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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.ArrayList;
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import java.util.Collections;
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import java.util.HashSet;
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import java.util.List;
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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.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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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.TaxonComparator;
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/**
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* The homotypical group class represents a set of {@link TaxonNameBase 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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* @created 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 = Logger.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<TaxonNameBase> typifiedNames = new HashSet<TaxonNameBase>();
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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 TaxonNameBase 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 TaxonNameBase taxon names}.
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*/
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public 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 TaxonNameBase 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<TaxonNameBase> getTypifiedNames() {
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return typifiedNames;
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}
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/**
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* Adds a new {@link TaxonNameBase 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(TaxonNameBase)
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*/
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public void addTypifiedName(TaxonNameBase typifiedName) {
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if (typifiedName != null){
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typifiedNames.add(typifiedName);
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typifiedName.setHomotypicalGroup(this);
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}
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}
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/**
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* Removes one element from the set of {@link TaxonNameBase taxon names}
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* that belong to <i>this</i> homotypical group.
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*
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* @param taxonBase the taxon name which should be removed from the corresponding set
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* @see #addTypifiedName(TaxonNameBase)
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*/
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public void removeTypifiedName(TaxonNameBase typifiedName) {
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HomotypicalGroup newHomotypicalGroup = HomotypicalGroup.NewInstance();
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typifiedName.setHomotypicalGroup(newHomotypicalGroup);
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typifiedNames.remove(typifiedName);
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}
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/**
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* Merges the typified {@link TaxonNameBase 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<TaxonNameBase> typifiedNames = new HashSet<TaxonNameBase>();
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typifiedNames.addAll(homotypicalGroupToMerge.getTypifiedNames());
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for (TaxonNameBase 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 TaxonNameBase 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 TaxonNameBase#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 (TaxonNameBase 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 TaxonNameBase 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 TaxonNameBase#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 (TaxonNameBase 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 TaxonNameBase 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 TaxonNameBase#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<TypeDesignationBase>();
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for (TaxonNameBase taxonName : typifiedNames){
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result.addAll(taxonName.getTypeDesignations());
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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 SpecimenTypeDesignation specimen type designations} that
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// * typify <i>this</i> homotypical group including the status of these designations.
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// *
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// * @see #getTypifiedNames()
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// */
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// @OneToMany
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// @Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
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// public Set<SpecimenTypeDesignation> getSpecimenTypeDesignations() {
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// return specimenTypeDesignations;
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// }
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// /**
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// * @see #getSpecimenTypeDesignations()
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// */
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// protected void setSpecimenTypeDesignations(Set<SpecimenTypeDesignation> specimenTypeDesignations) {
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// this.specimenTypeDesignations = specimenTypeDesignations;
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// }
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// /**
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// * Adds a new {@link SpecimenTypeDesignation specimen type designation} to the set
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// * of specimen type designations assigned to <i>this</i> homotypical group and eventually
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// * (with a boolean parameter) also to the corresponding set of each of the
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// * {@link TaxonNameBase taxon names} belonging to <i>this</i> homotypical group.
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// *
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// * @param specimenTypeDesignation the specimen type designation to be added
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// * @param addToAllNames the boolean flag indicating whether the addition will also
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// * carried out for each taxon name
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// *
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// * @see TaxonNameBase#getSpecimenTypeDesignations()
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// * @see SpecimenTypeDesignation
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// */
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// public void addSpecimenTypeDesignation(SpecimenTypeDesignation specimenTypeDesignation, boolean addToAllNames) {
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// if (specimenTypeDesignation != null){
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// specimenTypeDesignation.setHomotypicalGroup(this);
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// specimenTypeDesignations.add(specimenTypeDesignation);
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// }
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// if (addToAllNames){
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// for (TaxonNameBase taxonNameBase : this.typifiedNames){
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// taxonNameBase.addSpecimenTypeDesignation(specimenTypeDesignation);
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// }
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// }
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// }
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// /**
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// * Removes one element from the set of {@link SpecimenTypeDesignation specimen type designations} assigned to the
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// * {@link HomotypicalGroup homotypical group} to which this {@link TaxonNameBase taxon name} belongs.
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// * The same element will be removed from the corresponding set of each of
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// * the taxon names belonging to <i>this</i> homotypical group. Furthermore the
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// * homotypical group attribute of the specimen type designation will be
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// * nullified.
