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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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* @created 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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//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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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 ZoologicalName 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 TaxonNameBase 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(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 ZoologicalName 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 TaxonNameBase 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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){
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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 ZoologicalName 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 TaxonNameBase 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 TaxonNameBase 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 ZoologicalName 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 TaxonNameBase 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
|
|
311
|
* also "illegitimate" (("invalid" for {@link ZoologicalName zoological names}).
|
|
312
|
*
|
|
313
|
* @see #VALID()
|
|
314
|
* @see #REJECTED()
|
|
315
|
* @see #isIllegitimateType()
|
|
316
|
*/
|
|
317
|
public static final NomenclaturalStatusType DOUBTFUL(){
|
|
318
|
return getTermByUuid(uuidDoubtful);
|
|
319
|
}
|
|
320
|
|
|
321
|
/**
|
|
322
|
* Returns the nomenclatural status type "confusum". A "valid" ("available")
|
|
323
|
* {@link TaxonNameBase taxon name} is "confusum" if it has been widely
|
|
324
|
* and persistently used for a taxon or taxa not including its type.<BR>
|
|
325
|
* A "confusum" taxon name is treated as if "rejected" and is therefore
|
|
326
|
* also "illegitimate" ("invalid" for {@link ZoologicalName zoological names}).
|
|
327
|
*
|
|
328
|
* @see #VALID()
|
|
329
|
* @see #REJECTED()
|
|
330
|
* @see #isIllegitimateType()
|
|
331
|
*/
|
|
332
|
public static final NomenclaturalStatusType CONFUSUM(){
|
|
333
|
return getTermByUuid(uuidConfusum);
|
|
334
|
}
|
|
335
|
|
|
336
|
/**
|
|
337
|
* Returns the nomenclatural status type "illegitimate" ("invalid" for
|
|
338
|
* {@link ZoologicalName zoological names}). A "valid" ("available")
|
|
339
|
* {@link TaxonNameBase taxon name}, unless "conserved" or "sanctioned", is "illegitimate"
|
|
340
|
* if it was "superfluous" when published or has been later "rejected".<BR>
|
|
341
|
*
|
|
342
|
* @see #VALID()
|
|
343
|
* @see #SUPERFLUOUS()
|
|
344
|
* @see #REJECTED()
|
|
345
|
*/
|
|
346
|
public static final NomenclaturalStatusType ILLEGITIMATE(){
|
|
347
|
return getTermByUuid(uuidIllegitimate);
|
|
348
|
}
|
|
349
|
|
|
350
|
/**
|
|
351
|
* Returns the nomenclatural status type "superfluous". A "valid"
|
|
352
|
* ("available") {@link TaxonNameBase taxon name} is "superfluous" if, when published,
|
|
353
|
* the taxon to which it was applied, as circumscribed by its {@link NonViralName#getCombinationAuthorship() author},
|
|
354
|
* definitely included the type of a name which ought to have been adopted,
|
|
355
|
* or of which the epithet ought to have been adopted, under the rules of
|
|
356
|
* the {@link NomenclaturalCode nomenclature code}, and if it has not been later declared
|
|
357
|
* "conserved" or "sanctioned" by the competent authorities.<BR>
|
|
358
|
* A "superfluous" taxon name is therefore also "illegitimate" ("invalid" for
|
|
359
|
* {@link ZoologicalName zoological names}).
|
|
360
|
*
|
|
361
|
* @see #VALID()
|
|
362
|
* @see #CONSERVED()
|
|
363
|
* @see #SANCTIONED()
|
|
364
|
* @see #isIllegitimateType()
|
|
365
|
*/
|
|
366
|
public static final NomenclaturalStatusType SUPERFLUOUS(){
|
|
367
|
return getTermByUuid(uuidSuperfluous);
|
|
368
|
}
|
|
369
|
|
|
370
|
/**
|
|
371
|
* Returns the nomenclatural status type "rejected". A "valid" ("available")
|
|
372
|
* {@link TaxonNameBase taxon name} is "rejected" if, even though by the strict
|
|
373
|
* application of the rules of the {@link NomenclaturalCode nomenclature code}, and especially
|
|
374
|
* of the principle of priority, it should be "legitimate" ("valid" for
|
|
375
|
* {@link ZoologicalName zoological names}), competent authorities decided to handle
|
|
376
|
* it as "illegitimate".<BR>
|
|
377
|
* A "rejected" taxon name is therefore also "illegitimate" ("invalid" for
|
|
378
|
* zoological names). A "rejected" taxon name is always rejected in favour
|
|
379
|
* of a "conserved" taxon name.
