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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.HashMap;
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import java.util.List;
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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.log4j.Logger;
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import org.hibernate.envers.Audited;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.OrderedTermBase;
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import eu.etaxonomy.cdm.model.common.Representation;
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import eu.etaxonomy.cdm.model.common.TermType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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/**
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* The class representing categories of nomenclatural status (like "invalid",
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* "conserved" or "novum") to qualify the use of a particular taxon name string
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* depending on its {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} (original publication),
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* on its {@link NomenclaturalCode nomenclatural code} and on possible decisions of the corresponding
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* competent authorities. Unfortunately the ICBN and the ICZN use sometimes
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* different words for the same meaning or the same word for different meanings
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* (for instance "valid" and "legitimate").
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* <P>
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* A standard (ordered) list of nomenclatural status type 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 nomenclatural
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* status types if needed. The present standard list follows the ICBN
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* terminology.
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* <P>
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* This class corresponds more or less to: <ul>
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* <li> NomenclaturalNoteTypeTerm according to the TDWG ontology
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* <li> NomenclaturalNoteType according to the TCS
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* </ul>
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*
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* @author a.mueller
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* @since 10.07.2008
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "NomenclaturalStatusType")
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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.common.DefinedTermBase")
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@Audited
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public class NomenclaturalStatusType extends OrderedTermBase<NomenclaturalStatusType> {
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private static final long serialVersionUID = 1337101678484153972L;
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private static Logger logger = Logger.getLogger(NomenclaturalStatusType.class);
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//Botanical uuids
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public static final UUID uuidIcnafpNomStatusVocabulary = UUID.fromString("bb28cdca-2f8a-4f11-9c21-517e9ae87f1f");
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private static final UUID uuidAmbiguous = UUID.fromString("90f5012b-705b-4488-b4c6-002d2bc5198e");
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private static final UUID uuidDoubtful = UUID.fromString("0ffeb39e-872e-4c0f-85ba-a4150d9f9e7d");
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private static final UUID uuidConfusum = UUID.fromString("24955174-aa5c-4e71-a2fd-3efc79e885db");
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private static final UUID uuidIllegitimate = UUID.fromString("b7c544cf-a375-4145-9d3e-4b97f3f18108");
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private static final UUID uuidSuperfluous = UUID.fromString("6890483a-c6ba-4ae1-9ab1-9fbaa5736ce9");
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private static final UUID uuidRejected = UUID.fromString("48107cc8-7a5b-482e-b438-efbba050b851");
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private static final UUID uuidUtiqueRejected = UUID.fromString("04338fdd-c12a-402f-a1ca-68b4bf0be042");
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private static final UUID uuidConservedProp = UUID.fromString("82bab006-5aed-4301-93ec-980deb30cbb1");
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private static final UUID uuidOrthographyConservedProp = UUID.fromString("02f82bc5-1066-454b-a023-11967cba9092");
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private static final UUID uuidLegitimate = UUID.fromString("51a3613c-b53b-4561-b0cd-9163d91c15aa");
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private static final UUID uuidAlternative = UUID.fromString("3b8a8519-420f-4dfa-b050-b410cc257961");
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private static final UUID uuidNovum = UUID.fromString("05fcb68f-af60-4851-b912-892512058897");
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private static final UUID uuidUtiqueRejectedProp = UUID.fromString("643ee07f-026c-426c-b838-c778c8613383");
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private static final UUID uuidOrthographyConserved = UUID.fromString("34a7d383-988b-4117-b8c0-52b947f8c711");
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private static final UUID uuidRejectedProp = UUID.fromString("248e44c2-5436-4526-a352-f7467ecebd56");
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private static final UUID uuidConserved = UUID.fromString("6330f719-e2bc-485f-892b-9f882058a966");
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private static final UUID uuidSanctioned = UUID.fromString("1afe55c4-76aa-46c0-afce-4dc07f512733");
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private static final UUID uuidInvalid = UUID.fromString("b09d4f51-8a77-442a-bbce-e7832aaf46b7");
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private static final UUID uuidNudum = UUID.fromString("e0d733a8-7777-4b27-99a3-05ab50e9f312");
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private static final UUID uuidCombinationInvalid = UUID.fromString("f858e619-7b7f-4225-913b-880a2143ec83");
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private static final UUID uuidCombinationIllegitimate = UUID.fromString("d901d455-4e01-45cb-b653-01a840b97eed");
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private static final UUID uuidProvisional = UUID.fromString("a277507e-ad93-4978-9419-077eb889c951");
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private static final UUID uuidValid = UUID.fromString("bd036217-5499-4ccd-8f4c-72e06158db93");
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private static final UUID uuidOpusUtiqueOppr = UUID.fromString("a5055d80-dbba-4660-b091-a1835d59fe7c");
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private static final UUID uuidSubnudum = UUID.fromString("92a76bd0-6ea8-493f-98e0-4be0b98c092f");
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private static final UUID uuidCombNov = UUID.fromString("ed508710-deef-44b1-96f6-1ce6d2c9c884");
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private static final UUID uuidOrthographyRejected = UUID.fromString("39a25673-f716-4ec7-ae27-2498fce43166");
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private static final UUID uuidConservedDesig = UUID.fromString("4e9c9702-a74d-4033-9d47-792ad123712c");
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private static final UUID uuidIned = UUID.fromString("51429574-c6f9-4aa1-bab9-0bbc5b160ba1");
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//zoological uuids
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public static final UUID uuidIcznNomStatusVocabulary = UUID.fromString("5e3c08e9-13a9-498e-861e-b9b5656ab6ac");
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private static final UUID uuidZooNotAvailable = UUID.fromString("6d9ed462-b761-4da3-9304-4749e883d4eb");
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private static final UUID uuidZooInvalid = UUID.fromString("2bef7039-c129-410b-815e-2a1f7249127b");
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private static final UUID uuidZooSuppressed = UUID.fromString("a61602c7-fbd4-4eb4-98a2-44919db8920b");
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private static final UUID uuidZooOblitum = UUID.fromString("6a6f7a88-991f-4f76-8ce9-4110839fae8b");
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public static NomenclaturalStatusType NewInstance(String description, String label, String labelAbbrev, Language language) {
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return new NomenclaturalStatusType(description, label, labelAbbrev, language);
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}
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public static NomenclaturalStatusType NewInstance(String description, String label, String labelAbbrev) {
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return new NomenclaturalStatusType(description, label, labelAbbrev);
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}
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protected static Map<UUID, NomenclaturalStatusType> termMap = null;
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private static Map<String, UUID> abbrevMap = null;
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private static Map<String, UUID> labelMap = null;
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protected static Map<UUID, NomenclaturalStatusType> zooTermMap = null;
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private static Map<String, UUID> zooAbbrevMap = null;
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private static Map<String, UUID> zooLabelMap = null;
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protected static NomenclaturalStatusType getTermByUuid(UUID uuid){
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if ((termMap == null || termMap.isEmpty()) && (zooTermMap == null || zooTermMap.isEmpty())){
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return getTermByClassAndUUID(NomenclaturalStatusType.class, uuid);
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}
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NomenclaturalStatusType result = null;
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if (termMap != null){
