/*
 *                    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.scop;

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

import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlRootElement;

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;


/** Container for the information for a domain. Contains a line in the file
 * dir.cla.scop.txt_1.75
 *
 * e.g d1dlwa_  1dlw    A:      a.1.1.1 14982   cl=46456,cf=46457,sf=46458,fa=46459,dm=46460,sp=46461,px=14982
 *
 * Instantiated using {@link ScopDatabase#getDomainByScopID(String)}
 * @author Andreas Prlic
 *
 */
@XmlRootElement(name = "ScopDomain", namespace ="http://source.rcsb.org")
@XmlAccessorType(XmlAccessType.PUBLIC_MEMBER)
public class ScopDomain implements Serializable, Cloneable, StructureIdentifier {

        private static final long serialVersionUID = 5890476209571654301L;

        String scopId;
        String pdbId;
        List<String> ranges;
        String classificationId;
        Integer sunid;

        int classId;
        int foldId;
        int superfamilyId;
        int familyId;
        int domainId;
        int speciesId;
        int px;




        @Override
        public String toString() {
                StringBuilder buf = new StringBuilder();
                buf.append(scopId);
                buf.append("\t") ;
                buf.append(pdbId);
                buf.append( "\t");

                int rangePos = 0;
                for (String range: ranges){
                        rangePos++;

                        buf.append(range);

                        if ( ( ranges.size()> 1 ) && (rangePos < ranges.size()))
                                buf.append(",");
                }
                buf.append("\t") ;
                buf.append(classificationId);
                buf.append("\t") ;
                buf.append(String.valueOf(sunid));
                buf.append("\t") ;

                buf.append("cl=");
                buf.append(String.valueOf(classId));
                buf.append(",cf=");
                buf.append(String.valueOf(foldId));
                buf.append(",sf=");
                buf.append(String.valueOf(superfamilyId));
                buf.append(",fa=");
                buf.append(String.valueOf(familyId));
                buf.append(",dm=");
                buf.append(String.valueOf(domainId));
                buf.append(",sp=");
                buf.append(String.valueOf(speciesId));
                buf.append(",px=");
                buf.append(String.valueOf(px));


                return buf.toString();
        }

        public String getScopId() {
                return scopId;
        }
        public void setScopId(String scopId) {
                this.scopId = scopId;
        }
        public String getPdbId() {
                return pdbId;
        }
        public void setPdbId(String pdbId) {
                this.pdbId = pdbId;
        }
        public List<String> getRanges() {
                return ranges;
        }
        public void setRanges(List<String> ranges) {
                this.ranges = ranges;
        }
        public String getClassificationId() {
                return classificationId;
        }
        public void setClassificationId(String classificationId) {
                this.classificationId = classificationId;
        }
        public Integer getSunid() {
                return sunid;
        }
        public void setSunid(Integer sunid) {
                this.sunid = sunid;
        }
        public int getClassId() {
                return classId;
        }
        public void setClassId(int classId) {
                this.classId = classId;
        }
        public int getFoldId() {
                return foldId;
        }
        public void setFoldId(int foldId) {
                this.foldId = foldId;
        }
        public int getSuperfamilyId() {
                return superfamilyId;
        }
        public void setSuperfamilyId(int superfamilyId) {
                this.superfamilyId = superfamilyId;
        }
        public int getFamilyId() {
                return familyId;
        }
        public void setFamilyId(int familyId) {
                this.familyId = familyId;
        }
        public int getDomainId() {
                return domainId;
        }
        public void setDomainId(int domainId) {
                this.domainId = domainId;
        }
        public int getSpeciesId() {
                return speciesId;
        }
        public void setSpeciesId(int speciesId) {
                this.speciesId = speciesId;
        }
        public int getPx() {
                return px;
        }
        public void setPx(int px) {
                this.px = px;
        }

        @Override
        protected Object clone() throws CloneNotSupportedException {

                super.clone();

                ScopDomain n = new ScopDomain();
                n.setClassId(getClassId());
                n.setClassificationId(getClassificationId());
                n.setDomainId(getDomainId());
                n.setFamilyId(getFamilyId());
                n.setFoldId(getFoldId());
                n.setPdbId(getPdbId());
                n.setPx(getPx());
                n.setRanges(getRanges());
                n.setScopId(getScopId());
                n.setSpeciesId(getSpeciesId());
                n.setSunid(getSunid());
                n.setSuperfamilyId(getSuperfamilyId());


                return n;


        }

        /**
         * 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 = ResidueRange.parseMultiple(getRanges());
                for (ResidueRange rr : rrs) chains.add(rr.getChainId());
                return chains;
        }

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

        public List<ResidueRange> getResidueRanges() {
                return ResidueRange.parseMultiple(ranges);
        }

        @Override
        public SubstructureIdentifier toCanonical() {
                return new SubstructureIdentifier(getPdbId(), ResidueRange.parseMultiple(getRanges()));
        }

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

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

}