|
|
380
|
*
|
|
381
|
* @see #VALID()
|
|
382
|
* @see #isLegitimateType()
|
|
383
|
* @see #isIllegitimateType()
|
|
384
|
* @see #CONSERVED()
|
|
385
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
|
386
|
*/
|
|
387
|
public static final NomenclaturalStatusType REJECTED(){
|
|
388
|
return getTermByUuid(uuidRejected);
|
|
389
|
}
|
|
390
|
|
|
391
|
/**
|
|
392
|
* Returns the nomenclatural status type "utique rejected". A "valid"
|
|
393
|
* ("available") {@link TaxonNameBase taxon name} is "utique rejected" if it is rejected
|
|
394
|
* outright (without being rejected in favour of a "conserved" taxon name).<BR>
|
|
395
|
* An "utique rejected" taxon name is therefore also "illegitimate"
|
|
396
|
* ("invalid" for zoological names).
|
|
397
|
*
|
|
398
|
* @see #REJECTED()
|
|
399
|
* @see #VALID()
|
|
400
|
* @see #isIllegitimateType()
|
|
401
|
* @see #CONSERVED()
|
|
402
|
*/
|
|
403
|
public static final NomenclaturalStatusType UTIQUE_REJECTED(){
|
|
404
|
return getTermByUuid(uuidUtiqueRejected);
|
|
405
|
}
|
|
406
|
|
|
407
|
/**
|
|
408
|
* Returns the nomenclatural status type "proposed to be conserved". A
|
|
409
|
* "valid" ("available") {@link TaxonNameBase taxon name} is "proposed to be conserved"
|
|
410
|
* if, even though by the strict application of the rules of
|
|
411
|
* the {@link NomenclaturalCode nomenclature code}, and especially of the principle of priority,
|
|
412
|
* it is "illegitimate" ("invalid" for {@link ZoologicalName zoological names}),
|
|
413
|
* it has been submitted to competent authorities in order to decide whether
|
|
414
|
* it should be handled as "legitimate".<BR>
|
|
415
|
* A "proposed to be conserved" taxon name is therefore still "illegitimate"
|
|
416
|
* ("invalid" for zoological names).
|
|
417
|
*
|
|
418
|
* {@link https://dev.e-taxonomy.eu/trac/ticket/5662}
|
|
419
|
*
|
|
420
|
* @see #VALID()
|
|
421
|
* @see #isIllegitimateType()
|
|
422
|
* @see #isLegitimateType()
|
|
423
|
* @see #CONSERVED()
|
|
424
|
* @see #CONSERVED_DESIG()
|
|
425
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
|
426
|
*/
|
|
427
|
public static final NomenclaturalStatusType CONSERVED_PROP(){
|
|
428
|
return getTermByUuid(uuidConservedProp);
|
|
429
|
}
|
|
430
|
|
|
431
|
/**
|
|
432
|
* Returns the nomenclatural status type "designated to be conserved". A
|
|
433
|
* "valid" ("available") {@link TaxonNameBase taxon name} is "designated to be conserved"
|
|
434
|
* if, even though by the strict application of the rules of
|
|
435
|
* the {@link NomenclaturalCode nomenclature code}, and especially of the principle of priority,
|
|
436
|
* it is "illegitimate" ("invalid" for {@link ZoologicalName zoological names}),
|
|
437
|
* it has been submitted to competent authorities in order to decide whether
|
|
438
|
* it should be handled as "legitimate".<BR>
|
|
439
|
* A "proposed to be conserved" taxon name is therefore still "illegitimate"
|
|
440
|
* ("invalid" for zoological names).
|
|
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 TaxonNameBase 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 ZoologicalName 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 ZoologicalName zoological names}). A "valid" ("available")
|
|
479
|
* {@link TaxonNameBase 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 TaxonNameBase 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 ZoologicalName 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 TaxonNameBase 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 ZoologicalName 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 TaxonNameBase 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 ZoologicalName 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
|
* Returns the nomenclatural status type "orthography rejected". <BR>
|
|
566
|
* TBC.
|
|
567
|
* See also {@link http://dev.e-taxonomy.eu/trac/ticket/5649}
|
|
568
|
*
|
|
569
|
* @see #ORTHOGRAPHY_CONSERVED()
|
|
570
|
* @see #REJECTED()
|
|
571
|
* @see #isIllegitimateType()
|
|
572
|
*/
|
|
573
|
public static final NomenclaturalStatusType ORTHOGRAPHY_REJECTED(){
|
|
574
|
return getTermByUuid(uuidOrthographyRejected);
|
|
575
|
}
|
|
576
|
|
|
577
|
/**
|
|
578
|
* Returns the nomenclatural status type "proposed to be rejected". A
|
|
579
|
* "valid" ("available") {@link TaxonNameBase taxon name} is "proposed to be rejected"
|
|
580
|
* if, even though by the strict application of the rules of
|
|
581
|
* the {@link NomenclaturalCode nomenclature code}, and especially of the principle of priority,
|
|
582
|
* it should be "legitimate" ("valid" for {@link ZoologicalName zoological names}),
|
|
583
|
* it has been submitted to competent authorities in order to decide whether
|
|
584
|
* it should be handled as "illegitimate".<BR>
|
|
585
|
* A "proposed to be rejected" taxon name is therefore still "legitimate"
|
|
586
|
* ("valid" for zoological names). A "proposed to be rejected" taxon name is always
|
|
587
|
* to be rejected in favour of a "proposed to be conserved" taxon name.
