cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/SDDDataSet.java

   1 /**
   2 * Copyright (C) 2007 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.sdd;
  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 javassist.compiler.ast.Keyword;
  19
  20 import javax.xml.bind.annotation.XmlAccessType;
  21 import javax.xml.bind.annotation.XmlAccessorType;
  22 import javax.xml.bind.annotation.XmlElement;
  23 import javax.xml.bind.annotation.XmlElementWrapper;
  24 import javax.xml.bind.annotation.XmlElements;
  25 import javax.xml.bind.annotation.XmlRootElement;
  26 import javax.xml.bind.annotation.XmlType;
  27
  28 import eu.etaxonomy.cdm.model.agent.Address;
  29 import eu.etaxonomy.cdm.model.agent.AgentBase;
  30 import eu.etaxonomy.cdm.model.agent.Contact;
  31 import eu.etaxonomy.cdm.model.agent.Institution;
  32 import eu.etaxonomy.cdm.model.agent.InstitutionType;
  33 import eu.etaxonomy.cdm.model.agent.InstitutionalMembership;
  34 import eu.etaxonomy.cdm.model.agent.Person;
  35 import eu.etaxonomy.cdm.model.agent.Team;
  36 import eu.etaxonomy.cdm.model.common.AnnotationType;
  37 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  38 import eu.etaxonomy.cdm.model.common.ExtensionType;
  39 import eu.etaxonomy.cdm.model.common.Language;
  40 import eu.etaxonomy.cdm.model.common.LanguageString;
  41 import eu.etaxonomy.cdm.model.common.LanguageStringBase;
  42 import eu.etaxonomy.cdm.model.common.MarkerType;
  43 import eu.etaxonomy.cdm.model.common.ReferencedEntityBase;
  44 import eu.etaxonomy.cdm.model.common.RelationshipBase;
  45 import eu.etaxonomy.cdm.model.common.Representation;
  46 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  47 import eu.etaxonomy.cdm.model.common.VersionableEntity;
  48 import eu.etaxonomy.cdm.model.description.AbsenceTerm;
  49 import eu.etaxonomy.cdm.model.description.Feature;
  50 import eu.etaxonomy.cdm.model.description.FeatureNode;
  51 import eu.etaxonomy.cdm.model.description.FeatureTree;
  52 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
  53 import eu.etaxonomy.cdm.model.description.Modifier;
  54 import eu.etaxonomy.cdm.model.description.PresenceTerm;
  55 import eu.etaxonomy.cdm.model.description.Scope;
  56 import eu.etaxonomy.cdm.model.description.Sex;
  57 import eu.etaxonomy.cdm.model.description.Stage;
  58 import eu.etaxonomy.cdm.model.description.State;
  59 import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
  60 import eu.etaxonomy.cdm.model.description.TextFormat;
  61 import eu.etaxonomy.cdm.model.location.Continent;
  62 import eu.etaxonomy.cdm.model.location.NamedArea;
  63 import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
  64 import eu.etaxonomy.cdm.model.location.NamedAreaType;
  65 import eu.etaxonomy.cdm.model.location.ReferenceSystem;
  66 import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
  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.Rank;
  82 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  83 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  84 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  85 import eu.etaxonomy.cdm.model.name.ViralName;
  86 import eu.etaxonomy.cdm.model.name.ZoologicalName;
  87 import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
  88 import eu.etaxonomy.cdm.model.occurrence.DeterminationModifier;
  89 import eu.etaxonomy.cdm.model.occurrence.FieldObservation;
  90 import eu.etaxonomy.cdm.model.occurrence.Fossil;
  91 import eu.etaxonomy.cdm.model.occurrence.LivingBeing;
  92 import eu.etaxonomy.cdm.model.occurrence.Observation;
  93 import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
  94 import eu.etaxonomy.cdm.model.occurrence.Specimen;
  95 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  96 /*import eu.etaxonomy.cdm.model.reference.Article;
  97 import eu.etaxonomy.cdm.model.reference.Book;
  98 import eu.etaxonomy.cdm.model.reference.BookSection;
  99 import eu.etaxonomy.cdm.model.reference.CdDvd;
 100 import eu.etaxonomy.cdm.model.reference.Database;
 101 import eu.etaxonomy.cdm.model.reference.Generic;
 102 import eu.etaxonomy.cdm.model.reference.InProceedings;
 103 import eu.etaxonomy.cdm.model.reference.Journal;
 104 import eu.etaxonomy.cdm.model.reference.Map;
 105 import eu.etaxonomy.cdm.model.reference.Patent;
 106 import eu.etaxonomy.cdm.model.reference.PersonalCommunication;
 107 import eu.etaxonomy.cdm.model.reference.PrintSeries;
 108 import eu.etaxonomy.cdm.model.reference.Proceedings;*/
 109 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
 110 /*import eu.etaxonomy.cdm.model.reference.Report;
 111 import eu.etaxonomy.cdm.model.reference.Thesis;
 112 import eu.etaxonomy.cdm.model.reference.WebPage;*/
 113 import eu.etaxonomy.cdm.model.taxon.Synonym;
 114 import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
 115 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
 116 import eu.etaxonomy.cdm.model.taxon.Taxon;
 117 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
 118 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
 119 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
 120
 121 /**
