cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/jaxb/DataSet.java

   1 /**
   2 * Copyright (C) 2008 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5  *
   6  * The contents of this file are subject to the Mozilla Public License Version 1.1
   7  * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.io.jaxb;
  11
  12 import java.util.ArrayList;
  13 import java.util.Collection;
  14 import java.util.HashSet;
  15 import java.util.List;
  16 import java.util.Set;
  17
  18 import javax.xml.bind.annotation.XmlAccessType;
  19 import javax.xml.bind.annotation.XmlAccessorType;
  20 import javax.xml.bind.annotation.XmlElement;
  21 import javax.xml.bind.annotation.XmlElementWrapper;
  22 import javax.xml.bind.annotation.XmlElements;
  23 import javax.xml.bind.annotation.XmlRootElement;
  24 import javax.xml.bind.annotation.XmlType;
  25
  26 import eu.etaxonomy.cdm.model.agent.Address;
  27 import eu.etaxonomy.cdm.model.agent.Agent;
  28 import eu.etaxonomy.cdm.model.agent.Contact;
  29 import eu.etaxonomy.cdm.model.agent.Institution;
  30 import eu.etaxonomy.cdm.model.agent.InstitutionType;
  31 import eu.etaxonomy.cdm.model.agent.InstitutionalMembership;
  32 import eu.etaxonomy.cdm.model.agent.Person;
  33 import eu.etaxonomy.cdm.model.agent.Team;
  34 import eu.etaxonomy.cdm.model.common.AnnotationType;
  35 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  36 import eu.etaxonomy.cdm.model.common.ExtensionType;
  37 import eu.etaxonomy.cdm.model.common.Keyword;
  38 import eu.etaxonomy.cdm.model.common.Language;
  39 import eu.etaxonomy.cdm.model.common.LanguageString;
  40 import eu.etaxonomy.cdm.model.common.LanguageStringBase;
  41 import eu.etaxonomy.cdm.model.common.MarkerType;
  42 import eu.etaxonomy.cdm.model.common.ReferencedEntityBase;
  43 import eu.etaxonomy.cdm.model.common.RelationshipBase;
  44 import eu.etaxonomy.cdm.model.common.Representation;
  45 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  46 import eu.etaxonomy.cdm.model.common.VersionableEntity;
  47 import eu.etaxonomy.cdm.model.description.AbsenceTerm;
  48 import eu.etaxonomy.cdm.model.description.Feature;
  49 import eu.etaxonomy.cdm.model.description.FeatureNode;
  50 import eu.etaxonomy.cdm.model.description.FeatureTree;
  51 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
  52 import eu.etaxonomy.cdm.model.description.Modifier;
  53 import eu.etaxonomy.cdm.model.description.PresenceTerm;
  54 import eu.etaxonomy.cdm.model.description.Scope;
  55 import eu.etaxonomy.cdm.model.description.Sex;
  56 import eu.etaxonomy.cdm.model.description.Stage;
  57 import eu.etaxonomy.cdm.model.description.State;
  58 import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
  59 import eu.etaxonomy.cdm.model.description.TextFormat;
  60 import eu.etaxonomy.cdm.model.location.Continent;
  61 import eu.etaxonomy.cdm.model.location.NamedArea;
  62 import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
  63 import eu.etaxonomy.cdm.model.location.NamedAreaType;
  64 import eu.etaxonomy.cdm.model.location.ReferenceSystem;
  65 import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
  66 import eu.etaxonomy.cdm.model.media.Media;
  67 import eu.etaxonomy.cdm.model.media.RightsTerm;
  68 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  69 import eu.etaxonomy.cdm.model.name.BacterialName;
  70 import eu.etaxonomy.cdm.model.name.BotanicalName;
  71 import eu.etaxonomy.cdm.model.name.CultivarPlantName;
  72 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  73 import eu.etaxonomy.cdm.model.name.HybridRelationship;
  74 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
  75 import eu.etaxonomy.cdm.model.name.NameRelationship;
