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
   7 package eu.etaxonomy.cdm.io.jaxb;
   8
   9 import java.util.ArrayList;
  10 import java.util.Collection;
  11 import java.util.HashSet;
  12 import java.util.List;
  13 import java.util.Set;
  14
  15 import javax.xml.bind.annotation.XmlAccessType;
  16 import javax.xml.bind.annotation.XmlAccessorType;
  17 import javax.xml.bind.annotation.XmlElement;
  18 import javax.xml.bind.annotation.XmlElementWrapper;
  19 import javax.xml.bind.annotation.XmlElements;
  20 import javax.xml.bind.annotation.XmlRootElement;
  21 import javax.xml.bind.annotation.XmlType;
  22
  23 import eu.etaxonomy.cdm.model.agent.Address;
  24 import eu.etaxonomy.cdm.model.agent.Agent;
  25 import eu.etaxonomy.cdm.model.agent.Contact;
  26 import eu.etaxonomy.cdm.model.agent.Institution;
  27 import eu.etaxonomy.cdm.model.agent.InstitutionType;
  28 import eu.etaxonomy.cdm.model.agent.InstitutionalMembership;
  29 import eu.etaxonomy.cdm.model.agent.Person;
  30 import eu.etaxonomy.cdm.model.agent.Team;
  31 import eu.etaxonomy.cdm.model.common.AnnotationType;
  32 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  33 import eu.etaxonomy.cdm.model.common.ExtensionType;
  34 import eu.etaxonomy.cdm.model.common.Keyword;
  35 import eu.etaxonomy.cdm.model.common.Language;
  36 import eu.etaxonomy.cdm.model.common.LanguageString;
  37 import eu.etaxonomy.cdm.model.common.LanguageStringBase;
  38 import eu.etaxonomy.cdm.model.common.MarkerType;
  39 import eu.etaxonomy.cdm.model.common.MultilanguageText;
  40 import eu.etaxonomy.cdm.model.common.ReferencedEntityBase;
  41 import eu.etaxonomy.cdm.model.common.RelationshipBase;
  42 import eu.etaxonomy.cdm.model.common.Representation;
  43 import eu.etaxonomy.cdm.model.common.TermBase;
  44 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  45 import eu.etaxonomy.cdm.model.common.VersionableEntity;
  46 import eu.etaxonomy.cdm.model.description.AbsenceTerm;
  47 import eu.etaxonomy.cdm.model.description.Feature;
  48 import eu.etaxonomy.cdm.model.description.FeatureNode;
  49 import eu.etaxonomy.cdm.model.description.FeatureTree;
  50 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
  51 import eu.etaxonomy.cdm.model.description.Modifier;
  52 import eu.etaxonomy.cdm.model.description.PresenceTerm;
  53 import eu.etaxonomy.cdm.model.description.Scope;
  54 import eu.etaxonomy.cdm.model.description.Sex;
  55 import eu.etaxonomy.cdm.model.description.Stage;
  56 import eu.etaxonomy.cdm.model.description.State;
  57 import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
  58 import eu.etaxonomy.cdm.model.description.TextFormat;
  59 import eu.etaxonomy.cdm.model.location.Continent;
  60 import eu.etaxonomy.cdm.model.location.NamedArea;
  61 import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
  62 import eu.etaxonomy.cdm.model.location.NamedAreaType;
  63 import eu.etaxonomy.cdm.model.location.ReferenceSystem;
  64 import eu.etaxonomy.cdm.model.location.TdwgArea;
  65 import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
  66 import eu.etaxonomy.cdm.model.media.Media;
  67 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  68 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  69 import eu.etaxonomy.cdm.model.media.RightsTerm;
  70 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  71 import eu.etaxonomy.cdm.model.name.BacterialName;
  72 import eu.etaxonomy.cdm.model.name.BotanicalName;
  73 import eu.etaxonomy.cdm.model.name.CultivarPlantName;
  74 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  75 import eu.etaxonomy.cdm.model.name.HybridRelationship;
  76 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