 122  * @author a.babadshanjan
 123  */
 124 @XmlAccessorType(XmlAccessType.FIELD)
 125 @XmlType(name = "", propOrder = {
 126             "terms",
 127             "termVocabularies",
 128                 "agents",
 129                 "agentData",
 130                 "occurrences",
 131             "references",
 132             "referencedEntities",
 133             "featureData",
 134             "languageData",
 135             "taxonomicNames",
 136             "homotypicalGroups",
 137             "taxa",
 138             "synonyms",
 139             "relationships",
 140             "media"
 141 })
 142 @XmlRootElement(name = "DataSet", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 143 public class SDDDataSet {
 144
 145     // Some fields are of type List and some are of type Set.
 146         // This is mainly because
 147         // the service classes return lists, i.e.
 148     // TaxonServiceImpl.getRootTaxa() returns List<Taxon>
 149         // and the Taxon methods return sets, i.e.
 150     // Taxon.getTaxonomicChildren() returns Set<Taxon>.
 151
 152     @XmlElementWrapper(name = "Agents")
 153     @XmlElements({
 154         @XmlElement(name = "Team", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Team.class),
 155         @XmlElement(name = "Institution", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Institution.class),
 156         @XmlElement(name = "Person", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Person.class)
 157     })
 158     protected List<? extends AgentBase> agents;
 159
 160     @XmlElementWrapper(name = "AgentData")
 161     @XmlElements({
 162     @XmlElement(name = "Address", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Address.class),
 163     @XmlElement(name = "Contact", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Contact.class),
 164     @XmlElement(name = "InstitutionalMembership", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = InstitutionalMembership.class)
 165     })
 166     protected List<VersionableEntity> agentData;
 167
 168     @XmlElementWrapper(name = "FeatureData")
 169     @XmlElements({
 170     @XmlElement(name = "FeatureNode", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = FeatureNode.class),
 171     @XmlElement(name = "FeatureTree", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = FeatureTree.class)
 172     })
 173 //    protected List<VersionableEntity> featureData;
 174     protected List<VersionableEntity> featureData;
 175
 176     @XmlElementWrapper(name = "LanguageData")
 177     @XmlElements({
 178     @XmlElement(name = "Representation", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = Representation.class),
 179     @XmlElement(name = "LanguageString", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = LanguageString.class)
 180     })
 181     protected List<LanguageStringBase> languageData;
 182
 183     @XmlElementWrapper(name = "Terms")
 184     @XmlElements({
 185         @XmlElement(name = "AbsenceTerm", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = AbsenceTerm.class),
 186         @XmlElement(name = "AnnotationType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = AnnotationType.class),
 187         @XmlElement(name = "Continent", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = Continent.class),
 188         @XmlElement(name = "DerivationEventType", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DerivationEventType.class),
 189         @XmlElement(name = "DeterminationModifier", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DeterminationModifier.class),
 190         @XmlElement(name = "ExtensionType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = ExtensionType.class),
 191         @XmlElement(name = "Feature", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Feature.class),
 192         @XmlElement(name = "HybridRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = HybridRelationshipType.class),
 193         @XmlElement(name = "InstitutionType", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = InstitutionType.class),
 194         @XmlElement(name = "Language", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = Language.class),
 195         @XmlElement(name = "MarkerType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = MarkerType.class),
 196         @XmlElement(name = "MeasurementUnit", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = MeasurementUnit.class),
 197         @XmlElement(name = "Modifier", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Modifier.class),
 198         @XmlElement(name = "NamedArea", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedArea.class),
 199         @XmlElement(name = "NamedAreaLevel", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedAreaLevel.class),
 200         @XmlElement(name = "NamedAreaType", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedAreaType.class),
 201         @XmlElement(name = "NameRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameRelationshipType.class),
 202         @XmlElement(name = "NomenclaturalCode", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalCode.class),
