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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.taxon;
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import javax.persistence.Entity;
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import javax.persistence.FetchType;
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import javax.persistence.ManyToOne;
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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.XmlIDREF;
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import javax.xml.bind.annotation.XmlRootElement;
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import javax.xml.bind.annotation.XmlSchemaType;
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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.annotations.Cascade;
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import org.hibernate.annotations.CascadeType;
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import org.hibernate.envers.Audited;
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import org.hibernate.search.annotations.ContainedIn;
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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.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.strategy.cache.taxon.ITaxonCacheStrategy;
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import eu.etaxonomy.cdm.strategy.cache.taxon.TaxonBaseDefaultCacheStrategy;
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import eu.etaxonomy.cdm.validation.Level3;
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import eu.etaxonomy.cdm.validation.annotation.HomotypicSynonymsShouldBelongToGroup;
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/**
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* The class for synonyms: these are {@link TaxonBase taxa} the {@link name.TaxonNameBase taxon names}
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* of which are not used by the {@link TaxonBase#getSec() reference} to designate a real
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* taxon but are mentioned as taxon names that were oder are used by some other
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* unspecified references to designate (at least to some extent) the same
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* particular real taxon. Synonyms that are {@link #getAcceptedTaxon() attached} to an accepted {@link Taxon taxon}
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* are actually meaningless.<BR>
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* Splitting taxa in "accepted/valid" and "synonyms"
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* makes it easier to handle particular relationships between
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* ("accepted/valid") {@link Taxon taxa} on the one hand and ("synonym") taxa
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* on the other.
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*
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* @author m.doering
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* @created 08-Nov-2007 13:06:55
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "Synonym", propOrder = {
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"acceptedTaxon",
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"type",
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"proParte",
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"partial"
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})
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@XmlRootElement(name = "Synonym")
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@Entity
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@Indexed(index = "eu.etaxonomy.cdm.model.taxon.TaxonBase")
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@Audited
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@Configurable
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@HomotypicSynonymsShouldBelongToGroup(groups = Level3.class)
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public class Synonym extends TaxonBase<ITaxonCacheStrategy<Synonym>> {
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private static final long serialVersionUID = 6977221584815363620L;
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(Synonym.class);
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@XmlElement(name = "acceptedTaxon")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToOne(fetch = FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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@ContainedIn
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// @NotEmpty(groups = Level2.class,message="{eu.etaxonomy.cdm.model.taxon.Synonym.noOrphanedSynonyms.message}")
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// @NotNull(groups = Level2.class)
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private Taxon acceptedTaxon;
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@XmlElement(name = "IsProParte")
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private boolean proParte = false;
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@XmlElement(name = "IsPartial")
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private boolean partial = false;
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@XmlElement(name = "Type")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToOne(fetch=FetchType.EAGER)
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private SynonymType type;
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//************************************* FACTORY ****************************/
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/**
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* Creates a new synonym instance with
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* the {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} used and the {@link eu.etaxonomy.cdm.model.reference.Reference reference}
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* using it as a synonym and not as an ("accepted/correct") {@link Taxon taxon}.
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*
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* @param taxonNameBase the taxon name used
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* @param sec the reference using the taxon name
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* @see #Synonym(TaxonNameBase, Reference)
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*/
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public static Synonym NewInstance(TaxonNameBase taxonName, Reference sec){
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Synonym result = new Synonym(taxonName, sec, null);
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return result;
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}
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public static Synonym NewInstance(TaxonNameBase taxonName, Reference sec, String secDetail){
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Synonym result = new Synonym(taxonName, sec, secDetail);
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return result;
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}
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// ************* CONSTRUCTORS *************/
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/**
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* Class constructor: creates a new empty synonym instance.
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*
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* @see #Synonym(TaxonNameBase, Reference)
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*/
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//TODO should be private, but still produces Spring init errors
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public Synonym(){
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this.cacheStrategy = new TaxonBaseDefaultCacheStrategy<Synonym>();
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}
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private Synonym(TaxonNameBase taxonNameBase, Reference sec, String secDetail){
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super(taxonNameBase, sec, secDetail);
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this.cacheStrategy = new TaxonBaseDefaultCacheStrategy<Synonym>();
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}
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//********************** GETTER/SETTER ******************************/
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/**
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* Returns the "accepted/valid" {@link Taxon taxon}
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*
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*/
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public Taxon getAcceptedTaxon() {
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return this.acceptedTaxon;
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}
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/**
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* @param acceptedTaxon the acceptedTaxon to set
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*/
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protected void setAcceptedTaxon(Taxon acceptedTaxon) {
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if (acceptedTaxon == null){
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Taxon oldTaxon = this.acceptedTaxon;
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this.acceptedTaxon = null;
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oldTaxon.removeSynonym(this);
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}else{
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if (this.acceptedTaxon != null){
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this.acceptedTaxon.removeSynonym(this, false);
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}
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this.acceptedTaxon = acceptedTaxon;
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this.acceptedTaxon.addSynonym(this);
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checkHomotypic();
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}
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}
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/**
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* Returns "true" if the proParte flag is set.
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* This indicates that the {@link name.TaxonNameBase taxon name} used as a
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* {@link Synonym synonym} designated originally a real taxon which later has
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* been split. In this case the synonym is therefore the synonym of at least
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* two different ("accepted/valid") {@link Taxon taxa}.
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*/
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public boolean isProParte() {
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return proParte;
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}
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/**
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* @see #isProParte()
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*/
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public void setProParte(boolean proParte) {
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this.proParte = proParte;
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}
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/**
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* Returns "true" if the ProParte flag is set.
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* This indicates that the {@link name.TaxonNameBase taxon name} used as <code>this</code>
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* {@link Synonym synonym} designated originally a real taxon which later has
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* been lumped together with another one. In this case the
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* ("accepted/valid") {@link Taxon taxon} has therefore at least
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* two different synonyms (for the two lumped real taxa).
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*/
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public boolean isPartial() {
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return partial;
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}
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/**
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* @see #isPartial()
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*/
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public void setPartial(boolean partial) {
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this.partial = partial;
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}
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public SynonymType getType() {
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return type;
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}
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public void setType(SynonymType type) {
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this.type = type;
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checkHomotypic();
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}
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//***************** METHODS **************************/
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/**
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* Returns true if <i>this</i> is a synonym of the given taxon.
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*
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* @param taxon the taxon to check synonym for
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* @return true if <i>this</i> is a synonm of the given taxon
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*
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* @see #getAcceptedTaxon()
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*/
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@Transient
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public boolean isSynonymOf(Taxon taxon){
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return taxon != null && taxon.equals(this.acceptedTaxon);
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}
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@Override
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@Transient
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public boolean isOrphaned() {
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return this.acceptedTaxon == null || this.acceptedTaxon.isOrphaned();
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}
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/**
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* Checks if the synonym type is homotypic. If it is
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* the name of <code>this</code> synonym is added to the {@link HomotypicalGroup
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* homotypic group} of the {@link Taxon accepted taxon}.
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*/
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private void checkHomotypic() {
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if (type != null && type.equals(SynonymType.HOMOTYPIC_SYNONYM_OF())
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&& acceptedTaxon != null && acceptedTaxon.getName() != null){
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acceptedTaxon.getName().getHomotypicalGroup().addTypifiedName(this.getName());
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}
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}
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//*********************** CLONE ********************************************************/
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@Override
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public Object clone() {
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Synonym result;
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result = (Synonym)super.clone();
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//no changes to accepted taxon, type, partial, proParte
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return result;
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}
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}
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