|
|
588
|
*
|
|
589
|
* @see #VALID()
|
|
590
|
* @see #isLegitimateType()
|
|
591
|
* @see #isIllegitimateType()
|
|
592
|
* @see #REJECTED()
|
|
593
|
* @see #CONSERVED_PROP()
|
|
594
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
|
595
|
*/
|
|
596
|
public static final NomenclaturalStatusType REJECTED_PROP(){
|
|
597
|
return getTermByUuid(uuidRejectedProp);
|
|
598
|
}
|
|
599
|
|
|
600
|
|
|
601
|
/**
|
|
602
|
* Returns the nomenclatural status type "conserved". A "valid"
|
|
603
|
* ("available") {@link TaxonNameBase taxon name} is "conserved" if, even though by the strict
|
|
604
|
* application of the rules of the {@link NomenclaturalCode nomenclature code}, and especially of
|
|
605
|
* the principle of priority, it should be "illegitimate" ("invalid" for
|
|
606
|
* {@link ZoologicalName zoological names}), competent authorities decided to handle
|
|
607
|
* it as "legitimate".<BR>
|
|
608
|
* A "conserved" taxon name is therefore also "legitimate" ("valid" for
|
|
609
|
* zoological names).
|
|
610
|
*
|
|
611
|
* @see #VALID()
|
|
612
|
* @see #isIllegitimateType()
|
|
613
|
* @see #isLegitimateType()
|
|
614
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
|
615
|
*/
|
|
616
|
public static final NomenclaturalStatusType CONSERVED(){
|
|
617
|
return getTermByUuid(uuidConserved);
|
|
618
|
}
|
|
619
|
|
|
620
|
/**
|
|
621
|
* Returns the nomenclatural status type "sanctioned". {@link BotanicalName Botanical names}
|
|
622
|
* for fungi are "sanctioned" if they were published in the opera mentioned
|
|
623
|
* in Article 13.1d of the {@link NomenclaturalCode#ICBN() ICBN}.<BR>
|
|
624
|
* A "sanctioned" taxon name is treated as if "conserved" and is therefore
|
|
625
|
* also "legitimate".
|
|
626
|
*
|
|
627
|
* @see #VALID()
|
|
628
|
* @see #CONSERVED()
|
|
629
|
* @see #isLegitimateType()
|
|
630
|
*/
|
|
631
|
public static final NomenclaturalStatusType SANCTIONED(){
|
|
632
|
return getTermByUuid(uuidSanctioned);
|
|
633
|
}
|
|
634
|
|
|
635
|
/**
|
|
636
|
* Returns the nomenclatural status type "invalid" (this corresponds to
|
|
637
|
* "not available" for {@link ZoologicalName zoological names}). The use of "invalid"
|
|
638
|
* {@link TaxonNameBase taxon names} should be avoided.<BR>
|
|
639
|
* A taxon name is "invalid" if it is not "valid"; this means that
|
|
640
|
* the taxon name:<ul>
|
|
641
|
* <li>has not been effectively published or
|
|
642
|
* <li>has a form which does not comply with the rules of the
|
|
643
|
* {@link NomenclaturalCode nomenclature code} or
|
|
644
|
* <li>is not accompanied by a description or diagnosis or by a reference to
|
|
645
|
* such a previously published description or diagnosis
|
|
646
|
* </ul>
|
|
647
|
*
|
|
648
|
* @see #VALID()
|
|
649
|
* @see #isInvalidType()
|
|
650
|
* @see #ILLEGITIMATE()
|
|
651
|
*/
|
|
652
|
public static final NomenclaturalStatusType INVALID(){
|
|
653
|
return getTermByUuid(uuidInvalid);
|
|
654
|
}
|
|
655
|
|
|
656
|
/**
|
|
657
|
* Returns the nomenclatural status type "nudum". A {@link TaxonNameBase taxon name} is "nudum"
|
|
658
|
* if its publication is not accompanied by a description or diagnosis or
|
|
659
|
* by a reference to such a previously published description or diagnosis.<BR>
|
|
660
|
* A "nudum" taxon name is therefore also "invalid" ("not available" for
|
|
661
|
* {@link ZoologicalName zoological names}).
