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9479da48
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Andreas Müller
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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.model.name;
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1cfc54ab
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Andreas Müller
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import java.lang.reflect.Method;
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396aee74
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Andreas Müller
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import java.util.HashSet;
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b24d580a
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Andreas Kohlbecker
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import java.util.List;
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396aee74
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Andreas Müller
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import java.util.Set;
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import javax.persistence.Column;
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396aee74
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Andreas Müller
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import javax.persistence.Entity;
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import javax.persistence.FetchType;
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import javax.persistence.Inheritance;
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import javax.persistence.InheritanceType;
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import javax.persistence.ManyToMany;
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import javax.persistence.ManyToOne;
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import javax.persistence.OneToMany;
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b70a7f94
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Andreas Kohlbecker
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import javax.persistence.Transient;
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import javax.xml.bind.annotation.XmlAccessType;
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import javax.xml.bind.annotation.XmlAccessorType;
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import javax.xml.bind.annotation.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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9479da48
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Andreas Müller
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Andreas Müller
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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.annotations.Index;
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import org.hibernate.annotations.Table;
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ee91bcd9
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import org.hibernate.envers.Audited;
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import org.hibernate.search.annotations.Field;
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import org.springframework.util.ReflectionUtils;
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396aee74
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.IParsable;
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import eu.etaxonomy.cdm.model.common.IReferencedEntity;
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import eu.etaxonomy.cdm.model.common.IRelated;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
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import eu.etaxonomy.cdm.model.occurrence.Specimen;
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import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.reference.StrictReferenceBase;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy;
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Andreas Müller
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/**
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m.geoffroy
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* The upmost (abstract) class for scientific taxon names regardless of any
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c3440568
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* particular {@link NomenclaturalCode nomenclature code}. The scientific taxon name does not depend
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* on the use made of it in a publication or a treatment
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* ({@link eu.etaxonomy.cdm.model.taxon.TaxonBase taxon concept respectively potential taxon})
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* as an {@link eu.etaxonomy.cdm.model.taxon.Taxon "accepted" respectively "correct" (taxon) name}
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* or as a {@link eu.etaxonomy.cdm.model.taxon.Synonym synonym}.
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* <P>
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* This class corresponds partially to: <ul>
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* <li> TaxonName according to the TDWG ontology
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* <li> ScientificName and CanonicalName according to the TCS
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* <li> ScientificName according to the ABCD schema
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* </ul>
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m.geoffroy
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*
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9479da48
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Andreas Müller
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* @author m.doering
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* @version 1.0
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* @created 08-Nov-2007 13:06:57
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "TaxonNameBase", propOrder = {
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"appendedPhrase",
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"nomenclaturalMicroReference",
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"nomenclaturalReference",
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"rank",
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"fullTitleCache",
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"protectedFullTitleCache",
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"homotypicalGroup",
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"typeDesignations",
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"relationsFromThisName",
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"relationsToThisName",
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"status",
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"descriptions",
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"taxonBases"
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})
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@XmlRootElement(name = "TaxonNameBase")
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9479da48
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Andreas Müller
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@Entity
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@Audited
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Andreas Müller
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@Inheritance(strategy=InheritanceType.SINGLE_TABLE)
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Andreas Müller
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@Table(appliesTo="TaxonNameBase", indexes = { @Index(name = "taxonNameBaseTitleCacheIndex", columnNames = { "titleCache" }) })
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public abstract class TaxonNameBase<T extends TaxonNameBase<?,?>, S extends INameCacheStrategy> extends IdentifiableEntity<S> implements IReferencedEntity, IParsable, IRelated {
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Andreas Müller
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private static final long serialVersionUID = -4530368639601532116L;
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private static final Logger logger = Logger.getLogger(TaxonNameBase.class);
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@XmlElement(name = "FullTitleCache")
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@Column(length=330, name="fullTitleCache")
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private String fullTitleCache;
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//if true titleCache will not be automatically generated/updated
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@XmlElement(name = "ProtectedFullTitleCache")
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private boolean protectedFullTitleCache;
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@XmlElementWrapper(name = "Descriptions")
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@XmlElement(name = "Description")
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@OneToMany(mappedBy="taxonName", fetch= FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE})
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private Set<TaxonNameDescription> descriptions = new HashSet<TaxonNameDescription>();
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@XmlElement(name = "AppendedPhrase")
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@Field(index= org.hibernate.search.annotations.Index.TOKENIZED)
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Andreas Müller
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private String appendedPhrase;
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@XmlElement(name = "NomenclaturalMicroReference")
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@Field(index= org.hibernate.search.annotations.Index.TOKENIZED)
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Andreas Müller
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private String nomenclaturalMicroReference;
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@XmlAttribute
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Andreas Müller
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private boolean hasProblem = false;
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@XmlAttribute
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private int problemStarts = -1;
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@XmlAttribute
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private int problemEnds = -1;
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@XmlElementWrapper(name = "TypeDesignations")
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@XmlElement(name = "TypeDesignation")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToMany(fetch = FetchType.LAZY)
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//TODO @Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE_ORPHAN})
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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private Set<TypeDesignationBase> typeDesignations = new HashSet<TypeDesignationBase>();
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@XmlElement(name = "HomotypicalGroup")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToOne(fetch = FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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private HomotypicalGroup homotypicalGroup;
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@XmlElementWrapper(name = "RelationsFromThisName")
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@XmlElement(name = "RelationFromThisName")
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@OneToMany(mappedBy="relatedFrom", fetch= FetchType.LAZY)
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ec1f7873
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Andreas Müller
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//TODO @Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE_ORPHAN}) => DELETE_ORPHAN does not work ( org.hibernate.HibernateException: Don't change the reference to a collection with cascade="all-delete-orphan": eu.etaxonomy.cdm.model.name.TaxonNameBase.relationsFromThisName)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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private Set<NameRelationship> relationsFromThisName = new HashSet<NameRelationship>();
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@XmlElementWrapper(name = "RelationsToThisName")
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@XmlElement(name = "RelationToThisName")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@OneToMany(mappedBy="relatedTo", fetch= FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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private Set<NameRelationship> relationsToThisName = new HashSet<NameRelationship>();
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@XmlElementWrapper(name = "NomenclaturalStatuses")
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@XmlElement(name = "NomenclaturalStatus")
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@OneToMany(fetch= FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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private Set<NomenclaturalStatus> status = new HashSet<NomenclaturalStatus>();
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@XmlElementWrapper(name = "TaxonBases")
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@XmlElement(name = "TaxonBase")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@OneToMany(mappedBy="name", fetch= FetchType.LAZY)
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private Set<TaxonBase> taxonBases = new HashSet<TaxonBase>();
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@XmlElement(name = "Rank")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToOne(fetch = FetchType.EAGER)
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private Rank rank;
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@XmlElement(name = "NomenclaturalReference")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToOne(fetch = FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE})
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private ReferenceBase nomenclaturalReference;
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// ************* CONSTRUCTORS *************/
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m.geoffroy
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/**
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| 194 |
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m.geoffroy
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* Class constructor: creates a new empty taxon name.
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m.geoffroy
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*
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* @see #TaxonNameBase(Rank)
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* @see #TaxonNameBase(HomotypicalGroup)
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* @see #TaxonNameBase(Rank, HomotypicalGroup)
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*/
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| 200 |
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public TaxonNameBase() {
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super();
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| 202 |
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}
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| 203 |
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/**
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| 204 |
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m.geoffroy
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* Class constructor: creates a new taxon name
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| 205 |
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m.geoffroy
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* only containing its {@link Rank rank}.
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| 206 |
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m.geoffroy
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*
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m.geoffroy
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* @param rank the rank to be assigned to <i>this</i> taxon name
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| 208 |
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m.geoffroy
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* @see #TaxonNameBase()
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* @see #TaxonNameBase(HomotypicalGroup)
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* @see #TaxonNameBase(Rank, HomotypicalGroup)
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| 211 |
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m.geoffroy
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*/
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| 212 |
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public TaxonNameBase(Rank rank) {
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| 213 |
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this(rank, null);
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}
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| 215 |
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m.geoffroy
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/**
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| 216 |
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m.geoffroy
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* Class constructor: creates a new taxon name
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| 217 |
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m.geoffroy
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* only containing its {@link HomotypicalGroup homotypical group}.
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| 218 |
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m.geoffroy
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* The new taxon name will be also added to the set of taxon names
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| 219 |
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* belonging to this homotypical group.
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| 220 |
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*
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| 221 |
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m.geoffroy
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* @param homotypicalGroup the homotypical group to which <i>this</i> taxon name belongs
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| 222 |
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m.geoffroy
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* @see #TaxonNameBase()
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* @see #TaxonNameBase(Rank)
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* @see #TaxonNameBase(Rank, HomotypicalGroup)
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| 225 |
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*/
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| 226 |
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public TaxonNameBase(HomotypicalGroup homotypicalGroup) {
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| 227 |
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this(null, homotypicalGroup);
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| 228 |
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}
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| 229 |
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/**
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| 230 |
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m.geoffroy
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* Class constructor: creates a new taxon name
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| 231 |
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m.geoffroy
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* only containing its {@link Rank rank} and
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| 232 |
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* its {@link HomotypicalGroup homotypical group}.
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| 233 |
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* The new taxon name will be also added to the set of taxon names
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| 234 |
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* belonging to this homotypical group.
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| 235 |
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*
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6a9737e8
|
m.geoffroy
|
* @param rank the rank to be assigned to <i>this</i> taxon name
|
| 237 |
b9d0e8d2
|
m.geoffroy
|
* @param homotypicalGroup the homotypical group to which <i>this</i> taxon name belongs
|
| 238 |
6a9737e8
|
m.geoffroy
|
* @see #TaxonNameBase()
|
| 239 |
|
|
* @see #TaxonNameBase(Rank)
|
| 240 |
|
|
* @see #TaxonNameBase(HomotypicalGroup)
|
| 241 |
12655d36
|
m.geoffroy
|
*/
|
| 242 |
b18c6379
|
Andreas Müller
|
public TaxonNameBase(Rank rank, HomotypicalGroup homotypicalGroup) {
|
| 243 |
9479da48
|
Andreas Müller
|
super();
|
| 244 |
|
|
this.setRank(rank);
|
| 245 |
b18c6379
|
Andreas Müller
|
if (homotypicalGroup == null){
|
| 246 |
|
|
homotypicalGroup = new HomotypicalGroup();
|
| 247 |
|
|
}
|
| 248 |
|
|
homotypicalGroup.addTypifiedName(this);
|
| 249 |
9479da48
|
Andreas Müller
|
}
|
| 250 |
2a486d28
|
Andreas Müller
|
|
| 251 |
|
|
//********* METHODS **************************************/
|
| 252 |
9017e2de
|
Andreas Müller
|
|
| 253 |
12655d36
|
m.geoffroy
|
/**
|
| 254 |
b9d0e8d2
|
m.geoffroy
|
* Returns the boolean value "false" since the components of <i>this</i> taxon name
|
| 255 |
eb7e638a
|
m.geoffroy
|
* cannot follow the rules of a corresponding {@link NomenclaturalCode nomenclatural code}
|
| 256 |
|
|
* which is not defined for this class. The nomenclature code depends on
|
| 257 |
12655d36
|
m.geoffroy
|
* the concrete name subclass ({@link BacterialName BacterialName},
|
| 258 |
|
|
* {@link BotanicalName BotanicalName}, {@link CultivarPlantName CultivarPlantName},
|
| 259 |
|
|
* {@link ZoologicalName ZoologicalName} or {@link ViralName ViralName})
|
| 260 |
eb7e638a
|
m.geoffroy
|
* to which a taxon name belongs.