 203         @XmlElement(name = "NomenclaturalStatusType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalStatusType.class),
 204         @XmlElement(name = "PresenceTerm", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = PresenceTerm.class),
 205         @XmlElement(name = "PreservationMethod", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = PreservationMethod.class),
 206         @XmlElement(name = "Rank", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = Rank.class),
 207         @XmlElement(name = "ReferenceSystem", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = ReferenceSystem.class),
 208         @XmlElement(name = "RightsTerm", namespace = "http://etaxonomy.eu/cdm/model/media/1.0", type = RightsTerm.class),
 209         @XmlElement(name = "Scope", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Scope.class),
 210         @XmlElement(name = "Sex", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Sex.class),
 211         @XmlElement(name = "Stage", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Stage.class),
 212         @XmlElement(name = "State", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = State.class),
 213         @XmlElement(name = "StatisticalMeasure", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = StatisticalMeasure.class),
 214         @XmlElement(name = "SynonymRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = SynonymRelationshipType.class),
 215         @XmlElement(name = "TaxonRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = TaxonRelationshipType.class),
 216         @XmlElement(name = "TextFormat", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = TextFormat.class),
 217         @XmlElement(name = "TypeDesignationStatus", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = SpecimenTypeDesignationStatus.class),
 218         @XmlElement(name = "WaterbodyOrCountry", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = WaterbodyOrCountry.class)
 219     })
 220     protected List<DefinedTermBase> terms;
 221
 222     @XmlElementWrapper(name = "TermVocabularies")
 223     @XmlElement(name = "TermVocabulary", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
 224     protected List<TermVocabulary<DefinedTermBase>> termVocabularies;
 225
 226     @XmlElementWrapper(name = "Occurrences")
 227     @XmlElements({
 228         @XmlElement(name = "DnaSample", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DnaSample.class),
 229         @XmlElement(name = "FieldObservation", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = FieldObservation.class),
 230         @XmlElement(name = "Fossil", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = Fossil.class),
 231         @XmlElement(name = "LivingBeing", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = LivingBeing.class),
 232         @XmlElement(name = "Observation", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = Observation.class),
 233         @XmlElement(name = "Specimen", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = Specimen.class)
 234     })
 235     protected List<SpecimenOrObservationBase> occurrences;
 236
 237     @XmlElementWrapper(name = "References")
 238         @XmlElement(name = "Reference", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = ReferenceBase.class)
 239
 240     protected List<ReferenceBase> references;
 241
 242     @XmlElementWrapper(name = "ReferencedEntities")
 243     @XmlElements({
 244         @XmlElement(name = "NomenclaturalStatus", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalStatus.class),
 245         @XmlElement(name = "NameTypeDesignation", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameTypeDesignation.class),
 246         @XmlElement(name = "SpecimenTypeDesignation", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = SpecimenTypeDesignation.class)
 247     })
 248     protected List<ReferencedEntityBase> referencedEntities;
 249
 250
 251     @XmlElementWrapper(name = "TaxonomicNames")
 252     @XmlElements({
 253         @XmlElement(name = "BacterialName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = BacterialName.class),
 254         @XmlElement(name = "BotanicalName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = BotanicalName.class),
 255         @XmlElement(name = "CultivarPlantName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = CultivarPlantName.class),
 256         @XmlElement(name = "ViralName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = ViralName.class),
 257         @XmlElement(name = "ZoologicalName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = ZoologicalName.class)
 258     })
 259     protected List<TaxonNameBase> taxonomicNames;
 260
 261     @XmlElementWrapper(name = "Taxa")
 262     @XmlElement(name = "Taxon", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0")
 263     protected List<Taxon> taxa;
 264
 265     @XmlElementWrapper(name = "Synonyms")
 266     @XmlElement(name = "Synonym", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0")
 267     protected List<Synonym> synonyms;
 268
 269     @XmlElementWrapper(name = "Relationships")
