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.Entity;

import javax.persistence.FetchType;

import javax.persistence.ManyToOne;

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.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.annotations.Type;

import org.hibernate.envers.Audited;

import eu.etaxonomy.cdm.model.agent.AgentBase;

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

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

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

import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;

/**

 * Instances of this the {@link SingleRead} class describe the process and the result of a single

 * sequence generation (read). It has as an input the PCR result ({@link AmplificationResult}). A primer

 * is used for expressing the DNA in either {@link SequenceDirection#Forward forward} or

 * {@link SequenceDirection#Reverse reverse} direction.

 * The result of the process is a {@link #getPherogram() pherogram} which by interpretation results

 * in the most probable {@link #getSequence() sequence}.

 * The event dates like the sequencing date and the sequencing agent(person) are inherited by {@link EventBase}.

 *

 * @see AmplificationResult

 * @see SequenceString

 * @see Sequence

 *

 * @author a.mueller

 * @since 2013-07-05

 */

@XmlAccessorType(XmlAccessType.FIELD)

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

	"amplificationResult",

	"sequence",

	"primer",

	"direction",

	"pherogram",

	"materialOrMethod"

})

@XmlRootElement(name = "SingleRead")

@Entity

@Audited

public class SingleRead extends EventBase implements Cloneable{

	private static final long serialVersionUID = 1735535003073536132L;

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

	/** @see #getAmplificationResult()  */

	@XmlElement(name = "AmplificationResult")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

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

	private AmplificationResult amplificationResult;

	/** @see #getPrimer()*/

	@XmlElement(name = "Primer")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

	private Primer primer;

	/** @see #getSequence()*/

	/**{@link #getSequence()}*/

	@XmlElement(name = "Sequence")

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

    private SequenceString sequence = SequenceString.NewInstance();

	@XmlElement(name = "Pherogram")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

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

	private Media pherogram;

	/** @see #getDirection()*/

	@XmlAttribute(name ="direction")

	//TODO length = 3

	@Type(type = "eu.etaxonomy.cdm.hibernate.EnumUserType",

    	parameters = {@org.hibernate.annotations.Parameter(name  = "enumClass", value = "eu.etaxonomy.cdm.model.molecular.SequenceDirection")}

	)

	private SequenceDirection direction;

	@XmlElement(name = "MaterialOrMethod")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

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

	private MaterialOrMethodEvent materialOrMethod;

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

	public static SingleRead NewInstance(){

		return new SingleRead();

	}

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

	//protected for Javassist, otherwise private

	protected SingleRead(){};

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

	/**

	 * Returns the {@link AmplificationResult amplification product} that was the input for this

	 * {@link SingleRead single sequence}.

	 */

	public AmplificationResult getAmplificationResult() {

		return amplificationResult;

	}

	/**

	 * TODO this method is protected as long as bidirectionality is not clear.

	 * @see #getAmplificationResult()

	 */

	protected void setAmplificationResult(AmplificationResult amplificationResult) {

		this.amplificationResult = amplificationResult;

	}

	/**

	 * The {@link Primer primer} used for processing this single sequence.

	 * Often this primer already has been used in the according {@link Amplification amplification}.

	 * However, there are exceptions from this rule.

	 */

	public Primer getPrimer() {

		return primer;

	}

	/**

	 * @see #getPrimer()

	 */

	public void setPrimer(Primer primer) {

		this.primer = primer;

	}

	/**

	 * The {@link SequenceString sequence string} of this single sequence process (e.g. AGTGGTAGGATG)

	 */

	public SequenceString getSequence() {

		return sequence;

	}

	/**

	 * @see #getSequence()

	 */

	public void setSequence(SequenceString sequence) {

		if (sequence == null){

			SequenceString.NewInstance();

		}

		this.sequence = sequence;

	}

	/**

	 * The {@link SequenceDirection direction} in which this single sequence has been created.

	 * Usually an {@link Amplification amplification} leads to 2 single sequences per {@link DnaSample},

	 * a {@link SequenceDirection#Forward forward} and a {@link SequenceDirection#Reverse reverse} one.

	 * These 2 result then in a {@link Sequence consensus sequence}.

	 * But there are exceptions from this rule.

	 */

	public SequenceDirection getDirection() {

		return direction;

	}

	/**

	 * @see #getDirection()

	 */

	public void setDirection(SequenceDirection direction) {

		this.direction = direction;

	}

	/**

	 * The pherogram (chromatogram) which visualizes the result of this single sequence.

	 */

	public Media getPherogram() {

		return pherogram;

	}

	/**

	 * @see #getPherogram()

	 */

	public void setPherogram(Media pherogram) {

		this.pherogram = pherogram;

	}

	/**

	 * The material and/or method used for this sequencing.

	 */

	public MaterialOrMethodEvent getMaterialOrMethod() {

		return materialOrMethod;

	}

	/**

	 * @see #getMaterialOrMethod()

	 */

	public void setMaterialOrMethod(MaterialOrMethodEvent materialOrMethod) {

		this.materialOrMethod = materialOrMethod;

	}

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

	/**

	 * Delegate method to get the text representation of the {@link #getSequence() sequence}.

	 * @see #setSequenceString(String)

	 */

	@Transient

	public String getSequenceString() {

		return sequence.getString();

	}

	/**

	 * Delegate method to set the text representation of the {@link #getSequence() sequence}.

	 */

	@Transient

	public void setSequenceString(String sequence) {

		this.sequence.setString(sequence);

	}

	/**

	 * Transient convenience method which wrapps {@link EventBase#getActor()}.

	 * @return the {@link TimePeriod date/period} when this sequence was created.

	 */

	@Transient

	public TimePeriod getDateSequenced(){

		return ((EventBase)this).getTimeperiod();

	}

	/**

	 * @see #getDateSequenced()

	 */

	public void setDateSequenced(TimePeriod dateSequenced){

		this.setTimeperiod(dateSequenced);

	}

	/**

	 * Transient convenience method which wrapps {@link EventBase#getActor()}.

	 * @return the {@link AgentBase agent} who sequenced this single sequence.

	 */

	@Transient

	public AgentBase getSequencedBy(){

		return ((EventBase)this).getActor();

	}

	/**

	 * @see #getSequencedBy()

	 */

	public void setSequencedBy(AgentBase sequencedBy){

		this.setActor(sequencedBy);

	}

	// ********************* 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> sequencing by

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

	 *

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

	 */

	@Override

	public SingleRead clone()  {

		try{

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

    		//sequences

    		result.sequence = (SequenceString)this.sequence.clone();

    		//don't change amplification, pherogram, primer, sequence, direction

    		return result;

		}catch (CloneNotSupportedException e) {

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

			e.printStackTrace();

			return null;

		}

	}

}