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// *
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// * @param specimenTypeDesignation the specimen type designation which should be deleted
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// * @see #getSpecimenTypeDesignations()
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// * @see #addSpecimenTypeDesignation(SpecimenTypeDesignation, boolean)
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// * @see TaxonNameBase#removeSpecimenTypeDesignation(SpecimenTypeDesignation)
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// * @see SpecimenTypeDesignation#getHomotypicalGroup()
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// */
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// public void removeSpecimenTypeDesignation(SpecimenTypeDesignation specimenTypeDesignation) {
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// if (specimenTypeDesignation != null){
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// specimenTypeDesignation.setHomotypicalGroup(null);
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// specimenTypeDesignations.remove(specimenTypeDesignation);
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// }
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// for (TaxonNameBase taxonNameBase : this.typifiedNames){
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// taxonNameBase.removeSpecimenTypeDesignation(specimenTypeDesignation);
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// }
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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 <i>this</i> homotypical group including the status of these designations.
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// *
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// * @see #getTypifiedNames()
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// */
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// @OneToMany
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// @Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
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// public Set<NameTypeDesignation> getNameTypeDesignations() {
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// return nameTypeDesignations;
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// }
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// /**
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// * @see #getNameTypeDesignations()
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// */
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// protected void setNameTypeDesignations(Set<NameTypeDesignation> nameTypeDesignations) {
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// this.nameTypeDesignations = nameTypeDesignations;
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// }
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// /**
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// * Adds a new {@link NameTypeDesignation name type designation} to the set
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// * of name type designations assigned to <i>this</i> homotypical group and eventually
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// * (with a boolean parameter) also to the corresponding set of each of the
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// * {@link TaxonNameBase taxon names} belonging to <i>this</i> homotypical group.
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// *
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// * @param nameTypeDesignation the name type designation to be added
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// * @param addToAllNames the boolean flag indicating whether the addition will also
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// * carried out for each taxon name
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// *
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// * @see TaxonNameBase#getNameTypeDesignations()
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// * @see NameTypeDesignation
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// */
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// public void addNameTypeDesignation(NameTypeDesignation nameTypeDesignation, boolean addToAllNames) {
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// if (nameTypeDesignation != null){
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// nameTypeDesignation.setHomotypicalGroup(this);
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// nameTypeDesignations.add(nameTypeDesignation);
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// }
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// if (addToAllNames){
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// for (TaxonNameBase taxonNameBase : this.typifiedNames){
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// taxonNameBase.addNameTypeDesignation(nameTypeDesignation);
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// }
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// }
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// }
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// /**
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// * Removes one element from the set of {@link NameTypeDesignation name type designations} assigned to the
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// * {@link HomotypicalGroup homotypical group} to which this {@link TaxonNameBase taxon name} belongs.
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// * The same element will be removed from the corresponding set of each of
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// * the taxon names belonging to <i>this</i> homotypical group. Furthermore the
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// * homotypical group attribute of the name type designation will be
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// * nullified.
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// *
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// * @param nameTypeDesignation the name type designation which should be deleted
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// * @see #getNameTypeDesignations()
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// * @see #addNameTypeDesignation(NameTypeDesignation, boolean)
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// * @see TaxonNameBase#removeNameTypeDesignation(NameTypeDesignation)
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// * @see NameTypeDesignation#getHomotypicalGroup()
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// */
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// public void removeNameTypeDesignation(NameTypeDesignation nameTypeDesignation) {
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// if (nameTypeDesignation != null){
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// nameTypeDesignation.setHomotypicalGroup(null);
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// nameTypeDesignations.remove(nameTypeDesignation);
|
|
348
|
// }
|
|
349
|
// for (TaxonNameBase taxonNameBase : this.typifiedNames){
|
|
350
|
// taxonNameBase.removeNameTypeDesignation(nameTypeDesignation);
|
|
351
|
// }
|
|
352
|
// }
|
|
353
|
|
|
354
|
|
|
355
|
/**
|
|
356
|
* Retrieves the ordered list (depending on the date of publication) of
|
|
357
|
* {@link taxon.Synonym synonyms} (according to a given reference)
|
|
358
|
* the {@link TaxonNameBase taxon names} of which belong to <i>this</i> homotypical group.