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result = termMap.get(uuid);
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}
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if (result == null && zooTermMap != null){
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result = zooTermMap.get(uuid);
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}
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return result;
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}
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//********************************** Constructor *********************************/
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//for hibernate use only
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@Deprecated
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protected NomenclaturalStatusType() {
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super(TermType.NomenclaturalStatusType);
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}
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/**
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* Class constructor: creates an additional nomenclatural status type
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* instance 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 nomenclatural status type to be created
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* @param label the string identifying the new nomenclatural status
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* type to be created
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* @param labelAbbrev the string identifying (in abbreviated form) the
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* new nomenclatural status type to be created
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* @see #NomenclaturalStatusType()
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* @see #readCsvLine(List, Language)
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* @see #readCsvLine(List)
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*/
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private NomenclaturalStatusType(String term, String label, String labelAbbrev) {
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super(TermType.NomenclaturalStatusType, term, label, labelAbbrev);
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}
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private NomenclaturalStatusType(String term, String label, String labelAbbrev, Language language) {
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super(TermType.NomenclaturalStatusType);
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this.addRepresentation(new Representation(term, label, labelAbbrev, language));
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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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zooTermMap = null;
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}
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/**
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* Returns the boolean value indicating whether <i>this</i> nomenclatural status
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* type is itself "invalid" or a kind of "invalid" (true) or not (false) -
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* this corresponds to "not available" for {@link IZoologicalName zoological names} -.
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* Returns false if <i>this</i> nomenclatural status type is null. The use
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* of "invalid" {@link TaxonName taxon names} should be avoided.<BR>
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* A taxon name is "invalid" if it is not "valid"; this means that
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* the taxon name:<ul>
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* <li>has not been effectively published or
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* <li>has a form which does not comply with the rules of the
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* {@link NomenclaturalCode nomenclature code} or
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* <li>is not accompanied by a description or diagnosis or by a reference to
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* such a previously published description or diagnosis
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* </ul>
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*
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* @see #VALID()
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* @see #isIllegitimateType()
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* @see eu.etaxonomy.cdm.model.common.DefinedTermBase#getKindOf()
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*/
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@Transient
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public boolean isInvalidType(){
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if (this.equals(INVALID())
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|| this.equals(NUDUM())
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|| this.equals(PROVISIONAL())
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|| this.equals(INED())
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|| this.equals(COMBINATION_INVALID())
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|| this.equals(OPUS_UTIQUE_OPPR())
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|| this.equals(ZOO_NOT_AVAILABLE())
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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 boolean value indicating whether <i>this</i> nomenclatural status
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* type is itself "legitimate" or a kind of "legitimate" (true)
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* or not (false). Corresponds to "valid" for {@link IZoologicalName zoological names}.<BR>
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* Returns false if <i>this</i> nomenclatural status type is null.<BR>
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* A "valid" (zool.: "available") {@link TaxonName taxon name}, unless "rejected",
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* is "legitimate" if it was not "superfluous" when published
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* or has been later "conserved".<BR>
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*
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* @see #isInvalidType()
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* @see #isIllegitimateType()
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* @see eu.etaxonomy.cdm.model.common.DefinedTermBase#getKindOf()
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*/
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@Transient
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public boolean isLegitimateType(){
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if (this.equals(LEGITIMATE()) ||
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this.equals(NOVUM()) ||
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this.equals(ALTERNATIVE()) ||
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this.equals(CONSERVED()) ||
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this.equals(ORTHOGRAPHY_CONSERVED()) ||
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this.equals(REJECTED_PROP()) ||
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this.equals(UTIQUE_REJECTED_PROP()) ||
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this.equals(COMB_NOV())||
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this.equals(CONSERVED_DESIG())
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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 boolean value indicating whether <i>this</i> nomenclatural status
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* type is itself "illegitimate" or a kind of "illegitimate" (true)
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* or not (false) - this corresponds to "invalid" for {@link IZoologicalName zoological names} -.
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* Returns false if <i>this</i> nomenclatural status type is null.<BR>
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* A "valid" ("available") {@link TaxonName taxon name}, unless "conserved" or
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* "sanctioned", is "illegitimate" if it was "superfluous" when published
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* or has been later "rejected".
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*
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* @see #VALID()
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* @see #isInvalidType()
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* @see #ILLEGITIMATE()
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* @see #CONSERVED()
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* @see #SANCTIONED()
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* @see eu.etaxonomy.cdm.model.common.DefinedTermBase#getKindOf()
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*/
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@Transient
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public boolean isIllegitimateType(){
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if (this.equals(ILLEGITIMATE()) ||
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this.equals(SUPERFLUOUS()) ||
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this.equals(REJECTED()) ||
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this.equals(UTIQUE_REJECTED()) ||
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this.equals(CONSERVED_PROP()) ||
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this.equals(ORTHOGRAPHY_CONSERVED_PROP()) ||
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this.equals(ZOO_INVALID()) ||
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this.equals(ZOO_SUPPRESSED()) ||
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this.equals(ORTHOGRAPHY_REJECTED())
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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 nomenclatural status type "ambiguous". A "valid"
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* ("available") {@link TaxonName taxon name} is "ambiguous" if it has been used so long
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* by different authors in different senses (other than the originally
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* intended) that it has become a persistent cause of error and confusion.<BR>
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* An "ambiguous" taxon name is treated as if "rejected" and is therefore
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* also "illegitimate" ("invalid" for {@link IZoologicalName zoological names}).
