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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.io.sdd.out;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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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.XmlElements;
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import javax.xml.bind.annotation.XmlRootElement;
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import javax.xml.bind.annotation.XmlType;
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import eu.etaxonomy.cdm.model.agent.Address;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.agent.Contact;
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import eu.etaxonomy.cdm.model.agent.Institution;
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import eu.etaxonomy.cdm.model.agent.InstitutionalMembership;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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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.LanguageStringBase;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.ReferencedEntityBase;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.common.SourcedEntityBase;
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import eu.etaxonomy.cdm.model.common.VersionableEntity;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureNode;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.description.MeasurementUnit;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
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import eu.etaxonomy.cdm.model.description.TextFormat;
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import eu.etaxonomy.cdm.model.location.Country;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
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import eu.etaxonomy.cdm.model.location.NamedAreaType;
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import eu.etaxonomy.cdm.model.location.ReferenceSystem;
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import eu.etaxonomy.cdm.model.media.RightsType;
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import eu.etaxonomy.cdm.model.molecular.DnaSample;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
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import eu.etaxonomy.cdm.model.name.NameRelationship;
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import eu.etaxonomy.cdm.model.name.NameRelationshipType;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.model.term.Representation;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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/**
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* @author a.babadshanjan
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "", propOrder = {
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"terms",
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"termVocabularies",
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"agents",
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"agentData",
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"occurrences",
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"references",
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"referencedEntities",
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"featureData",
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"languageData",
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"taxonomicNames",
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"homotypicalGroups",
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"taxa",
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"synonyms",
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"relationships",
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"media"
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})
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@XmlRootElement(name = "DataSet", namespace = "http://etaxonomy.eu/cdm/model/1.0")
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public class SDDDataSet {
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// Some fields are of type List and some are of type Set.
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// This is mainly because
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// the service classes return lists, i.e.
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// TaxonServiceImpl.getRootTaxa() returns List<Taxon>
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// and the Taxon methods return sets, i.e.
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// Taxon.getTaxonomicChildren() returns Set<Taxon>.
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@XmlElementWrapper(name = "Agents")
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@XmlElements({
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@XmlElement(name = "Team", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Team.class),
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@XmlElement(name = "Institution", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Institution.class),
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@XmlElement(name = "Person", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Person.class)
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})
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protected List<? extends AgentBase> agents;
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@XmlElementWrapper(name = "AgentData")
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@XmlElements({
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@XmlElement(name = "Address", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Address.class),
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@XmlElement(name = "Contact", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Contact.class),
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@XmlElement(name = "InstitutionalMembership", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = InstitutionalMembership.class)
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})
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protected List<VersionableEntity> agentData;
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@XmlElementWrapper(name = "FeatureData")
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@XmlElements({
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@XmlElement(name = "FeatureNode", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = FeatureNode.class),
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@XmlElement(name = "FeatureTree", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = FeatureTree.class)
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})
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// protected List<VersionableEntity> featureData;
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protected List<VersionableEntity> featureData;
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@XmlElementWrapper(name = "LanguageData")
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@XmlElements({
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@XmlElement(name = "Representation", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = Representation.class),
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@XmlElement(name = "LanguageString", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = LanguageString.class)
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})
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protected List<LanguageStringBase> languageData;
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@XmlElementWrapper(name = "Terms")