|
|
359
|
* If other names are part of <i>this</i> group that are not considered synonyms
|
|
360
|
* according to the respective reference, then they will not be included in
|
|
361
|
* the result set.
|
|
362
|
*
|
|
363
|
* @deprecated synonyms should not depend on the sec. Therefore this method will be removed in
|
|
364
|
* version 3.1 or higher. Use {@link Taxon#getSynonymsInGroup(HomotypicalGroup)} instead. But be
|
|
365
|
* aware that the semantics is slightly different.
|
|
366
|
* @param sec the reference whose treatment is to be considered
|
|
367
|
* @return the ordered list of synonyms
|
|
368
|
* @see TaxonNameBase#getSynonyms()
|
|
369
|
* @see TaxonNameBase#getTaxa()
|
|
370
|
* @see taxon.Synonym
|
|
371
|
*/
|
|
372
|
@Deprecated
|
|
373
|
public List<Synonym> getSynonymsInGroup(Reference sec){
|
|
374
|
List<Synonym> result = new ArrayList<Synonym>();
|
|
375
|
for (TaxonNameBase<?, ?>name : this.getTypifiedNames()){
|
|
376
|
for (Synonym synonym : name.getSynonyms()){
|
|
377
|
if ( (synonym.getSec() == null && sec == null) ||
|
|
378
|
synonym.getSec() != null && synonym.getSec().equals(sec)){
|
|
379
|
result.add(synonym);
|
|
380
|
}
|
|
381
|
}
|
|
382
|
}
|
|
383
|
Collections.sort(result, new TaxonComparator());
|
|
384
|
return result;
|
|
385
|
}
|
|
386
|
|
|
387
|
/**
|
|
388
|
* Creates a basionym relationship to all other names in this names homotypical
|
|
389
|
* group.
|
|
390
|
*
|
|
391
|
* @see HomotypicalGroup.setGroupBasionym(TaxonNameBase basionymName)
|
|
392
|
*
|
|
393
|
* @param basionymName
|
|
394
|
* @throws IllegalArgumentException if basionymName is not member in this homotypical group
|
|
395
|
*/
|
|
396
|
@Transient
|
|
397
|
public void setGroupBasionym(TaxonNameBase basionymName) throws IllegalArgumentException{
|
|
398
|
setGroupBasionym(basionymName, null, null, null);
|
|
399
|
}
|
|
400
|
|
|
401
|
public void setGroupBasionym(TaxonNameBase basionymName, Reference citation, String microCitation, String ruleConsidered)
|
|
402
|
throws IllegalArgumentException {
|
|
403
|
if (! typifiedNames.contains(basionymName)){
|
|
404
|
throw new IllegalArgumentException("Name to be set as basionym/original combination must be part of the homotypical group but is not");
|
|
405
|
}
|
|
406
|
if (typifiedNames.size() < 2){return;}
|
|
407
|
//
|
|
408
|
//Add new relations
|
|
409
|
for (TaxonNameBase name : typifiedNames) {
|
|
410
|
if (!name.equals(basionymName)) {
|
|
411
|
name.addRelationshipFromName(basionymName, NameRelationshipType.BASIONYM(), citation, microCitation, ruleConsidered);
|
|
412
|
}
|
|
413
|
}
|
|
414
|
}
|
|
415
|
|
|
416
|
/**
|
|
417
|
* Removes all basionym relationships between basionymName and any other name
|
|
418
|
* in its homotypic group
|
|
419
|
*
|
|
420
|
* @param basionymName
|
|
421
|
*/
|
|
422
|
public static void removeGroupBasionym(TaxonNameBase basionymName) {
|
|
423
|
HomotypicalGroup homotypicalGroup = basionymName.getHomotypicalGroup();
|
|
424
|
Set<NameRelationship> relations = basionymName.getRelationsFromThisName();
|
|
425
|
Set<NameRelationship> removeRelations = new HashSet<NameRelationship>();
|
|
426
|
|
|
427
|
for (NameRelationship relation : relations) {
|
|
428
|
|
|
429
|
// If this is a basionym relation, and toName is in the homotypical group,
|
|
430
|
// remove the relationship.