  76 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
  77 import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
  78 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  79 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  80 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  81 import eu.etaxonomy.cdm.model.name.NonViralName;
  82 import eu.etaxonomy.cdm.model.name.Rank;
  83 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  84 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  85 import eu.etaxonomy.cdm.model.name.TypeDesignationStatus;
  86 import eu.etaxonomy.cdm.model.name.ViralName;
  87 import eu.etaxonomy.cdm.model.name.ZoologicalName;
  88 import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
  89 import eu.etaxonomy.cdm.model.occurrence.DeterminationModifier;
  90 import eu.etaxonomy.cdm.model.occurrence.FieldObservation;
  91 import eu.etaxonomy.cdm.model.occurrence.Fossil;
  92 import eu.etaxonomy.cdm.model.occurrence.LivingBeing;
  93 import eu.etaxonomy.cdm.model.occurrence.Observation;
  94 import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
  95 import eu.etaxonomy.cdm.model.occurrence.Specimen;
  96 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  97 import eu.etaxonomy.cdm.model.reference.Article;
  98 import eu.etaxonomy.cdm.model.reference.BibtexEntryType;
  99 import eu.etaxonomy.cdm.model.reference.Book;
 100 import eu.etaxonomy.cdm.model.reference.BookSection;
 101 import eu.etaxonomy.cdm.model.reference.CdDvd;
 102 import eu.etaxonomy.cdm.model.reference.Database;
 103 import eu.etaxonomy.cdm.model.reference.Generic;
 104 import eu.etaxonomy.cdm.model.reference.InProceedings;
 105 import eu.etaxonomy.cdm.model.reference.Journal;
 106 import eu.etaxonomy.cdm.model.reference.Map;
 107 import eu.etaxonomy.cdm.model.reference.Patent;
 108 import eu.etaxonomy.cdm.model.reference.PersonalCommunication;
 109 import eu.etaxonomy.cdm.model.reference.PrintSeries;
 110 import eu.etaxonomy.cdm.model.reference.Proceedings;
 111 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
 112 import eu.etaxonomy.cdm.model.reference.Report;
 113 import eu.etaxonomy.cdm.model.reference.Thesis;
 114 import eu.etaxonomy.cdm.model.reference.WebPage;
 115 import eu.etaxonomy.cdm.model.taxon.Synonym;
 116 import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
 117 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
 118 import eu.etaxonomy.cdm.model.taxon.Taxon;
 119 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
 120 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
 121 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
 122
 123 /**
 124  * @author a.babadshanjan
 125  */
 126 @XmlAccessorType(XmlAccessType.FIELD)
 127 @XmlType(name = "", propOrder = {
 128             "terms",
 129             "termVocabularies",
 130                 "agents",
 131                 "agentData",
 132                 "occurrences",
 133             "references",
 134             "referencedEntities",
 135             "featureData",
 136             "languageData",
 137             "taxonomicNames",
 138             "homotypicalGroups",
 139             "taxa",
 140             "synonyms",
 141             "relationships",
 142             "media"
 143 })
 144 @XmlRootElement(name = "DataSet", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 145 public class DataSet {
 146
 147     // Some fields are of type List and some are of type Set.
 148         // This is mainly because
 149         // the service classes return lists, i.e.
 150     // TaxonServiceImpl.getRootTaxa() returns List<Taxon>
 151         // and the Taxon methods return sets, i.e.
 152     // Taxon.getTaxonomicChildren() returns Set<Taxon>.
