cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/SpecimenTypeDesignation.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.name;
  11
  12
  13 import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;
  14 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  15 import eu.etaxonomy.cdm.model.common.ReferencedEntityBase;
  16 import org.apache.log4j.Logger;
  17 import org.hibernate.annotations.Cascade;
  18 import org.hibernate.annotations.CascadeType;
  19
  20 import java.util.*;
  21
  22 import javax.persistence.*;
  23 import javax.xml.bind.annotation.XmlAccessType;
  24 import javax.xml.bind.annotation.XmlAccessorType;
  25 import javax.xml.bind.annotation.XmlElement;
  26 import javax.xml.bind.annotation.XmlElementWrapper;
  27 import javax.xml.bind.annotation.XmlIDREF;
  28 import javax.xml.bind.annotation.XmlSchemaType;
  29 import javax.xml.bind.annotation.XmlType;
  30
  31 /**
  32  * The class representing a typification of an {@link HomotypicalGroup homotypical group} by a
  33  * {@link occurrence.DerivedUnitBase specimen or a figure}. This allows to define a specimen type designation
  34  * only once for the homotypical group instead of defining a type designation
  35  * for each one of the taxon names subsumed under one homotypical group.
  36  * All {@link TaxonNameBase taxon names} which have a {@link Rank rank}
  37  * "species aggregate" or lower can only be typified by specimens.
  38  * Moreover each typification by a specimen (or by a figure) has a {@link TypeDesignationStatus status}
  39  * like "holotype" or "isotype".
  40  * <P>
  41  * This class corresponds to: <ul>
  42  * <li> NomenclaturalType according to the TDWG ontology
  43  * <li> Typification (partially) according to the TCS
  44  * <li> NomenclaturalTypeDesignation according to the ABCD schema
  45  * </ul>
  46  *
  47  * @see         NameTypeDesignation
  48  * @author      m.doering
  49  * @version 1.0
  50  * @created 08-Nov-2007 13:06:38
  51  */
  52 @XmlAccessorType(XmlAccessType.FIELD)
  53 @XmlType(name = "SpecimenTypeDesignation", propOrder = {
  54     "homotypicalGroup",
  55     "typeSpecimen",
  56     "typeStatus",
  57     "typifiedNames"
  58 })
  59 @Entity
  60 public class SpecimenTypeDesignation extends TypeDesignationBase implements ITypeDesignation {
  61
  62         private static final Logger logger = Logger.getLogger(SpecimenTypeDesignation.class);
  63
  64         @XmlElement(name = "TypeSpecimen")
  65 //      @XmlIDREF
  66 //      @XmlSchemaType(name = "IDREF")
  67         private DerivedUnitBase typeSpecimen;
  68
  69         @XmlElement(name = "TypeStatus")
  70         private TypeDesignationStatus typeStatus;
  71
  72
  73
  74
  75 //      /**
  76 //       * Creates a new specimen type designation instance
  77 //       * (including its {@link reference.ReferenceBase reference source} and eventually
  78 //       * the taxon name string originally used by this reference when establishing
  79 //       * the former designation) and adds it to the corresponding
  80 //       * {@link HomotypicalGroup#getSpecimenTypeDesignations() specimen type designation set} of the
  81 //       * {@link HomotypicalGroup homotypical group}.
  82 //       *
  83 //       * @param specimen                              the derived unit (specimen or figure) used as type
  84 //       * @param status                                the type designation status
  85 //       * @param citation                              the reference source for the new designation
  86 //       * @param citationMicroReference        the string with the details describing the exact localisation within the reference
  87 //       * @param originalNameString    the taxon name string used originally in the reference source for the new designation
  88 //       * @see                                                 #SpecimenTypeDesignation(DerivedUnitBase, TypeDesignationStatus, ReferenceBase, String, String)
  89 //       * @see                                                 HomotypicalGroup#addSpecimenTypeDesignation(SpecimenTypeDesignation, boolean)
  90 //       * @see                                                 occurrence.DerivedUnitBase
  91 //       */
  92 //      protected static SpecimenTypeDesignation NewInstance2(DerivedUnitBase specimen, TypeDesignationStatus status,
  93 //                      ReferenceBase citation, String citationMicroReference, String originalNameString){
  94 //              SpecimenTypeDesignation specTypeDesig = new SpecimenTypeDesignation(specimen, status, citation, citationMicroReference, originalNameString);
  95 //              return specTypeDesig;
  96 //      }
  97
  98
  99         // ************* CONSTRUCTORS *************/
 100         /**
 101          * Class constructor: creates a new empty specimen type designation.
