/*
 * 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/
 *
 * Author: Daniel Asarnow
 * Date:   2012-7-23
 */

package org.biojava.nbio.structure.cath;

/**
 * @author Daniel Asarnow
 */

import java.io.IOException;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.biojava.nbio.structure.ResidueRange;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIdentifier;
import org.biojava.nbio.structure.SubstructureIdentifier;
import org.biojava.nbio.structure.align.util.AtomCache;

/**
 * A class which represents a single CATH domain.
 */
public class CathDomain implements Serializable, StructureIdentifier {

        public static final long serialVersionUID = 1L;

        /**
         * The CATH domain code. Always 7 characters in length, combining the PDB and chain letter with the number of the domain within CATH.
         * Example: 1aoiA00
         * If the chain letter '0', domain refers to an entire PDB entry.
         */
        String domainName; // 7 characters 1oaiA00

        /**
         * The class number of this domain.
         */
        Integer classId; // C

        /**
         * The architecture number of this domain.
         */
        Integer architectureId; // A

        /**
         * The topology number of this domain.
         */
        Integer topologyId; // T

        /**
         * The homologous superfamily number of this domain.
         */
        Integer homologyId; // H

        /**
         * The sequence family (35% identity) number of this domain.
         */
        Integer sequenceFamilyId; // S

        /**
         * The "orthologous" sequence family (60% identity) number of this domain.
         */
        Integer orthologousSequenceFamilyId; // O

        /**
         * The "Like" sequence family (95% identity) number of this domain.
         */
        Integer likeSequenceFamilyId; // L

        /**
         * The identical sequence family (100% identity) number of this domain.
         */

        Integer identicalSequenceFamilyId; // I

        /**
         * The count of this domain among the identical sequence family members.
         */
        Integer domainCounter; // D

        /**
         * The domain length..
         */
        Integer length;

        /**
         * The resolution of the domain structure. Nominally in Angstroms,
         * the values 999.000 and 1000.000 signify NMR structures and obsolete structures, respectively.
         */
        Double resolution;

        /**
         * The format and version of the CathDomainDescriptionFile.
         */
        String format;

        /**
         * The CATH version.
         */
        String version;

        Date date;

        /**
         * The so-called name field holds a potentially long description of the domain.
         */
        String name;

        /**
         * Complete source organism listing.
         */
        String source;

        /**
         * FASTA header.
         */
        String sequenceHeader;

        /**
         * FASTA sequence.
         */
        String sequence;

        /**
         * List of all sub-domain segments.
         */
        List<CathSegment> segments;

        /**
         * A (potentially long) comment. Usually empty.
         */
        String comment;

        public String getDomainName() {
                return domainName;
        }

        public void setDomainName(String domainName) {
                this.domainName = domainName;
        }

        /**
         * Returns a string of the form {@code PDBID.CHAIN}.
         * For example: {@code 1hiv.A}.
         * @deprecated This method is poorly named; use {@link #getThePdbId()} or {@link #getPdbIdAndChain()} instead
         */
        @Deprecated
        public String getPdbId() {
                 return getPdbIdAndChain();
        }

        /**
         * Returns the PDB ID.
         */
        public String getThePdbId() {
                return domainName.substring(0, 4);
        }

        /**
         * Returns a string of the form {@code PDBID.CHAIN}.
         * For example: {@code 1hiv.A}.
         */
        public String getPdbIdAndChain() {
                return domainName.substring(0, 4) +
                                (!domainName.substring(4, 5).equals("0") ? "." + domainName.substring(4, 5) : "");
        }

        public Integer getDomainId() {
                return Integer.parseInt(domainName.substring(5));
        }

        public Integer getClassId() {
                return classId;
        }

        public void setClassId(Integer classId) {
                this.classId = classId;
        }

        public Integer getArchitectureId() {
                return architectureId;
        }

        public void setArchitectureId(Integer architectureId) {
                this.architectureId = architectureId;
        }

        public Integer getTopologyId() {
                return topologyId;
        }

        public void setTopologyId(Integer topologyId) {
                this.topologyId = topologyId;
        }

        public Integer getHomologyId() {
                return homologyId;
        }

        public void setHomologyId(Integer homologyId) {
                this.homologyId = homologyId;
        }

        public Integer getSequenceFamilyId() {
                return sequenceFamilyId;
        }

        public void setSequenceFamilyId(Integer sequenceFamilyId) {
                this.sequenceFamilyId = sequenceFamilyId;
        }

        public Integer getOrthologousSequenceFamilyId() {
                return orthologousSequenceFamilyId;
        }

        public void setOrthologousSequenceFamilyId(Integer orthologousSequenceFamilyId) {
                this.orthologousSequenceFamilyId = orthologousSequenceFamilyId;
        }

        public Integer getLikeSequenceFamilyId() {
                return likeSequenceFamilyId;
        }

        public void setLikeSequenceFamilyId(Integer likeSequenceFamilyId) {
                this.likeSequenceFamilyId = likeSequenceFamilyId;
        }

        public Integer getIdenticalSequenceFamilyId() {
                return identicalSequenceFamilyId;
        }

        public void setIdenticalSequenceFamilyId(Integer identicalSequenceFamilyId) {
                this.identicalSequenceFamilyId = identicalSequenceFamilyId;
        }

        public Integer getDomainCounter() {
                return domainCounter;
        }

        public void setDomainCounter(Integer domainCounter) {
                this.domainCounter = domainCounter;
        }

