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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.model.taxon;
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import java.lang.reflect.Method;
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import java.util.List;
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import javax.persistence.Entity;
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import javax.persistence.FetchType;
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import javax.persistence.Index;
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import javax.persistence.ManyToOne;
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import javax.persistence.OneToOne;
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import javax.persistence.Table;
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import javax.persistence.Transient;
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import javax.validation.constraints.NotNull;
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import javax.xml.bind.annotation.XmlAccessType;
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import javax.xml.bind.annotation.XmlAccessorType;
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import javax.xml.bind.annotation.XmlAttribute;
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import javax.xml.bind.annotation.XmlElement;
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import javax.xml.bind.annotation.XmlIDREF;
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import javax.xml.bind.annotation.XmlSchemaType;
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import javax.xml.bind.annotation.XmlType;
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import org.apache.log4j.Logger;
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import org.hibernate.annotations.Cascade;
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import org.hibernate.annotations.CascadeType;
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import org.hibernate.envers.Audited;
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import org.hibernate.search.annotations.Analyze;
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import org.hibernate.search.annotations.ClassBridge;
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import org.hibernate.search.annotations.ClassBridges;
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import org.hibernate.search.annotations.Field;
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import org.hibernate.search.annotations.FieldBridge;
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import org.hibernate.search.annotations.IndexedEmbedded;
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import org.hibernate.search.annotations.Store;
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import org.hibernate.search.bridge.builtin.BooleanBridge;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.compare.taxon.TaxonComparator;
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import eu.etaxonomy.cdm.compare.taxon.TaxonNodeByNameComparator;
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import eu.etaxonomy.cdm.compare.taxon.TaxonNodeByRankAndNameComparator;
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import eu.etaxonomy.cdm.compare.taxon.TaxonNodeNaturalComparator;
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import eu.etaxonomy.cdm.hibernate.search.AcceptedTaxonBridge;
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import eu.etaxonomy.cdm.hibernate.search.ClassInfoBridge;
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import eu.etaxonomy.cdm.model.common.IIntextReferenceTarget;
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import eu.etaxonomy.cdm.model.common.IPublishable;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.ITaxonNameBase;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.strategy.cache.TaggedText;
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import eu.etaxonomy.cdm.strategy.cache.name.CacheUpdate;
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import eu.etaxonomy.cdm.strategy.cache.taxon.ITaxonCacheStrategy;
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import eu.etaxonomy.cdm.strategy.cache.taxon.TaxonBaseDefaultCacheStrategy;
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import eu.etaxonomy.cdm.validation.Level2;
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import eu.etaxonomy.cdm.validation.Level3;
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import eu.etaxonomy.cdm.validation.annotation.TaxonNameCannotBeAcceptedAndSynonym;
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/**
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* The upmost (abstract) class for the use of a {@link eu.etaxonomy.cdm.model.name.TaxonName taxon name} in a {@link eu.etaxonomy.cdm.model.reference.Reference reference}
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* or within a taxonomic view/treatment either as a {@link Taxon taxon}
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* ("accepted" respectively "correct" name) or as a (junior) {@link Synonym synonym}.
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* Within a taxonomic view/treatment or a reference a taxon name can be used
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* only in one of both described meanings. The reference using the taxon name
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* is generally cited with "sec." (secundum, sensu). For instance:
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* "<i>Juncus longirostris</i> Kuvaev sec. Kirschner, J. et al. 2002".
