/*
 *                    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 Jun 5, 2010
 * Author: Jianjiong Gao
 *
 */

package org.biojava.nbio.protmod.structure;

import org.biojava.nbio.protmod.ModificationCategory;
import org.biojava.nbio.protmod.ProteinModification;
import org.biojava.nbio.protmod.ProteinModificationImpl;
import org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter;

import java.io.Serializable;
import java.util.*;


/**
 *
 * @author Jianjiong Gao
 * @since 3.0
 */
public class ModifiedCompoundImpl
implements ModifiedCompound, Serializable, Comparable<ModifiedCompound> {

        /**
         *
         */
        private static final long serialVersionUID = 1656563037849815427L;

        ProteinModification originalModification;

        ProteinModification modification;

        Set<StructureGroup> groups;

        Map<Set<StructureGroup>, Set<StructureAtomLinkage>> atomLinkages;

        public static final String newline = System.getProperty("line.separator");

        public ModifiedCompoundImpl(){

        }

        /**
         * Create a ModifiedCompoundImpl that has only one involved component.
         * Use this constructor for a modified residue.
         * @param modification {@link ProteinModification}.
         * @param modifiedResidue modified group.
         * @return a {@link ModifiedCompound}.
         * @throws IllegalArgumentException if either argument is null.
         */
        public ModifiedCompoundImpl (
                        ProteinModification modification,
                        StructureGroup modifiedResidue) {
                if (modification==null || modifiedResidue==null) {
                        throw new IllegalArgumentException("Null argument(s)");
                }

                groups = new HashSet<StructureGroup>(1);
                groups.add(modifiedResidue);

                // is it possible that components be added by addLinkage later?
                atomLinkages = null;

                setModification(modification);
        }

        /**
         *
         * @param modification ProteinModification.
         * @param linkages a collection of atom linkages.
         * @see ProteinModification
         * @see StructureAtomLinkage
         */
        public ModifiedCompoundImpl( ProteinModification modification,
                        Collection<StructureAtomLinkage> linkages) {
                if (modification==null) {
                        throw new IllegalArgumentException("modification cannot be null");
                }

                if (linkages==null||linkages.isEmpty()) {
                        throw new IllegalArgumentException("at least one linkage.");
                }

                this.groups = new HashSet<StructureGroup>();

                addAtomLinkages(linkages);

                setModification(modification);

        }

        @Override
        public void setModification(ProteinModification protmod){
                originalModification = protmod;

                resetModification();
        }

        @Override
        public ProteinModification getModification() {
                return modification;
        }

        private void resetModification() {
                if (originalModification == null)
                        modification = originalModification;
                else if (originalModification.getCategory()!=ModificationCategory.UNDEFINED)
                        modification = originalModification;
                else {
                        int nRes = 0;
                        Set<String> ligands = new HashSet<String>();
                        for (StructureGroup group : groups) {
                                if (group.isAminoAcid()) {
                                        nRes ++;
                                } else {
                                        ligands.add(group.getPDBName().trim());
                                }
                        }

                        ModificationCategory cat;
                        switch (nRes) {
                        case 0:
                                modification = originalModification; return;
                        case 1:
                                cat = ModificationCategory.ATTACHMENT; break;
                        case 2:
                                cat = ModificationCategory.CROSS_LINK_2; break;
                        case 3:
                                cat = ModificationCategory.CROSS_LINK_3; break;
                        case 4:
                                cat = ModificationCategory.CROSS_LINK_4; break;
                        case 5:
                                cat = ModificationCategory.CROSS_LINK_5; break;
                        case 6:
                                cat = ModificationCategory.CROSS_LINK_6; break;
                        case 7:
                                cat = ModificationCategory.CROSS_LINK_7; break;
                        default:
                                cat = ModificationCategory.CROSS_LINK_8_OR_LARGE; break;
                        }

                        modification = new ProteinModificationImpl.Builder(originalModification)
                                        .setCategory(cat).addKeywords(ligands).build();
                }
        }

        /**
         *
         * @return the original modification ID.
         * @deprecated use getModification().getId()
         */
        @Deprecated
        public String getOriginalModificationId() {
                if (originalModification==null)
                        return null;

                return originalModification.getId();
        }

        @Override
        public Set<StructureGroup> getGroups() {
                if ( groups == null)
                        return null;

                return Collections.unmodifiableSet(groups);
        }

        @Override
        public Set<StructureGroup> getGroups(boolean isAminoAcid) {
                Set<StructureGroup> result = new HashSet<StructureGroup>();
                for (StructureGroup group : groups) {
                        if (group.isAminoAcid() == isAminoAcid) {
                                result.add(group);
                        }
                }
                return result;
        }

        @Override
        public void setGroups(Set<StructureGroup> groups){
                this.groups = groups;
                resetModification();
        }

        @Override
        public Set<StructureAtomLinkage> getAtomLinkages() {
                if (atomLinkages==null) {
                        return Collections.emptySet();
                } else {
                        Set<StructureAtomLinkage> result = new HashSet<StructureAtomLinkage>();
                        for (Set<StructureAtomLinkage> linkages : atomLinkages.values()) {
                                result.addAll(linkages);
                        }