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*
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* @see #VALID()
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* @see #REJECTED()
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* @see #isIllegitimateType()
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*/
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public static final NomenclaturalStatusType AMBIGUOUS(){
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return getTermByUuid(uuidAmbiguous);
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}
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/**
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* Returns the nomenclatural status type "doubtful" (dubious). A "valid"
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* ("available") {@link TaxonName taxon name} is "doubtful" if its
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* application is uncertain; the confusion being derived from an incomplete
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* or confusing description.<BR>
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* A "doubtful" taxon name is treated as if "rejected" and is therefore
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* also "illegitimate" (("invalid" for {@link IZoologicalName zoological names}).
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*
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* @see #VALID()
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* @see #REJECTED()
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* @see #isIllegitimateType()
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*/
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public static final NomenclaturalStatusType DOUBTFUL(){
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return getTermByUuid(uuidDoubtful);
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}
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/**
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* Returns the nomenclatural status type "confusum". A "valid" ("available")
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* {@link TaxonName taxon name} is "confusum" if it has been widely
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* and persistently used for a taxon or taxa not including its type.<BR>
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* A "confusum" taxon name is treated as if "rejected" and is therefore
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* also "illegitimate" ("invalid" for {@link IZoologicalName zoological names}).
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*
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* @see #VALID()
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* @see #REJECTED()
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* @see #isIllegitimateType()
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*/
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public static final NomenclaturalStatusType CONFUSUM(){
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return getTermByUuid(uuidConfusum);
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}
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/**
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* Returns the nomenclatural status type "illegitimate" ("invalid" for
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* {@link IZoologicalName zoological names}). A "valid" ("available")
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* {@link TaxonName taxon name}, unless "conserved" or "sanctioned", is "illegitimate"
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* if it was "superfluous" when published or has been later "rejected".<BR>
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*
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* @see #VALID()
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* @see #SUPERFLUOUS()
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* @see #REJECTED()
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*/
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public static final NomenclaturalStatusType ILLEGITIMATE(){
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350
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return getTermByUuid(uuidIllegitimate);
|
351
|
}
|
352
|
|
353
|
/**
|
354
|
* Returns the nomenclatural status type "superfluous". A "valid"
|
355
|
* ("available") {@link TaxonName taxon name} is "superfluous" if, when published,
|
356
|
* the taxon to which it was applied, as circumscribed by its {@link NonViralName#getCombinationAuthorship() author},
|
357
|
* definitely included the type of a name which ought to have been adopted,
|
358
|
* or of which the epithet ought to have been adopted, under the rules of
|
359
|
* the {@link NomenclaturalCode nomenclature code}, and if it has not been later declared
|
360
|
* "conserved" or "sanctioned" by the competent authorities.<BR>
|
361
|
* A "superfluous" taxon name is therefore also "illegitimate" ("invalid" for
|
362
|
* {@link IZoologicalName zoological names}).
|
363
|
*
|
364
|
* @see #VALID()
|
365
|
* @see #CONSERVED()
|
366
|
* @see #SANCTIONED()
|
367
|
* @see #isIllegitimateType()
|
368
|
*/
|
369
|
public static final NomenclaturalStatusType SUPERFLUOUS(){
|
370
|
return getTermByUuid(uuidSuperfluous);
|
371
|
}
|
372
|
|
373
|
/**
|
374
|
* Returns the nomenclatural status type "rejected". A "valid" ("available")
|
375
|
* {@link TaxonName taxon name} is "rejected" if, even though by the strict
|
376
|
* application of the rules of the {@link NomenclaturalCode nomenclature code}, and especially
|
377
|
* of the principle of priority, it should be "legitimate" ("valid" for
|
378
|
* {@link IZoologicalName zoological names}), competent authorities decided to handle
|
379
|
* it as "illegitimate".<BR>
|
380
|
* A "rejected" taxon name is therefore also "illegitimate" ("invalid" for
|
381
|
* zoological names). A "rejected" taxon name is always rejected in favour
|
382
|
* of a "conserved" taxon name.
|
383
|
*
|
384
|
* @see #VALID()
|
385
|
* @see #isLegitimateType()
|
386
|
* @see #isIllegitimateType()
|
387
|
* @see #CONSERVED()
|
388
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
389
|
*/
|
390
|
public static final NomenclaturalStatusType REJECTED(){
|
391
|
return getTermByUuid(uuidRejected);
|
392
|
}
|
393
|
|
394
|
/**
|
395
|
* Returns the nomenclatural status type "utique rejected". A "valid"
|
396
|
* ("available") {@link TaxonName taxon name} is "utique rejected" if it is rejected
|
397
|
* outright (without being rejected in favour of a "conserved" taxon name).<BR>
|
398
|
* An "utique rejected" taxon name is therefore also "illegitimate"
|
399
|
* ("invalid" for zoological names).
