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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 java.lang.reflect.Field;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import javax.persistence.Entity;
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import javax.persistence.FetchType;
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import javax.persistence.OneToMany;
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import javax.persistence.Transient;
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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.XmlAttribute;
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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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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.ClassBridge;
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import org.hibernate.search.annotations.ClassBridges;
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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.hibernate.search.annotations.IndexedEmbedded;
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import org.springframework.beans.factory.annotation.Configurable;
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import org.springframework.util.ReflectionUtils;
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import eu.etaxonomy.cdm.hibernate.search.GroupByTaxonClassBridge;
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import eu.etaxonomy.cdm.hibernate.search.TaxonRelationshipClassBridge;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IRelated;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.DescriptionType;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.IDescribable;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.ITaxonNameBase;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.ICdmTarget;
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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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/**
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* The class for "accepted/correct" {@link TaxonBase taxa} (only these taxa according to
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* the opinion of the {@link eu.etaxonomy.cdm.model.reference.Reference reference} can build a classification).
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* An {@link java.lang.Iterable interface} is supported to iterate through taxonomic children.<BR>
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* Splitting taxa in "accepted/correct" and {@link Synonym "synonyms"} makes it easier to handle
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* particular relationships between ("accepted/correct") taxa on the one hand
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* and between ("synonym") taxa and ("accepted/correct") taxa on the other.
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*
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* @author m.doering
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* @since 08-Nov-2007 13:06:56
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "Taxon", propOrder = {
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"taxonNodes",
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"synonyms",
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"relationsFromThisTaxon",
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"relationsToThisTaxon",
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"descriptions"
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})
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@XmlRootElement(name = "Taxon")
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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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@ClassBridges({
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@ClassBridge(impl = GroupByTaxonClassBridge.class),
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@ClassBridge(impl = TaxonRelationshipClassBridge.class)
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})
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public class Taxon
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extends TaxonBase<ITaxonCacheStrategy<Taxon>>
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implements IRelated<RelationshipBase>, IDescribable<TaxonDescription>, ICdmTarget{
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private static final long serialVersionUID = -584946869762749006L;
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private static final Logger logger = Logger.getLogger(Taxon.class);
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private static final TaxonComparator defaultTaxonComparator = new TaxonComparator();
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@XmlElementWrapper(name = "Descriptions")
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@XmlElement(name = "Description")
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@OneToMany(mappedBy="taxon", fetch= FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
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@NotNull
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@ContainedIn
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private Set<TaxonDescription> descriptions = new HashSet<>();
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// all related synonyms
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@XmlElementWrapper(name = "Synonyms")
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@XmlElement(name = "Synonym")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@OneToMany(mappedBy="acceptedTaxon", fetch=FetchType.LAZY, orphanRemoval=false) //we allow synonyms to stay on their own for dirty data and for intermediate states during e.g. imports
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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@NotNull
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@Valid
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@ContainedIn
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private Set<Synonym> synonyms = new HashSet<>();
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// all taxa relations with rel.fromTaxon==this
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@XmlElementWrapper(name = "RelationsFromThisTaxon")
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@XmlElement(name = "FromThisTaxonRelationship")
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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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// @Valid
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@ContainedIn
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private Set<TaxonRelationship> relationsFromThisTaxon = new HashSet<>();
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// all taxa relations with rel.toTaxon==this
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@XmlElementWrapper(name = "RelationsToThisTaxon")
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@XmlElement(name = "ToThisTaxonRelationship")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@OneToMany(mappedBy="relatedTo", fetch=FetchType.LAZY, orphanRemoval=true)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
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// @Valid
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@ContainedIn
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private Set<TaxonRelationship> relationsToThisTaxon = new HashSet<>();
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@XmlAttribute(name= "taxonStatusUnknown")
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private boolean taxonStatusUnknown = false;
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/**
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* The status of this taxon is unknown it could also be some kind of synonym.
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* @return the taxonStatusUnknown
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*/
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public boolean isTaxonStatusUnknown() {return taxonStatusUnknown;}
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/** @see #isTaxonStatusUnknown()*/
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public void setTaxonStatusUnknown(boolean taxonStatusUnknown) {this.taxonStatusUnknown = taxonStatusUnknown;}
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@XmlElementWrapper(name = "taxonNodes")
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@XmlElement(name = "taxonNode")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@OneToMany(mappedBy="taxon", fetch=FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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@IndexedEmbedded
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private Set<TaxonNode> taxonNodes = new HashSet<>();
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// ************************* FACTORY METHODS ********************************/
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/**
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* @see #NewInstance(TaxonName, Reference)
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* @param taxonName
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* @param sec
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* @return
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*/
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public static Taxon NewInstance(ITaxonNameBase taxonName, Reference sec){
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return NewInstance(TaxonName.castAndDeproxy(taxonName), sec);
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}
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/**
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* Creates a new (accepted/valid) taxon instance with
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* the {@link eu.etaxonomy.cdm.model.name.TaxonName taxon name} used and the {@link eu.etaxonomy.cdm.model.reference.Reference reference}
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* using it.
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*
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* @param taxonName the taxon name used
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* @param sec the reference using the taxon name
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* @see #Taxon(TaxonName, Reference)
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*/
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public static Taxon NewInstance(TaxonName taxonName, Reference sec){
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Taxon result = new Taxon(taxonName, sec);
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return result;
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}
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/**
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* Creates a new Taxon for the given name, secundum reference and secundum detail
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* @param taxonName
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* @param sec
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* @param secMicroReference
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* @see #
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*/
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public static Taxon NewInstance(TaxonName taxonName, Reference sec, String secMicroReference){
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Taxon result = new Taxon(taxonName, sec, secMicroReference);
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return result;
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}
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/**
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* Creates a new taxon instance with an unknown status (accepted/synonym) and with
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* the {@link eu.etaxonomy.cdm.model.name.TaxonName taxon name} used and the {@link eu.etaxonomy.cdm.model.reference.Reference reference}
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* using it.
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*
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* @param taxonName the taxon name used
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* @param sec the reference using the taxon name
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* @see #Taxon(TaxonName, Reference)
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*/
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public static Taxon NewUnknownStatusInstance(TaxonName taxonName, Reference sec){
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Taxon result = new Taxon(taxonName, sec);
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result.setTaxonStatusUnknown(true);
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return result;
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}
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// ************* CONSTRUCTORS *************/
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//TODO should be private, but still produces Spring init errors
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@Deprecated
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public Taxon(){
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this.cacheStrategy = new TaxonBaseDefaultCacheStrategy<>();
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}
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private Taxon(TaxonName taxonName, Reference sec){
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super(taxonName, sec, null);
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this.cacheStrategy = new TaxonBaseDefaultCacheStrategy<>();
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}
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private Taxon(TaxonName taxonName, Reference sec, String secMicroReference){
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super(taxonName, sec, secMicroReference);
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this.cacheStrategy = new TaxonBaseDefaultCacheStrategy<Taxon>();
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}
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//********* METHODS **************************************/
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/**
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* Returns the set of {@link eu.etaxonomy.cdm.model.description.TaxonDescription taxon descriptions}
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* concerning <i>this</i> taxon.
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*
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* @see #removeDescription(TaxonDescription)
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* @see #addDescription(TaxonDescription)
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* @see eu.etaxonomy.cdm.model.description.TaxonDescription#getTaxon()
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*/
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@Override
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public Set<TaxonDescription> getDescriptions() {
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if(descriptions == null) {
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descriptions = new HashSet<>();
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}
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return descriptions;
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}
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public Set<TaxonDescription> getDescriptions(DescriptionType type) {
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Set<TaxonDescription> result = new HashSet<>();
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for (TaxonDescription description : getDescriptions()){
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if (description.getTypes().contains(type)){
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result.add(description);
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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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* Adds a new {@link eu.etaxonomy.cdm.model.description.TaxonDescription taxon description} to the set
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* of taxon descriptions assigned to <i>this</i> (accepted/correct) taxon.
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* Due to bidirectionality the content of the {@link eu.etaxonomy.cdm.model.description.TaxonDescription#getTaxon() taxon attribute} of the
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* taxon description itself will be replaced with <i>this</i> taxon. The taxon
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* description will also be removed from the set of taxon descriptions
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* assigned to its previous taxon.
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*
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* @param description the taxon description to be added for <i>this</i> taxon
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* @see #getDescriptions()
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* @see #removeDescription(TaxonDescription)
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* @see eu.etaxonomy.cdm.model.description.TaxonDescription#getTaxon()
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*/
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@Override
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public void addDescription(TaxonDescription description) {
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if (description.getTaxon() != null){
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description.getTaxon().removeDescription(description);
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}
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Field field = ReflectionUtils.findField(TaxonDescription.class, "taxon", Taxon.class);
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ReflectionUtils.makeAccessible(field);
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ReflectionUtils.setField(field, description, this);
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descriptions.add(description);
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}
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/**
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* Removes one element from the set of {@link eu.etaxonomy.cdm.model.description.TaxonDescription taxon descriptions} assigned
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* to <i>this</i> (accepted/correct) taxon. Due to bidirectionality the content of
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* the {@link eu.etaxonomy.cdm.model.description.TaxonDescription#getTaxon() taxon attribute} of the taxon description
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* itself will be set to "null".
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*
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* @param description the taxon description which should be removed
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* @see #getDescriptions()
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* @see #addDescription(TaxonDescription)
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* @see eu.etaxonomy.cdm.model.description.TaxonDescription#getTaxon()
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*/
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@Override
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public void removeDescription(TaxonDescription description) {
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//description.setTaxon(null) for not visible method
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Field field = ReflectionUtils.findField(TaxonDescription.class, "taxon", Taxon.class);
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ReflectionUtils.makeAccessible(field);
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ReflectionUtils.setField(field, description, null);
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descriptions.remove(description);
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}
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public void removeDescription(TaxonDescription description, boolean removeElements){
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if (removeElements){
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Set<DescriptionElementBase> elements = new HashSet<DescriptionElementBase>(description.getElements());
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for (DescriptionElementBase el:elements){
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description.getElements().remove(el);
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}
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removeDescription(description);
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} else{
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removeDescription(description);
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}
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}
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/**
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* Returns the image gallery for a taxon. If there are multiple taxon descriptions
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* marked as image galleries an arbitrary one is chosen.
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* If no image gallery exists, a new one is created if <code>createNewIfNotExists</code>
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* is <code>true</code>.