|
| 261 |
12655d36
|
m.geoffroy
|
*
|
| 262 |
eb7e638a
|
m.geoffroy
|
* @return false
|
| 263 |
12655d36
|
m.geoffroy
|
*/
|
| 264 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 265 |
9479da48
|
Andreas Müller
|
public abstract boolean isCodeCompliant();
|
| 266 |
|
|
|
| 267 |
33508d06
|
a.babadshanjan
|
public abstract String generateFullTitle();
|
| 268 |
9479da48
|
Andreas Müller
|
|
| 269 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 270 |
33508d06
|
a.babadshanjan
|
public String getFullTitleCache(){
|
| 271 |
|
|
if (protectedFullTitleCache){
|
| 272 |
|
|
return this.fullTitleCache;
|
| 273 |
|
|
}
|
| 274 |
|
|
if (fullTitleCache == null){
|
| 275 |
e3a02794
|
a.babadshanjan
|
this.setFullTitleCache(generateFullTitle(), protectedFullTitleCache);
|
| 276 |
33508d06
|
a.babadshanjan
|
}
|
| 277 |
|
|
return fullTitleCache;
|
| 278 |
|
|
}
|
| 279 |
b24d580a
|
Andreas Kohlbecker
|
|
| 280 |
|
|
@Transient
|
| 281 |
|
|
public List<Object> getTaggedName(){
|
| 282 |
|
|
return getCacheStrategy().getTaggedName(this);
|
| 283 |
|
|
}
|
| 284 |
33508d06
|
a.babadshanjan
|
|
| 285 |
|
|
public void setFullTitleCache(String fullTitleCache){
|
| 286 |
|
|
setFullTitleCache(fullTitleCache, PROTECTED);
|
| 287 |
|
|
}
|
| 288 |
|
|
|
| 289 |
|
|
public void setFullTitleCache(String fullTitleCache, boolean protectCache){
|
| 290 |
|
|
//TODO truncation of full title cache
|
| 291 |
c0bd32ce
|
a.babadshanjan
|
if (fullTitleCache != null && fullTitleCache.length() > 329){
|
| 292 |
|
|
logger.warn("Truncation of full title cache: " + this.toString() + "/" + fullTitleCache);
|
| 293 |
|
|
fullTitleCache = fullTitleCache.substring(0, 329) + "...";
|
| 294 |
|
|
}
|
| 295 |
33508d06
|
a.babadshanjan
|
this.fullTitleCache = fullTitleCache;
|
| 296 |
|
|
this.setProtectedFullTitleCache(protectCache);
|
| 297 |
|
|
}
|
| 298 |
|
|
|
| 299 |
|
|
public boolean isProtectedFullTitleCache() {
|
| 300 |
|
|
return protectedFullTitleCache;
|
| 301 |
|
|
}
|
| 302 |
|
|
|
| 303 |
|
|
public void setProtectedFullTitleCache(boolean protectedFullTitleCache) {
|
| 304 |
|
|
this.protectedFullTitleCache = protectedFullTitleCache;
|
| 305 |
|
|
}
|
| 306 |
|
|
|
| 307 |
12655d36
|
m.geoffroy
|
/**
|
| 308 |
|
|
* Returns the set of all {@link NameRelationship name relationships}
|
| 309 |
b9d0e8d2
|
m.geoffroy
|
* in which <i>this</i> taxon name is involved. A taxon name can be both source
|
| 310 |
12655d36
|
m.geoffroy
|
* in some name relationships or target in some others.
|
| 311 |
|
|
*
|
| 312 |
09487e73
|
m.geoffroy
|
* @see #getRelationsToThisName()
|
| 313 |
|
|
* @see #getRelationsFromThisName()
|
| 314 |
|
|
* @see #addNameRelationship(NameRelationship)
|
| 315 |
12655d36
|
m.geoffroy
|
* @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
|
| 316 |
|
|
* @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
|
| 317 |
|
|
*/
|
| 318 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 319 |
9479da48
|
Andreas Müller
|
public Set<NameRelationship> getNameRelations() {
|
| 320 |
6ecda5d2
|
m.doering
|
Set<NameRelationship> rels = new HashSet<NameRelationship>();
|
| 321 |
|
|
rels.addAll(getRelationsFromThisName());
|
| 322 |
|
|
rels.addAll(getRelationsToThisName());
|
| 323 |
|
|
return rels;
|
| 324 |
|
|
}
|
| 325 |
b92a6173
|
a.babadshanjan
|
|
| 326 |
6ecda5d2
|
m.doering
|
/**
|
| 327 |
b9d0e8d2
|
m.geoffroy
|
* Creates a new {@link NameRelationship#NameRelationship(TaxonNameBase, TaxonNameBase, NameRelationshipType, String) name relationship} from <i>this</i> taxon name to another taxon name
|
| 328 |
|
|
* and adds it both to the set of {@link #getRelationsFromThisName() relations from <i>this</i> taxon name} and
|
| 329 |
12655d36
|
m.geoffroy
|
* to the set of {@link #getRelationsToThisName() relations to the other taxon name}.
|
| 330 |
|
|
*
|
| 331 |
|
|
* @param toName the taxon name of the target for this new name relationship
|
| 332 |
|
|
* @param type the type of this new name relationship
|
| 333 |
|
|
* @param ruleConsidered the string which specifies the rule on which this name relationship is based
|
| 334 |
09487e73
|
m.geoffroy
|
* @see #getRelationsToThisName()
|
| 335 |
|
|
* @see #getNameRelations()
|
| 336 |
12655d36
|
m.geoffroy
|
* @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
|
| 337 |
|
|
* @see #addNameRelationship(NameRelationship)
|
| 338 |
6ecda5d2
|
m.doering
|
*/
|
| 339 |
|
|
public void addRelationshipToName(TaxonNameBase toName, NameRelationshipType type, String ruleConsidered){
|
| 340 |
|
|
NameRelationship rel = new NameRelationship(toName, this, type, ruleConsidered);
|
| 341 |
|
|
}
|
| 342 |
21f31bf8
|
Andreas Müller
|
|
| 343 |
|
|
public void addRelationshipToName(TaxonNameBase toName, NameRelationshipType type, ReferenceBase citation, String microCitation, String ruleConsidered){
|
| 344 |
|
|
NameRelationship rel = new NameRelationship(toName, this, type, citation, microCitation, ruleConsidered);
|
| 345 |
|
|
}
|
| 346 |
|
|
|
| 347 |
12655d36
|
m.geoffroy
|
/**
|
| 348 |
b9d0e8d2
|
m.geoffroy
|
* Creates a new {@link NameRelationship#NameRelationship(TaxonNameBase, TaxonNameBase, NameRelationshipType, String) name relationship} from another taxon name to <i>this</i> taxon name
|
| 349 |
|
|
* and adds it both to the set of {@link #getRelationsToThisName() relations to <i>this</i> taxon name} and
|
| 350 |
12655d36
|
m.geoffroy
|
* to the set of {@link #getRelationsFromThisName() relations from the other taxon name}.
|
| 351 |
|
|
*
|
| 352 |
|
|
* @param fromName the taxon name of the source for this new name relationship
|
| 353 |
|
|
* @param type the type of this new name relationship
|
| 354 |
|
|
* @param ruleConsidered the string which specifies the rule on which this name relationship is based
|
| 355 |
09487e73
|
m.geoffroy
|
* @see #getRelationsFromThisName()
|
| 356 |
|
|
* @see #getNameRelations()
|
| 357 |
12655d36
|
m.geoffroy
|
* @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
|
| 358 |
|
|
* @see #addNameRelationship(NameRelationship)
|
| 359 |
|
|
*/
|
| 360 |
4dd3e141
|
m.doering
|
public void addRelationshipFromName(TaxonNameBase fromName, NameRelationshipType type, String ruleConsidered){
|
| 361 |
|
|
NameRelationship rel = new NameRelationship(this, fromName, type, ruleConsidered);
|
| 362 |
|
|
}
|
| 363 |
21f31bf8
|
Andreas Müller
|
public void addRelationshipFromName(TaxonNameBase fromName, NameRelationshipType type, ReferenceBase citation, String microCitation, String ruleConsidered){
|
| 364 |
|
|
NameRelationship rel = new NameRelationship(this, fromName, type, citation, microCitation, ruleConsidered);
|
| 365 |
|
|
}
|
| 366 |
|
|
|
| 367 |
12655d36
|
m.geoffroy
|
/**
|
| 368 |
|
|
* Adds an existing {@link NameRelationship name relationship} either to the set of
|
| 369 |
b9d0e8d2
|
m.geoffroy
|
* {@link #getRelationsToThisName() relations to <i>this</i> taxon name} or to the set of
|
| 370 |
|
|
* {@link #getRelationsFromThisName() relations from <i>this</i> taxon name}. If neither the
|
| 371 |
|
|
* source nor the target of the name relationship match with <i>this</i> taxon name
|
| 372 |
12655d36
|
m.geoffroy
|
* no addition will be carried out.
|
| 373 |
|
|
*
|
| 374 |
b9d0e8d2
|
m.geoffroy
|
* @param rel the name relationship to be added to one of <i>this</i> taxon name's name relationships sets
|
| 375 |
09487e73
|
m.geoffroy
|
* @see #getNameRelations()
|
| 376 |
12655d36
|
m.geoffroy
|
* @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
|
| 377 |
|
|
* @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
|
| 378 |
|
|
*/
|
| 379 |
6ecda5d2
|
m.doering
|
protected void addNameRelationship(NameRelationship rel) {
|
| 380 |
|
|
if (rel!=null && rel.getToName().equals(this)){
|
| 381 |
|
|
this.relationsToThisName.add(rel);
|
| 382 |
|
|
}else if(rel!=null && rel.getFromName().equals(this)){
|
| 383 |
|
|
this.relationsFromThisName.add(rel);
|
| 384 |
|
|
}else{
|
| 385 |
|
|
//TODO: raise error???
|
| 386 |
|
|
}
|
| 387 |
9479da48
|
Andreas Müller
|
}
|
| 388 |
12655d36
|
m.geoffroy
|
/**
|
| 389 |
|
|
* Removes one {@link NameRelationship name relationship} from one of both sets of
|
| 390 |
b9d0e8d2
|
m.geoffroy
|
* {@link #getNameRelations() name relationships} in which <i>this</i> taxon name is involved.
|
| 391 |
09487e73
|
m.geoffroy
|
* The name relationship will also be removed from one of both sets belonging
|
| 392 |
|
|
* to the second taxon name involved. Furthermore the fromName and toName
|
| 393 |
|
|
* attributes of the name relationship object will be nullified.
