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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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import java.util.Set;
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33508d06
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a.babadshanjan
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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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827f3b3c
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a.babadshanjan
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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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a.babadshanjan
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import javax.xml.bind.annotation.XmlIDREF;
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a.babadshanjan
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import javax.xml.bind.annotation.XmlRootElement;
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a.babadshanjan
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import javax.xml.bind.annotation.XmlSchemaType;
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827f3b3c
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a.babadshanjan
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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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396aee74
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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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ben.clark
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import org.hibernate.envers.Audited;
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fd7ee7b1
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ben.clark
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import org.hibernate.search.annotations.Field;
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ee91bcd9
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ben.clark
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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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9479da48
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Andreas Müller
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/**
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975192f9
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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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m.geoffroy
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* particular {@link NomenclaturalCode nomenclature code}. The scientific taxon name does not depend
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85629348
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m.geoffroy
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* on the use made of it in a publication or a treatment
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09887ea6
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m.geoffroy
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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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9e86cd74
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m.geoffroy
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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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19e7a39e
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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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827f3b3c
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a.babadshanjan
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@XmlAccessorType(XmlAccessType.FIELD)
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a.babadshanjan
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@XmlType(name = "TaxonNameBase", propOrder = {
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827f3b3c
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a.babadshanjan
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"appendedPhrase",
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"nomenclaturalMicroReference",
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64c4a14d
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a.babadshanjan
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"nomenclaturalReference",
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827f3b3c
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a.babadshanjan
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"rank",
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33508d06
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a.babadshanjan
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"fullTitleCache",
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"protectedFullTitleCache",
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827f3b3c
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a.babadshanjan
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"homotypicalGroup",
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ddae61ce
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a.babadshanjan
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"typeDesignations",
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827f3b3c
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a.babadshanjan
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"relationsFromThisName",
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"relationsToThisName",
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7baa835b
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a.babadshanjan
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"status",
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ee91bcd9
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ben.clark
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"descriptions",
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"taxonBases"
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})
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a.babadshanjan
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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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ee91bcd9
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ben.clark
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@Audited
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9479da48
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Andreas Müller
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@Inheritance(strategy=InheritanceType.SINGLE_TABLE)
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c281e68e
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Andreas Müller
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@Table(appliesTo="TaxonNameBase", indexes = { @Index(name = "taxonNameBaseTitleCacheIndex", columnNames = { "titleCache" }) })
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f6765014
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ben.clark
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public abstract class TaxonNameBase<T extends TaxonNameBase<?,?>, S extends INameCacheStrategy> extends IdentifiableEntity implements IReferencedEntity, IParsable, IRelated {
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168723a2
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a.babadshanjan
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961ee94b
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Andreas Müller
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private static final long serialVersionUID = -4530368639601532116L;
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b70a7f94
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Andreas Kohlbecker
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private static final Logger logger = Logger.getLogger(TaxonNameBase.class);
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a.babadshanjan
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33508d06
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@XmlElement(name = "FullTitleCache")
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ee91bcd9
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ben.clark
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@Column(length=330, name="fullTitleCache")
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33508d06
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a.babadshanjan
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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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2595daef
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a.babadshanjan
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@XmlElementWrapper(name = "Descriptions")
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@XmlElement(name = "Description")
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ee91bcd9
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ben.clark
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@OneToMany(mappedBy="taxonName", fetch= FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE})
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2595daef
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a.babadshanjan
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private Set<TaxonNameDescription> descriptions = new HashSet<TaxonNameDescription>();
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71dcc146
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Andreas Müller
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a.babadshanjan
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@XmlElement(name = "AppendedPhrase")
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fd7ee7b1
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ben.clark
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@Field(index= org.hibernate.search.annotations.Index.TOKENIZED)
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9479da48
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Andreas Müller
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private String appendedPhrase;
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a.babadshanjan
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a.babadshanjan
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@XmlElement(name = "NomenclaturalMicroReference")
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fd7ee7b1
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ben.clark
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@Field(index= org.hibernate.search.annotations.Index.TOKENIZED)
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9479da48
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Andreas Müller
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private String nomenclaturalMicroReference;
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a.babadshanjan
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@XmlAttribute
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9479da48
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Andreas Müller
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private boolean hasProblem = false;
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a.babadshanjan
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6680df00
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Andreas Müller
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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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dce4c9cb
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Andreas Müller
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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)
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dce4c9cb
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Andreas Müller
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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})
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private HomotypicalGroup homotypicalGroup;
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a.babadshanjan
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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)
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608eada2
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Andreas Müller
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private Set<NameRelationship> relationsFromThisName = new HashSet<NameRelationship>();
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a.babadshanjan
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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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ee91bcd9
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ben.clark
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@OneToMany(mappedBy="relatedTo", fetch= FetchType.LAZY)
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ec1f7873
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Andreas Müller
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//@Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE_ORPHAN})
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@Cascade(CascadeType.SAVE_UPDATE)
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608eada2
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Andreas Müller
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private Set<NameRelationship> relationsToThisName = new HashSet<NameRelationship>();
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a.babadshanjan
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ben.clark
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@XmlElementWrapper(name = "NomenclaturalStatuses")
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a.babadshanjan
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@XmlElement(name = "NomenclaturalStatus")
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ben.clark
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@OneToMany(fetch= FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE})
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608eada2
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Andreas Müller
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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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608eada2
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Andreas Müller
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private Set<TaxonBase> taxonBases = new HashSet<TaxonBase>();
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a.babadshanjan
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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.LAZY)
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9479da48
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Andreas Müller
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private Rank rank;
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@XmlElement(name = "NomenclaturalReference")
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a.babadshanjan
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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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1cfc54ab
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Andreas Müller
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2a486d28
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Andreas Müller
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// ************* CONSTRUCTORS *************/
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12655d36
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m.geoffroy
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/**
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85629348
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m.geoffroy
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* Class constructor: creates a new empty taxon name.
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12655d36
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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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9479da48
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Andreas Müller
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public TaxonNameBase() {
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ee91bcd9
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ben.clark
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super();
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9479da48
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Andreas Müller
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}
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12655d36
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m.geoffroy
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/**
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85629348
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m.geoffroy
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* Class constructor: creates a new taxon name
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09887ea6
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m.geoffroy
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* only containing its {@link Rank rank}.
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12655d36
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m.geoffroy
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*
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b9d0e8d2
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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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6a9737e8
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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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12655d36
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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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public TaxonNameBase(Rank rank) {
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b18c6379
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Andreas Müller
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this(rank, null);
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}
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12655d36
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m.geoffroy
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/**
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85629348
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m.geoffroy
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* Class constructor: creates a new taxon name
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9dac7f49
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m.geoffroy
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* only containing its {@link HomotypicalGroup homotypical group}.
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85629348
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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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740cb3b5
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m.geoffroy
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* belonging to this homotypical group.
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12655d36
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m.geoffroy
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*
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b9d0e8d2
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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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6a9737e8
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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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12655d36
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m.geoffroy
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*/
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227 |
b18c6379
|
Andreas Müller
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public TaxonNameBase(HomotypicalGroup homotypicalGroup) {
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this(null, homotypicalGroup);
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}
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12655d36
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m.geoffroy
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/**
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85629348
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m.geoffroy
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* Class constructor: creates a new taxon name
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09887ea6
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m.geoffroy
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* only containing its {@link Rank rank} and
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9dac7f49
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m.geoffroy
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* its {@link HomotypicalGroup homotypical group}.
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740cb3b5
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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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* belonging to this homotypical group.
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12655d36
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m.geoffroy
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*
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6a9737e8
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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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b9d0e8d2
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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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6a9737e8
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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(HomotypicalGroup)
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12655d36
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m.geoffroy
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*/
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243 |
b18c6379
|
Andreas Müller
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public TaxonNameBase(Rank rank, HomotypicalGroup homotypicalGroup) {
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244 |
9479da48
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Andreas Müller
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super();
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this.setRank(rank);
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246 |
b18c6379
|
Andreas Müller
|
if (homotypicalGroup == null){
|
247 |
|
|
homotypicalGroup = new HomotypicalGroup();
|
248 |
|
|
}
|
249 |
|
|
homotypicalGroup.addTypifiedName(this);
|
250 |
9479da48
|
Andreas Müller
|
}
|
251 |
2a486d28
|
Andreas Müller
|
|
252 |
|
|
//********* METHODS **************************************/
|
253 |
9017e2de
|
Andreas Müller
|
|
254 |
12655d36
|
m.geoffroy
|
/**
|
255 |
b9d0e8d2
|
m.geoffroy
|
* Returns the boolean value "false" since the components of <i>this</i> taxon name
|
256 |
eb7e638a
|
m.geoffroy
|
* cannot follow the rules of a corresponding {@link NomenclaturalCode nomenclatural code}
|
257 |
|
|
* which is not defined for this class. The nomenclature code depends on
|
258 |
12655d36
|
m.geoffroy
|
* the concrete name subclass ({@link BacterialName BacterialName},
|
259 |
|
|
* {@link BotanicalName BotanicalName}, {@link CultivarPlantName CultivarPlantName},
|
260 |
|
|
* {@link ZoologicalName ZoologicalName} or {@link ViralName ViralName})
|
261 |
eb7e638a
|
m.geoffroy
|
* to which a taxon name belongs.
