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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.model.name;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import javax.persistence.Transient;
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import javax.xml.bind.annotation.XmlEnum;
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import javax.xml.bind.annotation.XmlEnumValue;
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import javax.xml.bind.annotation.XmlType;
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import org.apache.log4j.Logger;
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import au.com.bytecode.opencsv.CSVWriter;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.IDefinedTerm;
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import eu.etaxonomy.cdm.model.media.Media;
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/**
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* The class for the five nomenclature codes (ICNB, ICBN, ICNCP, ICZN and ICVCN)
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* ruling {@link TaxonNameBase taxon names}.
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* <P>
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* The standard set of nomenclature code instances will be automatically created
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* as the project starts. But this class allows to extend this standard set by
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* creating new instances of additional nomenclature codes if unlikely needed.
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* <P>
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* This class corresponds to: <ul>
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* <li> NomenclaturalCodeTerm according to the TDWG ontology
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* <li> NomenclaturalCodesEnum according to the TCS
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* <li> CodeOfNomenclatureEnum according to the ABCD schema
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* </ul>
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*
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* @author a.mueller
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* @created 19.05.2008
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* @version 2.0
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*/
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@XmlType(name = "NomenclaturalCode")
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@XmlEnum
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public enum NomenclaturalCode implements IDefinedTerm<NomenclaturalCode> {
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//International Code of Nomenclature of Bacteria
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@XmlEnumValue("ICNB") ICNB(UUID.fromString("ff4b0979-7abf-4b40-95c0-8b8b1e8a4d5e")),
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//International Code of Botanical Nomenclature
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@XmlEnumValue("ICBN") ICBN(UUID.fromString("540fc02a-8a8e-4813-89d2-581dad4dd482")),
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//International Code of Cultivated Plants
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@XmlEnumValue("ICNCP") ICNCP(UUID.fromString("65a432b5-92b1-4c9a-8090-2a185e423d2e")),
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//International Code of Zoological Nomenclature
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@XmlEnumValue("ICZN") ICZN(UUID.fromString("b584c2f8-dbe5-4454-acad-2b45e63ec11b")),
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//International Code for Virus Classification and Nomenclature
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@XmlEnumValue("ICVCN") ICVCN(UUID.fromString("e9d6d6b4-ccb7-4f28-b828-0b1501f8c75a"));
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private static final Logger logger = Logger.getLogger(NomenclaturalCode.class);
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private UUID uuid;
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private NomenclaturalCode(UUID uuid){
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this.uuid = uuid;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.IDefinedTerm#getUuid()
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*/
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public UUID getUuid(){
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return this.uuid;
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}
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/* (non-Javadoc)
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* @see java.lang.Enum#toString()
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*/
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@Override
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public String toString() {
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return "NomenclaturalCode" + " <" + uuid + "> " + this.name();
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}
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public static NomenclaturalCode fromString(String string){
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for(NomenclaturalCode code : NomenclaturalCode.values()){
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if(code.name().equals(string)) return code;
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}
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return null;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.IDefinedTerm#getByUuid(java.util.UUID)
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*/
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public NomenclaturalCode getByUuid(UUID uuid) {
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for (NomenclaturalCode nomCode : NomenclaturalCode.values()){
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if (nomCode.getUuid().equals(uuid)){
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return nomCode;
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}
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}
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return null;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.IDefinedTerm#getGeneralizationOf()
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*/
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public Set<NomenclaturalCode> getGeneralizationOf() {
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return new HashSet<NomenclaturalCode>();
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.IDefinedTerm#getIncludes()
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*/
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public Set<NomenclaturalCode> getIncludes() {
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return new HashSet<NomenclaturalCode>();
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.IDefinedTerm#getKindOf()
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*/
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public NomenclaturalCode getKindOf() {
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return null;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.IDefinedTerm#getPartOf()
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*/
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public NomenclaturalCode getPartOf() {
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return null;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.IDefinedTerm#getMedia()
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*/
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public Set<Media> getMedia() {
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// TODO add links to codes
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return new HashSet<Media>();
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.ILoadableTerm#readCsvLine(java.lang.Class, java.util.List, java.util.Map)
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*/
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public NomenclaturalCode readCsvLine(Class<NomenclaturalCode> termClass,
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List<String> csvLine, Map<UUID, DefinedTermBase> terms) {
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// TODO Auto-generated method stub
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return null;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.ILoadableTerm#writeCsvLine(au.com.bytecode.opencsv.CSVWriter, eu.etaxonomy.cdm.model.common.IDefinedTerm)
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*/
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public void writeCsvLine(CSVWriter writer, NomenclaturalCode term) {
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// TODO Auto-generated method stub
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logger.warn("write csvLine not yet implemented");
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}
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/**
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* Creates a new particular {@link TaxonNameBase taxon name} (botanical, zoological,
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* cultivar plant, bacterial or viral name) instance depending on <i>this</i>
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* nomenclature code only containing the given {@link Rank rank}.