|
|
662
|
*
|
|
663
|
* @see #isInvalidType()
|
|
664
|
*/
|
|
665
|
public static final NomenclaturalStatusType NUDUM(){
|
|
666
|
return getTermByUuid(uuidNudum);
|
|
667
|
}
|
|
668
|
|
|
669
|
/**
|
|
670
|
* Returns the nomenclatural status type "invalid combination". A
|
|
671
|
* {@link TaxonNameBase bi- or trinomial} is an "invalid combination" if its
|
|
672
|
* {@link NonViralName#getCombinationAuthorship() author} did not definitely associate the final
|
|
673
|
* epithet with the name of the genus or species, or with its abbreviation.<BR>
|
|
674
|
* An "invalid combination" taxon name is therefore also "invalid"
|
|
675
|
* ("not available" for {@link ZoologicalName zoological names}).
|
|
676
|
*
|
|
677
|
* @see #isInvalidType()
|
|
678
|
*/
|
|
679
|
public static final NomenclaturalStatusType COMBINATION_INVALID(){
|
|
680
|
return getTermByUuid(uuidCombinationInvalid);
|
|
681
|
}
|
|
682
|
|
|
683
|
/**
|
|
684
|
* Returns the nomenclatural status type "illegitimate combination".
|
|
685
|
* TODO explanation
|
|
686
|
*
|
|
687
|
* @see #isInvalidType()
|
|
688
|
*/
|
|
689
|
public static final NomenclaturalStatusType COMBINATION_ILLEGITIMATE(){
|
|
690
|
return getTermByUuid(uuidCombinationIllegitimate);
|
|
691
|
}
|
|
692
|
|
|
693
|
/**
|
|
694
|
* Returns the nomenclatural status type "provisional". A {@link TaxonNameBase taxon name} is
|
|
695
|
* "provisional" if it has not been yet effectively published.<BR>
|
|
696
|
* A "provisional" taxon name is therefore also "invalid"
|
|
697
|
* ("not available" for {@link ZoologicalName zoological names}).
|
|
698
|
*
|
|
699
|
* @see #isInvalidType()
|
|
700
|
*/
|
|
701
|
public static final NomenclaturalStatusType PROVISIONAL(){
|
|
702
|
return getTermByUuid(uuidProvisional);
|
|
703
|
}
|
|
704
|
|
|
705
|
/**
|
|
706
|
* Returns the nomenclatural status type "valid" (this corresponds to
|
|
707
|
* "available" for {@link ZoologicalName zoological names}).<BR>
|
|
708
|
* A {@link TaxonNameBase taxon name} is "valid" if it:<ul>
|
|
709
|
* <li>has been effectively published and
|
|
710
|
* <li>has a form which complies with the rules of the
|
|
711
|
* {@link NomenclaturalCode nomenclature code} and
|
|
712
|
* <li>is accompanied by a description or diagnosis or by a reference to
|
|
713
|
* such a previously published description or diagnosis
|
|
714
|
* </ul>
|
|
715
|
*
|
|
716
|
* @see #INVALID()
|
|
717
|
* @see #LEGITIMATE()
|
|
718
|
*/
|
|
719
|
public static final NomenclaturalStatusType VALID(){
|
|
720
|
return getTermByUuid(uuidValid);
|
|
721
|
}
|
|
722
|
|
|
723
|
/**
|
|
724
|
* Returns the nomenclatural status type "subnudum". This type is not
|
|
725
|
* covered by {@link NomenclaturalCode nomenclature codes}. It appears sometimes in literature and
|
|
726
|
* represents the opinion of the author who considers the {@link TaxonNameBase taxon name} to be
|
|
727
|
* unusable for an unambiguous taxonomic use.
|
|
728
|
*
|
|
729
|
* @see #AMBIGUOUS()
|
|
730
|
* @see #CONFUSUM()
|
|
731
|
*
|
|
732
|
*/
|
|
733
|
public static final NomenclaturalStatusType SUBNUDUM(){
|
|
734
|
return getTermByUuid(uuidSubnudum);
|
|
735
|
}
|
|
736
|
|
|
737
|
/**
|
|
738
|
* Returns the nomenclatural status type "comb. nov.". No further information available for now.