  77 import eu.etaxonomy.cdm.model.name.NameRelationship;
  78 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
  79 import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
  80 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  81 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  82 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  83 import eu.etaxonomy.cdm.model.name.Rank;
  84 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  85 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  86 import eu.etaxonomy.cdm.model.name.TypeDesignationStatus;
  87 import eu.etaxonomy.cdm.model.name.ViralName;
  88 import eu.etaxonomy.cdm.model.name.ZoologicalName;
  89 import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
  90 import eu.etaxonomy.cdm.model.occurrence.DeterminationModifier;
  91 import eu.etaxonomy.cdm.model.occurrence.FieldObservation;
  92 import eu.etaxonomy.cdm.model.occurrence.Fossil;
  93 import eu.etaxonomy.cdm.model.occurrence.LivingBeing;
  94 import eu.etaxonomy.cdm.model.occurrence.Observation;
  95 import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
  96 import eu.etaxonomy.cdm.model.occurrence.Specimen;
  97 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  98 import eu.etaxonomy.cdm.model.reference.Article;
  99 import eu.etaxonomy.cdm.model.reference.BibtexEntryType;
 100 import eu.etaxonomy.cdm.model.reference.Book;
 101 import eu.etaxonomy.cdm.model.reference.BookSection;
 102 import eu.etaxonomy.cdm.model.reference.CdDvd;
 103 import eu.etaxonomy.cdm.model.reference.Database;
 104 import eu.etaxonomy.cdm.model.reference.Generic;
 105 import eu.etaxonomy.cdm.model.reference.InProceedings;
 106 import eu.etaxonomy.cdm.model.reference.Journal;
 107 import eu.etaxonomy.cdm.model.reference.Map;
 108 import eu.etaxonomy.cdm.model.reference.Patent;
 109 import eu.etaxonomy.cdm.model.reference.PersonalCommunication;
 110 import eu.etaxonomy.cdm.model.reference.PrintSeries;
 111 import eu.etaxonomy.cdm.model.reference.Proceedings;
 112 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
 113 import eu.etaxonomy.cdm.model.reference.Report;
 114 import eu.etaxonomy.cdm.model.reference.Thesis;
 115 import eu.etaxonomy.cdm.model.reference.WebPage;
 116 import eu.etaxonomy.cdm.model.taxon.Synonym;
 117 import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
 118 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
 119 import eu.etaxonomy.cdm.model.taxon.Taxon;
 120 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
 121 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
 122 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
 123
 124 /**
 125  * @author a.babadshanjan
 126  */
 127 @XmlAccessorType(XmlAccessType.FIELD)
 128 @XmlType(name = "", propOrder = {
 129             "terms",
 130             "termVocabularies",
 131                 "agents",
 132                 "agentData",
 133                 "occurrences",
 134             "references",
 135             "referencedEntities",
 136             "featureData",
 137             "languageData",
 138             "taxonomicNames",
 139             "homotypicalGroups",
 140             "taxa",
 141             "synonyms",
 142             "relationships",
 143             "media"
 144 })
 145 @XmlRootElement(name = "DataSet", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 146 public class DataSet {
 147
 148     // Some fields are of type List and some are of type Set.
 149         // This is mainly because
 150         // the service classes return lists, i.e.
 151     // TaxonServiceImpl.getRootTaxa() returns List<Taxon>
 152         // and the Taxon methods return sets, i.e.
 153     // Taxon.getTaxonomicChildren() returns Set<Taxon>.
