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.OneToMany;
  19 import javax.persistence.Transient;
  20
  21 import org.apache.log4j.Logger;
  22 import org.hibernate.annotations.Cascade;
  23 import org.hibernate.annotations.CascadeType;
  24
  25 import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
  26 import eu.etaxonomy.cdm.model.occurrence.Specimen;
  27 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  28 import eu.etaxonomy.cdm.model.taxon.Synonym;
  29 import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
  30 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  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 markus
  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 HomotypicalGroup() {
  48                 super();
  49         }
  50
  51
  52         @OneToMany
  53         public Set<TaxonNameBase> getTypifiedNames() {
  54                 return typifiedNames;
  55         }
  56         protected void setTypifiedNames(Set<TaxonNameBase> typifiedNames) {
  57                 this.typifiedNames = typifiedNames;
  58         }
  59         public void addTypifiedName(TaxonNameBase typifiedName) {
  60                 typifiedName.setHomotypicalGroup(this);
  61         }
  62         public void removeTypifiedName(TaxonNameBase typifiedName) {
  63                 typifiedName.setHomotypicalGroup(null);
  64         }
  65
  66
  67         @OneToMany
  68         @Cascade({CascadeType.SAVE_UPDATE})
  69         public Set<SpecimenTypeDesignation> getTypeDesignations() {
  70                 return typeDesignations;
  71         }
  72         protected void setTypeDesignations(Set<SpecimenTypeDesignation> typeDesignations) {
  73                 this.typeDesignations = typeDesignations;
  74         }
  75         public void addTypeDesignation(SpecimenTypeDesignation typeDesignation) {
  76                 typeDesignation.setHomotypicalGroup(this);
  77         }
  78         public void removeTypeDesignation(SpecimenTypeDesignation typeDesignation) {
  79                 typeDesignation.setHomotypicalGroup(null);
  80         }
  81         public void addTypeDesignation(Specimen typeSpecimen, TypeDesignationStatus status, ReferenceBase citation, String citationMicroReference, String originalNameString) {
  82                 SpecimenTypeDesignation td = new SpecimenTypeDesignation(this, typeSpecimen, status, citation, citationMicroReference, originalNameString);
  83                 td.setHomotypicalGroup(this);
  84         }
  85
  86         /**
  87          * Retrieves the synonyms of reference sec that are part of this homotypical group.
  88          * If other names are part of this group that are not considered synonyms in the respective sec-reference,
  89          * then they will not be included in the resultset.
  90          * @param sec
  91          * @return
  92          */
  93         @Transient
  94         public List<Synonym> getSynonymsInGroup(ReferenceBase sec){
  95                 List<Synonym> result = new ArrayList();
  96                 for (TaxonNameBase n:this.getTypifiedNames()){
  97                         for (Synonym s:n.getSynonyms()){
  98                                 if (s.getSec().equals(sec)){
  99                                         result.add(s);
 100                                 }
 101                         }
 102                 }
 103                 // TODO: sort result list according to date first published, see nomenclatural reference
 104                 return result;
 105         }
 106 }