|
| 394 |
12655d36
|
m.geoffroy
|
*
|
| 395 |
|
|
* @param nameRelation the name relationship which should be deleted from one of both sets
|
| 396 |
6a9737e8
|
m.geoffroy
|
* @see #getNameRelations()
|
| 397 |
12655d36
|
m.geoffroy
|
*/
|
| 398 |
6ecda5d2
|
m.doering
|
public void removeNameRelationship(NameRelationship nameRelation) {
|
| 399 |
b92a6173
|
a.babadshanjan
|
|
| 400 |
|
|
TaxonNameBase fromName = nameRelation.getFromName();
|
| 401 |
|
|
TaxonNameBase toName = nameRelation.getToName();
|
| 402 |
|
|
|
| 403 |
|
|
if (nameRelation != null) {
|
| 404 |
|
|
nameRelation.setToName(null);
|
| 405 |
|
|
nameRelation.setFromName(null);
|
| 406 |
|
|
}
|
| 407 |
|
|
|
| 408 |
|
|
if (fromName != null) {
|
| 409 |
|
|
fromName.removeNameRelationship(nameRelation);
|
| 410 |
|
|
}
|
| 411 |
|
|
|
| 412 |
|
|
if (toName != null) {
|
| 413 |
|
|
toName.removeNameRelationship(nameRelation);
|
| 414 |
|
|
}
|
| 415 |
|
|
|
| 416 |
|
|
this.relationsToThisName.remove(nameRelation);
|
| 417 |
|
|
this.relationsFromThisName.remove(nameRelation);
|
| 418 |
|
|
}
|
| 419 |
|
|
|
| 420 |
|
|
public void removeTaxonName(TaxonNameBase taxonName) {
|
| 421 |
|
|
Set<NameRelationship> nameRelationships = new HashSet<NameRelationship>();
|
| 422 |
|
|
// nameRelationships.addAll(this.getNameRelations());
|
| 423 |
|
|
nameRelationships.addAll(this.getRelationsFromThisName());
|
| 424 |
|
|
nameRelationships.addAll(this.getRelationsToThisName());
|
| 425 |
|
|
for(NameRelationship nameRelationship : nameRelationships) {
|
| 426 |
|
|
// remove name relationship from this side
|
| 427 |
|
|
if (nameRelationship.getFromName().equals(this) && nameRelationship.getToName().equals(taxonName)) {
|
| 428 |
|
|
this.removeNameRelation(nameRelationship);
|
| 429 |
|
|
}
|
| 430 |
|
|
}
|
| 431 |
|
|
}
|
| 432 |
|
|
|
| 433 |
|
|
public void removeNameRelation(NameRelationship nameRelation) {
|
| 434 |
|
|
nameRelation.setToName(null);
|
| 435 |
|
|
|
| 436 |
|
|
TaxonNameBase name = nameRelation.getFromName();
|
| 437 |
|
|
if (name != null){
|
| 438 |
|
|
nameRelation.setFromName(null);
|
| 439 |
|
|
name.removeNameRelation(nameRelation);
|
| 440 |
|
|
}
|
| 441 |
6ecda5d2
|
m.doering
|
this.relationsToThisName.remove(nameRelation);
|
| 442 |
|
|
this.relationsFromThisName.remove(nameRelation);
|
| 443 |
9479da48
|
Andreas Müller
|
}
|
| 444 |
6ecda5d2
|
m.doering
|
|
| 445 |
|
|
|
| 446 |
b3262b1b
|
m.geoffroy
|
/**
|
| 447 |
|
|
* Does exactly the same as the addNameRelationship method provided that
|
| 448 |
|
|
* the given relationship is a name relationship.
|
| 449 |
|
|
*
|
| 450 |
b9d0e8d2
|
m.geoffroy
|
* @param relation the relationship to be added to one of <i>this</i> taxon name's name relationships sets
|
| 451 |
b3262b1b
|
m.geoffroy
|
* @see #addNameRelationship(NameRelationship)
|
| 452 |
|
|
* @see #getNameRelations()
|
| 453 |
|
|
* @see NameRelationship
|
| 454 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.common.RelationshipBase
|
| 455 |
b3262b1b
|
m.geoffroy
|
*/
|
| 456 |
705e0850
|
Andreas Müller
|
public void addRelationship(RelationshipBase relation) {
|
| 457 |
|
|
if (relation instanceof NameRelationship){
|
| 458 |
|
|
addNameRelationship((NameRelationship)relation);
|
| 459 |
d27ee9b1
|
Andreas Müller
|
if (relation.getType() != null &&
|
| 460 |
bef42c31
|
Andreas Müller
|
( relation.getType().equals(NameRelationshipType.BASIONYM()) ||
|
| 461 |
|
|
relation.getType().equals(NameRelationshipType.REPLACED_SYNONYM())
|
| 462 |
|
|
)){
|
| 463 |
d27ee9b1
|
Andreas Müller
|
TaxonNameBase fromName = ((NameRelationship)relation).getFromName();
|
| 464 |
|
|
TaxonNameBase toName = ((NameRelationship)relation).getToName();
|
| 465 |
|
|
fromName.getHomotypicalGroup().merge(toName.getHomotypicalGroup());
|
| 466 |
|
|
}
|
| 467 |
705e0850
|
Andreas Müller
|
}else{
|
| 468 |
d27ee9b1
|
Andreas Müller
|
logger.warn("Relationship not of type NameRelationship!");
|
| 469 |
705e0850
|
Andreas Müller
|
//TODO exception handling
|
| 470 |
|
|
}
|
| 471 |
7ebeb288
|
Andreas Müller
|
}
|
| 472 |
|
|
|
| 473 |
|
|
|
| 474 |
09487e73
|
m.geoffroy
|
/**
|
| 475 |
|
|
* Returns the set of all {@link NameRelationship name relationships}
|
| 476 |
b9d0e8d2
|
m.geoffroy
|
* in which <i>this</i> taxon name is involved as a source.
|
| 477 |
09487e73
|
m.geoffroy
|
*
|
| 478 |
|
|
* @see #getNameRelations()
|
| 479 |
|
|
* @see #getRelationsToThisName()
|
| 480 |
|
|
* @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
|
| 481 |
|
|
*/
|
| 482 |
6ecda5d2
|
m.doering
|
public Set<NameRelationship> getRelationsFromThisName() {
|
| 483 |
|
|
return relationsFromThisName;
|
| 484 |
9479da48
|
Andreas Müller
|
}
|
| 485 |
ee91bcd9
|
ben.clark
|
|
| 486 |
09487e73
|
m.geoffroy
|
/**
|
| 487 |
|
|
* Returns the set of all {@link NameRelationship name relationships}
|
| 488 |
b9d0e8d2
|
m.geoffroy
|
* in which <i>this</i> taxon name is involved as a target.
|
| 489 |
09487e73
|
m.geoffroy
|
*
|
| 490 |
|
|
* @see #getNameRelations()
|
| 491 |
|
|
* @see #getRelationsFromThisName()
|
| 492 |
|
|
* @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
|
| 493 |
|
|
*/
|
| 494 |
6ecda5d2
|
m.doering
|
public Set<NameRelationship> getRelationsToThisName() {
|
| 495 |
|
|
return relationsToThisName;
|
| 496 |
9479da48
|
Andreas Müller
|
}
|
| 497 |
|
|
|
| 498 |
09487e73
|
m.geoffroy
|
/**
|
| 499 |
|
|
* Returns the set of {@link NomenclaturalStatus nomenclatural status} assigned
|
| 500 |
b9d0e8d2
|
m.geoffroy
|
* to <i>this</i> taxon name according to its corresponding nomenclature code.
|
| 501 |
09487e73
|
m.geoffroy
|
* This includes the {@link NomenclaturalStatusType type} of the nomenclatural status
|
| 502 |
|
|
* and the nomenclatural code rule considered.
|
| 503 |
|
|
*
|
| 504 |
|
|
* @see NomenclaturalStatus
|
| 505 |
|
|
* @see NomenclaturalStatusType
|
| 506 |
|
|
*/
|
| 507 |
9479da48
|
Andreas Müller
|
public Set<NomenclaturalStatus> getStatus() {
|
| 508 |
|
|
return status;
|
| 509 |
|
|
}
|
| 510 |
ee91bcd9
|
ben.clark
|
|
| 511 |
09487e73
|
m.geoffroy
|
/**
|
| 512 |
|
|
* Adds a new {@link NomenclaturalStatus nomenclatural status}
|
| 513 |
b9d0e8d2
|
m.geoffroy
|
* to <i>this</i> taxon name's set of nomenclatural status.
|
| 514 |
09487e73
|
m.geoffroy
|
*
|
| 515 |
|
|
* @param nomStatus the nomenclatural status to be added
|
| 516 |
|
|
* @see #getStatus()
|
| 517 |
|
|
*/
|
| 518 |
025f3199
|
Andreas Müller
|
public void addStatus(NomenclaturalStatus nomStatus) {
|
| 519 |
|
|
this.status.add(nomStatus);
|
| 520 |
9479da48
|
Andreas Müller
|
}
|
| 521 |
ee91bcd9
|
ben.clark
|
|
| 522 |
09487e73
|
m.geoffroy
|
/**
|
| 523 |
b9d0e8d2
|
m.geoffroy
|
* Removes one element from the set of nomenclatural status of <i>this</i> taxon name.
|
| 524 |
09487e73
|
m.geoffroy
|
* Type and ruleConsidered attributes of the nomenclatural status object
|
| 525 |
|
|
* will be nullified.
|
| 526 |
|
|
*
|
| 527 |
b9d0e8d2
|
m.geoffroy
|
* @param nomStatus the nomenclatural status of <i>this</i> taxon name which should be deleted
|
| 528 |
09487e73
|
m.geoffroy
|
* @see #getStatus()
|
| 529 |
|
|
*/
|
| 530 |
025f3199
|
Andreas Müller
|
public void removeStatus(NomenclaturalStatus nomStatus) {
|
| 531 |
09487e73
|
m.geoffroy
|
//TODO to be implemented?
|
| 532 |
|
|
logger.warn("not yet fully implemented?");
|
| 533 |
025f3199
|
Andreas Müller
|
this.status.remove(nomStatus);
|
| 534 |
9479da48
|
Andreas Müller
|
}
|
| 535 |
|
|
|
| 536 |
5c19d7f0
|
Andreas Müller
|
|
| 537 |
|
|
/**
|
| 538 |
09887ea6
|
m.geoffroy
|
* Indicates whether <i>this</i> taxon name is a {@link NameRelationshipType#BASIONYM() basionym}
|
| 539 |
|
|
* or a {@link NameRelationshipType#REPLACED_SYNONYM() replaced synonym}
|
| 540 |
abc6aceb
|
m.geoffroy
|
* of any other taxon name. Returns "true", if a basionym or a replaced
|
| 541 |
09887ea6
|
m.geoffroy
|
* synonym {@link NameRelationship relationship} from <i>this</i> taxon name to another taxon name exists,
|
| 542 |
b9d0e8d2
|
m.geoffroy
|
* false otherwise (also in case <i>this</i> taxon name is the only one in the
|
| 543 |
09487e73
|
m.geoffroy
|
* homotypical group).
|
| 544 |
5c19d7f0
|
Andreas Müller
|
*/
|
| 545 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 546 |
5c19d7f0
|
Andreas Müller
|
public boolean isOriginalCombination(){
|
| 547 |
|
|
Set<NameRelationship> relationsFromThisName = this.getRelationsFromThisName();
|
| 548 |
|
|
for (NameRelationship relation : relationsFromThisName) {
|
| 549 |
|
|
if (relation.getType().equals(NameRelationshipType.BASIONYM()) ||
|
| 550 |
|
|
relation.getType().equals(NameRelationshipType.REPLACED_SYNONYM())) {
|
| 551 |
|
|
return true;
|
| 552 |
|
|
}
|
| 553 |
|
|
}
|
| 554 |
|
|
return false;
|
| 555 |
|
|
}
|
| 556 |
|
|
|
| 557 |
09487e73
|
m.geoffroy
|
/**
|
| 558 |
09887ea6
|
m.geoffroy
|
* Returns the taxon name which is the {@link NameRelationshipType#BASIONYM() basionym} of <i>this</i> taxon name.