 154
 155     @XmlElementWrapper(name = "Agents", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 156     @XmlElements({
 157         @XmlElement(name = "Team", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Team.class),
 158         @XmlElement(name = "Institution", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Institution.class),
 159         @XmlElement(name = "Person", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Person.class)
 160     })
 161     protected List<? extends Agent> agents;
 162
 163     @XmlElementWrapper(name = "AgentData", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 164     @XmlElements({
 165     @XmlElement(name = "Address", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Address.class),
 166     @XmlElement(name = "Contact", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Contact.class),
 167     @XmlElement(name = "InstitutionalMembership", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = InstitutionalMembership.class)
 168     })
 169     protected List<VersionableEntity> agentData;
 170
 171     @XmlElementWrapper(name = "FeatureData", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 172     @XmlElements({
 173     @XmlElement(name = "FeatureNode", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = FeatureNode.class),
 174     @XmlElement(name = "FeatureTree", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = FeatureTree.class)
 175     })
 176 //    protected List<VersionableEntity> featureData;
 177     protected List<VersionableEntity<?>> featureData;
 178
 179     @XmlElementWrapper(name = "LanguageData", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 180     @XmlElements({
 181     @XmlElement(name = "Representation", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = Representation.class),
 182     @XmlElement(name = "LanguageString", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = LanguageString.class)
 183     })
 184     protected List<LanguageStringBase> languageData;
 185
 186     @XmlElementWrapper(name = "Terms", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 187     @XmlElements({
 188         @XmlElement(name = "AbsenceTerm", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = AbsenceTerm.class),
 189         @XmlElement(name = "AnnotationType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = AnnotationType.class),
 190         @XmlElement(name = "BibtexEntryType", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = BibtexEntryType.class),
 191         @XmlElement(name = "Continent", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = Continent.class),
 192         @XmlElement(name = "DerivationEventType", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DerivationEventType.class),
 193         @XmlElement(name = "DeterminationModifier", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DeterminationModifier.class),
 194         @XmlElement(name = "ExtensionType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = ExtensionType.class),
 195         @XmlElement(name = "Feature", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Feature.class),
 196         @XmlElement(name = "HybridRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = HybridRelationshipType.class),
 197         @XmlElement(name = "InstitutionType", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = InstitutionType.class),
 198         @XmlElement(name = "Keyword", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = Keyword.class),
 199         @XmlElement(name = "Language", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = Language.class),
 200         @XmlElement(name = "MarkerType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = MarkerType.class),
 201         @XmlElement(name = "MeasurementUnit", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = MeasurementUnit.class),
 202         @XmlElement(name = "Modifier", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Modifier.class),
 203         @XmlElement(name = "NamedArea", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedArea.class),
 204         @XmlElement(name = "NamedAreaLevel", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedAreaLevel.class),
 205         @XmlElement(name = "NamedAreaType", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedAreaType.class),
 206         @XmlElement(name = "NameRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameRelationshipType.class),
 207         @XmlElement(name = "NomenclaturalCode", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalCode.class),
 208         @XmlElement(name = "NomenclaturalStatusType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalStatusType.class),
 209         @XmlElement(name = "PresenceTerm", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = PresenceTerm.class),
 210         @XmlElement(name = "PreservationMethod", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = PreservationMethod.class),
 211         @XmlElement(name = "Rank", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = Rank.class),
 212         @XmlElement(name = "ReferenceSystem", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = ReferenceSystem.class),
 213         @XmlElement(name = "RightsTerm", namespace = "http://etaxonomy.eu/cdm/model/media/1.0", type = RightsTerm.class),
 214         @XmlElement(name = "Scope", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Scope.class),
 215         @XmlElement(name = "Sex", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Sex.class),
 216         @XmlElement(name = "Stage", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Stage.class),
 217         @XmlElement(name = "State", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = State.class),
 218         @XmlElement(name = "StatisticalMeasure", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = StatisticalMeasure.class),
 219         @XmlElement(name = "SynonymRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = SynonymRelationshipType.class),
 220         @XmlElement(name = "TaxonRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = TaxonRelationshipType.class),
 221         @XmlElement(name = "TextFormat", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = TextFormat.class),
 222         @XmlElement(name = "TypeDesignationStatus", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = TypeDesignationStatus.class),
