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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.description;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import javax.persistence.Entity;
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import javax.persistence.FetchType;
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import javax.persistence.Inheritance;
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import javax.persistence.InheritanceType;
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import javax.persistence.JoinTable;
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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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import javax.persistence.Transient;
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import javax.xml.bind.annotation.XmlAccessType;
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import javax.xml.bind.annotation.XmlAccessorType;
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import javax.xml.bind.annotation.XmlElement;
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import javax.xml.bind.annotation.XmlElementWrapper;
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import javax.xml.bind.annotation.XmlIDREF;
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import javax.xml.bind.annotation.XmlSchemaType;
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import javax.xml.bind.annotation.XmlType;
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import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
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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.IndexColumn;
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import org.hibernate.envers.Audited;
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import org.hibernate.search.annotations.IndexedEmbedded;
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import eu.etaxonomy.cdm.jaxb.MultilanguageTextAdapter;
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import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.common.ISourceable;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.LanguageString;
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import eu.etaxonomy.cdm.model.common.MultilanguageText;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.strategy.merge.Merge;
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import eu.etaxonomy.cdm.strategy.merge.MergeMode;
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/**
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* The upmost (abstract) class for a piece of information) about
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* a {@link SpecimenOrObservationBase specimen}, a {@link Taxon taxon} or even a {@link TaxonNameBase taxon name}.
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* A concrete description element assigns descriptive data to one {@link Feature feature}.<BR>
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* Experts use the word feature for the property itself but not for the actual
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* description element. Therefore naming this class FeatureBase would have
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* leaded to confusion.
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* <P>
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* This class corresponds to: <ul>
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* <li> DescriptionsBaseType according to the the SDD schema
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* <li> InfoItem according to the TDWG ontology
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* <li> MeasurementOrFactAtomised according to the ABCD schema
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* </ul>
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*
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* @author m.doering
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* @version 1.0
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* @created 08-Nov-2007 13:06:24
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "DescriptionElementBase", propOrder = {
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"feature",
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"modifiers",
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"modifyingText",
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"media",
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"inDescription",
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"sources"
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})
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@Entity
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@Audited
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@Inheritance(strategy=InheritanceType.SINGLE_TABLE)
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public abstract class DescriptionElementBase extends AnnotatableEntity implements ISourceable<DescriptionElementSource> {
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private static final long serialVersionUID = 5000910777835755905L;
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(DescriptionElementBase.class);
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//type, category of information. In structured descriptions characters
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@XmlElement(name = "Feature")
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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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@Cascade(CascadeType.MERGE)
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@IndexedEmbedded
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private Feature feature;
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@XmlElementWrapper(name = "Modifiers")
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@XmlElement(name = "Modifier")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToMany(fetch = FetchType.LAZY)
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@JoinTable(name="DescriptionElementBase_Modifier")
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private Set<Modifier> modifiers = new HashSet<Modifier>();
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@XmlElement(name = "ModifyingText")
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@XmlJavaTypeAdapter(MultilanguageTextAdapter.class)
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@OneToMany(fetch = FetchType.LAZY)
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@JoinTable(name = "DescriptionElementBase_ModifyingText")
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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private Map<Language,LanguageString> modifyingText = new HashMap<Language,LanguageString>();
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@XmlElementWrapper(name = "Media")
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@XmlElement(name = "Medium")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToMany(fetch = FetchType.LAZY)
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@IndexColumn(name="sortIndex", base = 0)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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private List<Media> media = new ArrayList<Media>();
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@XmlElement(name = "InDescription")
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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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@IndexedEmbedded
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private DescriptionBase inDescription;
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@XmlElementWrapper(name = "Sources")
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@XmlElement(name = "DescriptionElementSource")
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@OneToMany(fetch = FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE, CascadeType.DELETE_ORPHAN})
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@Merge(MergeMode.ADD_CLONE)
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private Set<DescriptionElementSource> sources = new HashSet<DescriptionElementSource>();
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// ************* CONSTRUCTORS *************/
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/**
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* Class constructor: creates a new empty description element instance.