|
| 559 |
09487e73
|
m.geoffroy
|
* The basionym of a taxon name is its epithet-bringing synonym.
|
| 560 |
09887ea6
|
m.geoffroy
|
* For instance <i>Pinus abies</i> L. was published by Linnaeus and the botanist
|
| 561 |
b9d0e8d2
|
m.geoffroy
|
* Karsten transferred later <i>this</i> taxon to the genus Picea. Therefore,
|
| 562 |
09887ea6
|
m.geoffroy
|
* <i>Pinus abies</i> L. is the basionym of the new combination <i>Picea abies</i> (L.) H. Karst.
|
| 563 |
09487e73
|
m.geoffroy
|
*/
|
| 564 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 565 |
2a486d28
|
Andreas Müller
|
public T getBasionym(){
|
| 566 |
6ecda5d2
|
m.doering
|
//TODO: pick the right name relationships...
|
| 567 |
d27ee9b1
|
Andreas Müller
|
logger.warn("get Basionym not yet implemented");
|
| 568 |
6ecda5d2
|
m.doering
|
return null;
|
| 569 |
9479da48
|
Andreas Müller
|
}
|
| 570 |
09487e73
|
m.geoffroy
|
/**
|
| 571 |
09887ea6
|
m.geoffroy
|
* Assigns a taxon name as {@link NameRelationshipType#BASIONYM() basionym} of <i>this</i> taxon name.
|
| 572 |
|
|
* The basionym {@link NameRelationship relationship} will be added to <i>this</i> taxon name
|
| 573 |
09487e73
|
m.geoffroy
|
* and to the basionym. The basionym cannot have itself a basionym.
|
| 574 |
09887ea6
|
m.geoffroy
|
* The {@link HomotypicalGroup homotypical groups} of <i>this</i> taxon name and of the basionym
|
| 575 |
|
|
* will be {@link HomotypicalGroup#merge(HomotypicalGroup) merged}.
|
| 576 |
|
|
*
|
| 577 |
|
|
* @param basionym the taxon name to be set as the basionym of <i>this</i> taxon name
|
| 578 |
|
|
* @see #getBasionym()
|
| 579 |
|
|
* @see #addBasionym(TaxonNameBase, String)
|
| 580 |
09487e73
|
m.geoffroy
|
*/
|
| 581 |
d27ee9b1
|
Andreas Müller
|
public void addBasionym(T basionym){
|
| 582 |
21f31bf8
|
Andreas Müller
|
addBasionym(basionym, null, null, null);
|
| 583 |
6ecda5d2
|
m.doering
|
}
|
| 584 |
09487e73
|
m.geoffroy
|
/**
|
| 585 |
09887ea6
|
m.geoffroy
|
* Assigns a taxon name as {@link NameRelationshipType#BASIONYM() basionym} of <i>this</i> taxon name
|
| 586 |
09487e73
|
m.geoffroy
|
* and keeps the nomenclatural rule considered for it. The basionym
|
| 587 |
09887ea6
|
m.geoffroy
|
* {@link NameRelationship relationship} will be added to <i>this</i> taxon name and to the basionym.
|
| 588 |
|
|
* The basionym cannot have itself a basionym.
|
| 589 |
|
|
* The {@link HomotypicalGroup homotypical groups} of <i>this</i> taxon name and of the basionym
|
| 590 |
|
|
* will be {@link HomotypicalGroup#merge(HomotypicalGroup) merged}.
|
| 591 |
|
|
*
|
| 592 |
|
|
* @param basionym the taxon name to be set as the basionym of <i>this</i> taxon name
|
| 593 |
|
|
* @param ruleConsidered the string identifying the nomenclatural rule
|
| 594 |
|
|
* @see #getBasionym()
|
| 595 |
|
|
* @see #addBasionym(TaxonNameBase)
|
| 596 |
09487e73
|
m.geoffroy
|
*/
|
| 597 |
21f31bf8
|
Andreas Müller
|
public void addBasionym(T basionym, ReferenceBase citation, String microcitation, String ruleConsidered){
|
| 598 |
d27ee9b1
|
Andreas Müller
|
if (basionym != null){
|
| 599 |
21f31bf8
|
Andreas Müller
|
basionym.addRelationshipToName(this, NameRelationshipType.BASIONYM(), citation, microcitation, ruleConsidered);
|
| 600 |
d27ee9b1
|
Andreas Müller
|
}
|
| 601 |
|
|
}
|
| 602 |
|
|
|
| 603 |
09887ea6
|
m.geoffroy
|
/**
|
| 604 |
|
|
* Removes the {@link NameRelationshipType#BASIONYM() basionym} {@link NameRelationship relationship} from the set of
|
| 605 |
|
|
* {@link #getRelationsToThisName() name relationships to} <i>this</i> taxon name. The same relationhip will be
|
| 606 |
|
|
* removed from the set of {@link #getRelationsFromThisName() name relationships from} the taxon name
|
| 607 |
|
|
* previously used as basionym.
|
| 608 |
|
|
*
|
| 609 |
|
|
* @see #getBasionym()
|
| 610 |
|
|
* @see #addBasionym(TaxonNameBase)
|
| 611 |
|
|
*/
|
| 612 |
d27ee9b1
|
Andreas Müller
|
public void removeBasionym(){
|
| 613 |
|
|
//TODO implement
|
| 614 |
|
|
logger.warn("not yet implemented");
|
| 615 |
9479da48
|
Andreas Müller
|
}
|
| 616 |
|
|
|
| 617 |
8eebe79d
|
m.geoffroy
|
/**
|
| 618 |
b9d0e8d2
|
m.geoffroy
|
* Returns the taxonomic {@link Rank rank} of <i>this</i> taxon name.
|
| 619 |
8eebe79d
|
m.geoffroy
|
*
|
| 620 |
|
|
* @see Rank
|
| 621 |
|
|
*/
|
| 622 |
9479da48
|
Andreas Müller
|
public Rank getRank(){
|
| 623 |
|
|
return this.rank;
|
| 624 |
|
|
}
|
| 625 |
ee91bcd9
|
ben.clark
|
|
| 626 |
8eebe79d
|
m.geoffroy
|
/**
|
| 627 |
|
|
* @see #getRank()
|
| 628 |
|
|
*/
|
| 629 |
9479da48
|
Andreas Müller
|
public void setRank(Rank rank){
|
| 630 |
|
|
this.rank = rank;
|
| 631 |
|
|
}
|
| 632 |
|
|
|
| 633 |
8eebe79d
|
m.geoffroy
|
/**
|
| 634 |
09887ea6
|
m.geoffroy
|
* Returns the {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} of <i>this</i> taxon name.
|
| 635 |
8eebe79d
|
m.geoffroy
|
* The nomenclatural reference is here meant to be the one publication
|
| 636 |
b9d0e8d2
|
m.geoffroy
|
* <i>this</i> taxon name was originally published in while fulfilling the formal
|
| 637 |
a7d9a8c1
|
m.geoffroy
|
* requirements as specified by the corresponding {@link NomenclaturalCode nomenclatural code}.
|
| 638 |
8eebe79d
|
m.geoffroy
|
*
|
| 639 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.reference.INomenclaturalReference
|
| 640 |
|
|
* @see eu.etaxonomy.cdm.model.reference.ReferenceBase
|
| 641 |
8eebe79d
|
m.geoffroy
|
*/
|
| 642 |
b70a7f94
|
Andreas Kohlbecker
|
public ReferenceBase getNomenclaturalReference(){
|
| 643 |
|
|
return this.nomenclaturalReference;
|
| 644 |
9479da48
|
Andreas Müller
|
}
|
| 645 |
8eebe79d
|
m.geoffroy
|
/**
|
| 646 |
09887ea6
|
m.geoffroy
|
* Assigns a {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} to <i>this</i> taxon name.
|
| 647 |
|
|
* The corresponding {@link eu.etaxonomy.cdm.model.reference.ReferenceBase.isNomenclaturallyRelevant nomenclaturally relevant flag} will be set to true
|
| 648 |
8eebe79d
|
m.geoffroy
|
* as it is obviously used for nomenclatural purposes.
|
| 649 |
|
|
*
|
| 650 |
b70a7f94
|
Andreas Kohlbecker
|
* @throws IllegalArgumentException if parameter <code>nomenclaturalReference</code> is not assignable from {@link INomenclaturalReference}
|
| 651 |
8eebe79d
|
m.geoffroy
|
* @see #getNomenclaturalReference()
|
| 652 |
|
|
*/
|
| 653 |
b70a7f94
|
Andreas Kohlbecker
|
public void setNomenclaturalReference(ReferenceBase nomenclaturalReference){
|
| 654 |
|
|
if(nomenclaturalReference != null){
|
| 655 |
|
|
if(!INomenclaturalReference.class.isAssignableFrom(nomenclaturalReference.getClass())){
|
| 656 |
|
|
throw new IllegalArgumentException("Parameter nomenclaturalReference is not assignable from INomenclaturalReference");
|
| 657 |
|
|
}
|
| 658 |
|
|
this.nomenclaturalReference = (ReferenceBase)nomenclaturalReference;
|
| 659 |
|
|
} else {
|
| 660 |
|
|
this.nomenclaturalReference = null;
|
| 661 |
|
|
}
|
| 662 |
9479da48
|
Andreas Müller
|
}
|
| 663 |
|
|
|
| 664 |
8eebe79d
|
m.geoffroy
|
/**
|
| 665 |
b9d0e8d2
|
m.geoffroy
|
* Returns the appended phrase string assigned to <i>this</i> taxon name.
|
| 666 |
8eebe79d
|
m.geoffroy
|
* The appended phrase is a non-atomised addition to a name. It is
|
| 667 |
|
|
* not ruled by a nomenclatural code.
|
| 668 |
|
|
*/
|
| 669 |
9479da48
|
Andreas Müller
|
public String getAppendedPhrase(){
|
| 670 |
|
|
return this.appendedPhrase;
|
| 671 |
|
|
}
|
| 672 |
ee91bcd9
|
ben.clark
|
|
| 673 |
8eebe79d
|
m.geoffroy
|
/**
|
| 674 |
|
|
* @see #getAppendedPhrase()
|
| 675 |
|
|
*/
|
| 676 |
9479da48
|
Andreas Müller
|
public void setAppendedPhrase(String appendedPhrase){
|
| 677 |
|
|
this.appendedPhrase = appendedPhrase;
|
| 678 |
|
|
}
|
| 679 |
|
|
|
| 680 |
8eebe79d
|
m.geoffroy
|
/**
|
| 681 |
09887ea6
|
m.geoffroy
|
* Returns the details string of the {@link #getNomenclaturalReference() nomenclatural reference} assigned
|
| 682 |
b9d0e8d2
|
m.geoffroy
|
* to <i>this</i> taxon name. The details describe the exact localisation within
|
| 683 |
8eebe79d
|
m.geoffroy
|
* the publication used as nomenclature reference. These are mostly
|
| 684 |
|
|
* (implicitly) pages but can also be figures or tables or any other
|
| 685 |
|
|
* element of a publication. A nomenclatural micro reference (details)
|
| 686 |
|
|
* requires the existence of a nomenclatural reference.
|
| 687 |
|
|
*/
|
| 688 |
|
|
//Details of the nomenclatural reference (protologue).
