EDIT

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy 

* http://www.e-taxonomy.eu

* 

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.model.molecular;

import java.util.HashSet;

import java.util.Set;

import javax.persistence.Basic;

import javax.persistence.Entity;

import javax.persistence.FetchType;

import javax.persistence.ManyToOne;

import javax.persistence.OneToMany;

import javax.persistence.Transient;

import javax.xml.bind.annotation.XmlAccessType;

import javax.xml.bind.annotation.XmlAccessorType;

import javax.xml.bind.annotation.XmlAttribute;

import javax.xml.bind.annotation.XmlElement;

import javax.xml.bind.annotation.XmlElementWrapper;

import javax.xml.bind.annotation.XmlIDREF;

import javax.xml.bind.annotation.XmlRootElement;

import javax.xml.bind.annotation.XmlSchemaType;

import javax.xml.bind.annotation.XmlType;

import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;

import org.apache.log4j.Logger;

import org.hibernate.annotations.Cascade;

import org.hibernate.annotations.CascadeType;

import org.hibernate.annotations.Index;

import org.hibernate.annotations.Table;

import org.hibernate.annotations.Type;

import org.hibernate.envers.Audited;

import org.joda.time.DateTime;

import org.springframework.beans.factory.annotation.Configurable;

import eu.etaxonomy.cdm.jaxb.DateTimeAdapter;

import eu.etaxonomy.cdm.model.common.IReferencedEntity;

import eu.etaxonomy.cdm.model.common.IdentifiableEntity;

import eu.etaxonomy.cdm.model.media.IMediaDocumented;

import eu.etaxonomy.cdm.model.media.Media;

import eu.etaxonomy.cdm.model.reference.Reference;

import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;

import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;

/**

 * @author m.doering

 * @version 1.0

 * @created 08-Nov-2007 13:06:51

 */

@XmlAccessorType(XmlAccessType.FIELD)

@XmlType(name = "Sequence", propOrder = {

    "sequence",

    "length",

    "dateSequenced",

    "barcode",

    "citationMicroReference",

    "publishedIn",

    "locus",

    "citations",

    "genBankAccession",

    "chromatograms"

})

@XmlRootElement(name = "Sequence")

@Entity

@Audited

@Configurable

@Table(appliesTo="Sequence", indexes = { @Index(name = "sequenceTitleCacheIndex", columnNames = { "titleCache" }) })

public class Sequence extends IdentifiableEntity<IIdentifiableEntityCacheStrategy<Sequence>> implements IReferencedEntity, IMediaDocumented{

	private static final long serialVersionUID = 8298983152731241775L;

	private static final Logger logger = Logger.getLogger(Sequence.class);

	//the sequence as a string of base pairs. 5'->3'

	@XmlElement(name = "Sequence")

	private String sequence;

	//should be calculated in case sequence is set

	@XmlElement(name = "Length")

	private Integer length;

	//should be calculated in case sequence is set

	@XmlElement (name = "DateSequenced", type= String.class)

	@XmlJavaTypeAdapter(DateTimeAdapter.class)

	@Type(type="dateTimeUserType")

	@Basic(fetch = FetchType.LAZY)

	private DateTime dateSequenced;

	//should be calculated in case sequence is set

	@XmlAttribute(name = "isBarcode")

	private boolean barcode;

	//the sequence as a string of base pairs. 5'->3'

	@XmlElement(name = "CitationMicroReference")

	private String citationMicroReference;

	@XmlElement(name = "PublishedIn")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

    @Cascade(CascadeType.SAVE_UPDATE)

	private Reference publishedIn;

	@XmlElementWrapper(name = "Citations")

	@XmlElement(name = "Citation")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @OneToMany(fetch = FetchType.LAZY)

	private Set<Reference> citations = new HashSet<Reference>();

	@XmlElementWrapper(name = "GenBankAccessions")

	@XmlElement(name = "GenBankAccession")

    @OneToMany(fetch = FetchType.LAZY)

	private Set<GenBankAccession> genBankAccession = new HashSet<GenBankAccession>();

	@XmlElement(name = "Locus")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

    @Cascade(CascadeType.SAVE_UPDATE)

	private Locus locus;

