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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.MapKeyJoinColumn;
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import javax.persistence.OneToMany;
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import javax.persistence.OrderColumn;
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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.XmlTransient;
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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.logging.log4j.LogManager;
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import org.apache.logging.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.ListIndexBase;
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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.IMultiLanguageTextHolder;
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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.TimePeriod;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.reference.ICdmTarget;
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import eu.etaxonomy.cdm.model.reference.IOriginalSource;
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import eu.etaxonomy.cdm.model.reference.ISourceable;
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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.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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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 TaxonName 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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* @since 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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"inDescription",
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"timeperiod",
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"modifiers",
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"modifyingText",
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"media",
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"sources",
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"sortIndex"
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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
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extends AnnotatableEntity
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implements ISourceable<DescriptionElementSource>, IModifiable, IMultiLanguageTextHolder{
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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 = LogManager.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.MERGE) remove cascade #5755
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@IndexedEmbedded // no depth for terms
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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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@IndexedEmbedded(depth=1)
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private Set<DefinedTerm> modifiers = new HashSet<>();
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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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@MapKeyJoinColumn(name="modifyingtext_mapkey_id")
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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@IndexedEmbedded
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private Map<Language,LanguageString> modifyingText = new HashMap<>();
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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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@OrderColumn(name="sortIndex")
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@ListIndexBase(value=0) //not really needed as this is the default
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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private List<Media> media = new ArrayList<>();
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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,CascadeType.MERGE})
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@IndexedEmbedded(includeEmbeddedObjectId=true)
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private DescriptionBase<?> inDescription;
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@XmlElement(name = "TimePeriod")
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private TimePeriod timeperiod = TimePeriod.NewInstance();
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@XmlElementWrapper(name = "Sources")
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@XmlElement(name = "DescriptionElementSource")
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@OneToMany(fetch = FetchType.LAZY, mappedBy = "sourcedElement", orphanRemoval=true)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
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@Merge(MergeMode.ADD_CLONE)
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private Set<DescriptionElementSource> sources = new HashSet<>();
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//#8004 optional sortIndex
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private Integer sortIndex = null;
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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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// ******************** GETTER / SETTER ***********************************/
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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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* 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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* The point in time, the time period or the season for which this description element
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* is valid. A season may be expressed by not filling the year part(s) of the time period.
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*/
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public TimePeriod getTimeperiod() {
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return timeperiod;
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}