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*
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* @param rank the rank of the new taxon name instance
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* @see BotanicalName#NewInstance(Rank)
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* @see ZoologicalName#NewInstance(Rank)
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* @see CultivarPlantName#NewInstance(Rank)
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* @see BacterialName#NewInstance(Rank)
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* @see ViralName#NewInstance(Rank)
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*/
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public TaxonNameBase<?,?> getNewTaxonNameInstance(Rank rank){
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TaxonNameBase<?,?> result;
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NomenclaturalCode nomCode = this;
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switch (this){
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case ICBN:
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result = BotanicalName.NewInstance(rank);
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break;
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case ICZN:
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result = ZoologicalName.NewInstance(rank);
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break;
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case ICNCP:
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result = CultivarPlantName.NewInstance(rank);
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break;
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case ICNB:
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result = BacterialName.NewInstance(rank);
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break;
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case ICVCN:
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result = ViralName.NewInstance(rank);
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break;
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default:
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logger.warn("Unknown nomenclatural code: " + this.getUuid());
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result = null;
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}
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return result;
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}
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/**
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* Creates a new particular {@link TaxonNameBase taxon name} (botanical, zoological,
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* cultivar plant, bacterial or viral name) instance depending on <i>this</i>
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* nomenclature code only containing the given {@link Rank rank}.
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*
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* @param rank the rank of the new taxon name instance
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* @see BotanicalName#NewInstance(Rank)
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* @see ZoologicalName#NewInstance(Rank)
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* @see CultivarPlantName#NewInstance(Rank)
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* @see BacterialName#NewInstance(Rank)
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* @see ViralName#NewInstance(Rank)
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*/
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@Transient
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public <T extends TaxonNameBase> Class<? extends T> getCdmClass(){
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Class<? extends T> result;
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switch (this){
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case ICBN:
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result = (Class<T>)BotanicalName.class;
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break;
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case ICZN:
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result = (Class<T>)ZoologicalName.class;
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break;
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case ICNCP:
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result = (Class<T>)CultivarPlantName.class;
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break;
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case ICNB:
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result = (Class<T>)BacterialName.class;
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break;
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case ICVCN:
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result = (Class<T>)ViralName.class;
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break;
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default:
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logger.warn("Unknown nomenclatural code: " + this.getUuid());
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result = null;
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}
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return result;
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}
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}
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//@XmlAccessorType(XmlAccessType.FIELD)
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//@Entity
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////@Audited
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//public class NomenclaturalCode extends DefinedTermBase<NomenclaturalCode> {
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// /**
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// * SerialVersionUID
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// */
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// private static final long serialVersionUID = -1011240079962589681L;
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// private static final Logger logger = Logger.getLogger(NomenclaturalCode.class);
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//
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// private static final UUID uuidIcnb = UUID.fromString("ff4b0979-7abf-4b40-95c0-8b8b1e8a4d5e");
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// private static final UUID uuidIcbn = UUID.fromString("540fc02a-8a8e-4813-89d2-581dad4dd482");
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// private static final UUID uuidIcncp = UUID.fromString("65a432b5-92b1-4c9a-8090-2a185e423d2e");
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// private static final UUID uuidIczn = UUID.fromString("b584c2f8-dbe5-4454-acad-2b45e63ec11b");
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// private static final UUID uuidIcvcn = UUID.fromString("e9d6d6b4-ccb7-4f28-b828-0b1501f8c75a");
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//
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// private static NomenclaturalCode ICZN;
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//
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// private static NomenclaturalCode ICVCN;
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//
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// private static NomenclaturalCode ICNCP;
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//
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// private static NomenclaturalCode ICBN;
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//
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// private static NomenclaturalCode ICNB;
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//
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//
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// protected static Map<UUID, NomenclaturalCode> termMap = null;
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//
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// protected static NomenclaturalCode getTermByUuid(UUID uuid){
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// if (termMap == null){
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// DefaultTermInitializer vocabularyStore = new DefaultTermInitializer();
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// vocabularyStore.initialize();
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// }
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// return (NomenclaturalCode)termMap.get(uuid);
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// }
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//
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//
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// // ************* CONSTRUCTORS *************/
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// /**
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// * Class constructor: creates a new empty nomenclature code instance.
