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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.model.name;
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import java.util.HashSet;
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import java.util.Set;
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import javax.persistence.Entity;
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import javax.persistence.FetchType;
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import javax.persistence.OneToMany;
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import javax.persistence.Transient;
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import javax.xml.bind.annotation.XmlAccessType;
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import javax.xml.bind.annotation.XmlAccessorType;
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import javax.xml.bind.annotation.XmlElement;
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import javax.xml.bind.annotation.XmlElementWrapper;
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import javax.xml.bind.annotation.XmlIDREF;
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import javax.xml.bind.annotation.XmlSchemaType;
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import javax.xml.bind.annotation.XmlType;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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import org.hibernate.envers.Audited;
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import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
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import eu.etaxonomy.cdm.model.reference.Reference;
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/**
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* The homotypical group class represents a set of {@link TaxonName taxon names} associated
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* on the base of their typifications. Since it can be asserted that two taxon
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* names are typified by the same type without mentioning the type itself, even
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* taxon names without explicit {@link TypeDesignationBase type designation} can belong
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* to an homotypical group.<BR>
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* Taxon names belonging to an homotypical group and the taxon names or
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* {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimens} used as types for their
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* {@link TypeDesignationBase type designations} have the following properties: <ul>
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* <li> A taxon name belongs exactly to one homotypical group
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* <li> A type specimen or a type name can be used as a type only for taxon
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* names belonging to the same homotypical group<BR>
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* - therefore an homotypical group circumscribes a set of types<BR>
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* - each taxon name shares a subset of these types<BR>
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* - each type is used by a subset of these taxon names
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* within the homotypical group
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* <li> Names that share at least one common type must belong to the same
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* homotypical group
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* <li> Names that share the same basionym or replaced synonym must belong to
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* the same homotypical group
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* </ul>
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*
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* @see TypeDesignationBase
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* @see NameTypeDesignation
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* @see SpecimenTypeDesignation
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* @author m.doering
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* @version 1.0
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* @since 08-Nov-2007
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "HomotypicalGroup", propOrder = {
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"typifiedNames"
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})
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@Entity
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@Audited
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public class HomotypicalGroup extends AnnotatableEntity {
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private static final long serialVersionUID = -2308347613205551766L;
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private static final Logger logger = LogManager.getLogger(HomotypicalGroup.class);
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@XmlElementWrapper(name = "TypifiedNames")
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@XmlElement(name = "TypifiedName")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@OneToMany(mappedBy="homotypicalGroup", fetch=FetchType.LAZY)
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protected Set<TaxonName> typifiedNames = new HashSet<>();
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// ******************** static methods **************************************/
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/**
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* Creates a new homotypical group instance with an empty set of typified
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* {@link TaxonName taxon names}.
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*
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* @see #HomotypicalGroup()
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*/
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public static HomotypicalGroup NewInstance(){
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return new HomotypicalGroup();
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}
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//********************** CONSTRUCTOR ********************************************/
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/**
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* Class constructor: creates a new homotypical group instance with an
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* empty set of typified {@link TaxonName taxon names}.
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*/
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protected HomotypicalGroup() {
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super();
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}
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// ********************** GETTER/SETTER/ADDER/REMOVER ********************************/
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/**
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* Returns the set of {@link TaxonName taxon names} that belong to <i>this</i> homotypical group.
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*
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* @see #getSpecimenTypeDesignations()
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*/
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public Set<TaxonName> getTypifiedNames() {
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return typifiedNames;
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}
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/**
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* Adds a new {@link TaxonName taxon name} to the set of taxon names that belong
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* to <i>this</i> homotypical group.
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*
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* @param typifiedName the taxon name to be added to <i>this</i> group
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* @see #getTypifiedNames()
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* @see #removeTypifiedName(TaxonName)
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*/
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public void addTypifiedName(TaxonName typifiedName) {
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if (typifiedName != null){
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typifiedNames.add(typifiedName);
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//if (typifiedName.getHomotypicalGroup() != null && !typifiedName.getHomotypicalGroup().equals(this))
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typifiedName.setHomotypicalGroup(this);
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}
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}
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/**
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* @see #removeTypifiedName(TaxonName, boolean)
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* @param typifiedName
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*/
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public void removeTypifiedName(TaxonName typifiedName) {
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removeTypifiedName(typifiedName, false);
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}
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/**
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* Removes one element from the set of {@link TaxonName taxon names}
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* that belong to <i>this</i> homotypical group.