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* @param createNewIfNotExists
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* @return
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*/
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public TaxonDescription getImageGallery(boolean createNewIfNotExists) {
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TaxonDescription result = null;
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Set<TaxonDescription> descriptions= getDescriptions();
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for (TaxonDescription description : descriptions){
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if (description.isImageGallery()){
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result = description;
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break;
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}
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}
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if (result == null && createNewIfNotExists){
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result = TaxonDescription.NewInstance(this);
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result.setImageGallery(true);
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}
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return result;
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}
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public Set<TaxonNode> getTaxonNodes() {
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return taxonNodes;
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}
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// protected void setTaxonNodes(Set<TaxonNode> taxonNodes) {
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// this.taxonNodes = taxonNodes;
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// }
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protected void addTaxonNode(TaxonNode taxonNode){
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taxonNodes.add(taxonNode);
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}
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public boolean removeTaxonNode(TaxonNode taxonNode){
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if (!taxonNodes.contains(taxonNode)){
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return false;
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}
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TaxonNode parent = taxonNode.getParent();
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if (parent != null){
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parent.removeChildNode(taxonNode);
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}
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taxonNode.setTaxon(null);
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return taxonNodes.remove(taxonNode);
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}
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public boolean removeTaxonNode(TaxonNode taxonNode, boolean deleteChildren){
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TaxonNode parent = taxonNode.getParent();
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boolean success = true;
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if ((!taxonNode.getChildNodes().isEmpty() && deleteChildren) || (taxonNode.getChildNodes().isEmpty()) ){
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taxonNode.delete();
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} else if (!taxonNode.isTopmostNode()){
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List<TaxonNode> nodes = new ArrayList<TaxonNode> (taxonNode.getChildNodes());
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for (TaxonNode childNode: nodes){
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taxonNode.getChildNodes().remove(childNode);
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parent.addChildNode(childNode, null, null);
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}
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taxonNode.delete();
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} else if (taxonNode.isTopmostNode()){
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success = false;
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}
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return success;
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}
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public boolean removeTaxonNodes(boolean deleteChildren){
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Iterator<TaxonNode> nodesIterator = taxonNodes.iterator();
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TaxonNode node;
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TaxonNode parent;
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boolean success = false;
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List<TaxonNode> removeNodes = new ArrayList<>();
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while (nodesIterator.hasNext()){
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node = nodesIterator.next();
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if (!deleteChildren){
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List<TaxonNode> children = node.getChildNodes();
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405
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Iterator<TaxonNode> childrenIterator = children.iterator();
|
406
|
parent = node.getParent();
|
407
|
while (childrenIterator.hasNext()){
|
408
|
TaxonNode childNode = childrenIterator.next();
|
409
|
if (parent != null){
|
410
|
parent.addChildNode(childNode, null, null);
|
411
|
}else{
|
412
|
childNode.setParent(null);
|
413
|
}
|
414
|
}
|
415
|
|
416
|
for (int i = 0; i<node.getChildNodes().size(); i++){
|
417
|
node.removeChild(i);
|
418
|
}
|
419
|
}
|
420
|
|
421
|
removeNodes.add(node);
|
422
|
}
|
423
|
for (int i = 0; i<removeNodes.size(); i++){
|
424
|
TaxonNode removeNode = removeNodes.get(i);
|
425
|
success = removeNode.delete(deleteChildren);
|
426
|
removeNode.setTaxon(null);
|
427
|
removeTaxonNode(removeNode);
|
428
|
}
|
429
|
return success;
|
430
|
|
431
|
}
|
432
|
|
433
|
public TaxonNode getTaxonNode(Classification classification) {
|
434
|
if (classification == null){
|
435
|
return null;
|
436
|
}
|
437
|
for (TaxonNode node : this.getTaxonNodes()){
|
438
|
if (classification.equals(node.getClassification())){
|
439
|
return node;
|
440
|
}
|
441
|
}
|
442
|
return null;
|
443
|
}
|
444
|
|
445
|
/**
|
446
|
* Returns the set of all {@link Synonym synonyms}
|
447
|
* for which <i>this</i> ("accepted/valid") taxon is the accepted taxon.
|
448
|
*
|
449
|
* @see #addSynonym(Synonym, SynonymType)
|
450
|
* @see #removeSynonym(Synonym)
|
451
|
*/
|
452
|
public Set<Synonym> getSynonyms() {
|
453
|
if(synonyms == null) {
|
454
|
this.synonyms = new HashSet<>();
|
455
|
}
|
456
|
return synonyms;
|
457
|
}
|
458
|
|
459
|
/**
|
460
|
* Returns the set of all {@link TaxonRelationship taxon relationships}
|
461
|
* between two taxa in which <i>this</i> taxon is involved as a source.
|
462
|
*
|
463
|
* @see #getRelationsToThisTaxon()
|
464
|
* @see #getTaxonRelations()
|
465
|
*/
|
466
|
public Set<TaxonRelationship> getRelationsFromThisTaxon() {
|
467
|
if(relationsFromThisTaxon == null) {
|
468
|
this.relationsFromThisTaxon = new HashSet<>();
|
469
|
}
|
470
|
return relationsFromThisTaxon;
|
471
|
}
|
472
|
|
473
|
/**
|
474
|
* Returns the set of all {@link TaxonRelationship taxon relationships}
|
475
|
* between two taxa in which <i>this</i> taxon is involved as a target.
|
476
|
*
|
477
|
* @see #getRelationsFromThisTaxon()
|
478
|
* @see #getTaxonRelations()
|
479
|
*/
|
480
|
public Set<TaxonRelationship> getRelationsToThisTaxon() {
|
481
|
if(relationsToThisTaxon == null) {
|
482
|
this.relationsToThisTaxon = new HashSet<>();
|
483
|
}
|
484
|
return relationsToThisTaxon;
|
485
|
}
|
486
|
|
487
|
/**
|
488
|
* Returns the set of all {@link TaxonRelationship taxon relationships}
|
489
|
* between two taxa in which <i>this</i> taxon is involved either as a source or
|
490
|
* as a target.
|
491
|
*
|
492
|
* @see #getRelationsFromThisTaxon()
|
493
|
* @see #getRelationsToThisTaxon()
|
494
|
*/
|
495
|
@Transient
|
496
|
public Set<TaxonRelationship> getTaxonRelations() {
|
497
|
Set<TaxonRelationship> rels = new HashSet<>();
|
498
|
rels.addAll(getRelationsToThisTaxon());
|
499
|
rels.addAll(getRelationsFromThisTaxon());
|
500
|
return rels;
|
501
|
}
|
502
|
|
503
|
/**
|
504
|
* @see #getRelationsToThisTaxon()
|
505
|
*/
|
506
|
protected void setRelationsToThisTaxon(Set<TaxonRelationship> relationsToThisTaxon) {
|
507
|
this.relationsToThisTaxon = relationsToThisTaxon;
|
508
|
}
|
509
|
|
510
|
/**
|
511
|
* @see #getRelationsFromThisTaxon()
|
512
|
*/
|
513
|
protected void setRelationsFromThisTaxon(Set<TaxonRelationship> relationsFromThisTaxon) {
|
514
|
this.relationsFromThisTaxon = relationsFromThisTaxon;
|
515
|
}
|
516
|
|
517
|
/**
|
518
|
* If a relationships between <i>this</i> and the given taxon exists they will be returned.
|
519
|
* <i>This</i> taxon is involved either as a source or as a target in the relationships.
|
520
|
* The method will return <code>null</code> if no relations exist between the two taxa.
|
521
|
*
|
522
|
* @param possiblyRelatedTaxon
|
523
|
* a taxon to check for a relationship
|
524
|
* @return
|
525
|
* a set of <code>TaxonRelationship</code>s or <code>null</null> if none exists.
|
526
|
*/
|
527
|
public Set<TaxonRelationship> getTaxonRelations(Taxon possiblyRelatedTaxon){
|
528
|
Set<TaxonRelationship> relations = new HashSet<>();
|
529
|
|
530
|
for(TaxonRelationship relationship : getTaxonRelations()){
|
531
|
if(relationship.getFromTaxon().equals(possiblyRelatedTaxon)) {
|
532
|
relations.add(relationship);
|
533
|
}
|
534
|
if(relationship.getToTaxon().equals(possiblyRelatedTaxon)) {
|
535
|
relations.add(relationship);
|
536
|
}
|
537
|
}
|
538
|
|
539
|
return relations.size() > 0 ? relations : null;
|
540
|
}
|
541
|
|
542
|
/**
|
543
|
* Removes one {@link TaxonRelationship taxon relationship} from one of both sets of
|
544
|
* {@link #getTaxonRelations() taxon relationships} in which <i>this</i> taxon is involved
|
545
|
* either as a {@link #getRelationsFromThisTaxon() source} or as a {@link #getRelationsToThisTaxon() target}.
|
546
|
* The taxon relationship will also be removed from one of both sets
|
547
|
* belonging to the second taxon involved. Furthermore the inherited RelatedFrom and
|
548
|
* RelatedTo attributes of the given taxon relationship will be nullified.<P>
|
549
|
*
|
550
|
* @param rel the taxon relationship which should be removed from one
|
551
|
* of both sets
|
552
|
* @see #getTaxonRelations()
|
553
|
* @see eu.etaxonomy.cdm.model.common.RelationshipBase#getRelatedFrom()
|
554
|
* @see eu.etaxonomy.cdm.model.common.RelationshipBase#getRelatedTo()
|
555
|
*
|
556
|
*/
|
557
|
public void removeTaxonRelation(TaxonRelationship rel) {
|
558
|
this.relationsToThisTaxon.remove(rel);
|
559
|
this.relationsFromThisTaxon.remove(rel);
|
560
|
Taxon fromTaxon = rel.getFromTaxon();
|
561
|
Taxon toTaxon = rel.getToTaxon();
|
562
|
|
563
|
//delete Relationship from other related Taxon
|
564
|
if (fromTaxon != this){
|
565
|
rel.setToTaxon(null); //remove this Taxon from relationship
|
566
|
if (fromTaxon != null){
|
567
|
if (fromTaxon.getTaxonRelations().contains(rel)){
|
568
|
fromTaxon.removeTaxonRelation(rel);
|
569
|
}
|
570
|
}
|
571
|
}
|
572
|
if (toTaxon != this ){
|
573
|
rel.setFromTaxon(null); //remove this Taxon from relationship
|
574
|
if (toTaxon != null){
|
575
|
if (toTaxon.getTaxonRelations().contains(rel)) {
|
576
|
toTaxon.removeTaxonRelation(rel);
|
577
|
}
|
578
|
}
|
579
|
}
|
580
|
}
|
581
|
|
582
|
/**
|
583
|
* Adds an existing {@link TaxonRelationship taxon relationship} either to the set of
|
584
|
* {@link #getRelationsToThisTaxon() taxon relationships to <i>this</i> taxon} or to the set of
|
585
|
* {@link #getRelationsFromThisTaxon() taxon relationships from <i>this</i> taxon}. If neither the
|
586
|
* source nor the target of the taxon relationship match with <i>this</i> taxon
|
587
|
* no addition will be carried out. The taxon relationship will also be
|
588
|
* added to the second taxon involved in the given relationship.<P>
|
589
|
*
|
590
|
* @param rel the taxon relationship to be added to one of <i>this</i> taxon's taxon relationships sets
|
591
|
* @see #addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String)
|
592
|
* @see #getTaxonRelations()
|
593
|
* @see #getRelationsFromThisTaxon()
|
594
|
* @see #getRelationsToThisTaxon()
|
595
|
*/
|
596
|
public void addTaxonRelation(TaxonRelationship rel) {
|
597
|
if (rel!=null && rel.getType()!=null && !getTaxonRelations().contains(rel) ){
|
598
|
Taxon toTaxon=rel.getToTaxon();
|
599
|
Taxon fromTaxon=rel.getFromTaxon();
|
600
|
if ( this.equals(toTaxon) || this.equals(fromTaxon) ){
|
601
|
if (this.equals(fromTaxon)){
|
602
|
relationsFromThisTaxon.add(rel);
|
603
|
// also add relation to other taxon object
|
604
|
if (toTaxon!=null){
|
605
|
toTaxon.addTaxonRelation(rel);
|
606
|
}
|
607
|
}else if (this.equals(toTaxon)){
|
608
|
relationsToThisTaxon.add(rel);
|
609
|
// also add relation to other taxon object
|
610
|
if (fromTaxon!=null){
|
611
|
fromTaxon.addTaxonRelation(rel);
|
612
|
}
|
613
|
}
|
614
|
}else if (toTaxon == null || fromTaxon == null){
|
615
|
if (toTaxon == null){
|
616
|
toTaxon = this;
|
617
|
relationsToThisTaxon.add(rel);
|
618
|
if (fromTaxon!= null){
|
619
|
fromTaxon.addTaxonRelation(rel);
|
620
|
}
|
621
|
}else if (fromTaxon == null && toTaxon != null){
|
622
|
fromTaxon = this;
|
623
|
relationsFromThisTaxon.add(rel);
|
624
|
toTaxon.addTaxonRelation(rel);
|
625
|
}
|
626
|
}
|
627
|
}
|
628
|
}
|
629
|
|
630
|
@Override
|
631
|
@Deprecated //for inner use by RelationshipBase only
|
632
|
public void addRelationship(RelationshipBase rel){
|
633
|
if (rel instanceof TaxonRelationship){
|
634
|
addTaxonRelation((TaxonRelationship)rel);
|
635
|
}else{
|
636
|
throw new ClassCastException("Wrong Relationsship type for Taxon.addRelationship");
|
637
|
}
|
638
|
}
|
639
|
|
640
|
/**
|
641
|
* Creates a new {@link TaxonRelationship taxon relationship} instance where <i>this</i> taxon
|
642
|
* plays the source role and adds it to the set of
|
643
|
* {@link #getRelationsFromThisTaxon() "taxon relationships from"} belonging to <i>this</i> taxon.
