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.XmlType;
  24 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
  25
  26 import org.apache.log4j.Logger;
  27 import org.hibernate.annotations.Type;
  28 import org.hibernate.envers.Audited;
  29 import org.hibernate.search.annotations.Analyze;
  30 import org.hibernate.search.annotations.Field;
  31 import org.hibernate.search.annotations.FieldBridge;
  32 import org.joda.time.DateTime;
  33
  34 import eu.etaxonomy.cdm.hibernate.search.DateTimeBridge;
  35 import eu.etaxonomy.cdm.jaxb.DateTimeAdapter;
  36 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  37 import eu.etaxonomy.cdm.model.common.VersionableEntity;
  38 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
  39 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  40 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  41
  42 /**
  43  * A DNA Quality describes the quality of a {@link SpecimenOrObservationType#DnaSample}
  44  *
  45  * @author a.mueller
  46  * @created 18-Oct-2014
  47  */
  48 @XmlAccessorType(XmlAccessType.FIELD)
  49 @XmlType(name = "DnaQuality", propOrder = {
  50         "purificationMethod",
  51         "ratioOfAbsorbance260_230",
  52     "ratioOfAbsorbance260_280",
  53     "concentration",
  54     "concentrationUnit",
  55     "qualityTerm",
  56     "qualityCheckDate"
  57 })
  58 @XmlRootElement(name = "DnaQuality")
  59 @Entity
  60 //@Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
  61 @Audited
  62 public class DnaQuality extends VersionableEntity implements Cloneable {
  63         private static final long serialVersionUID = -8829069331010573654L;
  64         @SuppressWarnings("unused")
  65         private static final Logger logger = Logger.getLogger(DnaQuality.class);
  66
  67 // ****************** FACTORY METHOD *****************/
  68
  69         /**
  70          * Factory method
  71          * @return
  72          */
  73         public static DnaQuality NewInstance(){
  74                 return new DnaQuality();
  75         }
  76
  77 // ************** ATTRIBUTES ****************************/
  78
  79     //TODO
  80 //    @XmlTransient
  81 //    @Transient
  82 //    private MaterialOrMethodEvent purificationMethod;
  83     private String purificationMethod;
  84
  85
  86         private Double ratioOfAbsorbance260_230;
  87
  88         private Double ratioOfAbsorbance260_280;
  89
  90         private Double concentration;
  91
  92         @XmlElement(name = "Type")
  93     @XmlIDREF
  94     @XmlSchemaType(name = "IDREF")
  95     @ManyToOne(fetch = FetchType.LAZY)
  96         private MeasurementUnit concentrationUnit;
  97
  98
  99         @XmlElement(name = "Type")
 100     @XmlIDREF
 101     @XmlSchemaType(name = "IDREF")
 102     @ManyToOne(fetch = FetchType.LAZY)
 103         private DefinedTerm qualityTerm;
 104
 105     @XmlElement (name = "QualityCheckDate", type= String.class)
 106     @XmlJavaTypeAdapter(DateTimeAdapter.class)
 107     @Type(type="dateTimeUserType")
 108     @Basic(fetch = FetchType.LAZY)
 109     @Field(analyze = Analyze.NO)
 110     @FieldBridge(impl = DateTimeBridge.class)
 111     @Audited
 112     private DateTime qualityCheckDate;
 113
 114
 115 // ******************* CONSTRUCTOR *************************/
 116
 117         /**
 118          * Constructor
 119          */
 120         private DnaQuality() {}
 121
 122 //************ GETTER / SETTER  **********************************/
 123
 124
 125         public String getPurificationMethod() {
 126                 return purificationMethod;
 127         }
 128
 129         public void setPurificationMethod(String purificationMethod) {
 130                 this.purificationMethod = purificationMethod;
 131         }
 132
 133         public Double getRatioOfAbsorbance260_230() {
 134                 return ratioOfAbsorbance260_230;
 135         }
 136
 137         public void setRatioOfAbsorbance260_230(Double ratioOfAbsorbance260_230) {
 138                 this.ratioOfAbsorbance260_230 = ratioOfAbsorbance260_230;
 139         }
 140
 141         public Double getRatioOfAbsorbance260_280() {
 142                 return ratioOfAbsorbance260_280;
 143         }
 144
 145         public void setRatioOfAbsorbance260_280(Double ratioOfAbsorbance260_280) {
 146                 this.ratioOfAbsorbance260_280 = ratioOfAbsorbance260_280;
 147         }
 148
 149
 150     public Double getConcentration() {
 151                 return concentration;
 152         }
 153
 154         public void setConcentration(Double concentration) {
 155                 this.concentration = concentration;
 156         }
 157
 158         public MeasurementUnit getConcentrationUnit() {
 159                 return concentrationUnit;
 160         }
 161
 162         public void setConcentrationUnit(MeasurementUnit concentrationUnit) {
 163                 this.concentrationUnit = concentrationUnit;
 164         }
 165
 166         public DateTime getQualityCheckDate() {
 167                 return qualityCheckDate;
 168         }
 169
 170         public void setQualityCheckDate(DateTime qualityCheckDate) {
 171                 this.qualityCheckDate = qualityCheckDate;
 172         }
 173
 174         public DefinedTerm getQualityTerm() {
 175                 return qualityTerm;
 176         }
 177
 178         public void setQualityTerm(DefinedTerm qualityTerm) {
 179                 this.qualityTerm = qualityTerm;
 180         }
 181
 182
 183
 184 //*********** CLONE **********************************/
 185
 186         /**
 187          * Clones <i>this</i> dna quality. This is a shortcut that enables to
 188          * create a new instance that differs only slightly from <i>this</i> dna quality
 189          * by modifying only some of the attributes.<BR>
 190          * @throws CloneNotSupportedException
 191          *
 192          * @see Specimen#clone()
 193          * @see DerivedUnit#clone()
 194          * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
 195          * @see java.lang.Object#clone()
 196          */
 197         @Override
 198         public DnaQuality clone() {
 199                 try {
 200                         DnaQuality result = (DnaQuality)super.clone();
 201
 202                         //purification method ??
 203
 204                         //no changes to: rationXXX, concentration, qualityCheckDate, qualityTerm,
 205                         return result;
 206
 207                 } catch (CloneNotSupportedException e) {
 208                         throw new RuntimeException(e);  //may not occur as Clonable is implemented
 209                 }
 210         }
 211
 212 }