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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.HashMap;
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import java.util.Map;
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import java.util.UUID;
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import javax.persistence.Entity;
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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.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.term.TermType;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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/**
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* The class representing status (categories) of {@link SpecimenTypeDesignation specimen type designations}
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* for a {@link TaxonName taxon name} or a set of them. Within this set {@link NameRelationshipType#BASIONYM() basionyms}
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* or {@link NameRelationshipType#REPLACED_SYNONYM() replaced synonyms}, in case of reclassifications,
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* will be here referred as "type-bringing" taxon names.
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* <P>
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* The different status indicate whether the {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimens} used as types
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* in a designation are duplicates, replacements, related specimens etc.
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* <P>
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* A standard (ordered) list of type designation status instances will be
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* automatically created as the project starts. But this class allows to extend
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* this standard list by creating new instances of additional type designation
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* status if needed.
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* <P>
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* This class corresponds to: <ul>
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* <li> NomencalturalTypeTypeTerm according to the TDWG ontology
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* <li> NomenclaturalTypeStatusOfUnitsEnum according to the TCS
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* </ul>
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*
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* @author m.doering
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* @since 08-Nov-2007 13:07:00
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "SpecimenTypeDesignationStatus")
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@Entity
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//@Indexed disabled to reduce clutter in indexes, since this type is not used by any search
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//@Indexed(index = "eu.etaxonomy.cdm.model.term.DefinedTermBase")
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@Audited
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public class SpecimenTypeDesignationStatus extends TypeDesignationStatusBase<SpecimenTypeDesignationStatus> {
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private static final long serialVersionUID = -7918261741824966182L;
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@SuppressWarnings("unused")
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private static final Logger logger = LogManager.getLogger(SpecimenTypeDesignationStatus.class);
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protected static Map<UUID, SpecimenTypeDesignationStatus> termMap = null;
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private static final UUID uuidType = UUID.fromString("7194020b-a326-4b47-9bfe-9f31a30aba7f");
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private static final UUID uuidHolotype = UUID.fromString("a407dbc7-e60c-46ff-be11-eddf4c5a970d");
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private static final UUID uuidLectotype = UUID.fromString("05002d46-083e-4b27-8731-2e7c28a8825c");
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private static final UUID uuidNeotype = UUID.fromString("26e13359-8f77-4e40-a85a-56c01782fce0");
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private static final UUID uuidEpitype = UUID.fromString("989a2715-71d5-4fbe-aa9a-db9168353744");
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private static final UUID uuidIsolectotype = UUID.fromString("7a1a8a53-78f4-4fc0-89f7-782e94992d08");
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private static final UUID uuidIsoneotype = UUID.fromString("7afc2f4f-f70a-4aa5-80a5-87764f746bde");
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private static final UUID uuidIsotype = UUID.fromString("93ef8257-0a08-47bb-9b36-542417ae7560");
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private static final UUID uuidParaneotype = UUID.fromString("0c39e2a5-2fe0-4d4f-819a-f609b5340339");
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private static final UUID uuidParatype = UUID.fromString("eb7df2e5-d9a7-479d-970c-c6f2b0a761d7");
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private static final UUID uuidSecondStepLectotype = UUID.fromString("01d91053-7004-4984-aa0d-9f4de59d6205");
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private static final UUID uuidSecondStepNeotype = UUID.fromString("8d2fed1f-242e-4bcf-bbd7-e85133e479dc");
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private static final UUID uuidSyntype = UUID.fromString("f3b60bdb-4638-4ca9-a0c7-36e77d8459bb");
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private static final UUID uuidParalectotype = UUID.fromString("7244bc51-14d8-41a6-9524-7dc5303bba29");
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private static final UUID uuidIsoepitype = UUID.fromString("95b90696-e103-4bc0-b60b-c594983fb566");
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private static final UUID uuidIconotype = UUID.fromString("643513d0-32f5-46ba-840b-d9b9caf8160f");
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private static final UUID uuidPhototype = UUID.fromString("b7807acc-f559-474e-ad4a-e7a41e085e34");
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private static final UUID uuidUnspecified = UUID.fromString("230fd762-b143-49de-ac2e-744bcc48a63b");
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private static final UUID uuidOriginalMaterial = UUID.fromString("49c96cae-6be6-401e-9b36-1bc12d9dc8f9");
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private static final UUID uuidIsosyntype = UUID.fromString("052a5ff0-8e9a-4355-b24f-5e4bb6071f44");
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private static final UUID uuidIsoparatype = UUID.fromString("497137f3-b614-4183-8a22-97fcd6e2bdd8");
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//********************************** Constructor *********************************/
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//for hibernate use only
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@Deprecated
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protected SpecimenTypeDesignationStatus() {
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super(TermType.SpecimenTypeDesignationStatus);
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}
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/**
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* Class constructor: creates an additional type designation status instance
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* with a description (in the {@link eu.etaxonomy.cdm.model.common.Language#DEFAULT() default language}), a label
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* and a label abbreviation.