 223         @XmlElement(name = "WaterbodyOrCountry", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = WaterbodyOrCountry.class)
 224     })
 225     protected List<DefinedTermBase> terms;
 226
 227     @XmlElementWrapper(name = "TermVocabularies", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 228     @XmlElement(name = "TermVocabulary", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
 229     protected List<TermVocabulary<DefinedTermBase>> termVocabularies;
 230
 231     @XmlElementWrapper(name = "Occurrences", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 232     @XmlElements({
 233         @XmlElement(name = "DnaSample", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DnaSample.class),
 234         @XmlElement(name = "FieldObservation", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = FieldObservation.class),
 235         @XmlElement(name = "Fossil", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = Fossil.class),
 236         @XmlElement(name = "LivingBeing", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = LivingBeing.class),
 237         @XmlElement(name = "Observation", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = Observation.class),
 238         @XmlElement(name = "Specimen", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = Specimen.class)
 239     })
 240     protected List<SpecimenOrObservationBase> occurrences;
 241
 242     @XmlElementWrapper(name = "References", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 243     @XmlElements({
 244         @XmlElement(name = "Article", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Article.class),
 245         @XmlElement(name = "Book", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Book.class),
 246         @XmlElement(name = "BookSection", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = BookSection.class),
 247         @XmlElement(name = "CdDvd", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = CdDvd.class),
 248         @XmlElement(name = "Database", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Database.class),
 249         @XmlElement(name = "Generic", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Generic.class),
 250         @XmlElement(name = "InProceedings", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = InProceedings.class),
 251         @XmlElement(name = "Journal", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Journal.class),
 252         @XmlElement(name = "Map", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Map.class),
 253         @XmlElement(name = "Patent", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Patent.class),
 254         @XmlElement(name = "PersonalCommunication", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = PersonalCommunication.class),
 255         @XmlElement(name = "PrintSeries", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = PrintSeries.class),
 256         @XmlElement(name = "Proceedings", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Proceedings.class),
 257         @XmlElement(name = "Report", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Report.class),
 258         @XmlElement(name = "Thesis", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Thesis.class),
 259         @XmlElement(name = "WebPage", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = WebPage.class)
 260     })
 261     protected List<ReferenceBase> references;
 262
 263     @XmlElementWrapper(name = "ReferencedEntities", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 264     @XmlElements({
 265         @XmlElement(name = "NomenclaturalStatus", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalStatus.class),
 266         @XmlElement(name = "NameTypeDesignation", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameTypeDesignation.class),
 267         @XmlElement(name = "SpecimenTypeDesignation", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = SpecimenTypeDesignation.class)
 268     })
 269     protected List<ReferencedEntityBase> referencedEntities;
 270
 271
 272     @XmlElementWrapper(name = "TaxonomicNames", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 273     @XmlElements({
 274         @XmlElement(name = "BacterialName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = BacterialName.class),
 275         @XmlElement(name = "BotanicalName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = BotanicalName.class),
 276         @XmlElement(name = "CultivarPlantName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = CultivarPlantName.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     //protected List<VersionableEntity> media;
 303
 304     @XmlElementWrapper(name = "HomotypicalGroups", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 305     @XmlElement(name = "HomotypicalGroup", namespace = "http://etaxonomy.eu/cdm/model/name/1.0")
 306     protected List<HomotypicalGroup> homotypicalGroups;
 307
 308 //      @XmlElement(name = "TdwgArea", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = TdwgArea.class),
 309
 310         public DataSet () {
 311
 312                 agents = new ArrayList<Agent>();
 313                 agentData = new ArrayList<VersionableEntity>();
 314 //              featureData = new ArrayList<VersionableEntity>();
 315                 featureData = new ArrayList<VersionableEntity<?>>();
 316                 languageData = new ArrayList<LanguageStringBase>();
 317                 terms = new ArrayList<DefinedTermBase>();
 318                 termVocabularies = new ArrayList<TermVocabulary<DefinedTermBase>>();
 319                 occurrences = new ArrayList<SpecimenOrObservationBase>();
 320                 references = new ArrayList<ReferenceBase>();
 321                 referencedEntities = new ArrayList<ReferencedEntityBase>();
 322                 taxonomicNames = new ArrayList<TaxonNameBase>();
 323                 taxa = new ArrayList<Taxon>();
 324                 synonyms = new ArrayList<Synonym>();
 325                 relationships = new HashSet<RelationshipBase>();
 326                 media = new ArrayList<Media>();
 327                 //media = new ArrayList<VersionableEntity>();
 328                 homotypicalGroups = new ArrayList<HomotypicalGroup>();
 329         }
 330
 331     /**
 332      * Gets the value of the agents property.