|
|
431
|
if (relation.getType().isBasionymRelation() &&
|
|
432
|
relation.getToName().getHomotypicalGroup().equals(homotypicalGroup)) {
|
|
433
|
removeRelations.add(relation);
|
|
434
|
}
|
|
435
|
}
|
|
436
|
|
|
437
|
// Removing relations from a set through which we are iterating causes a
|
|
438
|
// ConcurrentModificationException. Therefore, we delete the targeted
|
|
439
|
// relations in a second step.
|
|
440
|
for (NameRelationship relation : removeRelations) {
|
|
441
|
basionymName.removeNameRelationship(relation);
|
|
442
|
}
|
|
443
|
}
|
|
444
|
|
|
445
|
|
|
446
|
/**
|
|
447
|
* Returns all taxon names in the homotypical group that do not have an 'is_basionym_for' (zool.: 'is_original_combination_for')
|
|
448
|
* or a replaced synonym relationship.
|
|
449
|
* @return
|
|
450
|
*/
|
|
451
|
@Transient
|
|
452
|
public Set<TaxonNameBase> getUnrelatedNames(){
|
|
453
|
Set<NameRelationship> set = getBasionymOrReplacedSynonymRelations(true, true);
|
|
454
|
Set<TaxonNameBase> result = new HashSet<TaxonNameBase>();
|
|
455
|
result.addAll(this.getTypifiedNames());
|
|
456
|
for (NameRelationship nameRelationship : set){
|
|
457
|
result.remove(nameRelationship.getFromName());
|
|
458
|
result.remove(nameRelationship.getToName());
|
|
459
|
}
|
|
460
|
return result;
|
|
461
|
}
|
|
462
|
|
|
463
|
/**
|
|
464
|
* Returns all taxon names in the homotypical group that are new combinations (have a basionym/original combination
|
|
465
|
* or a replaced synonym).
|
|
466
|
* @return
|
|
467
|
*/
|
|
468
|
@Transient
|
|
469
|
public Set<TaxonNameBase> getNewCombinations(){
|
|
470
|
Set<NameRelationship> set = getBasionymOrReplacedSynonymRelations(true, true);
|
|
471
|
Set<TaxonNameBase> result = new HashSet<TaxonNameBase>();
|
|
472
|
for (NameRelationship nameRelationship : set){
|
|
473
|
result.add(nameRelationship.getToName());
|
|
474
|
}
|
|
475
|
return result;
|
|
476
|
}
|
|
477
|
|
|
478
|
|
|
479
|
|
|
480
|
/**
|
|
481
|
* Returns all taxon names in the homotypical group that have an 'is_basionym_for' (zool.: 'is_original_combination_for')
|
|
482
|
* or a replaced synonym relationship.
|
|
483
|
* @return
|
|
484
|
*/
|
|
485
|
@Transient
|
|
486
|
public Set<TaxonNameBase> getBasionymsOrReplacedSynonyms(){
|
|
487
|
Set<NameRelationship> set = getBasionymOrReplacedSynonymRelations(true, true);
|
|
488
|
Set<TaxonNameBase> result = new HashSet<TaxonNameBase>();
|
|
489
|
for (NameRelationship nameRelationship : set){
|
|
490
|
result.add(nameRelationship.getFromName());
|
|
491
|
}
|
|
492
|
return result;
|
|
493
|
}
|
|
494
|
|
|
495
|
/**
|
|
496
|
* Returns all taxon names in the homotypical group that have a 'is_basionym_for' (zool.: 'is_original_combination_for') relationship.
|
|
497
|
* @return
|
|
498
|
*/
|
|
499
|
@Transient
|
|
500
|
public Set<TaxonNameBase> getBasionyms(){
|
|
501
|
Set<NameRelationship> set = getBasionymOrReplacedSynonymRelations(true, false);
|
|
502
|
Set<TaxonNameBase> result = new HashSet<TaxonNameBase>();
|
|
503
|
for (NameRelationship nameRelationship : set){
|
|
504
|
result.add(nameRelationship.getFromName());
|
|
505
|
}
|
|
506
|
return result;
|
|
507
|
}
|
|
508
|
|
|
509
|
/**
|
|
510
|
* Returns all taxon names in the homotypical group that have a 'is_replaced_synonym_for' relationship.