 153
 154     @XmlElementWrapper(name = "Agents", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 155     @XmlElements({
 156         @XmlElement(name = "Team", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Team.class),
 157         @XmlElement(name = "Institution", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Institution.class),
 158         @XmlElement(name = "Person", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Person.class)
 159     })
 160     protected List<? extends Agent> agents;
 161
 162     @XmlElementWrapper(name = "AgentData", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 163     @XmlElements({
 164     @XmlElement(name = "Address", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Address.class),
 165     @XmlElement(name = "Contact", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Contact.class),
 166     @XmlElement(name = "InstitutionalMembership", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = InstitutionalMembership.class)
 167     })
 168     protected List<VersionableEntity> agentData;
 169
 170     @XmlElementWrapper(name = "FeatureData", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 171     @XmlElements({
 172     @XmlElement(name = "FeatureNode", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = FeatureNode.class),
 173     @XmlElement(name = "FeatureTree", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = FeatureTree.class)
 174     })
 175 //    protected List<VersionableEntity> featureData;
 176     protected List<VersionableEntity> featureData;
 177
 178     @XmlElementWrapper(name = "LanguageData", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 179     @XmlElements({
 180     @XmlElement(name = "Representation", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = Representation.class),
 181     @XmlElement(name = "LanguageString", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = LanguageString.class)
 182     })
 183     protected List<LanguageStringBase> languageData;
 184
 185     @XmlElementWrapper(name = "Terms", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 186     @XmlElements({
 187         @XmlElement(name = "AbsenceTerm", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = AbsenceTerm.class),
 188         @XmlElement(name = "AnnotationType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = AnnotationType.class),
 189         @XmlElement(name = "BibtexEntryType", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = BibtexEntryType.class),
 190         @XmlElement(name = "Continent", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = Continent.class),
 191         @XmlElement(name = "DerivationEventType", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DerivationEventType.class),
 192         @XmlElement(name = "DeterminationModifier", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DeterminationModifier.class),
 193         @XmlElement(name = "ExtensionType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = ExtensionType.class),
 194         @XmlElement(name = "Feature", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Feature.class),
 195         @XmlElement(name = "HybridRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = HybridRelationshipType.class),
 196         @XmlElement(name = "InstitutionType", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = InstitutionType.class),
 197         @XmlElement(name = "Keyword", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = Keyword.class),
 198         @XmlElement(name = "Language", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = Language.class),
 199         @XmlElement(name = "MarkerType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = MarkerType.class),
 200         @XmlElement(name = "MeasurementUnit", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = MeasurementUnit.class),
 201         @XmlElement(name = "Modifier", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Modifier.class),
 202         @XmlElement(name = "NamedArea", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedArea.class),
 203         @XmlElement(name = "NamedAreaLevel", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedAreaLevel.class),
 204         @XmlElement(name = "NamedAreaType", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedAreaType.class),
 205         @XmlElement(name = "NameRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameRelationshipType.class),
 206         @XmlElement(name = "NomenclaturalCode", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalCode.class),
 207         @XmlElement(name = "NomenclaturalStatusType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalStatusType.class),
 208         @XmlElement(name = "PresenceTerm", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = PresenceTerm.class),
 209         @XmlElement(name = "PreservationMethod", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = PreservationMethod.class),
 210         @XmlElement(name = "Rank", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = Rank.class),
 211         @XmlElement(name = "ReferenceSystem", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = ReferenceSystem.class),
 212         @XmlElement(name = "RightsTerm", namespace = "http://etaxonomy.eu/cdm/model/media/1.0", type = RightsTerm.class),
 213         @XmlElement(name = "Scope", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Scope.class),
 214         @XmlElement(name = "Sex", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Sex.class),
 215         @XmlElement(name = "Stage", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Stage.class),