 333      *
 334      * @return
 335      *     possible object is
 336      *     {@link List<Agent> }
 337      *
 338      */
 339     public List<? extends Agent> getAgents() {
 340         return agents;
 341     }
 342
 343     /**
 344      * Sets the value of the agents property.
 345      *
 346      * @param value
 347      *     allowed object is
 348      *     {@link List<Agent> }
 349      *
 350      */
 351     public void setAgents(List<? extends Agent> value) {
 352         this.agents = value;
 353     }
 354
 355     /**
 356      * Gets the value of the agentData property.
 357      *
 358      * @return
 359      *     possible object is
 360      *     {@link List<VersionableEntity> }
 361      *
 362      */
 363     public List<VersionableEntity> getAgentData() {
 364         return agentData;
 365     }
 366
 367     /**
 368      * Sets the value of the agentData property.
 369      *
 370      * @param value
 371      *     allowed object is
 372      *     {@link List<VersionableEntity> }
 373      *
 374      */
 375     public void setAgentData(List<VersionableEntity> value) {
 376         this.agentData = value;
 377     }
 378
 379     /**
 380      * Gets the value of the terms property.
 381      *
 382      * @return
 383      *     possible object is
 384      *     {@link List<TermBase> }
 385      *
 386      */
 387
 388     //public List<? extends TermBase> getTerms() {
 389     public List<DefinedTermBase> getTerms() {
 390         return terms;
 391     }
 392
 393     /**
 394      * Sets the value of the terms property.
 395      *
 396      * @param value
 397      *     allowed object is
 398      *     {@link List<TermBase> }
 399      *
 400      */
 401     //public void setTerms(List<? extends TermBase> value) {
 402     public void setTerms(List<DefinedTermBase> value) {
 403         this.terms = value;
 404     }
 405
 406     /**
 407      * Gets the value of the term vocabularies property.
 408      *
 409      * @return
 410      *     possible object is
 411      *     {@link List<TermVocabulary> }
 412      *
 413      */
 414
 415     public List<TermVocabulary<DefinedTermBase>> getTermVocabularies() {
 416         return termVocabularies;
 417     }
 418
 419     /**
 420      * Sets the value of the term vocabularies property.
 421      *
 422      * @param value
 423      *     allowed object is
 424      *     {@link List<TermVocabulary> }
 425      *
 426      */
 427     public void setTermVocabularies(List<TermVocabulary<DefinedTermBase>> value) {
 428         this.termVocabularies = value;
 429     }
 430
 431     /**
 432      * Gets the value of the taxonomicNames property.
 433      *
 434      * @return
 435      *     possible object is
 436      *     {@link List<axonNameBase> }
 437      *
 438      */
 439     public List<TaxonNameBase> getTaxonomicNames() {
 440         return taxonomicNames;
 441     }
 442
 443     /**
 444      * Sets the value of the taxonomicNames property.