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* <P>
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* This class corresponds to: <ul>
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* <li> TaxonConcept according to the TDWG ontology
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* <li> TaxonConcept according to the TCS
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* </ul>
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*
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* @author m.doering
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* @since 08-Nov-2007 13:06:56
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "TaxonBase", propOrder = {
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"name",
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"secSource",
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"doubtful",
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"appendedPhrase",
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"useNameCache",
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"publish"
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})
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@Entity
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@Audited
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//@PreFilter("hasPermission(filterObject, 'edit')")
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@Table(name="TaxonBase", indexes = { @Index(name = "taxonBaseTitleCacheIndex", columnList = "titleCache") })
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@TaxonNameCannotBeAcceptedAndSynonym(groups = Level3.class)
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@ClassBridges({
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@ClassBridge(name="classInfo",
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index = org.hibernate.search.annotations.Index.YES,
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store = Store.YES,
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impl = ClassInfoBridge.class),
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@ClassBridge(name=AcceptedTaxonBridge.ACC_TAXON, // TODO rename to acceptedTaxon, since we are usually not using abbreviations for field names, see also ACC_TAXON_BRIDGE_PREFIX
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index = org.hibernate.search.annotations.Index.YES,
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store = Store.YES,
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impl = AcceptedTaxonBridge.class),
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@ClassBridge(impl = eu.etaxonomy.cdm.hibernate.search.NomenclaturalSortOrderBrigde.class)
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})
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public abstract class TaxonBase<S extends ITaxonCacheStrategy>
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extends IdentifiableEntity<S>
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implements IPublishable, IIntextReferenceTarget{
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private static final long serialVersionUID = -3589185949928938529L;
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private static final Logger logger = Logger.getLogger(TaxonBase.class);
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public static final String ACC_TAXON_BRIDGE_PREFIX = "accTaxon";
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private static Method methodTaxonNameAddTaxonBase;
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static {
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try {
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methodTaxonNameAddTaxonBase = TaxonName.class.getDeclaredMethod("addTaxonBase", TaxonBase.class);
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methodTaxonNameAddTaxonBase.setAccessible(true);
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} catch (Exception e) {
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logger.error(e);
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for(StackTraceElement ste : e.getStackTrace()) {
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logger.error(ste);
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}
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}
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}
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//The assignment to the Taxon or to the Synonym class is not definitive
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@XmlAttribute(name = "isDoubtful")
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private boolean doubtful;
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@XmlElement(name = "Name")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToOne(fetch = FetchType.LAZY)
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@IndexedEmbedded(includeEmbeddedObjectId=true)
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@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
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@NotNull(groups = Level2.class)
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private TaxonName name;
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//#9327
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@XmlElement(name = "SecSource")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@OneToOne(fetch = FetchType.LAZY, orphanRemoval=true, mappedBy="sourcedTaxon")
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@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE,CascadeType.DELETE})
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@CacheUpdate(noUpdate ="titleCache")
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@IndexedEmbedded
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private SecundumSource secSource;
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@XmlElement(name = "AppendedPhrase")
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private String appendedPhrase;
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@XmlAttribute(name= "UseNameCache")
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private boolean useNameCache = false;
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@XmlAttribute(name = "publish")
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@Field(analyze = Analyze.NO, store = Store.YES, bridge= @FieldBridge(impl=BooleanBridge.class))
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private boolean publish = true;
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// ************* CONSTRUCTORS *************/
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/**
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* Class constructor: creates a new empty (abstract) taxon.
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*
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* @see #TaxonBase(TaxonName, Reference)
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*/
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protected TaxonBase(){
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super();
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}
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/**
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* Class constructor: creates a new (abstract) taxon with the
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* {@link eu.etaxonomy.cdm.model.name.TaxonName taxon name} used and the {@link eu.etaxonomy.cdm.model.reference.Reference reference}
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* using it.
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*
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* @param taxonName the taxon name used
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* @param sec the reference using the taxon name
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* @see #TaxonBase()
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*/
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protected TaxonBase(TaxonName taxonName, Reference sec, String secDetail){
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super();
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if (taxonName != null){
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this.invokeSetMethod(methodTaxonNameAddTaxonBase, taxonName);
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}
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this.setSec(sec);
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this.setSecMicroReference(secDetail);
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}
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@Override
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protected void initDefaultCacheStrategy() {
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this.cacheStrategy = (S)new TaxonBaseDefaultCacheStrategy();
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}
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//********* METHODS **************************************/
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@Transient
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public List<TaggedText> getTaggedTitle(){
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return getCacheStrategy().getTaggedTitle(this);
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}
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/**
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* Returns the {@link TaxonName taxon name} used in <i>this</i> (abstract) taxon.
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*/
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public TaxonName getName(){
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return this.name;
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}
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public void setName(TaxonName name) {
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if (this.name != null){
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this.name.getTaxonBases().remove(this);
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}
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if(name != null) {
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name.getTaxonBases().add(this);
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}
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this.name = name;
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}
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/**
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* Returns the {@link eu.etaxonomy.cdm.model.name.HomotypicalGroup homotypical group} of the
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* {@link eu.etaxonomy.cdm.model.name.TaxonName taxon name} used in <i>this</i> (abstract) taxon.