|
|
511
|
* @return
|
|
512
|
*/
|
|
513
|
@Transient
|
|
514
|
public Set<TaxonNameBase> getReplacedSynonym(){
|
|
515
|
Set<NameRelationship> set = getBasionymOrReplacedSynonymRelations(false, true);
|
|
516
|
Set<TaxonNameBase> result = new HashSet<TaxonNameBase>();
|
|
517
|
for (NameRelationship nameRelationship : set){
|
|
518
|
result.add(nameRelationship.getFromName());
|
|
519
|
}
|
|
520
|
return result;
|
|
521
|
}
|
|
522
|
|
|
523
|
/**
|
|
524
|
* Returns the name relationships that represent either a basionym (original combination) relationship or
|
|
525
|
* a replaced synonym relationship.
|
|
526
|
* @return
|
|
527
|
*/
|
|
528
|
@Transient
|
|
529
|
public Set<NameRelationship> getBasionymAndReplacedSynonymRelations(){
|
|
530
|
return getBasionymOrReplacedSynonymRelations(true, true);
|
|
531
|
}
|
|
532
|
|
|
533
|
/**
|
|
534
|
* Computes all basionym and replaced synonym relationships between names in this group.
|
|
535
|
* If <code>doBasionym</code> is <code>false</code> basionym relationships are excluded.
|
|
536
|
* If <code>doReplacedSynonym</code> is <code>false</code> replaced synonym relationships are excluded.
|
|
537
|
* @param doBasionym
|
|
538
|
* @param doReplacedSynonym
|
|
539
|
* @return
|
|
540
|
*/
|
|
541
|
@Transient
|
|
542
|
private Set<NameRelationship> getBasionymOrReplacedSynonymRelations(boolean doBasionym, boolean doReplacedSynonym){
|
|
543
|
Set<NameRelationship> result = new HashSet<NameRelationship>();
|
|
544
|
Set<TaxonNameBase> names = this.getTypifiedNames();
|
|
545
|
if (names.size() > 1){
|
|
546
|
for (TaxonNameBase name : names){
|
|
547
|
Set nameRels = name.getNameRelations();
|
|
548
|
//TODO make getNameRelations generic
|
|
549
|
for (Object obj : nameRels){
|
|
550
|
NameRelationship nameRel = (NameRelationship)obj;
|
|
551
|
NameRelationshipType type = nameRel.getType();
|
|
552
|
if ( type.isBasionymRelation() && doBasionym){
|
|
553
|
if (testRelatedNameInThisGroup(nameRel)){
|
|
554
|
result.add(nameRel);
|
|
555
|
}else{
|
|
556
|
logger.warn("Name has basionym relation to a name that is not in the same homotypical group");
|
|
557
|
}
|
|
558
|
}else if (type.isReplacedSynonymRelation() && doReplacedSynonym) {
|
|
559
|
if (testRelatedNameInThisGroup(nameRel)){
|
|
560
|
result.add(nameRel);
|
|
561
|
}else{
|
|
562
|
logger.warn("Name has replaced synonym relation to a name that is not in the same homotypical group");
|
|
563
|
}
|
|
564
|
}
|
|
565
|
}
|
|
566
|
}
|
|
567
|
}
|
|
568
|
return result;
|
|
569
|
}
|
|
570
|
|
|
571
|
private boolean testRelatedNameInThisGroup(NameRelationship nameRel){
|
|
572
|
TaxonNameBase toName = nameRel.getToName();
|
|
573
|
return (this.getTypifiedNames().contains(toName));
|
|
574
|
}
|
|
575
|
|
|
576
|
private boolean isBasionymOrRepSynRel(NameRelationshipType relType){
|
|
577
|
if (relType == null){
|
|
578
|
throw new IllegalArgumentException("NameRelationshipType should never be null");
|
|
579
|
}else if (relType.equals(NameRelationshipType.BASIONYM())) {
|
|
580
|
return true;
|
|
581
|
}else if (relType.equals(NameRelationshipType.REPLACED_SYNONYM())){
|
|
582
|
return true;
|
|
583
|
}else{
|
|
584
|
return false;
|
|
585
|
}
|
|
586
|
}
|
|
587
|
|
|
588
|
|
|
589
|
}
|