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.OneToMany;
  19 import javax.persistence.Transient;
  20 import javax.validation.constraints.NotNull;
  21 import javax.xml.bind.annotation.XmlAccessType;
  22 import javax.xml.bind.annotation.XmlAccessorType;
  23 import javax.xml.bind.annotation.XmlElement;
  24 import javax.xml.bind.annotation.XmlElementWrapper;
  25 import javax.xml.bind.annotation.XmlIDREF;
  26 import javax.xml.bind.annotation.XmlRootElement;
  27 import javax.xml.bind.annotation.XmlSchemaType;
  28 import javax.xml.bind.annotation.XmlType;
  29
  30 import org.apache.log4j.Logger;
  31 import org.hibernate.annotations.Cascade;
  32 import org.hibernate.annotations.CascadeType;
  33 import org.hibernate.envers.Audited;
  34 import org.hibernate.search.annotations.ContainedIn;
  35 import org.hibernate.search.annotations.Indexed;
  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  * @created 08-Nov-2007
  51  */
  52 @XmlAccessorType(XmlAccessType.FIELD)
  53 @XmlType(name = "DnaSample", propOrder = {
  54     "sequences",
  55     "amplifications"
  56 })
  57 @XmlRootElement(name = "DnaSample")
  58 @Entity
  59 @Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
  60 @Audited
  61 public class DnaSample extends DerivedUnit implements Cloneable {
  62         private static final long serialVersionUID = -2978411330023671805L;
  63         @SuppressWarnings("unused")
  64         private static final Logger logger = Logger.getLogger(DnaSample.class);
  65
  66 // ****************** FACTORY METHOD *****************/
  67
  68         /**
  69          * Factory method
  70          * @return
  71          */
  72         public static DnaSample NewInstance(){
  73                 return new DnaSample();
  74         }
  75
  76 // ************** ATTRIBUTES ****************************/
  77
  78 //      @XmlElement(name = "BankNumber")
  79 //      private String bankNumber;
  80
  81         @XmlElementWrapper(name = "Sequences")
  82         @XmlElement(name = "sequence")
  83     @XmlIDREF
  84     @XmlSchemaType(name = "IDREF")
  85     @OneToMany(fetch = FetchType.LAZY)
  86         @Cascade(CascadeType.SAVE_UPDATE)
  87     private Set<Sequence> sequences = new HashSet<Sequence>();
  88
  89
  90         @XmlElementWrapper(name = "Amplifications")
  91         @XmlElement(name = "Amplification")
  92         @OneToMany(mappedBy="dnaSample", fetch = FetchType.LAZY)
  93         @Cascade( { CascadeType.SAVE_UPDATE, CascadeType.DELETE})
  94     @ContainedIn
  95     @NotNull
  96         private Set<Amplification> amplifications = new HashSet<Amplification>();
  97
  98
  99 // ******************* CONSTRUCTOR *************************/
 100
 101         /**
 102          * Constructor
 103          */
 104         private DnaSample() {
 105                 super(SpecimenOrObservationType.DnaSample);
 106                 this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<DerivedUnit>();
 107         }
 108
 109 //************ GETTER / SETTER  **********************************/
 110
 111         //sequencings
 112         public Set<Sequence> getSequences() {
 113                 return sequences;
 114         }
 115
 116         public void addSequence(Sequence sequence) {
 117                 if (sequence.getDnaSample() != null){
 118                         sequence.getDnaSample().removeSequence(sequence);
 119                 }
 120                 this.sequences.add(sequence);
 121                 sequence.setDnaSample(this);
 122         }
 123
 124         public void removeSequence(Sequence sequence) {
 125                 sequence.setDnaSample(null);
 126                 this.sequences.remove(sequence);
 127         }
 128
 129
 130
 131         //amplifications
 132         public Set<Amplification> getAmplifications() {
 133                 return amplifications;
 134         }
 135
 136         public void addAmplification(Amplification amplification) {
 137                 this.amplifications.add(amplification);
 138                 amplification.setDnaSample(this);
 139         }
 140
 141         public void removeAmplification(Amplification amplification) {
 142                 this.amplifications.remove(amplification);
 143         }
 144
 145 // ************* Convenience Getter / Setter ************/
 146
 147         @Transient
 148         public Collection getStoredAt(){
 149                 return this.getCollection();
 150         }
 151
 152         public void setStoredAt(Collection storedAt){
 153                 this.setCollection(storedAt);
 154         }
 155
 156         @Transient
 157         public Set<SpecimenOrObservationBase> getExtractedFrom(){
 158                 return getOriginals();
 159         }
 160
 161         @Transient
 162         public String getBankNumber(){
 163                 return this.getCatalogNumber();
 164         }
 165
 166         public void setBankNumber(String bankNumber){
 167                 this.setCatalogNumber(bankNumber);
 168         }
 169
 170
 171 //*********** CLONE **********************************/
 172
 173         /**
 174          * Clones <i>this</i> dna sample. This is a shortcut that enables to
 175          * create a new instance that differs only slightly from <i>this</i> dna sample
 176          * by modifying only some of the attributes.<BR>
 177          * This method overrides the clone method from {@link Specimen Specimen}.
 178          * @throws CloneNotSupportedException
 179          *
 180          * @see Specimen#clone()
 181          * @see DerivedUnit#clone()
 182          * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
 183          * @see java.lang.Object#clone()
 184          */
 185         @Override
 186         public DnaSample clone() {
 187                 DnaSample result = (DnaSample)super.clone();
 188                 //sequenceSet
 189                 result.sequences = new HashSet<Sequence>();
 190                 for(Sequence sequence : this.sequences) {
 191                         result.addSequence(sequence);
 192                 }
 193                 //no changes to: bankNumber
 194                 return result;
 195         }
 196 }