressionSystemVariant() {
                return expressionSystemVariant;
        }

        public void setExpressionSystemVariant(String expressionSystemVariant) {
                this.expressionSystemVariant = expressionSystemVariant;
        }

        public String getExpressionSystemCellLine() {
                return expressionSystemCellLine;
        }

        public void setExpressionSystemCellLine(String expressionSystemCellLine) {
                this.expressionSystemCellLine = expressionSystemCellLine;
        }

        public String getExpressionSystemAtccNumber() {
                return expressionSystemAtccNumber;
        }

        public void setExpressionSystemAtccNumber(String expressionSystemAtccNumber) {
                this.expressionSystemAtccNumber = expressionSystemAtccNumber;
        }

        public String getExpressionSystemOrgan() {
                return expressionSystemOrgan;
        }

        public void setExpressionSystemOrgan(String expressionSystemOrgan) {
                this.expressionSystemOrgan = expressionSystemOrgan;
        }

        public String getExpressionSystemTissue() {
                return expressionSystemTissue;
        }

        public void setExpressionSystemTissue(String expressionSystemTissue) {
                this.expressionSystemTissue = expressionSystemTissue;
        }

        public String getExpressionSystemCell() {
                return expressionSystemCell;
        }

        public void setExpressionSystemCell(String expressionSystemCell) {
                this.expressionSystemCell = expressionSystemCell;
        }

        public String getExpressionSystemOrganelle() {
                return expressionSystemOrganelle;
        }

        public void setExpressionSystemOrganelle(String expressionSystemOrganelle) {
                this.expressionSystemOrganelle = expressionSystemOrganelle;
        }

        public String getExpressionSystemCellularLocation() {
                return expressionSystemCellularLocation;
        }

        public void setExpressionSystemCellularLocation(String expressionSystemCellularLocation) {
                this.expressionSystemCellularLocation = expressionSystemCellularLocation;
        }

        public String getExpressionSystemVectorType() {
                return expressionSystemVectorType;
        }

        public void setExpressionSystemVectorType(String expressionSystemVectorType) {
                this.expressionSystemVectorType = expressionSystemVectorType;
        }

        public String getExpressionSystemVector() {
                return expressionSystemVector;
        }

        public void setExpressionSystemVector(String expressionSystemVector) {
                this.expressionSystemVector = expressionSystemVector;
        }

        public String getExpressionSystemPlasmid() {
                return expressionSystemPlasmid;
        }

        public void setExpressionSystemPlasmid(String expressionSystemPlasmid) {
                this.expressionSystemPlasmid = expressionSystemPlasmid;
        }

        public String getExpressionSystemGene() {
                return expressionSystemGene;
        }

        public void setExpressionSystemGene(String expressionSystemGene) {
                this.expressionSystemGene = expressionSystemGene;
        }

        public String getExpressionSystemOtherDetails() {
                return expressionSystemOtherDetails;
        }

        public void setExpressionSystemOtherDetails(String expressionSystemOtherDetails) {
                this.expressionSystemOtherDetails = expressionSystemOtherDetails;
        }

        /**
         * Get the list of chains that are part of this EntityInfo. Note that for multi-model
         * structures chains from all models are returned.
         *
         * @return a List of Chain objects
         */
        public List<Chain> getChains(){
                return this.chains;
        }

        private List<Chain> getFirstModelChains() {

                Map<String, Chain> firstModelChains = new LinkedHashMap<>();
                Set<String> lookupChainIds = new HashSet<>(getChainIds());

                for (Chain chain : chains) {
                        if (lookupChainIds.contains(chain.getId())) {
                                if (!firstModelChains.containsKey(chain.getId())) {
                                        firstModelChains.put(chain.getId(), chain);
                                }
                        }
                }

                return new ArrayList<>(firstModelChains.values());
        }

         /**
          * Add new Chain to this EntityInfo
          * @param chain
          */
        public void addChain(Chain chain){
                this.chains.add(chain);
        }

        /**
         * Set the chains for this EntityInfo
         * @param chains
         */
        public void setChains(List<Chain> chains){
                this.chains = chains;
        }

        /**
         * Get the type of entity this EntityInfo describes.
         * Options are polymer, non-polymer or water.
         * @return a string describing the type of entity. (polymer, non-polymer or water).
         */
        public EntityType getType() {
                return this.type;
        }

        /**
         * Set the type of entity this EntityInfo describes.
         * Options are polymer, non-polymer or water.
         * @param type a string describing the type of entity. (polymer, non-polymer or water).
         */
        public void setType(EntityType type) {
                this.type = type;
        }
}