 216         @XmlElement(name = "State", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = State.class),
 217         @XmlElement(name = "StatisticalMeasure", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = StatisticalMeasure.class),
 218         @XmlElement(name = "SynonymRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = SynonymRelationshipType.class),
 219         @XmlElement(name = "TaxonRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = TaxonRelationshipType.class),
 220         @XmlElement(name = "TextFormat", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = TextFormat.class),
 221         @XmlElement(name = "TypeDesignationStatus", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = TypeDesignationStatus.class),
 222         @XmlElement(name = "WaterbodyOrCountry", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = WaterbodyOrCountry.class)
 223     })
 224     protected List<DefinedTermBase> terms;
 225
 226     @XmlElementWrapper(name = "TermVocabularies", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 227     @XmlElement(name = "TermVocabulary", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
 228     protected List<TermVocabulary<DefinedTermBase>> termVocabularies;
 229
 230     @XmlElementWrapper(name = "Occurrences", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 231     @XmlElements({
 232         @XmlElement(name = "DnaSample", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DnaSample.class),
 233         @XmlElement(name = "FieldObservation", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = FieldObservation.class),
 234         @XmlElement(name = "Fossil", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = Fossil.class),
 235         @XmlElement(name = "LivingBeing", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = LivingBeing.class),
 236         @XmlElement(name = "Observation", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = Observation.class),
 237         @XmlElement(name = "Specimen", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = Specimen.class)
 238     })
 239     protected List<SpecimenOrObservationBase> occurrences;
 240
 241     @XmlElementWrapper(name = "References", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 242     @XmlElements({
 243         @XmlElement(name = "Article", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Article.class),
 244         @XmlElement(name = "Book", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Book.class),
 245         @XmlElement(name = "BookSection", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = BookSection.class),
 246         @XmlElement(name = "CdDvd", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = CdDvd.class),
 247         @XmlElement(name = "Database", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Database.class),
 248         @XmlElement(name = "Generic", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Generic.class),
 249         @XmlElement(name = "InProceedings", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = InProceedings.class),
 250         @XmlElement(name = "Journal", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Journal.class),
 251         @XmlElement(name = "Map", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Map.class),
 252         @XmlElement(name = "Patent", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Patent.class),
 253         @XmlElement(name = "PersonalCommunication", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = PersonalCommunication.class),
 254         @XmlElement(name = "PrintSeries", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = PrintSeries.class),
 255         @XmlElement(name = "Proceedings", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Proceedings.class),
 256         @XmlElement(name = "Report", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Report.class),
 257         @XmlElement(name = "Thesis", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Thesis.class),
 258         @XmlElement(name = "WebPage", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = WebPage.class)
 259     })
 260     protected List<ReferenceBase> references;
 261
 262     @XmlElementWrapper(name = "ReferencedEntities", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 263     @XmlElements({
 264         @XmlElement(name = "NomenclaturalStatus", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalStatus.class),
 265         @XmlElement(name = "NameTypeDesignation", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameTypeDesignation.class),
 266         @XmlElement(name = "SpecimenTypeDesignation", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = SpecimenTypeDesignation.class)
 267     })
 268     protected List<ReferencedEntityBase> referencedEntities;
 269
 270
 271     @XmlElementWrapper(name = "TaxonomicNames", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 272     @XmlElements({
 273         @XmlElement(name = "BacterialName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = BacterialName.class),
 274         @XmlElement(name = "BotanicalName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = BotanicalName.class),
 275         @XmlElement(name = "CultivarPlantName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = CultivarPlantName.class),
 276         @XmlElement(name = "NonViralName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NonViralName.class),
 277         @XmlElement(name = "ViralName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = ViralName.class),
