cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/HomotypicalGroup.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 import java.util.ArrayList;
  13 import java.util.HashSet;
  14 import java.util.List;
  15 import java.util.Set;
  16
  17 import javax.persistence.Entity;
  18 import javax.persistence.FetchType;
  19 import javax.persistence.OneToMany;
  20 import javax.persistence.Transient;
  21
  22 import org.apache.log4j.Logger;
  23 import org.hibernate.annotations.Cascade;
  24 import org.hibernate.annotations.CascadeType;
  25
  26 import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
  27 import eu.etaxonomy.cdm.model.occurrence.Specimen;
  28 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  29 import eu.etaxonomy.cdm.model.taxon.Synonym;
  30
  31
  32 /**
  33  * A homotypical group represents all names that share the same type specimens.
  34  * This also includes supergeneric names like genera or families which usually have a name type designation
  35  * that finally (a name type designation can also point to another supergeneric name) points to a species name,
  36  * which in turn has a (set of) physical type specimen(s).
  37  * @author m.doering
  38  *
  39  */
  40 @Entity
  41 public class HomotypicalGroup extends AnnotatableEntity {
  42         static Logger logger = Logger.getLogger(HomotypicalGroup.class);
  43
  44         protected Set<TaxonNameBase> typifiedNames = new HashSet();
  45         protected Set<SpecimenTypeDesignation> typeDesignations = new HashSet();
  46
  47         public static HomotypicalGroup NewInstance(){
  48                 return new HomotypicalGroup();
  49         }
  50
  51
  52         public HomotypicalGroup() {
  53                 super();
  54         }
  55
  56
  57         @OneToMany(mappedBy="homotypicalGroup", fetch=FetchType.EAGER)
  58         public Set<TaxonNameBase> getTypifiedNames() {
  59                 return typifiedNames;
  60         }
  61         protected void setTypifiedNames(Set<TaxonNameBase> typifiedNames) {
  62                 this.typifiedNames = typifiedNames;
  63         }
  64         public void addTypifiedName(TaxonNameBase typifiedName) {
  65                 typifiedName.setHomotypicalGroup(this);
  66         }
  67         public void removeTypifiedName(TaxonNameBase typifiedName) {
  68                 typifiedName.setHomotypicalGroup(null);
  69         }
  70
  71
  72         @OneToMany
  73         @Cascade({CascadeType.SAVE_UPDATE})
  74         public Set<SpecimenTypeDesignation> getTypeDesignations() {
  75                 return typeDesignations;
  76         }
  77         protected void setTypeDesignations(Set<SpecimenTypeDesignation> typeDesignations) {
  78                 this.typeDesignations = typeDesignations;
  79         }
  80         public void addTypeDesignation(SpecimenTypeDesignation typeDesignation) {
  81                 typeDesignation.setHomotypicalGroup(this);
  82         }
  83         public void removeTypeDesignation(SpecimenTypeDesignation typeDesignation) {
  84                 typeDesignation.setHomotypicalGroup(null);
  85         }
  86         public void addTypeDesignation(Specimen typeSpecimen, TypeDesignationStatus status, ReferenceBase citation, String citationMicroReference, String originalNameString) {
  87                 SpecimenTypeDesignation td = new SpecimenTypeDesignation(this, typeSpecimen, status, citation, citationMicroReference, originalNameString);
  88                 td.setHomotypicalGroup(this);
  89         }
  90
  91         /**
  92          * Retrieves the synonyms of reference sec that are part of this homotypical group.
  93          * If other names are part of this group that are not considered synonyms in the respective sec-reference,
  94          * then they will not be included in the resultset.
  95          * @param sec
  96          * @return
  97          */
  98         @Transient
  99         public List<Synonym> getSynonymsInGroup(ReferenceBase sec){
 100                 List<Synonym> result = new ArrayList();
 101                 for (TaxonNameBase<TaxonNameBase> n:this.getTypifiedNames()){
 102                         for (Synonym s:n.getSynonyms()){
 103                                 if ( (s.getSec() == null && sec == null) ||
 104                                                 s.getSec().equals(sec)){
 105                                         result.add(s);
 106                                 }
 107                         }
 108                 }
 109                 // TODO: sort result list according to date first published, see nomenclatural reference
 110                 return result;
 111         }
 112 }