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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.Map;
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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.XmlElement;
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import javax.xml.bind.annotation.XmlRootElement;
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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 org.hibernate.search.annotations.Field;
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import org.hibernate.search.annotations.Index;
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import org.hibernate.search.annotations.Indexed;
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import org.hibernate.validator.constraints.Length;
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import org.springframework.beans.factory.annotation.Configurable;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy;
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import eu.etaxonomy.cdm.validation.annotation.NullOrNotEmpty;
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/**
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* The taxon name class for viral taxa. The scientific name will be stored
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* as a string (consisting eventually of several words even combined also with
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* non alphabetical characters) in the inherited {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#setTitleCache(String) titleCache} attribute.
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* Classification has no influence on the names of viral taxon names and no
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* viral taxon must be taxonomically included in another viral taxon with
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* higher rank. For examples see ICTVdb:
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* "http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/vn_indxA.htm"
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* <P>
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* This class corresponds to: NameViral according to the ABCD schema.
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*
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* @author m.doering
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* @version 1.0
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* @created 08-Nov-2007 13:07:02
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "", propOrder = {
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"acronym"
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})
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@XmlRootElement(name = "ViralName")
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@Entity
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@Indexed(index = "eu.etaxonomy.cdm.model.name.TaxonNameBase")
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@Audited
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@Configurable
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public class ViralName extends TaxonNameBase<ViralName, INameCacheStrategy<ViralName>> implements Cloneable {
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private static final long serialVersionUID = 4516625507432071817L;
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private static final Logger logger = Logger.getLogger(ViralName.class);
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// @XmlTransient
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// @Transient
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// protected INameCacheStrategy<ViralName> cacheStrategy;
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@XmlElement(name = "Acronym")
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@Field(index=Index.TOKENIZED)
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@NullOrNotEmpty
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@Length(max = 255)
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private String acronym;
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// ************* CONSTRUCTORS *************/
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protected ViralName(){
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super();
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}
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/**
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* Class constructor: creates a new viral taxon name instance
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* only containing its {@link Rank rank}.
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*
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* @param rank the rank to be assigned to <i>this</i> viral taxon name
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* @see TaxonNameBase#TaxonNameBase(Rank)
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*/
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public ViralName(Rank rank) {
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super(rank);
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}
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//***********************
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private static Map<String, java.lang.reflect.Field> allFields = null;
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@Override
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protected Map<String, java.lang.reflect.Field> getAllFields(){
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if (allFields == null){
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allFields = CdmUtils.getAllFields(this.getClass(), CdmBase.class, false, false, false, true);
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}
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return allFields;
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}
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//*************************
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//********* METHODS **************************************/
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/**
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* Creates a new viral taxon name instance only containing its {@link Rank rank}.
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*
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* @param rank the rank to be assigned to <i>this</i> viral taxon name
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* @see #ViralName(Rank)
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*/
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public static ViralName NewInstance(Rank rank){
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return new ViralName(rank);
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}
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/**
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* Returns the accepted acronym (an assigned abbreviation) string for <i>this</i>
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* viral taxon name. For instance PCV stays for Peanut Clump Virus.
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*
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* @return the string containing the accepted acronym of <i>this</i> viral taxon name
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*/
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public String getAcronym(){
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return this.acronym;
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}
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/**
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* @see #getAcronym()
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*/
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public void setAcronym(String acronym){
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this.acronym = acronym;
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}
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/**
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* Generates and returns the string with the scientific name of <i>this</i>
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* viral taxon name. This string may be stored in the inherited
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* {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache() titleCache} attribute.
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* This method overrides the generic and inherited
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* method from {@link TaxonNameBase TaxonNameBase} .
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*
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* @return the string with the composed name of <i>this</i> viral taxon name with authorship (and maybe year)
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* @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()
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* @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache()
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* @see TaxonNameBase#generateTitle()
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*/
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// @Override
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// public String generateTitle(){
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// logger.warn("not yet implemented");
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// return this.toString();
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// }
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@Override
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public String generateFullTitle(){
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logger.warn("not yet implemented");
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return this.toString();
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}
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/**
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* Returns the boolean value "true" if the components of <i>this</i> viral taxon name
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* follow the rules of the corresponding
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* {@link NomenclaturalCode International Code of Virus Classification and Nomenclature},
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* "false" otherwise.
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* This method overrides and implements the isCodeCompliant method from
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* the abstract {@link TaxonNameBase#isCodeCompliant() TaxonNameBase} class.
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*
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* @return the boolean value expressing the compliance of <i>this</i> viral taxon name to its nomenclatural code
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* @see TaxonNameBase#isCodeCompliant()
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*/
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@Override
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@Transient
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public boolean isCodeCompliant() {
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logger.warn("not yet implemented");
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return false;
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}
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/**
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* Returns the {@link NomenclaturalCode nomenclatural code} that governs
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* the construction of <i>this</i> viral taxon name, that is the
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* International Code of Virus Classification and Nomenclature.
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* This method overrides the getNomeclaturalCode method from {@link TaxonNameBase TaxonNameBase}.
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*
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* @return the nomenclatural code for viruses
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* @see #isCodeCompliant()
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* @see TaxonNameBase#getHasProblem()
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* @see TaxonNameBase#getNomenclaturalCode()
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*/
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@Override
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public NomenclaturalCode getNomenclaturalCode(){
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return NomenclaturalCode.ICVCN;
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}
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/**
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* Returns the {@link eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy cache strategy} used to generate
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* several strings corresponding to <i>this</i> viral taxon name.
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*
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* @return the cache strategy used for <i>this</i> viral taxon name
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* @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy
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* @see eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
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*/
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// @Override
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// @Transient
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// public INameCacheStrategy getCacheStrategy() {
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// return cacheStrategy;
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// }
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/**
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* @see #getCacheStrategy()
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*/
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// @Override
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// public void setCacheStrategy(INameCacheStrategy cacheStrategy) {
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// this.cacheStrategy = cacheStrategy;
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// }
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//*********************** CLONE ********************************************************/
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/**
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* Clones <i>this</i> viral name. This is a shortcut that enables to create
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* a new instance that differs only slightly from <i>this</i> viral name by
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* modifying only some of the attributes.
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*
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* @see eu.etaxonomy.cdm.model.name.TaxonNameBase#clone()
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* @see java.lang.Object#clone()
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*/
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@Override
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public Object clone() {
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ViralName result = (ViralName)super.clone();
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//no changes to: acronym
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return result;
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}
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}
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