cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaQuality.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.model.molecular;
  11
  12
  13 import javax.persistence.Entity;
  14 import javax.persistence.FetchType;
  15 import javax.persistence.ManyToOne;
  16 import javax.persistence.Transient;
  17 import javax.xml.bind.annotation.XmlAccessType;
  18 import javax.xml.bind.annotation.XmlAccessorType;
  19 import javax.xml.bind.annotation.XmlElement;
  20 import javax.xml.bind.annotation.XmlIDREF;
  21 import javax.xml.bind.annotation.XmlRootElement;
  22 import javax.xml.bind.annotation.XmlSchemaType;
  23 import javax.xml.bind.annotation.XmlTransient;
  24 import javax.xml.bind.annotation.XmlType;
  25
  26 import org.apache.log4j.Logger;
  27 import org.hibernate.envers.Audited;
  28 import org.joda.time.DateTime;
  29
  30 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  31 import eu.etaxonomy.cdm.model.common.VersionableEntity;
  32 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  33 import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;
  34 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  35
  36 /**
  37  * A DNA Quality describes the quality of a {@link SpecimenOrObservationType#DnaSample}
  38  *
  39  * @author a.mueller
  40  * @created 18-Oct-2014
  41  */
  42 @XmlAccessorType(XmlAccessType.FIELD)
  43 @XmlType(name = "DnaQuality", propOrder = {
  44     "ratioOfAbsorbance230_260",
  45     "ratioOfAbsorbance260_280",
  46     "concentration",
  47     "qualityTerm"
  48 //    ,"purificationMethod"
  49 //    ,"dateQualityCheck"
  50 //    ,"dateNanoDrop"
  51
  52 })
  53 @XmlRootElement(name = "DnaQuality")
  54 @Entity
  55 //@Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
  56 @Audited
  57 public class DnaQuality extends VersionableEntity implements Cloneable {
  58         private static final long serialVersionUID = -8829069331010573654L;
  59         @SuppressWarnings("unused")
  60         private static final Logger logger = Logger.getLogger(DnaQuality.class);
  61
  62 // ****************** FACTORY METHOD *****************/
  63
  64         /**
  65          * Factory method
  66          * @return
  67          */
  68         public static DnaQuality NewInstance(){
  69                 return new DnaQuality();
  70         }
  71
  72 // ************** ATTRIBUTES ****************************/
  73
  74         private Double ratioOfAbsorbance230_260;
  75
  76         private Double ratioOfAbsorbance260_280;
  77
  78         private Double concentration;
  79
  80         @XmlElement(name = "Type")
  81     @XmlIDREF
  82     @XmlSchemaType(name = "IDREF")
  83     @ManyToOne(fetch = FetchType.LAZY)
  84         private DefinedTerm qualityTerm;
  85
  86     //TODO
  87     @XmlTransient
  88     @Transient
  89     private MaterialOrMethodEvent purificationMethod;
  90
  91   //TODO
  92     @XmlTransient
  93     @Transient
  94     private DateTime dateQualityCheck;
  95
  96   //TODO
  97     @XmlTransient
  98     @Transient
  99     private DateTime dateNanoDrop;
 100
 101
 102 // ******************* CONSTRUCTOR *************************/
 103
 104         /**
 105          * Constructor
 106          */
 107         private DnaQuality() {}
 108
 109 //************ GETTER / SETTER  **********************************/
 110
 111         public Double getRatioOfAbsorbance230_260() {
 112                 return ratioOfAbsorbance230_260;
 113         }
 114
 115         public void setRatioOfAbsorbance230_260(Double ratioOfAbsorbance230_260) {
 116                 this.ratioOfAbsorbance230_260 = ratioOfAbsorbance230_260;
 117         }
 118
 119         public Double getRatioOfAbsorbance260_280() {
 120                 return ratioOfAbsorbance260_280;
 121         }
 122
 123         public void setRatioOfAbsorbance260_280(Double ratioOfAbsorbance260_280) {
 124                 this.ratioOfAbsorbance260_280 = ratioOfAbsorbance260_280;
 125         }
 126
 127
 128     public Double getConcentration() {
 129                 return concentration;
 130         }
 131
 132         public void setConcentration(Double concentration) {
 133                 this.concentration = concentration;
 134         }
 135
 136         public DefinedTerm getQualityTerm() {
 137                 return qualityTerm;
 138         }
 139
 140         public void setQualityTerm(DefinedTerm qualityTerm) {
 141                 this.qualityTerm = qualityTerm;
 142         }
 143
 144
 145
 146 //*********** CLONE **********************************/
 147
 148         /**
 149          * Clones <i>this</i> dna quality. This is a shortcut that enables to
 150          * create a new instance that differs only slightly from <i>this</i> dna quality
 151          * by modifying only some of the attributes.<BR>
 152          * @throws CloneNotSupportedException
 153          *
 154          * @see Specimen#clone()
 155          * @see DerivedUnit#clone()
 156          * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
 157          * @see java.lang.Object#clone()
 158          */
 159         @Override
 160         public DnaQuality clone() {
 161                 try {
 162                         DnaQuality result = (DnaQuality)super.clone();
 163
 164                         //purification method ??
 165
 166                         //no changes to: rationXXX, concentration, dates, qualityTerm,
 167                         return result;
 168
 169                 } catch (CloneNotSupportedException e) {
 170                         throw new RuntimeException(e);  //may not occur as Clonable is implemented
 171                 }
 172         }
 173 }