 278         @XmlElement(name = "ZoologicalName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = ZoologicalName.class)
 279     })
 280     protected List<TaxonNameBase> taxonomicNames;
 281
 282     @XmlElementWrapper(name = "Taxa", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 283     @XmlElement(name = "Taxon", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0")
 284     protected List<Taxon> taxa;
 285
 286     @XmlElementWrapper(name = "Synonyms", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 287     @XmlElement(name = "Synonym", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0")
 288     protected List<Synonym> synonyms;
 289
 290     @XmlElementWrapper(name = "Relationships", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 291     @XmlElements({
 292         @XmlElement(name = "TaxonRelationship", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = TaxonRelationship.class),
 293         @XmlElement(name = "SynonymRelationship", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = SynonymRelationship.class),
 294         @XmlElement(name = "NameRelationship", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameRelationship.class),
 295         @XmlElement(name = "HybridRelationship", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = HybridRelationship.class)
 296     })
 297     protected Set<RelationshipBase> relationships;
 298
 299     @XmlElementWrapper(name = "Media", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 300     @XmlElement(name = "Media", namespace = "http://etaxonomy.eu/cdm/model/media/1.0")
 301     protected List<Media> media;
 302
 303     @XmlElementWrapper(name = "HomotypicalGroups", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 304     @XmlElement(name = "HomotypicalGroup", namespace = "http://etaxonomy.eu/cdm/model/name/1.0")
 305     protected List<HomotypicalGroup> homotypicalGroups;
 306
 307 //      @XmlElement(name = "TdwgArea", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = TdwgArea.class),
 308
 309         public DataSet () {
 310
 311                 agents = new ArrayList<Agent>();
 312                 agentData = new ArrayList<VersionableEntity>();
 313 //              featureData = new ArrayList<VersionableEntity>();
 314                 featureData = new ArrayList<VersionableEntity>();
 315                 languageData = new ArrayList<LanguageStringBase>();
 316                 terms = new ArrayList<DefinedTermBase>();
 317                 termVocabularies = new ArrayList<TermVocabulary<DefinedTermBase>>();
 318                 occurrences = new ArrayList<SpecimenOrObservationBase>();
 319                 references = new ArrayList<ReferenceBase>();
 320                 referencedEntities = new ArrayList<ReferencedEntityBase>();
 321                 taxonomicNames = new ArrayList<TaxonNameBase>();
 322                 taxa = new ArrayList<Taxon>();
 323                 synonyms = new ArrayList<Synonym>();
 324                 relationships = new HashSet<RelationshipBase>();
 325                 media = new ArrayList<Media>();
 326                 homotypicalGroups = new ArrayList<HomotypicalGroup>();
 327         }
 328
 329     /**
 330      * Gets the value of the agents property.
 331      *
 332      * @return
 333      *     possible object is
 334      *     {@link List<Agent> }
 335      *
 336      */
 337     public List<? extends Agent> getAgents() {
 338         return agents;
 339     }
 340
 341     /**
 342      * Sets the value of the agents property.
 343      *
 344      * @param value
 345      *     allowed object is
 346      *     {@link List<Agent> }
 347      *
 348      */
 349     public void setAgents(List<? extends Agent> value) {
 350         this.agents = value;
 351     }
 352
 353     /**
 354      * Gets the value of the agentData property.
 355      *
 356      * @return
 357      *     possible object is
 358      *     {@link List<VersionableEntity> }
 359      *
 360      */
 361     public List<VersionableEntity> getAgentData() {
 362         return agentData;
 363     }
 364
 365     /**
 366      * Sets the value of the agentData property.
 367      *
 368      * @param value
 369      *     allowed object is
 370      *     {@link List<VersionableEntity> }
 371      *
 372      */
 373     public void setAgentData(List<VersionableEntity> value) {
 374         this.agentData = value;
 375     }
 376
 377     /**
 378      * Gets the value of the terms property.
 379      *
 380      * @return
 381      *     possible object is
 382      *     {@link List<TermBase> }
 383      *
 384      */
 385
 386     //public List<? extends TermBase> getTerms() {
 387     public List<DefinedTermBase> getTerms() {
 388         return terms;
 389     }
 390
 391     /**
 392      * Sets the value of the terms property.
 393      *
 394      * @param value
 395      *     allowed object is
 396      *     {@link List<TermBase> }
 397      *
 398      */
 399     //public void setTerms(List<? extends TermBase> value) {
 400     public void setTerms(List<DefinedTermBase> value) {
 401         this.terms = value;
 402     }
 403
 404     /**
 405      * Gets the value of the term vocabularies property.
 406      *
 407      * @return
 408      *     possible object is
 409      *     {@link List<TermVocabulary> }
 410      *
 411      */
 412
 413     public List<TermVocabulary<DefinedTermBase>> getTermVocabularies() {
 414         return termVocabularies;
 415     }
 416
 417     /**
 418      * Sets the value of the term vocabularies property.