|
644
|
* The taxon relationship will also be added to the set of taxon
|
645
|
* relationships to the second taxon involved in the created relationship.<P>
|
646
|
*
|
647
|
* @param toTaxon the taxon which plays the target role in the new taxon relationship
|
648
|
* @param type the taxon relationship type for the new taxon relationship
|
649
|
* @param citation the reference source for the new taxon relationship
|
650
|
* @param microcitation the string with the details describing the exact localisation within the reference
|
651
|
* @return
|
652
|
* @see #addTaxonRelation(TaxonRelationship)
|
653
|
* @see #getTaxonRelations()
|
654
|
* @see #getRelationsFromThisTaxon()
|
655
|
* @see #getRelationsToThisTaxon()
|
656
|
*/
|
657
|
public TaxonRelationship addTaxonRelation(Taxon toTaxon, TaxonRelationshipType type, Reference citation, String microcitation) {
|
658
|
return new TaxonRelationship(this, toTaxon, type, citation, microcitation);
|
659
|
}
|
660
|
|
661
|
/**
|
662
|
* Creates a new {@link TaxonRelationship taxon relationship} (with {@link TaxonRelationshipType taxon relationship type}
|
663
|
* "misapplied name for") instance where <i>this</i> taxon plays the target role
|
664
|
* and adds it to the set of {@link #getRelationsToThisTaxon() taxon relationships to <i>this</i> taxon}.
|
665
|
* The taxon relationship will also be added to the set of taxon
|
666
|
* relationships to the other (misapplied name) taxon involved in the created relationship.
|
667
|
*
|
668
|
* @param misappliedNameTaxon the taxon which plays the source role in the new taxon relationship
|
669
|
* @param citation the reference source for the new taxon relationship
|
670
|
* @param microcitation the string with the details describing the exact localisation within the reference
|
671
|
* @return
|
672
|
* @see #getMisappliedNames()
|
673
|
* @see #addProParteMisappliedName(Taxon, Reference, String)
|
674
|
* @see #addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String)
|
675
|
* @see #addTaxonRelation(TaxonRelationship)
|
676
|
* @see #getTaxonRelations()
|
677
|
* @see #getRelationsFromThisTaxon()
|
678
|
* @see #getRelationsToThisTaxon()
|
679
|
*/
|
680
|
public TaxonRelationship addMisappliedName(Taxon misappliedNameTaxon, Reference citation, String microcitation) {
|
681
|
return misappliedNameTaxon.addTaxonRelation(this, TaxonRelationshipType.MISAPPLIED_NAME_FOR(), citation, microcitation);
|
682
|
}
|
683
|
|
684
|
// public void removeMisappliedName(Taxon misappliedNameTaxon){
|
685
|
// Set<TaxonRelationship> taxRels = this.getTaxonRelations();
|
686
|
// for (TaxonRelationship taxRel : taxRels ){
|
687
|
// if (taxRel.getType().equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())
|
688
|
// && taxRel.getFromTaxon().equals(misappliedNameTaxon)){
|
689
|
// this.removeTaxonRelation(taxRel);
|
690
|
// }
|
691
|
// }
|
692
|
// }
|
693
|
|
694
|
/**
|
695
|
* Creates a new {@link TaxonRelationship taxon relationship} (with {@link TaxonRelationshipType taxon relationship type}
|
696
|
* "pro parte misapplied name for") instance where <i>this</i> taxon plays the target role
|
697
|
* and adds it to the set of {@link #getRelationsToThisTaxon() taxon relationships to <i>this</i> taxon}.
|
698
|
* The taxon relationship will also be added to the set of taxon
|
699
|
* relationships to the other (pro parte misapplied name) taxon involved in the created relationship.
|
700
|
*
|
701
|
* @param proParteMisappliedNameTaxon the taxon which plays the source role in the new taxon relationship
|
702
|
* @param citation the reference source for the new taxon relationship
|
703
|
* @param microcitation the string with the details describing the exact localisation within the reference
|
704
|
* @return
|
705
|
* @see #addMisappliedName(Taxon, Reference, String)
|
706
|
* @see #getMisappliedNames()
|
707
|
* @see #addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String)
|
708
|
* @see #addTaxonRelation(TaxonRelationship)
|
709
|
* @see #getTaxonRelations()
|
710
|
* @see #getRelationsFromThisTaxon()
|
711
|
* @see #getRelationsToThisTaxon()
|
712
|
*/
|
713
|
public TaxonRelationship addProParteMisappliedName(Taxon proParteMisappliedNameTaxon, Reference citation, String microcitation) {
|
714
|
return proParteMisappliedNameTaxon.addTaxonRelation(this, TaxonRelationshipType.PRO_PARTE_MISAPPLIED_NAME_FOR(), citation, microcitation);
|
715
|
}
|
716
|
|
717
|
/**
|
718
|
* Creates a new {@link TaxonRelationship taxon relationship} (with {@link TaxonRelationshipType taxon relationship type}
|
719
|
* "partial misapplied name for") instance where <i>this</i> taxon plays the target role
|
720
|
* and adds it to the set of {@link #getRelationsToThisTaxon() taxon relationships to <i>this</i> taxon}.
|
721
|
* The taxon relationship will also be added to the set of taxon
|
722
|
* relationships to the other (pro parte misapplied name) taxon involved in the created relationship.
|
723
|
*
|
724
|
* @param partialMisappliedNameTaxon the taxon which plays the source role in the new taxon relationship
|
725
|
* @param citation the reference source for the new taxon relationship
|
726
|
* @param microcitation the string with the details describing the exact localization within the reference
|
727
|
* @return
|
728
|
* @see #addMisappliedName(Taxon, Reference, String)
|
729
|
* @see #addProParteMisappliedName(Taxon, Reference, String)
|
730
|
* @see #getMisappliedNames()
|
731
|
* @see #addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String)
|
732
|
* @see #addTaxonRelation(TaxonRelationship)
|
733
|
* @see #getTaxonRelations()
|
734
|
* @see #getRelationsFromThisTaxon()
|
735
|
* @see #getRelationsToThisTaxon()
|
736
|
*/
|
737
|
public TaxonRelationship addPartialMisappliedName(Taxon partialMisappliedNameTaxon, Reference citation, String microcitation) {
|
738
|
return partialMisappliedNameTaxon.addTaxonRelation(this, TaxonRelationshipType.PARTIAL_MISAPPLIED_NAME_FOR(), citation, microcitation);
|
739
|
}
|
740
|
|
741
|
/**
|
742
|
* Creates a new {@link TaxonRelationship taxon relationship} (with {@link TaxonRelationshipType taxon relationship type}
|
743
|
* "pro parte synonym for") instance where <i>this</i> taxon plays the target role
|
744
|
* and adds it to the set of {@link #getRelationsToThisTaxon() taxon relationships to <i>this</i> taxon}.
|
745
|
* The taxon relationship will also be added to the set of taxon
|
746
|
* relationships to the other (pro parte synonym) taxon involved in the created relationship.
|
747
|
*
|
748
|
* @param proParteTaxon the taxon which plays the source role in the new taxon relationship
|
749
|
* @param citation the reference source for the new taxon relationship
|
750
|
* @param microcitation the string with the details describing the exact localisation within the reference
|
751
|
* @return
|
752
|
* @see #getMisappliedNames()
|
753
|
* @see #addProParteMisappliedName(Taxon, Reference, String)
|
754
|
* @see #addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String)
|
755
|
* @see #addTaxonRelation(TaxonRelationship)
|
756
|
* @see #getTaxonRelations()
|
757
|
* @see #getRelationsFromThisTaxon()
|
758
|
* @see #getRelationsToThisTaxon()
|
759
|
*/
|
760
|
public TaxonRelationship addProparteSynonym(Taxon proParteTaxon, Reference citation, String microcitation) {
|
761
|
return proParteTaxon.addTaxonRelation(this, TaxonRelationshipType.PRO_PARTE_SYNONYM_FOR(), citation, microcitation);
|
762
|
}
|
763
|
|
764
|
/**
|
765
|
* Creates a new {@link TaxonRelationship taxon relationship} instance with
|
766
|
* {@link TaxonRelationshipType taxon relationship type} {@link TaxonRelationshipType#PARTIAL_SYNONYM_FOR()
|
767
|
* partial synonym for} where <i>this</i> taxon plays the target role
|
768
|
* and adds it to the set of {@link #getRelationsToThisTaxon() taxon relationships to <i>this</i> taxon}.