 270     @XmlElements({
 271         @XmlElement(name = "TaxonRelationship", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = TaxonRelationship.class),
 272         @XmlElement(name = "SynonymRelationship", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = SynonymRelationship.class),
 273         @XmlElement(name = "NameRelationship", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameRelationship.class),
 274         @XmlElement(name = "HybridRelationship", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = HybridRelationship.class)
 275     })
 276     protected Set<RelationshipBase> relationships;
 277
 278     @XmlElementWrapper(name = "Media_")
 279     @XmlElement(name = "Media", namespace = "http://etaxonomy.eu/cdm/model/media/1.0")
 280     protected List<VersionableEntity> media;
 281
 282     @XmlElementWrapper(name = "HomotypicalGroups")
 283     @XmlElement(name = "HomotypicalGroup", namespace = "http://etaxonomy.eu/cdm/model/name/1.0")
 284     protected List<HomotypicalGroup> homotypicalGroups;
 285
 286 //      @XmlElement(name = "TdwgArea", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = TdwgArea.class),
 287
 288         public SDDDataSet () {
 289
 290                 agents = new ArrayList<AgentBase>();
 291                 agentData = new ArrayList<VersionableEntity>();
 292 //              featureData = new ArrayList<VersionableEntity>();
 293                 featureData = new ArrayList<VersionableEntity>();
 294                 languageData = new ArrayList<LanguageStringBase>();
 295                 terms = new ArrayList<DefinedTermBase>();
 296                 termVocabularies = new ArrayList<TermVocabulary<DefinedTermBase>>();
 297                 occurrences = new ArrayList<SpecimenOrObservationBase>();
 298                 references = new ArrayList<ReferenceBase>();
 299                 referencedEntities = new ArrayList<ReferencedEntityBase>();
 300                 taxonomicNames = new ArrayList<TaxonNameBase>();
 301                 taxa = new ArrayList<Taxon>();
 302                 synonyms = new ArrayList<Synonym>();
 303                 relationships = new HashSet<RelationshipBase>();
 304                 media = new ArrayList<VersionableEntity>();
 305                 homotypicalGroups = new ArrayList<HomotypicalGroup>();
 306         }
 307
 308     /**
 309      * Gets the value of the agents property.
 310      *
 311      * @return
 312      *     possible object is
 313      *     {@link List<Agent> }
 314      *
 315      */
 316     public List<? extends AgentBase> getAgents() {
 317         return agents;
 318     }
 319
 320     /**
 321      * Sets the value of the agents property.
 322      *
 323      * @param value
 324      *     allowed object is
 325      *     {@link List<Agent> }
 326      *
 327      */
 328     public void setAgents(List<? extends AgentBase> value) {
 329         this.agents = value;
 330     }
 331
 332     /**
 333      * Gets the value of the agentData property.
 334      *
 335      * @return
 336      *     possible object is
 337      *     {@link List<VersionableEntity> }
 338      *
 339      */
 340     public List<VersionableEntity> getAgentData() {
 341         return agentData;
 342     }
 343
 344     /**
 345      * Sets the value of the agentData property.
 346      *
 347      * @param value
 348      *     allowed object is
 349      *     {@link List<VersionableEntity> }
 350      *
 351      */
 352     public void setAgentData(List<VersionableEntity> value) {
 353         this.agentData = value;
 354     }
 355
 356     /**
 357      * Gets the value of the terms property.
 358      *
 359      * @return
 360      *     possible object is
 361      *     {@link List<TermBase> }
 362      *
 363      */
 364
 365     //public List<? extends TermBase> getTerms() {
 366     public List<DefinedTermBase> getTerms() {
 367         return terms;
 368     }
 369
 370     /**
 371      * Sets the value of the terms property.
 372      *
 373      * @param value
 374      *     allowed object is
 375      *     {@link List<TermBase> }
 376      *
 377      */
 378     //public void setTerms(List<? extends TermBase> value) {
 379     public void setTerms(List<DefinedTermBase> value) {
 380         this.terms = value;
 381     }
 382
 383     /**
 384      * Gets the value of the term vocabularies property.
 385      *
 386      * @return
 387      *     possible object is
 388      *     {@link List<TermVocabulary> }
 389      *
 390      */
 391
 392     public List<TermVocabulary<DefinedTermBase>> getTermVocabularies() {
 393         return termVocabularies;
 394     }
 395
 396     /**
 397      * Sets the value of the term vocabularies property.
 398      *
 399      * @param value
 400      *     allowed object is
 401      *     {@link List<TermVocabulary> }
 402      *
 403      */
 404     public void setTermVocabularies(List<TermVocabulary<DefinedTermBase>> value) {
 405         this.termVocabularies = value;
 406     }
 407
 408     /**
 409      * Gets the value of the taxonomicNames property.