 419      *
 420      * @param value
 421      *     allowed object is
 422      *     {@link List<TermVocabulary> }
 423      *
 424      */
 425     public void setTermVocabularies(List<TermVocabulary<DefinedTermBase>> value) {
 426         this.termVocabularies = value;
 427     }
 428
 429     /**
 430      * Gets the value of the taxonomicNames property.
 431      *
 432      * @return
 433      *     possible object is
 434      *     {@link List<axonNameBase> }
 435      *
 436      */
 437     public List<TaxonNameBase> getTaxonomicNames() {
 438         return taxonomicNames;
 439     }
 440
 441     /**
 442      * Sets the value of the taxonomicNames property.
 443      *
 444      * @param value
 445      *     allowed object is
 446      *     {@link List<TaxonNameBase> }
 447      *
 448      */
 449     public void setTaxonomicNames(List<TaxonNameBase> value) {
 450         this.taxonomicNames = value;
 451     }
 452
 453     /**
 454      * Gets the value of the references property.
 455      *
 456      * @return
 457      *     possible object is
 458      *     {@link List<SpecimenOrObservationBase> }
 459      *
 460      */
 461     public List<SpecimenOrObservationBase> getOccurrences() {
 462         return occurrences;
 463     }
 464
 465     /**
 466      * Sets the value of the references property.
 467      *
 468      * @param value
 469      *     allowed object is
 470      *     {@link List<SpecimenOrObservationBase> }
 471      *
 472      */
 473     public void setOccurrences(List<SpecimenOrObservationBase> value) {
 474         this.occurrences = value;
 475     }
 476
 477     /**
 478      * Gets the value of the references property.
 479      *
 480      * @return
 481      *     possible object is
 482      *     {@link List<ReferenceBase> }
 483      *
 484      */
 485     public List<ReferenceBase> getReferences() {
 486         return references;
 487     }
 488
 489     /**
 490      * Sets the value of the references property.
 491      *
 492      * @param value
 493      *     allowed object is
 494      *     {@link List<ReferenceBase> }
 495      *
 496      */
 497     public void setReferences(List<ReferenceBase> value) {
 498         this.references = value;
 499     }
 500
 501     /**
 502      * Adds the referenced entities in value to the referenced entity property list.
 503      *
 504      * @param value
 505      *     allowed object is
 506      *     {@link Collection<ReferencedEntityBase> }
 507      *
 508      */
 509     public <T extends ReferencedEntityBase> void addReferencedEntities(Collection<T> value) {
 510         for (T referencedEntity: value) {
 511                 this.referencedEntities.add(referencedEntity);
 512         }
 513     }
 514
 515     /**
 516      * Gets the value of the  property.
 517      *
 518      * @return
 519      *     possible object is
 520      *     {@link List<ReferencedEntityBase> }
 521      *
 522      */
 523     public List<ReferencedEntityBase> getReferencedEntities() {
 524         return referencedEntities;
 525     }
 526
 527     /**
 528      * Sets the value of the referencedEntities property.
 529      *
 530      * @param value
 531      *     allowed object is
 532      *     {@link List<ReferencedEntityBase> }
 533      *
 534      */
 535     public void setReferencedEntities(List<? extends ReferencedEntityBase> value) {
 536         this.referencedEntities = new ArrayList<ReferencedEntityBase>();
 537         referencedEntities.addAll(value);
 538     }
 539
 540     /**
 541      * Adds the features in value to the feature data property list.
 542      *
 543      * @param value
 544      *     allowed object is
 545      *     {@link Collection<VersionableEntity> }
 546      *
 547      */
 548     public <T extends VersionableEntity> void addFeatureData(Collection<T> value) {
 549         for (T featureItem: value) {
 550                 this.featureData.add(featureItem);
 551         }
 552     }
 553
 554     /**
 555      * Gets the value of the feature data property.
 556      *
 557      * @return
 558      *     possible object is
 559      *     {@link List<VersionableEntity> }
 560      *
 561      */
 562 //    public List<VersionableEntity> getFeatureData() {
 563     public List<VersionableEntity> getFeatureData() {
 564         return featureData;
 565     }
 566
 567     /**
 568      * Sets the value of the feature data property.