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*
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* @see #DescriptionElementBase(Feature)
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*/
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protected DescriptionElementBase(){
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}
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/**
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* Class constructor: creates a new description element instance with the
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* given {@link Feature feature} that is described or measured.
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*
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* @param feature the feature described or measured
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* @see #DescriptionElementBase()
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*/
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protected DescriptionElementBase(Feature feature){
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if (feature == null){
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feature = Feature.UNKNOWN();
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}
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this.feature = feature;
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}
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/**
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* Returns the list of {@link Media media} (that is pictures, movies,
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* recorded sounds ...) <i>this</i> description element is based on.
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*/
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public List<Media> getMedia(){
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return this.media;
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}
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/**
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* Adds a {@link Media media} to the list of {@link #getMedia() media}
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* <i>this</i> description element is based on.
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*
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* @param media the media to be added to <i>this</i> description element
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* @see #getMedia()
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*/
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public void addMedia(Media media){
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this.media.add(media);
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}
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/**
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* Removes one element from the list of {@link #getMedia() media}
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* <i>this</i> description element is based on.
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*
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* @param media the media which should be removed
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* @see #getMedia()
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* @see #addMedia(Media)
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*/
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public void removeMedia(Media media){
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this.media.remove(media);
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}
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/**
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* Returns the {@link DescriptionBase description} that <i>this</i> DescriptionElement is
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* part of.
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* @return
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*/
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public DescriptionBase getInDescription() {
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return this.inDescription;
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}
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/**
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* @see #setInDescription()
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*/
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protected void setInDescription(DescriptionBase inDescription) {
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this.inDescription = inDescription;
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}
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/**
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* Does exactly the same as getFeature().
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* @author ben.clark
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* FIXME Is there a need to have two methods with different names which do the same thing?
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*
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* @see #getFeature()
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*/
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@Transient
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@Deprecated //will be removed in version 3.
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public Feature getType(){
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return this.getFeature();
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}
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/**
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* Does exactly the same as setFeature(Feature).
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*
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* @param type the feature to be described or measured
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* @see #setFeature(Feature)
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* @see #getFeature()
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*/
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@Deprecated //will be removed in version 3
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public void setType(Feature type){
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this.setFeature(type);
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}
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/**
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* Returns the {@link Feature feature} <i>this</i> description element is for.
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* A feature is a property that can be described or measured but not the
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* description or the measurement itself.
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*/
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public Feature getFeature(){
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return this.feature;
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}
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/**
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* @see #getFeature()
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*/
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public void setFeature(Feature feature){
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this.feature = feature;
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}
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/**
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* Returns the set of {@link Modifier modifiers} used to qualify the validity of
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* <i>this</i> description element. This is only metainformation.
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*/
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public Set<Modifier> getModifiers(){
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return this.modifiers;
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}
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/**
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* Adds a {@link Modifier modifier} to the set of {@link #getModifiers() modifiers}
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* used to qualify the validity of <i>this</i> description element.
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*
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* @param modifier the modifier to be added to <i>this</i> description element
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* @see #getModifiers()
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*/
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public void addModifier(Modifier modifier){
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this.modifiers.add(modifier);
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}
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/**
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* Removes one element from the set of {@link #getModifiers() modifiers}
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* used to qualify the validity of <i>this</i> description element.
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*
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* @param modifier the modifier which should be removed
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* @see #getModifiers()
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* @see #addModifier(Modifier)
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*/
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public void removeModifier(Modifier modifier){
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this.modifiers.remove(modifier);
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}
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/**
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* Returns the {@link MultilanguageText multilanguage text} used to qualify the validity
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* of <i>this</i> description element. The different {@link LanguageString language strings}
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* contained in the multilanguage text should all have the same meaning.<BR>
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* A multilanguage text does not belong to a controlled {@link TermVocabulary term vocabulary}
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* as a {@link Modifier modifier} does.