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@XmlElements({
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@XmlElement(name = "AnnotationType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = AnnotationType.class),
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@XmlElement(name = "Continent", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedArea.class),
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@XmlElement(name = "DerivationEventType", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DerivationEventType.class),
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@XmlElement(name = "DeterminationModifier", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DefinedTerm.class),
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@XmlElement(name = "ExtensionType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = ExtensionType.class),
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@XmlElement(name = "Feature", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Feature.class),
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@XmlElement(name = "HybridRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = HybridRelationshipType.class),
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@XmlElement(name = "InstitutionType", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = DefinedTerm.class),
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@XmlElement(name = "Language", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = Language.class),
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@XmlElement(name = "MarkerType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = MarkerType.class),
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@XmlElement(name = "MeasurementUnit", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = MeasurementUnit.class),
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@XmlElement(name = "Modifier", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = DefinedTerm.class),
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@XmlElement(name = "NamedArea", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedArea.class),
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@XmlElement(name = "NamedAreaLevel", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedAreaLevel.class),
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@XmlElement(name = "NamedAreaType", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedAreaType.class),
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@XmlElement(name = "NameRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameRelationshipType.class),
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@XmlElement(name = "NomenclaturalCode", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalCode.class),
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@XmlElement(name = "NomenclaturalStatusType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalStatusType.class),
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@XmlElement(name = "PresenceAbsenceTerm", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = PresenceAbsenceTerm.class),
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@XmlElement(name = "PreservationMethod", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = PreservationMethod.class),
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@XmlElement(name = "Rank", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = Rank.class),
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@XmlElement(name = "ReferenceSystem", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = ReferenceSystem.class),
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@XmlElement(name = "RightsType", namespace = "http://etaxonomy.eu/cdm/model/media/1.0", type = RightsType.class),
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@XmlElement(name = "Scope", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = DefinedTerm.class),
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@XmlElement(name = "Sex", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = DefinedTerm.class),
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@XmlElement(name = "Stage", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = DefinedTerm.class),
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@XmlElement(name = "State", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = State.class),
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@XmlElement(name = "StatisticalMeasure", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = StatisticalMeasure.class),
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@XmlElement(name = "SynonymType", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = SynonymType.class),
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@XmlElement(name = "TaxonRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = TaxonRelationshipType.class),
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@XmlElement(name = "TextFormat", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = TextFormat.class),
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@XmlElement(name = "TypeDesignationStatus", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = SpecimenTypeDesignationStatus.class),
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@XmlElement(name = "Country", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = Country.class)
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})
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protected List<DefinedTermBase> terms;
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@XmlElementWrapper(name = "TermVocabularies")
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@XmlElement(name = "TermVocabulary", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
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protected List<TermVocabulary<DefinedTermBase>> termVocabularies;
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@XmlElementWrapper(name = "Occurrences")
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@XmlElements({
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@XmlElement(name = "DnaSample", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DnaSample.class),
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@XmlElement(name = "FieldUnit", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = FieldUnit.class)
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})
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protected List<SpecimenOrObservationBase> occurrences;
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@XmlElementWrapper(name = "References")
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@XmlElement(name = "Reference", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Reference.class)
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protected List<Reference> references;
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@XmlElementWrapper(name = "ReferencedEntities")
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@XmlElements({
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@XmlElement(name = "NomenclaturalStatus", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalStatus.class),
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})
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protected List<ReferencedEntityBase> referencedEntities;
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@XmlElementWrapper(name = "SourcedEntities")
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@XmlElements({
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@XmlElement(name = "NameTypeDesignation", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameTypeDesignation.class),