                        return result;
                }
        }


        @Override
        public void setAtomLinkages(Set<StructureAtomLinkage> linkages) {
                for (StructureAtomLinkage sali : linkages){
                        addAtomLinkage(sali);
                }
                resetModification();
        }

        @Override
        public boolean addAtomLinkage(StructureAtomLinkage linkage) {
                if (linkage==null) {
                        throw new IllegalArgumentException("Null linkage");
                }

                Set<StructureGroup> gs = new HashSet<StructureGroup>(2);
                gs.add(linkage.getAtom1().getGroup());
                gs.add(linkage.getAtom2().getGroup());

                if (atomLinkages==null) {
                        atomLinkages = new HashMap<Set<StructureGroup>, Set<StructureAtomLinkage>>();
                }

                Set<StructureAtomLinkage> linkages = atomLinkages.get(gs);
                if (linkages == null) {
                        linkages = new HashSet<StructureAtomLinkage>();
                        atomLinkages.put(gs, linkages);
                        groups.addAll(gs); // it's possible of new groups
                };

                return linkages.add(linkage);
        }

        @Override
        public void addAtomLinkages(Collection<StructureAtomLinkage> linkages) {
                if (linkages==null) {
                        throw new IllegalArgumentException("Null linkages");
                }

                for (StructureAtomLinkage link : linkages) {
                        addAtomLinkage(link);
                }

                resetModification();
        }

        @Override
        public boolean crossChains() {
                if (groups==null || groups.isEmpty())
                        return false;

                Iterator<StructureGroup> it = groups.iterator();
                String chain = it.next().getChainId();
                while (it.hasNext()) {
                        if (!it.next().getChainId().equals(chain))
                                return true;
                }

                return false;
        }


        @Override
        public String toString(){
                StringBuilder sb = new StringBuilder();
                if ( originalModification == null)
                        return "ModifiedCompoundImpl -- not initialized";

                //sb.append("Modification_");
                sb.append(originalModification.getId());
                ModificationCategory cat ;
                if (originalModification.getCategory()==ModificationCategory.UNDEFINED) {
                        cat = getModification().getCategory();
                } else
                        cat = originalModification.getCategory();
                sb.append("_");
                sb.append(cat.toString());
                return sb.toString();
        }


        @Override
        public String getDescription() {

                StringBuilder sb = new StringBuilder();
                //sb.append("Category: ");

                if ( getModification()  == null) {
                        sb.append(" !!! not initialized !!!");
                        return sb.toString();
                }

                sb.append(originalModification.toString());
//              sb.append(getModification().getCategory());
//              if (!modification.getKeywords().isEmpty()) {
//                      sb.append("; ");
//                      sb.append(modification.getKeywords());
//              }
//              sb.append("; Modification ID: ");
//              sb.append(modification.getId());
//
//              if (modification.getResidId()!=null) {
//                      sb.append("; RESID: ");
//                      sb.append(modification.getResidId());
//                      sb.append(" [");
//                      sb.append(modification.getResidName());
//                      sb.append(']');
//              }
//
//              sb.append(" | ");
//
//              if (atomLinkages==null) {
//                      for (StructureGroup group : groups) {
//                              sb.append(group);
//                              sb.append(" | ");
//                      }
//              } else {
//                      for (Set<StructureAtomLinkage> linkages : atomLinkages.values()) {
//                              for (StructureAtomLinkage linkage : linkages) {
//                                      sb.append(linkage);
//                                      sb.append(" | ");
//                              }
//                      }
//              }

                return sb.toString();
        }

        @Override
        public void setDescription(String desc){
                // do nothing....

        }

        @Override
        public int compareTo(ModifiedCompound compound){
                try {
                        // quite complex objects so the easiest is to just wrap it as XML
                        // and compare the two strings...
                        String xml  = ModifiedCompoundXMLConverter.toXML(this);
                        String xml2 = ModifiedCompoundXMLConverter.toXML(compound);
                        return xml.compareTo(xml2);
                } catch (Exception e){

                }
                return this.toString().compareTo(compound.toString());
        }

        /**
         * @return true if same modification and same components; false, otherwise.
         */
        @Override
        public boolean equals(Object obj) {
                if (!(obj instanceof ModifiedCompound)) {
                        return false;
                }

                ModifiedCompound mci = (ModifiedCompound)obj;
                if (mci.getModification() != originalModification) {
                        return false;
                }

                if (!groups.equals(mci.getGroups())) {
                        return false;
                }

                return true;

                // Do not need to consider linkage, since they can be determined by
                // modification and groups.
        }

        @Override
        public int hashCode() {
                int result = 17;
                result = result * 32 + originalModification.hashCode();

                int sum = 0;
                for (StructureGroup group : groups) {
                        sum += group.hashCode();
                }

                result = result * 32 + sum;

                return result;
        }
}