|
|
739
|
* @return
|
|
740
|
*/
|
|
741
|
//TODO javadoc. this term was added for Flore du Gabon
|
|
742
|
public static final NomenclaturalStatusType COMB_NOV(){
|
|
743
|
return getTermByUuid(uuidCombNov);
|
|
744
|
}
|
|
745
|
|
|
746
|
/**
|
|
747
|
* Returns the nomenclatural status type "opus utique oppressum". This type
|
|
748
|
* relates to article 32.7 (old ICBN) and article 32.9 as well as App. 6
|
|
749
|
* (new {@link NomenclaturalCode#ICBN() ICBN}). This is a reference list of botanical opera, in which all
|
|
750
|
* {@link BotanicalName taxon names} (or names of a certain rank) are oppressed. Such a name has the
|
|
751
|
* status "invalid" but in contrary to "rejected" not a single name
|
|
752
|
* is rejected by the commission but an opus with regard to the validity of
|
|
753
|
* all taxon names occurring in it.<BR>
|
|
754
|
* An "opus utique oppressum" taxon name is therefore also "invalid"
|
|
755
|
* ("not available" for {@link ZoologicalName zoological names}).
|
|
756
|
*
|
|
757
|
* @see #isInvalidType()
|
|
758
|
*/
|
|
759
|
public static final NomenclaturalStatusType OPUS_UTIQUE_OPPR(){
|
|
760
|
return getTermByUuid(uuidOpusUtiqueOppr);
|
|
761
|
}
|
|
762
|
|
|
763
|
/**
|
|
764
|
* TODO
|
|
765
|
* @return
|
|
766
|
*/
|
|
767
|
public static final NomenclaturalStatusType ZOO_NOT_AVAILABLE (){
|
|
768
|
return getTermByUuid(uuidZooNotAvailable);
|
|
769
|
}
|
|
770
|
|
|
771
|
/**
|
|
772
|
* TODO
|
|
773
|
* @return
|
|
774
|
*/
|
|
775
|
public static final NomenclaturalStatusType ZOO_INVALID (){
|
|
776
|
return getTermByUuid(uuidZooInvalid);
|
|
777
|
}
|
|
778
|
|
|
779
|
/**
|
|
780
|
* TODO
|
|
781
|
* @return
|
|
782
|
*/
|
|
783
|
public static final NomenclaturalStatusType ZOO_SUPPRESSED (){
|
|
784
|
return getTermByUuid(uuidZooSuppressed);
|
|
785
|
}
|
|
786
|
|
|
787
|
//TODO further Zoological status
|
|
788
|
|
|
789
|
|
|
790
|
//TODO Soraya
|
|
791
|
// orth. var.: orthographic variant
|
|
792
|
// pro syn.: pro synonymo
|
|
793
|
|
|
794
|
// TODO
|
|
795
|
// Preliminary implementation for BotanicalNameParser.
|
|
796
|
// not yet complete
|
|
797
|
/**
|
|
798
|
* Returns the nomenclatural status type identified through its label
|
|
799
|
* abbreviation. Preliminary implementation for BotanicalNameParser.
|
|
800
|
*
|
|
801
|
* @param statusAbbreviation the label abbreviation
|
|
802
|
* @param name
|
|
803
|
* @return the nomenclatural status type
|
|
804
|
*
|
|
805
|
*/
|
|
806
|
public static NomenclaturalStatusType getNomenclaturalStatusTypeByAbbreviation(String statusAbbreviation, NonViralName<?> name) throws UnknownCdmTypeException{
|
|
807
|
if (statusAbbreviation == null){
|
|
808
|
throw new NullPointerException("Abbreviation is NULL in getNomenclaturalStatusTypeByAbbreviation");
|
|
809
|
}
|
|
810
|
NomenclaturalStatusType result = null;
|
|
811
|
|
|
812
|
//TODO handle undefined names correctly
|
|
813
|
boolean isZooname = name.getNomenclaturalCode().equals(NomenclaturalCode.ICZN);
|
|
814
|
|
|
815
|
Map<String, UUID> map = isZooname ? zooAbbrevMap : abbrevMap;
|
|
816
|
if (map == null ){
|
|
817
|
return null;
|
|
818
|
}
|
|
819
|
//non unique abbrev
|
|
820
|
if (! isZooname && statusAbbreviation.equalsIgnoreCase("nom. alternativ.")){
|
|
821
|
return NomenclaturalStatusType.ALTERNATIVE();
|
|
822
|
}
|
|
823
|
UUID uuid = map.get(statusAbbreviation);
|
|
824
|
if (uuid != null ){
|
|
825
|
result = getTermByUuid(uuid);
|
|
826
|
}
|
|
827
|
if (result != null){
|
|
828
|
return result;
|
|
829
|
}else {
|
|
830
|
if (statusAbbreviation == null){
|
|
831
|
statusAbbreviation = "(null)";
|
|
832
|
}
|
|
833
|
throw new UnknownCdmTypeException("Unknown nom. status abbreviation: " + statusAbbreviation);
|
|
834
|
}
|
|
835
|
|
|
836
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. ambig.")) { return NomenclaturalStatusType.AMBIGUOUS();
|
|
837
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. dub.")) { return NomenclaturalStatusType.DOUBTFUL();