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*
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* @param typifiedName the taxon name which should be removed from the corresponding set
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* @param removeGroup if <code>true</code> the typified name is given a new
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* homotypical group
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* @see #addTypifiedName(TaxonName)
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*/
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public void removeTypifiedName(TaxonName typifiedName, boolean removeGroup) {
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if (removeGroup){
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HomotypicalGroup newHomotypicalGroup = HomotypicalGroup.NewInstance();
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typifiedName.setHomotypicalGroup(newHomotypicalGroup);
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}
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typifiedNames.remove(typifiedName);
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}
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/**
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* Merges the typified {@link TaxonName taxon names} from one homotypical group into
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* the set of typified taxon names of <i>this</i> homotypical group.
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*
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* @param homotypicalGroupToMerge the homotypical group the typified names of which
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* are to be transferred to <i>this</i> homotypical group
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*/
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public void merge(HomotypicalGroup homotypicalGroupToMerge){
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if (homotypicalGroupToMerge != null){
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Set<TaxonName> typifiedNames = new HashSet<>();
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typifiedNames.addAll(homotypicalGroupToMerge.getTypifiedNames());
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for (TaxonName typifiedName: typifiedNames){
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this.addTypifiedName(typifiedName);
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}
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}
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}
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/**
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* Returns the set of {@link SpecimenTypeDesignation specimen type designations} that
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* typify the {@link TaxonName taxon names} belonging to <i>this</i> homotypical group
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* including the status of these designations.
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*
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* @see #getTypifiedNames()
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* @see #getNameTypeDesignations()
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* @see #getTypeDesignations()
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* @see TaxonName#getSpecimenTypeDesignations()
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*/
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@Transient
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public Set<SpecimenTypeDesignation> getSpecimenTypeDesignations(){
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Set<SpecimenTypeDesignation> result = new HashSet<SpecimenTypeDesignation>();
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for (TaxonName taxonName : typifiedNames){
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result.addAll(taxonName.getSpecimenTypeDesignations());
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}
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return result;
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}
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/**
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* Returns the set of {@link NameTypeDesignation name type designations} that
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* typify the {@link TaxonName taxon names} belonging to <i>this</i> homotypical group
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* including the status of these designations.
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*
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* @see #getTypifiedNames()
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* @see #getSpecimenTypeDesignations()
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* @see #getTypeDesignations()
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* @see TaxonName#getNameTypeDesignations()
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*/
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@Transient
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public Set<NameTypeDesignation> getNameTypeDesignations(){
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Set<NameTypeDesignation> result = new HashSet<NameTypeDesignation>();
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for (TaxonName taxonName : typifiedNames){
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result.addAll(taxonName.getNameTypeDesignations());
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}
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return result;
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}
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/**
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* Returns the set of all {@link TypeDesignationBase type designations} that
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* typify the {@link TaxonName taxon names} belonging to <i>this</i> homotypical group
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* (this includes either {@link NameTypeDesignation name type designations} or
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* {@link SpecimenTypeDesignation specimen type designations}).
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*
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* @see #getTypifiedNames()
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* @see #getNameTypeDesignations()
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* @see #getSpecimenTypeDesignations()
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* @see TaxonName#getTypeDesignations()
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*/
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@Transient
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public Set<TypeDesignationBase<?>> getTypeDesignations(){
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Set<TypeDesignationBase<?>> result = new HashSet<>();
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for (TaxonName taxonName : typifiedNames){
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result.addAll((Set)taxonName.getTypeDesignations());
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}
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return result;
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}
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/**
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* Creates a basionym relationship to all other names in this names homotypical
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* group.