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*
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* @param term the string (in the default language) describing the
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* new type designation status to be created
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* @param label the string identifying the new type designation
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* status to be created
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* @param labelAbbrev the string identifying (in abbreviated form) the
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* new type designation status to be created
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* @see #TypeDesignationStatus()
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*/
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private SpecimenTypeDesignationStatus(String term, String label, String labelAbbrev) {
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super(TermType.SpecimenTypeDesignationStatus, term, label, labelAbbrev);
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}
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//************************** METHODS ********************************
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@Override
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public void resetTerms(){
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termMap = null;
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}
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protected static SpecimenTypeDesignationStatus findTermByUuid(UUID uuid){
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if (termMap == null || termMap.isEmpty()){
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return getTermByClassAndUUID(SpecimenTypeDesignationStatus.class, uuid);
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} else {
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return termMap.get(uuid);
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}
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}
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//#8140
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@Transient
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@Override
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public boolean hasDesignationSource(){
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if (this.equals(LECTOTYPE()) ||
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this.equals(ISOLECTOTYPE()) ||
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this.equals(SECOND_STEP_LECTOTYPE()) ||
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// this.equals(PARALECTOTYPE()) || //removed due to #8140#note-5
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//with source but not "lecto"
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this.equals(EPITYPE()) ||
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this.equals(ISOEPITYPE()) ||
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this.equals(NEOTYPE()) ||
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this.equals(ISONEOTYPE()) ||
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this.equals(SECOND_STEP_NEOTYPE())
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){
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return true;
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}else{
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return false;
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}
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}
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/**
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* Returns the "unknown" designation status. One may choose this status to indicate that the type
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* designation is not
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*
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*/
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public static final SpecimenTypeDesignationStatus TYPE(){
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return findTermByUuid(uuidType);
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}
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/**
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* Returns the "holotype" designation status. A holotype of a
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* set of names is the one {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or illustration}
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* designated as the nomenclatural type by the {@link NonViralName#getCombinationAuthorship() author} of the
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* "type-bringing" {@link TaxonName taxon name} (or by the author of a later validated
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* "invalid" taxon name).
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*
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* @see NameRelationshipType#VALIDATED_BY_NAME()
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*/
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public static final SpecimenTypeDesignationStatus HOLOTYPE(){
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return findTermByUuid(uuidHolotype);
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}
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/**
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* Returns the "lectotype" designation status. A lectotype is a
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* {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or illustration} designated as the nomenclatural type,
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* when no holotype was indicated at the time of publication of the
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* "type-bringing" {@link TaxonName taxon name}, when the
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* holotype is found to to be assigned to taxon names belonging to more than one
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* {@link HomotypicalGroup homotypical group}, or as long as it is missing.
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*
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* @see #HOLOTYPE()
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*/
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public static final SpecimenTypeDesignationStatus LECTOTYPE(){
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return findTermByUuid(uuidLectotype);
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}
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/**
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* Returns the "neotype" designation status. A neotype is a
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* {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or illustration} selected to serve as nomenclatural type
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* as long as all of the material on which the "type-bringing" {@link TaxonName taxon name} was based
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* is missing.
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*
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* @see #HOLOTYPE()
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*/
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public static final SpecimenTypeDesignationStatus NEOTYPE(){
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return findTermByUuid(uuidNeotype);
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}
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/**
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* Returns the "epitype" designation status. An epitype is a
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* {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or illustration} selected to serve as an interpretative type
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* when the holotype, lectotype or previously designated neotype, or all
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* original material associated with the {@link NomenclaturalStatusType#VALID() validly} published "type-bringing"
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* {@link TaxonName taxon name}, is demonstrably ambiguous and cannot be critically
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* identified for purposes of the precise application of the taxon name.