|
769
|
* The taxon relationship will also be added to the set of taxon
|
770
|
* relationships to the other (partial synonym) taxon involved in the created relationship.
|
771
|
*
|
772
|
* @param partialTaxon the taxon which plays the source role in the new taxon relationship
|
773
|
* @param citation the reference source for the new taxon relationship
|
774
|
* @param microcitation the string with the details describing the exact localisation within the reference
|
775
|
* @return
|
776
|
* @see #addProparteSynonym(Taxon, Reference, String)
|
777
|
* @see #addTaxonRelation(Taxon, TaxonRelationshipType, Reference, String)
|
778
|
* @see #addTaxonRelation(TaxonRelationship)
|
779
|
* @see #getTaxonRelations()
|
780
|
* @see #getRelationsFromThisTaxon()
|
781
|
* @see #getRelationsToThisTaxon()
|
782
|
*/
|
783
|
public TaxonRelationship addPartialSynonym(Taxon partialTaxon, Reference citation, String microcitation) {
|
784
|
return partialTaxon.addTaxonRelation(this, TaxonRelationshipType.PARTIAL_SYNONYM_FOR(), citation, microcitation);
|
785
|
}
|
786
|
|
787
|
/**
|
788
|
* TODO update documentation
|
789
|
* Removes one {@link TaxonRelationship taxon relationship} with {@link TaxonRelationshipType taxon relationship type}
|
790
|
* taxonRelType and with the given child taxon playing the
|
791
|
* source role from the set of {@link #getRelationsToThisTaxon() "taxon relationships to"} belonging
|
792
|
* to <i>this</i> taxon. The taxon relationship will also be removed from the set
|
793
|
* of {@link #getRelationsFromThisTaxon() "taxon relationships from"} belonging to the other side taxon.
|
794
|
* Furthermore, the inherited RelatedFrom and RelatedTo attributes of the
|
795
|
* taxon relationship will be nullified.<P>
|
796
|
*
|
797
|
* @param taxon the taxon which plays the source role in the taxon relationship
|
798
|
* @param taxonRelType the taxon relationship type
|
799
|
*/
|
800
|
public void removeTaxon(Taxon taxon, TaxonRelationshipType taxonRelType){
|
801
|
Set<TaxonRelationship> taxRels = this.getTaxonRelations();
|
802
|
for (TaxonRelationship taxRel : taxRels ){
|
803
|
if (taxRel.getType().equals(taxonRelType)
|
804
|
&& taxRel.getFromTaxon().equals(taxon)){
|
805
|
this.removeTaxonRelation(taxRel);
|
806
|
}
|
807
|
}
|
808
|
}
|
809
|
|
810
|
/**
|
811
|
* Returns the boolean value indicating whether <i>this</i> taxon is a misapplication
|
812
|
* (misapplied name) for at least one other taxon.
|
813
|
*/
|
814
|
// TODO cache as for #hasTaxonomicChildren
|
815
|
@Transient
|
816
|
public boolean isMisapplication(){
|
817
|
return computeMisapliedNameRelations() > 0;
|
818
|
}
|
819
|
|
820
|
/**
|
821
|
* Counts the number of misapplied name relationships (including pro parte and partial
|
822
|
* misapplied names) where this taxon represents the
|
823
|
* misapplied name for another taxon.
|
824
|
* @return
|
825
|
*/
|
826
|
private int computeMisapliedNameRelations(){
|
827
|
int count = 0;
|
828
|
for (TaxonRelationship rel: this.getRelationsFromThisTaxon()){
|
829
|
if (rel.getType().isAnyMisappliedName()){
|
830
|
count++;
|
831
|
}
|
832
|
}
|
833
|
return count;
|
834
|
}
|
835
|
|
836
|
/**
|
837
|
* Returns the boolean value indicating whether <i>this</i> taxon is a misapplication
|
838
|
* (misapplied name) for at least one other taxon.
|
839
|
*/
|
840
|
// TODO cache as for #hasTaxonomicChildren
|
841
|
@Transient
|
842
|
public boolean isProparteSynonym(){
|
843
|
return computeProparteSynonymRelations() > 0;
|
844
|
}
|
845
|
|
846
|
/**
|
847
|
* Counts the number of misapplied name relationships (including pro parte misapplied
|
848
|
* names) where this taxon represents the
|
849
|
* misapplied name for another taxon.
|
850
|
* @return
|
851
|
*/
|
852
|
private int computeProparteSynonymRelations(){
|
853
|
int count = 0;
|
854
|
for (TaxonRelationship rel: this.getRelationsFromThisTaxon()){
|
855
|
if (rel.getType().isAnySynonym()){
|
856
|
count++;
|
857
|
}
|
858
|
}
|
859
|
return count;
|
860
|
}
|
861
|
|
862
|
/**
|
863
|
* Returns the boolean value indicating whether <i>this</i> taxon is a related
|
864
|
* concept for at least one other taxon.
|
865
|
*/
|
866
|
@Transient
|
867
|
public boolean isRelatedConcept(){
|
868
|
return computeConceptRelations() > 0;
|
869
|
}
|
870
|
|
871
|
/**
|
872
|
* Counts the number of concept relationships where this taxon represents the
|
873
|
* related concept for another taxon.
|
874
|
* @return
|
875
|
*/
|
876
|
private int computeConceptRelations(){
|
877
|
int count = 0;
|
878
|
for (TaxonRelationship rel: this.getRelationsFromThisTaxon()){
|
879
|
TaxonRelationshipType type = rel.getType();
|
880
|
if (type.isConceptRelationship()){
|
881
|
count++;
|
882
|
}
|
883
|
}
|
884
|
return count;
|
885
|
}
|
886
|
|
887
|
/**
|
888
|
* Returns the boolean value indicating whether <i>this</i> taxon has at least one
|
889
|
* {@link Synonym synonym} (true) or not (false). If true the {@link #getSynonyms() set of synonyms}
|
890
|
* belonging to <i>this</i> ("accepted/valid") taxon is not empty .
|
891
|
*
|
892
|
* @see #getSynonyms()
|
893
|
* @see #getSynonymNames()
|
894
|
* @see #removeSynonym(Synonym)
|
895
|
*/
|
896
|
@Transient
|
897
|
public boolean hasSynonyms(){
|
898
|
return this.getSynonyms().size() > 0;
|
899
|
}
|
900
|
|
901
|
/**
|
902
|
* Returns the boolean value indicating whether <i>this</i> taxon is at least
|
903
|
* involved in one {@link #getTaxonRelations() taxon relationship} between
|
904
|
* two taxa (true), either as a source or as a target, or not (false).
|
905
|
*
|
906
|
* @see #getTaxonRelations()
|
907
|
* @see #getRelationsToThisTaxon()
|
908
|
* @see #getRelationsFromThisTaxon()
|
909
|
* @see #removeTaxonRelation(TaxonRelationship)
|
910
|
* @see TaxonRelationship
|
911
|
*/
|
912
|
public boolean hasTaxonRelationships(){
|
913
|
return this.getTaxonRelations().size() > 0;
|
914
|
}
|
915
|
|
916
|
/*
|
917
|
* MISAPPLIED NAMES
|
918
|
*/
|
919
|
/**
|
920
|
* Returns the set of taxa playing the source role in {@link TaxonRelationship taxon relationships}
|
921
|
* (with {@link TaxonRelationshipType taxon relationship type} "misapplied name for") where
|
922
|
* <i>this</i> taxon plays the target role. A misapplied name is a taxon the
|
923
|
* {@link eu.etaxonomy.cdm.model.name.TaxonName taxon name} of which has been erroneously used
|
924
|
* by its {@link TaxonBase#getSec() taxon reference} to denominate the same real taxon
|
925
|
* as the one meant by <i>this</i> ("accepted/correct") taxon.
|
926
|
*
|
927
|
* @see #getTaxonRelations()
|
928
|
* @see #getRelationsToThisTaxon()
|
929
|
* @see #addMisappliedName(Taxon, Reference, String)
|
930
|
* @param includeNonCongruent if <code>true</code> also those taxa are returned that are related
|
931
|
* via a non congruent relationship like {@link TaxonRelationshipType#PRO_PARTE_MISAPPLIED_NAME_FOR()
|
932
|
* pro parte misapplied name}
|
933
|
*/
|
934
|
@Transient
|
935
|
public Set<Taxon> getMisappliedNames(boolean includeNonCongruent){
|
936
|
Set<Taxon> taxa = new HashSet<>();
|
937
|
Set<TaxonRelationship> rels = this.getRelationsToThisTaxon();
|
938
|
for (TaxonRelationship rel: rels){
|
939
|
TaxonRelationshipType relType = rel.getType();
|
940
|
if ( (includeNonCongruent && relType.isAnyMisappliedName())
|
941
|
|| relType.equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())){
|
942
|
taxa.add(rel.getFromTaxon());
|
943
|
}
|
944
|
}
|
945
|
return taxa;
|
946
|
}
|
947
|
|
948
|
/**
|
949
|
* Returns the set of misapplied name relationships in which this taxon
|
950
|
* plays the role of the correctly accepted taxon (target). A misapplied name is a taxon the
|
951
|
* {@link eu.etaxonomy.cdm.model.name.TaxonName taxon name} of which has been erroneously used
|
952
|
* by its {@link TaxonBase#getSec() taxon reference} to denominate the same real taxon
|
953
|
* as the one meant by <i>this</i> ("accepted/correct") taxon.
|
954
|
*/
|
955
|
@Transient
|
956
|
public Set<TaxonRelationship> getMisappliedNameRelations(){
|
957
|
Set<TaxonRelationship> result = new HashSet<>();
|
958
|
Set<TaxonRelationship> rels = this.getRelationsToThisTaxon();
|
959
|
for (TaxonRelationship rel: rels){
|
960
|
TaxonRelationshipType relType = rel.getType();
|
961
|
if (relType.isAnyMisappliedName()){
|
962
|
result.add(rel);
|
963
|
}
|
964
|
}
|
965
|
return result;
|
966
|
}
|
967
|
|
968
|
/**
|
969
|
* Returns the set of taxa playing the target role in {@link TaxonRelationship taxon relationships}
|
970
|
* (with {@link TaxonRelationshipType taxon relationship type} "misapplied name for"
|
971
|
* or "pro parte misapplied name for") where
|
972
|
* <i>this</i> taxon plays the source role. A misapplied name is a taxon the
|
973
|
* {@link eu.etaxonomy.cdm.model.name.TaxonName taxon name} of which has been erroneously used
|
974
|
* by its {@link TaxonBase#getSec() taxon reference} to denominate the same real taxon
|
975
|
* as the one meant by <i>this</i> ("accepted/correct") taxon.
