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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 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.Indexed;
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import org.hibernate.validator.constraints.NotEmpty;
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import org.springframework.beans.factory.annotation.Configurable;
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import eu.etaxonomy.cdm.model.common.IRelated;
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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.common.IIdentifiableEntityCacheStrategy;
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import eu.etaxonomy.cdm.strategy.cache.taxon.TaxonBaseDefaultCacheStrategy;
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import eu.etaxonomy.cdm.validation.Level2;
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import java.util.*;
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import javax.persistence.*;
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import javax.validation.Valid;
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import javax.validation.constraints.NotNull;
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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.XmlElementWrapper;
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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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/**
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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 involved in no
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* {@link SynonymRelationship synonym relationship} are actually meaningless.<BR>
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* Splitting taxa in "accepted/correct" and "synonyms"
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* makes it easier to handle particular relationships between
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* ("accepted/correct") {@link Taxon taxa} on the one hand and between ("synonym") taxa
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* and ("accepted/correct") taxa on the other.
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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 13:06:55
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "Synonym", propOrder = {
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"synonymRelations"
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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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public class Synonym extends TaxonBase<IIdentifiableEntityCacheStrategy<Synonym>> implements IRelated<SynonymRelationship>{
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private static final long serialVersionUID = -454067515022159757L;
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(Synonym.class);
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// Don't need the synonym relations here since they are stored at taxon side?
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@XmlElementWrapper(name = "SynonymRelations")
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@XmlElement(name = "SynonymRelationship")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@OneToMany(mappedBy="relatedFrom", fetch=FetchType.LAZY, orphanRemoval=true)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
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@NotNull
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@NotEmpty(groups = Level2.class,message="{eu.etaxonomy.cdm.model.taxon.Synonym.noOrphanedSynonyms.message}")
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@Valid
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private Set<SynonymRelationship> synonymRelations = new HashSet<SynonymRelationship>();
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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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/**
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* Class constructor: 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#Synonym(TaxonNameBase, Reference)
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*/
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public Synonym(TaxonNameBase taxonNameBase, Reference sec){
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super(taxonNameBase, sec);
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this.cacheStrategy = new TaxonBaseDefaultCacheStrategy<Synonym>();
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}
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//********* METHODS **************************************/
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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);
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return result;
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}
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/**
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* Returns the set of all {@link SynonymRelationship synonym relationships}
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* in which <i>this</i> synonym is involved. <i>This</i> synonym can only
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* be the source within these synonym relationships.
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*
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* @see #addSynonymRelation(SynonymRelationship)
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* @see #addRelationship(SynonymRelationship)
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* @see #removeSynonymRelation(SynonymRelationship)
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*/
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public Set<SynonymRelationship> getSynonymRelations() {
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if(synonymRelations == null) {
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this.synonymRelations = new HashSet<SynonymRelationship>();
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}
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return synonymRelations;
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}
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/**
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* @see #getSynonymRelations()
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*/
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protected void setSynonymRelations(Set<SynonymRelationship> synonymRelations) {
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this.synonymRelations = synonymRelations;
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}
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/**
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* Adds an existing {@link SynonymRelationship synonym relationship} to the set of
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* {@link #getSynonymRelations() synonym relationships} assigned to <i>this</i> synonym. If
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* the source of the synonym relationship does not match with <i>this</i>
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* synonym no addition will be carried out.<BR>
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* This methods does the same as the {@link #addRelationship() addRelationship} method.
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*
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* @param synonymRelation the synonym relationship to be added to <i>this</i> synonym's
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* synonym relationships set
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* @see #addRelationship(SynonymRelationship)
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* @see #getSynonymRelations()
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* @see #removeSynonymRelation(SynonymRelationship)
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*/
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protected void addSynonymRelation(SynonymRelationship synonymRelation) {
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this.synonymRelations.add(synonymRelation);
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}
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/**
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* Removes one element from the set of {@link SynonymRelationship synonym relationships} assigned
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* to <i>this</i> synonym. Due to bidirectionality the given
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* synonym relationship will also be removed from the set of synonym
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* relationships assigned to the {@link Taxon#getSynonymRelations() taxon} involved in the
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* relationship. Furthermore the content of
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* the {@link SynonymRelationship#getAcceptedTaxon() accepted taxon} attribute and of the
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* {@link SynonymRelationship#getSynonym() synonym} attribute within the synonym relationship
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* itself will be set to "null".
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*
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* @param synonymRelation the synonym relationship which should be deleted
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* @see #getSynonymRelations()
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* @see #addRelationship(SynonymRelationship)
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*/
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public void removeSynonymRelation(SynonymRelationship synonymRelation) {
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synonymRelation.setSynonym(null);
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Taxon taxon = synonymRelation.getAcceptedTaxon();
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if (taxon != null){
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synonymRelation.setAcceptedTaxon(null);
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taxon.removeSynonymRelation(synonymRelation);
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}
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this.synonymRelations.remove(synonymRelation);
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}
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/**
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* Adds an existing {@link SynonymRelationship synonym relationship} to the set of
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* {@link #getSynonymRelations() synonym relationships} assigned to <i>this</i> synonym. If
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* the source of the synonym relationship does not match with <i>this</i>
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* synonym no addition will be carried out.<BR>
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* This methods does the same as the {@link #addSynonymRelation(SynonymRelationship) addSynonymRelation} method.
