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.Basic;

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.XmlTransient;

import javax.xml.bind.annotation.XmlType;

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

import org.apache.log4j.Logger;

import org.hibernate.annotations.Type;

import org.hibernate.envers.Audited;

import org.hibernate.search.annotations.Analyze;

import org.hibernate.search.annotations.Field;

import org.hibernate.search.annotations.FieldBridge;

import org.joda.time.DateTime;

import eu.etaxonomy.cdm.hibernate.search.DateTimeBridge;

import eu.etaxonomy.cdm.jaxb.DateTimeAdapter;

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

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

import eu.etaxonomy.cdm.model.description.MeasurementUnit;

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

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

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

/**

 * A DNA Quality describes the quality of a {@link SpecimenOrObservationType#DnaSample}

 *

 * @author a.mueller

 * @since 18-Oct-2014

 */

@XmlAccessorType(XmlAccessType.FIELD)

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

	"purificationMethod",

	"ratioOfAbsorbance260_230",

    "ratioOfAbsorbance260_280",

    "concentration",

    "concentrationUnit",

    "qualityTerm",

    "qualityCheckDate"

})

@XmlRootElement(name = "DnaQuality")

@Entity

//@Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")

@Audited

public class DnaQuality extends VersionableEntity implements Cloneable {

	private static final long serialVersionUID = -8829069331010573654L;

	@SuppressWarnings("unused")

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

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

	/**

	 * Factory method

	 * @return

	 */

	public static DnaQuality NewInstance(){

		return new DnaQuality();

	}

// ************** ATTRIBUTES ****************************/

    //TODO

//	@XmlElement(name = "PurificationMethod")

//    @XmlIDREF

//    @XmlSchemaType(name = "IDREF")

	@XmlTransient

    @ManyToOne(fetch = FetchType.LAZY)

	//FIXME preliminary as it is not yet decided if we will use a string or a MoME #4552

    private MaterialOrMethodEvent typedPurificationMethod;

    private String purificationMethod;

	private Double ratioOfAbsorbance260_230;

	private Double ratioOfAbsorbance260_280;

	private Double concentration;

	@XmlElement(name = "concentrationUnit")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

	private MeasurementUnit concentrationUnit;

	@XmlElement(name = "Type")

    @XmlIDREF

    @XmlSchemaType(name = "IDREF")

    @ManyToOne(fetch = FetchType.LAZY)

	private OrderedTerm qualityTerm;

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

    @XmlJavaTypeAdapter(DateTimeAdapter.class)

    @Type(type="dateTimeUserType")

    @Basic(fetch = FetchType.LAZY)

    @Field(analyze = Analyze.NO)

    @FieldBridge(impl = DateTimeBridge.class)

    @Audited

    private DateTime qualityCheckDate;

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

	/**

	 * Constructor

	 */

	protected DnaQuality() {}

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

	public String getPurificationMethod() {

		return purificationMethod;

	}

	public void setPurificationMethod(String purificationMethod) {

		this.purificationMethod = purificationMethod;

	}

	public Double getRatioOfAbsorbance260_230() {

		return ratioOfAbsorbance260_230;

	}

	public void setRatioOfAbsorbance260_230(Double ratioOfAbsorbance260_230) {

		this.ratioOfAbsorbance260_230 = ratioOfAbsorbance260_230;

	}

	public Double getRatioOfAbsorbance260_280() {

		return ratioOfAbsorbance260_280;

	}

	public void setRatioOfAbsorbance260_280(Double ratioOfAbsorbance260_280) {

		this.ratioOfAbsorbance260_280 = ratioOfAbsorbance260_280;

	}

    public Double getConcentration() {

		return concentration;

	}

	public void setConcentration(Double concentration) {

		this.concentration = concentration;

	}

	public MeasurementUnit getConcentrationUnit() {

		return concentrationUnit;

	}

	public void setConcentrationUnit(MeasurementUnit concentrationUnit) {

		this.concentrationUnit = concentrationUnit;

	}

	public DateTime getQualityCheckDate() {

		return qualityCheckDate;

	}

	public void setQualityCheckDate(DateTime qualityCheckDate) {

		this.qualityCheckDate = qualityCheckDate;

	}

	public OrderedTerm getQualityTerm() {

		return qualityTerm;

	}

	public void setQualityTerm(OrderedTerm qualityTerm) {

		this.qualityTerm = qualityTerm;

	}

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

	/**

	 * Clones <i>this</i> dna quality. This is a shortcut that enables to

	 * create a new instance that differs only slightly from <i>this</i> dna quality

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

	 * @throws CloneNotSupportedException

	 *

	 * @see Specimen#clone()

	 * @see DerivedUnit#clone()

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

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

	 */

	@Override

	public DnaQuality clone() {

		try {

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

			//purification method ??

			//no changes to: rationXXX, concentration, qualityCheckDate, qualityTerm,

			return result;

		} catch (CloneNotSupportedException e) {

			throw new RuntimeException(e);  //may not occur as Clonable is implemented

		}

	}

}