 410      *
 411      * @return
 412      *     possible object is
 413      *     {@link List<axonNameBase> }
 414      *
 415      */
 416     public List<TaxonNameBase> getTaxonomicNames() {
 417         return taxonomicNames;
 418     }
 419
 420     /**
 421      * Sets the value of the taxonomicNames property.
 422      *
 423      * @param value
 424      *     allowed object is
 425      *     {@link List<TaxonNameBase> }
 426      *
 427      */
 428     public void setTaxonomicNames(List<TaxonNameBase> value) {
 429         this.taxonomicNames = value;
 430     }
 431
 432     /**
 433      * Gets the value of the references property.
 434      *
 435      * @return
 436      *     possible object is
 437      *     {@link List<SpecimenOrObservationBase> }
 438      *
 439      */
 440     public List<SpecimenOrObservationBase> getOccurrences() {
 441         return occurrences;
 442     }
 443
 444     /**
 445      * Sets the value of the references property.
 446      *
 447      * @param value
 448      *     allowed object is
 449      *     {@link List<SpecimenOrObservationBase> }
 450      *
 451      */
 452     public void setOccurrences(List<SpecimenOrObservationBase> value) {
 453         this.occurrences = value;
 454     }
 455
 456     /**
 457      * Gets the value of the references property.
 458      *
 459      * @return
 460      *     possible object is
 461      *     {@link List<ReferenceBase> }
 462      *
 463      */
 464     public List<ReferenceBase> getReferences() {
 465         return references;
 466     }
 467
 468     /**
 469      * Sets the value of the references property.
 470      *
 471      * @param value
 472      *     allowed object is
 473      *     {@link List<ReferenceBase> }
 474      *
 475      */
 476     public void setReferences(List<ReferenceBase> value) {
 477         this.references = value;
 478     }
 479
 480     /**
 481      * Adds the referenced entities in value to the referenced entity property list.
 482      *
 483      * @param value
 484      *     allowed object is
 485      *     {@link Collection<ReferencedEntityBase> }
 486      *
 487      */
 488     public <T extends ReferencedEntityBase> void addReferencedEntities(Collection<T> value) {
 489         for (T referencedEntity: value) {
 490                 this.referencedEntities.add(referencedEntity);
 491         }
 492     }
 493
 494     /**
 495      * Gets the value of the  property.
 496      *
 497      * @return
 498      *     possible object is
 499      *     {@link List<ReferencedEntityBase> }
 500      *
 501      */
 502     public List<ReferencedEntityBase> getReferencedEntities() {
 503         return referencedEntities;
 504     }
 505
 506     /**
 507      * Sets the value of the referencedEntities property.
 508      *
 509      * @param value
 510      *     allowed object is
 511      *     {@link List<ReferencedEntityBase> }
 512      *
 513      */
 514     public void setReferencedEntities(List<? extends ReferencedEntityBase> value) {
 515         this.referencedEntities = new ArrayList<ReferencedEntityBase>();
 516         referencedEntities.addAll(value);
 517     }
 518
 519     /**
 520      * Adds the features in value to the feature data property list.
 521      *
 522      * @param value
 523      *     allowed object is
 524      *     {@link Collection<VersionableEntity> }
 525      *
 526      */
 527     public <T extends VersionableEntity> void addFeatureData(Collection<T> value) {
 528         for (T featureItem: value) {
 529                 this.featureData.add(featureItem);
 530         }
 531     }
 532
 533     /**
 534      * Gets the value of the feature data property.
 535      *
 536      * @return
 537      *     possible object is
 538      *     {@link List<VersionableEntity> }
 539      *
 540      */
 541 //    public List<VersionableEntity> getFeatureData() {
 542     public List<VersionableEntity> getFeatureData() {
 543         return featureData;
 544     }
 545
 546     /**
 547      * Sets the value of the feature data property.
 548      *
 549      * @param value
 550      *     allowed object is
 551      *     {@link List<VersionableEntity> }
 552      *
 553      */
 554     public <T extends VersionableEntity> void setFeatureData(List<T> value) {
 555         featureData = new ArrayList<VersionableEntity>();
 556         for (T featureItem: value) {
 557                 this.featureData.add(featureItem);
 558         }
 559     }
 560
 561 //    public void setFeatureData(List<? extends VersionableEntity> value) {
 562     //public void setFeatureData(List<? extends VersionableEntity<?>> value) {
 563 //        this.featureData = new ArrayList<VersionableEntity>();
 564     //    this.featureData = new ArrayList<VersionableEntity<?>>();
 565     //    featureData.addAll(value);
 566     //}
 567
 568     /**
 569      * Adds the features in value to the language data property list.