 569      *
 570      * @param value
 571      *     allowed object is
 572      *     {@link List<VersionableEntity> }
 573      *
 574      */
 575     public <T extends VersionableEntity> void setFeatureData(List<T> value) {
 576         featureData = new ArrayList<VersionableEntity>();
 577         for (T featureItem: value) {
 578                 this.featureData.add(featureItem);
 579         }
 580     }
 581
 582 //    public void setFeatureData(List<? extends VersionableEntity> value) {
 583     //public void setFeatureData(List<? extends VersionableEntity<?>> value) {
 584 //        this.featureData = new ArrayList<VersionableEntity>();
 585     //    this.featureData = new ArrayList<VersionableEntity<?>>();
 586     //    featureData.addAll(value);
 587     //}
 588
 589     /**
 590      * Adds the features in value to the language data property list.
 591      *
 592      * @param value
 593      *     allowed object is
 594      *     {@link Collection<LanguageStringBase> }
 595      *
 596      */
 597     public <T extends LanguageStringBase> void addLanguageData(Collection<T> value) {
 598         for (T languageItem: value) {
 599                 this.languageData.add(languageItem);
 600         }
 601     }
 602
 603     /**
 604      * Gets the value of the language data property.
 605      *
 606      * @return
 607      *     possible object is
 608      *     {@link List<LanguageStringBase> }
 609      *
 610      */
 611     public List<LanguageStringBase> getLanguageData() {
 612         return languageData;
 613     }
 614
 615     /**
 616      * Sets the value of the feature data property.
 617      *
 618      * @param value
 619      *     allowed object is
 620      *     {@link List<LanguageStringBase> }
 621      *
 622      */
 623     public void setLanguageData(List<? extends LanguageStringBase> value) {
 624         this.languageData = new ArrayList<LanguageStringBase>();
 625         languageData.addAll(value);
 626     }
 627
 628     /**
 629      * Adds the taxa in value to the taxa property list.
 630      *
 631      * @param value
 632      *     allowed object is
 633      *     {@link Collection<Taxon> }
 634      *
 635      */
 636     public void addTaxa(Collection<Taxon> value) {
 637         for (Taxon taxon: value) {
 638                 this.taxa.add(taxon);
 639         }
 640     }
 641
 642     /**
 643      * Gets the value of the taxa property.
 644      *
 645      * @return
 646      *     possible object is
 647      *     {@link List<Taxon> }
 648      *
 649      */
 650 //    public List<Taxon> getTaxa() {
 651 //        return taxa;
 652 //    }
 653
 654     /**
 655      * Gets the value of the taxa property as {@link Collection<TaxonBase> }
 656      *
 657      * @return
 658      *     possible object is
 659      *     {@link Collection<TaxonBase> }
 660      *
 661      */
 662     public Collection<? extends TaxonBase> getTaxa() {
 663
 664         //TODO can be deleted when everything works
 665         //Object obj = taxa;
 666         //Collection<TaxonBase> taxonBases = (Collection<TaxonBase>)obj;
 667         List<Taxon> list = taxa;
 668         return list;
 669     }
 670
 671     public Collection<TaxonBase> getTaxonBases() {
 672
 673         Collection<TaxonBase> result = new HashSet<TaxonBase>();;
 674         if (taxa != null) {
 675                 result.addAll(taxa);
 676         }
 677         if (synonyms != null) {
 678                 result.addAll(synonyms);
 679         }
 680         return result;
 681     }
 682
 683     /**
 684      * Sets the value of the taxa property.
 685      *
 686      * @param value
 687      *     allowed object is
 688      *     {@link List<Taxon> }
 689      *
 690      */
 691     public void setTaxa(List<Taxon> value) {
 692         this.taxa = value;
 693     }
 694
 695     /**
 696      * Adds the taxon in value to the taxa property list.