|
| 689 |
9479da48
|
Andreas Müller
|
public String getNomenclaturalMicroReference(){
|
| 690 |
|
|
return this.nomenclaturalMicroReference;
|
| 691 |
|
|
}
|
| 692 |
8eebe79d
|
m.geoffroy
|
/**
|
| 693 |
|
|
* @see #getNomenclaturalMicroReference()
|
| 694 |
|
|
*/
|
| 695 |
9479da48
|
Andreas Müller
|
public void setNomenclaturalMicroReference(String nomenclaturalMicroReference){
|
| 696 |
|
|
this.nomenclaturalMicroReference = nomenclaturalMicroReference;
|
| 697 |
|
|
}
|
| 698 |
|
|
|
| 699 |
6680df00
|
Andreas Müller
|
/* (non-Javadoc)
|
| 700 |
|
|
* @see eu.etaxonomy.cdm.model.common.IParsable#getHasProblem()
|
| 701 |
8eebe79d
|
m.geoffroy
|
*/
|
| 702 |
9479da48
|
Andreas Müller
|
public boolean getHasProblem(){
|
| 703 |
|
|
return this.hasProblem;
|
| 704 |
|
|
}
|
| 705 |
6680df00
|
Andreas Müller
|
|
| 706 |
|
|
/* (non-Javadoc)
|
| 707 |
|
|
* @see eu.etaxonomy.cdm.model.common.IParsable#setHasProblem(boolean)
|
| 708 |
8eebe79d
|
m.geoffroy
|
*/
|
| 709 |
9479da48
|
Andreas Müller
|
public void setHasProblem(boolean hasProblem){
|
| 710 |
|
|
this.hasProblem = hasProblem;
|
| 711 |
|
|
}
|
| 712 |
6680df00
|
Andreas Müller
|
|
| 713 |
|
|
/* (non-Javadoc)
|
| 714 |
|
|
* @see eu.etaxonomy.cdm.model.common.IParsable#hasProblem()
|
| 715 |
81c31b35
|
Andreas Müller
|
*/
|
| 716 |
|
|
public boolean hasProblem(){
|
| 717 |
|
|
return getHasProblem();
|
| 718 |
|
|
}
|
| 719 |
6680df00
|
Andreas Müller
|
|
| 720 |
|
|
/* (non-Javadoc)
|
| 721 |
|
|
* @see eu.etaxonomy.cdm.model.common.IParsable#problemStarts()
|
| 722 |
|
|
*/
|
| 723 |
|
|
public int getProblemStarts(){
|
| 724 |
|
|
return this.problemStarts;
|
| 725 |
|
|
}
|
| 726 |
|
|
|
| 727 |
|
|
/* (non-Javadoc)
|
| 728 |
|
|
* @see eu.etaxonomy.cdm.model.common.IParsable#setProblemStarts(int)
|
| 729 |
|
|
*/
|
| 730 |
|
|
public void setProblemStarts(int start) {
|
| 731 |
|
|
this.problemStarts = start;
|
| 732 |
|
|
}
|
| 733 |
|
|
|
| 734 |
|
|
/* (non-Javadoc)
|
| 735 |
|
|
* @see eu.etaxonomy.cdm.model.common.IParsable#problemEnds()
|
| 736 |
|
|
*/
|
| 737 |
|
|
public int getProblemEnds(){
|
| 738 |
|
|
return this.problemEnds;
|
| 739 |
|
|
}
|
| 740 |
|
|
|
| 741 |
|
|
/* (non-Javadoc)
|
| 742 |
|
|
* @see eu.etaxonomy.cdm.model.common.IParsable#setProblemEnds(int)
|
| 743 |
|
|
*/
|
| 744 |
|
|
public void setProblemEnds(int end) {
|
| 745 |
|
|
this.problemEnds = end;
|
| 746 |
|
|
}
|
| 747 |
|
|
|
| 748 |
dce4c9cb
|
Andreas Müller
|
//*********************** TYPE DESIGNATION *********************************************//
|
| 749 |
|
|
|
| 750 |
79263e24
|
m.geoffroy
|
/**
|
| 751 |
dce4c9cb
|
Andreas Müller
|
* Returns the set of {@link TypeDesignationBase type designations} assigned
|
| 752 |
|
|
* to <i>this</i> taxon name.
|
| 753 |
79263e24
|
m.geoffroy
|
* @see NameTypeDesignation
|
| 754 |
|
|
* @see SpecimenTypeDesignation
|
| 755 |
|
|
*/
|
| 756 |
dce4c9cb
|
Andreas Müller
|
public Set<TypeDesignationBase> getTypeDesignations() {
|
| 757 |
|
|
return typeDesignations;
|
| 758 |
9479da48
|
Andreas Müller
|
}
|
| 759 |
dce4c9cb
|
Andreas Müller
|
|
| 760 |
|
|
/**
|
| 761 |
6a9737e8
|
m.geoffroy
|
* Removes one element from the set of {@link TypeDesignationBase type designations} assigned to
|
| 762 |
|
|
* <i>this</i> taxon name. The type designation itself will be nullified.
|
| 763 |
dce4c9cb
|
Andreas Müller
|
*
|
| 764 |
|
|
* @param typeDesignation the type designation which should be deleted
|
| 765 |
|
|
*/
|
| 766 |
|
|
public void removeTypeDesignation(TypeDesignationBase typeDesignation) {
|
| 767 |
|
|
logger.warn("not yet fully implemented: nullify the specimen type designation itself?");
|
| 768 |
|
|
this.typeDesignations.remove(typeDesignation);
|
| 769 |
|
|
}
|
| 770 |
|
|
|
| 771 |
|
|
/**
|
| 772 |
|
|
* Returns the set of {@link SpecimenTypeDesignation specimen type designations} assigned
|
| 773 |
6a9737e8
|
m.geoffroy
|
* to <i>this</i> taxon name. The {@link Rank rank} of <i>this</i> taxon name is generally
|
| 774 |
|
|
* "species" or below. The specimen type designations include all the
|
| 775 |
|
|
* specimens on which the typification of this name is based (which are
|
| 776 |
09887ea6
|
m.geoffroy
|
* exclusively used to typify taxon names belonging to the same
|
| 777 |
6a9737e8
|
m.geoffroy
|
* {@link HomotypicalGroup homotypical group} to which <i>this</i> taxon name
|
| 778 |
|
|
* belongs) and eventually the status of these designations.
|
| 779 |
dce4c9cb
|
Andreas Müller
|
*
|
| 780 |
|
|
* @see SpecimenTypeDesignation
|
| 781 |
|
|
* @see NameTypeDesignation
|
| 782 |
6a9737e8
|
m.geoffroy
|
* @see HomotypicalGroup
|
| 783 |
dce4c9cb
|
Andreas Müller
|
*/
|
| 784 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 785 |
dce4c9cb
|
Andreas Müller
|
public Set<SpecimenTypeDesignation> getSpecimenTypeDesignationsOfHomotypicalGroup() {
|
| 786 |
|
|
return this.getHomotypicalGroup().getSpecimenTypeDesignations();
|
| 787 |
|
|
}
|
| 788 |
|
|
|
| 789 |
|
|
//*********************** NAME TYPE DESIGNATION *********************************************//
|
| 790 |
|
|
|
| 791 |
|
|
/**
|
| 792 |
|
|
* Returns the set of {@link NameTypeDesignation name type designations} assigned
|
| 793 |
|
|
* to <i>this</i> taxon name the rank of which must be above "species".
|
| 794 |
|
|
* The name type designations include all the taxon names used to typify
|
| 795 |
d82717cb
|
m.geoffroy
|
* <i>this</i> taxon name and eventually the rejected or conserved status
|
| 796 |
dce4c9cb
|
Andreas Müller
|
* of these designations.
|
| 797 |
|
|
*
|
| 798 |
|
|
* @see NameTypeDesignation
|
| 799 |
|
|
* @see SpecimenTypeDesignation
|
| 800 |
|
|
*/
|
| 801 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 802 |
dce4c9cb
|
Andreas Müller
|
public Set<NameTypeDesignation> getNameTypeDesignations() {
|
| 803 |
|
|
Set<NameTypeDesignation> result = new HashSet<NameTypeDesignation>();
|
| 804 |
|
|
for (TypeDesignationBase typeDesignation : this.typeDesignations){
|
| 805 |
|
|
if (typeDesignation instanceof NameTypeDesignation){
|
| 806 |
|
|
result.add((NameTypeDesignation)typeDesignation);
|
| 807 |
c79406dd
|
n.hoffmann
|
}
|
| 808 |
|
|
}
|
| 809 |
dce4c9cb
|
Andreas Müller
|
return result;
|
| 810 |
c79406dd
|
n.hoffmann
|
}
|
| 811 |
ed85df08
|
Andreas Müller
|
|
| 812 |
|
|
/**
|
| 813 |
|
|
* Creates and adds a new {@link NameTypeDesignation name type designation}
|
| 814 |
09887ea6
|
m.geoffroy
|
* to <i>this</i> taxon name's set of type designations.
|
| 815 |
ed85df08
|
Andreas Müller
|
*
|
| 816 |
b9d0e8d2
|
m.geoffroy
|
* @param typeSpecies the taxon name to be used as type of <i>this</i> taxon name
|
| 817 |
ed85df08
|
Andreas Müller
|
* @param citation the reference for this new designation
|
| 818 |
|
|
* @param citationMicroReference the string with the details (generally pages) within the reference
|
| 819 |
7d954fd9
|
m.geoffroy
|
* @param originalNameString the taxon name string used in the reference to assert this designation
|
| 820 |
6a9737e8
|
m.geoffroy
|
* @param isRejectedType the boolean status for a rejected name type designation
|
| 821 |
|
|
* @param isConservedType the boolean status for a conserved name type designation
|
| 822 |
|
|
* @param isLectoType the boolean status for a lectotype name type designation
|
| 823 |
d82717cb
|
m.geoffroy
|
* @param isNotDesignated the boolean status for a name type designation without name type
|
| 824 |
|
|
* @param addToAllHomotypicNames the boolean indicating whether the name type designation should be
|
| 825 |
|
|
* added to all taxon names of the homotypical group this taxon name belongs to
|
| 826 |
ed85df08
|
Andreas Müller
|
* @see #getNameTypeDesignations()
|
| 827 |
6a9737e8
|
m.geoffroy
|
* @see NameTypeDesignation
|
| 828 |
57883822
|
m.geoffroy
|
* @see TypeDesignationBase#isNotDesignated()
|
| 829 |
ed85df08
|
Andreas Müller
|
*/
|
| 830 |
dce4c9cb
|
Andreas Müller
|
public void addNameTypeDesignation(TaxonNameBase typeSpecies,
|
| 831 |
|
|
ReferenceBase citation,
|
| 832 |
|
|
String citationMicroReference,
|
| 833 |
|
|
String originalNameString,
|
| 834 |
|
|
boolean isRejectedType,
|
| 835 |
|
|
boolean isConservedType,
|
| 836 |
|
|
boolean isLectoType,
|
| 837 |
|
|
boolean isNotDesignated,
|
| 838 |
|
|
boolean addToAllHomotypicNames) {
|
| 839 |
ec1f7873
|
Andreas Müller
|
NameTypeDesignation nameTypeDesignation = new NameTypeDesignation(typeSpecies, citation, citationMicroReference, originalNameString, isRejectedType, isConservedType, isLectoType, isNotDesignated);
|
| 840 |
168723a2
|
a.babadshanjan
|
nameTypeDesignation.setLectoType(isLectoType);
|
| 841 |
dce4c9cb
|
Andreas Müller
|
addTypeDesignation(nameTypeDesignation, addToAllHomotypicNames);
|
| 842 |
ed85df08
|
Andreas Müller
|
}
|
| 843 |
|
|
|
| 844 |
dce4c9cb
|
Andreas Müller
|
//*********************** SPECIMEN TYPE DESIGNATION *********************************************//
|
| 845 |
ed85df08
|
Andreas Müller
|
|
| 846 |
61106138
|
m.geoffroy
|
/**
|
| 847 |
|
|
* Returns the set of {@link SpecimenTypeDesignation specimen type designations}
|
| 848 |
b9d0e8d2
|
m.geoffroy
|
* that typify <i>this</i> taxon name.
