/*
 *                    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 May 27, 2010
 * Author: Jianjiong Gao
 *
 */

package org.biojava.nbio.protmod;

import java.util.Collection;
import java.util.LinkedHashSet;
import java.util.Set;

/**
 * This class contains information about a specific protein
 * modification.
 *
 * @author Jianjiong Gao
 * @since 3.0
 */
public class ProteinModificationImpl
implements ProteinModification , Comparable<ProteinModification> {

        private final String id;
        private final ModificationCondition condition;
        private final ModificationCategory category;
        private final ModificationOccurrenceType occurrenceType;

        private final String pdbccId;
        private final String pdbccName;
        private final String residId;
        private final String residName;
        private final String psimodId;
        private final String psimodName;
        private final String sysName;
        private final String formula;

        private final Set<String> keywords;

        @Override
        public String getId() {
                return id;
        }

        @Override
        public String getPdbccId() {
                return pdbccId;
        }

        @Override
        public String getPdbccName() {
                return pdbccName;
        }

        @Override
        public String getResidId() {
                return residId;
        }

        @Override
        public String getResidName() {
                return residName;
        }

        @Override
        public String getPsimodId() {
                return psimodId;
        }

        @Override
        public String getPsimodName() {
                return psimodName;
        }

        @Override
        public String getSystematicName() {
                return sysName;
        }

        @Override
        public String getDescription() {
                return toString();
                //return description;
        }

        @Override
        public Set<String> getKeywords() {
                return keywords;
        }

        @Override
        public ModificationCondition getCondition() {
                return condition;
        }

        @Override
        public String getFormula() {
                return formula;
        }

        @Override
        public ModificationCategory getCategory() {
                return category;
        }

        @Override
        public ModificationOccurrenceType getOccurrenceType() {
                return occurrenceType;
        }

        @Override
        public String toString() {
                return "ProteinModificationImpl [id=" + id + ", condition=" + condition
                                + ", category=" + category + ", occurrenceType="
                                + occurrenceType + ", pdbccId=" + pdbccId + ", pdbccName="
                                + pdbccName + ", residId=" + residId + ", residName="
                                + residName + ", psimodId=" + psimodId + ", psimodName="
                                + psimodName + ", sysName=" + sysName + ", formula=" + formula
                                + ", keywords=" + keywords + "]";
        }

        /*
        private String printModification(ProteinModificationImpl mod) {
                StringBuilder sb = new StringBuilder();

                String name = getBestPossibleName(mod);
                boolean hasName = true;
                if (  name.equals(""))
                        hasName = false;
                sb.append(name);

                Set<String> keywords = mod.getKeywords();
                if (keywords!=null && !keywords.isEmpty()) {
                        if ( hasName)
                                sb.append(" (");
                        for (String keyword : keywords) {

                                sb.append(keyword);
                                sb.append(", ");
                        }
                        sb.delete(sb.length()-2,sb.length());
                }
                if ( hasName)
                        sb.append(")");
                return sb.toString();
        }


        private String getBestPossibleName(ProteinModificationImpl mod) {

                //System.out.println(mod.getResidName() + " : " + mod.getPsimodName() + " : " + mod.getPdbccName() + " : " + mod.getSystematicName());

                // first: get resid
                String resid = mod.getResidId();
                if (resid != null) {
                        String residname = mod.getResidName();
                        if (residname != null) {
                                return residname;
                        }
                }

                // 2nd: PSI-MOD

                String name = mod.getPsimodName();
                if ( name != null) {
                        //System.out.println("PSI_MOD name:" + name);
                        return name;
                }

                // 3rd PDB-CC

                String pdbcc = mod.getPdbccName();
                if ( pdbcc != null ) {
                        //System.out.println("PDBCC name: " + pdbcc);
                        return pdbcc;
                }


                // no public name know, use the systematic name

                String systematic = mod.getSystematicName();
                if ( systematic != null) {
                        //System.out.println("SYSTEMATIC NAME: " + mod.getSystematicName());
                        return systematic;
                }


                return "";

        }
        */

        @Override
        public int hashCode() {
                int ret = id.hashCode();
                ret = ret * 31 + category.hashCode();
                return ret;
        }

        @Override
        public boolean equals(Object obj) {
                if (!(obj instanceof ProteinModification))
                        return false;

                ProteinModification mod = (ProteinModification)obj;
                if (!id.equals(mod.getId()))
                        return false;

                if (category != mod.getCategory())
                        return false;

                return true;
        }




        /**
         * Uses Builder pattern to build a ProteinModification.
         */
        public static class Builder {
                private final String id;

                private ModificationCondition condition;
                private ModificationCategory category;
                private ModificationOccurrenceType occurrenceType;

                private String pdbccId = null;
                private String pdbccName = null;
                private String residId = null;
                private String residName = null;
                private String psimodId = null;
                private String psimodName = null;
                private String sysName = null;
                private String formula = null;

                private Set<String> keywords = new LinkedHashSet<String>();

                /**
                 *
                 * @param id
                 * @param cat
                 * @param occType
                 * @param condition
                 */
                public Builder(final String id, final ModificationCategory cat,
                                final ModificationOccurrenceType occType,
                                final ModificationCondition condition) {
                        if ( id == null) throw new IllegalArgumentException("id == null!");
                        if ( cat == null) throw new IllegalArgumentException("cat == null!");
                        if ( occType == null) throw new IllegalArgumentException("occType == null!");
                        if ( condition == null) throw new IllegalArgumentException("condition == null!");