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/**
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* @see #getTimeperiod()
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*/
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public void setTimeperiod(TimePeriod timeperiod) {
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if (timeperiod == null){
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timeperiod = TimePeriod.NewInstance();
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}
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this.timeperiod = timeperiod;
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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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@Override
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public Set<DefinedTerm> 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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@Override
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public void addModifier(DefinedTerm 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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@Override
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public void removeModifier(DefinedTerm 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 #putModifyingText(Language, String)
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* @deprecated should follow the put semantic of maps, this method will be removed in v4.0
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* Use the {@link #putModifyingText(LanguageString) putModifyingText} method
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*/
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@Deprecated
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public LanguageString addModifyingText(LanguageString description){
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return this.putModifyingText(description);
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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 #putModifyingText(Language, String)
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*/
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public LanguageString putModifyingText(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 #putModifyingText(LanguageString)
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* @deprecated should follow the put semantic of maps, this method will be removed in v4.0
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* Use the {@link #putModifyingText(Language, String) putModifyingText} method
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*/
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@Deprecated
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public LanguageString addModifyingText(String text, Language language){
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return this.putModifyingText(language, text);
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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 language the language in which the text string is formulated
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* @param text the string describing the validity
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* in a particular language
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*
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* @see #getModifyingText()
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* @see #putModifyingText(LanguageString)
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*
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*/
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public LanguageString putModifyingText(Language language, String text){
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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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@Override
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public Set<DescriptionElementSource> getSources() {
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return this.sources;
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}
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@Override
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public void addSource(DescriptionElementSource source) {
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if (source != null){
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this.sources.add(source);
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source.setSourcedElement(this);
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}
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}
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@Override
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public DescriptionElementSource addSource(OriginalSourceType type, String id, String idNamespace,
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Reference reference, String microReference) {
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if (id == null && idNamespace == null && reference == null && microReference == null){
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return null;
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}
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DescriptionElementSource source = DescriptionElementSource.NewInstance(type, id, idNamespace,
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reference, microReference);
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addSource(source);
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return source;
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}
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@Override
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public void addSources(Set<DescriptionElementSource> sources){
|
427
|
for (DescriptionElementSource source:sources){
|
428
|
addSource(source);
|
429
|
}
|
430
|
}
|
431
|
|
432
|
@Override
|
433
|
public DescriptionElementSource addImportSource(String id, String idNamespace, Reference reference, String microReference) {
|
434
|
if (id == null && idNamespace == null && reference == null && microReference == null){
|
435
|