|
| 849 |
ed85df08
|
Andreas Müller
|
*/
|
| 850 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 851 |
dce4c9cb
|
Andreas Müller
|
public Set<SpecimenTypeDesignation> getSpecimenTypeDesignations() {
|
| 852 |
|
|
Set<SpecimenTypeDesignation> result = new HashSet<SpecimenTypeDesignation>();
|
| 853 |
|
|
for (TypeDesignationBase typeDesignation : this.typeDesignations){
|
| 854 |
|
|
if (typeDesignation instanceof SpecimenTypeDesignation){
|
| 855 |
|
|
result.add((SpecimenTypeDesignation)typeDesignation);
|
| 856 |
|
|
}
|
| 857 |
|
|
}
|
| 858 |
|
|
return result;
|
| 859 |
66b77c3e
|
m.geoffroy
|
}
|
| 860 |
dce4c9cb
|
Andreas Müller
|
|
| 861 |
66b77c3e
|
m.geoffroy
|
|
| 862 |
79263e24
|
m.geoffroy
|
/**
|
| 863 |
d82717cb
|
m.geoffroy
|
* Creates and adds a new {@link SpecimenTypeDesignation specimen type designation}
|
| 864 |
09887ea6
|
m.geoffroy
|
* to <i>this</i> taxon name's set of type designations.
|
| 865 |
79263e24
|
m.geoffroy
|
*
|
| 866 |
d82717cb
|
m.geoffroy
|
* @param typeSpecimen the specimen to be used as a type for <i>this</i> taxon name
|
| 867 |
79263e24
|
m.geoffroy
|
* @param status the specimen type designation status
|
| 868 |
|
|
* @param citation the reference for this new specimen type designation
|
| 869 |
|
|
* @param citationMicroReference the string with the details (generally pages) within the reference
|
| 870 |
|
|
* @param originalNameString the taxon name used in the reference to assert this designation
|
| 871 |
57883822
|
m.geoffroy
|
* @param isNotDesignated the boolean status for a specimen type designation without specimen type
|
| 872 |
d82717cb
|
m.geoffroy
|
* @param addToAllHomotypicNames the boolean indicating whether the specimen type designation should be
|
| 873 |
|
|
* added to all taxon names of the homotypical group the typified
|
| 874 |
|
|
* taxon name belongs to
|
| 875 |
|
|
* @see #getSpecimenTypeDesignations()
|
| 876 |
2d4607f2
|
a.babadshanjan
|
* @see SpecimenTypeDesignationStatus
|
| 877 |
d82717cb
|
m.geoffroy
|
* @see SpecimenTypeDesignation
|
| 878 |
57883822
|
m.geoffroy
|
* @see TypeDesignationBase#isNotDesignated()
|
| 879 |
79263e24
|
m.geoffroy
|
*/
|
| 880 |
dce4c9cb
|
Andreas Müller
|
public void addSpecimenTypeDesignation(Specimen typeSpecimen,
|
| 881 |
2d4607f2
|
a.babadshanjan
|
SpecimenTypeDesignationStatus status,
|
| 882 |
dce4c9cb
|
Andreas Müller
|
ReferenceBase citation,
|
| 883 |
|
|
String citationMicroReference,
|
| 884 |
|
|
String originalNameString,
|
| 885 |
57883822
|
m.geoffroy
|
boolean isNotDesignated,
|
| 886 |
dce4c9cb
|
Andreas Müller
|
boolean addToAllHomotypicNames) {
|
| 887 |
57883822
|
m.geoffroy
|
SpecimenTypeDesignation specimenTypeDesignation = new SpecimenTypeDesignation(typeSpecimen, status, citation, citationMicroReference, originalNameString, isNotDesignated);
|
| 888 |
dce4c9cb
|
Andreas Müller
|
addTypeDesignation(specimenTypeDesignation, addToAllHomotypicNames);
|
| 889 |
9479da48
|
Andreas Müller
|
}
|
| 890 |
ed85df08
|
Andreas Müller
|
|
| 891 |
dce4c9cb
|
Andreas Müller
|
private boolean addTypeDesignation(TypeDesignationBase typeDesignation, boolean addToAllNames){
|
| 892 |
|
|
//at them moment typeDesignations are not persisted with the homotypical group
|
| 893 |
|
|
//so explicit adding to the homotypical group is not necessary.
|
| 894 |
|
|
if (typeDesignation != null){
|
| 895 |
|
|
this.typeDesignations.add(typeDesignation);
|
| 896 |
|
|
typeDesignation.addTypifiedName(this);
|
| 897 |
|
|
|
| 898 |
|
|
if (addToAllNames){
|
| 899 |
|
|
for (TaxonNameBase taxonName : this.getHomotypicalGroup().getTypifiedNames()){
|
| 900 |
|
|
if (taxonName != this){
|
| 901 |
|
|
taxonName.addTypeDesignation(typeDesignation, false);
|
| 902 |
|
|
}
|
| 903 |
|
|
}
|
| 904 |
|
|
}
|
| 905 |
|
|
}
|
| 906 |
|
|
return true;
|
| 907 |
ed85df08
|
Andreas Müller
|
}
|
| 908 |
dce4c9cb
|
Andreas Müller
|
|
| 909 |
ed85df08
|
Andreas Müller
|
|
| 910 |
dce4c9cb
|
Andreas Müller
|
|
| 911 |
|
|
//*********************** HOMOTYPICAL GROUP *********************************************//
|
| 912 |
9479da48
|
Andreas Müller
|
|
| 913 |
dce4c9cb
|
Andreas Müller
|
|
| 914 |
79263e24
|
m.geoffroy
|
/**
|
| 915 |
|
|
* Returns the {@link HomotypicalGroup homotypical group} to which
|
| 916 |
b9d0e8d2
|
m.geoffroy
|
* <i>this</i> taxon name belongs. A homotypical group represents all taxon names
|
| 917 |
d82717cb
|
m.geoffroy
|
* that share the same types.
|
| 918 |
79263e24
|
m.geoffroy
|
*
|
| 919 |
|
|
* @see HomotypicalGroup
|
| 920 |
|
|
*/
|
| 921 |
ee91bcd9
|
ben.clark
|
|
| 922 |
9479da48
|
Andreas Müller
|
public HomotypicalGroup getHomotypicalGroup() {
|
| 923 |
|
|
return homotypicalGroup;
|
| 924 |
|
|
}
|
| 925 |
ee91bcd9
|
ben.clark
|
|
| 926 |
|
|
/*
|
| 927 |
|
|
* @see #getHomotypicalGroup()
|
| 928 |
|
|
*/
|
| 929 |
|
|
protected void setHomotypicalGroup(HomotypicalGroup homotypicalGroup) {
|
| 930 |
|
|
this.homotypicalGroup = homotypicalGroup;
|
| 931 |
9479da48
|
Andreas Müller
|
}
|
| 932 |
|
|
|
| 933 |
dce4c9cb
|
Andreas Müller
|
// *************************************************************************//
|
| 934 |
|
|
|
| 935 |
b3262b1b
|
m.geoffroy
|
/**
|
| 936 |
|
|
* @see #getNomenclaturalReference()
|
| 937 |
|
|
*/
|
| 938 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 939 |
9479da48
|
Andreas Müller
|
public StrictReferenceBase getCitation(){
|
| 940 |
66b77c3e
|
m.geoffroy
|
//TODO What is the purpose of this method differing from the getNomenclaturalReference method?
|
| 941 |
c19dfdc5
|
Andreas Müller
|
logger.warn("getCitation not yet implemented");
|
| 942 |
9479da48
|
Andreas Müller
|
return null;
|
| 943 |
|
|
}
|
| 944 |
|
|
|
| 945 |
66b77c3e
|
m.geoffroy
|
/**
|
| 946 |
|
|
* Returns the complete string containing the
|
| 947 |
09887ea6
|
m.geoffroy
|
* {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference#getNomenclaturalCitation() nomenclatural reference citation}
|
| 948 |
|
|
* and the {@link #getNomenclaturalMicroReference() details} assigned to <i>this</i> taxon name.
|
| 949 |
66b77c3e
|
m.geoffroy
|
*
|
| 950 |
b9d0e8d2
|
m.geoffroy
|
* @return the string containing the nomenclatural reference of <i>this</i> taxon name
|
| 951 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.reference.INomenclaturalReference#getNomenclaturalCitation()
|
| 952 |
b3262b1b
|
m.geoffroy
|
* @see #getNomenclaturalReference()
|
| 953 |
|
|
* @see #getNomenclaturalMicroReference()
|
| 954 |
66b77c3e
|
m.geoffroy
|
*/
|
| 955 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 956 |
6680df00
|
Andreas Müller
|
@Deprecated
|
| 957 |
9479da48
|
Andreas Müller
|
public String getCitationString(){
|
| 958 |
c19dfdc5
|
Andreas Müller
|
logger.warn("getCitationString not yet implemented");
|
| 959 |
9479da48
|
Andreas Müller
|
return null;
|
| 960 |
|
|
}
|
| 961 |
|
|
|
| 962 |
09887ea6
|
m.geoffroy
|
/**
|
| 963 |
|
|
* Not yet implemented
|
| 964 |
|
|
*/
|
| 965 |
6680df00
|
Andreas Müller
|
@Deprecated
|
| 966 |
9479da48
|
Andreas Müller
|
public String[] getProblems(){
|
| 967 |
c19dfdc5
|
Andreas Müller
|
logger.warn("getProblems not yet implemented");
|
| 968 |
9479da48
|
Andreas Müller
|
return null;
|
| 969 |
|
|
}
|
| 970 |
|
|
|
| 971 |
|
|
/**
|
| 972 |
66b77c3e
|
m.geoffroy
|
* Returns the string containing the publication date (generally only year)
|
| 973 |
09887ea6
|
m.geoffroy
|
* of the {@link #getNomenclaturalReference() nomenclatural reference} for <i>this</i> taxon name, null if there is
|
| 974 |
b3262b1b
|
m.geoffroy
|
* no nomenclatural reference.
|
| 975 |
66b77c3e
|
m.geoffroy
|
*
|
| 976 |
b9d0e8d2
|
m.geoffroy
|
* @return the string containing the publication date of <i>this</i> taxon name
|
| 977 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.reference.INomenclaturalReference#getYear()
|
| 978 |
9479da48
|
Andreas Müller
|
*/
|
| 979 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 980 |
b0b7280d
|
Andreas Müller
|
public String getReferenceYear(){
|
| 981 |
|
|
if (this.getNomenclaturalReference() != null ){
|
| 982 |
|
|
return this.getNomenclaturalReference().getYear();
|
| 983 |
|
|
}else{
|
| 984 |
|
|
return null;
|
| 985 |
|
|
}
|
| 986 |
9479da48
|
Andreas Müller
|
}
|
| 987 |
|
|
|
| 988 |
66b77c3e
|
m.geoffroy
|
/**
|
| 989 |
09887ea6
|
m.geoffroy
|
* Returns the set of {@link eu.etaxonomy.cdm.model.taxon.TaxonBase taxon bases} that refer to <i>this</i> taxon name.