                        this.id = id;
                        this.category = cat;
                        this.occurrenceType = occType;
                        this.condition = condition;
                }

                /**
                 * Create a Builder from an existing ProteinModification.
                 * @param copyFrom the ProteinModification to be copied from.
                 */
                public Builder(final ProteinModification copyFrom) {
                        this(copyFrom.getId(), copyFrom.getCategory(), copyFrom.getOccurrenceType(), copyFrom.getCondition());
                        this.pdbccId = copyFrom.getPdbccId();
                        this.pdbccName = copyFrom.getPdbccName();
                        this.residId = copyFrom.getResidId();
                        this.residName = copyFrom.getResidName();
                        this.psimodId = copyFrom.getPsimodId();
                        this.psimodName = copyFrom.getPsimodName();
                        this.sysName = copyFrom.getSystematicName();
                        this.formula = copyFrom.getFormula();

                        this.keywords = new LinkedHashSet<String>(copyFrom.getKeywords());
                }

                public Builder setCategory(final ModificationCategory cat) {
                        if (cat == null) throw new IllegalArgumentException("cat == null!");
                        this.category = cat;
                        return this;
                }

                public Builder setOccurrenceType(final ModificationOccurrenceType occType) {
                        if (occType == null) throw new IllegalArgumentException("occType == null!");
                        this.occurrenceType =occType;
                        return this;
                }

                public Builder setCondition(final ModificationCondition condition) {
                        if (condition == null) throw new IllegalArgumentException("condition == null!");
                        this.condition = condition;
                        return this;
                }

                /**
                 * Set the Protein Data Bank Chemical Component ID.
                 * @param pdbccId Protein Data Bank Chemical Component ID.
                 * @return the same Builder object so you can chain setters.
                 */
                public Builder setPdbccId(final String pdbccId) {
                        this.pdbccId = pdbccId;
                        return this;
                }

                /**
                 * Set the Protein Data Bank Chemical Component name.
                 * @param pdbccName Protein Data Bank Chemical Component name.
                 * @return the same Builder object so you can chain setters.
                 */
                public Builder setPdbccName(final String pdbccName) {
                        this.pdbccName = pdbccName;
                        return this;
                }

                /**
                 * Set the RESID ID.
                 * @param residId RESID ID.
                 * @return the same Builder object so you can chain setters.
                 */
                public Builder setResidId(final String residId) {
                        this.residId = residId;
                        return this;
                }

                /**
                 * Set the RESID name.
                 * @param residName RESID name.
                 * @return the same Builder object so you can chain setters.
                 */
                public Builder setResidName(final String residName) {
                        this.residName = residName;
                        return this;
                }

                /**
                 * Set the PSI-MOD ID.
                 * @param psimodId PSI-MOD ID.
                 * @return the same Builder object so you can chain setters.
                 */
                public Builder setPsimodId(final String psimodId) {
                        this.psimodId = psimodId;
                        return this;
                }

                /**
                 * Set the PSI-MOD name.
                 * @param psimodName PSI-MOD name.
                 * @return the same Builder object so you can chain setters.
                 */
                public Builder setPsimodName(final String psimodName) {
                        this.psimodName = psimodName;
                        return this;
                }

                /**
                 * Set the systematic name.
                 * @param sysName systematic name.
                 * @return the same Builder object so you can chain setters.
                 */
                public Builder setSystematicName(final String sysName) {
                        this.sysName = sysName;
                        return this;
                }

                /**
                 *
                 * @param description description of the modification.
                 * @return the same Builder object so you can chain setters.
                 */
                public Builder setDescription(final String description) {
                        // description is created on the fly in getDescription
                        return this;
                }

                /**
                 * Add a keyword associate with the PTM.
                 * @param keyword a keyword.
                 * @return the same Builder object so you can chain setters.
                 * @throws IllegalArgumentException if the keyword is null.
                 */
                public Builder addKeyword(String keyword) {
                        if (keyword == null) throw new IllegalArgumentException("Keyword cannot be null.");
                        keywords.add(keyword);
                        return this;
                }

                public Builder addKeywords(Collection<String> keywords) {
                        if (keywords==null)     throw new IllegalArgumentException("Keywords cannot be null.");

                        for (String keyword : keywords) {
                                addKeyword(keyword);
                        }

                        return this;
                }

                /**
                 * Set the residue formula.
                 * @param formula residue formula.
                 * @return the same Builder object so you can chain setters.
                 */
                public Builder setFormula(final String formula) {
                        this.formula = formula;
                        return this;
                }

                /**
                 *
                 * @return build ProteinModification.
                 */
                public ProteinModificationImpl build() {
                        return new ProteinModificationImpl(this);
                }
        }

        /**
         *
         */
        private ProteinModificationImpl(Builder builder) {
                this.id = builder.id;
                this.category = builder.category;
                this.occurrenceType = builder.occurrenceType;
                this.condition = builder.condition;
                this.pdbccId = builder.pdbccId;
                this.pdbccName = builder.pdbccName;
                this.residId = builder.residId;
                this.residName = builder.residName;
                this.psimodId = builder.psimodId;
                this.psimodName = builder.psimodName;
                this.sysName = builder.sysName;
                this.formula = builder.formula;

                this.keywords = new LinkedHashSet<String>(builder.keywords);
        }

        @Override
        public int compareTo(ProteinModification arg0) {
                if ( this.equals(arg0))
                        return 0;

                return this.toString().compareTo(arg0.toString());
        }
}