|
400
|
*
|
401
|
* @see #REJECTED()
|
402
|
* @see #VALID()
|
403
|
* @see #isIllegitimateType()
|
404
|
* @see #CONSERVED()
|
405
|
*/
|
406
|
public static final NomenclaturalStatusType UTIQUE_REJECTED(){
|
407
|
return getTermByUuid(uuidUtiqueRejected);
|
408
|
}
|
409
|
|
410
|
/**
|
411
|
* Returns the nomenclatural status type "proposed to be conserved". A
|
412
|
* "valid" ("available") {@link TaxonName taxon name} is "proposed to be conserved"
|
413
|
* if, even though by the strict application of the rules of
|
414
|
* the {@link NomenclaturalCode nomenclature code}, and especially of the principle of priority,
|
415
|
* it is "illegitimate" ("invalid" for {@link IZoologicalName zoological names}),
|
416
|
* it has been submitted to competent authorities in order to decide whether
|
417
|
* it should be handled as "legitimate".<BR>
|
418
|
* A "proposed to be conserved" taxon name is therefore still "illegitimate"
|
419
|
* ("invalid" for zoological names).
|
420
|
*
|
421
|
* {@link https://dev.e-taxonomy.eu/trac/ticket/5662}
|
422
|
*
|
423
|
* @see #VALID()
|
424
|
* @see #isIllegitimateType()
|
425
|
* @see #isLegitimateType()
|
426
|
* @see #CONSERVED()
|
427
|
* @see #CONSERVED_DESIG()
|
428
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
429
|
*/
|
430
|
public static final NomenclaturalStatusType CONSERVED_PROP(){
|
431
|
return getTermByUuid(uuidConservedProp);
|
432
|
}
|
433
|
|
434
|
/**
|
435
|
* Returns the nomenclatural status type "designated to be conserved". A
|
436
|
* "valid" ("available") {@link TaxonName taxon name} is "designated to be conserved".
|
437
|
* The name is considered to be legitimate as it has been decided by the General Committee
|
438
|
* though not yet ratified by the Int. Bot./Zool. Congr.
|
439
|
*
|
440
|
* NOTE: This interpretation needs further clarification.
|
441
|
*
|
442
|
* {@link https://dev.e-taxonomy.eu/trac/ticket/5662}
|
443
|
*
|
444
|
* @see #VALID()
|
445
|
* @see #isIllegitimateType()
|
446
|
* @see #isLegitimateType()
|
447
|
* @see #CONSERVED()
|
448
|
* @see #CONSERVED_PROP()()
|
449
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
450
|
*/
|
451
|
public static final NomenclaturalStatusType CONSERVED_DESIG(){
|
452
|
return getTermByUuid(uuidConservedDesig);
|
453
|
}
|
454
|
|
455
|
|
456
|
|
457
|
/**
|
458
|
* Returns the nomenclatural status type "proposed to be conserved
|
459
|
* (orthography)". A {@link TaxonName taxon name} is "proposed to be conserved
|
460
|
* (orthography)" if, even though originally published with another
|
461
|
* spelling, it has been submitted to competent authorities in order to
|
462
|
* decide whether the proposed alternative spelling should be "conserved".<BR>
|
463
|
* A "proposed to be conserved (orthography)" taxon name is therefore still
|
464
|
* "illegitimate" ("invalid" for {@link IZoologicalName zoological names}).
|
465
|
*
|
466
|
* @see #isIllegitimateType()
|
467
|
* @see #CONSERVED_PROP()
|
468
|
* @see #CONSERVED()
|
469
|
* @see NameRelationshipType#ORTHOGRAPHIC_VARIANT()
|
470
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
471
|
*/
|
472
|
public static final NomenclaturalStatusType ORTHOGRAPHY_CONSERVED_PROP(){
|
473
|
return getTermByUuid(uuidOrthographyConservedProp);
|
474
|
}
|
475
|
|
476
|
/**
|
477
|
* Returns the nomenclatural status type "legitimate" ("valid" for
|
478
|
* {@link IZoologicalName zoological names}). A "valid" ("available")
|
479
|
* {@link TaxonName taxon name}, unless "rejected", is "legitimate" if it was not
|
480
|
* "superfluous" when published or has been later "conserved".<BR>
|
481
|
*
|
482
|
* @see #VALID()
|
483
|
* @see #SUPERFLUOUS()
|
484
|
* @see #CONSERVED()
|
485
|
*/
|
486
|
public static final NomenclaturalStatusType LEGITIMATE(){
|
487
|
return getTermByUuid(uuidLegitimate);
|
488
|
}
|
489
|
|
490
|
/**
|
491
|
* Returns the nomenclatural status type "alternative". A family
|
492
|
* {@link BotanicalName botanical name} is "alternative" if it is a classical name
|
493
|
* long in use, in some cases even before 1753, and is considered as
|
494
|
* {@link NomenclaturalStatusType#VALID() "valid"} although it does not follow the rules for
|
495
|
* family names (see Article 18 of the ICBN).<BR>
|
496
|
* An "alternative" taxon name is treated as if "conserved" and is therefore
|
497
|
* also "legitimate".
|
498
|
*
|
499
|
* @see #VALID()
|
500
|
* @see #CONSERVED()
|
501
|
* @see #isLegitimateType()
|
502
|
* @see NameRelationshipType#ALTERNATIVE_NAME()
|
503
|
*/
|
504
|
public static final NomenclaturalStatusType ALTERNATIVE(){
|
505
|
return getTermByUuid(uuidAlternative);
|
506
|
}
|
507
|
|
508
|
/**
|
509
|
* Returns the nomenclatural status type "novum". A "valid"
|
510
|
* ("available") {@link TaxonName taxon name} is "novum" if it has been created
|
511
|
* in order either to replace an earlier name that is "illegitimate" or to
|
512
|
* avoid the building of a "later homonym".<BR>
|
513
|
* A "novum" taxon name is therefore also "legitimate" ("valid" for
|
514
|
* {@link IZoologicalName zoological names}).