|
| 990 |
66b77c3e
|
m.geoffroy
|
* In this context a taxon base means the use of a taxon name by a reference
|
| 991 |
09887ea6
|
m.geoffroy
|
* either as a {@link eu.etaxonomy.cdm.model.taxon.Taxon taxon} ("accepted/correct" name) or
|
| 992 |
|
|
* as a (junior) {@link eu.etaxonomy.cdm.model.taxon.Synonym synonym}.
|
| 993 |
|
|
* A taxon name can be used by several distinct {@link eu.etaxonomy.cdm.model.reference.ReferenceBase references} but only once
|
| 994 |
66b77c3e
|
m.geoffroy
|
* within a taxonomic treatment (identified by one reference).
|
| 995 |
|
|
*
|
| 996 |
|
|
* @see #getTaxa()
|
| 997 |
|
|
* @see #getSynonyms()
|
| 998 |
|
|
*/
|
| 999 |
608eada2
|
Andreas Müller
|
public Set<TaxonBase> getTaxonBases() {
|
| 1000 |
|
|
return this.taxonBases;
|
| 1001 |
|
|
}
|
| 1002 |
ee91bcd9
|
ben.clark
|
|
| 1003 |
66b77c3e
|
m.geoffroy
|
/**
|
| 1004 |
09887ea6
|
m.geoffroy
|
* Adds a new {@link eu.etaxonomy.cdm.model.taxon.TaxonBase taxon base}
|
| 1005 |
b9d0e8d2
|
m.geoffroy
|
* to the set of taxon bases using <i>this</i> taxon name.
|
| 1006 |
66b77c3e
|
m.geoffroy
|
*
|
| 1007 |
|
|
* @param taxonBase the taxon base to be added
|
| 1008 |
|
|
* @see #getTaxonBases()
|
| 1009 |
61106138
|
m.geoffroy
|
* @see #removeTaxonBase(TaxonBase)
|
| 1010 |
66b77c3e
|
m.geoffroy
|
*/
|
| 1011 |
1cfc54ab
|
Andreas Müller
|
//TODO protected
|
| 1012 |
|
|
public void addTaxonBase(TaxonBase taxonBase){
|
| 1013 |
ee91bcd9
|
ben.clark
|
Method method = ReflectionUtils.findMethod(TaxonBase.class, "setName", new Class[] {TaxonNameBase.class});
|
| 1014 |
|
|
ReflectionUtils.makeAccessible(method);
|
| 1015 |
|
|
ReflectionUtils.invokeMethod(method, taxonBase, new Object[] {this});
|
| 1016 |
1cfc54ab
|
Andreas Müller
|
taxonBases.add(taxonBase);
|
| 1017 |
|
|
}
|
| 1018 |
b3262b1b
|
m.geoffroy
|
/**
|
| 1019 |
09887ea6
|
m.geoffroy
|
* Removes one element from the set of {@link eu.etaxonomy.cdm.model.taxon.TaxonBase taxon bases} that refer to <i>this</i> taxon name.
|
| 1020 |
b3262b1b
|
m.geoffroy
|
*
|
| 1021 |
|
|
* @param taxonBase the taxon base which should be removed from the corresponding set
|
| 1022 |
09887ea6
|
m.geoffroy
|
* @see #getTaxonBases()
|
| 1023 |
b3262b1b
|
m.geoffroy
|
* @see #addTaxonBase(TaxonBase)
|
| 1024 |
|
|
*/
|
| 1025 |
c1c3a21a
|
Andreas Müller
|
public void removeTaxonBase(TaxonBase taxonBase){
|
| 1026 |
ee91bcd9
|
ben.clark
|
Method method = ReflectionUtils.findMethod(TaxonBase.class, "setName", new Class[] {TaxonNameBase.class});
|
| 1027 |
|
|
ReflectionUtils.makeAccessible(method);
|
| 1028 |
|
|
ReflectionUtils.invokeMethod(method, taxonBase, new Object[] {null});
|
| 1029 |
d163fbf6
|
Andreas Müller
|
taxonBases.remove(taxonBase);
|
| 1030 |
1cfc54ab
|
Andreas Müller
|
}
|
| 1031 |
|
|
|
| 1032 |
0d4d2092
|
m.doering
|
/**
|
| 1033 |
09887ea6
|
m.geoffroy
|
* Returns the set of {@link eu.etaxonomy.cdm.model.taxon.Taxon taxa} ("accepted/correct" names according to any
|
| 1034 |
b9d0e8d2
|
m.geoffroy
|
* reference) that are based on <i>this</i> taxon name. This set is a subset of
|
| 1035 |
66b77c3e
|
m.geoffroy
|
* the set returned by getTaxonBases().
|
| 1036 |
|
|
*
|
| 1037 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.taxon.Taxon
|
| 1038 |
66b77c3e
|
m.geoffroy
|
* @see #getTaxonBases()
|
| 1039 |
|
|
* @see #getSynonyms()
|
| 1040 |
0d4d2092
|
m.doering
|
*/
|
| 1041 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 1042 |
0d4d2092
|
m.doering
|
public Set<Taxon> getTaxa(){
|
| 1043 |
608eada2
|
Andreas Müller
|
Set<Taxon> result = new HashSet<Taxon>();
|
| 1044 |
|
|
for (TaxonBase taxonBase : this.taxonBases){
|
| 1045 |
|
|
if (taxonBase instanceof Taxon){
|
| 1046 |
|
|
result.add((Taxon)taxonBase);
|
| 1047 |
|
|
}
|
| 1048 |
|
|
}
|
| 1049 |
|
|
return result;
|
| 1050 |
0d4d2092
|
m.doering
|
}
|
| 1051 |
608eada2
|
Andreas Müller
|
|
| 1052 |
0d4d2092
|
m.doering
|
/**
|
| 1053 |
09887ea6
|
m.geoffroy
|
* Returns the set of {@link eu.etaxonomy.cdm.model.taxon.Synonym (junior) synonyms} (according to any
|
| 1054 |
b9d0e8d2
|
m.geoffroy
|
* reference) that are based on <i>this</i> taxon name. This set is a subset of
|
| 1055 |
66b77c3e
|
m.geoffroy
|
* the set returned by getTaxonBases().
|
| 1056 |
|
|
*
|
| 1057 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.taxon.Synonym
|
| 1058 |
66b77c3e
|
m.geoffroy
|
* @see #getTaxonBases()
|
| 1059 |
|
|
* @see #getTaxa()
|
| 1060 |
0d4d2092
|
m.doering
|
*/
|
| 1061 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 1062 |
608eada2
|
Andreas Müller
|
public Set<Synonym> getSynonyms() {
|
| 1063 |
|
|
Set<Synonym> result = new HashSet<Synonym>();
|
| 1064 |
|
|
for (TaxonBase taxonBase : this.taxonBases){
|
| 1065 |
|
|
if (taxonBase instanceof Synonym){
|
| 1066 |
|
|
result.add((Synonym)taxonBase);
|
| 1067 |
|
|
}
|
| 1068 |
|
|
}
|
| 1069 |
|
|
return result;
|
| 1070 |
0d4d2092
|
m.doering
|
}
|
| 1071 |
9118658f
|
m.doering
|
|
| 1072 |
71dcc146
|
Andreas Müller
|
|
| 1073 |
|
|
// *********** DESCRIPTIONS *************************************
|
| 1074 |
|
|
|
| 1075 |
0880a77c
|
m.geoffroy
|
/**
|
| 1076 |
09887ea6
|
m.geoffroy
|
* Returns the set of {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription taxon name descriptions} assigned
|
| 1077 |
b9d0e8d2
|
m.geoffroy
|
* to <i>this</i> taxon name. A taxon name description is a piece of information
|
| 1078 |
0880a77c
|
m.geoffroy
|
* concerning the taxon name like for instance the content of its first
|
| 1079 |
|
|
* publication (protolog) or a picture of this publication.
|
| 1080 |
|
|
*
|
| 1081 |
|
|
* @see #addDescription(TaxonNameDescription)
|
| 1082 |
|
|
* @see #removeDescription(TaxonNameDescription)
|
| 1083 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.description.TaxonNameDescription
|
| 1084 |
0880a77c
|
m.geoffroy
|
*/
|
| 1085 |
71dcc146
|
Andreas Müller
|
public Set<TaxonNameDescription> getDescriptions() {
|
| 1086 |
|
|
return descriptions;
|
| 1087 |
|
|
}
|
| 1088 |
ee91bcd9
|
ben.clark
|
|
| 1089 |
0880a77c
|
m.geoffroy
|
/**
|
| 1090 |
09887ea6
|
m.geoffroy
|
* Adds a new {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription taxon name description}
|
| 1091 |
b9d0e8d2
|
m.geoffroy
|
* to the set of taxon name descriptions assigned to <i>this</i> taxon name. The
|
| 1092 |
09887ea6
|
m.geoffroy
|
* content of the {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription#getTaxonName() taxonName attribute} of the
|
| 1093 |
b9d0e8d2
|
m.geoffroy
|
* taxon name description itself will be replaced with <i>this</i> taxon name.
|
| 1094 |
0880a77c
|
m.geoffroy
|
*
|
| 1095 |
|
|
* @param description the taxon name description to be added
|
| 1096 |
|
|
* @see #getDescriptions()
|
| 1097 |
|
|
* @see #removeDescription(TaxonNameDescription)
|
| 1098 |
71dcc146
|
Andreas Müller
|
*/
|
| 1099 |
|
|
public void addDescription(TaxonNameDescription description) {
|
| 1100 |
fd7ee7b1
|
ben.clark
|
java.lang.reflect.Field field = ReflectionUtils.findField(TaxonNameDescription.class, "taxonName", TaxonNameBase.class);
|
| 1101 |
c49c125c
|
Andreas Müller
|
ReflectionUtils.makeAccessible(field);
|
| 1102 |
|
|
ReflectionUtils.setField(field, description, this);
|
| 1103 |
71dcc146
|
Andreas Müller
|
descriptions.add(description);
|
| 1104 |
|
|
}
|
| 1105 |
0880a77c
|
m.geoffroy
|
/**
|
| 1106 |
09887ea6
|
m.geoffroy
|
* Removes one element from the set of {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription taxon name descriptions} assigned
|
| 1107 |
|
|
* to <i>this</i> taxon name. The content of the {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription#getTaxonName() taxonName attribute}
|
| 1108 |
0880a77c
|
m.geoffroy
|
* of the description itself will be set to "null".