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* <P>
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* NOTE: the actual content of <i>this</i> description element is NOT
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* stored in the modifying text. This is only metainformation
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* (like "Some experts express doubt about this assertion").
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*/
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public Map<Language,LanguageString> getModifyingText(){
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return this.modifyingText;
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}
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/**
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* Adds a translated {@link LanguageString text in a particular language}
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* to the {@link MultilanguageText multilanguage text} used to qualify the validity
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* of <i>this</i> description element.
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*
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* @param description the language string describing the validity
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* in a particular language
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* @see #getModifyingText()
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* @see #addModifyingText(String, Language)
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*/
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public LanguageString addModifyingText(LanguageString description){
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return this.modifyingText.put(description.getLanguage(),description);
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}
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/**
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* Creates a {@link LanguageString language string} based on the given text string
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* and the given {@link Language language} and adds it to the {@link MultilanguageText multilanguage text}
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* used to qualify the validity of <i>this</i> description element.
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*
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* @param text the string describing the validity
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* in a particular language
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* @param language the language in which the text string is formulated
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* @see #getModifyingText()
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* @see #addModifyingText(LanguageString)
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*/
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public LanguageString addModifyingText(String text, Language language){
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return this.modifyingText.put(language, LanguageString.NewInstance(text, language));
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}
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/**
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* Removes from the {@link MultilanguageText multilanguage text} used to qualify the validity
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* of <i>this</i> description element the one {@link LanguageString language string}
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* with the given {@link Language language}.
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*
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* @param language the language in which the language string to be removed
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* has been formulated
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* @see #getModifyingText()
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*/
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public LanguageString removeModifyingText(Language language){
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return this.modifyingText.remove(language);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.ISourceable#getSources()
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*/
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public Set<DescriptionElementSource> getSources() {
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return this.sources;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.ISourceable#addSource(eu.etaxonomy.cdm.model.common.IOriginalSource)
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*/
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public void addSource(DescriptionElementSource source) {
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if (source != null){
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DescriptionElementBase oldSourcedObj = source.getSourcedObj();
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if (oldSourcedObj != null && oldSourcedObj != this){
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oldSourcedObj.getSources().remove(source);
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}
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this.sources.add(source);
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source.setSourcedObj(this);
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}
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}
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/* (non-Javadoc)
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366
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* @see eu.etaxonomy.cdm.model.common.ISourceable#addSource(java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.reference.ReferenceBase, java.lang.String)
|
|
367
|
*/
|
|
368
|
public DescriptionElementSource addSource(String id, String idNamespace, ReferenceBase citation, String microCitation) {
|
|
369
|
if (id == null && idNamespace == null && citation == null && microCitation == null){
|
|
370
|
return null;
|
|
371
|
}
|
|
372
|
DescriptionElementSource source = DescriptionElementSource.NewInstance(id, idNamespace, citation, microCitation);
|
|
373
|
addSource(source);
|
|
374
|
return source;
|
|
375
|
}
|
|
376
|
|
|
377
|
public void addSource(String id, String idNamespace, ReferenceBase citation, String microReference, TaxonNameBase nameUsedInSource, String originalNameString){
|
|
378
|
DescriptionElementSource newSource = DescriptionElementSource.NewInstance(id, idNamespace, citation, microReference, nameUsedInSource, originalNameString);
|
|
379
|
addSource(newSource);
|
|
380
|
}
|
|
381
|
|
|
382
|
/* (non-Javadoc)
|
|
383
|
* @see eu.etaxonomy.cdm.model.common.ISourceable#removeSource(eu.etaxonomy.cdm.model.common.IOriginalSource)
|
|
384
|
*/
|
|
385
|
public void removeSource(DescriptionElementSource source) {
|
|
386
|
this.sources.remove(source);
|
|
387
|
}
|
|
388
|
|
|
389
|
|
|
390
|
/**
|
|
391
|
* Gets the citation micro reference of the first source. This method is deprecated and exists only to be compliant with version 2.0.