        public Integer getLength() {
                return length;
        }

        public void setLength(Integer length) {
                this.length = length;
        }

        public Double getResolution() {
                return resolution;
        }

        public void setResolution(Double resolution) {
                this.resolution = resolution;
        }

        public void setCATH(String cathCode) {
                String[] token = cathCode.split("[.]");
                setClassId(Integer.parseInt(token[0]));
                setArchitectureId(Integer.parseInt(token[1]));
                setTopologyId(Integer.parseInt(token[2]));
                setHomologyId(Integer.parseInt(token[3]));
        }

        public String getCATH() {
                return Integer.toString(getClassId()) + "." +
                                Integer.toString(getArchitectureId()) + "." +
                                Integer.toString(getTopologyId()) + "." +
                                Integer.toString(getHomologyId());
        }

        public void setSOLID(String cathCode) {
                String[] token = cathCode.split("[.]");
                setSequenceFamilyId(Integer.parseInt(token[0]));
                setOrthologousSequenceFamilyId(Integer.parseInt(token[1]));
                setLikeSequenceFamilyId(Integer.parseInt(token[2]));
                setIdenticalSequenceFamilyId(Integer.parseInt(token[3]));
                setDomainCounter(Integer.parseInt(token[4]));
        }

        public String getSOILD() {
                return Integer.toString(getSequenceFamilyId()) + "." +
                                Integer.toString(getOrthologousSequenceFamilyId()) + "." +
                                Integer.toString(getLikeSequenceFamilyId()) + "." +
                                Integer.toString(getIdenticalSequenceFamilyId()) + "." +
                                Integer.toString(getDomainCounter());
        }

        public Integer getClassificationId(CathCategory cathCategory) {
                switch (cathCategory) {
                        case Class:
                                return getClassId();
                        case Architecture:
                                return getArchitectureId();
                        case Topolgy:
                                return getTopologyId();
                        case Homology:
                                return getHomologyId();
                        case SequenceFamily:
                                return getSequenceFamilyId();
                        case OrthologousSequenceFamily:
                                return getOrthologousSequenceFamilyId();
                        case LikeSequenceFamily:
                                return getLikeSequenceFamilyId();
                        case IdenticalSequenceFamily:
                                return getIdenticalSequenceFamilyId();
                        case DomainCounter:
                                return getDomainCounter();
                        default:
                                return null;
                }
        }

        public String getFormat() {
                return format;
        }

        public void setFormat(String format) {
                this.format = format;
        }

        public String getVersion() {
                return version;
        }

        public void setVersion(String version) {
                this.version = version;
        }

        public Date getDate() {
                return date;
        }

        public void setDate(Date date) {
                this.date = date;
        }

        public String getName() {
                return name;
        }

        public void setName(String name) {
                this.name = name;
        }

        public String getSource() {
                return source;
        }

        public void setSource(String source) {
                this.source = source;
        }

        public String getSequenceHeader() {
                return sequenceHeader;
        }

        public void setSequenceHeader(String sequenceHeader) {
                this.sequenceHeader = sequenceHeader;
        }

        public String getSequence() {
                return sequence;
        }

        public void setSequence(String sequence) {
                this.sequence = sequence;
        }

        public List<CathSegment> getSegments() {
                return segments;
        }

        public void setSegments(List<CathSegment> segments) {
                this.segments = segments;
        }

        public String getComment() {
                return comment;
        }

        public void setComment(String comment) {
                this.comment = comment;
        }

        @Override
        public String toString() {
                return "CathDomain [domainName=" + domainName + ", classId=" + classId
                                + ", architectureId=" + architectureId + ", topologyId="
                                + topologyId + ", homologyId=" + homologyId
                                + ", sequenceFamilyId=" + sequenceFamilyId
                                + ", orthologousSequenceFamilyId="
                                + orthologousSequenceFamilyId + ", likeSequenceFamilyId="
                                + likeSequenceFamilyId + ", identicalSequenceFamilyId="
                                + identicalSequenceFamilyId + ", domainCounter="
                                + domainCounter + ", length=" + length + ", resolution="
                                + resolution + ", format=" + format + ", version=" + version
                                + ", date=" + date + ", name=" + name + ", source=" + source
                                + ", sequenceHeader=" + sequenceHeader + ", sequence="
                                + sequence + ", segments=" + segments + ", comment=" + comment
                                + "]";
        }

        /**
         * Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
         */
        public Set<String> getChains() {
                Set<String> chains = new HashSet<String>();
                List<ResidueRange> rrs = toCanonical().getResidueRanges();
                for (ResidueRange rr : rrs) chains.add(rr.getChainId());
                return chains;
        }

        @Override
        public String getIdentifier() {
                return getCATH();
        }

        @Override
        public SubstructureIdentifier toCanonical() {
                List<ResidueRange> ranges = new ArrayList<ResidueRange>();
                String chain = String.valueOf(getDomainName().charAt(getDomainName().length() - 3));
                for (CathSegment segment : this.getSegments()) {
                        ranges.add(new ResidueRange(chain, segment.getStart(), segment.getStop()));
                }

                return new SubstructureIdentifier(getThePdbId(), ranges);
        }

        @Override
        public Structure reduce(Structure input) throws StructureException {
                return toCanonical().reduce(input);
        }

        @Override
        public Structure loadStructure(AtomCache cache) throws StructureException,
                        IOException {
                return cache.getStructure(getThePdbId());
        }


}