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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.Column;
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import javax.persistence.Entity;
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import javax.validation.constraints.Min;
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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.commons.lang.StringUtils;
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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.Analyze;
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import org.hibernate.search.annotations.Field;
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import org.hibernate.search.annotations.Indexed;
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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.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
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import eu.etaxonomy.cdm.strategy.cache.name.CacheUpdate;
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import eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy;
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import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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import eu.etaxonomy.cdm.validation.annotation.NullOrNotEmpty;
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/**
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* The taxon name class for animals.
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* <P>
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* This class corresponds to: NameZoological 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 13:07:03
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* @see NonViralName
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "ZoologicalName", propOrder = {
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"breed",
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"publicationYear",
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"originalPublicationYear"
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})
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@XmlRootElement(name = "ZoologicalName")
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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 ZoologicalName extends NonViralName<ZoologicalName> implements Cloneable{
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private static final long serialVersionUID = 845745609734814484L;
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(ZoologicalName.class);
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//Name of the breed of an animal
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@XmlElement(name = "Breed")
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@Field
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@NullOrNotEmpty
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@Column(length=255)
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private String breed;
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@XmlElement(name = "PublicationYear")
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@Field(analyze = Analyze.NO)
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@CacheUpdate(value ="authorshipCache")
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@Min(0)
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private Integer publicationYear;
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@XmlElement(name = "OriginalPublicationYear")
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@Field(analyze = Analyze.NO)
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@CacheUpdate(value ="authorshipCache")
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@Min(0)
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private Integer originalPublicationYear;
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static private INonViralNameParser nameParser = new NonViralNameParserImpl();
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// ************* CONSTRUCTORS *************/
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/**
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* Class constructor: creates a new zoological taxon name instance
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* only containing the {@link eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy default cache strategy}.
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*
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* @see #ZoologicalName(Rank, HomotypicalGroup)
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* @see #ZoologicalName(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
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* @see eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy
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*/
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protected ZoologicalName() {
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this.cacheStrategy = ZooNameDefaultCacheStrategy.NewInstance();
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}
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/**
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* Class constructor: creates a new zoological taxon name instance
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* only containing its {@link Rank rank},
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* its {@link HomotypicalGroup homotypical group} and
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* the {@link eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy default cache strategy}.
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* The new zoological taxon name instance will be also added to the set of
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* zoological taxon names belonging to the given homotypical group.
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*
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* @param rank the rank to be assigned to <i>this</i> zoological taxon name
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* @param homotypicalGroup the homotypical group to which <i>this</i> zoological taxon name belongs
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* @see #ZoologicalName()
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* @see #ZoologicalName(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
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* @see eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy
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*/
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protected ZoologicalName(Rank rank, HomotypicalGroup homotypicalGroup) {
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super(rank, homotypicalGroup);
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this.cacheStrategy = ZooNameDefaultCacheStrategy.NewInstance();
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}
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/**
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* Class constructor: creates a new zoological taxon name instance
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* containing its {@link Rank rank},
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* its {@link HomotypicalGroup homotypical group},
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* its scientific name components, its {@link eu.etaxonomy.cdm.agent.TeamOrPersonBase author(team)},
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* its {@link eu.etaxonomy.cdm.reference.INomenclaturalReference nomenclatural reference} and
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* the {@link eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy default cache strategy}.
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* The new zoological taxon name instance will be also added to the set of
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* zoological taxon names belonging to the given homotypical group.
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*
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* @param rank the rank to be assigned to <i>this</i> zoological taxon name
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* @param genusOrUninomial the string for <i>this</i> zoological taxon name
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* if its rank is genus or higher or for the genus part
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* if its rank is lower than genus
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* @param infraGenericEpithet the string for the first epithet of
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* <i>this</i> zoological taxon name if its rank is lower than genus
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* and higher than species aggregate
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* @param specificEpithet the string for the first epithet of
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* <i>this</i> zoological taxon name if its rank is species aggregate or lower
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* @param infraSpecificEpithet the string for the second epithet of
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* <i>this</i> zoological taxon name if its rank is lower than species
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* @param combinationAuthorship the author or the team who published <i>this</i> zoological taxon name
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* @param nomenclaturalReference the nomenclatural reference where <i>this</i> zoological taxon name was published
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* @param nomenclMicroRef the string with the details for precise location within the nomenclatural reference
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* @param homotypicalGroup the homotypical group to which <i>this</i> zoological taxon name belongs
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* @see #ZoologicalName()
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* @see #ZoologicalName(Rank, HomotypicalGroup)
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* @see #NewInstance(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
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* @see eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy
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* @see eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy
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* @see eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
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*/
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protected ZoologicalName (Rank rank, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, TeamOrPersonBase combinationAuthorship, INomenclaturalReference nomenclaturalReference, String nomenclMicroRef, HomotypicalGroup homotypicalGroup) {
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super(rank, genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet, combinationAuthorship, nomenclaturalReference, nomenclMicroRef, homotypicalGroup);
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this.cacheStrategy = ZooNameDefaultCacheStrategy.NewInstance();
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}
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//********* METHODS **************************************/
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/**
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* Creates a new zoological taxon name instance
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* only containing its {@link Rank rank} and
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* the {@link eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy default cache strategy}.
