/*
 * 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.getChainName());
		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());
	}


}