|
262 |
12655d36
|
m.geoffroy
|
*
|
263 |
eb7e638a
|
m.geoffroy
|
* @return false
|
264 |
12655d36
|
m.geoffroy
|
*/
|
265 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
266 |
9479da48
|
Andreas Müller
|
public abstract boolean isCodeCompliant();
|
267 |
|
|
|
268 |
33508d06
|
a.babadshanjan
|
public abstract String generateFullTitle();
|
269 |
9479da48
|
Andreas Müller
|
|
270 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
271 |
33508d06
|
a.babadshanjan
|
public String getFullTitleCache(){
|
272 |
|
|
if (protectedFullTitleCache){
|
273 |
|
|
return this.fullTitleCache;
|
274 |
|
|
}
|
275 |
|
|
if (fullTitleCache == null){
|
276 |
e3a02794
|
a.babadshanjan
|
this.setFullTitleCache(generateFullTitle(), protectedFullTitleCache);
|
277 |
33508d06
|
a.babadshanjan
|
}
|
278 |
|
|
return fullTitleCache;
|
279 |
|
|
}
|
280 |
|
|
|
281 |
|
|
public void setFullTitleCache(String fullTitleCache){
|
282 |
|
|
setFullTitleCache(fullTitleCache, PROTECTED);
|
283 |
|
|
}
|
284 |
|
|
|
285 |
|
|
public void setFullTitleCache(String fullTitleCache, boolean protectCache){
|
286 |
|
|
//TODO truncation of full title cache
|
287 |
c0bd32ce
|
a.babadshanjan
|
if (fullTitleCache != null && fullTitleCache.length() > 329){
|
288 |
|
|
logger.warn("Truncation of full title cache: " + this.toString() + "/" + fullTitleCache);
|
289 |
|
|
fullTitleCache = fullTitleCache.substring(0, 329) + "...";
|
290 |
|
|
}
|
291 |
33508d06
|
a.babadshanjan
|
this.fullTitleCache = fullTitleCache;
|
292 |
|
|
this.setProtectedFullTitleCache(protectCache);
|
293 |
|
|
}
|
294 |
|
|
|
295 |
|
|
public boolean isProtectedFullTitleCache() {
|
296 |
|
|
return protectedFullTitleCache;
|
297 |
|
|
}
|
298 |
|
|
|
299 |
|
|
public void setProtectedFullTitleCache(boolean protectedFullTitleCache) {
|
300 |
|
|
this.protectedFullTitleCache = protectedFullTitleCache;
|
301 |
|
|
}
|
302 |
|
|
|
303 |
12655d36
|
m.geoffroy
|
/**
|
304 |
|
|
* Returns the set of all {@link NameRelationship name relationships}
|
305 |
b9d0e8d2
|
m.geoffroy
|
* in which <i>this</i> taxon name is involved. A taxon name can be both source
|
306 |
12655d36
|
m.geoffroy
|
* in some name relationships or target in some others.
|
307 |
|
|
*
|
308 |
09487e73
|
m.geoffroy
|
* @see #getRelationsToThisName()
|
309 |
|
|
* @see #getRelationsFromThisName()
|
310 |
|
|
* @see #addNameRelationship(NameRelationship)
|
311 |
12655d36
|
m.geoffroy
|
* @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
|
312 |
|
|
* @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
|
313 |
|
|
*/
|
314 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
315 |
9479da48
|
Andreas Müller
|
public Set<NameRelationship> getNameRelations() {
|
316 |
6ecda5d2
|
m.doering
|
Set<NameRelationship> rels = new HashSet<NameRelationship>();
|
317 |
|
|
rels.addAll(getRelationsFromThisName());
|
318 |
|
|
rels.addAll(getRelationsToThisName());
|
319 |
|
|
return rels;
|
320 |
|
|
}
|
321 |
b92a6173
|
a.babadshanjan
|
|
322 |
6ecda5d2
|
m.doering
|
/**
|
323 |
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
|
324 |
|
|
* and adds it both to the set of {@link #getRelationsFromThisName() relations from <i>this</i> taxon name} and
|
325 |
12655d36
|
m.geoffroy
|
* to the set of {@link #getRelationsToThisName() relations to the other taxon name}.
|
326 |
|
|
*
|
327 |
|
|
* @param toName the taxon name of the target for this new name relationship
|
328 |
|
|
* @param type the type of this new name relationship
|
329 |
|
|
* @param ruleConsidered the string which specifies the rule on which this name relationship is based
|
330 |
09487e73
|
m.geoffroy
|
* @see #getRelationsToThisName()
|
331 |
|
|
* @see #getNameRelations()
|
332 |
12655d36
|
m.geoffroy
|
* @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
|
333 |
|
|
* @see #addNameRelationship(NameRelationship)
|
334 |
6ecda5d2
|
m.doering
|
*/
|
335 |
|
|
public void addRelationshipToName(TaxonNameBase toName, NameRelationshipType type, String ruleConsidered){
|
336 |
|
|
NameRelationship rel = new NameRelationship(toName, this, type, ruleConsidered);
|
337 |
|
|
}
|
338 |
12655d36
|
m.geoffroy
|
/**
|
339 |
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
|
340 |
|
|
* and adds it both to the set of {@link #getRelationsToThisName() relations to <i>this</i> taxon name} and
|
341 |
12655d36
|
m.geoffroy
|
* to the set of {@link #getRelationsFromThisName() relations from the other taxon name}.
|
342 |
|
|
*
|
343 |
|
|
* @param fromName the taxon name of the source for this new name relationship
|
344 |
|
|
* @param type the type of this new name relationship
|
345 |
|
|
* @param ruleConsidered the string which specifies the rule on which this name relationship is based
|
346 |
09487e73
|
m.geoffroy
|
* @see #getRelationsFromThisName()
|
347 |
|
|
* @see #getNameRelations()
|
348 |
12655d36
|
m.geoffroy
|
* @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
|
349 |
|
|
* @see #addNameRelationship(NameRelationship)
|
350 |
|
|
*/
|
351 |
4dd3e141
|
m.doering
|
public void addRelationshipFromName(TaxonNameBase fromName, NameRelationshipType type, String ruleConsidered){
|
352 |
|
|
NameRelationship rel = new NameRelationship(this, fromName, type, ruleConsidered);
|
353 |
|
|
}
|
354 |
12655d36
|
m.geoffroy
|
/**
|
355 |
|
|
* Adds an existing {@link NameRelationship name relationship} either to the set of
|
356 |
b9d0e8d2
|
m.geoffroy
|
* {@link #getRelationsToThisName() relations to <i>this</i> taxon name} or to the set of
|
357 |
|
|
* {@link #getRelationsFromThisName() relations from <i>this</i> taxon name}. If neither the
|
358 |
|
|
* source nor the target of the name relationship match with <i>this</i> taxon name
|
359 |
12655d36
|
m.geoffroy
|
* no addition will be carried out.
|
360 |
|
|
*
|
361 |
b9d0e8d2
|
m.geoffroy
|
* @param rel the name relationship to be added to one of <i>this</i> taxon name's name relationships sets
|
362 |
09487e73
|
m.geoffroy
|
* @see #getNameRelations()
|
363 |
12655d36
|
m.geoffroy
|
* @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
|
364 |
|
|
* @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
|
365 |
|
|
*/
|
366 |
6ecda5d2
|
m.doering
|
protected void addNameRelationship(NameRelationship rel) {
|
367 |
|
|
if (rel!=null && rel.getToName().equals(this)){
|
368 |
|
|
this.relationsToThisName.add(rel);
|
369 |
|
|
}else if(rel!=null && rel.getFromName().equals(this)){
|
370 |
|
|
this.relationsFromThisName.add(rel);
|
371 |
|
|
}else{
|
372 |
|
|
//TODO: raise error???
|
373 |
|
|
}
|
374 |
9479da48
|
Andreas Müller
|
}
|
375 |
12655d36
|
m.geoffroy
|
/**
|
376 |
|
|
* Removes one {@link NameRelationship name relationship} from one of both sets of
|
377 |
b9d0e8d2
|
m.geoffroy
|
* {@link #getNameRelations() name relationships} in which <i>this</i> taxon name is involved.
|
378 |
09487e73
|
m.geoffroy
|
* The name relationship will also be removed from one of both sets belonging
|
379 |
|
|
* to the second taxon name involved. Furthermore the fromName and toName
|
380 |
|
|
* attributes of the name relationship object will be nullified.
|
381 |
12655d36
|
m.geoffroy
|
*
|
382 |
|
|
* @param nameRelation the name relationship which should be deleted from one of both sets
|
383 |
6a9737e8
|
m.geoffroy
|
* @see #getNameRelations()
|
384 |
12655d36
|
m.geoffroy
|
*/
|
385 |
6ecda5d2
|
m.doering
|
public void removeNameRelationship(NameRelationship nameRelation) {
|
386 |
b92a6173
|
a.babadshanjan
|
|
387 |
|
|
TaxonNameBase fromName = nameRelation.getFromName();
|
388 |
|
|
TaxonNameBase toName = nameRelation.getToName();
|
389 |
|
|
|
390 |
|
|
if (nameRelation != null) {
|
391 |
|
|
nameRelation.setToName(null);
|
392 |
|
|
nameRelation.setFromName(null);
|
393 |
|
|
}
|
394 |
|
|
|
395 |
|
|
if (fromName != null) {
|
396 |
|
|
fromName.removeNameRelationship(nameRelation);
|
397 |
|
|
}
|
398 |
|
|
|
399 |
|
|
if (toName != null) {
|
400 |
|
|
toName.removeNameRelationship(nameRelation);
|
401 |
|
|
}
|
402 |
|
|
|
403 |
|
|
this.relationsToThisName.remove(nameRelation);
|
404 |
|
|
this.relationsFromThisName.remove(nameRelation);
|
405 |
|
|
}
|
406 |
|
|
|
407 |
|
|
public void removeTaxonName(TaxonNameBase taxonName) {
|
408 |
|
|
Set<NameRelationship> nameRelationships = new HashSet<NameRelationship>();
|
409 |
|
|
// nameRelationships.addAll(this.getNameRelations());
|
410 |
|
|
nameRelationships.addAll(this.getRelationsFromThisName());
|
411 |
|
|
nameRelationships.addAll(this.getRelationsToThisName());
|
412 |
|
|
for(NameRelationship nameRelationship : nameRelationships) {
|
413 |
|
|
// remove name relationship from this side
|
414 |
|
|
if (nameRelationship.getFromName().equals(this) && nameRelationship.getToName().equals(taxonName)) {
|
415 |
|
|
this.removeNameRelation(nameRelationship);
|
416 |
|
|
}
|
417 |
|
|
}
|
418 |
|
|
}
|
419 |
|
|
|
420 |
|
|
public void removeNameRelation(NameRelationship nameRelation) {
|
421 |
|
|
nameRelation.setToName(null);
|
422 |
|
|
|
423 |
|
|
TaxonNameBase name = nameRelation.getFromName();
|
424 |
|
|
if (name != null){
|
425 |
|
|
nameRelation.setFromName(null);
|
426 |
|
|
name.removeNameRelation(nameRelation);
|
427 |
|
|
}
|
428 |
6ecda5d2
|
m.doering
|
this.relationsToThisName.remove(nameRelation);
|
429 |
|
|
this.relationsFromThisName.remove(nameRelation);
|
430 |
9479da48
|
Andreas Müller
|
}
|
431 |
6ecda5d2
|
m.doering
|
|
432 |
|
|
|
433 |
b3262b1b
|
m.geoffroy
|
/**
|
434 |
|
|
* Does exactly the same as the addNameRelationship method provided that
|
435 |
|
|
* the given relationship is a name relationship.