|
976
|
|
977
|
* @param includeNonCongruent if <code>true</code> also those taxa are returned that are related
|
978
|
* via a non congruent relationship like {@link TaxonRelationshipType#PRO_PARTE_MISAPPLIED_NAME_FOR()
|
979
|
* pro parte misapplied name}
|
980
|
*
|
981
|
* @see #getTaxonRelations()
|
982
|
* @see #getRelationsToThisTaxon()
|
983
|
* @see #addMisappliedName(Taxon, Reference, String)
|
984
|
* @see #addProParteMisappliedName(Taxon, Reference, String)
|
985
|
*/
|
986
|
@Transient
|
987
|
public Set<Taxon> getTaxaForMisappliedName(boolean includeNonCongruent){
|
988
|
Set<Taxon> taxa = new HashSet<>();
|
989
|
Set<TaxonRelationship> rels = this.getRelationsFromThisTaxon();
|
990
|
for (TaxonRelationship rel: rels){
|
991
|
TaxonRelationshipType relType = rel.getType();
|
992
|
if ( (includeNonCongruent && relType.isAnyMisappliedName())
|
993
|
|| relType.equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())){
|
994
|
taxa.add(rel.getToTaxon());
|
995
|
}
|
996
|
}
|
997
|
return taxa;
|
998
|
}
|
999
|
|
1000
|
/**
|
1001
|
* Returns the set of pro parte or partial synonym relationships in which this taxon
|
1002
|
* plays the role of the "correctly" accepted taxon (target).
|
1003
|
*
|
1004
|
* @see #getProParteAndPartialSynonyms()
|
1005
|
* @see #getMisappliedNameRelations()
|
1006
|
*/
|
1007
|
@Transient
|
1008
|
public Set<TaxonRelationship> getProParteAndPartialSynonymRelations(){
|
1009
|
Set<TaxonRelationship> result = new HashSet<>();
|
1010
|
Set<TaxonRelationship> rels = this.getRelationsToThisTaxon();
|
1011
|
for (TaxonRelationship rel: rels){
|
1012
|
TaxonRelationshipType relType = rel.getType();
|
1013
|
if (relType.isAnySynonym()){
|
1014
|
result.add(rel);
|
1015
|
}
|
1016
|
}
|
1017
|
return result;
|
1018
|
}
|
1019
|
|
1020
|
/**
|
1021
|
* Returns the set of pro parte or partial synonyms in which this taxon
|
1022
|
* plays the role of the "correctly" accepted taxon (target).
|
1023
|
*
|
1024
|
* @see #getProParteAndPartialSynonymRelations()
|
1025
|
* @see #getMisappliedNames(boolean)
|
1026
|
*/
|
1027
|
@Transient
|
1028
|
public Set<Taxon> getProParteAndPartialSynonyms(){
|
1029
|
Set<Taxon> synonyms = new HashSet<>();
|
1030
|
Set<TaxonRelationship> rels = this.getProParteAndPartialSynonymRelations();
|
1031
|
for (TaxonRelationship rel: rels){
|
1032
|
synonyms.add(rel.getFromTaxon());
|
1033
|
}
|
1034
|
return synonyms;
|
1035
|
}
|
1036
|
|
1037
|
/**
|
1038
|
* Returns the set of all {@link TaxonName taxon names} used as {@link Synonym synonyms}
|
1039
|
* of <i>this</i> ("accepted/valid") taxon.
|
1040
|
*
|
1041
|
* @see #getSynonyms()
|
1042
|
* @see #getSynonymsSortedByType()
|
1043
|
* @see #addSynonymName(TaxonName, SynonymType)
|
1044
|
* @see #addSynonym(Synonym, SynonymType, Reference, String)
|
1045
|
* @see #removeSynonym(Synonym)
|
1046
|
*/
|
1047
|
@Transient
|
1048
|
public Set<TaxonName> getSynonymNames(){
|
1049
|
Set<TaxonName> names = new HashSet<>();
|
1050
|
for (Synonym syn: this.getSynonyms()){
|
1051
|
names.add(syn.getName());
|
1052
|
}
|
1053
|
return names;
|
1054
|
}
|
1055
|
|
1056
|
/**
|
1057
|
* Might be public in future. For the moment protected to ensure that
|
1058
|
* synonym type is always set after refactoring.
|
1059
|
*
|
1060
|
* @param synonym
|
1061
|
*/
|
1062
|
protected void addSynonym(Synonym synonym){
|
1063
|
if (! this.equals(synonym.getAcceptedTaxon())){
|
1064
|
synonym.setAcceptedTaxon(this);
|
1065
|
}
|
1066
|
if (!synonyms.contains(synonym)){
|
1067
|
synonyms.add(synonym);
|
1068
|
}
|
1069
|
}
|
1070
|
|
1071
|
/**
|
1072
|
* Adds the given {@link Synonym synonym} to <code>this</code> taxon
|
1073
|
* and changes the {@link SynonymType
|
1074
|
* synonym type} before.
|
1075
|
*
|
1076
|
* @param synonym the synonym to be added
|
1077
|
* @param synonymType the synonym type of the synonym to be added. If not <code>null</code>
|
1078
|
* and if the synonym already has a type the existing type will be overwritten.<BR>
|
1079
|
* If synonymType is {@link SynonymType#HOMOTYPIC_SYNONYM_OF()}
|
1080
|
* the homotypic group of the synonym is changed to that of <code>this</code> taxon.<BR>
|
1081
|
* To explicitly set the type to <code>null</code> use {@link Synonym#setType(SynonymType)}
|
1082
|
* @see #addSynonym(Synonym)
|
1083
|
* @see #addSynonym(Synonym, SynonymType, Reference, String)
|
1084
|
* @see #addSynonymName(TaxonName, SynonymType)
|
1085
|
* @see #addSynonymName(TaxonName, SynonymType, Reference, String)
|
1086
|
* @see #addHomotypicSynonymName(TaxonName, Reference, String)
|
1087
|
* @see #addHeterotypicSynonymName(TaxonName)
|
1088
|
* @see #addHeterotypicSynonymName(TaxonName, Reference, String, HomotypicalGroup)
|
1089
|
* @see #getSynonyms()
|
1090
|
* @see #removeSynonym(Synonym)
|
1091
|
* @see Synonym#getAcceptedTaxon()
|
1092
|
*/
|
1093
|
public void addSynonym(Synonym synonym, SynonymType synonymType){
|
1094
|
synonym.setType(synonymType); //must be set before as otherwise merging of homotypical groups may not work correctly in Synonym.checkHomotypic()
|
1095
|
addSynonym(synonym);
|
1096
|
}
|
1097
|
|
1098
|
/**
|
1099
|
* Adds the given {@link Synonym synonym} with the given {@link SynonymType
|
1100
|
* synonym relationship type}
|
1101
|
*
|
1102
|
* @param synonym the synonym to be added
|
1103
|
* @param synonymType the synonym type of the synonym to be added. If not null
|
1104
|
* and if the synonym already has a type the existing type will be overwritten.
|
1105
|
// * @param citation the reference source for the new synonym relationship
|
1106
|
// * @param microcitation the string with the details describing the exact localization within the reference
|
1107
|
* @see #addSynonym(Synonym)
|
1108
|
* @see #addSynonym(Synonym, SynonymType, Reference, String)
|
1109
|
* @see #addSynonymName(TaxonName, SynonymType)
|
1110
|
* @see #addSynonymName(TaxonName, SynonymType, Reference, String)
|
1111
|
* @see #addHomotypicSynonymName(TaxonName, Reference, String)
|
1112
|
* @see #addHeterotypicSynonymName(TaxonName)
|
1113
|
* @see #addHeterotypicSynonymName(TaxonName, HomotypicalGroup, Reference, String)
|
1114
|
* @see #getSynonyms()
|
1115
|
* @see #removeSynonym(Synonym)
|
1116
|
* @see Synonym#getAcceptedTaxon()
|
1117
|
*/
|
1118
|
private void addSynonym(Synonym synonym, SynonymType synonymType, Reference newSecReference, String newSecMicroReference){
|
1119
|
if (newSecReference != null){
|
1120
|
synonym.setSec(newSecReference);
|
1121
|
}
|
1122
|
if (newSecMicroReference != null){
|
1123
|
synonym.setSecMicroReference(newSecMicroReference);
|
1124
|
}
|
1125
|
addSynonym(synonym, synonymType);
|
1126
|
return;
|
1127
|
}
|
1128
|
|
1129
|
/**
|
1130
|
* Creates a new {@link Synonym synonym} to <code>this</code> {@link Taxon taxon}) using the
|
1131
|
* given {@link TaxonName synonym name} and with the given
|
1132
|
* {@link SynonymType synonym type}. If the later is
|
1133
|
* {@link SynonymType#HOMOTYPIC_SYNONYM_OF() homotypic synonym}
|
1134
|
* the name will be added to the same {@link HomotypicalGroup homotypical group}
|
1135
|
* as the <code>this</code> accepted taxon.<BR>
|
1136
|
* The secundum reference of the new synonym is taken from <code>this</code> taxon.
|
1137
|
* A secundum detail is not set.
|
1138
|
*
|
1139
|
* @param synonymName the taxon name to be used as a synonym to be added
|
1140
|
* to <i>this</i> taxon's set of synonyms
|
1141
|
* @param synonymType the synonym type of the synonym
|
1142
|
* relationship to be added
|
1143
|
* @return the created synonym
|
1144
|
* @see #addSynonymName(TaxonName, SynonymType, Reference, String)
|
1145
|
* @see #addSynonym(Synonym, SynonymType)
|
1146
|
* @see #addSynonym(Synonym, SynonymType, Reference, String)
|
1147
|
* @see #addHomotypicSynonym(Synonym, Reference, String)
|
1148
|
* @see #addHomotypicSynonymName(TaxonName, Reference, String)
|
1149
|
* @see #addHeterotypicSynonymName(TaxonName)
|
1150
|
* @see #addHeterotypicSynonymName(TaxonName, HomotypicalGroup, Reference, String)
|
1151
|
* @see #getSynonyms()
|
1152
|
* @see #removeSynonym(Synonym)
|
1153
|
*/
|
1154
|
public Synonym addSynonymName(TaxonName synonymName, SynonymType synonymType){
|
1155
|
return addSynonymName(synonymName, null, null, synonymType);
|
1156
|
}
|
1157
|
|
1158
|
/**
|
1159
|
* Creates a new {@link Synonym synonym} to <code>this</code> {@link Taxon taxon}) using the
|
1160
|
* given {@link TaxonName synonym name} and with the given
|
1161
|
* {@link SynonymType synonym type}. If the later is
|
1162
|
* {@link SynonymType#HOMOTYPIC_SYNONYM_OF() homotypic synonym}
|
1163
|
* the name will be added to the same {@link HomotypicalGroup homotypical group}
|
1164
|
* as the <code>this</code> accepted taxon.<BR>
|
1165
|
*
|
1166
|
* If secReference is not <code>null</code>, the new synonym will have this as
|
1167
|
* secundum reference. Otherwise <code>this</code> taxons sec reference is taken
|
1168
|
* as secundum reference for the synonym. SecDetail will be the secMicroReference of the
|
1169
|
* new synonym.<BR>
|
1170
|
*
|
1171
|
* @param synonymName the taxon name to be used as a synonym to be added
|
1172
|
* to <i>this</i> taxon's set of synonyms
|
1173
|
* @param secReference the secundum reference for the new synonym (if <code>null</code>
|
1174
|
* <code>this</code> taxon's secundum reference is taken.
