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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.Inheritance;
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import javax.persistence.InheritanceType;
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import javax.persistence.ManyToMany;
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import javax.persistence.ManyToOne;
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import javax.persistence.Transient;
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import javax.validation.constraints.NotNull;
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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.XmlRootElement;
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import javax.xml.bind.annotation.XmlSchemaType;
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import javax.xml.bind.annotation.XmlSeeAlso;
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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.annotations.Cascade;
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import org.hibernate.annotations.CascadeType;
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import org.hibernate.envers.Audited;
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import org.hibernate.search.annotations.IndexedEmbedded;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.common.SourcedEntityBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.validation.Level2;
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import eu.etaxonomy.cdm.validation.annotation.ValidLectotypeSource;
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import eu.etaxonomy.cdm.validation.annotation.ValidTypeDesignation;
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/**
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* The (abstract) class representing a typification of one or several {@link TaxonName taxon names}.<BR>
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* All taxon names which have a {@link Rank rank} "species aggregate" or lower
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* can only be typified by specimens (a {@link SpecimenTypeDesignation specimen type designation}), but taxon
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* names with a higher rank might be typified by an other taxon name with
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* rank "species" or "genus" (a {@link NameTypeDesignation name type designation}).
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*
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* @see TaxonName
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* @see NameTypeDesignation
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* @see SpecimenTypeDesignation
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* @author a.mueller
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* @since 07.08.2008
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*/
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@XmlRootElement(name = "TypeDesignationBase")
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@XmlType(name = "TypeDesignationBase", propOrder = {
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"typeStatus",
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"notDesignated",
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"typifiedNames",
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"citation",
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"citationMicroReference",
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"registrations",
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})
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@XmlSeeAlso({
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NameTypeDesignation.class,
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SpecimenTypeDesignation.class,
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TextualTypeDesignation.class
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})
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@Entity
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@Audited
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@Inheritance(strategy=InheritanceType.SINGLE_TABLE)
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@ValidTypeDesignation(groups=Level2.class)
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@ValidLectotypeSource(groups=Level2.class)
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public abstract class TypeDesignationBase<T extends TypeDesignationStatusBase<T>>
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extends SourcedEntityBase<IdentifiableSource>
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implements ITypeDesignation {
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private static final long serialVersionUID = 4838214337140859787L;
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(TypeDesignationBase.class);
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@XmlElement(name = "IsNotDesignated")
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private boolean notDesignated;
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@XmlElement(name = "TypeStatus")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToOne(fetch = FetchType.LAZY, targetEntity = TypeDesignationStatusBase.class)
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private T typeStatus;
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//the lectotype (or similar) reference
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@XmlElement(name = "Citation")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToOne(fetch = FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
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private Reference citation;
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//Details of the lectotype reference.
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@XmlElement(name = "CitationMicroReference")
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private String citationMicroReference;
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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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@ManyToMany(fetch = FetchType.LAZY , mappedBy="typeDesignations")
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@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
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private Set<TaxonName> typifiedNames = new HashSet<>();
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//******* REGISTRATION *****************/
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@XmlElementWrapper(name = "Registrations")
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@XmlElement(name = "Registration")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToMany(mappedBy="typeDesignations", fetch= FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
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@NotNull
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@IndexedEmbedded(depth=1)
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private Set<Registration> registrations = new HashSet<>();
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// **************** CONSTRUCTOR *************************************/
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protected TypeDesignationBase(){
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super();
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}
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/**
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* Class constructor: creates a new type designation
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* (including its {@link Reference reference source} and eventually
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* the taxon name string originally used by this reference when establishing
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* the former designation).
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*
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* @param citation the reference source for the new designation
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* @param citationMicroReference the string with the details describing the exact localisation within the reference
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* @param originalNameString the taxon name string used originally in the reference source for the new designation
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* @see #TypeDesignationBase()
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* @see #isNotDesignated()
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* @see TaxonName#getTypeDesignations()
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*/
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protected TypeDesignationBase(Reference citation, String citationMicroReference, String originalNameString) {
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this(citation, citationMicroReference, originalNameString, false);
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}
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/**
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* Class constructor: creates a new type designation
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* (including its {@link Reference reference source} and eventually
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* the taxon name string originally used by this reference when establishing
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* the former designation).
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*
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* @param citation the reference source for the new designation
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* @param citationMicroReference the string with the details describing the exact localisation within the reference
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* @param originalNameString the taxon name string used originally in the reference source for the new designation
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* @param isNotDesignated the boolean flag indicating whether there is no type at all for
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* <i>this</i> type designation
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* @see #TypeDesignationBase()
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* @see #isNotDesignated()
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* @see TaxonName#getTypeDesignations()
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*/
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protected TypeDesignationBase(Reference citation, String citationMicroReference, String originalNameString, boolean notDesignated){
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super();
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this.notDesignated = notDesignated;
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this.citationMicroReference = citationMicroReference;
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this.citation = citation;
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}
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// **************** METHODS *************************************/
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/**
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* Returns the {@link TypeDesignationStatusBase type designation status} for <i>this</i> specimen type
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* designation. This status describes which of the possible categories of
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* types like "holotype", "neotype", "syntype" or "isotype" applies to <i>this</i>
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* specimen type designation.