|
436 |
|
|
*
|
437 |
b9d0e8d2
|
m.geoffroy
|
* @param relation the relationship to be added to one of <i>this</i> taxon name's name relationships sets
|
438 |
b3262b1b
|
m.geoffroy
|
* @see #addNameRelationship(NameRelationship)
|
439 |
|
|
* @see #getNameRelations()
|
440 |
|
|
* @see NameRelationship
|
441 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.common.RelationshipBase
|
442 |
b3262b1b
|
m.geoffroy
|
*/
|
443 |
705e0850
|
Andreas Müller
|
public void addRelationship(RelationshipBase relation) {
|
444 |
|
|
if (relation instanceof NameRelationship){
|
445 |
|
|
addNameRelationship((NameRelationship)relation);
|
446 |
d27ee9b1
|
Andreas Müller
|
if (relation.getType() != null &&
|
447 |
bef42c31
|
Andreas Müller
|
( relation.getType().equals(NameRelationshipType.BASIONYM()) ||
|
448 |
|
|
relation.getType().equals(NameRelationshipType.REPLACED_SYNONYM())
|
449 |
|
|
)){
|
450 |
d27ee9b1
|
Andreas Müller
|
TaxonNameBase fromName = ((NameRelationship)relation).getFromName();
|
451 |
|
|
TaxonNameBase toName = ((NameRelationship)relation).getToName();
|
452 |
|
|
fromName.getHomotypicalGroup().merge(toName.getHomotypicalGroup());
|
453 |
|
|
}
|
454 |
705e0850
|
Andreas Müller
|
}else{
|
455 |
d27ee9b1
|
Andreas Müller
|
logger.warn("Relationship not of type NameRelationship!");
|
456 |
705e0850
|
Andreas Müller
|
//TODO exception handling
|
457 |
|
|
}
|
458 |
7ebeb288
|
Andreas Müller
|
}
|
459 |
|
|
|
460 |
|
|
|
461 |
09487e73
|
m.geoffroy
|
/**
|
462 |
|
|
* Returns the set of all {@link NameRelationship name relationships}
|
463 |
b9d0e8d2
|
m.geoffroy
|
* in which <i>this</i> taxon name is involved as a source.
|
464 |
09487e73
|
m.geoffroy
|
*
|
465 |
|
|
* @see #getNameRelations()
|
466 |
|
|
* @see #getRelationsToThisName()
|
467 |
|
|
* @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
|
468 |
|
|
*/
|
469 |
6ecda5d2
|
m.doering
|
public Set<NameRelationship> getRelationsFromThisName() {
|
470 |
|
|
return relationsFromThisName;
|
471 |
9479da48
|
Andreas Müller
|
}
|
472 |
ee91bcd9
|
ben.clark
|
|
473 |
09487e73
|
m.geoffroy
|
/**
|
474 |
|
|
* Returns the set of all {@link NameRelationship name relationships}
|
475 |
b9d0e8d2
|
m.geoffroy
|
* in which <i>this</i> taxon name is involved as a target.
|
476 |
09487e73
|
m.geoffroy
|
*
|
477 |
|
|
* @see #getNameRelations()
|
478 |
|
|
* @see #getRelationsFromThisName()
|
479 |
|
|
* @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
|
480 |
|
|
*/
|
481 |
6ecda5d2
|
m.doering
|
public Set<NameRelationship> getRelationsToThisName() {
|
482 |
|
|
return relationsToThisName;
|
483 |
9479da48
|
Andreas Müller
|
}
|
484 |
|
|
|
485 |
09487e73
|
m.geoffroy
|
/**
|
486 |
|
|
* Returns the set of {@link NomenclaturalStatus nomenclatural status} assigned
|
487 |
b9d0e8d2
|
m.geoffroy
|
* to <i>this</i> taxon name according to its corresponding nomenclature code.
|
488 |
09487e73
|
m.geoffroy
|
* This includes the {@link NomenclaturalStatusType type} of the nomenclatural status
|
489 |
|
|
* and the nomenclatural code rule considered.
|
490 |
|
|
*
|
491 |
|
|
* @see NomenclaturalStatus
|
492 |
|
|
* @see NomenclaturalStatusType
|
493 |
|
|
*/
|
494 |
9479da48
|
Andreas Müller
|
public Set<NomenclaturalStatus> getStatus() {
|
495 |
|
|
return status;
|
496 |
|
|
}
|
497 |
ee91bcd9
|
ben.clark
|
|
498 |
09487e73
|
m.geoffroy
|
/**
|
499 |
|
|
* Adds a new {@link NomenclaturalStatus nomenclatural status}
|
500 |
b9d0e8d2
|
m.geoffroy
|
* to <i>this</i> taxon name's set of nomenclatural status.
|
501 |
09487e73
|
m.geoffroy
|
*
|
502 |
|
|
* @param nomStatus the nomenclatural status to be added
|
503 |
|
|
* @see #getStatus()
|
504 |
|
|
*/
|
505 |
025f3199
|
Andreas Müller
|
public void addStatus(NomenclaturalStatus nomStatus) {
|
506 |
|
|
this.status.add(nomStatus);
|
507 |
9479da48
|
Andreas Müller
|
}
|
508 |
ee91bcd9
|
ben.clark
|
|
509 |
09487e73
|
m.geoffroy
|
/**
|
510 |
b9d0e8d2
|
m.geoffroy
|
* Removes one element from the set of nomenclatural status of <i>this</i> taxon name.
|
511 |
09487e73
|
m.geoffroy
|
* Type and ruleConsidered attributes of the nomenclatural status object
|
512 |
|
|
* will be nullified.
|
513 |
|
|
*
|
514 |
b9d0e8d2
|
m.geoffroy
|
* @param nomStatus the nomenclatural status of <i>this</i> taxon name which should be deleted
|
515 |
09487e73
|
m.geoffroy
|
* @see #getStatus()
|
516 |
|
|
*/
|
517 |
025f3199
|
Andreas Müller
|
public void removeStatus(NomenclaturalStatus nomStatus) {
|
518 |
09487e73
|
m.geoffroy
|
//TODO to be implemented?
|
519 |
|
|
logger.warn("not yet fully implemented?");
|
520 |
025f3199
|
Andreas Müller
|
this.status.remove(nomStatus);
|
521 |
9479da48
|
Andreas Müller
|
}
|
522 |
|
|
|
523 |
5c19d7f0
|
Andreas Müller
|
|
524 |
|
|
/**
|
525 |
09887ea6
|
m.geoffroy
|
* Indicates whether <i>this</i> taxon name is a {@link NameRelationshipType#BASIONYM() basionym}
|
526 |
|
|
* or a {@link NameRelationshipType#REPLACED_SYNONYM() replaced synonym}
|
527 |
abc6aceb
|
m.geoffroy
|
* of any other taxon name. Returns "true", if a basionym or a replaced
|
528 |
09887ea6
|
m.geoffroy
|
* synonym {@link NameRelationship relationship} from <i>this</i> taxon name to another taxon name exists,
|
529 |
b9d0e8d2
|
m.geoffroy
|
* false otherwise (also in case <i>this</i> taxon name is the only one in the
|
530 |
09487e73
|
m.geoffroy
|
* homotypical group).
|
531 |
5c19d7f0
|
Andreas Müller
|
*/
|
532 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
533 |
5c19d7f0
|
Andreas Müller
|
public boolean isOriginalCombination(){
|
534 |
|
|
Set<NameRelationship> relationsFromThisName = this.getRelationsFromThisName();
|
535 |
|
|
for (NameRelationship relation : relationsFromThisName) {
|
536 |
|
|
if (relation.getType().equals(NameRelationshipType.BASIONYM()) ||
|
537 |
|
|
relation.getType().equals(NameRelationshipType.REPLACED_SYNONYM())) {
|
538 |
|
|
return true;
|
539 |
|
|
}
|
540 |
|
|
}
|
541 |
|
|
return false;
|
542 |
|
|
}
|
543 |
|
|
|
544 |
09487e73
|
m.geoffroy
|
/**
|
545 |
09887ea6
|
m.geoffroy
|
* Returns the taxon name which is the {@link NameRelationshipType#BASIONYM() basionym} of <i>this</i> taxon name.
|
546 |
09487e73
|
m.geoffroy
|
* The basionym of a taxon name is its epithet-bringing synonym.
|
547 |
09887ea6
|
m.geoffroy
|
* For instance <i>Pinus abies</i> L. was published by Linnaeus and the botanist
|
548 |
b9d0e8d2
|
m.geoffroy
|
* Karsten transferred later <i>this</i> taxon to the genus Picea. Therefore,
|
549 |
09887ea6
|
m.geoffroy
|
* <i>Pinus abies</i> L. is the basionym of the new combination <i>Picea abies</i> (L.) H. Karst.
|
550 |
09487e73
|
m.geoffroy
|
*/
|
551 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
552 |
2a486d28
|
Andreas Müller
|
public T getBasionym(){
|
553 |
6ecda5d2
|
m.doering
|
//TODO: pick the right name relationships...
|
554 |
d27ee9b1
|
Andreas Müller
|
logger.warn("get Basionym not yet implemented");
|
555 |
6ecda5d2
|
m.doering
|
return null;
|
556 |
9479da48
|
Andreas Müller
|
}
|
557 |
09487e73
|
m.geoffroy
|
/**
|
558 |
09887ea6
|
m.geoffroy
|
* Assigns a taxon name as {@link NameRelationshipType#BASIONYM() basionym} of <i>this</i> taxon name.
|
559 |
|
|
* The basionym {@link NameRelationship relationship} will be added to <i>this</i> taxon name
|
560 |
09487e73
|
m.geoffroy
|
* and to the basionym. The basionym cannot have itself a basionym.
|
561 |
09887ea6
|
m.geoffroy
|
* The {@link HomotypicalGroup homotypical groups} of <i>this</i> taxon name and of the basionym
|
562 |
|
|
* will be {@link HomotypicalGroup#merge(HomotypicalGroup) merged}.
|
563 |
|
|
*
|
564 |
|
|
* @param basionym the taxon name to be set as the basionym of <i>this</i> taxon name
|
565 |
|
|
* @see #getBasionym()
|
566 |
|
|
* @see #addBasionym(TaxonNameBase, String)
|
567 |
09487e73
|
m.geoffroy
|
*/
|
568 |
d27ee9b1
|
Andreas Müller
|
public void addBasionym(T basionym){
|
569 |
|
|
addBasionym(basionym, null);
|
570 |
6ecda5d2
|
m.doering
|
}
|
571 |
09487e73
|
m.geoffroy
|
/**
|
572 |
09887ea6
|
m.geoffroy
|
* Assigns a taxon name as {@link NameRelationshipType#BASIONYM() basionym} of <i>this</i> taxon name
|
573 |
09487e73
|
m.geoffroy
|
* and keeps the nomenclatural rule considered for it. The basionym
|
574 |
09887ea6
|
m.geoffroy
|
* {@link NameRelationship relationship} will be added to <i>this</i> taxon name and to the basionym.