 445      *
 446      * @param value
 447      *     allowed object is
 448      *     {@link List<TaxonNameBase> }
 449      *
 450      */
 451     public void setTaxonomicNames(List<TaxonNameBase> value) {
 452         this.taxonomicNames = value;
 453     }
 454
 455     /**
 456      * Gets the value of the references property.
 457      *
 458      * @return
 459      *     possible object is
 460      *     {@link List<SpecimenOrObservationBase> }
 461      *
 462      */
 463     public List<SpecimenOrObservationBase> getOccurrences() {
 464         return occurrences;
 465     }
 466
 467     /**
 468      * Sets the value of the references property.
 469      *
 470      * @param value
 471      *     allowed object is
 472      *     {@link List<SpecimenOrObservationBase> }
 473      *
 474      */
 475     public void setOccurrences(List<SpecimenOrObservationBase> value) {
 476         this.occurrences = value;
 477     }
 478
 479     /**
 480      * Gets the value of the references property.
 481      *
 482      * @return
 483      *     possible object is
 484      *     {@link List<ReferenceBase> }
 485      *
 486      */
 487     public List<ReferenceBase> getReferences() {
 488         return references;
 489     }
 490
 491     /**
 492      * Sets the value of the references property.
 493      *
 494      * @param value
 495      *     allowed object is
 496      *     {@link List<ReferenceBase> }
 497      *
 498      */
 499     public void setReferences(List<ReferenceBase> value) {
 500         this.references = value;
 501     }
 502
 503     /**
 504      * Adds the referenced entities in value to the referenced entity property list.
 505      *
 506      * @param value
 507      *     allowed object is
 508      *     {@link Collection<ReferencedEntityBase> }
 509      *
 510      */
 511     public <T extends ReferencedEntityBase> void addReferencedEntities(Collection<T> value) {
 512         for (T referencedEntity: value) {
 513                 this.referencedEntities.add(referencedEntity);
 514         }
 515     }
 516
 517     /**
 518      * Gets the value of the  property.
 519      *
 520      * @return
 521      *     possible object is
 522      *     {@link List<ReferencedEntityBase> }
 523      *
 524      */
 525     public List<ReferencedEntityBase> getReferencedEntities() {
 526         return referencedEntities;
 527     }
 528
 529     /**
 530      * Sets the value of the referencedEntities property.
 531      *
 532      * @param value
 533      *     allowed object is
 534      *     {@link List<ReferencedEntityBase> }
 535      *
 536      */
 537     public void setReferencedEntities(List<? extends ReferencedEntityBase> value) {
 538         this.referencedEntities = new ArrayList<ReferencedEntityBase>();
 539         referencedEntities.addAll(value);
 540     }
 541
 542     /**
 543      * Adds the features in value to the feature data property list.
 544      *
 545      * @param value
 546      *     allowed object is
 547      *     {@link Collection<VersionableEntity> }
 548      *
 549      */
 550     public <T extends VersionableEntity> void addFeatureData(Collection<T> value) {
 551         for (T featureItem: value) {
 552                 this.featureData.add(featureItem);
 553         }
 554     }
 555
 556     /**
 557      * Gets the value of the feature data property.
 558      *
 559      * @return
 560      *     possible object is
 561      *     {@link List<VersionableEntity> }
 562      *
 563      */
 564 //    public List<VersionableEntity> getFeatureData() {
 565     public List<VersionableEntity<?>> getFeatureData() {
 566         return featureData;
 567     }
 568
 569     /**
 570      * Sets the value of the feature data property.