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// *
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// * @see #NomenclaturalCode(String, String, String)
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// */
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// public NomenclaturalCode() {
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// super();
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// }
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//
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// /**
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// * Class constructor: creates an additional nomenclature code instance with
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// * a description (in the {@link eu.etaxonomy.cdm.model.common.Language#DEFAULT() default language}), a label and
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// * 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 nomenclature code to be created
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// * @param label the string identifying the new nomenclature code
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// * to be created
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// * @param labelAbbrev the string identifying (in abbreviated form) the
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// * new nomenclature code to be created
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// * @see #NomenclaturalCode()
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// */
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// public NomenclaturalCode(String term, String label, String labelAbbrev) {
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// super(term, label, labelAbbrev);
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// }
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//
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//
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// //********* METHODS **************************************/
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//
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// /**
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// * Returns the International Code of Nomenclature of Bacteria
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// */
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// public static final NomenclaturalCode ICNB(){
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// return getTermByUuid(uuidIcnb);
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//// return ICNB;
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// }
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//
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// /**
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// * Returns the International Code of Botanical Nomenclature
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// */
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// public static final NomenclaturalCode ICBN(){
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// return getTermByUuid(uuidIcbn);
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//// return ICBN;
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// }
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// /**
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// * Returns the International Code of Cultivated Plants
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// */
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// public static final NomenclaturalCode ICNCP(){
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// return getTermByUuid(uuidIcncp);
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//// return ICNCP;
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// }
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//
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// /**
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// * Returns the International Code of Zoological Nomenclature
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// */
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// public static final NomenclaturalCode ICZN(){
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// return getTermByUuid(uuidIczn);
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//// return ICZN;
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// }
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//
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//
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// /**
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// * Returns the International Code for Virus Classification and Nomenclature
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// */
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// public static final NomenclaturalCode ICVCN(){
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// return getTermByUuid(uuidIcvcn);
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//// return ICVCN; // FIXME(uuidIcvcn);
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// }
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//
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// /**
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// * Creates a new particular {@link TaxonNameBase taxon name} (botanical, zoological,
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// * cultivar plant, bacterial or viral name) instance depending on <i>this</i>
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// * nomenclature code only containing the given {@link Rank rank}.
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// *
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// * @param rank the rank of the new taxon name instance
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// * @see BotanicalName#NewInstance(Rank)
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// * @see ZoologicalName#NewInstance(Rank)
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// * @see CultivarPlantName#NewInstance(Rank)
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// * @see BacterialName#NewInstance(Rank)
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// * @see ViralName#NewInstance(Rank)
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// */
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362
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// @Transient
|
|
363
|
// public TaxonNameBase<?,?> getNewTaxonNameInstance(Rank rank){
|
|
364
|
// TaxonNameBase<?,?> result;
|
|
365
|
// if (this.equals(NomenclaturalCode.ICBN())){
|
|
366
|
// result = BotanicalName.NewInstance(rank);
|
|
367
|
// }else if (this.equals(NomenclaturalCode.ICZN())){
|
|
368
|
// result = ZoologicalName.NewInstance(rank);
|
|
369
|
// }else if (this.equals(NomenclaturalCode.ICNCP())){
|
|
370
|
// result = CultivarPlantName.NewInstance(rank);
|
|
371
|
// }else if (this.equals(NomenclaturalCode.ICNB())){
|
|
372
|
// result = BacterialName.NewInstance(rank);
|
|
373
|
// }else if (this.equals(NomenclaturalCode.ICVCN())){
|
|
374
|
// result = ViralName.NewInstance(rank);
|
|
375
|
// }else {
|
|
376
|
// logger.warn("Unknown nomenclatural code: " + this.getUuid());
|
|
377
|
// result = null;
|
|
378
|
// }
|
|
379
|
// return result;
|
|
380
|
// }
|
|
381
|
//
|
|
382
|
// /**
|
|
383
|
// * Creates a new particular {@link TaxonNameBase taxon name} (botanical, zoological,
|
|
384
|
// * cultivar plant, bacterial or viral name) instance depending on <i>this</i>
|
|
385
|
// * nomenclature code only containing the given {@link Rank rank}.