|
575 |
|
|
* The basionym cannot have itself a basionym.
|
576 |
|
|
* The {@link HomotypicalGroup homotypical groups} of <i>this</i> taxon name and of the basionym
|
577 |
|
|
* will be {@link HomotypicalGroup#merge(HomotypicalGroup) merged}.
|
578 |
|
|
*
|
579 |
|
|
* @param basionym the taxon name to be set as the basionym of <i>this</i> taxon name
|
580 |
|
|
* @param ruleConsidered the string identifying the nomenclatural rule
|
581 |
|
|
* @see #getBasionym()
|
582 |
|
|
* @see #addBasionym(TaxonNameBase)
|
583 |
09487e73
|
m.geoffroy
|
*/
|
584 |
d27ee9b1
|
Andreas Müller
|
public void addBasionym(T basionym, String ruleConsidered){
|
585 |
|
|
if (basionym != null){
|
586 |
|
|
basionym.addRelationshipToName(this, NameRelationshipType.BASIONYM(), ruleConsidered);
|
587 |
|
|
}
|
588 |
|
|
}
|
589 |
|
|
|
590 |
09887ea6
|
m.geoffroy
|
/**
|
591 |
|
|
* Removes the {@link NameRelationshipType#BASIONYM() basionym} {@link NameRelationship relationship} from the set of
|
592 |
|
|
* {@link #getRelationsToThisName() name relationships to} <i>this</i> taxon name. The same relationhip will be
|
593 |
|
|
* removed from the set of {@link #getRelationsFromThisName() name relationships from} the taxon name
|
594 |
|
|
* previously used as basionym.
|
595 |
|
|
*
|
596 |
|
|
* @see #getBasionym()
|
597 |
|
|
* @see #addBasionym(TaxonNameBase)
|
598 |
|
|
*/
|
599 |
d27ee9b1
|
Andreas Müller
|
public void removeBasionym(){
|
600 |
|
|
//TODO implement
|
601 |
|
|
logger.warn("not yet implemented");
|
602 |
9479da48
|
Andreas Müller
|
}
|
603 |
|
|
|
604 |
09887ea6
|
m.geoffroy
|
/**
|
605 |
|
|
* Returns the {@link eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy cache strategy} used to generate
|
606 |
|
|
* several strings corresponding to <i>this</i> taxon name
|
607 |
|
|
* (in particular taxon name caches and author strings).
|
608 |
|
|
*
|
609 |
|
|
* @return the cache strategy used for <i>this</i> taxon name
|
610 |
|
|
* @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy
|
611 |
|
|
* @see eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
|
612 |
|
|
*/
|
613 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
614 |
dadf5cd0
|
Andreas Kohlbecker
|
public abstract S getCacheStrategy();
|
615 |
09887ea6
|
m.geoffroy
|
/**
|
616 |
|
|
* @see #getCacheStrategy()
|
617 |
|
|
*/
|
618 |
ee91bcd9
|
ben.clark
|
|
619 |
dadf5cd0
|
Andreas Kohlbecker
|
public abstract void setCacheStrategy(S cacheStrategy);
|
620 |
9479da48
|
Andreas Müller
|
|
621 |
8eebe79d
|
m.geoffroy
|
/**
|
622 |
b9d0e8d2
|
m.geoffroy
|
* Returns the taxonomic {@link Rank rank} of <i>this</i> taxon name.
|
623 |
8eebe79d
|
m.geoffroy
|
*
|
624 |
|
|
* @see Rank
|
625 |
|
|
*/
|
626 |
9479da48
|
Andreas Müller
|
public Rank getRank(){
|
627 |
|
|
return this.rank;
|
628 |
|
|
}
|
629 |
ee91bcd9
|
ben.clark
|
|
630 |
8eebe79d
|
m.geoffroy
|
/**
|
631 |
|
|
* @see #getRank()
|
632 |
|
|
*/
|
633 |
9479da48
|
Andreas Müller
|
public void setRank(Rank rank){
|
634 |
|
|
this.rank = rank;
|
635 |
|
|
}
|
636 |
|
|
|
637 |
8eebe79d
|
m.geoffroy
|
/**
|
638 |
09887ea6
|
m.geoffroy
|
* Returns the {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} of <i>this</i> taxon name.
|
639 |
8eebe79d
|
m.geoffroy
|
* The nomenclatural reference is here meant to be the one publication
|
640 |
b9d0e8d2
|
m.geoffroy
|
* <i>this</i> taxon name was originally published in while fulfilling the formal
|
641 |
a7d9a8c1
|
m.geoffroy
|
* requirements as specified by the corresponding {@link NomenclaturalCode nomenclatural code}.
|
642 |
8eebe79d
|
m.geoffroy
|
*
|
643 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.reference.INomenclaturalReference
|
644 |
|
|
* @see eu.etaxonomy.cdm.model.reference.ReferenceBase
|
645 |
8eebe79d
|
m.geoffroy
|
*/
|
646 |
b70a7f94
|
Andreas Kohlbecker
|
public ReferenceBase getNomenclaturalReference(){
|
647 |
|
|
return this.nomenclaturalReference;
|
648 |
9479da48
|
Andreas Müller
|
}
|
649 |
8eebe79d
|
m.geoffroy
|
/**
|
650 |
09887ea6
|
m.geoffroy
|
* Assigns a {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} to <i>this</i> taxon name.
|
651 |
|
|
* The corresponding {@link eu.etaxonomy.cdm.model.reference.ReferenceBase.isNomenclaturallyRelevant nomenclaturally relevant flag} will be set to true
|
652 |
8eebe79d
|
m.geoffroy
|
* as it is obviously used for nomenclatural purposes.
|
653 |
|
|
*
|
654 |
b70a7f94
|
Andreas Kohlbecker
|
* @throws IllegalArgumentException if parameter <code>nomenclaturalReference</code> is not assignable from {@link INomenclaturalReference}
|
655 |
8eebe79d
|
m.geoffroy
|
* @see #getNomenclaturalReference()
|
656 |
|
|
*/
|
657 |
b70a7f94
|
Andreas Kohlbecker
|
public void setNomenclaturalReference(ReferenceBase nomenclaturalReference){
|
658 |
|
|
if(nomenclaturalReference != null){
|
659 |
|
|
if(!INomenclaturalReference.class.isAssignableFrom(nomenclaturalReference.getClass())){
|
660 |
|
|
throw new IllegalArgumentException("Parameter nomenclaturalReference is not assignable from INomenclaturalReference");
|
661 |
|
|
}
|
662 |
|
|
this.nomenclaturalReference = (ReferenceBase)nomenclaturalReference;
|
663 |
|
|
} else {
|
664 |
|
|
this.nomenclaturalReference = null;
|
665 |
|
|
}
|
666 |
9479da48
|
Andreas Müller
|
}
|
667 |
|
|
|
668 |
8eebe79d
|
m.geoffroy
|
/**
|
669 |
b9d0e8d2
|
m.geoffroy
|
* Returns the appended phrase string assigned to <i>this</i> taxon name.
|
670 |
8eebe79d
|
m.geoffroy
|
* The appended phrase is a non-atomised addition to a name. It is
|
671 |
|
|
* not ruled by a nomenclatural code.
|
672 |
|
|
*/
|
673 |
9479da48
|
Andreas Müller
|
public String getAppendedPhrase(){
|
674 |
|
|
return this.appendedPhrase;
|
675 |
|
|
}
|
676 |
ee91bcd9
|
ben.clark
|
|
677 |
8eebe79d
|
m.geoffroy
|
/**
|
678 |
|
|
* @see #getAppendedPhrase()
|
679 |
|
|
*/
|
680 |
9479da48
|
Andreas Müller
|
public void setAppendedPhrase(String appendedPhrase){
|
681 |
|
|
this.appendedPhrase = appendedPhrase;
|
682 |
|
|
}
|
683 |
|
|
|
684 |
8eebe79d
|
m.geoffroy
|
/**
|
685 |
09887ea6
|
m.geoffroy
|
* Returns the details string of the {@link #getNomenclaturalReference() nomenclatural reference} assigned
|
686 |
b9d0e8d2
|
m.geoffroy
|
* to <i>this</i> taxon name. The details describe the exact localisation within
|
687 |
8eebe79d
|
m.geoffroy
|
* the publication used as nomenclature reference. These are mostly
|
688 |
|
|
* (implicitly) pages but can also be figures or tables or any other
|
689 |
|
|
* element of a publication. A nomenclatural micro reference (details)
|
690 |
|
|
* requires the existence of a nomenclatural reference.
|
691 |
|
|
*/
|
692 |
|
|
//Details of the nomenclatural reference (protologue).