|
| 1109 |
|
|
*
|
| 1110 |
|
|
* @param description the taxon name description which should be removed
|
| 1111 |
|
|
* @see #getDescriptions()
|
| 1112 |
|
|
* @see #addDescription(TaxonNameDescription)
|
| 1113 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.description.TaxonNameDescription#getTaxonName()
|
| 1114 |
0880a77c
|
m.geoffroy
|
*/
|
| 1115 |
71dcc146
|
Andreas Müller
|
public void removeDescription(TaxonNameDescription description) {
|
| 1116 |
fd7ee7b1
|
ben.clark
|
java.lang.reflect.Field field = ReflectionUtils.findField(TaxonNameDescription.class, "taxonName", TaxonNameBase.class);
|
| 1117 |
c49c125c
|
Andreas Müller
|
ReflectionUtils.makeAccessible(field);
|
| 1118 |
|
|
ReflectionUtils.setField(field, description, null);
|
| 1119 |
71dcc146
|
Andreas Müller
|
descriptions.remove(description);
|
| 1120 |
|
|
}
|
| 1121 |
|
|
|
| 1122 |
95449e99
|
Andreas Müller
|
// ***********
|
| 1123 |
66b77c3e
|
m.geoffroy
|
/**
|
| 1124 |
|
|
* Returns the boolean value indicating whether a given taxon name belongs
|
| 1125 |
b9d0e8d2
|
m.geoffroy
|
* to the same {@link HomotypicalGroup homotypical group} as <i>this</i> taxon name (true)
|
| 1126 |
66b77c3e
|
m.geoffroy
|
* or not (false). Returns "true" only if the homotypical groups of both
|
| 1127 |
|
|
* taxon names exist and if they are identical.
|
| 1128 |
|
|
*
|
| 1129 |
|
|
* @param homoTypicName the taxon name the homotypical group of which is to be checked
|
| 1130 |
|
|
* @return the boolean value of the check
|
| 1131 |
|
|
* @see HomotypicalGroup
|
| 1132 |
|
|
*/
|
| 1133 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 1134 |
95449e99
|
Andreas Müller
|
public boolean isHomotypic(TaxonNameBase homoTypicName) {
|
| 1135 |
|
|
if (homoTypicName == null) {
|
| 1136 |
|
|
return false;
|
| 1137 |
|
|
}
|
| 1138 |
|
|
HomotypicalGroup homotypicGroup = homoTypicName.getHomotypicalGroup();
|
| 1139 |
|
|
if (homotypicGroup == null || this.getHomotypicalGroup() == null) {
|
| 1140 |
|
|
return false;
|
| 1141 |
|
|
}
|
| 1142 |
|
|
if (homotypicGroup.equals(this.getHomotypicalGroup())) {
|
| 1143 |
|
|
return true;
|
| 1144 |
|
|
}
|
| 1145 |
|
|
return false;
|
| 1146 |
|
|
}
|
| 1147 |
|
|
|
| 1148 |
|
|
//********* Rank comparison shortcuts ********************//
|
| 1149 |
4cc4f6f7
|
m.geoffroy
|
/**
|
| 1150 |
b9d0e8d2
|
m.geoffroy
|
* Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
|
| 1151 |
4cc4f6f7
|
m.geoffroy
|
* taxon name is higher than the genus rank (true) or not (false).
|
| 1152 |
|
|
* Suprageneric non viral names are monomials.
|
| 1153 |
bef42c31
|
Andreas Müller
|
* Returns false if rank is null.
|
| 1154 |
4cc4f6f7
|
m.geoffroy
|
*
|
| 1155 |
|
|
* @see #isGenus()
|
| 1156 |
|
|
* @see #isInfraGeneric()
|
| 1157 |
|
|
* @see #isSpecies()
|
| 1158 |
|
|
* @see #isInfraSpecific()
|
| 1159 |
|
|
*/
|
| 1160 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 1161 |
451c6005
|
m.doering
|
public boolean isSupraGeneric() {
|
| 1162 |
bef42c31
|
Andreas Müller
|
if (rank == null){
|
| 1163 |
|
|
return false;
|
| 1164 |
|
|
}
|
| 1165 |
451c6005
|
m.doering
|
return getRank().isSupraGeneric();
|
| 1166 |
|
|
}
|
| 1167 |
4cc4f6f7
|
m.geoffroy
|
/**
|
| 1168 |
b9d0e8d2
|
m.geoffroy
|
* Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
|
| 1169 |
4cc4f6f7
|
m.geoffroy
|
* taxon name is the genus rank (true) or not (false). Non viral names with
|
| 1170 |
10a54497
|
m.geoffroy
|
* genus rank are monomials. Returns false if rank is null.
|
| 1171 |
4cc4f6f7
|
m.geoffroy
|
*
|
| 1172 |
|
|
* @see #isSupraGeneric()
|
| 1173 |
|
|
* @see #isInfraGeneric()
|
| 1174 |
|
|
* @see #isSpecies()
|
| 1175 |
|
|
* @see #isInfraSpecific()
|
| 1176 |
|
|
*/
|
| 1177 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 1178 |
451c6005
|
m.doering
|
public boolean isGenus() {
|
| 1179 |
bef42c31
|
Andreas Müller
|
if (rank == null){
|
| 1180 |
|
|
return false;
|
| 1181 |
|
|
}
|
| 1182 |
451c6005
|
m.doering
|
return getRank().isGenus();
|
| 1183 |
|
|
}
|
| 1184 |
4cc4f6f7
|
m.geoffroy
|
/**
|
| 1185 |
b9d0e8d2
|
m.geoffroy
|
* Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
|
| 1186 |
10a54497
|
m.geoffroy
|
* taxon name is higher than the species rank and lower than the
|
| 1187 |
|
|
* genus rank (true) or not (false). Infrageneric non viral names are
|
| 1188 |
|
|
* binomials. Returns false if rank is null.
|
| 1189 |
4cc4f6f7
|
m.geoffroy
|
*
|
| 1190 |
|
|
* @see #isSupraGeneric()
|
| 1191 |
|
|
* @see #isGenus()
|
| 1192 |
|
|
* @see #isSpecies()
|
| 1193 |
|
|
* @see #isInfraSpecific()
|
| 1194 |
|
|
*/
|
| 1195 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 1196 |
451c6005
|
m.doering
|
public boolean isInfraGeneric() {
|
| 1197 |
bef42c31
|
Andreas Müller
|
if (rank == null){
|
| 1198 |
|
|
return false;
|
| 1199 |
|
|
}
|
| 1200 |
451c6005
|
m.doering
|
return getRank().isInfraGeneric();
|
| 1201 |
|
|
}
|
| 1202 |
4cc4f6f7
|
m.geoffroy
|
/**
|
| 1203 |
b9d0e8d2
|
m.geoffroy
|
* Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
|
| 1204 |
10a54497
|
m.geoffroy
|
* taxon name is the species rank (true) or not (false). Non viral names
|
| 1205 |
4cc4f6f7
|
m.geoffroy
|
* with species rank are binomials.
|
| 1206 |
bef42c31
|
Andreas Müller
|
* Returns false if rank is null.
|
| 1207 |
4cc4f6f7
|
m.geoffroy
|
*
|
| 1208 |
|
|
* @see #isSupraGeneric()
|
| 1209 |
|
|
* @see #isGenus()
|
| 1210 |
|
|
* @see #isInfraGeneric()
|
| 1211 |
|
|
* @see #isInfraSpecific()
|
| 1212 |
|
|
*/
|
| 1213 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 1214 |
451c6005
|
m.doering
|
public boolean isSpecies() {
|
| 1215 |
bef42c31
|
Andreas Müller
|
if (rank == null){
|
| 1216 |
|
|
return false;
|
| 1217 |
|
|
}
|
| 1218 |
451c6005
|
m.doering
|
return getRank().isSpecies();
|
| 1219 |
|
|
}
|
| 1220 |
4cc4f6f7
|
m.geoffroy
|
/**
|
| 1221 |
b9d0e8d2
|
m.geoffroy
|
* Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
|
| 1222 |
4cc4f6f7
|
m.geoffroy
|
* taxon name is lower than the species rank (true) or not (false).
|
| 1223 |
|
|
* Infraspecific non viral names are trinomials.
|
| 1224 |
bef42c31
|
Andreas Müller
|
* Returns false if rank is null.
|
| 1225 |
4cc4f6f7
|
m.geoffroy
|
*
|
| 1226 |
|
|
* @see #isSupraGeneric()
|
| 1227 |
|
|
* @see #isGenus()
|
| 1228 |
|
|
* @see #isInfraGeneric()
|
| 1229 |
|
|
* @see #isSpecies()
|
| 1230 |
|
|
*/
|
| 1231 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
| 1232 |
451c6005
|
m.doering
|
public boolean isInfraSpecific() {
|
| 1233 |
bef42c31
|
Andreas Müller
|
if (rank == null){
|
| 1234 |
|
|
return false;
|
| 1235 |
|
|
}
|
| 1236 |
451c6005
|
m.doering
|
return getRank().isInfraSpecific();
|
| 1237 |
|
|
}
|
| 1238 |
5c19d7f0
|
Andreas Müller
|
|
| 1239 |
7ebeb288
|
Andreas Müller
|
|
| 1240 |
4cc4f6f7
|
m.geoffroy
|
/**
|
| 1241 |
eb7e638a
|
m.geoffroy
|
* Returns null as the {@link NomenclaturalCode nomenclatural code} that governs
|
| 1242 |
b9d0e8d2
|
m.geoffroy
|
* the construction of <i>this</i> taxon name since there is no specific
|
| 1243 |
eb7e638a
|
m.geoffroy
|
* nomenclatural code defined. The real implementention takes place in the
|
| 1244 |
|
|
* subclasses {@link ViralName ViralName}, {@link BacterialName BacterialName},
|
| 1245 |
|
|
* {@link BotanicalName BotanicalName}, {@link CultivarPlantName CultivarPlantName} and
|
| 1246 |
|
|
* {@link ZoologicalName ZoologicalName}. Each taxon name is governed by one
|
| 1247 |
4cc4f6f7
|
m.geoffroy
|
* and only one nomenclatural code.
|
| 1248 |
|
|
*
|
| 1249 |
eb7e638a
|
m.geoffroy
|
* @return null
|
| 1250 |
b3262b1b
|
m.geoffroy
|
* @see #isCodeCompliant()
|
| 1251 |
|
|
* @see #getHasProblem()
|
| 1252 |
4cc4f6f7
|
m.geoffroy
|
*/
|
| 1253 |
bef42c31
|
Andreas Müller
|
abstract public NomenclaturalCode getNomenclaturalCode();
|
| 1254 |
d50a2c5d
|
Andreas Müller
|
/* (non-Javadoc)
|
| 1255 |
|
|
* @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()
|
| 1256 |
|
|
*/
|
| 1257 |
b3262b1b
|
m.geoffroy
|
/**
|
| 1258 |
b9d0e8d2
|
m.geoffroy
|
* Generates and returns the string with the scientific name of <i>this</i>
|
| 1259 |
7e759003
|
m.geoffroy
|
* taxon name (only non viral taxon names can be generated from their
|
| 1260 |
|
|
* components). This string may be stored in the inherited
|
| 1261 |
09887ea6
|
m.geoffroy
|
* {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache() titleCache} attribute.
|
| 1262 |
b3262b1b
|
m.geoffroy
|
* This method overrides the generic and inherited
|
| 1263 |
09887ea6
|
m.geoffroy
|
* {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle() method} from
|
| 1264 |
|
|
* {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity IdentifiableEntity}.
|
| 1265 |
b3262b1b
|
m.geoffroy
|
*
|
| 1266 |
|
|
* @return the string with the composed name of this non viral taxon name with authorship (and maybe year)
|
| 1267 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()
|
| 1268 |
|
|
* @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache()
|
| 1269 |
b3262b1b
|
m.geoffroy
|
*/
|
| 1270 |
4208745a
|
ben.clark
|
// @Override
|
| 1271 |
|
|
// public abstract String generateTitle();
|
| 1272 |
dadf5cd0
|
Andreas Kohlbecker
|
}
|