 697      *
 698      * @param value
 699      *
 700      */
 701     public void addTaxon(Taxon value) {
 702                 this.taxa.add(value);
 703     }
 704
 705
 706     /**
 707      * Gets the value of the synonyms property.
 708      *
 709      * @return
 710      *     possible object is
 711      *     {@link List<Synonym> }
 712      *
 713      */
 714     public List<Synonym> getSynonyms() {
 715         return synonyms;
 716     }
 717
 718     /**
 719      * Sets the value of the synonyms property.
 720      *
 721      * @param value
 722      *     allowed object is
 723      *     {@link List<Synonym> }
 724      *
 725      */
 726     public void setSynonyms(List<Synonym> value) {
 727         this.synonyms = value;
 728     }
 729
 730     /**
 731      * Adds the synonym in value to the taxa property list.
 732      *
 733      * @param value
 734      *
 735      */
 736     public void addSynonym(Synonym value) {
 737                 this.synonyms.add(value);
 738     }
 739
 740     /**
 741      * Adds the synonym in value to the synonyms property list.
 742      *
 743      * @param value
 744      *     allowed object is
 745      *     {@link Collection<Synonym> }
 746      *
 747      */
 748     public void addSynonyms(Collection<Synonym> value) {
 749         for (Synonym synonym: value) {
 750                 this.synonyms.add(synonym);
 751         }
 752     }
 753
 754     /**
 755      * Gets the value of the relationships property.
 756      *
 757      * @return
 758      *     possible object is
 759      *     {@link Set<RelationshipBase> }
 760      *
 761      */
 762     public Set<RelationshipBase> getRelationships() {
 763         return relationships;
 764     }
 765
 766     /**
 767      * Sets the value of the relationships property.
 768      *
 769      * @param value
 770      *     allowed object is
 771      *     {@link Set<RelationshipBase> }
 772      *
 773      */
 774     public void setRelationships(Set<RelationshipBase> value) {
 775         this.relationships = value;
 776     }
 777
 778     /**
 779      * Adds the relationship in value to the relationships property list.
 780      *
 781      * @param value
 782      *     allowed object is
 783      *     {@link Collection<RelationshipBase> }
 784      *
 785      */
 786     public void addRelationships(Collection<? extends RelationshipBase> value) {
 787         for (RelationshipBase relationship: value) {
 788                 this.relationships.add(relationship);
 789         }
 790     }
 791
 792     /**
 793      * Adds the media in value to the media property list.
 794      *
 795      * @param value
 796      *     allowed object is
 797      *     {@link Collection<VersionableEntity> }
 798      *
 799      */
 800     public <T extends Media> void addMedia(Collection<T> value) {
 801         for (T medium: value) {
 802                 this.media.add(medium);
 803         }
 804     }
 805
 806     /**
 807      * Gets the value of the  property.
 808      *
 809      * @return
 810      *     possible object is
 811      *     {@link List<ReferencedEntityBase> }
 812      *
 813      */
 814     public List<Media> getMedia() {
 815         return media;
 816     }
 817
 818     /**
 819      * Sets the value of the referencedEntities property.
 820      *
 821      * @param value
 822      *     allowed object is
 823      *     {@link List<ReferencedEntityBase> }
 824      *
 825      */
 826     public void setMedia(List<Media> value) {
 827         this.media = new ArrayList<Media>();
 828         media.addAll(value);
 829     }
 830
 831     /**
 832      * Gets the value of the synonyms property.
 833      *
 834      * @return
 835      *     possible object is
 836      *     {@link List<Synonym> }
 837      *
 838      */
 839     public List<HomotypicalGroup> getHomotypicalGroups() {
 840         return homotypicalGroups;
 841     }
 842
 843     /**
 844      * Sets the value of the synonyms property.
 845      *
 846      * @param value
 847      *     allowed object is
 848      *     {@link List<Synonym> }
 849      *
 850      */
 851     public void setHomotypicalGroups(List<HomotypicalGroup> value) {
 852         this.homotypicalGroups = value;
 853     }
 854
 855 }