|
693 |
9479da48
|
Andreas Müller
|
public String getNomenclaturalMicroReference(){
|
694 |
|
|
return this.nomenclaturalMicroReference;
|
695 |
|
|
}
|
696 |
8eebe79d
|
m.geoffroy
|
/**
|
697 |
|
|
* @see #getNomenclaturalMicroReference()
|
698 |
|
|
*/
|
699 |
9479da48
|
Andreas Müller
|
public void setNomenclaturalMicroReference(String nomenclaturalMicroReference){
|
700 |
|
|
this.nomenclaturalMicroReference = nomenclaturalMicroReference;
|
701 |
|
|
}
|
702 |
|
|
|
703 |
6680df00
|
Andreas Müller
|
/* (non-Javadoc)
|
704 |
|
|
* @see eu.etaxonomy.cdm.model.common.IParsable#getHasProblem()
|
705 |
8eebe79d
|
m.geoffroy
|
*/
|
706 |
9479da48
|
Andreas Müller
|
public boolean getHasProblem(){
|
707 |
|
|
return this.hasProblem;
|
708 |
|
|
}
|
709 |
6680df00
|
Andreas Müller
|
|
710 |
|
|
/* (non-Javadoc)
|
711 |
|
|
* @see eu.etaxonomy.cdm.model.common.IParsable#setHasProblem(boolean)
|
712 |
8eebe79d
|
m.geoffroy
|
*/
|
713 |
9479da48
|
Andreas Müller
|
public void setHasProblem(boolean hasProblem){
|
714 |
|
|
this.hasProblem = hasProblem;
|
715 |
|
|
}
|
716 |
6680df00
|
Andreas Müller
|
|
717 |
|
|
/* (non-Javadoc)
|
718 |
|
|
* @see eu.etaxonomy.cdm.model.common.IParsable#hasProblem()
|
719 |
81c31b35
|
Andreas Müller
|
*/
|
720 |
|
|
public boolean hasProblem(){
|
721 |
|
|
return getHasProblem();
|
722 |
|
|
}
|
723 |
6680df00
|
Andreas Müller
|
|
724 |
|
|
/* (non-Javadoc)
|
725 |
|
|
* @see eu.etaxonomy.cdm.model.common.IParsable#problemStarts()
|
726 |
|
|
*/
|
727 |
|
|
public int getProblemStarts(){
|
728 |
|
|
return this.problemStarts;
|
729 |
|
|
}
|
730 |
|
|
|
731 |
|
|
/* (non-Javadoc)
|
732 |
|
|
* @see eu.etaxonomy.cdm.model.common.IParsable#setProblemStarts(int)
|
733 |
|
|
*/
|
734 |
|
|
public void setProblemStarts(int start) {
|
735 |
|
|
this.problemStarts = start;
|
736 |
|
|
}
|
737 |
|
|
|
738 |
|
|
/* (non-Javadoc)
|
739 |
|
|
* @see eu.etaxonomy.cdm.model.common.IParsable#problemEnds()
|
740 |
|
|
*/
|
741 |
|
|
public int getProblemEnds(){
|
742 |
|
|
return this.problemEnds;
|
743 |
|
|
}
|
744 |
|
|
|
745 |
|
|
/* (non-Javadoc)
|
746 |
|
|
* @see eu.etaxonomy.cdm.model.common.IParsable#setProblemEnds(int)
|
747 |
|
|
*/
|
748 |
|
|
public void setProblemEnds(int end) {
|
749 |
|
|
this.problemEnds = end;
|
750 |
|
|
}
|
751 |
|
|
|
752 |
dce4c9cb
|
Andreas Müller
|
//*********************** TYPE DESIGNATION *********************************************//
|
753 |
|
|
|
754 |
79263e24
|
m.geoffroy
|
/**
|
755 |
dce4c9cb
|
Andreas Müller
|
* Returns the set of {@link TypeDesignationBase type designations} assigned
|
756 |
|
|
* to <i>this</i> taxon name.
|
757 |
79263e24
|
m.geoffroy
|
* @see NameTypeDesignation
|
758 |
|
|
* @see SpecimenTypeDesignation
|
759 |
|
|
*/
|
760 |
dce4c9cb
|
Andreas Müller
|
public Set<TypeDesignationBase> getTypeDesignations() {
|
761 |
|
|
return typeDesignations;
|
762 |
9479da48
|
Andreas Müller
|
}
|
763 |
dce4c9cb
|
Andreas Müller
|
|
764 |
|
|
/**
|
765 |
6a9737e8
|
m.geoffroy
|
* Removes one element from the set of {@link TypeDesignationBase type designations} assigned to
|
766 |
|
|
* <i>this</i> taxon name. The type designation itself will be nullified.
|
767 |
dce4c9cb
|
Andreas Müller
|
*
|
768 |
|
|
* @param typeDesignation the type designation which should be deleted
|
769 |
|
|
*/
|
770 |
|
|
public void removeTypeDesignation(TypeDesignationBase typeDesignation) {
|
771 |
|
|
logger.warn("not yet fully implemented: nullify the specimen type designation itself?");
|
772 |
|
|
this.typeDesignations.remove(typeDesignation);
|
773 |
|
|
}
|
774 |
|
|
|
775 |
|
|
/**
|
776 |
|
|
* Returns the set of {@link SpecimenTypeDesignation specimen type designations} assigned
|
777 |
6a9737e8
|
m.geoffroy
|
* to <i>this</i> taxon name. The {@link Rank rank} of <i>this</i> taxon name is generally
|
778 |
|
|
* "species" or below. The specimen type designations include all the
|
779 |
|
|
* specimens on which the typification of this name is based (which are
|
780 |
09887ea6
|
m.geoffroy
|
* exclusively used to typify taxon names belonging to the same
|
781 |
6a9737e8
|
m.geoffroy
|
* {@link HomotypicalGroup homotypical group} to which <i>this</i> taxon name
|
782 |
|
|
* belongs) and eventually the status of these designations.
|
783 |
dce4c9cb
|
Andreas Müller
|
*
|
784 |
|
|
* @see SpecimenTypeDesignation
|
785 |
|
|
* @see NameTypeDesignation
|
786 |
6a9737e8
|
m.geoffroy
|
* @see HomotypicalGroup
|
787 |
dce4c9cb
|
Andreas Müller
|
*/
|
788 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
789 |
dce4c9cb
|
Andreas Müller
|
public Set<SpecimenTypeDesignation> getSpecimenTypeDesignationsOfHomotypicalGroup() {
|
790 |
|
|
return this.getHomotypicalGroup().getSpecimenTypeDesignations();
|
791 |
|
|
}
|
792 |
|
|
|
793 |
|
|
//*********************** NAME TYPE DESIGNATION *********************************************//
|
794 |
|
|
|
795 |
|
|
/**
|
796 |
|
|
* Returns the set of {@link NameTypeDesignation name type designations} assigned
|
797 |
|
|
* to <i>this</i> taxon name the rank of which must be above "species".
|
798 |
|
|
* The name type designations include all the taxon names used to typify
|
799 |
d82717cb
|
m.geoffroy
|
* <i>this</i> taxon name and eventually the rejected or conserved status
|
800 |
dce4c9cb
|
Andreas Müller
|
* of these designations.
|
801 |
|
|
*
|
802 |
|
|
* @see NameTypeDesignation
|
803 |
|
|
* @see SpecimenTypeDesignation
|
804 |
|
|
*/
|
805 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
806 |
dce4c9cb
|
Andreas Müller
|
public Set<NameTypeDesignation> getNameTypeDesignations() {
|
807 |
|
|
Set<NameTypeDesignation> result = new HashSet<NameTypeDesignation>();
|
808 |
|
|
for (TypeDesignationBase typeDesignation : this.typeDesignations){
|
809 |
|
|
if (typeDesignation instanceof NameTypeDesignation){
|
810 |
|
|
result.add((NameTypeDesignation)typeDesignation);
|
811 |
c79406dd
|
n.hoffmann
|
}
|
812 |
|
|
}
|
813 |
dce4c9cb
|
Andreas Müller
|
return result;
|
814 |
c79406dd
|
n.hoffmann
|
}
|
815 |
ed85df08
|
Andreas Müller
|
|
816 |
|
|
/**
|
817 |
|
|
* Creates and adds a new {@link NameTypeDesignation name type designation}
|
818 |
09887ea6
|
m.geoffroy
|
* to <i>this</i> taxon name's set of type designations.
|
819 |
ed85df08
|
Andreas Müller
|
*
|
820 |
b9d0e8d2
|
m.geoffroy
|
* @param typeSpecies the taxon name to be used as type of <i>this</i> taxon name
|
821 |
ed85df08
|
Andreas Müller
|
* @param citation the reference for this new designation
|
822 |
|
|
* @param citationMicroReference the string with the details (generally pages) within the reference
|
823 |
7d954fd9
|
m.geoffroy
|
* @param originalNameString the taxon name string used in the reference to assert this designation
|
824 |
6a9737e8
|
m.geoffroy
|
* @param isRejectedType the boolean status for a rejected name type designation
|
825 |
|
|
* @param isConservedType the boolean status for a conserved name type designation
|
826 |
|
|
* @param isLectoType the boolean status for a lectotype name type designation
|
827 |
d82717cb
|
m.geoffroy
|
* @param isNotDesignated the boolean status for a name type designation without name type
|
828 |
|
|
* @param addToAllHomotypicNames the boolean indicating whether the name type designation should be
|
829 |
|
|
* added to all taxon names of the homotypical group this taxon name belongs to
|
830 |
ed85df08
|
Andreas Müller
|
* @see #getNameTypeDesignations()
|
831 |
6a9737e8
|
m.geoffroy
|
* @see NameTypeDesignation
|
832 |
57883822
|
m.geoffroy
|
* @see TypeDesignationBase#isNotDesignated()
|
833 |
ed85df08
|
Andreas Müller
|
*/
|
834 |
dce4c9cb
|
Andreas Müller
|
public void addNameTypeDesignation(TaxonNameBase typeSpecies,
|
835 |
|
|
ReferenceBase citation,
|
836 |
|
|
String citationMicroReference,
|
837 |
|
|
String originalNameString,
|
838 |
|
|
boolean isRejectedType,
|
839 |
|
|
boolean isConservedType,
|
840 |
|
|
boolean isLectoType,
|
841 |
|
|
boolean isNotDesignated,
|
842 |
|
|
boolean addToAllHomotypicNames) {
|
843 |
ec1f7873
|
Andreas Müller
|
NameTypeDesignation nameTypeDesignation = new NameTypeDesignation(typeSpecies, citation, citationMicroReference, originalNameString, isRejectedType, isConservedType, isLectoType, isNotDesignated);
|
844 |
168723a2
|
a.babadshanjan
|
nameTypeDesignation.setLectoType(isLectoType);
|
845 |
dce4c9cb
|
Andreas Müller
|
addTypeDesignation(nameTypeDesignation, addToAllHomotypicNames);
|
846 |
ed85df08
|
Andreas Müller
|
}
|
847 |
|
|
|
848 |
dce4c9cb
|
Andreas Müller
|
//*********************** SPECIMEN TYPE DESIGNATION *********************************************//
|
849 |
ed85df08
|
Andreas Müller
|
|
850 |
61106138
|
m.geoffroy
|
/**
|
851 |
|
|
* Returns the set of {@link SpecimenTypeDesignation specimen type designations}
|
852 |
b9d0e8d2
|
m.geoffroy
|
* that typify <i>this</i> taxon name.