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*/
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public T getTypeStatus(){
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return (CdmBase.deproxy(this.typeStatus)); //otherwise for some error we get an error in TypeDesignationDaoHibernateImplTest
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}
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/**
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* @see #getTypeStatus()
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*/
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public void setTypeStatus(T typeStatus){
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this.typeStatus = typeStatus;
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}
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/**
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* Returns the boolean value "true" if it is known that a type does not
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* exist and therefore the {@link TaxonName taxon name} to which <i>this</i>
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* type designation is assigned must still be typified. Two
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* cases must be differentiated: <BR><ul>
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* <li> a) it is unknown whether a type exists and
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* <li> b) it is known that no type exists
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* </ul>
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* If a) is true there should be no TypeDesignation instance at all
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* assigned to the "typified" taxon name.<BR>
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* If b) is true there should be a TypeDesignation instance with the
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* flag isNotDesignated set. The typeName attribute, in case of a
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* {@link NameTypeDesignation name type designation}, or the typeSpecimen attribute,
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* in case of a {@link SpecimenTypeDesignation specimen type designation}, should then be "null".
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*/
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public boolean isNotDesignated() {
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return notDesignated;
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}
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/**
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* @see #isNotDesignated()
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*/
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public void setNotDesignated(boolean notDesignated) {
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this.notDesignated = notDesignated;
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}
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public String getCitationMicroReference(){
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return this.citationMicroReference;
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}
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public void setCitationMicroReference(String citationMicroReference){
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this.citationMicroReference = citationMicroReference;
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}
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public Reference getCitation(){
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return this.citation;
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}
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public void setCitation(Reference citation) {
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this.citation = citation;
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}
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/**
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* Returns the {@link Registration registrations} available for this
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* type designation.
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*/
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public Set<Registration> getRegistrations() {
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return this.registrations;
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}
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/**
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* Remove the type (specimen or name) from this type designation
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*/
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public abstract void removeType();
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/**
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* Returns the set of {@link TaxonName taxon names} typified in <i>this</i>
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* type designation. This is a subset of the taxon names belonging to the
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* corresponding {@link #getHomotypicalGroup() homotypical group}.
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*/
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@Override
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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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* @deprecated for bidirectional use only
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*/
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@Deprecated
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protected void addTypifiedName(TaxonName taxonName){
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this.typifiedNames.add(taxonName);
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}
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/**
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* @deprecated for bidirectional use only
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*/
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@Deprecated
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protected void removeTypifiedName(TaxonName taxonName){
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this.typifiedNames.remove(taxonName);
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if (taxonName.getTypeDesignations().contains(this)){
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taxonName.removeTypeDesignation(this);
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}
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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protected IdentifiableSource createNewInstance(OriginalSourceType type, String idInSource, String idNamespace,
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Reference reference, String microReference, String originalInfo) {
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return IdentifiableSource.NewInstance(type, idInSource, idNamespace, reference, microReference, originalInfo);
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}
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@Override
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@Transient
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public boolean isLectoType() {
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if (getTypeStatus() == null) {
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return false;
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}
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return getTypeStatus().isLectotype();
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}
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//*********************** CLONE ********************************************************/
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/**
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* Clones <i>this</i> type designation. This is a shortcut that enables to create
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* a new instance that differs only slightly from <i>this</i> type designation by
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* modifying only some of the attributes.<BR>
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* CAUTION: the typifiedNames set is also cloned by adding the new type designation
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* to the typifiedNames of the original type designation. If this is unwanted
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* th
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*
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* not cloned but empty after cloning as the typified
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* names is considered to be the not owning part of a bidirectional relationship.
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* This may be changed in future.
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*
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* @throws CloneNotSupportedException
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*
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* @see eu.etaxonomy.cdm.model.common.ReferencedEntityBase#clone()
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* @see java.lang.Object#clone()
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*/
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@Override
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public Object clone() throws CloneNotSupportedException {
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TypeDesignationBase<?> result = (TypeDesignationBase<?>)super.clone();
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//registrations
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result.registrations = new HashSet<>();
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for (Registration registration : registrations){
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registration.addTypeDesignation(result);
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}
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//typified names
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result.typifiedNames = new HashSet<>();
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for (TaxonName taxonName : getTypifiedNames()){
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taxonName.addTypeDesignation(result, false);
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}
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//no changes to: notDesignated, typeStatus, homotypicalGroup
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return result;
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}
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}
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