 571      *
 572      * @param value
 573      *     allowed object is
 574      *     {@link List<VersionableEntity> }
 575      *
 576      */
 577     public <T extends VersionableEntity> void setFeatureData(List<T> value) {
 578         featureData = new ArrayList<VersionableEntity<?>>();
 579         for (T featureItem: value) {
 580                 this.featureData.add(featureItem);
 581         }
 582     }
 583
 584 //    public void setFeatureData(List<? extends VersionableEntity> value) {
 585     //public void setFeatureData(List<? extends VersionableEntity<?>> value) {
 586 //        this.featureData = new ArrayList<VersionableEntity>();
 587     //    this.featureData = new ArrayList<VersionableEntity<?>>();
 588     //    featureData.addAll(value);
 589     //}
 590
 591     /**
 592      * Adds the features in value to the language data property list.
 593      *
 594      * @param value
 595      *     allowed object is
 596      *     {@link Collection<LanguageStringBase> }
 597      *
 598      */
 599     public <T extends LanguageStringBase> void addLanguageData(Collection<T> value) {
 600         for (T languageItem: value) {
 601                 this.languageData.add(languageItem);
 602         }
 603     }
 604
 605     /**
 606      * Gets the value of the language data property.
 607      *
 608      * @return
 609      *     possible object is
 610      *     {@link List<LanguageStringBase> }
 611      *
 612      */
 613     public List<LanguageStringBase> getLanguageData() {
 614         return languageData;
 615     }
 616
 617     /**
 618      * Sets the value of the feature data property.
 619      *
 620      * @param value
 621      *     allowed object is
 622      *     {@link List<LanguageStringBase> }
 623      *
 624      */
 625     public void setLanguageData(List<? extends LanguageStringBase> value) {
 626         this.languageData = new ArrayList<LanguageStringBase>();
 627         languageData.addAll(value);
 628     }
 629
 630     /**
 631      * Adds the taxa in value to the taxa property list.
 632      *
 633      * @param value
 634      *     allowed object is
 635      *     {@link Collection<Taxon> }
 636      *
 637      */
 638     public void addTaxa(Collection<Taxon> value) {
 639         for (Taxon taxon: value) {
 640                 this.taxa.add(taxon);
 641         }
 642     }
 643
 644     /**
 645      * Gets the value of the taxa property.
 646      *
 647      * @return
 648      *     possible object is
 649      *     {@link List<Taxon> }
 650      *
 651      */
 652 //    public List<Taxon> getTaxa() {
 653 //        return taxa;
 654 //    }
 655
 656     /**
 657      * Gets the value of the taxa property as {@link Collection<TaxonBase> }
 658      *
 659      * @return
 660      *     possible object is
 661      *     {@link Collection<TaxonBase> }
 662      *
 663      */
 664     public Collection<? extends TaxonBase> getTaxa() {
 665
 666         //TODO can be deleted when everything works
 667         //Object obj = taxa;
 668         //Collection<TaxonBase> taxonBases = (Collection<TaxonBase>)obj;
 669         List<Taxon> list = taxa;
 670         return list;
 671     }
 672
 673     public Collection<TaxonBase> getTaxonBases() {
 674
 675         Collection<TaxonBase> result = new HashSet<TaxonBase>();;
 676         if (taxa != null) {
 677                 result.addAll(taxa);
 678         }
 679         if (synonyms != null) {
 680                 result.addAll(synonyms);
 681         }
 682         return result;
 683     }
 684
 685     /**
 686      * Sets the value of the taxa property.
 687      *
 688      * @param value
 689      *     allowed object is
 690      *     {@link List<Taxon> }
 691      *
 692      */
 693     public void setTaxa(List<Taxon> value) {
 694         this.taxa = value;
 695     }
 696
 697     /**
 698      * Adds the taxon in value to the taxa property list.
 699      *
 700      * @param value
 701      *
 702      */
 703     public void addTaxon(Taxon value) {
 704                 this.taxa.add(value);
 705     }
 706
 707
 708     /**
 709      * Gets the value of the synonyms property.
 710      *
 711      * @return
 712      *     possible object is
 713      *     {@link List<Synonym> }
 714      *
 715      */
 716     public List<Synonym> getSynonyms() {
 717         return synonyms;
 718     }
 719
 720     /**
 721      * Sets the value of the synonyms property.