|
853 |
ed85df08
|
Andreas Müller
|
*/
|
854 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
855 |
dce4c9cb
|
Andreas Müller
|
public Set<SpecimenTypeDesignation> getSpecimenTypeDesignations() {
|
856 |
|
|
Set<SpecimenTypeDesignation> result = new HashSet<SpecimenTypeDesignation>();
|
857 |
|
|
for (TypeDesignationBase typeDesignation : this.typeDesignations){
|
858 |
|
|
if (typeDesignation instanceof SpecimenTypeDesignation){
|
859 |
|
|
result.add((SpecimenTypeDesignation)typeDesignation);
|
860 |
|
|
}
|
861 |
|
|
}
|
862 |
|
|
return result;
|
863 |
66b77c3e
|
m.geoffroy
|
}
|
864 |
dce4c9cb
|
Andreas Müller
|
|
865 |
66b77c3e
|
m.geoffroy
|
|
866 |
79263e24
|
m.geoffroy
|
/**
|
867 |
d82717cb
|
m.geoffroy
|
* Creates and adds a new {@link SpecimenTypeDesignation specimen type designation}
|
868 |
09887ea6
|
m.geoffroy
|
* to <i>this</i> taxon name's set of type designations.
|
869 |
79263e24
|
m.geoffroy
|
*
|
870 |
d82717cb
|
m.geoffroy
|
* @param typeSpecimen the specimen to be used as a type for <i>this</i> taxon name
|
871 |
79263e24
|
m.geoffroy
|
* @param status the specimen type designation status
|
872 |
|
|
* @param citation the reference for this new specimen type designation
|
873 |
|
|
* @param citationMicroReference the string with the details (generally pages) within the reference
|
874 |
|
|
* @param originalNameString the taxon name used in the reference to assert this designation
|
875 |
57883822
|
m.geoffroy
|
* @param isNotDesignated the boolean status for a specimen type designation without specimen type
|
876 |
d82717cb
|
m.geoffroy
|
* @param addToAllHomotypicNames the boolean indicating whether the specimen type designation should be
|
877 |
|
|
* added to all taxon names of the homotypical group the typified
|
878 |
|
|
* taxon name belongs to
|
879 |
|
|
* @see #getSpecimenTypeDesignations()
|
880 |
2d4607f2
|
a.babadshanjan
|
* @see SpecimenTypeDesignationStatus
|
881 |
d82717cb
|
m.geoffroy
|
* @see SpecimenTypeDesignation
|
882 |
57883822
|
m.geoffroy
|
* @see TypeDesignationBase#isNotDesignated()
|
883 |
79263e24
|
m.geoffroy
|
*/
|
884 |
dce4c9cb
|
Andreas Müller
|
public void addSpecimenTypeDesignation(Specimen typeSpecimen,
|
885 |
2d4607f2
|
a.babadshanjan
|
SpecimenTypeDesignationStatus status,
|
886 |
dce4c9cb
|
Andreas Müller
|
ReferenceBase citation,
|
887 |
|
|
String citationMicroReference,
|
888 |
|
|
String originalNameString,
|
889 |
57883822
|
m.geoffroy
|
boolean isNotDesignated,
|
890 |
dce4c9cb
|
Andreas Müller
|
boolean addToAllHomotypicNames) {
|
891 |
57883822
|
m.geoffroy
|
SpecimenTypeDesignation specimenTypeDesignation = new SpecimenTypeDesignation(typeSpecimen, status, citation, citationMicroReference, originalNameString, isNotDesignated);
|
892 |
dce4c9cb
|
Andreas Müller
|
addTypeDesignation(specimenTypeDesignation, addToAllHomotypicNames);
|
893 |
9479da48
|
Andreas Müller
|
}
|
894 |
ed85df08
|
Andreas Müller
|
|
895 |
dce4c9cb
|
Andreas Müller
|
private boolean addTypeDesignation(TypeDesignationBase typeDesignation, boolean addToAllNames){
|
896 |
|
|
//at them moment typeDesignations are not persisted with the homotypical group
|
897 |
|
|
//so explicit adding to the homotypical group is not necessary.
|
898 |
|
|
if (typeDesignation != null){
|
899 |
|
|
this.typeDesignations.add(typeDesignation);
|
900 |
|
|
typeDesignation.addTypifiedName(this);
|
901 |
|
|
|
902 |
|
|
if (addToAllNames){
|
903 |
|
|
for (TaxonNameBase taxonName : this.getHomotypicalGroup().getTypifiedNames()){
|
904 |
|
|
if (taxonName != this){
|
905 |
|
|
taxonName.addTypeDesignation(typeDesignation, false);
|
906 |
|
|
}
|
907 |
|
|
}
|
908 |
|
|
}
|
909 |
|
|
}
|
910 |
|
|
return true;
|
911 |
ed85df08
|
Andreas Müller
|
}
|
912 |
dce4c9cb
|
Andreas Müller
|
|
913 |
ed85df08
|
Andreas Müller
|
|
914 |
dce4c9cb
|
Andreas Müller
|
|
915 |
|
|
//*********************** HOMOTYPICAL GROUP *********************************************//
|
916 |
9479da48
|
Andreas Müller
|
|
917 |
dce4c9cb
|
Andreas Müller
|
|
918 |
79263e24
|
m.geoffroy
|
/**
|
919 |
|
|
* Returns the {@link HomotypicalGroup homotypical group} to which
|
920 |
b9d0e8d2
|
m.geoffroy
|
* <i>this</i> taxon name belongs. A homotypical group represents all taxon names
|
921 |
d82717cb
|
m.geoffroy
|
* that share the same types.
|
922 |
79263e24
|
m.geoffroy
|
*
|
923 |
|
|
* @see HomotypicalGroup
|
924 |
|
|
*/
|
925 |
ee91bcd9
|
ben.clark
|
|
926 |
9479da48
|
Andreas Müller
|
public HomotypicalGroup getHomotypicalGroup() {
|
927 |
|
|
return homotypicalGroup;
|
928 |
|
|
}
|
929 |
ee91bcd9
|
ben.clark
|
|
930 |
|
|
/*
|
931 |
|
|
* @see #getHomotypicalGroup()
|
932 |
|
|
*/
|
933 |
|
|
protected void setHomotypicalGroup(HomotypicalGroup homotypicalGroup) {
|
934 |
|
|
this.homotypicalGroup = homotypicalGroup;
|
935 |
9479da48
|
Andreas Müller
|
}
|
936 |
|
|
|
937 |
dce4c9cb
|
Andreas Müller
|
// *************************************************************************//
|
938 |
|
|
|
939 |
b3262b1b
|
m.geoffroy
|
/**
|
940 |
|
|
* @see #getNomenclaturalReference()
|
941 |
|
|
*/
|
942 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
943 |
9479da48
|
Andreas Müller
|
public StrictReferenceBase getCitation(){
|
944 |
66b77c3e
|
m.geoffroy
|
//TODO What is the purpose of this method differing from the getNomenclaturalReference method?
|
945 |
c19dfdc5
|
Andreas Müller
|
logger.warn("getCitation not yet implemented");
|
946 |
9479da48
|
Andreas Müller
|
return null;
|
947 |
|
|
}
|
948 |
|
|
|
949 |
66b77c3e
|
m.geoffroy
|
/**
|
950 |
|
|
* Returns the complete string containing the
|
951 |
09887ea6
|
m.geoffroy
|
* {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference#getNomenclaturalCitation() nomenclatural reference citation}
|
952 |
|
|
* and the {@link #getNomenclaturalMicroReference() details} assigned to <i>this</i> taxon name.
|
953 |
66b77c3e
|
m.geoffroy
|
*
|
954 |
b9d0e8d2
|
m.geoffroy
|
* @return the string containing the nomenclatural reference of <i>this</i> taxon name
|
955 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.reference.INomenclaturalReference#getNomenclaturalCitation()
|
956 |
b3262b1b
|
m.geoffroy
|
* @see #getNomenclaturalReference()
|
957 |
|
|
* @see #getNomenclaturalMicroReference()
|
958 |
66b77c3e
|
m.geoffroy
|
*/
|
959 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
960 |
6680df00
|
Andreas Müller
|
@Deprecated
|
961 |
9479da48
|
Andreas Müller
|
public String getCitationString(){
|
962 |
c19dfdc5
|
Andreas Müller
|
logger.warn("getCitationString not yet implemented");
|
963 |
9479da48
|
Andreas Müller
|
return null;
|
964 |
|
|
}
|
965 |
|
|
|
966 |
09887ea6
|
m.geoffroy
|
/**
|
967 |
|
|
* Not yet implemented
|
968 |
|
|
*/
|
969 |
6680df00
|
Andreas Müller
|
@Deprecated
|
970 |
9479da48
|
Andreas Müller
|
public String[] getProblems(){
|
971 |
c19dfdc5
|
Andreas Müller
|
logger.warn("getProblems not yet implemented");
|
972 |
9479da48
|
Andreas Müller
|
return null;
|
973 |
|
|
}
|
974 |
|
|
|
975 |
|
|
/**
|
976 |
66b77c3e
|
m.geoffroy
|
* Returns the string containing the publication date (generally only year)
|
977 |
09887ea6
|
m.geoffroy
|
* of the {@link #getNomenclaturalReference() nomenclatural reference} for <i>this</i> taxon name, null if there is
|
978 |
b3262b1b
|
m.geoffroy
|
* no nomenclatural reference.
|
979 |
66b77c3e
|
m.geoffroy
|
*
|
980 |
b9d0e8d2
|
m.geoffroy
|
* @return the string containing the publication date of <i>this</i> taxon name
|
981 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.reference.INomenclaturalReference#getYear()
|
982 |
9479da48
|
Andreas Müller
|
*/
|
983 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
984 |
b0b7280d
|
Andreas Müller
|
public String getReferenceYear(){
|
985 |
|
|
if (this.getNomenclaturalReference() != null ){
|
986 |
|
|
return this.getNomenclaturalReference().getYear();
|
987 |
|
|
}else{
|
988 |
|
|
return null;
|
989 |
|
|
}
|
990 |
9479da48
|
Andreas Müller
|
}
|
991 |
|
|
|
992 |
66b77c3e
|
m.geoffroy
|
/**
|
993 |
09887ea6
|
m.geoffroy
|
* Returns the set of {@link eu.etaxonomy.cdm.model.taxon.TaxonBase taxon bases} that refer to <i>this</i> taxon name.
|
994 |
66b77c3e
|
m.geoffroy
|
* In this context a taxon base means the use of a taxon name by a reference
|
995 |
09887ea6
|
m.geoffroy
|
* either as a {@link eu.etaxonomy.cdm.model.taxon.Taxon taxon} ("accepted/correct" name) or
|
996 |
|
|
* as a (junior) {@link eu.etaxonomy.cdm.model.taxon.Synonym synonym}.