|
|
392
|
* It will be removed in v2.3
|
|
393
|
* @return
|
|
394
|
*/
|
|
395
|
@Transient
|
|
396
|
@Deprecated
|
|
397
|
public String getCitationMicroReference(){
|
|
398
|
if (this.sources.size() < 1){
|
|
399
|
return null;
|
|
400
|
}else{
|
|
401
|
return this.sources.iterator().next().getCitationMicroReference();
|
|
402
|
}
|
|
403
|
}
|
|
404
|
|
|
405
|
/**
|
|
406
|
* Sets the citation micro reference of the first source. This method is deprecated and exists only to be compliant with version 2.0.
|
|
407
|
* It will be removed in v2.3
|
|
408
|
* If more than one source exists an IllegalStateException is thrown
|
|
409
|
**/
|
|
410
|
@Transient
|
|
411
|
@Deprecated
|
|
412
|
public void setCitationMicroReference(String citationMicroReference){
|
|
413
|
if (this.sources.size() < 1){
|
|
414
|
ReferenceBase citation = null;
|
|
415
|
this.addSource(DescriptionElementSource.NewInstance(null, null, citation, citationMicroReference));
|
|
416
|
}else if (this.sources.size() > 1){
|
|
417
|
throw new IllegalStateException("When adding a microcitation via the setCitationMicroReference method there must be only one source available");
|
|
418
|
}else{
|
|
419
|
this.sources.iterator().next().setCitationMicroReference(citationMicroReference);
|
|
420
|
}
|
|
421
|
}
|
|
422
|
|
|
423
|
/**
|
|
424
|
* Gets the citation of the first source. This method is deprecated and exists only to be compliant with version 2.0.
|
|
425
|
* It will be removed in v2.3
|
|
426
|
*/
|
|
427
|
@Transient
|
|
428
|
@Deprecated
|
|
429
|
public ReferenceBase getCitation(){
|
|
430
|
if (this.sources.size() < 1){
|
|
431
|
return null;
|
|
432
|
}else{
|
|
433
|
return this.sources.iterator().next().getCitation();
|
|
434
|
}
|
|
435
|
}
|
|
436
|
|
|
437
|
/**
|
|
438
|
* Sets the citation of the first source. This method is deprecated and exists only to be compliant with version 2.0.
|
|
439
|
* It will be removed in v2.3
|
|
440
|
* If more than one source exists an IllegalStateException is thrown
|
|
441
|
**/
|
|
442
|
@Deprecated
|
|
443
|
public void setCitation(ReferenceBase citation) {
|
|
444
|
if (this.sources.size() < 1){
|
|
445
|
this.addSource(DescriptionElementSource.NewInstance(null, null, citation, null));
|
|
446
|
}else if (this.sources.size() > 1){
|
|
447
|
throw new IllegalStateException("When adding a citation via the setCitation method there must be only one source available");
|
|
448
|
}else{
|
|
449
|
this.sources.iterator().next().setCitation(citation);
|
|
450
|
}
|
|
451
|
}
|
|
452
|
|
|
453
|
|
|
454
|
/**
|
|
455
|
* Gets the original name string of the first source. This method is deprecated and exists only to be compliant with version 2.0.
|
|
456
|
* It will be removed in v2.3
|
|
457
|
* @return
|
|
458
|
*/
|
|
459
|
@Transient
|
|
460
|
@Deprecated
|
|
461
|
public String getOriginalNameString(){
|
|
462
|
if (this.sources.size() < 1){
|
|
463
|
return null;
|
|
464
|
}else{
|
|
465
|
return this.sources.iterator().next().getOriginalNameString();
|
|
466
|
}
|
|
467
|
}
|
|
468
|
|
|
469
|
/**
|
|
470
|
* Sets the original name string of the first source. This method is deprecated and exists only to be compliant with version 2.0.