|
515
|
*
|
516
|
* @see #VALID()
|
517
|
* @see #isIllegitimateType()
|
518
|
* @see NameRelationshipType#REPLACED_SYNONYM()
|
519
|
* @see NameRelationshipType#BLOCKING_NAME_FOR()
|
520
|
*/
|
521
|
public static final NomenclaturalStatusType NOVUM(){
|
522
|
return getTermByUuid(uuidNovum);
|
523
|
}
|
524
|
|
525
|
/**
|
526
|
* Returns the nomenclatural status type "proposed to be utique rejected". A
|
527
|
* "valid" ("available") {@link TaxonName taxon name} is "proposed to be utique rejected"
|
528
|
* if, even though by the strict application of the rules of
|
529
|
* the {@link NomenclaturalCode nomenclature code}, and especially of the principle of priority,
|
530
|
* it is "legitimate" ("valid" for {@link IZoologicalName zoological names}),
|
531
|
* it has been submitted to competent authorities in order to decide whether
|
532
|
* it should be handled as "illegitimate" (without to be rejected in favour
|
533
|
* of a "conserved" taxon name).<BR>
|
534
|
* A "proposed to be utique rejected" taxon name is therefore still "legitimate"
|
535
|
* ("valid" for zoological names).
|
536
|
*
|
537
|
* @see #VALID()
|
538
|
* @see #isLegitimateType()
|
539
|
* @see #isIllegitimateType()
|
540
|
* @see #REJECTED()
|
541
|
* @see #REJECTED_PROP()
|
542
|
*/
|
543
|
public static final NomenclaturalStatusType UTIQUE_REJECTED_PROP(){
|
544
|
return getTermByUuid(uuidUtiqueRejectedProp);
|
545
|
}
|
546
|
|
547
|
/**
|
548
|
* Returns the nomenclatural status type "conserved (orthography)". A
|
549
|
* {@link TaxonName taxon name} is "conserved (orthography)" if competent authorities
|
550
|
* decided to conserve a different spelling to the one published originally.<BR>
|
551
|
* A "conserved (orthography)" taxon name is "conserved" and hence
|
552
|
* "legitimate" ("valid" for {@link IZoologicalName zoological names}).
|
553
|
*
|
554
|
* @see #isLegitimateType()
|
555
|
* @see #CONSERVED()
|
556
|
* @see #ORTHOGRAPHY_CONSERVED_PROP()
|
557
|
* @see NameRelationshipType#ORTHOGRAPHIC_VARIANT()
|
558
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
559
|
*/
|
560
|
public static final NomenclaturalStatusType ORTHOGRAPHY_CONSERVED(){
|
561
|
return getTermByUuid(uuidOrthographyConserved);
|
562
|
}
|
563
|
|
564
|
|
565
|
|
566
|
|
567
|
/**
|
568
|
* Returns the nomenclatural status type "orthography rejected". <BR>
|
569
|
* TBC.
|
570
|
* See also {@link http://dev.e-taxonomy.eu/trac/ticket/5649}
|
571
|
*
|
572
|
* @see #ORTHOGRAPHY_CONSERVED()
|
573
|
* @see #REJECTED()
|
574
|
* @see #isIllegitimateType()
|
575
|
*/
|
576
|
public static final NomenclaturalStatusType ORTHOGRAPHY_REJECTED(){
|
577
|
return getTermByUuid(uuidOrthographyRejected);
|
578
|
}
|
579
|
|
580
|
/**
|
581
|
* Returns the nomenclatural status type "proposed to be rejected". A
|
582
|
* "valid" ("available") {@link TaxonName taxon name} is "proposed to be rejected"
|
583
|
* if, even though by the strict application of the rules of
|
584
|
* the {@link NomenclaturalCode nomenclature code}, and especially of the principle of priority,
|
585
|
* it should be "legitimate" ("valid" for {@link IZoologicalName zoological names}),
|
586
|
* it has been submitted to competent authorities in order to decide whether
|
587
|
* it should be handled as "illegitimate".<BR>
|
588
|
* A "proposed to be rejected" taxon name is therefore still "legitimate"
|
589
|
* ("valid" for zoological names). A "proposed to be rejected" taxon name is always
|
590
|
* to be rejected in favour of a "proposed to be conserved" taxon name.
|
591
|
*
|
592
|
* @see #VALID()
|
593
|
* @see #isLegitimateType()
|
594
|
* @see #isIllegitimateType()
|
595
|
* @see #REJECTED()
|
596
|
* @see #CONSERVED_PROP()
|
597
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
598
|
*/
|
599
|
public static final NomenclaturalStatusType REJECTED_PROP(){
|
600
|
return getTermByUuid(uuidRejectedProp);
|
601
|
}
|
602
|
|
603
|
|
604
|
/**
|
605
|
* Returns the nomenclatural status type "conserved". A "valid"
|
606
|
* ("available") {@link TaxonName taxon name} is "conserved" if, even though by the strict
|
607
|
* application of the rules of the {@link NomenclaturalCode nomenclature code}, and especially of
|
608
|
* the principle of priority, it should be "illegitimate" ("invalid" for
|
609
|
* {@link IZoologicalName zoological names}), competent authorities decided to handle
|
610
|
* it as "legitimate".<BR>
|
611
|
* A "conserved" taxon name is therefore also "legitimate" ("valid" for
|
612
|
* zoological names).
|
613
|
*
|
614
|
* @see #VALID()
|
615
|
* @see #isIllegitimateType()
|
616
|
* @see #isLegitimateType()
|
617
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
618
|
*/
|
619
|
public static final NomenclaturalStatusType CONSERVED(){
|
620
|
return getTermByUuid(uuidConserved);
|
621
|
}
|
622
|
|
623
|
/**
|
624
|
* Returns the nomenclatural status type "sanctioned". {@link BotanicalName Botanical names}
|
625
|
* for fungi are "sanctioned" if they were published in the opera mentioned
|
626
|
* in Article 13.1d of the {@link NomenclaturalCode#ICBN() ICBN}.<BR>
|
627
|
* A "sanctioned" taxon name is treated as if "conserved" and is therefore
|
628
|
* also "legitimate".
