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 import eu.etaxonomy.cdm.strategy.cache.INameCacheStrategy;
  31
  32
  33 /**
  34  * A homotypical group represents all taxon names that share the same type
  35  * specimens. This also includes suprageneric names like genera or families
  36  * which usually have a name type designation that finally (a name type
  37  * designation can also point to another suprageneric name) points to a species
  38  * name, which in turn has a (set of) physical type specimen(s). This class
  39  * allows to define the type designation only once for the homotypical group
  40  * instead of defining a type designation for each one of the taxon names
  41  * subsumed under one homotypical group.
  42  *
  43  * @author m.doering
  44  *
  45  */
  46 @Entity
  47 public class HomotypicalGroup extends AnnotatableEntity {
  48         static Logger logger = Logger.getLogger(HomotypicalGroup.class);
  49
  50         protected Set<TaxonNameBase> typifiedNames = new HashSet();
  51         protected Set<SpecimenTypeDesignation> typeDesignations = new HashSet();
  52
  53         public static HomotypicalGroup NewInstance(){
  54                 return new HomotypicalGroup();
  55         }
  56
  57
  58         public HomotypicalGroup() {
  59                 super();
  60         }
  61
  62
  63         @OneToMany(mappedBy="homotypicalGroup", fetch=FetchType.EAGER)
  64         public Set<TaxonNameBase> getTypifiedNames() {
  65                 return typifiedNames;
  66         }
  67         protected void setTypifiedNames(Set<TaxonNameBase> typifiedNames) {
  68                 this.typifiedNames = typifiedNames;
  69         }
  70         public void addTypifiedName(TaxonNameBase typifiedName) {
  71                 if (typifiedName != null){
  72                         typifiedName.setHomotypicalGroup(this);
  73                         typifiedNames.add(typifiedName);
  74                 }
  75         }
  76         public void removeTypifiedName(TaxonNameBase typifiedName) {
  77                 typifiedName.setHomotypicalGroup(null);
  78                 typifiedNames.remove(typifiedName);
  79         }
  80
  81
  82         @OneToMany
  83         @Cascade({CascadeType.SAVE_UPDATE})
  84         public Set<SpecimenTypeDesignation> getTypeDesignations() {
  85                 return typeDesignations;
  86         }
  87         protected void setTypeDesignations(Set<SpecimenTypeDesignation> typeDesignations) {
  88                 this.typeDesignations = typeDesignations;
  89         }
  90         public void addTypeDesignation(SpecimenTypeDesignation typeDesignation, boolean addToAllNames) {
  91                 if (typeDesignation != null){
  92                         typeDesignation.setHomotypicalGroup(this);
  93                         typeDesignations.add(typeDesignation);
  94                 }
  95                 if (addToAllNames){
  96                         for (TaxonNameBase taxonNameBase : this.typifiedNames){
  97                                 taxonNameBase.addSpecimenTypeDesignation(typeDesignation);
  98                         }
  99                 }
 100         }
 101         public void removeTypeDesignation(SpecimenTypeDesignation typeDesignation) {
 102                 if (typeDesignation != null){
 103                         typeDesignation.setHomotypicalGroup(null);
 104                         typeDesignations.remove(typeDesignation);
 105                 }
 106                 for (TaxonNameBase taxonNameBase : this.typifiedNames){
 107                         taxonNameBase.removeSpecimenTypeDesignation(typeDesignation);
 108                 }
 109         }
 110
 111
 112         /**
 113          * Retrieves the synonyms of reference sec that are part of this homotypical group.
 114          * If other names are part of this group that are not considered synonyms in the respective sec-reference,
 115          * then they will not be included in the resultset.
 116          * @param sec
 117          * @return
 118          */
 119         @Transient
 120         public List<Synonym> getSynonymsInGroup(ReferenceBase sec){
 121                 List<Synonym> result = new ArrayList();
 122                 for (TaxonNameBase<TaxonNameBase, INameCacheStrategy> n:this.getTypifiedNames()){
 123                         for (Synonym s:n.getSynonyms()){
 124                                 if ( (s.getSec() == null && sec == null) ||
 125                                                 s.getSec().equals(sec)){
 126                                         result.add(s);
 127                                 }
 128                         }
 129                 }
 130                 // TODO: sort result list according to date first published, see nomenclatural reference
 131                 return result;
 132         }
 133 }