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*
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* @param rank the rank to be assigned to <i>this</i> zoological taxon name
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* @see #ZoologicalName(Rank, HomotypicalGroup)
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* @see #NewInstance(Rank, HomotypicalGroup)
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* @see #NewInstance(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
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* @see eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy
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*/
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public static ZoologicalName NewInstance(Rank rank){
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return new ZoologicalName(rank, null);
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}
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/**
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* Creates a new zoological taxon name instance
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* only containing its {@link Rank rank},
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* its {@link HomotypicalGroup homotypical group} and
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* the {@link eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy default cache strategy}.
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* The new zoological taxon name instance will be also added to the set of
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* zoological taxon names belonging to the given homotypical group.
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*
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* @param rank the rank to be assigned to <i>this</i> zoological taxon name
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* @param homotypicalGroup the homotypical group to which <i>this</i> zoological taxon name belongs
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* @see #NewInstance(Rank)
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* @see #NewInstance(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
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* @see #ZoologicalName(Rank, HomotypicalGroup)
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* @see eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy
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*/
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public static ZoologicalName NewInstance(Rank rank, HomotypicalGroup homotypicalGroup){
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return new ZoologicalName(rank, homotypicalGroup);
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}
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/**
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* Creates a new zoological taxon name instance
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* containing its {@link Rank rank},
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* its {@link HomotypicalGroup homotypical group},
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* its scientific name components, its {@link eu.etaxonomy.cdm.agent.TeamOrPersonBase author(team)},
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* its {@link eu.etaxonomy.cdm.reference.INomenclaturalReference nomenclatural reference} and
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* the {@link eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy default cache strategy}.
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* The new zoological taxon name instance will be also added to the set of
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* zoological taxon names belonging to the given homotypical group.
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*
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* @param rank the rank to be assigned to <i>this</i> zoological taxon name
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* @param genusOrUninomial the string for <i>this</i> zoological taxon name
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* if its rank is genus or higher or for the genus part
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* if its rank is lower than genus
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* @param infraGenericEpithet the string for the first epithet of
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* <i>this</i> zoological taxon name if its rank is lower than genus
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* and higher than species aggregate
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* @param specificEpithet the string for the first epithet of
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* <i>this</i> zoological taxon name if its rank is species aggregate or lower
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* @param infraSpecificEpithet the string for the second epithet of
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* <i>this</i> zoological taxon name if its rank is lower than species
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* @param combinationAuthorship the author or the team who published <i>this</i> zoological taxon name
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* @param nomenclaturalReference the nomenclatural reference where <i>this</i> zoological taxon name was published
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* @param nomenclMicroRef the string with the details for precise location within the nomenclatural reference
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* @param homotypicalGroup the homotypical group to which <i>this</i> zoological taxon name belongs
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* @see #NewInstance(Rank)
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* @see #NewInstance(Rank, HomotypicalGroup)
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* @see #ZoologicalName(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
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* @see eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy
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*/
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public static ZoologicalName NewInstance(Rank rank, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, TeamOrPersonBase combinationAuthorship, INomenclaturalReference nomenclaturalReference, String nomenclMicroRef, HomotypicalGroup homotypicalGroup) {
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return new ZoologicalName(rank, genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet, combinationAuthorship, nomenclaturalReference, nomenclMicroRef, homotypicalGroup);
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}
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/**
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* Returns a zoological taxon name based on parsing a string representing
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* all elements (according to the {@link NomenclaturalCode#ICZN() ICZN}) of a zoological taxon name (where
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* the scientific name is an uninomial) including authorship but without
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* nomenclatural reference.
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*
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* @param fullNameString the string to be parsed
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* @return the new zoological taxon name
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*/
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public static ZoologicalName PARSED_NAME(String fullNameString){
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return PARSED_NAME(fullNameString, Rank.GENUS());
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}
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/**
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* Returns a zoological taxon name based on parsing a string representing
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* all elements (according to the {@link NomenclaturalCode#ICZN() ICZN})) of a zoological taxon name including
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* authorship but without nomenclatural reference. The parsing result
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* depends on the given rank of the zoological taxon name to be created.
