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.JoinColumn;

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.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import org.hibernate.annotations.Cascade;

import org.hibernate.annotations.CascadeType;

import org.hibernate.envers.Audited;

import org.hibernate.search.annotations.Analyze;

import org.hibernate.search.annotations.Field;

import org.hibernate.search.annotations.IndexedEmbedded;

import org.hibernate.search.annotations.NumericField;

import eu.etaxonomy.cdm.common.CdmUtils;

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

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

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

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

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

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

/**

 * The physical process of amplification (also called PCR) extracts and replicates parts of the DNA of

 * a given {@link #getDnaSample() DNA Sample} . The part of the DNA being replicated is defined by the

 * {@link Amplification#getDnaMarker() marker} (also called locus) - implemented in CDM as a {@link DefinedTerm}

 * of term type {@link TermType#DnaMarker}.

 *

 * <BR>

 * To execute the replication {@link Primer primers} (short DNA fractions) are

 * used. They may work in both directions of the DNA part therefore we do have a

 * {@link #getForwardPrimer() forward primer} and a {@link #getReversePrimer() reverse primer}.

 * Most (or all?) amplifications require a {@link #getPurification() purification process}. Additionally

 * some use {@link #getCloning()} for replication.

 *

 * <H3>Quality control</H3>

 * <BR>

 * For quality control the resulting product (PCR) is tested using a chromatographic method called

 * electrophoresis. The parameters (voltage, ladder used, running time, and gel concentration) used

 * for this electrophoresis as well as the resulting

 * {@link #getGelPhoto() photo} are also relevant for an amplification.

 *

 * We have 2 classes to store the core data for an amplification: {@link Amplification} and {@link AmplificationResult}.

 * <BR>

 * In {@link Amplification} we store all data that is equal for an amplification event which includes amplification

 * of many {@link DnaSample dna samples}. Those data which are relevant only for a specific dna sample are

 * stored in {@link AmplificationResult}. Theoretically this includes data on the resulting PCR. However, as the

 * PCR itself is not persistent we do not store further information on it in the CDM and do not handle

 * {@link AmplificationResult} as a {@link DerivedUnit}.

 * <BR>

 * This may change in future: http://dev.e-taxonomy.eu/trac/ticket/3717.

 * <BR>

 *

 * @author a.mueller

 * @since 2013-07-05

 *

 * @see AmplificationResult

 */

@XmlAccessorType(XmlAccessType.FIELD)

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

	"dnaMarker",

	"forwardPrimer",

	"reversePrimer",

	"purification",

	"institution",

	"ladderUsed",

	"electrophoresisVoltage",

	"gelRunningTime",

	"gelConcentration",

	"labelCache"

})

@XmlRootElement(name = "Amplification")

@Entity

@Audited

public class Amplification extends EventBase implements Cloneable{

	private static final long serialVersionUID = -6382383300974316261L;

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

    /** @see #getDnaMarker()*/

    @XmlElement(name = "DnaMarker")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    //TODO why is this eager?

    @ManyToOne(fetch=FetchType.EAGER)

    private DefinedTerm dnaMarker;

    /** @see #getForwardPrimer() */

    @XmlElement(name = "ForwardPrimer")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch=FetchType.LAZY)

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

    private Primer forwardPrimer;

    /** @see #getReversePrimer()*/

    @XmlElement(name = "ReversePrimer")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch=FetchType.LAZY)

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

    private Primer reversePrimer;

    @XmlElement(name = "Purification")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch=FetchType.LAZY)

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

    private MaterialOrMethodEvent purification;

	@XmlElement(name = "Institution")

	@XmlIDREF

	@XmlSchemaType(name = "IDREF")

	@ManyToOne(fetch = FetchType.LAZY)

	@IndexedEmbedded

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

	@JoinColumn(name="institution_id")

	private Institution institution;

    /** @see #getLadderUsed() */

    @XmlElement(name = "ladderUsed")

	@Field

    @Column(length=255)

	private String ladderUsed;

    /** @see #getElectrophoresisVoltage()*/

	@XmlElement(name = "electrophoresisVoltage")

	@Field(analyze = Analyze.NO)

	@NumericField

	private Double electrophoresisVoltage;

    /** @see #getGelRunningTime() */

	@XmlElement(name = "gelRunningTime")

	@Field(analyze = Analyze.NO)

	@NumericField

	private Double gelRunningTime;

    /** @see #getGelConcentration() */

	@XmlElement(name = "gelConcentration")

	@Field(analyze = Analyze.NO)

	@NumericField

	private Double gelConcentration;

	//automatically created

	private String labelCache;

// ********************* FACTORY METHODS ************************/

	public static Amplification NewInstance(){

	    return new Amplification();

	}

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

	protected Amplification(){}

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

	/**

	 * The {@link TermType#DnaMarker DNA marker} used for this amplification.

	 * The DNA marker also defines the part (locality) of the DNA/RNA examined.