|
997 |
|
|
* A taxon name can be used by several distinct {@link eu.etaxonomy.cdm.model.reference.ReferenceBase references} but only once
|
998 |
66b77c3e
|
m.geoffroy
|
* within a taxonomic treatment (identified by one reference).
|
999 |
|
|
*
|
1000 |
|
|
* @see #getTaxa()
|
1001 |
|
|
* @see #getSynonyms()
|
1002 |
|
|
*/
|
1003 |
608eada2
|
Andreas Müller
|
public Set<TaxonBase> getTaxonBases() {
|
1004 |
|
|
return this.taxonBases;
|
1005 |
|
|
}
|
1006 |
ee91bcd9
|
ben.clark
|
|
1007 |
66b77c3e
|
m.geoffroy
|
/**
|
1008 |
09887ea6
|
m.geoffroy
|
* Adds a new {@link eu.etaxonomy.cdm.model.taxon.TaxonBase taxon base}
|
1009 |
b9d0e8d2
|
m.geoffroy
|
* to the set of taxon bases using <i>this</i> taxon name.
|
1010 |
66b77c3e
|
m.geoffroy
|
*
|
1011 |
|
|
* @param taxonBase the taxon base to be added
|
1012 |
|
|
* @see #getTaxonBases()
|
1013 |
61106138
|
m.geoffroy
|
* @see #removeTaxonBase(TaxonBase)
|
1014 |
66b77c3e
|
m.geoffroy
|
*/
|
1015 |
1cfc54ab
|
Andreas Müller
|
//TODO protected
|
1016 |
|
|
public void addTaxonBase(TaxonBase taxonBase){
|
1017 |
ee91bcd9
|
ben.clark
|
Method method = ReflectionUtils.findMethod(TaxonBase.class, "setName", new Class[] {TaxonNameBase.class});
|
1018 |
|
|
ReflectionUtils.makeAccessible(method);
|
1019 |
|
|
ReflectionUtils.invokeMethod(method, taxonBase, new Object[] {this});
|
1020 |
1cfc54ab
|
Andreas Müller
|
taxonBases.add(taxonBase);
|
1021 |
|
|
}
|
1022 |
b3262b1b
|
m.geoffroy
|
/**
|
1023 |
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.
|
1024 |
b3262b1b
|
m.geoffroy
|
*
|
1025 |
|
|
* @param taxonBase the taxon base which should be removed from the corresponding set
|
1026 |
09887ea6
|
m.geoffroy
|
* @see #getTaxonBases()
|
1027 |
b3262b1b
|
m.geoffroy
|
* @see #addTaxonBase(TaxonBase)
|
1028 |
|
|
*/
|
1029 |
c1c3a21a
|
Andreas Müller
|
public void removeTaxonBase(TaxonBase taxonBase){
|
1030 |
ee91bcd9
|
ben.clark
|
Method method = ReflectionUtils.findMethod(TaxonBase.class, "setName", new Class[] {TaxonNameBase.class});
|
1031 |
|
|
ReflectionUtils.makeAccessible(method);
|
1032 |
|
|
ReflectionUtils.invokeMethod(method, taxonBase, new Object[] {null});
|
1033 |
d163fbf6
|
Andreas Müller
|
taxonBases.remove(taxonBase);
|
1034 |
1cfc54ab
|
Andreas Müller
|
}
|
1035 |
|
|
|
1036 |
0d4d2092
|
m.doering
|
/**
|
1037 |
09887ea6
|
m.geoffroy
|
* Returns the set of {@link eu.etaxonomy.cdm.model.taxon.Taxon taxa} ("accepted/correct" names according to any
|
1038 |
b9d0e8d2
|
m.geoffroy
|
* reference) that are based on <i>this</i> taxon name. This set is a subset of
|
1039 |
66b77c3e
|
m.geoffroy
|
* the set returned by getTaxonBases().
|
1040 |
|
|
*
|
1041 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.taxon.Taxon
|
1042 |
66b77c3e
|
m.geoffroy
|
* @see #getTaxonBases()
|
1043 |
|
|
* @see #getSynonyms()
|
1044 |
0d4d2092
|
m.doering
|
*/
|
1045 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
1046 |
0d4d2092
|
m.doering
|
public Set<Taxon> getTaxa(){
|
1047 |
608eada2
|
Andreas Müller
|
Set<Taxon> result = new HashSet<Taxon>();
|
1048 |
|
|
for (TaxonBase taxonBase : this.taxonBases){
|
1049 |
|
|
if (taxonBase instanceof Taxon){
|
1050 |
|
|
result.add((Taxon)taxonBase);
|
1051 |
|
|
}
|
1052 |
|
|
}
|
1053 |
|
|
return result;
|
1054 |
0d4d2092
|
m.doering
|
}
|
1055 |
608eada2
|
Andreas Müller
|
|
1056 |
0d4d2092
|
m.doering
|
/**
|
1057 |
09887ea6
|
m.geoffroy
|
* Returns the set of {@link eu.etaxonomy.cdm.model.taxon.Synonym (junior) synonyms} (according to any
|
1058 |
b9d0e8d2
|
m.geoffroy
|
* reference) that are based on <i>this</i> taxon name. This set is a subset of
|
1059 |
66b77c3e
|
m.geoffroy
|
* the set returned by getTaxonBases().
|
1060 |
|
|
*
|
1061 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.taxon.Synonym
|
1062 |
66b77c3e
|
m.geoffroy
|
* @see #getTaxonBases()
|
1063 |
|
|
* @see #getTaxa()
|
1064 |
0d4d2092
|
m.doering
|
*/
|
1065 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
1066 |
608eada2
|
Andreas Müller
|
public Set<Synonym> getSynonyms() {
|
1067 |
|
|
Set<Synonym> result = new HashSet<Synonym>();
|
1068 |
|
|
for (TaxonBase taxonBase : this.taxonBases){
|
1069 |
|
|
if (taxonBase instanceof Synonym){
|
1070 |
|
|
result.add((Synonym)taxonBase);
|
1071 |
|
|
}
|
1072 |
|
|
}
|
1073 |
|
|
return result;
|
1074 |
0d4d2092
|
m.doering
|
}
|
1075 |
9118658f
|
m.doering
|
|
1076 |
71dcc146
|
Andreas Müller
|
|
1077 |
|
|
// *********** DESCRIPTIONS *************************************
|
1078 |
|
|
|
1079 |
0880a77c
|
m.geoffroy
|
/**
|
1080 |
09887ea6
|
m.geoffroy
|
* Returns the set of {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription taxon name descriptions} assigned
|
1081 |
b9d0e8d2
|
m.geoffroy
|
* to <i>this</i> taxon name. A taxon name description is a piece of information
|
1082 |
0880a77c
|
m.geoffroy
|
* concerning the taxon name like for instance the content of its first
|
1083 |
|
|
* publication (protolog) or a picture of this publication.
|
1084 |
|
|
*
|
1085 |
|
|
* @see #addDescription(TaxonNameDescription)
|
1086 |
|
|
* @see #removeDescription(TaxonNameDescription)
|
1087 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.description.TaxonNameDescription
|
1088 |
0880a77c
|
m.geoffroy
|
*/
|
1089 |
71dcc146
|
Andreas Müller
|
public Set<TaxonNameDescription> getDescriptions() {
|
1090 |
|
|
return descriptions;
|
1091 |
|
|
}
|
1092 |
ee91bcd9
|
ben.clark
|
|
1093 |
0880a77c
|
m.geoffroy
|
/**
|
1094 |
09887ea6
|
m.geoffroy
|
* Adds a new {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription taxon name description}
|
1095 |
b9d0e8d2
|
m.geoffroy
|
* to the set of taxon name descriptions assigned to <i>this</i> taxon name. The
|
1096 |
09887ea6
|
m.geoffroy
|
* content of the {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription#getTaxonName() taxonName attribute} of the
|
1097 |
b9d0e8d2
|
m.geoffroy
|
* taxon name description itself will be replaced with <i>this</i> taxon name.
|
1098 |
0880a77c
|
m.geoffroy
|
*
|
1099 |
|
|
* @param description the taxon name description to be added
|
1100 |
|
|
* @see #getDescriptions()
|
1101 |
|
|
* @see #removeDescription(TaxonNameDescription)
|
1102 |
71dcc146
|
Andreas Müller
|
*/
|
1103 |
|
|
public void addDescription(TaxonNameDescription description) {
|
1104 |
fd7ee7b1
|
ben.clark
|
java.lang.reflect.Field field = ReflectionUtils.findField(TaxonNameDescription.class, "taxonName", TaxonNameBase.class);
|
1105 |
c49c125c
|
Andreas Müller
|
ReflectionUtils.makeAccessible(field);
|
1106 |
|
|
ReflectionUtils.setField(field, description, this);
|
1107 |
71dcc146
|
Andreas Müller
|
descriptions.add(description);
|
1108 |
|
|
}
|
1109 |
0880a77c
|
m.geoffroy
|
/**
|
1110 |
09887ea6
|
m.geoffroy
|
* Removes one element from the set of {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription taxon name descriptions} assigned
|
1111 |
|
|
* to <i>this</i> taxon name. The content of the {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription#getTaxonName() taxonName attribute}
|
1112 |
0880a77c
|
m.geoffroy
|
* of the description itself will be set to "null".
|
1113 |
|
|
*
|
1114 |
|
|
* @param description the taxon name description which should be removed
|
1115 |
|
|
* @see #getDescriptions()
|
1116 |
|
|
* @see #addDescription(TaxonNameDescription)
|
1117 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.description.TaxonNameDescription#getTaxonName()
|
1118 |
0880a77c
|
m.geoffroy
|
*/
|
1119 |
71dcc146
|
Andreas Müller
|
public void removeDescription(TaxonNameDescription description) {
|
1120 |
fd7ee7b1
|
ben.clark
|
java.lang.reflect.Field field = ReflectionUtils.findField(TaxonNameDescription.class, "taxonName", TaxonNameBase.class);
|
1121 |
c49c125c
|
Andreas Müller
|
ReflectionUtils.makeAccessible(field);
|
1122 |
|
|
ReflectionUtils.setField(field, description, null);
|
1123 |
71dcc146
|
Andreas Müller
|
descriptions.remove(description);
|
1124 |
|
|
}
|
1125 |
|
|
|
1126 |
95449e99
|
Andreas Müller
|
// ***********
|
1127 |
66b77c3e
|
m.geoffroy
|
/**
|
1128 |
|
|
* Returns the boolean value indicating whether a given taxon name belongs
|
1129 |
b9d0e8d2
|
m.geoffroy
|
* to the same {@link HomotypicalGroup homotypical group} as <i>this</i> taxon name (true)
|
1130 |
66b77c3e
|
m.geoffroy
|
* or not (false). Returns "true" only if the homotypical groups of both
|
1131 |
|
|
* taxon names exist and if they are identical.