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* When an epitype is designated, the holotype, lectotype or neotype that
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* the epitype supports must be explicitly cited.
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*
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* @see #HOLOTYPE()
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* @see #LECTOTYPE()
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* @see #NEOTYPE()
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*/
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public static final SpecimenTypeDesignationStatus EPITYPE(){
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return findTermByUuid(uuidEpitype);
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}
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/**
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* Returns the "isotype" designation status. </BR>An isotype is any duplicate of
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* the holotype; it is always a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}.
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*
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* @see #HOLOTYPE()
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*/
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public static final SpecimenTypeDesignationStatus ISOTYPE(){
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return findTermByUuid(uuidIsotype);
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}
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/**
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* Returns the "syntype" designation status. </BR>A syntype is any one of two or
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* more {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimens} cited in the {@link TaxonName#getNomenclaturalReference() protologue} of the
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* "type-bringing" {@link TaxonName taxon name} when no holotype was designated,
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* or any one of two or more specimens simultaneously designated as types.
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*
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* @see #HOLOTYPE()
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*/
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public static final SpecimenTypeDesignationStatus SYNTYPE(){
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return findTermByUuid(uuidSyntype);
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}
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/**
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* Returns the "isosyntype" designation status. </BR>An isosyntype is any
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* {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen} cited in the
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* protologue of the type-bringing {@link TaxonName taxon name} which is
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* a duplicate of a {@link eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus#SYNTYPE() syntype}.
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* See also article 9.10 of the ICBN
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*
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* @see #HOLOTYPE()
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*/
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public static final SpecimenTypeDesignationStatus ISOSYNTYPE(){
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return findTermByUuid(uuidIsosyntype);
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}
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/**
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* Returns the "paratype" designation status. </BR>A paratype is a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}
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* cited in the {@link TaxonName#getNomenclaturalReference() protologue} of the "type-bringing"
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* {@link TaxonName taxon name} that is neither the holotype nor an isotype,
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* nor one of the syntypes if two or more specimens were simultaneously
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* designated as types.
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*
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* @see #HOLOTYPE()
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* @see #ISOTYPE()
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* @see #SYNTYPE()
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*/
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public static final SpecimenTypeDesignationStatus PARATYPE(){
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return findTermByUuid(uuidParatype);
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}
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/**
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* Returns the "isolectotype" designation status. </BR>
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* An isolectotype is any
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* duplicate of the lectotype; it is always a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}.
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*
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* @see #LECTOTYPE()
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*/
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public static final SpecimenTypeDesignationStatus ISOLECTOTYPE(){
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return findTermByUuid(uuidIsolectotype);
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}
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/**
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* Returns the "isoneotype" designation status. </BR>
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* An isoneotype is any
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* duplicate of the neotype; it is always a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}.
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*
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* @see #NEOTYPE()
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*/
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public static final SpecimenTypeDesignationStatus ISONEOTYPE(){
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return findTermByUuid(uuidIsoneotype);
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}
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/**
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* Returns the "isoparatype" designation status. </BR>
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* An isoparatype is any
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* duplicate of a paratype; it is always a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}.
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*
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* @see #PARATYPE()
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* @see #ISOTYPE()
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*/
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public static final SpecimenTypeDesignationStatus ISOPARATYPE(){
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return findTermByUuid(uuidIsoparatype);
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}
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/**
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* Returns the "paraneotype" designation status. </BR>
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* A paraneotype is a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen},
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* cited when selecting a neotype, other than the neotype itself. Also
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* called "neoparatype" in zoology.
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*
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* @see #NEOTYPE()
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*/
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public static final SpecimenTypeDesignationStatus PARANEOTYPE(){
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return findTermByUuid(uuidParaneotype);
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}
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/**
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* Returns the "second step lectotype" designation status. </BR>
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* A second step lectotype is a {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or illustration}, designated as lectotype
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* in order to substitute another already existing lectotype.