|
629
|
*
|
630
|
* @see #VALID()
|
631
|
* @see #CONSERVED()
|
632
|
* @see #isLegitimateType()
|
633
|
*/
|
634
|
public static final NomenclaturalStatusType SANCTIONED(){
|
635
|
return getTermByUuid(uuidSanctioned);
|
636
|
}
|
637
|
|
638
|
/**
|
639
|
* Returns the nomenclatural status type "invalid" (this corresponds to
|
640
|
* "not available" for {@link IZoologicalName zoological names}). The use of "invalid"
|
641
|
* {@link TaxonName taxon names} should be avoided.<BR>
|
642
|
* A taxon name is "invalid" if it is not "valid"; this means that
|
643
|
* the taxon name:<ul>
|
644
|
* <li>has not been effectively published or
|
645
|
* <li>has a form which does not comply with the rules of the
|
646
|
* {@link NomenclaturalCode nomenclature code} or
|
647
|
* <li>is not accompanied by a description or diagnosis or by a reference to
|
648
|
* such a previously published description or diagnosis
|
649
|
* </ul>
|
650
|
*
|
651
|
* @see #VALID()
|
652
|
* @see #isInvalidType()
|
653
|
* @see #ILLEGITIMATE()
|
654
|
*/
|
655
|
public static final NomenclaturalStatusType INVALID(){
|
656
|
return getTermByUuid(uuidInvalid);
|
657
|
}
|
658
|
|
659
|
/**
|
660
|
* Returns the nomenclatural status type "nudum". A {@link TaxonName taxon name} is "nudum"
|
661
|
* if its publication is not accompanied by a description or diagnosis or
|
662
|
* by a reference to such a previously published description or diagnosis.<BR>
|
663
|
* A "nudum" taxon name is therefore also "invalid" ("not available" for
|
664
|
* {@link IZoologicalName zoological names}).
|
665
|
*
|
666
|
* @see #isInvalidType()
|
667
|
*/
|
668
|
public static final NomenclaturalStatusType NUDUM(){
|
669
|
return getTermByUuid(uuidNudum);
|
670
|
}
|
671
|
|
672
|
/**
|
673
|
* Returns the nomenclatural status type "invalid combination". A
|
674
|
* {@link TaxonName bi- or trinomial} is an "invalid combination" if its
|
675
|
* {@link NonViralName#getCombinationAuthorship() author} did not definitely associate the final
|
676
|
* epithet with the name of the genus or species, or with its abbreviation.<BR>
|
677
|
* An "invalid combination" taxon name is therefore also "invalid"
|
678
|
* ("not available" for {@link IZoologicalName zoological names}).
|
679
|
*
|
680
|
* @see #isInvalidType()
|
681
|
*/
|
682
|
public static final NomenclaturalStatusType COMBINATION_INVALID(){
|
683
|
return getTermByUuid(uuidCombinationInvalid);
|
684
|
}
|
685
|
|
686
|
/**
|
687
|
* Returns the nomenclatural status type "illegitimate combination".
|
688
|
* TODO explanation
|
689
|
*
|
690
|
* @see #isInvalidType()
|
691
|
*/
|
692
|
public static final NomenclaturalStatusType COMBINATION_ILLEGITIMATE(){
|
693
|
return getTermByUuid(uuidCombinationIllegitimate);
|
694
|
}
|
695
|
|
696
|
/**
|
697
|
* Returns the nomenclatural status type "provisional". A {@link TaxonName taxon name} is
|
698
|
* "provisional" if it is not validly published, because not finally accepted by the author<BR>
|
699
|
* Some people use it in the same way as {@link #INED() ined.}
|
700
|
*
|
701
|
* @see #INED()
|
702
|
* @see #isInvalidType()
|
703
|
*/
|
704
|
public static final NomenclaturalStatusType PROVISIONAL(){
|
705
|
return getTermByUuid(uuidProvisional);
|
706
|
}
|
707
|
|
708
|
/**
|
709
|
* Returns the nomenclatural status type "ined.". A {@link TaxonName taxon name} is
|
710
|
* "inedited" if it it has not yet been published.<BR>
|
711
|
* An inedited taxon name is therefore also "invalid" (bot.) / "not available (zool.)
|
712
|
*<BR>
|
713
|
* see also http://dev.e-taxonomy.eu/trac/ticket/5896
|
714
|
*
|
715
|
* @see #PROVISIONAL()
|
716
|
* @see #isInvalidType()
|
717
|
* @return
|
718
|
*/
|
719
|
public static final NomenclaturalStatusType INED(){
|
720
|
return getTermByUuid(uuidIned);
|
721
|
}
|
722
|
|
723
|
/**
|
724
|
* Returns the nomenclatural status type "valid" (this corresponds to
|
725
|
* "available" for {@link IZoologicalName zoological names}).<BR>
|
726
|
* A {@link TaxonName taxon name} is "valid" if it:<ul>
|
727
|
* <li>has been effectively published and
|
728
|
* <li>has a form which complies with the rules of the
|
729
|
* {@link NomenclaturalCode nomenclature code} and
|
730
|
* <li>is accompanied by a description or diagnosis or by a reference to
|
731
|
* such a previously published description or diagnosis
|
732
|
* </ul>
|
733
|
*
|
734
|
* @see #INVALID()
|
735
|
* @see #LEGITIMATE()
|
736
|
*/
|
737
|
public static final NomenclaturalStatusType VALID(){
|
738
|
return getTermByUuid(uuidValid);
|
739
|
}
|
740
|
|
741
|
/**
|
742
|
* Returns the nomenclatural status type "subnudum". This type is not
|
743
|
* covered by {@link NomenclaturalCode nomenclature codes}. It appears sometimes in literature and
|
744
|
* represents the opinion of the author who considers the {@link TaxonName taxon name} to be
|
745
|
* unusable for an unambiguous taxonomic use.
|
746
|
*
|
747
|
* @see #AMBIGUOUS()
|
748
|
* @see #CONFUSUM()
|
749
|
*
|
750
|
*/
|
751
|
public static final NomenclaturalStatusType SUBNUDUM(){
|
752
|
return getTermByUuid(uuidSubnudum);
|
753
|
}
|
754
|
|
755
|
/**
|
756
|
* Returns the nomenclatural status type "comb. nov.". No further information available for now.