|
1175
|
* @param secMicroReference the secundum micro reference of the new synonym
|
1176
|
* @param synonymType the synonym type of the synonym to be added
|
1177
|
*
|
1178
|
* @see #addSynonymName(TaxonName, SynonymType, Reference, String)
|
1179
|
* @see #addSynonym(Synonym, SynonymType)
|
1180
|
* @see #addSynonym(Synonym, SynonymType, Reference, String)
|
1181
|
* @see #addHomotypicSynonym(Synonym, Reference, String)
|
1182
|
* @see #addHomotypicSynonymName(TaxonName, Reference, String)
|
1183
|
* @see #addHeterotypicSynonymName(TaxonName)
|
1184
|
* @see #addHeterotypicSynonymName(TaxonName, HomotypicalGroup, Reference, String)
|
1185
|
* @see #getSynonyms()
|
1186
|
* @see #removeSynonym(Synonym)
|
1187
|
*/
|
1188
|
public Synonym addSynonymName(TaxonName synonymName, Reference secReference, String secMicroReference, SynonymType synonymType){
|
1189
|
Synonym synonym = Synonym.NewInstance(synonymName, this.getSec()); //default sec
|
1190
|
addSynonym(synonym, synonymType, secReference, secMicroReference);
|
1191
|
return synonym;
|
1192
|
}
|
1193
|
|
1194
|
/**
|
1195
|
* Creates a new {@link Synonym synonym} to <code>this</code> {@link Taxon taxon}) using the given
|
1196
|
* {@link TaxonName synonym name}. The synonym will have the synonym type
|
1197
|
* {@link SynonymType#HETEROTYPIC_SYNONYM_OF() "is heterotypic synonym of"}.<BR>
|
1198
|
* The secundum reference is taken from <code>this</code> taxon.
|
1199
|
* No secMicroReference will be set for the new synonym.<BR>
|
1200
|
* The synonym will keep it's old homotypical group.<BR>
|
1201
|
*
|
1202
|
* @param synonymName the taxon name to be used as an heterotypic synonym
|
1203
|
* to be added to <i>this</i> taxon's set of synonyms
|
1204
|
* @return the created synonym
|
1205
|
* @see #addHeterotypicSynonymName(TaxonName, Reference, String, HomotypicalGroup)
|
1206
|
* @see #addSynonymName(TaxonName, SynonymType)
|
1207
|
* @see #addSynonymName(TaxonName, SynonymType, Reference, String)
|
1208
|
* @see #addSynonym(Synonym, SynonymType)
|
1209
|
* @see #addSynonym(Synonym, SynonymType, Reference, String)
|
1210
|
* @see #addHomotypicSynonym(Synonym, Reference, String)
|
1211
|
* @see #addHomotypicSynonymName(TaxonName, Reference, String)
|
1212
|
* @see #getSynonyms()
|
1213
|
* @see #removeSynonym(Synonym)
|
1214
|
*/
|
1215
|
public Synonym addHeterotypicSynonymName(TaxonName synonymName){
|
1216
|
return addHeterotypicSynonymName(synonymName, null, null, null);
|
1217
|
}
|
1218
|
|
1219
|
/**
|
1220
|
* Creates a new {@link Synonym synonym} to <code>this</code> {@link Taxon taxon}) using the given
|
1221
|
* {@link TaxonName synonym name}. The synonym will have the synonym type
|
1222
|
* {@link SynonymType#HETEROTYPIC_SYNONYM_OF() "is heterotypic synonym of"}.<BR>
|
1223
|
*
|
1224
|
* If secReference is not <code>null</code>, the new synonym will have this as
|
1225
|
* secundum reference. Otherwise <code>this</code> taxons sec reference is taken
|
1226
|
* as secundum reference for the synonym. SecDetail will be the secMicroReference of the
|
1227
|
* new synonym.<BR>
|
1228
|
* Furthermore the taxon name used as synonym will be added
|
1229
|
* to the given {@link name.HomotypicalGroup homotypical group} (if not <code>null</code>).<BR>
|
1230
|
*
|
1231
|
* @param synonymName the taxon name to be used as an heterotypic synonym
|
1232
|
* to be added to <i>this</i> taxon's set of synonyms
|
1233
|
* @param secReference the secundum reference for the new synonym
|
1234
|
* @param secDetail the secundum detil for the new synonym
|
1235
|
* @param homotypicalGroup the homotypical group to which the taxon name
|
1236
|
* of the synonym will be added. If <code>null</code>
|
1237
|
* the homotypical group of synonymName is not changed
|
1238
|
* @return the created synonym
|
1239
|
* @see #addHeterotypicSynonymName(TaxonName)
|
1240
|
* @see #addSynonymName(TaxonName, SynonymType, Reference, String)
|
1241
|
* @see #addSynonymName(TaxonName, SynonymType)
|
1242
|
* @see #addSynonym(Synonym, SynonymType)
|
1243
|
* @see #addSynonym(Synonym, SynonymType, Reference, String)
|
1244
|
* @see #addHomotypicSynonym(Synonym, Reference, String)
|
1245
|
* @see #addHomotypicSynonymName(TaxonName, Reference, String)
|
1246
|
* @see #getSynonyms()
|
1247
|
* @see #removeSynonym(Synonym)
|
1248
|
*/
|
1249
|
public Synonym addHeterotypicSynonymName(TaxonName synonymName, Reference secReference, String secDetail, HomotypicalGroup homotypicalGroup){
|
1250
|
Synonym synonym = Synonym.NewInstance(synonymName, this.getSec());
|
1251
|
if (homotypicalGroup != null){
|
1252
|
homotypicalGroup.addTypifiedName(synonymName);
|
1253
|
}
|
1254
|
addSynonym(synonym, SynonymType.HETEROTYPIC_SYNONYM_OF(), secReference, secDetail);
|
1255
|
return synonym;
|
1256
|
}
|
1257
|
|
1258
|
/**
|
1259
|
* Creates a new {@link Synonym synonym} to <code>this</code> {@link Taxon taxon}) using the given
|
1260
|
* {@link TaxonName synonym name}. The synonym will have the synonym type
|
1261
|
* {@link SynonymType#HOMOTYPIC_SYNONYM_OF() "is homotypic synonym of"}.<BR>
|
1262
|
* The secundum reference is taken from <code>this</code> taxon.
|
1263
|
* No secMicroReference will be set for the new synonym.<BR>
|
1264
|
* The synonym's homotypic group will be changed to <code>this</code> taxon's group.<BR>
|
1265
|
*
|
1266
|
* @param synonymName the taxon name to be used as an homotypic synonym
|
1267
|
* to be added to <i>this</i> taxon's set of synonyms
|
1268
|
* @return the created synonym
|
1269
|
* @see #addHomotypicSynonym(Synonym, Reference, String)
|
1270
|
* @see #addSynonymName(TaxonName, SynonymType, Reference, String)
|
1271
|
* @see #addSynonymName(TaxonName, SynonymType)
|
1272
|
* @see #addSynonym(Synonym, SynonymType)
|
1273
|
* @see #addSynonym(Synonym, SynonymType, Reference, String)
|
1274
|
* @see #addHeterotypicSynonymName(TaxonName)
|
1275
|
* @see #addHeterotypicSynonymName(TaxonName, Reference, String, HomotypicalGroup)
|
1276
|
* @see #getSynonyms()
|
1277
|
* @see #removeSynonym(Synonym)
|
1278
|
*/
|
1279
|
public Synonym addHomotypicSynonymName(TaxonName synonymName){
|
1280
|
Synonym synonym = Synonym.NewInstance(synonymName, this.getSec());
|
1281
|
addHomotypicSynonym(synonym);
|
1282
|
return synonym;
|
1283
|
}
|
1284
|
|
1285
|
/**
|
1286
|
* Adds the given {@link Synonym synonym} to <code>this</code> taxon,
|
1287
|
* with the {@link SynonymType#HOMOTYPIC_SYNONYM_OF() "is homotypic synonym of"
|
1288
|
* relationship type} and returns it.
|
1289
|
* Furthermore the {@link TaxonName taxon name}
|
1290
|
* used as synonym will be added to the same {@link HomotypicalGroup homotypic group}
|
1291
|
* to which the taxon name of <i>this</i> taxon belongs.<BR>
|
1292
|
*
|
1293
|
* @param synonym the synonym added to <i>this</i> taxon's synonym set
|
1294
|
* @see #addHomotypicSynonymName(TaxonName, Reference, String)
|
1295
|
* @see #addSynonym(Synonym, SynonymType)
|
1296
|
* @see #addSynonym(Synonym, SynonymType, Reference, String)
|
1297
|
* @see #addSynonymName(TaxonName, SynonymType, Reference, String)
|
1298
|
* @see #addSynonymName(TaxonName, SynonymType)
|
1299
|
* @see #addHeterotypicSynonymName(TaxonName)
|
1300
|
* @see #addHeterotypicSynonymName(TaxonName, Reference, String, HomotypicalGroup)
|
1301
|
* @see #getSynonyms()
|
1302
|
* @see #removeSynonym(Synonym)
|
1303
|
*/
|
1304
|
public void addHomotypicSynonym(Synonym synonym){
|
1305
|
if (!this.getSynonyms().contains(synonym)){
|
1306
|
addSynonym(synonym, SynonymType.HOMOTYPIC_SYNONYM_OF());
|
1307
|
} else{
|
1308
|
logger.warn("Tried to add a synonym to an accepted taxon that already is a synonym of this taxon.");
|
1309
|
}
|
1310
|
return;
|
1311
|
}
|
1312
|
|
1313
|
/**
|
1314
|
* Like {@link #removeSynonym(Synonym, boolean)} with <code>removeSynonymNameFromHomotypicalGroup</code> set to true.
|
1315
|
* @see #removeSynonym(Synonym, boolean)
|
1316
|
*/
|
1317
|
public void removeSynonym(Synonym synonym){
|
1318
|
removeSynonym(synonym, true);
|
1319
|
}
|
1320
|
|
1321
|
|
1322
|
/**
|
1323
|
* Removes one element from the set of {@link Synonym synonyms} assigned
|
1324
|
* to <i>this</i> (accepted/valid) taxon.