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*
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* @see HomotypicalGroup.setGroupBasionym(TaxonName basionymName)
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*
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* @param basionymName
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* @throws IllegalArgumentException if basionymName is not member in this homotypical group
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*/
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@Transient
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public void setGroupBasionym(TaxonName basionymName) throws IllegalArgumentException{
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setGroupBasionym(basionymName, null, null, null, null);
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}
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public void setGroupBasionym(TaxonName basionymName, Reference citation, String microCitation, String ruleConsidered, NomenclaturalCodeEdition codeEdition)
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throws IllegalArgumentException {
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if (! typifiedNames.contains(basionymName)){
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throw new IllegalArgumentException("Name to be set as basionym/original combination must be part of the homotypical group but is not");
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}
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if (typifiedNames.size() < 2){return;}
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//
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//Add new relations
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Set<TaxonName> typified = new HashSet<>();
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for (TaxonName name : typifiedNames){
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typified.add(name);
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}
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for (TaxonName name : typified) {
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if (!name.equals(basionymName)) {
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name.addRelationshipFromName(basionymName, NameRelationshipType.BASIONYM(), citation, microCitation, ruleConsidered, codeEdition);
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}
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}
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typifiedNames= typified;
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}
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/**
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* Removes all basionym relationships between basionymName and any other name
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* in it's homotypic group
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*
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* @param basionymName
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*/
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public static void removeGroupBasionym(TaxonName basionymName) {
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HomotypicalGroup homotypicalGroup = basionymName.getHomotypicalGroup();
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Set<NameRelationship> relations = basionymName.getRelationsFromThisName();
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Set<NameRelationship> removeRelations = new HashSet<NameRelationship>();
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for (NameRelationship relation : relations) {
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// If this is a basionym relation, and toName is in the homotypical group,
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// remove the relationship.
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if (relation.getType().isBasionymRelation() &&
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relation.getToName().getHomotypicalGroup().equals(homotypicalGroup)) {
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removeRelations.add(relation);
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}
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}
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// Removing relations from a set through which we are iterating causes a
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// ConcurrentModificationException. Therefore, we delete the targeted
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// relations in a second step.
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for (NameRelationship relation : removeRelations) {
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basionymName.removeNameRelationship(relation);
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}
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}
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// /**
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// * TODO
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// * This method tries to set basionym(s) for a homotypical group
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// * Rule: Basionym must not have basionym author and not protectedAuthorshipCache
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// * Others must have basionymAuthor
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// * BasionymAuhtors must have equal NomenclaturalTitleCache to basionym
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// * last epithet must fit (be equal except for ending), otherwise we expect it to be replaced synonym
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// * those names fitting to a basionym relationship must remove all other basionym (and replaced synonym?) relationships
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// * Open: All types of relationships to replaced synonyms
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// */
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// public void guessAndSetBasionym(){
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// Map<String, INonViralName> candidates = new HashMap<>();
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// for (TaxonName typifiedName : this.typifiedNames){
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// if (! typifiedName.protectedAuthorshipCache && nvn.getBasionymAuthorship() == null){
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// candidates.add(typifiedName);
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// }
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// }
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// if (candidates.size() == 1){
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// for (TaxonName typifiedName : this.typifiedNames){
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// removeGroupBasionym(typifiedName);
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// }
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// this.setGroupBasionym(candidates.iterator().next());
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// }
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//
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// }
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/**
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* Returns all taxon names in the homotypic group that do not have an
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* 'is_basionym_for' (zool.: 'is_original_combination_for')
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* or a replaced synonym relationship.
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* @return
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*/
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@Transient
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public Set<TaxonName> getUnrelatedNames(){
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Set<NameRelationship> set = getBasionymOrReplacedSynonymRelations(true, true);
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Set<TaxonName> result = new HashSet<>();
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result.addAll(this.getTypifiedNames());
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for (NameRelationship nameRelationship : set){
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result.remove(nameRelationship.getFromName());
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result.remove(nameRelationship.getToName());
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}
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return result;
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}
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/**
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* Returns all taxon names in the homotypical group that are new combinations (have a basionym/original combination
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* or a replaced synonym).
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* @return
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*/
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@Transient
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public Set<TaxonName> getNewCombinations(){
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Set<NameRelationship> set = getBasionymOrReplacedSynonymRelations(true, true);
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Set<TaxonName> result = new HashSet<>();
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for (NameRelationship nameRelationship : set){
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result.add(nameRelationship.getToName());
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}
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return result;
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}
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/**
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* Returns all taxon names in the homotypical group that have an 'is_basionym_for' (zool.: 'is_original_combination_for')
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* or a replaced synonym relationship.