|
|
386
|
// *
|
|
387
|
// * @param rank the rank of the new taxon name instance
|
|
388
|
// * @see BotanicalName#NewInstance(Rank)
|
|
389
|
// * @see ZoologicalName#NewInstance(Rank)
|
|
390
|
// * @see CultivarPlantName#NewInstance(Rank)
|
|
391
|
// * @see BacterialName#NewInstance(Rank)
|
|
392
|
// * @see ViralName#NewInstance(Rank)
|
|
393
|
// */
|
|
394
|
// @Transient
|
|
395
|
// public <T extends TaxonNameBase> Class<? extends T> getCdmClass(){
|
|
396
|
// Class<? extends T> result;
|
|
397
|
// if (this.equals(NomenclaturalCode.ICBN())){
|
|
398
|
// result = (Class<T>)BotanicalName.class;
|
|
399
|
// }else if (this.equals(NomenclaturalCode.ICZN())){
|
|
400
|
// result = (Class<T>)ZoologicalName.class;
|
|
401
|
// }else if (this.equals(NomenclaturalCode.ICNCP())){
|
|
402
|
// result = (Class<T>)CultivarPlantName.class;
|
|
403
|
// }else if (this.equals(NomenclaturalCode.ICNB())){
|
|
404
|
// result = (Class<T>)BacterialName.class;
|
|
405
|
// }else if (this.equals(NomenclaturalCode.ICVCN())){
|
|
406
|
// result = (Class<T>)ViralName.class;
|
|
407
|
// }else {
|
|
408
|
// logger.warn("Unknown nomenclatural code: " + this.getUuid());
|
|
409
|
// result = null;
|
|
410
|
// }
|
|
411
|
// return result;
|
|
412
|
// }
|
|
413
|
//
|
|
414
|
// @Override
|
|
415
|
// protected void setDefaultTerms(TermVocabulary<NomenclaturalCode> termVocabulary) {
|
|
416
|
// termMap = new HashMap<UUID, NomenclaturalCode>();
|
|
417
|
// for (NomenclaturalCode term : termVocabulary.getTerms()){
|
|
418
|
// termMap.put(term.getUuid(), term);
|
|
419
|
// }
|
|
420
|
//
|
|
421
|
//// termMap.put(uuidIcbn, termVocabulary.findTermByUuid(NomenclaturalCode.uuidIcbn));
|
|
422
|
//// termMap.put(uuidIcnb, termVocabulary.findTermByUuid(NomenclaturalCode.uuidIcnb));
|
|
423
|
//// termMap.put(uuidIcncp, termVocabulary.findTermByUuid(NomenclaturalCode.uuidIcncp));
|
|
424
|
//// termMap.put(uuidIcvcn, termVocabulary.findTermByUuid(NomenclaturalCode.uuidIcvcn));
|
|
425
|
//// termMap.put(uuidIczn, termVocabulary.findTermByUuid(NomenclaturalCode.uuidIczn));
|
|
426
|
//
|
|
427
|
//// NomenclaturalCode.ICBN = termVocabulary.findTermByUuid(NomenclaturalCode.uuidIcbn);
|
|
428
|
//// NomenclaturalCode.ICNB = termVocabulary.findTermByUuid(NomenclaturalCode.uuidIcnb);
|
|
429
|
//// NomenclaturalCode.ICNCP = termVocabulary.findTermByUuid(NomenclaturalCode.uuidIcncp);
|
|
430
|
//// NomenclaturalCode.ICVCN = termVocabulary.findTermByUuid(NomenclaturalCode.uuidIcvcn);
|
|
431
|
//// NomenclaturalCode.ICZN = termVocabulary.findTermByUuid(NomenclaturalCode.uuidIczn);
|
|
432
|
// }
|
|
433
|
//
|
|
434
|
//
|
|
435
|
//}
|