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*
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* @param fullNameString the string to be parsed
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* @param rank the rank of the taxon name
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* @return the new zoological taxon name
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*/
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public static ZoologicalName PARSED_NAME(String fullNameString, Rank rank){
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if (nameParser == null){
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nameParser = new NonViralNameParserImpl();
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}
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return (ZoologicalName)nameParser.parseFullName(fullNameString, NomenclaturalCode.ICZN, rank);
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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> zoological taxon name, that is the
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* International Code of Zoological Nomenclature. This method overrides
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* the getNomenclaturalCode method from {@link NonViralName NonViralName}.
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*
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* @return the nomenclatural code for animals
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* @see NonViralName#isCodeCompliant()
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* @see NonViralName#getNomenclaturalCode()
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* @see TaxonNameBase#getHasProblem()
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*/
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@Override
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public NomenclaturalCode getNomenclaturalCode(){
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return NomenclaturalCode.ICZN;
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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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/* ***************** GETTER / SETTER ***************************/
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/**
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* Returns the breed name string for <i>this</i> animal (zoological taxon name).
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*
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* @return the string containing the breed name for <i>this</i> zoological taxon name
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*/
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public String getBreed(){
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return this.breed;
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}
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/**
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* @see #getBreed()
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*/
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public void setBreed(String breed){
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this.breed = StringUtils.isBlank(breed) ? null : breed;
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}
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/**
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* Returns the publication year (as an integer) for <i>this</i> zoological taxon
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* name. If the publicationYear attribute is null and a nomenclatural
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* reference exists the year could be computed from the
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* {@link eu.etaxonomy.cdm.reference.INomenclaturalReference nomenclatural reference}.
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*
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* @return the integer representing the publication year for <i>this</i> zoological taxon name
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* @see #getOriginalPublicationYear()
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*/
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public Integer getPublicationYear() {
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return publicationYear;
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}
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/**
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* @see #getPublicationYear()
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*/
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public void setPublicationYear(Integer publicationYear) {
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322
|
this.publicationYear = publicationYear;
|
|
323
|
}
|
|
324
|
|
|
325
|
/**
|
|
326
|
* Returns the publication year (as an integer) of the original validly
|
|
327
|
* published species epithet for <i>this</i> zoological taxon name. This only
|
|
328
|
* applies for zoological taxon names that are no {@link TaxonNameBase#isOriginalCombination() original combinations}.
|
|
329
|
* If the originalPublicationYear attribute is null the year could be taken
|
|
330
|
* from the publication year of the corresponding original name (basionym)
|
|
331
|
* or from the {@link eu.etaxonomy.cdm.reference.INomenclaturalReference nomenclatural reference} of the basionym
|
|
332
|
* if it exists.
|
|
333
|
*
|
|
334
|
* @return the integer representing the publication year of the original
|
|
335
|
* species epithet corresponding to <i>this</i> zoological taxon name
|
|
336
|
* @see #getPublicationYear()
|
|
337
|
*/
|
|
338
|
public Integer getOriginalPublicationYear() {
|
|
339
|
return originalPublicationYear;
|
|
340
|
}
|
|
341
|
/**
|
|
342
|
* @see #getOriginalPublicationYear()
|
|
343
|
*/
|
|
344
|
public void setOriginalPublicationYear(Integer originalPublicationYear) {
|
|
345
|
this.originalPublicationYear = originalPublicationYear;
|
|
346
|
}
|
|
347
|
|
|
348
|
|
|
349
|
//*********************** CLONE ********************************************************/
|
|
350
|
|
|
351
|
/**
|
|
352
|
* Clones <i>this</i> zoological name. This is a shortcut that enables to create
|
|
353
|
* a new instance that differs only slightly from <i>this</i> zoological name by
|
|
354
|
* modifying only some of the attributes.
|
|
355
|
*
|
|
356
|
* @see eu.etaxonomy.cdm.model.name.NonViralName#clone()
|
|
357
|
* @see java.lang.Object#clone()
|
|
358
|
*/
|
|
359
|
@Override
|
|
360
|
public Object clone() {
|
|
361
|
ZoologicalName result = (ZoologicalName)super.clone();
|
|
362
|
//no changes to: breed, publicationYear, originalPublicationYear
|
|
363
|
return result;
|
|
364
|
}
|
|
365
|
}
|