|
1325
|
*
|
1326
|
* @param synonym the synonym to be removed
|
1327
|
* @param removeSynonymNameFromHomotypicalGroup
|
1328
|
* if <code>true</code> the synonym name will also be deleted from its homotypical group if the
|
1329
|
* group contains other names
|
1330
|
* @see #getSynonyms()
|
1331
|
* @see #removeSynonym(Synonym)
|
1332
|
*/
|
1333
|
public void removeSynonym(Synonym synonym, boolean removeSynonymNameFromHomotypicalGroup) {
|
1334
|
if (synonym != null && this.equals(synonym.getAcceptedTaxon())){
|
1335
|
if(removeSynonymNameFromHomotypicalGroup){
|
1336
|
HomotypicalGroup synHG = synonym.getName().getHomotypicalGroup();
|
1337
|
if (synHG.getTypifiedNames().size() > 1){
|
1338
|
synHG.removeTypifiedName(synonym.getName(), false);
|
1339
|
}
|
1340
|
}
|
1341
|
this.synonyms.remove(synonym);
|
1342
|
synonym.setAcceptedTaxon(null);
|
1343
|
}
|
1344
|
}
|
1345
|
|
1346
|
/**
|
1347
|
* @see #getHomotypicSynonymsByHomotypicGroup(TaxonComparator)
|
1348
|
*/
|
1349
|
@Transient
|
1350
|
public List<Synonym> getHomotypicSynonymsByHomotypicGroup(){
|
1351
|
return getHomotypicSynonymsByHomotypicGroup(null);
|
1352
|
}
|
1353
|
|
1354
|
/**
|
1355
|
* Retrieves the ordered list (depending on the date of publication) of
|
1356
|
* homotypic {@link Synonym synonyms} (according to the same {@link eu.etaxonomy.cdm.model.reference.Reference reference}
|
1357
|
* as for <i>this</i> taxon) under the condition that the {@link eu.etaxonomy.cdm.model.name.TaxonName taxon names}
|
1358
|
* of these synonyms and the taxon name of <i>this</i> taxon belong to the
|
1359
|
* same {@link eu.etaxonomy.cdm.model.name.HomotypicalGroup homotypical group}.
|
1360
|
*
|
1361
|
* @param comparator the taxon comparator to use, if <code>null</code> the default comparator is taken.
|
1362
|
* @return the ordered list of homotypic synonyms
|
1363
|
* @see #getHomotypicSynonymsByHomotypicSynonymType()
|
1364
|
* @see #getSynonyms()
|
1365
|
* @see #getHomotypicSynonymyGroups()
|
1366
|
* @see eu.etaxonomy.cdm.model.name.HomotypicalGroup
|
1367
|
* @see eu.etaxonomy.cdm.model.name.HomotypicalGroup#getSynonymsInGroup(Reference)
|
1368
|
*/
|
1369
|
@Transient
|
1370
|
public List<Synonym> getHomotypicSynonymsByHomotypicGroup(TaxonComparator comparator){
|
1371
|
if (this.getHomotypicGroup() == null){
|
1372
|
return null;
|
1373
|
}else if (comparator == null){
|
1374
|
return this.getSynonymsInGroup(this.getHomotypicGroup());
|
1375
|
}else{
|
1376
|
return this.getSynonymsInGroup(this.getHomotypicGroup(), comparator);
|
1377
|
}
|
1378
|
}
|
1379
|
|
1380
|
/**
|
1381
|
* Retrieves the list of homotypic {@link Synonym synonyms}
|
1382
|
* (according to the same {@link eu.etaxonomy.cdm.model.reference.Reference reference}
|
1383
|
* as for <i>this</i> taxon) under the condition that these synonyms and
|
1384
|
* <i>this</i> taxon are involved in {@link SynonymRelationship synonym relationships} with an
|
1385
|
* "is homotypic synonym of" {@link SynonymType#HOMOTYPIC_SYNONYM_OF() synonym relationship type}.
|
1386
|
*
|
1387
|
* @return the ordered list of homotypic synonyms
|
1388
|
* @see #getHomotypicSynonymsByHomotypicGroup()
|
1389
|
* @see #getSynonyms()
|
1390
|
* @see #getHomotypicSynonymyGroups()
|
1391
|
* @see SynonymType
|
1392
|
* @deprecated as the method currently returns data not matching the original description of the method
|
1393
|
* as an ordered list (according to date of publication) of synonyms with same secundum as <i>this</i> taxon.
|
1394
|
* In future this method will either be removed or semantics may change.
|
1395
|
*/
|
1396
|
@Deprecated
|
1397
|
@Transient
|
1398
|
public List<Synonym> getHomotypicSynonymsByHomotypicSynonymType(){
|
1399
|
Set<Synonym> synonyms = this.getSynonyms();
|
1400
|
List<Synonym> result = new ArrayList<>();
|
1401
|
for(Synonym synonym : synonyms) {
|
1402
|
if(synonym.getType().equals(SynonymType.HOMOTYPIC_SYNONYM_OF())){
|
1403
|
result.add(synonym);
|
1404
|
}
|
1405
|
}
|
1406
|
return result;
|
1407
|
}
|
1408
|
|
1409
|
/**
|
1410
|
* Returns the ordered list of all {@link eu.etaxonomy.cdm.model.name.HomotypicalGroup homotypical groups} {@link Synonym synonyms} of
|
1411
|
* <i>this</i> taxon belong to. {@link eu.etaxonomy.cdm.model.name.TaxonName Taxon names} of homotypic synonyms
|
1412
|
* belong to the same homotypical group as the taxon name of <i>this</i>
|
1413
|
* taxon. Taxon names of heterotypic synonyms belong to at least one other
|
1414
|
* homotypical group. <BR>
|
1415
|
* The list returned is ordered according to the date of publication of the
|
1416
|
* first published name within each homotypical group.
|
1417
|
*
|
1418
|
* @see #getHeterotypicSynonymyGroups()
|
1419
|
* @see #getSynonyms()
|
1420
|
* @see eu.etaxonomy.cdm.model.name.HomotypicalGroup
|
1421
|
*/
|
1422
|
@Transient
|
1423
|
public List<HomotypicalGroup> getHomotypicSynonymyGroups(){
|
1424
|
List<HomotypicalGroup> result = new ArrayList<>();
|
1425
|
HomotypicalGroup myGroup = this.getHomotypicGroup();
|
1426
|
if (myGroup != null){ //if taxon has no name HG might be null
|
1427
|
result.add(myGroup);
|
1428
|
}
|
1429
|
for (TaxonName taxonName :this.getSynonymNames()){
|
1430
|
if (taxonName != null) {
|
1431
|
if (!result.contains(taxonName.getHomotypicalGroup())){
|
1432
|
result.add(taxonName.getHomotypicalGroup());
|
1433
|
}
|
1434
|
}
|
1435
|
}
|
1436
|
return result;
|
1437
|
}
|
1438
|
|
1439
|
/**
|
1440
|
* {@inheritDoc}.
|
1441
|
* <BR>Also returns <code>false</code> if it is a misapplied name or has a similar concept relationship that
|
1442
|
* is similar to synonym relationship (shows up in the synonymy of applications)
|
1443
|
*/
|
1444
|
@Override
|
1445
|
@Transient
|
1446
|
public boolean isOrphaned() {
|
1447
|
|
1448
|
if(taxonNodes == null || taxonNodes.isEmpty()) {
|
1449
|
if(getRelationsFromThisTaxon().isEmpty()) {
|
1450
|
return true;
|
1451
|
}else{
|
1452
|
for (TaxonRelationship rel : getRelationsFromThisTaxon()){
|
1453
|
if (rel.getType() != null && ! rel.getType().isConceptRelationship()){
|
1454
|
return false; //a synonym relationship type similar relationship exists => not orphaned
|
1455
|
}
|
1456
|
}
|
1457
|
return true; //all relations are real concept relations and therefore not relevant
|
1458
|
}
|
1459
|
}else{
|
1460
|
return false;
|
1461
|
}
|
1462
|
}
|
1463
|
|
1464
|
/**
|
1465
|
* Returns the ordered list of all
|
1466
|
* {@link eu.etaxonomy.cdm.model.name.HomotypicalGroup homotypical groups}
|
1467
|
* that contain {@link Synonym synonyms} that are heterotypic to <i>this</i> taxon.<BR>
|
1468
|
*
|
1469
|
* {@link eu.etaxonomy.cdm.model.name.TaxonName Taxon names} of heterotypic synonyms
|
1470
|
* belong to a homotypical group which cannot be the homotypical group to which the
|
1471
|
* taxon name of <i>this</i> taxon belongs.
|
1472
|
* This method returns the same
|
1473
|
* list as the {@link #getHomotypicSynonymyGroups() getHomotypicSynonymyGroups} method
|
1474
|
* but without the homotypical group to which the taxon name of <i>this</i> taxon
|
1475
|
* belongs.<BR>
|
1476
|
* The list returned is <B>ordered</B> according to the rules defined for
|
1477
|
* the {@link HomotypicGroupTaxonComparator} which includes 1) grouping of
|
1478
|
* basionym groups, 2) replaced synonym relationships, 3) publication date,
|
1479
|
* 4) ranks and 5) alphabetical order.
|
1480
|
*
|
1481
|
* @see #getHeterotypicSynonymyGroups()
|
1482
|
* @see #getSynonyms()
|
1483
|
* @see SynonymType#HETEROTYPIC_SYNONYM_OF()
|
1484
|
* @see eu.etaxonomy.cdm.model.name.HomotypicalGroup
|
1485
|
*/
|
1486
|
@Transient
|
1487
|
public List<HomotypicalGroup> getHeterotypicSynonymyGroups(){
|
1488
|
List<HomotypicalGroup> list = getHomotypicSynonymyGroups();
|
1489
|
//remove homotypic group
|
1490
|
list.remove(this.getHomotypicGroup());
|
1491
|
//sort
|
1492
|
Map<Synonym, HomotypicalGroup> map = new HashMap<>();
|
1493
|
for (HomotypicalGroup homotypicalGroup: list){
|
1494
|
List<Synonym> synonymList = getSynonymsInGroup(homotypicalGroup);
|
1495
|
if (synonymList.size() > 0){
|
1496
|
//select the first synonym in the group
|
1497
|
map.put(synonymList.get(0), homotypicalGroup);
|
1498
|
}
|
1499
|
}
|
1500
|
List<Synonym> keyList = new ArrayList<>();
|
1501
|
keyList.addAll(map.keySet());
|
1502
|
//order by first synonym
|
1503
|
Collections.sort(keyList, defaultTaxonComparator);
|
1504
|
|
1505
|
List<HomotypicalGroup> result = new ArrayList<>();
|
1506
|
for(Synonym synonym: keyList){
|
1507
|
//"replace" synonyms by homotypic groups
|
1508
|
result.add(map.get(synonym));
|
1509
|
}
|
1510
|
//sort end
|
1511
|
return result;
|
1512
|
}
|
1513
|
|
1514
|
/**
|
1515
|
* Retrieves the ordered list (depending on the rules defined for
|
1516
|
* the {@link HomotypicGroupTaxonComparator}) of
|
1517
|
* {@link taxon.Synonym synonyms} (according to a given reference)
|
1518
|
* the {@link TaxonName taxon names} of which belong to the homotypical group.