|
757
|
* @return
|
758
|
*/
|
759
|
//TODO javadoc. this term was added for Flore du Gabon
|
760
|
public static final NomenclaturalStatusType COMB_NOV(){
|
761
|
return getTermByUuid(uuidCombNov);
|
762
|
}
|
763
|
|
764
|
/**
|
765
|
* Returns the nomenclatural status type "opus utique oppressum". This type
|
766
|
* relates to article 32.7 (old ICBN) and article 32.9 as well as App. 6
|
767
|
* (new {@link NomenclaturalCode#ICBN() ICBN}). This is a reference list of botanical opera, in which all
|
768
|
* {@link BotanicalName taxon names} (or names of a certain rank) are oppressed. Such a name has the
|
769
|
* status "invalid" but in contrary to "rejected" not a single name
|
770
|
* is rejected by the commission but an opus with regard to the validity of
|
771
|
* all taxon names occurring in it.<BR>
|
772
|
* An "opus utique oppressum" taxon name is therefore also "invalid"
|
773
|
* ("not available" for {@link IZoologicalName zoological names}).
|
774
|
*
|
775
|
* @see #isInvalidType()
|
776
|
*/
|
777
|
public static final NomenclaturalStatusType OPUS_UTIQUE_OPPR(){
|
778
|
return getTermByUuid(uuidOpusUtiqueOppr);
|
779
|
}
|
780
|
|
781
|
/**
|
782
|
* TODO
|
783
|
* @return
|
784
|
*/
|
785
|
public static final NomenclaturalStatusType ZOO_NOT_AVAILABLE (){
|
786
|
return getTermByUuid(uuidZooNotAvailable);
|
787
|
}
|
788
|
|
789
|
/**
|
790
|
* TODO
|
791
|
* @return
|
792
|
*/
|
793
|
public static final NomenclaturalStatusType ZOO_INVALID (){
|
794
|
return getTermByUuid(uuidZooInvalid);
|
795
|
}
|
796
|
|
797
|
/**
|
798
|
* TODO
|
799
|
* @return
|
800
|
*/
|
801
|
public static final NomenclaturalStatusType ZOO_SUPPRESSED (){
|
802
|
return getTermByUuid(uuidZooSuppressed);
|
803
|
}
|
804
|
|
805
|
public static final NomenclaturalStatusType ZOO_OBLITUM (){
|
806
|
return getTermByUuid(uuidZooOblitum);
|
807
|
}
|
808
|
|
809
|
|
810
|
|
811
|
//TODO further Zoological status
|
812
|
|
813
|
|
814
|
//TODO Soraya
|
815
|
// orth. var.: orthographic variant
|
816
|
// pro syn.: pro synonymo
|
817
|
|
818
|
// TODO
|
819
|
// Preliminary implementation for BotanicalNameParser.
|
820
|
// not yet complete
|
821
|
/**
|
822
|
* Returns the nomenclatural status type identified through its label
|
823
|
* abbreviation. Preliminary implementation for BotanicalNameParser.
|
824
|
*
|
825
|
* @param statusAbbreviation the label abbreviation
|
826
|
* @param name the taxon name
|
827
|
* @return the nomenclatural status type
|
828
|
*
|
829
|
*/
|
830
|
public static NomenclaturalStatusType getNomenclaturalStatusTypeByAbbreviation(String statusAbbreviation, ITaxonNameBase name) throws UnknownCdmTypeException{
|
831
|
if (statusAbbreviation == null){
|
832
|
throw new NullPointerException("Abbreviation is NULL in getNomenclaturalStatusTypeByAbbreviation");
|
833
|
}
|
834
|
NomenclaturalStatusType result = null;
|
835
|
statusAbbreviation = normalizeStatusAbbrev(statusAbbreviation);
|
836
|
|
837
|
//TODO handle undefined names correctly
|
838
|
boolean isZooname = name == null? false : name.getNameType().equals(NomenclaturalCode.ICZN);
|
839
|
|
840
|
Map<String, UUID> map = isZooname ? zooAbbrevMap : abbrevMap;
|
841
|
if (map == null ){
|
842
|
return null;
|
843
|
}
|
844
|
//non unique abbrev
|
845
|
if (! isZooname && statusAbbreviation.equalsIgnoreCase("nom. alternativ.")){
|
846
|
return NomenclaturalStatusType.ALTERNATIVE();
|
847
|
}
|
848
|
UUID uuid = map.get(statusAbbreviation);
|
849
|
if (uuid != null ){
|
850
|
result = getTermByUuid(uuid);
|
851
|
}
|
852
|
if (result != null){
|
853
|
return result;
|
854
|
}else {
|
855
|
throw new UnknownCdmTypeException("Unknown nom. status abbreviation: " + statusAbbreviation);
|
856
|
}
|
857
|
}
|
858
|
|
859
|
/**
|
860
|
* @param statusAbbreviation
|
861
|
* @return
|
862
|
*/
|
863
|
private static String normalizeStatusAbbrev(String statusAbbreviation) {
|
864
|
//#7109 should not happen anymore
|
865
|
if (statusAbbreviation.equalsIgnoreCase("nom. valid")){
|
866
|
statusAbbreviation = "nom. val.";
|
867
|
}
|
868
|
return statusAbbreviation;
|
869
|
}
|
870
|
|
871
|
/**
|
872
|
* Returns the nomenclatural status type identified through its label.
|
873
|
*
|
874
|
* @param statusLabel the nomenclatural status label
|
875
|
* @return the nomenclatural status type
|
876
|
*
|
877
|
*/
|
878
|
public static NomenclaturalStatusType getNomenclaturalStatusTypeByLabel(String statusLabel) throws UnknownCdmTypeException{
|
879
|
if (statusLabel == null){
|
880
|
throw new NullPointerException("Status label is NULL in getNomenclaturalStatusTypeBylabel");
|
881
|
}
|
882
|
NomenclaturalStatusType result = null;
|
883
|
if (labelMap == null){
|
884
|
return null;
|
885
|
}
|
886
|
statusLabel = statusLabel.toLowerCase();
|
887
|
UUID uuid = labelMap.get(statusLabel);
|
888
|
if (uuid != null ){
|
889
|
result = getTermByUuid(uuid);
|
890
|
}
|
891
|
if (result != null){
|
892
|
return result;
|
893
|
}else {
|
894
|
if (statusLabel == null){
|
895
|
statusLabel = "(null)";
|
896
|
}
|
897
|
throw new UnknownCdmTypeException("Unknown nom. status label: " + statusLabel);
|
898
|
}
|
899
|
}
|
900
|
|
901
|
|
902
|
/**
|
903
|
* Fills <i>this</i> nomenclatural status type with contents (uuid, uri,
|
904
|
* description text, label and label abbreviation) coming from a csv line.