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*
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* @param synonymRelation the synonym relationship to be added to <i>this</i> synonym's
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* synonym relationships set
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* @see #addSynonymRelation(SynonymRelationship)
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* @see #getSynonymRelations()
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* @see #removeSynonymRelation(SynonymRelationship)
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*/
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.IRelated#addRelationship(eu.etaxonomy.cdm.model.common.RelationshipBase)
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*/
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public void addRelationship(SynonymRelationship rel){
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addSynonymRelation(rel);
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}
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/**
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* Returns the set of all ("accepted/correct") {@link Taxon taxa} involved in the same
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* {@link SynonymRelationship synonym relationships} as <i>this</i> synonym.
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* Each taxon is the target and <i>this</i> synonym is the source of a {@link SynonymRelationship synonym relationship}
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* belonging to the {@link #getSynonymRelations() set of synonym relationships} assigned to
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* <i>this</i> synonym. For a particular synonym there are more than one
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* ("accepted/correct") taxon only if the {@link SynonymRelationship#isProParte() "is pro parte" flag}
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* of the corresponding {@link SynonymRelationship synonym relationships} is set.
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*
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* @see #getSynonymRelations()
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* @see #getRelationType(Taxon)
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* @see SynonymRelationship#isProParte()
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*/
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@Transient
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public Set<Taxon> getAcceptedTaxa() {
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Set<Taxon>taxa=new HashSet<Taxon>();
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for (SynonymRelationship rel:getSynonymRelations()){
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taxa.add(rel.getAcceptedTaxon());
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}
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return taxa;
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}
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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 ynonms of the given taxon
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*
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* @see #getAcceptedTaxa()
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*/
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@Transient
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public boolean isSynonymOf(Taxon taxon){
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return getAcceptedTaxa().contains(taxon);
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}
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@Transient
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public boolean isOrphaned() {
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return false;
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}
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/**
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* Returns the set of {@link SynonymRelationshipType synonym relationship types} of the
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* {@link SynonymRelationship synonym relationships} where the {@link SynonymRelationship#getSynonym() synonym}
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* is <i>this</i> synonym and the {@link SynonymRelationship#getAcceptedTaxon() taxon}
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* is the given one. "Null" is returned if the given taxon is "null" or if
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* no synonym relationship exists from <i>this</i> synonym to the
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* given taxon.
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*
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* @param taxon the ("accepted/correct") taxon which a synonym relationship
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* from <i>this</i> synonym should point to
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* @see #getSynonymRelations()
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* @see #getAcceptedTaxa()
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*/
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public Set<SynonymRelationshipType> getRelationType(Taxon taxon){
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Set<SynonymRelationshipType> result = new HashSet<SynonymRelationshipType>();
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if (taxon == null ){
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return result;
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}
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for (SynonymRelationship rel : getSynonymRelations()){
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Taxon acceptedTaxon = rel.getAcceptedTaxon();
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if (taxon.equals(acceptedTaxon)){
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result.add(rel.getType());
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}
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}
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return result;
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}
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/**
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* Replaces ALL accepted taxa of this synonym by the new accepted taxon.
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* The citation information (citation /microcitation) of the synonym relationship
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* is kept.
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* @param newAcceptedTaxon
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* the new accepted taxon
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* @param relType
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* if not <code>null</code> the relationship type is changed to relType
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* @param copyCitationInfo
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* if true the citation and the microcitation of relationship
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* is not changed.
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* @param citation
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* if copyCitationInfo is <code>false</code> this citation is set
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* to the synonym relationship.
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* @param microCitation
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* if copyCitationInfo is <code>false</code> this micro citation is set
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* to the synonym relationship.
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* @param acceptedTaxon
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*/
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public void replaceAcceptedTaxon(Taxon newAcceptedTaxon, SynonymRelationshipType relType, boolean copyCitationInfo, Reference citation, String microCitation) {
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Set<SynonymRelationship> rels = new HashSet<SynonymRelationship>();
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rels.addAll(this.getSynonymRelations()); //avoid concurrent modification exception
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for (SynonymRelationship rel : rels){
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Taxon oldAcceptedTaxon = rel.getAcceptedTaxon();
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Synonym syn = rel.getSynonym();
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oldAcceptedTaxon.removeSynonym(rel.getSynonym(), false);
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SynonymRelationship newRel = (SynonymRelationship)rel.clone();
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newRel.setAcceptedTaxon(newAcceptedTaxon);
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newAcceptedTaxon.getSynonymRelations().add(newRel);
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newRel.setSynonym(syn);
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syn.addSynonymRelation(newRel);
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newRel.setType(relType);
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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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result.setSynonymRelations(new HashSet<SynonymRelationship>());
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for (SynonymRelationship synRelationship : this.getSynonymRelations()){
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SynonymRelationship newRelationship = (SynonymRelationship)synRelationship.clone();
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newRelationship.setRelatedFrom(result);
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result.synonymRelations.add(newRelationship);
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}
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return result;
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}
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}
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