|
|
838
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. confus.")) { return NomenclaturalStatusType.CONFUSUM();
|
|
839
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. illeg.")){return NomenclaturalStatusType.ILLEGITIMATE();
|
|
840
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. superfl.")){ return NomenclaturalStatusType.SUPERFLUOUS();
|
|
841
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. rej.")) { return NomenclaturalStatusType.REJECTED();
|
|
842
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. utique rej.")) { return NomenclaturalStatusType.UTIQUE_REJECTED();
|
|
843
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. cons. prop.")) { return NomenclaturalStatusType.CONSERVED_PROP();
|
|
844
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. orth. cons. prop.")) { return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP();
|
|
845
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. legit.")) { return NomenclaturalStatusType.LEGITIMATE();
|
|
846
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. altern.")) { return NomenclaturalStatusType.ALTERNATIVE();
|
|
847
|
|
|
848
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. alternativ.")) { return NomenclaturalStatusType.ALTERNATIVE();
|
|
849
|
|
|
850
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. nov.")) { return NomenclaturalStatusType.NOVUM();
|
|
851
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. utique rej. prop.")) { return NomenclaturalStatusType.UTIQUE_REJECTED_PROP();
|
|
852
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. orth. cons.")) { return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED();
|
|
853
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. rej. prop.")) { return NomenclaturalStatusType.REJECTED_PROP();
|
|
854
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. cons.")) { return NomenclaturalStatusType.CONSERVED();
|
|
855
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. sanct.")) { return NomenclaturalStatusType.SANCTIONED();
|
|
856
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. inval.")) { return NomenclaturalStatusType.INVALID();
|
|
857
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. nud.")){ return NomenclaturalStatusType.NUDUM();
|
|
858
|
// }else if (statusAbbreviation.equalsIgnoreCase("comb. inval.")){ return NomenclaturalStatusType.COMBINATION_INVALID();
|
|
859
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. provis.")) { return NomenclaturalStatusType.PROVISIONAL();
|
|
860
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. valid")) { return NomenclaturalStatusType.VALID();
|
|
861
|
// }else if (statusAbbreviation.equalsIgnoreCase("opus. utique oppr.")) { return NomenclaturalStatusType.OPUS_UTIQUE_OPPR();
|
|
862
|
// }else if (statusAbbreviation.equalsIgnoreCase("nom. subnud.")) { return NomenclaturalStatusType.SUBNUDUM();
|
|
863
|
// //TODO make generic, use labels for map
|
|
864
|
// }else {
|
|
865
|
// if (statusAbbreviation == null){
|
|
866
|
// statusAbbreviation = "(null)";
|
|
867
|
// }
|
|
868
|
// throw new eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException("Unknown NomenclaturalStatusType abbreviation: " + statusAbbreviation);
|
|
869
|
// }
|
|
870
|
}
|
|
871
|
|
|
872
|
/**
|
|
873
|
* Returns the nomenclatural status type identified through its label.
|
|
874
|
*
|
|
875
|
* @param statusLabel the nomenclatural status label
|
|
876
|
* @return the nomenclatural status type
|
|
877
|
*
|
|
878
|
*/
|
|
879
|
public static NomenclaturalStatusType getNomenclaturalStatusTypeByLabel(String statusLabel) throws UnknownCdmTypeException{
|
|
880
|
if (statusLabel == null){
|
|
881
|
throw new NullPointerException("Status label is NULL in getNomenclaturalStatusTypeBylabel");
|
|
882
|
}
|
|
883
|
NomenclaturalStatusType result = null;
|
|
884
|
if (labelMap == null){
|
|
885
|
return null;
|
|
886
|
}
|
|
887
|
statusLabel = statusLabel.toLowerCase();
|
|
888
|
UUID uuid = labelMap.get(statusLabel);