	@XmlElementWrapper(name = "Chromatograms")

	@XmlElement(name = "Chromatogram")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @OneToMany(fetch = FetchType.LAZY)

	private Set<Media> chromatograms = new HashSet<Media>();

	protected Sequence() {

		super(); // FIXME I think this is explicit - do we really need to call this?

		this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<Sequence>();

	}

	public Locus getLocus(){

		logger.debug("getLocus");

		return this.locus;

	}

	public void setLocus(Locus locus){

		this.locus = locus;

	}

	public Reference getPublishedIn(){

		return this.publishedIn;

	}

	public void setPublishedIn(Reference publishedIn){

		this.publishedIn = publishedIn;

	}

	public Set<Reference> getCitations() {

		return citations;

	}

	protected void setCitations(Set<Reference> citations) {

		this.citations = citations;

	}

	public void addCitation(Reference citation) {

		this.citations.add(citation);

	}

	public void removeCitation(Reference citation) {

		this.citations.remove(citation);

	}

	public Set<GenBankAccession> getGenBankAccession() {

		return genBankAccession;

	}

	public void addGenBankAccession(GenBankAccession genBankAccession) {

		this.genBankAccession.add(genBankAccession);

	}

	public void removeGenBankAccession(GenBankAccession genBankAccession) {

		this.genBankAccession.remove(genBankAccession);

	}

	public Set<Media> getChromatograms() {

		return chromatograms;

	}

	public void addChromatogram(Media chromatogram) {

		this.chromatograms.add(chromatogram);

	}

	public void removeChromatogram(Media chromatogram) {

		this.chromatograms.remove(chromatogram);

	}

	@Transient

	public Set<Media> getMedia() {

		return getChromatograms();

	}

	public String getSequence(){

		return this.sequence;

	}

	/**

	 * 

	 * @param sequence    sequence

	 */

	public void setSequence(String sequence){

		this.sequence = sequence;

	}

	public Integer getLength(){

		return this.length;

	}

	/**

	 * 

	 * @param length    length

	 */

	public void setLength(Integer length){

		this.length = length;

	}

	public DateTime getDateSequenced(){

		return this.dateSequenced;

	}

	/**

	 * 

	 * @param dateSequenced    dateSequenced

	 */

	public void setDateSequenced(DateTime dateSequenced){

		this.dateSequenced = dateSequenced;

	}

	public boolean isBarcode(){

		return this.barcode;

	}

	/**

	 * 

	 * @param isBarcode    isBarcode

	 */

	public void setBarcode(boolean barcode){

		this.barcode = barcode;

	}

	public String getCitationMicroReference(){

		return this.citationMicroReference;

	}

	/**

	 * 

	 * @param citationMicroReference    citationMicroReference

	 */

	public void setCitationMicroReference(String citationMicroReference){

		this.citationMicroReference = citationMicroReference;

	}

	public Reference getCitation(){

		return publishedIn;

	}

	//*********************** CLONE ********************************************************/

	/** 

	 * Clones <i>this</i> sequence. This is a shortcut that enables to create

	 * a new instance that differs only slightly from <i>this</i> sequence by

	 * modifying only some of the attributes.<BR><BR>

	 * 

	 *  

	 * @see eu.etaxonomy.cdm.model.media.IdentifiableEntity#clone()

	 * @see java.lang.Object#clone()

	 */

	@Override

	public Object clone()  {

		try{

		Sequence result = (Sequence)super.clone();

		result.citations = new HashSet<Reference>();

		for (Reference ref: this.citations){

			result.citations.add((Reference) ref.clone());

		}

		result.genBankAccession = new HashSet<GenBankAccession>();

		for (GenBankAccession genBankAcc: this.genBankAccession){

			result.genBankAccession.add((GenBankAccession)genBankAcc.clone());

		}

		result.chromatograms = new HashSet<Media>();

		for (Media chromatogram: this.chromatograms){

			result.chromatograms.add((Media)chromatogram.clone());

		}

		return result;

		}catch (CloneNotSupportedException e) {

			logger.warn("Object does not implement cloneable");

			e.printStackTrace();

			return null;

		}

	}

}