|
|
471
|
* It will be removed in v2.3
|
|
472
|
* If more than one source exists an IllegalStateException is thrown
|
|
473
|
**/
|
|
474
|
@Transient
|
|
475
|
@Deprecated
|
|
476
|
public void setOriginalNameString(String originalNameString){
|
|
477
|
if (this.sources.size() < 1){
|
|
478
|
this.addSource(DescriptionElementSource.NewInstance(null, null, null, null, null, originalNameString));
|
|
479
|
}else if (this.sources.size() > 1){
|
|
480
|
throw new IllegalStateException("When adding a microcitation via the setCitationMicroReference method there must be only one source available");
|
|
481
|
}else{
|
|
482
|
this.sources.iterator().next().setOriginalNameString(originalNameString);
|
|
483
|
}
|
|
484
|
}
|
|
485
|
|
|
486
|
|
|
487
|
/**
|
|
488
|
* Gets the name used in source of the first source. This method is deprecated and exists only to be compliant with version 2.0.
|
|
489
|
* It will be removed in v2.3
|
|
490
|
*/
|
|
491
|
@Transient
|
|
492
|
@Deprecated
|
|
493
|
public TaxonNameBase getNameUsedInReference(){
|
|
494
|
if (this.sources.size() < 1){
|
|
495
|
return null;
|
|
496
|
}else{
|
|
497
|
return this.sources.iterator().next().getNameUsedInSource();
|
|
498
|
}
|
|
499
|
}
|
|
500
|
|
|
501
|
/**
|
|
502
|
* Sets the name used in reference of the first source. This method is deprecated and exists only to be compliant with version 2.0.
|
|
503
|
* It will be removed in v2.3
|
|
504
|
* If more than one source exists an IllegalStateException is thrown
|
|
505
|
**/
|
|
506
|
@Deprecated
|
|
507
|
public void setNameUsedInReference(TaxonNameBase nameUsedInSource) {
|
|
508
|
if (this.sources.size() < 1){
|
|
509
|
this.addSource(DescriptionElementSource.NewInstance(null, null, null, null, nameUsedInSource, null));
|
|
510
|
}else if (this.sources.size() > 1){
|
|
511
|
throw new IllegalStateException("When adding a citation via the setCitation method there must be only one source available");
|
|
512
|
}else{
|
|
513
|
this.sources.iterator().next().setNameUsedInSource(nameUsedInSource);
|
|
514
|
}
|
|
515
|
}
|
|
516
|
|
|
517
|
//************************** CLONE **********************************************************/
|
|
518
|
|
|
519
|
/**
|
|
520
|
* Clones the description element. The element is <b>not</b> added to the same
|
|
521
|
* description as the orginal element (inDescription is set to <code>null</null>.
|
|
522
|
* @see eu.etaxonomy.cdm.model.common.AnnotatableEntity#clone()
|
|
523
|
*/
|
|
524
|
@Override
|
|
525
|
public Object clone() throws CloneNotSupportedException{
|
|
526
|
DescriptionElementBase result = (DescriptionElementBase)super.clone();
|
|
527
|
|
|
528
|
//Sources
|
|
529
|
result.sources = new HashSet<DescriptionElementSource>();
|
|
530
|
for (DescriptionElementSource source : getSources()){
|
|
531
|
DescriptionElementSource newSource = (DescriptionElementSource)source.clone();
|
|
532
|
result.addSource(newSource);
|
|
533
|
}
|
|
534
|
|
|
535
|
//inDescription
|
|
536
|
result.inDescription = null;
|
|
537
|
|
|
538
|
return result;
|
|
539
|
}
|
|
540
|
|
|
541
|
/**
|
|
542
|
* Clones the description element.<BR>
|
|
543
|
* The new element is added to the <code>description</code>.<BR>
|
|
544
|
* @see eu.etaxonomy.cdm.model.common.AnnotatableEntity#clone()
|
|
545
|
*/
|
|
546
|
public DescriptionElementBase clone(DescriptionBase description) throws CloneNotSupportedException{
|
|
547
|
DescriptionElementBase result = (DescriptionElementBase)clone();
|
|
548
|
description.addElement(result);
|
|
549
|
return result;
|
|
550
|
}
|
|
551
|
|
|
552
|
|
|
553
|
}
|