return null;
|
436
|
}
|
437
|
DescriptionElementSource source = DescriptionElementSource.NewInstance(OriginalSourceType.Import, id, idNamespace, reference, microReference);
|
438
|
addSource(source);
|
439
|
return source;
|
440
|
}
|
441
|
|
442
|
@Override
|
443
|
public DescriptionElementSource addPrimaryTaxonomicSource(Reference reference, String microReference) {
|
444
|
if (reference == null && microReference == null){
|
445
|
return null;
|
446
|
}
|
447
|
DescriptionElementSource source = DescriptionElementSource.NewPrimarySourceInstance(reference, microReference);
|
448
|
addSource(source);
|
449
|
return source;
|
450
|
}
|
451
|
|
452
|
@Override
|
453
|
public DescriptionElementSource addPrimaryTaxonomicSource(Reference reference) {
|
454
|
return addPrimaryTaxonomicSource(reference, null);
|
455
|
}
|
456
|
|
457
|
|
458
|
|
459
|
@Override
|
460
|
public DescriptionElementSource addSource(OriginalSourceType type, Reference reference,
|
461
|
String microReference, String originalInformation) {
|
462
|
DescriptionElementSource newSource = DescriptionElementSource.NewInstance(type, null, null,
|
463
|
reference, microReference, null, originalInformation);
|
464
|
addSource(newSource);
|
465
|
return newSource;
|
466
|
}
|
467
|
|
468
|
/**
|
469
|
* Adds a {@link IOriginalSource source} to this description element.
|
470
|
* @param type the type of the source
|
471
|
* @param idInSource the id used in the source
|
472
|
* @param idNamespace the namespace for the id in the source
|
473
|
* @param reference the source as a {@link Reference reference}
|
474
|
* @param microReference the details (e.g. page number) in the reference
|
475
|
* @param nameUsedInSource the taxon name used in the source
|
476
|
* @param originalNameString the name as text used in the source
|
477
|
*/
|
478
|
public DescriptionElementSource addSource(OriginalSourceType type, String idInSource, String idNamespace,
|
479
|
Reference reference, String microReference, TaxonName nameUsedInSource, String originalNameString){
|
480
|
DescriptionElementSource newSource = DescriptionElementSource.NewInstance(type, idInSource, idNamespace,
|
481
|
reference, microReference, nameUsedInSource, originalNameString);
|
482
|
addSource(newSource);
|
483
|
return newSource;
|
484
|
}
|
485
|
|
486
|
@Override
|
487
|
public DescriptionElementSource addAggregationSource(ICdmTarget target) {
|
488
|
DescriptionElementSource source = DescriptionElementSource.NewInstance(
|
489
|
OriginalSourceType.Aggregation, null, null, null, null,
|
490
|
null, null, target);
|
491
|
addSource(source);
|
492
|
return source;
|
493
|
}
|
494
|
|
495
|
@Override
|
496
|
public void removeSource(DescriptionElementSource source) {
|
497
|
this.sources.remove(source);
|
498
|
}
|
499
|
|
500
|
|
501
|
public Integer getSortIndex() {
|
502
|
return sortIndex;
|
503
|
}
|
504
|
public void setSortIndex(Integer sortIndex) {
|
505
|
this.sortIndex = sortIndex;
|
506
|
}
|
507
|
|
508
|
// ******************* METHODS *************************************************************/
|
509
|
|
510
|
protected Map<TermVocabulary, List<DefinedTerm>> makeModifierMap(){
|
511
|
Map<TermVocabulary, List<DefinedTerm>> result = new HashMap<>();
|
512
|
for (DefinedTerm modifier : getModifiers()){
|
513
|
TermVocabulary<DefinedTerm> voc = modifier.getVocabulary();
|
514
|
if (result.get(voc) == null){
|
515
|
result.put(voc, new ArrayList<>());
|
516
|
}
|
517
|
result.get(voc).add(modifier);
|
518
|
}
|
519
|
return result;
|
520
|
}
|
521
|
|
522
|
public List<DefinedTerm> getModifiers(TermVocabulary voc){
|
523
|
List<DefinedTerm> result = makeModifierMap().get(voc);
|
524
|
if (result == null){
|
525
|
result = new ArrayList<>();
|
526
|
}
|
527
|
return result;
|
528
|
}
|
529
|
|
530
|
|
531
|
/**
|
532
|
* Is this description item of a class type which is considered to
|
533
|
* represent character data? These classes are {@link QuantitativeData}
|
534
|
* and {@link CategoricalData}.
|
535
|
* To be overridden by these classes.
|
536
|
*/
|
537
|
@Transient
|
538
|
@XmlTransient
|
539
|
public boolean isCharacterData() {
|
540
|
return false;
|
541
|
}
|
542
|
|
543
|
//************************** CLONE **********************************************************/
|
544
|
|
545
|
/**
|
546
|
* Clones the description element. The element is <b>not</b> added to the same
|
547
|
* description as the original element (inDescription is set to <code>null</null>).
|
548
|
* @see eu.etaxonomy.cdm.model.common.AnnotatableEntity#clone()
|
549
|
*/
|
550
|
@Override
|
551
|
public DescriptionElementBase clone() {
|
552
|
|
553
|
try {
|
554
|
DescriptionElementBase result = (DescriptionElementBase)super.clone();
|
555
|
|
556
|
//inDescription
|
557
|
if (result.inDescription != null){
|
558
|
result.inDescription.removeElement(result);
|
559
|
result.inDescription = null;
|
560
|
}
|
561
|
|
562
|
//Sources
|
563
|
result.sources = new HashSet<>();
|
564
|
for (DescriptionElementSource source : getSources()){
|
565
|
DescriptionElementSource newSource = source.clone();
|
566
|
result.addSource(newSource);
|
567
|
}
|
568
|
|
569
|
//media
|
570
|
result.media = new ArrayList<>();
|
571
|
for (Media media : getMedia()){
|
572
|
result.media.add(media);
|
573
|
}
|
574
|
|
575
|
//modifying text
|
576
|
result.modifyingText = cloneLanguageString(getModifyingText());
|
577
|
|
578
|
//modifiers
|
579
|
result.modifiers = new HashSet<>();
|
580
|
for (DefinedTerm modifier : getModifiers()){
|
581
|
result.modifiers.add(modifier);
|
582
|
}
|
583
|
|
584
|
result.setTimeperiod(timeperiod == null? null:timeperiod.clone());
|
585
|
|
586
|
//no changes to: feature
|
587
|
return result;
|
588
|
} catch (CloneNotSupportedException e) {
|
589
|
throw new RuntimeException(e);
|
590
|
}
|
591
|
}
|
592
|
|
593
|
/**
|
594
|
* Clones the description element.<BR>
|
595
|
* The new element is added to the <code>description</code>.<BR>
|
596
|
* @see eu.etaxonomy.cdm.model.common.AnnotatableEntity#clone()
|
597
|
*/
|
598
|
public DescriptionElementBase clone(DescriptionBase description) {
|
599
|
DescriptionElementBase result = clone();
|
600
|
description.addElement(result);
|
601
|
return result;
|
602
|
}
|
603
|
}
|