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.Basic;
  14 import javax.persistence.Entity;
  15 import javax.persistence.FetchType;
  16 import javax.persistence.ManyToOne;
  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 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
  26
  27 import org.apache.log4j.Logger;
  28 import org.hibernate.annotations.Type;
  29 import org.hibernate.envers.Audited;
  30 import org.hibernate.search.annotations.Analyze;
  31 import org.hibernate.search.annotations.Field;
  32 import org.hibernate.search.annotations.FieldBridge;
  33 import org.joda.time.DateTime;
  34
  35 import eu.etaxonomy.cdm.hibernate.search.DateTimeBridge;
  36 import eu.etaxonomy.cdm.jaxb.DateTimeAdapter;
  37 import eu.etaxonomy.cdm.model.common.OrderedTerm;
  38 import eu.etaxonomy.cdm.model.common.VersionableEntity;
  39 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
  40 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  41 import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;
  42 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  43
  44 /**
  45  * A DNA Quality describes the quality of a {@link SpecimenOrObservationType#DnaSample}
  46  *
  47  * @author a.mueller
  48  * @created 18-Oct-2014
  49  */
  50 @XmlAccessorType(XmlAccessType.FIELD)
  51 @XmlType(name = "DnaQuality", propOrder = {
  52         "purificationMethod",
  53         "ratioOfAbsorbance260_230",
  54     "ratioOfAbsorbance260_280",
  55     "concentration",
  56     "concentrationUnit",
  57     "qualityTerm",
  58     "qualityCheckDate"
  59 })
  60 @XmlRootElement(name = "DnaQuality")
  61 @Entity
  62 //@Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
  63 @Audited
  64 public class DnaQuality extends VersionableEntity implements Cloneable {
  65         private static final long serialVersionUID = -8829069331010573654L;
  66         @SuppressWarnings("unused")
  67         private static final Logger logger = Logger.getLogger(DnaQuality.class);
  68
  69 // ****************** FACTORY METHOD *****************/
  70
  71         /**
  72          * Factory method
  73          * @return
  74          */
  75         public static DnaQuality NewInstance(){
  76                 return new DnaQuality();
  77         }
  78
  79 // ************** ATTRIBUTES ****************************/
  80
  81     //TODO
  82 //      @XmlElement(name = "PurificationMethod")
  83 //    @XmlIDREF
  84 //    @XmlSchemaType(name = "IDREF")
  85         @XmlTransient
  86     @ManyToOne(fetch = FetchType.LAZY)
  87         //FIXME preliminary as it is not yet decided if we will use a string or a MoME #4552
  88     private MaterialOrMethodEvent typedPurificationMethod;
  89
  90     private String purificationMethod;
  91
  92
  93         private Double ratioOfAbsorbance260_230;
  94
  95         private Double ratioOfAbsorbance260_280;
  96
  97         private Double concentration;
  98
  99         @XmlElement(name = "concentrationUnit")
 100     @XmlIDREF
 101     @XmlSchemaType(name = "IDREF")
 102     @ManyToOne(fetch = FetchType.LAZY)
 103         private MeasurementUnit concentrationUnit;
 104
 105
 106         @XmlElement(name = "Type")
 107     @XmlIDREF
 108     @XmlSchemaType(name = "IDREF")
 109     @ManyToOne(fetch = FetchType.LAZY)
 110         private OrderedTerm qualityTerm;
 111
 112     @XmlElement (name = "QualityCheckDate", type= String.class)
 113     @XmlJavaTypeAdapter(DateTimeAdapter.class)
 114     @Type(type="dateTimeUserType")
 115     @Basic(fetch = FetchType.LAZY)
 116     @Field(analyze = Analyze.NO)
 117     @FieldBridge(impl = DateTimeBridge.class)
 118     @Audited
 119     private DateTime qualityCheckDate;
 120
 121
 122 // ******************* CONSTRUCTOR *************************/
 123
 124         /**
 125          * Constructor
 126          */
 127         protected DnaQuality() {}
 128
 129 //************ GETTER / SETTER  **********************************/
 130
 131
 132         public String getPurificationMethod() {
 133                 return purificationMethod;
 134         }
 135
 136         public void setPurificationMethod(String purificationMethod) {
 137                 this.purificationMethod = purificationMethod;
 138         }
 139
 140         public Double getRatioOfAbsorbance260_230() {
 141                 return ratioOfAbsorbance260_230;
 142         }
 143
 144         public void setRatioOfAbsorbance260_230(Double ratioOfAbsorbance260_230) {
 145                 this.ratioOfAbsorbance260_230 = ratioOfAbsorbance260_230;
 146         }
 147
 148         public Double getRatioOfAbsorbance260_280() {
 149                 return ratioOfAbsorbance260_280;
 150         }
 151
 152         public void setRatioOfAbsorbance260_280(Double ratioOfAbsorbance260_280) {
 153                 this.ratioOfAbsorbance260_280 = ratioOfAbsorbance260_280;
 154         }
 155
 156
 157     public Double getConcentration() {
 158                 return concentration;
 159         }
 160
 161         public void setConcentration(Double concentration) {
 162                 this.concentration = concentration;
 163         }
 164
 165         public MeasurementUnit getConcentrationUnit() {
 166                 return concentrationUnit;
 167         }
 168
 169         public void setConcentrationUnit(MeasurementUnit concentrationUnit) {
 170                 this.concentrationUnit = concentrationUnit;
 171         }
 172
 173         public DateTime getQualityCheckDate() {
 174                 return qualityCheckDate;
 175         }
 176
 177         public void setQualityCheckDate(DateTime qualityCheckDate) {
 178                 this.qualityCheckDate = qualityCheckDate;
 179         }
 180
 181         public OrderedTerm getQualityTerm() {
 182                 return qualityTerm;
 183         }
 184
 185         public void setQualityTerm(OrderedTerm qualityTerm) {
 186                 this.qualityTerm = qualityTerm;
 187         }
 188
 189
 190
 191 //*********** CLONE **********************************/
 192
 193         /**
 194          * Clones <i>this</i> dna quality. This is a shortcut that enables to
 195          * create a new instance that differs only slightly from <i>this</i> dna quality
 196          * by modifying only some of the attributes.<BR>
 197          * @throws CloneNotSupportedException
 198          *
 199          * @see Specimen#clone()
 200          * @see DerivedUnit#clone()
 201          * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
 202          * @see java.lang.Object#clone()
 203          */
 204         @Override
 205         public DnaQuality clone() {
 206                 try {
 207                         DnaQuality result = (DnaQuality)super.clone();
 208
 209                         //purification method ??
 210
 211                         //no changes to: rationXXX, concentration, qualityCheckDate, qualityTerm,
 212                         return result;
 213
 214                 } catch (CloneNotSupportedException e) {
 215                         throw new RuntimeException(e);  //may not occur as Clonable is implemented
 216                 }
 217         }
 218
 219 }