|
905
|
* The implicit language for the description text is "latin".
|
906
|
* This method overrides the method of {@link eu.etaxonomy.cdm.model.common.DefinedTermBase DefinedTermBase}.
|
907
|
*
|
908
|
* @param csvLine the (ordered) list of substrings from a csv string
|
909
|
* to be used to fill <i>this</i> nomenclatural status type
|
910
|
* @see #NomenclaturalStatusType(String, String, String)
|
911
|
* @see #readCsvLine(List, Language)
|
912
|
* @see eu.etaxonomy.cdm.model.common.DefinedTermBase#readCsvLine(List)
|
913
|
*/
|
914
|
|
915
|
@Override
|
916
|
public NomenclaturalStatusType readCsvLine(Class<NomenclaturalStatusType> termClass, List<String> csvLine, Map<UUID,DefinedTermBase> terms, boolean abbrevAsId) { //TODO should be List<String> but makes error for some strange reason
|
917
|
try {
|
918
|
NomenclaturalStatusType newInstance = termClass.newInstance();
|
919
|
DefinedTermBase.readCsvLine(newInstance, csvLine, Language.LATIN(), abbrevAsId);
|
920
|
return newInstance;
|
921
|
} catch (Exception e) {
|
922
|
e.printStackTrace();
|
923
|
throw new RuntimeException(e);
|
924
|
}
|
925
|
}
|
926
|
|
927
|
@Override
|
928
|
protected void setDefaultTerms(TermVocabulary<NomenclaturalStatusType> termVocabulary) {
|
929
|
if (termVocabulary.getUuid().equals(uuidIcnafpNomStatusVocabulary)){
|
930
|
termMap = new HashMap<UUID, NomenclaturalStatusType>();
|
931
|
abbrevMap = new HashMap<String, UUID>();
|
932
|
labelMap = new HashMap<String, UUID>();
|
933
|
for (NomenclaturalStatusType term : termVocabulary.getTerms()){
|
934
|
termMap.put(term.getUuid(), term);
|
935
|
addStatusType(term, abbrevMap, labelMap);
|
936
|
}
|
937
|
}else if (termVocabulary.getUuid().equals(uuidIcznNomStatusVocabulary)){
|
938
|
zooTermMap = new HashMap<UUID, NomenclaturalStatusType>();
|
939
|
zooAbbrevMap = new HashMap<String, UUID>();
|
940
|
zooLabelMap = new HashMap<String, UUID>();
|
941
|
for (NomenclaturalStatusType term : termVocabulary.getTerms()){
|
942
|
zooTermMap.put(term.getUuid(), term);
|
943
|
addStatusType(term, zooAbbrevMap, zooLabelMap);
|
944
|
}
|
945
|
}else{
|
946
|
throw new IllegalArgumentException("Unknown Nom.Status Vocabulary");
|
947
|
}
|
948
|
}
|
949
|
|
950
|
public static void initDefaultTerms() {
|
951
|
TermVocabulary<NomenclaturalStatusType> vocabulary = getTermByUuid(uuidDoubtful).getVocabulary();
|
952
|
|
953
|
(new NomenclaturalStatusType()).setDefaultTerms(vocabulary);
|
954
|
}
|
955
|
|
956
|
/**
|
957
|
* Adds the status type to the (abbreviated) label maps
|
958
|
* @param term
|
959
|
*/
|
960
|
private void addStatusType(NomenclaturalStatusType statusType, Map<String, UUID> abbrevMap, Map<String, UUID> labelMap ) {
|
961
|
if (statusType == null){
|
962
|
logger.warn("statusType is NULL");
|
963
|
return;
|
964
|
}
|
965
|
List<Language> list = new ArrayList<Language>();
|
966
|
list.add(Language.LATIN());
|
967
|
list.add(Language.ENGLISH());
|
968
|
list.add(Language.DEFAULT());
|
969
|
|
970
|
Representation representation = statusType.getPreferredRepresentation(list);
|
971
|
if (representation != null){
|
972
|
|
973
|
String abbrevLabel = representation.getAbbreviatedLabel();
|
974
|
String label = representation.getLabel();
|
975
|
if (abbrevLabel == null){
|
976
|
logger.warn("label is NULL");
|
977
|
return;
|
978
|
}
|
979
|
|
980
|
//add to map
|
981
|
abbrevMap.put(abbrevLabel, statusType.getUuid());
|
982
|
labelMap.put(label.toLowerCase(), statusType.getUuid());
|
983
|
}
|
984
|
|
985
|
}
|
986
|
|
987
|
|
988
|
|
989
|
/**
|
990
|
* NomenclaturalStatusType should always be shown in latin, therefore the only existing representation
|
991
|
* is the latin one. In case we pass in another Language to this method it will return a <code>null</code> representation.
|
992
|
*
|
993
|
* In case the representation becomes null, we fall back to the latin representation.
|
994
|
*
|
995
|
*/
|
996
|
@Override
|
997
|
public Representation getRepresentation(Language lang) {
|
998
|
Representation representation = super.getRepresentation(lang);
|
999
|
|
1000
|
if(representation == null){
|
1001
|
representation = super.getRepresentation(Language.LATIN());
|
1002
|
}
|
1003
|
|
1004
|
return representation;
|
1005
|
}
|
1006
|
|
1007
|
|
1008
|
}
|