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@XmlElement(name = "SpecimenTypeDesignation", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = SpecimenTypeDesignation.class)
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})
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protected List<SourcedEntityBase> sourcedEntities;
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@XmlElementWrapper(name = "TaxonomicNames")
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@XmlElements({
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@XmlElement(name = "TaxonName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = TaxonName.class),
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})
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protected List<TaxonName> taxonomicNames;
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@XmlElementWrapper(name = "Taxa")
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@XmlElement(name = "Taxon", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0")
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protected List<Taxon> taxa;
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@XmlElementWrapper(name = "Synonyms")
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@XmlElement(name = "Synonym", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0")
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protected List<Synonym> synonyms;
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@XmlElementWrapper(name = "Relationships")
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@XmlElements({
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@XmlElement(name = "TaxonRelationship", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = TaxonRelationship.class),
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@XmlElement(name = "NameRelationship", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameRelationship.class),
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@XmlElement(name = "HybridRelationship", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = HybridRelationship.class)
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})
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protected Set<RelationshipBase> relationships;
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@XmlElementWrapper(name = "Media_")
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@XmlElement(name = "Media", namespace = "http://etaxonomy.eu/cdm/model/media/1.0")
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protected List<VersionableEntity> media;
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@XmlElementWrapper(name = "HomotypicalGroups")
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@XmlElement(name = "HomotypicalGroup", namespace = "http://etaxonomy.eu/cdm/model/name/1.0")
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protected List<HomotypicalGroup> homotypicalGroups;
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// @XmlElement(name = "TdwgArea", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = TdwgArea.class),
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public SDDDataSet () {
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agents = new ArrayList<>();
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agentData = new ArrayList<>();
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featureData = new ArrayList<>();
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languageData = new ArrayList<>();
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terms = new ArrayList<>();
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termVocabularies = new ArrayList<>();
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occurrences = new ArrayList<>();
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references = new ArrayList<>();
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referencedEntities = new ArrayList<>();
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taxonomicNames = new ArrayList<>();
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taxa = new ArrayList<>();
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synonyms = new ArrayList<>();
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media = new ArrayList<>();
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homotypicalGroups = new ArrayList<>();
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}
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public List<? extends AgentBase> getAgents() {
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return agents;
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}
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public void setAgents(List<? extends AgentBase> value) {
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this.agents = value;
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}
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public List<VersionableEntity> getAgentData() {
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return agentData;
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}
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278
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public void setAgentData(List<VersionableEntity> value) {
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279
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this.agentData = value;
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280
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}
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281
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282
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//public List<? extends TermBase> getTerms() {
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283
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public List<DefinedTermBase> getTerms() {
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284
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return terms;
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285
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}
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286
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287
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//public void setTerms(List<? extends TermBase> value) {
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288
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public void setTerms(List<DefinedTermBase> value) {
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289
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this.terms = value;
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290
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}
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291
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292
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public List<TermVocabulary<DefinedTermBase>> getTermVocabularies() {
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293
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return termVocabularies;
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294
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}
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295
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296
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public void setTermVocabularies(List<TermVocabulary<DefinedTermBase>> value) {
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297
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this.termVocabularies = value;
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298
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}