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* @return
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*/
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@Transient
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public Set<TaxonName> getBasionymsOrReplacedSynonyms(){
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Set<NameRelationship> set = getBasionymOrReplacedSynonymRelations(true, true);
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Set<TaxonName> result = new HashSet<>();
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for (NameRelationship nameRelationship : set){
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result.add(nameRelationship.getFromName());
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}
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return result;
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}
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/**
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* Returns all taxon names in the homotypical group that have a 'is_basionym_for' (zool.: 'is_original_combination_for') relationship.
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*/
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@Transient
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public Set<TaxonName> getBasionyms(){
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Set<NameRelationship> set = getBasionymOrReplacedSynonymRelations(true, false);
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Set<TaxonName> result = new HashSet<>();
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for (NameRelationship nameRelationship : set){
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result.add(nameRelationship.getFromName());
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}
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return result;
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}
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/**
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* Returns all taxon names in the homotypical group that have a 'is_replaced_synonym_for' relationship.
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*/
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@Transient
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public Set<TaxonName> getReplacedSynonym(){
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Set<NameRelationship> set = getBasionymOrReplacedSynonymRelations(false, true);
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Set<TaxonName> result = new HashSet<>();
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for (NameRelationship nameRelationship : set){
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result.add(nameRelationship.getFromName());
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}
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return result;
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}
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/**
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* Returns the name relationships that represent either a basionym (original combination) relationship or
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* a replaced synonym relationship.
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*/
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@Transient
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public Set<NameRelationship> getBasionymAndReplacedSynonymRelations(){
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return getBasionymOrReplacedSynonymRelations(true, true);
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}
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/**
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* Computes all basionym and replaced synonym relationships between names in this group.
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* If <code>doBasionym</code> is <code>false</code> basionym relationships are excluded.
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* If <code>doReplacedSynonym</code> is <code>false</code> replaced synonym relationships are excluded.
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* @param doBasionym
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* @param doReplacedSynonym
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* @return
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*/
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@Transient
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419
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private Set<NameRelationship> getBasionymOrReplacedSynonymRelations(boolean doBasionym, boolean doReplacedSynonym){
|
420
|
Set<NameRelationship> result = new HashSet<NameRelationship>();
|
421
|
Set<TaxonName> names = this.getTypifiedNames();
|
422
|
if (names.size() > 1){
|
423
|
for (TaxonName name : names){
|
424
|
Set nameRels = name.getNameRelations();
|
425
|
//TODO make getNameRelations generic
|
426
|
for (Object obj : nameRels){
|
427
|
NameRelationship nameRel = (NameRelationship)obj;
|
428
|
NameRelationshipType type = nameRel.getType();
|
429
|
if ( type.isBasionymRelation() && doBasionym){
|
430
|
if (testRelatedNameInThisGroup(nameRel)){
|
431
|
result.add(nameRel);
|
432
|
}else{
|
433
|
logger.warn("Name has basionym relation to a name that is not in the same homotypical group");
|
434
|
}
|
435
|
}else if (type.isReplacedSynonymRelation() && doReplacedSynonym) {
|
436
|
if (testRelatedNameInThisGroup(nameRel)){
|
437
|
result.add(nameRel);
|
438
|
}else{
|
439
|
logger.warn("Name has replaced synonym relation to a name that is not in the same homotypical group");
|
440
|
}
|
441
|
}
|
442
|
}
|
443
|
}
|
444
|
}
|
445
|
return result;
|
446
|
}
|
447
|
|
448
|
private boolean testRelatedNameInThisGroup(NameRelationship nameRel){
|
449
|
TaxonName toName = nameRel.getToName();
|
450
|
return (this.getTypifiedNames().contains(toName));
|
451
|
}
|
452
|
|
453
|
private boolean isBasionymOrRepSynRel(NameRelationshipType relType){
|
454
|
if (relType == null){
|
455
|
throw new IllegalArgumentException("NameRelationshipType should never be null");
|
456
|
}else if (relType.equals(NameRelationshipType.BASIONYM())) {
|
457
|
return true;
|
458
|
}else if (relType.equals(NameRelationshipType.REPLACED_SYNONYM())){
|
459
|
return true;
|
460
|
}else{
|
461
|
return false;
|
462
|
}
|
463
|
}
|
464
|
}
|