	 * It may also be called <i>locus</i>

	 */

	public DefinedTerm getDnaMarker() {

		return dnaMarker;

	}

	/** @see #getDnaMarker()*/

	public void setDnaMarker(DefinedTerm marker) {

		this.dnaMarker = marker;

	}

	/**

	 * The primer used for forward amplification.

	 * @see #getReversePrimer()

	 */

	public Primer getForwardPrimer() {

		return forwardPrimer;

	}

	/**

	 * @see #getForwardPrimer()

	 * @see #getReversePrimer()

	 */

	public void setForwardPrimer(Primer forwardPrimer) {

		this.forwardPrimer = forwardPrimer;

	}

	/**

	 * The primer used for reverse amplification.

	 * @see #getForwardPrimer()

	 */

	public Primer getReversePrimer() {

		return reversePrimer;

	}

	/**

	 * @see #getReversePrimer()

	 * @see #getForwardPrimer()

	 */

	public void setReversePrimer(Primer reversePrimer) {

		this.reversePrimer = reversePrimer;

	}

	/**

	 * The material and/or method used for purification.

	 */

	public MaterialOrMethodEvent getPurification() {

		return purification;

	}

	/**

	 * @see #getPurification()

	 */

	public void setPurification(MaterialOrMethodEvent purification) {

		this.purification = purification;

	}

    /**

     * The institution in which the amplification event took place.

     * Usually the {@link Amplification#getActor()} should be a person

     * or team that works for this institution at the given time

     * @return the institution

     */

//	#4498

    public Institution getInstitution() {

		return institution;

	}

	/**

	 * @see #getInstitution()

	 */

	public void setInstitution(Institution institution) {

		this.institution = institution;

	}

	/**

	 * The voltage used for running the electrophoresis quality check.

	 * Base unit is voltage [V].

	 * @see #getGelRunningTime()

	 * @see #getGelPhoto()

	 * @see #getLadderUsed()

	 * @see #getGelConcentration()

	 */

	public Double getElectrophoresisVoltage() {

		return electrophoresisVoltage;

	}

	/**

	 * @see #getElectrophoresisVoltage()

	 */

	public void setElectrophoresisVoltage(Double electrophoresisVoltage) {

		this.electrophoresisVoltage = electrophoresisVoltage;

	}

	/**

	 * The time for running the electrophoresis quality check.

	 * Base unit is minutes [min].

	 */

	public Double getGelRunningTime() {

		return gelRunningTime;

	}

	/**

	 * @see #getGelRunningTime()

	 */

	public void setGelRunningTime(Double gelRunningTime) {

		this.gelRunningTime = gelRunningTime;

	}

	/**

	 * The gel concentration used for the electrophoresis.

	 * Base unit is [%]

	 * @see #getElectrophoresisVoltage()

	 * @see #getGelRunningTime()

	 * @see #getGelPhoto()

	 * @see #getLadderUsed()

	 */

	public Double getGelConcentration() {

		return gelConcentration;

	}

	/**

	 * @see #getGelConcentration()

	 */

	public void setGelConcentration(Double gelConcentration) {

		this.gelConcentration = gelConcentration;

	}

	/**

	 * Material and method used for testing quality of this amplification.

	 * @see #getElectrophoresisVoltage()

	 * @see #getGelPhoto()

	 * @see #getGelConcentration()

	 * @see #getGelRunningTime()

	 */

	public String getLadderUsed() {

		return ladderUsed;

	}

	/**

	 * @see #getLadderUsed()

	 */

	public void setLadderUsed(String ladderUsed) {

		this.ladderUsed = ladderUsed;

	}

	/**

	 * Returns the labelCache

	 * @return

	 */

	public String getLabelCache() {

		return labelCache;

	}

	/**

	 * This method pushes the {@link Amplification#labelCache label cache} update.

	 * The cache is otherwise updated during persist in CacheStrategyUpdater.

	 */

	public void updateCache(){

        //retrieve data

		 String institutionName = getInstitution() == null ? "" :getInstitution().getTitleCache();

         String staffName = getActor() == null ? "" :getActor().getTitleCache();

         String dnaMarkerString = getDnaMarker() == null ? "" :getDnaMarker().getTitleCache();

         String dateString = getTimeperiod() == null ? "" :getTimeperiod().toString();

         //assemble string

         String designation = CdmUtils.concat("_", new String[]{institutionName, staffName, dnaMarkerString, dateString});

         this.labelCache = StringUtils.isBlank(designation) ? "<Amplification:" + getUuid() + ">" : designation ;

	}

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

	/**

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

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

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

	 *

	 *

	 * @see EventBase#clone()

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

	 */

	@Override

	public Object clone()  {

		try{

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

			//don't change marker, forwardPrimer, reversePrimer,

			//purifiaction, ladderUsed, electrophoresisVoltage,

			//gelRunningTime, gelConcentration

			return result;

		}catch (CloneNotSupportedException e) {

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

			e.printStackTrace();

			return null;

		}

	}

}