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.xml.bind.annotation.XmlAccessType;
  21 import javax.xml.bind.annotation.XmlAccessorType;
  22 import javax.xml.bind.annotation.XmlElement;
  23 import javax.xml.bind.annotation.XmlElementWrapper;
  24 import javax.xml.bind.annotation.XmlIDREF;
  25 import javax.xml.bind.annotation.XmlRootElement;
  26 import javax.xml.bind.annotation.XmlSchemaType;
  27 import javax.xml.bind.annotation.XmlType;
  28
  29 import org.apache.log4j.Logger;
  30 import org.hibernate.envers.Audited;
  31 import org.hibernate.search.annotations.Indexed;
  32
  33 import eu.etaxonomy.cdm.model.occurrence.Collection;
  34 import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;
  35 import eu.etaxonomy.cdm.model.occurrence.Specimen;
  36 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  37 import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;
  38
  39 /**
  40  * @author m.doering
  41  * @version 1.0
  42  * @created 08-Nov-2007 13:06:22
  43  */
  44 @XmlAccessorType(XmlAccessType.FIELD)
  45 @XmlType(name = "DnaSample", propOrder = {
  46     "sequences"
  47 })
  48 @XmlRootElement(name = "DnaSample")
  49 @Entity
  50 @Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
  51 @Audited
  52 public class DnaSample extends Specimen implements Cloneable {
  53         private static final long serialVersionUID = -2978411330023671805L;
  54         private static final Logger logger = Logger.getLogger(DnaSample.class);
  55
  56         /**
  57          * Factory method
  58          * @return
  59          */
  60         public static DnaSample NewInstance(){
  61                 return new DnaSample();
  62         }
  63
  64
  65 //      @XmlElement(name = "BankNumber")
  66 //      private String bankNumber;
  67
  68         @XmlElementWrapper(name = "Sequences")
  69         @XmlElement(name = "sequence")
  70     @XmlIDREF
  71     @XmlSchemaType(name = "IDREF")
  72     @OneToMany(fetch = FetchType.LAZY)
  73         private Set<Sequence> sequences = new HashSet<Sequence>();
  74
  75
  76
  77         /**
  78          * Constructor
  79          */
  80         private DnaSample() {
  81                 super();
  82                 this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<Specimen>();
  83         }
  84
  85         public Set<Sequence> getSequences() {
  86                 return sequences;
  87         }
  88
  89         // FIXME shouldn't this be the singular? i.e. addSequence( . . . )
  90         public void addSequences(Sequence sequence) {
  91                 this.sequences.add(sequence);
  92         }
  93
  94         // FIXME shouldn't this be the singular? i.e. removeSequence( . . . )
  95         public void removeSequences(Sequence sequence) {
  96                 this.sequences.remove(sequence);
  97         }
  98
  99         @Transient
 100         public Collection getStoredAt(){
 101                 return this.getCollection();
 102         }
 103
 104         public void setStoredAt(Collection storedAt){
 105                 this.setCollection(storedAt);
 106         }
 107
 108         @Transient
 109         public Set<SpecimenOrObservationBase> getExtractedFrom(){
 110                 return getOriginals();
 111         }
 112
 113         @Transient
 114         public String getBankNumber(){
 115                 return this.getCatalogNumber();
 116         }
 117
 118         public void setBankNumber(String bankNumber){
 119                 this.setCatalogNumber(bankNumber);
 120         }
 121
 122
 123 //*********** CLONE **********************************/
 124
 125         /**
 126          * Clones <i>this</i> dna sample. This is a shortcut that enables to
 127          * create a new instance that differs only slightly from <i>this</i> dna sample
 128          * by modifying only some of the attributes.<BR>
 129          * This method overrides the clone method from {@link Specimen Specimen}.
 130          *
 131          * @see Specimen#clone()
 132          * @see DerivedUnitBase#clone()
 133          * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
 134          * @see java.lang.Object#clone()
 135          */
 136         @Override
 137         public DnaSample clone(){
 138                 DnaSample result = (DnaSample)super.clone();
 139                 //sequenceSet
 140                 result.sequences = new HashSet<Sequence>();
 141                 for(Sequence sequence : this.sequences) {
 142                         result.addSequences(sequence);
 143                 }
 144                 //no changes to: bankNumber
 145                 return result;
 146         }
 147 }