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*
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* @see #LECTOTYPE()
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*/
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public static final SpecimenTypeDesignationStatus SECOND_STEP_LECTOTYPE(){
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return findTermByUuid(uuidSecondStepLectotype);
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}
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/**
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* Returns the "second step neotype" designation status. </BR>
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* A second step neotype is a {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or illustration}, designated as neotype
|
|
326
|
* in order to substitute another already existing neotype.
|
|
327
|
*
|
|
328
|
* @see #LECTOTYPE()
|
|
329
|
*/
|
|
330
|
public static final SpecimenTypeDesignationStatus SECOND_STEP_NEOTYPE(){
|
|
331
|
return findTermByUuid(uuidSecondStepNeotype);
|
|
332
|
}
|
|
333
|
|
|
334
|
/**
|
|
335
|
* Returns the "paralectotype" designation status. </BR>
|
|
336
|
* A paralectotype is a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}, cited when designating a lectotype, other than
|
|
337
|
* the lectotype itself. Also called "lectoparatype" in zoology.
|
|
338
|
*
|
|
339
|
* @see #LECTOTYPE()
|
|
340
|
*/
|
|
341
|
public static final SpecimenTypeDesignationStatus PARALECTOTYPE(){
|
|
342
|
return findTermByUuid(uuidParalectotype);
|
|
343
|
}
|
|
344
|
|
|
345
|
/**
|
|
346
|
* Returns the "isoepitype" designation status. An isoepitype is any
|
|
347
|
* duplicate of the epitype; it is always a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}.
|
|
348
|
*
|
|
349
|
* @see #EPITYPE()
|
|
350
|
*/
|
|
351
|
public static final SpecimenTypeDesignationStatus ISOEPITYPE(){
|
|
352
|
return findTermByUuid(uuidIsoepitype);
|
|
353
|
}
|
|
354
|
|
|
355
|
/**
|
|
356
|
* Returns the "iconotype" designation status. An iconotype is a holotype or
|
|
357
|
* a lectotype that is a {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit drawing}
|
|
358
|
* and not a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}.
|
|
359
|
* "Iconotype" does not have type status according to the ICBN.
|
|
360
|
*
|
|
361
|
* @see #HOLOTYPE()
|
|
362
|
* @see #LECTOTYPE()
|
|
363
|
*/
|
|
364
|
public static final SpecimenTypeDesignationStatus ICONOTYPE(){
|
|
365
|
return findTermByUuid(uuidIconotype);
|
|
366
|
}
|
|
367
|
|
|
368
|
/**
|
|
369
|
* Returns the "unspecific" type designation status. Used if from literature where it is not
|
|
370
|
* clear if it refers to another publication not cited or if it is a new designation.
|
|
371
|
*
|
|
372
|
*/
|
|
373
|
public static final SpecimenTypeDesignationStatus UNSPECIFIC(){
|
|
374
|
return findTermByUuid(uuidUnspecified);
|
|
375
|
}
|
|
376
|
|
|
377
|
/**
|
|
378
|
* Returns the "original material" type designation status.
|
|
379
|
* Botanical term for material from which a lectotype can be designated.
|
|
380
|
* "Original material" does not have type status according to the ICBN.
|
|
381
|
*
|
|
382
|
*/
|
|
383
|
public static final SpecimenTypeDesignationStatus ORIGINAL_MATERIAL(){
|
|
384
|
return findTermByUuid(uuidOriginalMaterial);
|
|
385
|
}
|
|
386
|
|
|
387
|
|
|
388
|
/**
|
|
389
|
* Returns the "phototype" type designation status.
|
|
390
|
* "Phototype" does not have type status according to the ICBN.
|
|
391
|
*
|
|
392
|
*/
|
|
393
|
public static final SpecimenTypeDesignationStatus PHOTOTYPE(){
|
|
394
|
return findTermByUuid(uuidPhototype);
|
|
395
|
}
|
|
396
|
|
|
397
|
@Override
|
|
398
|
protected void setDefaultTerms(TermVocabulary<SpecimenTypeDesignationStatus> termVocabulary) {
|
|
399
|
termMap = new HashMap<>();
|
|
400
|
for (SpecimenTypeDesignationStatus term : termVocabulary.getTerms()){
|
|
401
|
termMap.put(term.getUuid(), term);
|
|
402
|
}
|
|
403
|
}
|
|
404
|
|
|
405
|
}
|