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 javax.persistence.Column;

import javax.persistence.Entity;

import javax.persistence.FetchType;

import javax.persistence.ManyToOne;

import javax.xml.bind.annotation.XmlAccessType;

import javax.xml.bind.annotation.XmlAccessorType;

import javax.xml.bind.annotation.XmlElement;

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 org.apache.logging.log4j.LogManager;

import org.apache.logging.log4j.Logger;

import org.hibernate.annotations.Cascade;

import org.hibernate.annotations.CascadeType;

import org.hibernate.envers.Audited;

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

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

import eu.etaxonomy.cdm.model.term.DefinedTerm;

/**

 * A primer is a (short) DNA Sequence used for replication and extraction

 * of DNA parts during e.g. {@link Amplification amplification} or

 * {@link SingleRead sequence reading}.

 *

 * @author a.mueller

 * @since 2013-07-08

 */

@XmlAccessorType(XmlAccessType.FIELD)

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

	"label",

	"sequence",

	"dnaMarker",

	"publishedIn"

})

@XmlRootElement(name = "Primer")

@Entity

@Audited

//TODO which base class  (..., identifiable, definedTerm, ...)

public class Primer extends AnnotatableEntity {

	private static final long serialVersionUID = 6179007910988646989L;

	private static final Logger logger = LogManager.getLogger();

	/** @see #getLabel() */

	@XmlElement(name = "Label")

    @Column(length=255)

	private String label;

	/** @see #getSequence() */

	//(see #4139)

	@XmlElement(name = "Sequence")

 	private SequenceString sequence = SequenceString.NewInstance();

    /** @see #getDnaMarker()*/

    @XmlElement(name = "DnaMarker")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch=FetchType.LAZY)

    private DefinedTerm dnaMarker;

	/** @see #getPublishedIn() */

	@XmlElement(name = "PublishedIn")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch=FetchType.LAZY)

    @Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})

	private Reference publishedIn;

// ******************** FACTORY METHOD ******************/

	public static Primer NewInstance(String label){

		Primer result = new Primer();

		result.setLabel(label);

		return result;

	}

// ********************* CONSTRUCTOR ********************/

	//for hibernate use only, *packet* private required by bytebuddy

	//made protected to fix a java.lang.InstantiationException which occurred while loading an Amplification

	//and its primer. see https://stackoverflow.com/questions/7273125/hibernate-envers-and-javassist-enhancement-failed-exception

	Primer(){}

// ********************* GETTER / SETTER ********************/

	/**

	 * The name of this primer, usually given by the producers.

	 * @return the label of this primer.

	 */

	public String getLabel() {

		return label;

	}

	/**

	 * @see #getLabel()

	 */

	public void setLabel(String label) {

		this.label = label;

	}

	/**

	 * The DNA {@link Sequence} of this primer. A primer is usually a

	 * small piece of DNA and therefore can be expressed as a sequence.

	 */

	public SequenceString getSequence() {

		return sequence;

	}

	/**

	 * @see Primer#getSequence()

	 */

	public void setSequence(SequenceString sequence) {

		if (sequence == null){

			sequence = SequenceString.NewInstance();

		}

		this.sequence = sequence;

	}

	/**

	 * #4470

	 */

	public DefinedTerm getDnaMarker() {

		return dnaMarker;

	}

	public void setDnaMarker(DefinedTerm dnaMarker) {

		this.dnaMarker = dnaMarker;

	}

	/**

	 * The reference in which this primer was published and described

	 * for the first time. It is not a reference or citation for the

	 * sequence of this primer.<BR>

	 * Links to this reference are stored with the reference itself.

	 * @return the describing publication of this primer

	 */

	public Reference getPublishedIn() {

		return publishedIn;

	}

	/**

	 * @see #getPublishedIn()

	 */

	public void setPublishedIn(Reference publishedIn) {

		this.publishedIn = publishedIn;

	}

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

	/**

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

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

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

	 *

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

	 */

	@Override

	public Primer clone()  {

		try{

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

//		don't change label, sequence

		result.publishedIn = this.publishedIn;

		return result;

		}catch (CloneNotSupportedException e) {

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

			e.printStackTrace();

			return null;

		}

	}

}