|
1132 |
|
|
*
|
1133 |
|
|
* @param homoTypicName the taxon name the homotypical group of which is to be checked
|
1134 |
|
|
* @return the boolean value of the check
|
1135 |
|
|
* @see HomotypicalGroup
|
1136 |
|
|
*/
|
1137 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
1138 |
95449e99
|
Andreas Müller
|
public boolean isHomotypic(TaxonNameBase homoTypicName) {
|
1139 |
|
|
if (homoTypicName == null) {
|
1140 |
|
|
return false;
|
1141 |
|
|
}
|
1142 |
|
|
HomotypicalGroup homotypicGroup = homoTypicName.getHomotypicalGroup();
|
1143 |
|
|
if (homotypicGroup == null || this.getHomotypicalGroup() == null) {
|
1144 |
|
|
return false;
|
1145 |
|
|
}
|
1146 |
|
|
if (homotypicGroup.equals(this.getHomotypicalGroup())) {
|
1147 |
|
|
return true;
|
1148 |
|
|
}
|
1149 |
|
|
return false;
|
1150 |
|
|
}
|
1151 |
|
|
|
1152 |
|
|
//********* Rank comparison shortcuts ********************//
|
1153 |
4cc4f6f7
|
m.geoffroy
|
/**
|
1154 |
b9d0e8d2
|
m.geoffroy
|
* Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
|
1155 |
4cc4f6f7
|
m.geoffroy
|
* taxon name is higher than the genus rank (true) or not (false).
|
1156 |
|
|
* Suprageneric non viral names are monomials.
|
1157 |
bef42c31
|
Andreas Müller
|
* Returns false if rank is null.
|
1158 |
4cc4f6f7
|
m.geoffroy
|
*
|
1159 |
|
|
* @see #isGenus()
|
1160 |
|
|
* @see #isInfraGeneric()
|
1161 |
|
|
* @see #isSpecies()
|
1162 |
|
|
* @see #isInfraSpecific()
|
1163 |
|
|
*/
|
1164 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
1165 |
451c6005
|
m.doering
|
public boolean isSupraGeneric() {
|
1166 |
bef42c31
|
Andreas Müller
|
if (rank == null){
|
1167 |
|
|
return false;
|
1168 |
|
|
}
|
1169 |
451c6005
|
m.doering
|
return getRank().isSupraGeneric();
|
1170 |
|
|
}
|
1171 |
4cc4f6f7
|
m.geoffroy
|
/**
|
1172 |
b9d0e8d2
|
m.geoffroy
|
* Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
|
1173 |
4cc4f6f7
|
m.geoffroy
|
* taxon name is the genus rank (true) or not (false). Non viral names with
|
1174 |
10a54497
|
m.geoffroy
|
* genus rank are monomials. Returns false if rank is null.
|
1175 |
4cc4f6f7
|
m.geoffroy
|
*
|
1176 |
|
|
* @see #isSupraGeneric()
|
1177 |
|
|
* @see #isInfraGeneric()
|
1178 |
|
|
* @see #isSpecies()
|
1179 |
|
|
* @see #isInfraSpecific()
|
1180 |
|
|
*/
|
1181 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
1182 |
451c6005
|
m.doering
|
public boolean isGenus() {
|
1183 |
bef42c31
|
Andreas Müller
|
if (rank == null){
|
1184 |
|
|
return false;
|
1185 |
|
|
}
|
1186 |
451c6005
|
m.doering
|
return getRank().isGenus();
|
1187 |
|
|
}
|
1188 |
4cc4f6f7
|
m.geoffroy
|
/**
|
1189 |
b9d0e8d2
|
m.geoffroy
|
* Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
|
1190 |
10a54497
|
m.geoffroy
|
* taxon name is higher than the species rank and lower than the
|
1191 |
|
|
* genus rank (true) or not (false). Infrageneric non viral names are
|
1192 |
|
|
* binomials. Returns false if rank is null.
|
1193 |
4cc4f6f7
|
m.geoffroy
|
*
|
1194 |
|
|
* @see #isSupraGeneric()
|
1195 |
|
|
* @see #isGenus()
|
1196 |
|
|
* @see #isSpecies()
|
1197 |
|
|
* @see #isInfraSpecific()
|
1198 |
|
|
*/
|
1199 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
1200 |
451c6005
|
m.doering
|
public boolean isInfraGeneric() {
|
1201 |
bef42c31
|
Andreas Müller
|
if (rank == null){
|
1202 |
|
|
return false;
|
1203 |
|
|
}
|
1204 |
451c6005
|
m.doering
|
return getRank().isInfraGeneric();
|
1205 |
|
|
}
|
1206 |
4cc4f6f7
|
m.geoffroy
|
/**
|
1207 |
b9d0e8d2
|
m.geoffroy
|
* Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
|
1208 |
10a54497
|
m.geoffroy
|
* taxon name is the species rank (true) or not (false). Non viral names
|
1209 |
4cc4f6f7
|
m.geoffroy
|
* with species rank are binomials.
|
1210 |
bef42c31
|
Andreas Müller
|
* Returns false if rank is null.
|
1211 |
4cc4f6f7
|
m.geoffroy
|
*
|
1212 |
|
|
* @see #isSupraGeneric()
|
1213 |
|
|
* @see #isGenus()
|
1214 |
|
|
* @see #isInfraGeneric()
|
1215 |
|
|
* @see #isInfraSpecific()
|
1216 |
|
|
*/
|
1217 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
1218 |
451c6005
|
m.doering
|
public boolean isSpecies() {
|
1219 |
bef42c31
|
Andreas Müller
|
if (rank == null){
|
1220 |
|
|
return false;
|
1221 |
|
|
}
|
1222 |
451c6005
|
m.doering
|
return getRank().isSpecies();
|
1223 |
|
|
}
|
1224 |
4cc4f6f7
|
m.geoffroy
|
/**
|
1225 |
b9d0e8d2
|
m.geoffroy
|
* Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
|
1226 |
4cc4f6f7
|
m.geoffroy
|
* taxon name is lower than the species rank (true) or not (false).
|
1227 |
|
|
* Infraspecific non viral names are trinomials.
|
1228 |
bef42c31
|
Andreas Müller
|
* Returns false if rank is null.
|
1229 |
4cc4f6f7
|
m.geoffroy
|
*
|
1230 |
|
|
* @see #isSupraGeneric()
|
1231 |
|
|
* @see #isGenus()
|
1232 |
|
|
* @see #isInfraGeneric()
|
1233 |
|
|
* @see #isSpecies()
|
1234 |
|
|
*/
|
1235 |
b70a7f94
|
Andreas Kohlbecker
|
@Transient
|
1236 |
451c6005
|
m.doering
|
public boolean isInfraSpecific() {
|
1237 |
bef42c31
|
Andreas Müller
|
if (rank == null){
|
1238 |
|
|
return false;
|
1239 |
|
|
}
|
1240 |
451c6005
|
m.doering
|
return getRank().isInfraSpecific();
|
1241 |
|
|
}
|
1242 |
5c19d7f0
|
Andreas Müller
|
|
1243 |
7ebeb288
|
Andreas Müller
|
|
1244 |
4cc4f6f7
|
m.geoffroy
|
/**
|
1245 |
eb7e638a
|
m.geoffroy
|
* Returns null as the {@link NomenclaturalCode nomenclatural code} that governs
|
1246 |
b9d0e8d2
|
m.geoffroy
|
* the construction of <i>this</i> taxon name since there is no specific
|
1247 |
eb7e638a
|
m.geoffroy
|
* nomenclatural code defined. The real implementention takes place in the
|
1248 |
|
|
* subclasses {@link ViralName ViralName}, {@link BacterialName BacterialName},
|
1249 |
|
|
* {@link BotanicalName BotanicalName}, {@link CultivarPlantName CultivarPlantName} and
|
1250 |
|
|
* {@link ZoologicalName ZoologicalName}. Each taxon name is governed by one
|
1251 |
4cc4f6f7
|
m.geoffroy
|
* and only one nomenclatural code.
|
1252 |
|
|
*
|
1253 |
eb7e638a
|
m.geoffroy
|
* @return null
|
1254 |
b3262b1b
|
m.geoffroy
|
* @see #isCodeCompliant()
|
1255 |
|
|
* @see #getHasProblem()
|
1256 |
4cc4f6f7
|
m.geoffroy
|
*/
|
1257 |
bef42c31
|
Andreas Müller
|
abstract public NomenclaturalCode getNomenclaturalCode();
|
1258 |
d50a2c5d
|
Andreas Müller
|
/* (non-Javadoc)
|
1259 |
|
|
* @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()
|
1260 |
|
|
*/
|
1261 |
b3262b1b
|
m.geoffroy
|
/**
|
1262 |
b9d0e8d2
|
m.geoffroy
|
* Generates and returns the string with the scientific name of <i>this</i>
|
1263 |
7e759003
|
m.geoffroy
|
* taxon name (only non viral taxon names can be generated from their
|
1264 |
|
|
* components). This string may be stored in the inherited
|
1265 |
09887ea6
|
m.geoffroy
|
* {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache() titleCache} attribute.
|
1266 |
b3262b1b
|
m.geoffroy
|
* This method overrides the generic and inherited
|
1267 |
09887ea6
|
m.geoffroy
|
* {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle() method} from
|
1268 |
|
|
* {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity IdentifiableEntity}.
|
1269 |
b3262b1b
|
m.geoffroy
|
*
|
1270 |
|
|
* @return the string with the composed name of this non viral taxon name with authorship (and maybe year)
|
1271 |
09887ea6
|
m.geoffroy
|
* @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()
|
1272 |
|
|
* @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache()
|
1273 |
b3262b1b
|
m.geoffroy
|
*/
|
1274 |
d50a2c5d
|
Andreas Müller
|
@Override
|
1275 |
|
|
public String generateTitle() {
|
1276 |
|
|
// TODO Auto-generated method stub
|
1277 |
788ff862
|
Andreas Müller
|
logger.warn("not yet implemented");
|
1278 |
d50a2c5d
|
Andreas Müller
|
return null;
|
1279 |
ee91bcd9
|
ben.clark
|
}
|
1280 |
dadf5cd0
|
Andreas Kohlbecker
|
}
|