|
1519
|
* If other names are part of the group that are not considered synonyms of
|
1520
|
* <i>this</i> taxon, then they will not be included in
|
1521
|
* the result set.
|
1522
|
*
|
1523
|
* @param homotypicGroup
|
1524
|
* @see #getHeterotypicSynonymyGroups()
|
1525
|
* @see TaxonName#getSynonyms()
|
1526
|
* @see TaxonName#getTaxa()
|
1527
|
* @see taxon.Synonym
|
1528
|
*/
|
1529
|
@Transient
|
1530
|
public List<Synonym> getSynonymsInGroup(HomotypicalGroup homotypicGroup){
|
1531
|
return getSynonymsInGroup(homotypicGroup, new HomotypicGroupTaxonComparator(this));
|
1532
|
}
|
1533
|
|
1534
|
/**
|
1535
|
* @param homotypicGroup
|
1536
|
* @param comparator
|
1537
|
* @return
|
1538
|
* @see #getSynonymsInGroup(HomotypicalGroup)
|
1539
|
* @see #getHeterotypicSynonymyGroups()
|
1540
|
*/
|
1541
|
@Transient
|
1542
|
public List<Synonym> getSynonymsInGroup(HomotypicalGroup homotypicGroup, TaxonComparator comparator){
|
1543
|
List<Synonym> result = new ArrayList<>();
|
1544
|
if (homotypicGroup == null){
|
1545
|
return result; //always empty
|
1546
|
}
|
1547
|
|
1548
|
for (Synonym synonym : this.getSynonyms()){
|
1549
|
if (homotypicGroup.equals(synonym.getHomotypicGroup())){
|
1550
|
result.add(synonym);
|
1551
|
}
|
1552
|
}
|
1553
|
|
1554
|
Collections.sort(result, comparator);
|
1555
|
return result;
|
1556
|
}
|
1557
|
|
1558
|
/**
|
1559
|
* @see #getSynonymsGroups()
|
1560
|
*/
|
1561
|
@Transient
|
1562
|
public List<Taxon> getAllMisappliedNames(){
|
1563
|
List<Taxon> result = new ArrayList<>();
|
1564
|
|
1565
|
for (TaxonRelationship rel : this.getRelationsToThisTaxon()){
|
1566
|
if (rel.getType().isAnyMisappliedName() ){
|
1567
|
result.add(rel.getFromTaxon());
|
1568
|
}
|
1569
|
}
|
1570
|
sortBySimpleTitleCacheComparator(result);
|
1571
|
return result;
|
1572
|
}
|
1573
|
|
1574
|
|
1575
|
/**
|
1576
|
* @see #getSynonymsGroups()
|
1577
|
*/
|
1578
|
@Transient
|
1579
|
public List<Taxon> getAllProParteSynonyms(){
|
1580
|
List<Taxon> result = new ArrayList<>();
|
1581
|
|
1582
|
for (TaxonRelationship rel : this.getRelationsToThisTaxon()){
|
1583
|
if (rel.getType().isAnySynonym()){
|
1584
|
result.add(rel.getFromTaxon());
|
1585
|
}
|
1586
|
}
|
1587
|
sortBySimpleTitleCacheComparator(result);
|
1588
|
return result;
|
1589
|
}
|
1590
|
|
1591
|
private void sortBySimpleTitleCacheComparator(List<Taxon> result) {
|
1592
|
|
1593
|
Comparator<Taxon> taxonComparator = new Comparator<Taxon>(){
|
1594
|
|
1595
|
@Override
|
1596
|
public int compare(Taxon o1, Taxon o2) {
|
1597
|
|
1598
|
if (o1.getTitleCache() == o2.getTitleCache()){
|
1599
|
return 0;
|
1600
|
}
|
1601
|
if (o1.getTitleCache() == null){
|
1602
|
return -1;
|
1603
|
}
|
1604
|
if (o2.getTitleCache() == null){
|
1605
|
return 1;
|
1606
|
}
|
1607
|
return o1.getTitleCache().compareTo(o2.getTitleCache());
|
1608
|
|
1609
|
}
|
1610
|
};
|
1611
|
Collections.sort(result, taxonComparator);
|
1612
|
}
|
1613
|
|
1614
|
/**
|
1615
|
* Returns the image gallery description. If no image gallery exists, a new one is created using the
|
1616
|
* defined title and adds the string "-Image Gallery" to the title.</BR>
|
1617
|
* If multiple image galleries exist an arbitrary one is choosen.
|
1618
|
* @param title
|
1619
|
* @return
|
1620
|
*/
|
1621
|
public TaxonDescription getOrCreateImageGallery(String title){
|
1622
|
return getOrCreateImageGallery(title, true, false);
|
1623
|
}
|
1624
|
|
1625
|
/**
|
1626
|
* Returns the image gallery description. If no image gallery exists, a new one is created using the
|
1627
|
* defined title.</BR>
|
1628
|
* If onlyTitle == true we look only for an image gallery with this title, create a new one otherwise.
|
1629
|
* If multiple image galleries exist that match the conditions an arbitrary one is choosen.
|
1630
|
* @param title
|
1631
|
* @param onlyTitle
|
1632
|
* @param if true, the String "Image Gallery
|
1633
|
* @return
|
1634
|
*/
|
1635
|
@Transient
|
1636
|
public TaxonDescription getOrCreateImageGallery(String title, boolean addImageGalleryToTitle, boolean onlyTitle){
|
1637
|
TaxonDescription result = null;
|
1638
|
String titleCache = (title == null) ? "Image Gallery" : title;
|
1639
|
if (title != null && addImageGalleryToTitle){
|
1640
|
titleCache = titleCache+ "-Image Gallery";
|
1641
|
}
|
1642
|
Set<TaxonDescription> descriptionSet = this.getDescriptions();
|
1643
|
for (TaxonDescription desc: descriptionSet){
|
1644
|
if (desc.isImageGallery()){
|
1645
|
if (onlyTitle && ! titleCache.equals(desc.getTitleCache())){
|
1646
|
continue;
|
1647
|
}
|
1648
|
result = desc;
|
1649
|
if (onlyTitle && titleCache.equals(desc.getTitleCache())){
|
1650
|
break;
|
1651
|
}
|
1652
|
}
|
1653
|
}
|
1654
|
if (result == null){
|
1655
|
result = TaxonDescription.NewInstance();
|
1656
|
result.setTitleCache(titleCache, true);
|
1657
|
this.addDescription(result);
|
1658
|
result.setImageGallery(true);
|
1659
|
}
|
1660
|
return result;
|
1661
|
}
|
1662
|
|
1663
|
public void clearDescriptions() {
|
1664
|
this.descriptions = new HashSet<>();
|
1665
|
}
|
1666
|
|
1667
|
/**
|
1668
|
* Compiles all description items attached to this taxon having the given feature
|
1669
|
* and being of the given class. If feature or clazz is null no according filter
|
1670
|
* is applied.
|
1671
|
*/
|
1672
|
public <T extends DescriptionElementBase> Set<T> getDescriptionItems(Feature feature, Class<T> clazz) {
|
1673
|
Set<T> result = new HashSet<>();
|
1674
|
Set<TaxonDescription> descriptions = this.getDescriptions();
|
1675
|
for (TaxonDescription description : descriptions) {
|
1676
|
for (DescriptionElementBase deb : description.getElements()) {
|
1677
|
if (clazz == null || deb.isInstanceOf(clazz)) {
|
1678
|
if (feature == null || feature.equals(deb.getFeature())) {
|
1679
|
T matchingDeb = CdmBase.deproxy(deb, clazz);
|
1680
|
result.add(matchingDeb);
|
1681
|
}
|
1682
|
}
|
1683
|
}
|
1684
|
}
|
1685
|
return result;
|
1686
|
}
|
1687
|
|
1688
|
//*********************** CLONE ********************************************************/
|
1689
|
|
1690
|
/**
|
1691
|
* Clones <i>this</i> taxon. This is a shortcut that enables to create
|
1692
|
* a new instance that differs only slightly from <i>this</i> taxon by
|
1693
|
* modifying only some of the attributes.<BR><BR>
|
1694
|
* The TaxonNodes are not cloned, the list is empty.<BR>
|
1695
|
* (CAUTION: this behaviour needs to be discussed and may change in future).<BR><BR>
|
1696
|
* The taxon relationships and synonym relationships are cloned <BR>
|
1697
|
*
|
1698
|
* @see eu.etaxonomy.cdm.model.taxon.TaxonBase#clone()
|
1699
|
* @see eu.etaxonomy.cdm.model.media.IdentifiableEntity#clone()
|
1700
|
* @see java.lang.Object#clone()
|
1701
|
*/
|
1702
|
@Override
|
1703
|
public Taxon clone() {
|
1704
|
Taxon result;
|
1705
|
result = (Taxon)super.clone();
|
1706
|
|
1707
|
result.setRelationsFromThisTaxon(new HashSet<>());
|
1708
|
|
1709
|
for (TaxonRelationship fromRelationship : this.getRelationsFromThisTaxon()){
|
1710
|
TaxonRelationship newRelationship = (TaxonRelationship)fromRelationship.clone();
|
1711
|
newRelationship.setRelatedFrom(result);
|
1712
|
result.relationsFromThisTaxon.add(newRelationship);
|
1713
|
}
|
1714
|
|
1715
|
result.setRelationsToThisTaxon(new HashSet<>());
|
1716
|
for (TaxonRelationship toRelationship : this.getRelationsToThisTaxon()){
|
1717
|
TaxonRelationship newRelationship = (TaxonRelationship)toRelationship.clone();
|
1718
|
newRelationship.setRelatedTo(result);
|
1719
|
result.relationsToThisTaxon.add(newRelationship);
|
1720
|
}
|
1721
|
|
1722
|
//clone synonyms (is this wanted or should we remove synonyms
|
1723
|
result.synonyms = new HashSet<>();
|
1724
|
for (Synonym synonym : this.getSynonyms()){
|
1725
|
Synonym newSyn = synonym.clone();
|
1726
|
newSyn.setAcceptedTaxon(result);
|
1727
|
}
|
1728
|
|
1729
|
result.descriptions = new HashSet<>();
|
1730
|
for (TaxonDescription description : this.getDescriptions()){
|
1731
|
TaxonDescription newDescription = description.clone();
|
1732
|
result.addDescription(newDescription);
|
1733
|
}
|
1734
|
|
1735
|
result.taxonNodes = new HashSet<>();
|
1736
|
|
1737
|
/*for (TaxonNode taxonNode : this.getTaxonNodes()){
|
1738
|
TaxonNode newTaxonNode = (TaxonNode)taxonNode.clone();
|
1739
|
newTaxonNode.setTaxon(result);
|
1740
|
result.addTaxonNode(newTaxonNode);
|
1741
|
}*/
|
1742
|
|
1743
|
return result;
|
1744
|
}
|
1745
|
}
|