|
|
889
|
if (uuid != null ){
|
|
890
|
result = getTermByUuid(uuid);
|
|
891
|
}
|
|
892
|
if (result != null){
|
|
893
|
return result;
|
|
894
|
}else {
|
|
895
|
if (statusLabel == null){
|
|
896
|
statusLabel = "(null)";
|
|
897
|
}
|
|
898
|
throw new UnknownCdmTypeException("Unknown nom. status label: " + statusLabel);
|
|
899
|
}
|
|
900
|
|
|
901
|
// if (statusLabel == null){ throw new NullPointerException("statusLabel is 'null' in getNomenclaturalStatusTypeByLabel");
|
|
902
|
// }else if (statusLabel.equalsIgnoreCase("Ambiguous")) { return NomenclaturalStatusType.AMBIGUOUS();
|
|
903
|
// }else if (statusLabel.equalsIgnoreCase("Doubtful")) { return NomenclaturalStatusType.DOUBTFUL();
|
|
904
|
// }else if (statusLabel.equalsIgnoreCase("Confusum")) { return NomenclaturalStatusType.CONFUSUM();
|
|
905
|
// }else if (statusLabel.equalsIgnoreCase("Illegitimate")){return NomenclaturalStatusType.ILLEGITIMATE();
|
|
906
|
// }else if (statusLabel.equalsIgnoreCase("Superfluous")){ return NomenclaturalStatusType.SUPERFLUOUS();
|
|
907
|
// }else if (statusLabel.equalsIgnoreCase("Rejected")) { return NomenclaturalStatusType.REJECTED();
|
|
908
|
// }else if (statusLabel.equalsIgnoreCase("Utique Rejected")) { return NomenclaturalStatusType.UTIQUE_REJECTED();
|
|
909
|
// }else if (statusLabel.equalsIgnoreCase("Conserved Prop")) { return NomenclaturalStatusType.CONSERVED_PROP();
|
|
910
|
// }else if (statusLabel.equalsIgnoreCase("Orthography Conserved Prop")) { return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP();
|
|
911
|
// }else if (statusLabel.equalsIgnoreCase("Legitimate")) { return NomenclaturalStatusType.LEGITIMATE();
|
|
912
|
// }else if (statusLabel.equalsIgnoreCase("Alternative")) { return NomenclaturalStatusType.ALTERNATIVE();
|
|
913
|
// }else if (statusLabel.equalsIgnoreCase("Novum")) { return NomenclaturalStatusType.NOVUM();
|
|
914
|
// }else if (statusLabel.equalsIgnoreCase("Utique Rejected Prop")) { return NomenclaturalStatusType.UTIQUE_REJECTED_PROP();
|
|
915
|
// }else if (statusLabel.equalsIgnoreCase("Orthography Conserved")) { return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED();
|
|
916
|
// }else if (statusLabel.equalsIgnoreCase("Rejected Prop")) { return NomenclaturalStatusType.REJECTED_PROP();
|
|
917
|
// }else if (statusLabel.equalsIgnoreCase("Conserved")) { return NomenclaturalStatusType.CONSERVED();
|
|
918
|
// }else if (statusLabel.equalsIgnoreCase("Sanctioned")) { return NomenclaturalStatusType.SANCTIONED();
|
|
919
|
// }else if (statusLabel.equalsIgnoreCase("Invalid")) { return NomenclaturalStatusType.INVALID();
|
|
920
|
// }else if (statusLabel.equalsIgnoreCase("Nudum")){ return NomenclaturalStatusType.NUDUM();
|
|
921
|
// }else if (statusLabel.equalsIgnoreCase("Combination Invalid")){ return NomenclaturalStatusType.COMBINATION_INVALID();
|
|
922
|
// }else if (statusLabel.equalsIgnoreCase("Provisional")) { return NomenclaturalStatusType.PROVISIONAL();
|
|
923
|
// }else if (statusLabel.equalsIgnoreCase("Valid")) { return NomenclaturalStatusType.VALID();
|
|
924
|
// }else if (statusLabel.equalsIgnoreCase("Opus Utique Oppr")) { return NomenclaturalStatusType.OPUS_UTIQUE_OPPR();
|
|
925
|
// }else if (statusLabel.equalsIgnoreCase("Subnudum")) { return NomenclaturalStatusType.SUBNUDUM();
|
|
926
|
// }else {
|
|
927
|
// if (statusLabel == null){
|
|
928
|
// statusLabel = "(null)";
|
|
929
|
// }
|
|
930
|
// throw new eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException("Unknown NomenclaturalStatusType abbreviation: " + statusLabel);
|
|
931
|
// }
|
|
932
|
}
|
|
933
|
|
|
934
|
|
|
935
|
/**
|
|
936
|
* Fills <i>this</i> nomenclatural status type with contents (uuid, uri,
|
|
937
|
* description text, label and label abbreviation) coming from a csv line.
|
|
938
|
* The implicit language for the description text is "latin".
|
|
939
|
* This method overrides the method of {@link eu.etaxonomy.cdm.model.common.DefinedTermBase DefinedTermBase}.
