cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.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 java.util.HashSet;
  14 import java.util.Set;
  15
  16 import javax.persistence.Entity;
  17 import javax.persistence.FetchType;
  18 import javax.persistence.ManyToOne;
  19 import javax.persistence.OneToMany;
  20 import javax.persistence.Transient;
  21 import javax.validation.constraints.NotNull;
  22 import javax.xml.bind.annotation.XmlAccessType;
  23 import javax.xml.bind.annotation.XmlAccessorType;
  24 import javax.xml.bind.annotation.XmlElement;
  25 import javax.xml.bind.annotation.XmlElementWrapper;
  26 import javax.xml.bind.annotation.XmlIDREF;
  27 import javax.xml.bind.annotation.XmlRootElement;
  28 import javax.xml.bind.annotation.XmlSchemaType;
  29 import javax.xml.bind.annotation.XmlType;
  30
  31 import org.apache.log4j.Logger;
  32 import org.hibernate.annotations.Cascade;
  33 import org.hibernate.annotations.CascadeType;
  34 import org.hibernate.envers.Audited;
  35 import org.hibernate.search.annotations.ContainedIn;
  36 import org.hibernate.search.annotations.Indexed;
  37 import org.hibernate.search.annotations.IndexedEmbedded;
  38
  39 import eu.etaxonomy.cdm.model.occurrence.Collection;
  40 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  41 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  42 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  43 import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;
  44
  45 /**
  46  * A DNA Sample is the extracted DNA of a given tissue sample. It may be stored in
  47  * a DNA Bank and should then be handled as a collection unit.
  48  * DNA Sample are used to determine their {@link Sequence DNA sequences}
  49  * starting with a process called {@link Amplification amplification}.
  50  *
  51  * @author m.doering
  52  * @created 08-Nov-2007
  53  */
  54 @XmlAccessorType(XmlAccessType.FIELD)
  55 @XmlType(name = "DnaSample", propOrder = {
  56     "sequences",
  57     "amplifications",
  58     "dnaQuality"
  59 })
  60 @XmlRootElement(name = "DnaSample")
  61 @Entity
  62 @Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
  63 @Audited
  64 public class DnaSample extends DerivedUnit implements Cloneable {
  65         private static final long serialVersionUID = -2978411330023671805L;
  66         @SuppressWarnings("unused")
  67         private static final Logger logger = Logger.getLogger(DnaSample.class);
  68
  69 // ****************** FACTORY METHOD *****************/
  70
  71         /**
  72          * Factory method
  73          * @return
  74          */
  75         public static DnaSample NewInstance(){
  76                 return new DnaSample();
  77         }
  78
  79
  80 // ************** ATTRIBUTES ****************************/
  81
  82 //      @XmlElement(name = "BankNumber")
  83 //      private String bankNumber;
  84
  85         @XmlElementWrapper(name = "Sequences")
  86         @XmlElement(name = "sequence")
  87     @XmlIDREF
  88     @XmlSchemaType(name = "IDREF")
  89     @OneToMany(fetch = FetchType.LAZY)
  90         @Cascade(CascadeType.SAVE_UPDATE)
  91     private Set<Sequence> sequences = new HashSet<Sequence>();
  92
  93
  94         @XmlElementWrapper(name = "Amplifications")
  95         @XmlElement(name = "Amplification")
  96         @OneToMany(mappedBy="dnaSample", fetch = FetchType.LAZY)
  97         @Cascade( { CascadeType.SAVE_UPDATE, CascadeType.DELETE})
  98     @ContainedIn
  99     @NotNull
 100         private Set<Amplification> amplifications = new HashSet<Amplification>();
 101
 102     @XmlElement(name = "DnaQuality", required = true)
 103     @XmlIDREF
 104     @XmlSchemaType(name = "IDREF")
 105     @ManyToOne(fetch = FetchType.LAZY)
 106     @IndexedEmbedded
 107     @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
 108     private DnaQuality dnaQuality;
 109
 110
 111 // ******************* CONSTRUCTOR *************************/
 112
 113         /**
 114          * Constructor
 115          */
 116         protected DnaSample() {  //protected for Javassist, otherwise private
 117                 super(SpecimenOrObservationType.DnaSample);
 118                 this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<DerivedUnit>();
 119         }
 120
 121 //************ GETTER / SETTER  **********************************/
 122
 123         //sequencings
 124         public Set<Sequence> getSequences() {
 125                 return sequences;
 126         }
 127
 128         public void addSequence(Sequence sequence) {
 129                 if (sequence.getDnaSample() != null){
 130                         sequence.getDnaSample().removeSequence(sequence);
 131                 }
 132                 this.sequences.add(sequence);
 133                 sequence.setDnaSample(this);
 134         }
 135
 136         public void removeSequence(Sequence sequence) {
 137                 sequence.setDnaSample(null);
 138                 this.sequences.remove(sequence);
 139         }
 140
 141
 142
 143         //amplifications
 144         public Set<Amplification> getAmplifications() {
 145                 return amplifications;
 146         }
 147
 148         public void addAmplification(Amplification amplification) {
 149                 this.amplifications.add(amplification);
 150                 amplification.setDnaSample(this);
 151         }
 152
 153         public void removeAmplification(Amplification amplification) {
 154                 this.amplifications.remove(amplification);
 155         }
 156
 157         public DnaQuality getDnaQuality() {
 158                 return dnaQuality;
 159         }
 160
 161         public void setDnaQuality(DnaQuality dnaQuality) {
 162                 this.dnaQuality = dnaQuality;
 163         }
 164
 165
 166 // ************* Convenience Getter / Setter ************/
 167
 168
 169         @Transient
 170         public Collection getStoredAt(){
 171                 return this.getCollection();
 172         }
 173
 174         public void setStoredAt(Collection storedAt){
 175                 this.setCollection(storedAt);
 176         }
 177
 178         @Transient
 179         public Set<SpecimenOrObservationBase> getExtractedFrom(){
 180                 return getOriginals();
 181         }
 182
 183         @Transient
 184         public String getBankNumber(){
 185                 return this.getCatalogNumber();
 186         }
 187
 188         public void setBankNumber(String bankNumber){
 189                 this.setCatalogNumber(bankNumber);
 190         }
 191
 192
 193 //*********** CLONE **********************************/
 194
 195         /**
 196          * Clones <i>this</i> dna sample. This is a shortcut that enables to
 197          * create a new instance that differs only slightly from <i>this</i> dna sample
 198          * by modifying only some of the attributes.<BR>
 199          * This method overrides the clone method from {@link Specimen Specimen}.
 200          * @throws CloneNotSupportedException
 201          *
 202          * @see Specimen#clone()
 203          * @see DerivedUnit#clone()
 204          * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
 205          * @see java.lang.Object#clone()
 206          */
 207         @Override
 208         public DnaSample clone() {
 209                 DnaSample result = (DnaSample)super.clone();
 210                 //sequenceSet
 211                 result.sequences = new HashSet<Sequence>();
 212                 for(Sequence sequence : this.sequences) {
 213                         result.addSequence((Sequence)sequence.clone());
 214                 }
 215                 //no changes to: bankNumber
 216                 return result;
 217         }
 218 }