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.IndexedEmbedded;
  36
  37 import eu.etaxonomy.cdm.model.occurrence.Collection;
  38 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  39 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  40 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  41 import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;
  42
  43 /**
  44  * A DNA Sample is the extracted DNA of a given tissue sample. It may be stored in
  45  * a DNA Bank and should then be handled as a collection unit.
  46  * DNA Sample are used to determine their {@link Sequence DNA sequences}
  47  * starting with a process called {@link Amplification amplification}.
  48  *
  49  * @author m.doering
  50  * @since 08-Nov-2007
  51  */
  52 @XmlAccessorType(XmlAccessType.FIELD)
  53 @XmlType(name = "DnaSample", propOrder = {
  54     "sequences",
  55     "amplificationResults",
  56     "dnaQuality"
  57 })
  58 @XmlRootElement(name = "DnaSample")
  59 @Entity
  60 //@Indexed disabled to reduce clutter in indexes, since this type is not used by any search
  61 //@Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
  62 @Audited
  63 public class DnaSample extends DerivedUnit implements Cloneable {
  64         private static final long serialVersionUID = -2978411330023671805L;
  65         @SuppressWarnings("unused")
  66         private static final Logger logger = Logger.getLogger(DnaSample.class);
  67
  68 // ****************** FACTORY METHOD *****************/
  69
  70         /**
  71          * Factory method
  72          * @return
  73          */
  74         public static DnaSample NewInstance(){
  75                 return new DnaSample();
  76         }
  77
  78
  79 // ************** ATTRIBUTES ****************************/
  80
  81 //      @XmlElement(name = "BankNumber")
  82 //      private String bankNumber;
  83
  84         @XmlElementWrapper(name = "Sequences")
  85         @XmlElement(name = "sequence")
  86     @XmlIDREF
  87     @XmlSchemaType(name = "IDREF")
  88     @OneToMany(mappedBy="dnaSample", fetch = FetchType.LAZY)
  89         @Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
  90     private Set<Sequence> sequences = new HashSet<Sequence>();
  91
  92
  93         @XmlElementWrapper(name = "AmplificationResults")
  94         @XmlElement(name = "AmplificationResult")
  95         @OneToMany(mappedBy="dnaSample", fetch = FetchType.LAZY)
  96         @Cascade( { CascadeType.SAVE_UPDATE,CascadeType.MERGE, CascadeType.DELETE})
  97     @NotNull
  98         private final Set<AmplificationResult> amplificationResults = new HashSet<AmplificationResult>();
  99
 100     @XmlElement(name = "DnaQuality", required = true)
 101     @XmlIDREF
 102     @XmlSchemaType(name = "IDREF")
 103     @ManyToOne(fetch = FetchType.LAZY)
 104     @IndexedEmbedded
 105     @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
 106     private DnaQuality dnaQuality;
 107
 108
 109 // ******************* CONSTRUCTOR *************************/
 110
 111         /**
 112          * Constructor
 113          */
 114         protected DnaSample() {  //protected for Javassist, otherwise private
 115                 super(SpecimenOrObservationType.DnaSample);
 116                 this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<DerivedUnit>();
 117         }
 118
 119 //************ GETTER / SETTER  **********************************/
 120
 121         //sequencings
 122         public Set<Sequence> getSequences() {
 123                 return sequences;
 124         }
 125
 126         public void addSequence(Sequence sequence) {
 127                 if (sequence.getDnaSample() != null){
 128                         sequence.getDnaSample().removeSequence(sequence);
 129                 }
 130                 this.sequences.add(sequence);
 131                 sequence.setDnaSample(this);
 132         }
 133
 134         public void removeSequence(Sequence sequence) {
 135                 sequence.setDnaSample(null);
 136                 this.sequences.remove(sequence);
 137         }
 138
 139
 140
 141         //amplifications
 142         public Set<AmplificationResult> getAmplificationResults() {
 143                 return amplificationResults;
 144         }
 145
 146         public void addAmplificationResult(AmplificationResult amplificationResult) {
 147                 this.amplificationResults.add(amplificationResult);
 148                 amplificationResult.setDnaSample(this);
 149         }
 150
 151         public void removeAmplificationResult(AmplificationResult amplificationResult) {
 152                 this.amplificationResults.remove(amplificationResult);
 153                 amplificationResult.setDnaSample(null);
 154         }
 155
 156
 157         public DnaQuality getDnaQuality() {
 158                 return dnaQuality;
 159         }
 160         public void setDnaQuality(DnaQuality dnaQuality) {
 161                 this.dnaQuality = dnaQuality;
 162         }
 163
 164
 165 // ************* Convenience Getter / Setter ************/
 166
 167
 168         @Transient
 169         public Collection getStoredAt(){
 170                 return this.getCollection();
 171         }
 172
 173         public void setStoredAt(Collection storedAt){
 174                 this.setCollection(storedAt);
 175         }
 176
 177         @Transient
 178         public Set<SpecimenOrObservationBase> getExtractedFrom(){
 179                 return getOriginals();
 180         }
 181
 182         @Transient
 183         public String getBankNumber(){
 184                 return this.getCatalogNumber();
 185         }
 186
 187         public void setBankNumber(String bankNumber){
 188                 this.setCatalogNumber(bankNumber);
 189         }
 190
 191
 192 //*********** CLONE **********************************/
 193
 194         /**
 195          * Clones <i>this</i> dna sample. This is a shortcut that enables to
 196          * create a new instance that differs only slightly from <i>this</i> dna sample
 197          * by modifying only some of the attributes.<BR>
 198          * This method overrides the clone method from {@link Specimen Specimen}.
 199          * @throws CloneNotSupportedException
 200          *
 201          * @see Specimen#clone()
 202          * @see DerivedUnit#clone()
 203          * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
 204          * @see java.lang.Object#clone()
 205          */
 206         @Override
 207         public DnaSample clone() {
 208                 DnaSample result = (DnaSample)super.clone();
 209                 //sequenceSet
 210                 result.sequences = new HashSet<Sequence>();
 211                 for(Sequence sequence : this.sequences) {
 212                         result.addSequence((Sequence)sequence.clone());
 213                 }
 214                 //no changes to: bankNumber
 215                 return result;
 216         }
 217 }