 722      *
 723      * @param value
 724      *     allowed object is
 725      *     {@link List<Synonym> }
 726      *
 727      */
 728     public void setSynonyms(List<Synonym> value) {
 729         this.synonyms = value;
 730     }
 731
 732     /**
 733      * Adds the synonym in value to the taxa property list.
 734      *
 735      * @param value
 736      *
 737      */
 738     public void addSynonym(Synonym value) {
 739                 this.synonyms.add(value);
 740     }
 741
 742     /**
 743      * Adds the synonym in value to the synonyms property list.
 744      *
 745      * @param value
 746      *     allowed object is
 747      *     {@link Collection<Synonym> }
 748      *
 749      */
 750     public void addSynonyms(Collection<Synonym> value) {
 751         for (Synonym synonym: value) {
 752                 this.synonyms.add(synonym);
 753         }
 754     }
 755
 756     /**
 757      * Gets the value of the relationships property.
 758      *
 759      * @return
 760      *     possible object is
 761      *     {@link Set<RelationshipBase> }
 762      *
 763      */
 764     public Set<RelationshipBase> getRelationships() {
 765         return relationships;
 766     }
 767
 768     /**
 769      * Sets the value of the relationships property.
 770      *
 771      * @param value
 772      *     allowed object is
 773      *     {@link Set<RelationshipBase> }
 774      *
 775      */
 776     public void setRelationships(Set<RelationshipBase> value) {
 777         this.relationships = value;
 778     }
 779
 780     /**
 781      * Adds the relationship in value to the relationships property list.
 782      *
 783      * @param value
 784      *     allowed object is
 785      *     {@link Collection<RelationshipBase> }
 786      *
 787      */
 788     public void addRelationships(Collection<? extends RelationshipBase> value) {
 789         for (RelationshipBase relationship: value) {
 790                 this.relationships.add(relationship);
 791         }
 792     }
 793
 794     /**
 795      * Adds the media in value to the media property list.
 796      *
 797      * @param value
 798      *     allowed object is
 799      *     {@link Collection<VersionableEntity> }
 800      *
 801      */
 802     public <T extends Media> void addMedia(Collection<T> value) {
 803     //public <T extends VersionableEntity> void addMedia(Collection<T> value) {
 804         for (T medium: value) {
 805                 this.media.add(medium);
 806         }
 807     }
 808
 809     /**
 810      * Gets the value of the  property.
 811      *
 812      * @return
 813      *     possible object is
 814      *     {@link List<ReferencedEntityBase> }
 815      *
 816      */
 817     public List<Media> getMedia() {
 818     //public List<VersionableEntity> getMedia() {
 819         return media;
 820     }
 821
 822     /**
 823      * Sets the value of the referencedEntities property.
 824      *
 825      * @param value
 826      *     allowed object is
 827      *     {@link List<ReferencedEntityBase> }
 828      *
 829      */
 830     public void setMedia(List<? extends Media> value) {
 831     //public void setMedia(List<? extends VersionableEntity> value) {
 832         this.media = new ArrayList<Media>();
 833         //this.media = new ArrayList<VersionableEntity>();
 834         media.addAll(value);
 835     }
 836
 837     /**
 838      * Gets the value of the synonyms property.
 839      *
 840      * @return
 841      *     possible object is
 842      *     {@link List<Synonym> }
 843      *
 844      */
 845     public List<HomotypicalGroup> getHomotypicalGroups() {
 846         return homotypicalGroups;
 847     }
 848
 849     /**
 850      * Sets the value of the synonyms property.
 851      *
 852      * @param value
 853      *     allowed object is
 854      *     {@link List<Synonym> }
 855      *
 856      */
 857     public void setHomotypicalGroups(List<HomotypicalGroup> value) {
 858         this.homotypicalGroups = value;
 859     }
 860
 861 }