 102          *
 103          * @see #SpecimenTypeDesignation(DerivedUnitBase, TypeDesignationStatus,
 104          * ReferenceBase, String, String)
 105          */
 106         protected SpecimenTypeDesignation(){
 107
 108         }
 109
 110         /**
 111          * Class constructor: creates a new specimen type designation instance
 112          * (including its {@link reference.ReferenceBase reference source} and
 113          * eventually the taxon name string originally used by this reference when
 114          * establishing the former designation) and adds it to the corresponding
 115          * {@link HomotypicalGroup#getSpecimenTypeDesignations() specimen type
 116          * designation set} of the {@link HomotypicalGroup homotypical group}.
 117          *
 118          * @param specimen                              the derived unit (specimen or figure) used
 119          *                                                              as type
 120          * @param status                                the type designation status
 121          * @param citation                              the reference source for the new designation
 122          * @param citationMicroReference        the string with the details describing
 123          *                                                              the exact localisation within the reference
 124          * @param originalNameString    the taxon name string used originally in the
 125          *                                                              reference source for the new designation
 126          * @see                                                 #SpecimenTypeDesignation()
 127          * @see                                                 HomotypicalGroup#addSpecimenTypeDesignation(SpecimenTypeDesignation, boolean)
 128          * @see                                                 occurrence.DerivedUnitBase
 129          */
 130         protected SpecimenTypeDesignation(DerivedUnitBase specimen, TypeDesignationStatus status, ReferenceBase citation, String citationMicroReference,
 131                         String originalNameString) {
 132                 super(citation, citationMicroReference, originalNameString);
 133                 this.setTypeSpecimen(specimen);
 134                 this.setTypeStatus(status);
 135         }
 136
 137
 138
 139
 140         //********* METHODS **************************************/
 141
 142
 143
 144         /**
 145          * Returns the {@link occurrence.DerivedUnitBase derived unit} (specimen or figure) that is used
 146          * in <i>this</i> specimen type designation to typify the {@link HomotypicalGroup homotypical group}.
 147          *
 148          * @see   #getHomotypicalGroup()
 149          */
 150         @ManyToOne
 151         @Cascade({CascadeType.SAVE_UPDATE})
 152         public DerivedUnitBase getTypeSpecimen(){
 153                 return this.typeSpecimen;
 154         }
 155         /**
 156          * @see  #getTypeSpecimen()
 157          */
 158         public void setTypeSpecimen(DerivedUnitBase typeSpecimen){
 159                 this.typeSpecimen = typeSpecimen;
 160         }
 161
 162         /**
 163          * Returns the {@link TypeDesignationStatus type designation status} for <i>this</i> specimen type
 164          * designation. This status describes which of the possible categories of
 165          * types like "holotype", "neotype", "syntype" or "isotype" applies to <i>this</i>
 166          * specimen type designation.
 167          */
 168         @ManyToOne
 169         public TypeDesignationStatus getTypeStatus(){
 170                 return this.typeStatus;
 171         }
 172         /**
 173          * @see  #getTypeStatus()
 174          */
 175         public void setTypeStatus(TypeDesignationStatus typeStatus){
 176                 this.typeStatus = typeStatus;
 177         }
 178
 179         /* (non-Javadoc)
 180          * @see eu.etaxonomy.cdm.model.name.ITypeDesignation#isLectoType()
 181          */
 182         /**
 183          * Returns the boolean value indicating whether <i>this</i> specimen type
 184          * designation has a "lectotype" status (true) or not (false).<BR>
 185          * A lectotype is a {@link occurrence.DerivedUnitBase specimen or illustration} designated as the
 186          * nomenclatural type, when no holotype was indicated at the time of
 187          * publication of the "type-bringing" {@link TaxonNameBase taxon name}, when the
 188          * holotype is found to belong to more than one {@link HomotypicalGroup homotypical group},
 189          * or as long as it is missing.
 190          *
 191          * @see  TypeDesignationStatus#isLectotype()
 192          * @see  TypeDesignationStatus#HOLOTYPE()
 193          */
 194         @Transient
 195         public boolean isLectoType() {
 196                 return typeStatus.isLectotype();
 197         }
 198
 199 }