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*/
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@Transient
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public HomotypicalGroup getHomotypicGroup(){
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if (this.getName() == null){
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return null;
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}else{
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return this.getName().getHomotypicalGroup();
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}
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}
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/**
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* Returns the boolean value indicating whether the assignment of <i>this</i>
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* (abstract) taxon to the {@link Taxon Taxon} or to the {@link Synonym Synonym} class
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* is definitive (false) or not (true). If this flag is set the use of <i>this</i> (abstract)
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* taxon as an "accepted/correct" name or as a (junior) "synonym" might
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* still change in the course of taxonomical working process.
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*/
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public boolean isDoubtful(){
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return this.doubtful;
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}
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/**
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* @see #isDoubtful()
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*/
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public void setDoubtful(boolean doubtful){
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this.doubtful = doubtful;
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}
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/**
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* Returns the boolean value indicating if this taxon should be withheld (<code>publish=false</code>) or not
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* (<code>publish=true</code>) during any publication process to the general public.
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* This publish flag implementation is preliminary and may be replaced by a more general
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* implementation of READ rights in future.<BR>
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* The default value is <code>true</code>.
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*/
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@Override
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public boolean isPublish() {
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return publish;
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}
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@Override
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public void setPublish(boolean publish) {
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this.publish = publish;
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}
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//*************** sec source *******************/
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public SecundumSource getSecSource(){
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return this.secSource;
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}
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protected DescriptionElementSource getSecSource(boolean createIfNotExist){
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if (this.secSource == null && createIfNotExist){
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setSecSource(SecundumSource.NewSecundumInstance(this));
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}
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return secSource;
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}
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public void setSecSource(SecundumSource secSource) throws IllegalArgumentException {
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//check state
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if (secSource != null && !OriginalSourceType.SecundumReference.equals(secSource.getType())
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){
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throw new IllegalArgumentException("Secundum source must be of type " + OriginalSourceType.SecundumReference.getLabel());
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}
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this.secSource = secSource;
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if (secSource != null && secSource.getSourcedTaxon() != this){
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secSource.setSourcedTaxon(this);
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}
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}
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@Transient
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public Reference getSec(){
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return this.secSource == null? null:this.secSource.getCitation();
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}
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@Transient
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public void setSec(Reference secReference){
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if (secReference == null && this.getSecSource()==null){
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return;
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}else{
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getSecSource(true).setCitation(secReference);
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}
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}
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/**
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* Returns the details string of the {@link #getSec() sec reference} assigned
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* to <i>this</i> taxon base. The details describe the exact localisation within
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* the publication used as sec reference. These are mostly
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* (implicitly) pages but can also be figures or tables or any other
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* element of a publication. A sec micro reference (details)
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* requires the existence of a sec reference.
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*/
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@Transient
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public String getSecMicroReference(){
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return this.secSource == null? null: this.secSource.getCitationMicroReference();
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}
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/**
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* @see #getSecMicroReference()
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*/
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public void setSecMicroReference(String secMicroReference){
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secMicroReference = isBlank(secMicroReference)? null : secMicroReference;
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if (secMicroReference == null && this.getSecSource()==null){
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return;
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}else{
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this.getSecSource(true).setCitationMicroReference(secMicroReference);
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}
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}
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/**
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* Checks if the source is completely empty and if empty removes it from the name.
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*/
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//TODO maybe this should be moved to a hibernate listener, but the listener solution may
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//work only for sec single sources as they are the only which are bidirectional
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protected void checkNullSource() {
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if (this.secSource != null && this.secSource.checkEmpty(true)){
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this.secSource = null;
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}
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}
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// *********************************************
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/**
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* An appended phrase is a phrase that is added to the {@link eu.etaxonomy.cdm.model.name.TaxonName taxon name}
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* 's title cache to be used just in this taxon. E.g. the phrase "sensu latu" may be added
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* to the name to describe this taxon more precisely.
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* If {@link #isUseNameCache()}
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* @return the appendedPhrase
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*/
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public String getAppendedPhrase() {
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return appendedPhrase;
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}
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/**
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* @param appendedPhrase the appendedPhrase to set
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*/
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public void setAppendedPhrase(String appendedPhrase) {
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this.appendedPhrase = appendedPhrase;
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}
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/**
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* @return the useNameCache
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*/
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public boolean isUseNameCache() {
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return useNameCache;
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}
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/**
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* @param useNameCache the useNameCache to set
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*/
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public void setUseNameCache(boolean useNameCache) {
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this.useNameCache = useNameCache;
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}
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/**
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* Returns <code>true</code> if <code>this</code>
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* taxon base is not part of any classification.