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299
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300
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public List<TaxonName> getTaxonomicNames() {
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301
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return taxonomicNames;
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302
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}
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303
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public void setTaxonomicNames(List<TaxonName> value) {
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304
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this.taxonomicNames = value;
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305
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}
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306
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307
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public List<SpecimenOrObservationBase> getOccurrences() {
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308
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return occurrences;
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309
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}
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310
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311
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public void setOccurrences(List<SpecimenOrObservationBase> value) {
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312
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this.occurrences = value;
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313
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}
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314
|
|
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315
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public List<Reference> getReferences() {
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316
|
return references;
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|
317
|
}
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318
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public void setReferences(List<Reference> value) {
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319
|
this.references = value;
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|
320
|
}
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321
|
|
|
322
|
public <T extends ReferencedEntityBase> void addReferencedEntities(Collection<T> value) {
|
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323
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for (T referencedEntity: value) {
|
|
324
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this.referencedEntities.add(referencedEntity);
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|
325
|
}
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|
326
|
}
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|
327
|
public List<ReferencedEntityBase> getReferencedEntities() {
|
|
328
|
return referencedEntities;
|
|
329
|
}
|
|
330
|
public void setReferencedEntities(List<? extends ReferencedEntityBase> value) {
|
|
331
|
this.referencedEntities = new ArrayList<>();
|
|
332
|
referencedEntities.addAll(value);
|
|
333
|
}
|
|
334
|
|
|
335
|
public <T extends SourcedEntityBase> void addSourcedEntities(Collection<T> value) {
|
|
336
|
if (sourcedEntities == null){
|
|
337
|
this.sourcedEntities = new ArrayList<>();
|
|
338
|
}
|
|
339
|
for (T sourcedEntity: value) {
|
|
340
|
this.sourcedEntities.add(sourcedEntity);
|
|
341
|
}
|
|
342
|
}
|
|
343
|
|
|
344
|
public List<SourcedEntityBase> getSourcedEntities() {
|
|
345
|
return sourcedEntities;
|
|
346
|
}
|
|
347
|
public void setSourcedEntities(List<? extends SourcedEntityBase> value) {
|
|
348
|
this.sourcedEntities = new ArrayList<>();
|
|
349
|
sourcedEntities.addAll(value);
|
|
350
|
}
|
|
351
|
|
|
352
|
public <T extends VersionableEntity> void addFeatureData(Collection<T> value) {
|
|
353
|
for (T featureItem: value) {
|
|
354
|
this.featureData.add(featureItem);
|
|
355
|
}
|
|
356
|
}
|
|
357
|
// public List<VersionableEntity> getFeatureData() {
|
|
358
|
public List<VersionableEntity> getFeatureData() {
|
|
359
|
return featureData;
|
|
360
|
}
|
|
361
|
public <T extends VersionableEntity> void setFeatureData(List<T> value) {
|
|
362
|
featureData = new ArrayList<>();
|
|
363
|
for (T featureItem: value) {
|
|
364
|
this.featureData.add(featureItem);
|
|
365
|
}
|
|
366
|
}
|
|
367
|
|
|
368
|
// public void setFeatureData(List<? extends VersionableEntity> value) {
|
|
369
|
//public void setFeatureData(List<? extends VersionableEntity<?>> value) {
|
|
370
|
// this.featureData = new ArrayList<VersionableEntity>();
|
|
371
|
// this.featureData = new ArrayList<VersionableEntity<?>>();
|
|
372
|
// featureData.addAll(value);
|
|
373
|
//}
|
|
374
|
|
|
375
|
public <T extends LanguageStringBase> void addLanguageData(Collection<T> value) {
|
|
376
|
for (T languageItem: value) {
|
|
377
|
this.languageData.add(languageItem);
|
|
378
|
}
|
|
379
|
}
|
|
380
|
public List<LanguageStringBase> getLanguageData() {
|
|
381
|
return languageData;
|
|
382
|
}
|
|
383
|
public void setLanguageData(List<? extends LanguageStringBase> value) {
|
|
384
|
this.languageData = new ArrayList<>();
|
|
385
|
languageData.addAll(value);
|
|
386
|
}
|
|
387
|
|
|
388
|
public void addTaxa(Collection<Taxon> value) {
|
|
389
|
for (Taxon taxon: value) {
|
|
390
|
this.taxa.add(taxon);
|
|
391
|
}
|
|
392
|
}
|
|
393
|
|
|
394
|
public Collection<? extends TaxonBase> getTaxa() {
|
|
395
|
|
|
396
|
//TODO can be deleted when everything works
|
|
397
|
//Object obj = taxa;
|
|
398
|
//Collection<TaxonBase> taxonBases = (Collection<TaxonBase>)obj;
|
|
399
|
List<Taxon> list = taxa;
|
|
400
|
return list;
|
|
401
|
}
|
|
402
|
|
|
403
|
public Collection<TaxonBase> getTaxonBases() {
|
|
404
|
|
|
405
|
Collection<TaxonBase> result = new HashSet<>();
|
|
406
|
if (taxa != null) {
|
|
407
|
result.addAll(taxa);
|
|
408
|
}
|
|
409
|
if (synonyms != null) {
|
|
410
|
result.addAll(synonyms);
|
|
411
|
}
|
|
412
|
return result;
|
|
413
|
}
|
|
414
|
|
|
415
|
public void setTaxa(List<Taxon> value) {
|
|
416
|
this.taxa = value;
|
|
417
|
}
|
|
418
|
public void addTaxon(Taxon value) {
|
|
419
|
this.taxa.add(value);
|
|
420
|
}
|
|
421
|
|
|
422
|
public List<Synonym> getSynonyms() {
|
|
423
|
return synonyms;
|
|
424
|
}
|
|
425
|
public void setSynonyms(List<Synonym> value) {
|
|
426
|
this.synonyms = value;
|
|
427
|
}
|
|
428
|
|
|
429
|
public void addSynonym(Synonym value) {
|
|
430
|
this.synonyms.add(value);
|
|
431
|
}
|
|
432
|
public void addSynonyms(Collection<Synonym> value) {
|
|
433
|
for (Synonym synonym: value) {
|
|
434
|
this.synonyms.add(synonym);
|
|
435
|
}
|
|
436
|
}
|
|
437
|
|
|
438
|
public <T extends VersionableEntity> void addMedia(Collection<T> value) {
|
|
439
|
for (T medium: value) {
|
|
440
|
this.media.add(medium);
|
|
441
|
}
|
|
442
|
}
|
|
443
|
|
|
444
|
public List<VersionableEntity> getMedia() {
|
|
445
|
return media;
|
|
446
|
}
|
|
447
|
|
|
448
|
public void setMedia(List<? extends VersionableEntity> value) {
|
|
449
|
this.media = new ArrayList<>();
|
|
450
|
media.addAll(value);
|
|
451
|
}
|
|
452
|
|
|
453
|
public List<HomotypicalGroup> getHomotypicalGroups() {
|
|
454
|
return homotypicalGroups;
|
|
455
|
}
|
|
456
|
|
|
457
|
public void setHomotypicalGroups(List<HomotypicalGroup> value) {
|
|
458
|
this.homotypicalGroups = value;
|
|
459
|
}
|
|
460
|
|
|
461
|
}
|