|
|
940
|
*
|
|
941
|
* @param csvLine the (ordered) list of substrings from a csv string
|
|
942
|
* to be used to fill <i>this</i> nomenclatural status type
|
|
943
|
* @see #NomenclaturalStatusType(String, String, String)
|
|
944
|
* @see #readCsvLine(List, Language)
|
|
945
|
* @see eu.etaxonomy.cdm.model.common.DefinedTermBase#readCsvLine(List)
|
|
946
|
*/
|
|
947
|
|
|
948
|
@Override
|
|
949
|
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
|
|
950
|
try {
|
|
951
|
NomenclaturalStatusType newInstance = termClass.newInstance();
|
|
952
|
DefinedTermBase.readCsvLine(newInstance, csvLine, Language.LATIN(), abbrevAsId);
|
|
953
|
return newInstance;
|
|
954
|
} catch (Exception e) {
|
|
955
|
e.printStackTrace();
|
|
956
|
throw new RuntimeException(e);
|
|
957
|
}
|
|
958
|
}
|
|
959
|
|
|
960
|
@Override
|
|
961
|
protected void setDefaultTerms(TermVocabulary<NomenclaturalStatusType> termVocabulary) {
|
|
962
|
if (termVocabulary.getUuid().equals(uuidIcnafpNomStatusVocabulary)){
|
|
963
|
termMap = new HashMap<UUID, NomenclaturalStatusType>();
|
|
964
|
abbrevMap = new HashMap<String, UUID>();
|
|
965
|
labelMap = new HashMap<String, UUID>();
|
|
966
|
for (NomenclaturalStatusType term : termVocabulary.getTerms()){
|
|
967
|
termMap.put(term.getUuid(), term);
|
|
968
|
addStatusType(term, abbrevMap, labelMap);
|
|
969
|
}
|
|
970
|
}else if (termVocabulary.getUuid().equals(uuidIcznNomStatusVocabulary)){
|
|
971
|
zooTermMap = new HashMap<UUID, NomenclaturalStatusType>();
|
|
972
|
zooAbbrevMap = new HashMap<String, UUID>();
|
|
973
|
zooLabelMap = new HashMap<String, UUID>();
|
|
974
|
for (NomenclaturalStatusType term : termVocabulary.getTerms()){
|
|
975
|
zooTermMap.put(term.getUuid(), term);
|
|
976
|
addStatusType(term, zooAbbrevMap, zooLabelMap);
|
|
977
|
}
|
|
978
|
}else{
|
|
979
|
throw new IllegalArgumentException("Unknown Nom.Status Vocabulary");
|
|
980
|
}
|
|
981
|
}
|
|
982
|
|
|
983
|
/**
|
|
984
|
* Adds the status type to the (abbreviated) label maps
|
|
985
|
* @param term
|
|
986
|
*/
|
|
987
|
private void addStatusType(NomenclaturalStatusType statusType, Map<String, UUID> abbrevMap, Map<String, UUID> labelMap ) {
|
|
988
|
if (statusType == null){
|
|
989
|
logger.warn("statusType is NULL");
|
|
990
|
return;
|
|
991
|
}
|
|
992
|
List<Language> list = new ArrayList<Language>();
|
|
993
|
list.add(Language.LATIN());
|
|
994
|
list.add(Language.ENGLISH());
|
|
995
|
list.add(Language.DEFAULT());
|
|
996
|
|
|
997
|
Representation representation = statusType.getPreferredRepresentation(list);
|
|
998
|
if (representation != null){
|
|
999
|
|
|
1000
|
String abbrevLabel = representation.getAbbreviatedLabel();
|
|
1001
|
String label = representation.getLabel();
|
|
1002
|
if (abbrevLabel == null){
|
|
1003
|
logger.warn("label is NULL");
|
|
1004
|
return;
|
|
1005
|
}
|
|
1006
|
|
|
1007
|
//add to map
|
|
1008
|
abbrevMap.put(abbrevLabel, statusType.getUuid());
|
|
1009
|
labelMap.put(label.toLowerCase(), statusType.getUuid());
|
|
1010
|
}
|
|
1011
|
|
|
1012
|
}
|
|
1013
|
|
|
1014
|
|
|
1015
|
|
|
1016
|
/**
|
|
1017
|
* NomenclaturalStatusType should always be shown in latin, therefore the only existing representation
|
|
1018
|
* is the latin one. In case we pass in another Language to this method it will return a <code>null</code> representation.
|
|
1019
|
*
|
|
1020
|
* In case the representation becomes null, we fall back to the latin representation.
|
|
1021
|
*
|
|
1022
|
*/
|
|
1023
|
@Override
|
|
1024
|
public Representation getRepresentation(Language lang) {
|
|
1025
|
Representation representation = super.getRepresentation(lang);
|
|
1026
|
|
|
1027
|
if(representation == null){
|
|
1028
|
representation = super.getRepresentation(Language.LATIN());
|
|
1029
|
}
|
|
1030
|
|
|
1031
|
return representation;
|
|
1032
|
}
|
|
1033
|
|
|
1034
|
|
|
1035
|
}
|