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* False otherwise
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* @return boolean
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*/
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@Transient
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public abstract boolean isOrphaned();
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/**
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* @return
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*/
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@Transient
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public Rank getNullSafeRank() {
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return name == null ? null : name.getRank();
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}
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/**
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* This method compares 2 taxa on it's name titles and caches.
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* If both are equal it compares on the secundum titleCache as well.
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* It is not fully clear/defined how this method relates to
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* explicit comparators like {@link TaxonComparator}. The later
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* currently uses this method.
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* Historically it was a compareTo method in {@link IdentifiableEntity}
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* but did not fulfill the {@link Comparable} contract.
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* <BR><BR>
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* {@link https://dev.e-taxonomy.eu/redmine/issues/922}<BR>
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* {@link https://dev.e-taxonomy.eu/redmine/issues/6311}
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*
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* @see ITaxonNameBase#compareToName(TaxonName)
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* @see TaxonComparator
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* @see TaxonNodeNaturalComparator
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* @see TaxonNodeByNameComparator
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* @see TaxonNodeByRankAndNameComparator
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* @param otherTaxon
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416
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* @return the compareTo result similar to {@link Comparable#compareTo(Object)}
|
417
|
* @throws NullPointerException if otherTaxon is <code>null</code>
|
418
|
*/
|
419
|
//TODO handling of protected titleCache
|
420
|
public int compareToTaxon(TaxonBase otherTaxon){
|
421
|
|
422
|
int result = 0;
|
423
|
|
424
|
if (otherTaxon == null) {
|
425
|
throw new NullPointerException("Cannot compare to null.");
|
426
|
}
|
427
|
|
428
|
otherTaxon = deproxy(otherTaxon);
|
429
|
|
430
|
TaxonName otherName = deproxy(otherTaxon.getName());
|
431
|
ITaxonNameBase thisName = this.getName();
|
432
|
if ((otherName == null || thisName == null)){
|
433
|
if (otherName != thisName){
|
434
|
result = thisName == null ? -1 : 1;
|
435
|
}
|
436
|
}else{
|
437
|
result = thisName.compareToName(otherName);
|
438
|
}
|
439
|
|
440
|
if (result == 0){
|
441
|
String otherReferenceTitleCache = "";
|
442
|
String thisReferenceTitleCache = "";
|
443
|
|
444
|
Reference otherRef = deproxy(otherTaxon.getSec());
|
445
|
if (otherRef != null) {
|
446
|
otherReferenceTitleCache = otherRef.getTitleCache();
|
447
|
}
|
448
|
Reference thisRef = deproxy(this.getSec());
|
449
|
if (thisRef != null) {
|
450
|
thisReferenceTitleCache = thisRef.getTitleCache();
|
451
|
}
|
452
|
if ((CdmUtils.isNotBlank(otherReferenceTitleCache) || CdmUtils.isNotBlank(thisReferenceTitleCache))) {
|
453
|
result = thisReferenceTitleCache.compareTo(otherReferenceTitleCache);
|
454
|
}
|
455
|
}
|
456
|
|
457
|
return result;
|
458
|
}
|
459
|
|
460
|
//*********************** CLONE ********************************************************/
|
461
|
|
462
|
/**
|
463
|
* Clones <i>this</i> taxon. This is a shortcut that enables to create
|
464
|
* a new instance with exactly the same taxon name and sec reference.
|
465
|
*
|
466
|
* @see java.lang.Object#clone()
|
467
|
*/
|
468
|
@Override
|
469
|
public TaxonBase<S> clone() {
|
470
|
TaxonBase<S> result;
|
471
|
try {
|
472
|
result = (TaxonBase<S>)super.clone();
|
473
|
|
474
|
// result.setSec(null);
|
475
|
|
476
|
return result;
|
477
|
} catch (CloneNotSupportedException e) {
|
478
|
logger.warn("Object does not implement cloneable");
|
479
|
e.printStackTrace();
|
480
|
return null;
|
481
|
}
|
482
|
}
|
483
|
}
|