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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.model.molecular;
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import javax.persistence.Basic;
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import javax.persistence.Entity;
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import javax.persistence.FetchType;
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import javax.persistence.ManyToOne;
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import javax.xml.bind.annotation.XmlAccessType;
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import javax.xml.bind.annotation.XmlAccessorType;
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import javax.xml.bind.annotation.XmlElement;
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import javax.xml.bind.annotation.XmlIDREF;
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import javax.xml.bind.annotation.XmlRootElement;
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import javax.xml.bind.annotation.XmlSchemaType;
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import javax.xml.bind.annotation.XmlTransient;
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import javax.xml.bind.annotation.XmlType;
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import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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import org.hibernate.annotations.Type;
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import org.hibernate.envers.Audited;
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import org.hibernate.search.annotations.Analyze;
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import org.hibernate.search.annotations.Field;
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import org.hibernate.search.annotations.FieldBridge;
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import org.joda.time.DateTime;
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import eu.etaxonomy.cdm.hibernate.search.DateTimeBridge;
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import eu.etaxonomy.cdm.jaxb.DateTimeAdapter;
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import eu.etaxonomy.cdm.model.common.VersionableEntity;
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import eu.etaxonomy.cdm.model.description.MeasurementUnit;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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import eu.etaxonomy.cdm.model.term.OrderedTerm;
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/**
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* A DNA Quality describes the quality of a {@link SpecimenOrObservationType#DnaSample}
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*
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* @author a.mueller
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* @since 18-Oct-2014
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "DnaQuality", propOrder = {
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"purificationMethod",
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"ratioOfAbsorbance260_230",
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"ratioOfAbsorbance260_280",
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"concentration",
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"concentrationUnit",
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"qualityTerm",
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"qualityCheckDate"
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})
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@XmlRootElement(name = "DnaQuality")
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@Entity
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//@Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
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@Audited
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public class DnaQuality extends VersionableEntity implements Cloneable {
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private static final long serialVersionUID = -8829069331010573654L;
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@SuppressWarnings("unused")
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private static final Logger logger = LogManager.getLogger(DnaQuality.class);
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// ****************** FACTORY METHOD *****************/
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/**
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* Factory method
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* @return
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*/
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public static DnaQuality NewInstance(){
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return new DnaQuality();
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}
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// ************** ATTRIBUTES ****************************/
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//TODO
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// @XmlElement(name = "PurificationMethod")
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// @XmlIDREF
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// @XmlSchemaType(name = "IDREF")
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@XmlTransient
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@ManyToOne(fetch = FetchType.LAZY)
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//FIXME preliminary as it is not yet decided if we will use a string or a MoME #4552
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private MaterialOrMethodEvent typedPurificationMethod;
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private String purificationMethod;
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private Double ratioOfAbsorbance260_230;
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private Double ratioOfAbsorbance260_280;
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private Double concentration;
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@XmlElement(name = "concentrationUnit")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToOne(fetch = FetchType.LAZY)
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private MeasurementUnit concentrationUnit;
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@XmlElement(name = "Type")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToOne(fetch = FetchType.LAZY)
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private OrderedTerm qualityTerm;
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@XmlElement (name = "QualityCheckDate", type= String.class)
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@XmlJavaTypeAdapter(DateTimeAdapter.class)
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@Type(type="dateTimeUserType")
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@Basic(fetch = FetchType.LAZY)
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@Field(analyze = Analyze.NO)
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@FieldBridge(impl = DateTimeBridge.class)
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@Audited
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private DateTime qualityCheckDate;
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// ******************* CONSTRUCTOR *************************/
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/**
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* Constructor
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*/
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protected DnaQuality() {}
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//************ GETTER / SETTER **********************************/
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public String getPurificationMethod() {
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return purificationMethod;
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}
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public void setPurificationMethod(String purificationMethod) {
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this.purificationMethod = purificationMethod;
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}
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public Double getRatioOfAbsorbance260_230() {
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return ratioOfAbsorbance260_230;
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}
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public void setRatioOfAbsorbance260_230(Double ratioOfAbsorbance260_230) {
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this.ratioOfAbsorbance260_230 = ratioOfAbsorbance260_230;
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}
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public Double getRatioOfAbsorbance260_280() {
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return ratioOfAbsorbance260_280;
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}
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public void setRatioOfAbsorbance260_280(Double ratioOfAbsorbance260_280) {
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this.ratioOfAbsorbance260_280 = ratioOfAbsorbance260_280;
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}
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public Double getConcentration() {
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return concentration;
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}
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public void setConcentration(Double concentration) {
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this.concentration = concentration;
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}
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public MeasurementUnit getConcentrationUnit() {
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return concentrationUnit;
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}
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public void setConcentrationUnit(MeasurementUnit concentrationUnit) {
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this.concentrationUnit = concentrationUnit;
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}
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public DateTime getQualityCheckDate() {
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return qualityCheckDate;
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}
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public void setQualityCheckDate(DateTime qualityCheckDate) {
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this.qualityCheckDate = qualityCheckDate;
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}
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public OrderedTerm getQualityTerm() {
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return qualityTerm;
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}
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public void setQualityTerm(OrderedTerm qualityTerm) {
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this.qualityTerm = qualityTerm;
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}
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//*********** CLONE **********************************/
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/**
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* Clones <i>this</i> dna quality. This is a shortcut that enables to
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* create a new instance that differs only slightly from <i>this</i> dna quality
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* by modifying only some of the attributes.<BR>
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* @throws CloneNotSupportedException
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*
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* @see Specimen#clone()
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* @see DerivedUnit#clone()
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* @see java.lang.Object#clone()
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*/
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@Override
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public DnaQuality clone() {
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try {
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DnaQuality result = (DnaQuality)super.clone();
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//purification method ??
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//no changes to: rationXXX, concentration, qualityCheckDate, qualityTerm,
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return result;
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} catch (CloneNotSupportedException e) {
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throw new RuntimeException(e); //may not occur as Clonable is implemented
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}
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}
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}
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