 570      *
 571      * @param value
 572      *     allowed object is
 573      *     {@link Collection<LanguageStringBase> }
 574      *
 575      */
 576     public <T extends LanguageStringBase> void addLanguageData(Collection<T> value) {
 577         for (T languageItem: value) {
 578                 this.languageData.add(languageItem);
 579         }
 580     }
 581
 582     /**
 583      * Gets the value of the language data property.
 584      *
 585      * @return
 586      *     possible object is
 587      *     {@link List<LanguageStringBase> }
 588      *
 589      */
 590     public List<LanguageStringBase> getLanguageData() {
 591         return languageData;
 592     }
 593
 594     /**
 595      * Sets the value of the feature data property.
 596      *
 597      * @param value
 598      *     allowed object is
 599      *     {@link List<LanguageStringBase> }
 600      *
 601      */
 602     public void setLanguageData(List<? extends LanguageStringBase> value) {
 603         this.languageData = new ArrayList<LanguageStringBase>();
 604         languageData.addAll(value);
 605     }
 606
 607     /**
 608      * Adds the taxa in value to the taxa property list.
 609      *
 610      * @param value
 611      *     allowed object is
 612      *     {@link Collection<Taxon> }
 613      *
 614      */
 615     public void addTaxa(Collection<Taxon> value) {
 616         for (Taxon taxon: value) {
 617                 this.taxa.add(taxon);
 618         }
 619     }
 620
 621     /**
 622      * Gets the value of the taxa property.
 623      *
 624      * @return
 625      *     possible object is
 626      *     {@link List<Taxon> }
 627      *
 628      */
 629 //    public List<Taxon> getTaxa() {
 630 //        return taxa;
 631 //    }
 632
 633     /**
 634      * Gets the value of the taxa property as {@link Collection<TaxonBase> }
 635      *
 636      * @return
 637      *     possible object is
 638      *     {@link Collection<TaxonBase> }
 639      *
 640      */
 641     public Collection<? extends TaxonBase> getTaxa() {
 642
 643         //TODO can be deleted when everything works
 644         //Object obj = taxa;
 645         //Collection<TaxonBase> taxonBases = (Collection<TaxonBase>)obj;
 646         List<Taxon> list = taxa;
 647         return list;
 648     }
 649
 650     public Collection<TaxonBase> getTaxonBases() {
 651
 652         Collection<TaxonBase> result = new HashSet<TaxonBase>();;
 653         if (taxa != null) {
 654                 result.addAll(taxa);
 655         }
 656         if (synonyms != null) {
 657                 result.addAll(synonyms);
 658         }
 659         return result;
 660     }
 661
 662     /**
 663      * Sets the value of the taxa property.
 664      *
 665      * @param value
 666      *     allowed object is
 667      *     {@link List<Taxon> }
 668      *
 669      */
 670     public void setTaxa(List<Taxon> value) {
 671         this.taxa = value;
 672     }
 673
 674     /**
 675      * Adds the taxon in value to the taxa property list.
 676      *
 677      * @param value
 678      *
 679      */
 680     public void addTaxon(Taxon value) {
 681                 this.taxa.add(value);
 682     }
 683
 684
 685     /**
 686      * Gets the value of the synonyms property.
 687      *
 688      * @return
 689      *     possible object is
 690      *     {@link List<Synonym> }
 691      *
 692      */
 693     public List<Synonym> getSynonyms() {
 694         return synonyms;
 695     }
 696
 697     /**
 698      * Sets the value of the synonyms property.
 699      *
 700      * @param value
 701      *     allowed object is
 702      *     {@link List<Synonym> }
 703      *
 704      */
 705     public void setSynonyms(List<Synonym> value) {
 706         this.synonyms = value;
 707     }
 708
 709     /**
 710      * Adds the synonym in value to the taxa property list.
 711      *
 712      * @param value
 713      *
 714      */
 715     public void addSynonym(Synonym value) {
 716                 this.synonyms.add(value);
 717     }
 718
 719     /**
 720      * Adds the synonym in value to the synonyms property list.
 721      *
 722      * @param value
 723      *     allowed object is
 724      *     {@link Collection<Synonym> }
 725      *
 726      */
 727     public void addSynonyms(Collection<Synonym> value) {
 728         for (Synonym synonym: value) {
 729                 this.synonyms.add(synonym);
 730         }
 731     }
 732
 733     /**
 734      * Gets the value of the relationships property.
 735      *
 736      * @return
 737      *     possible object is
 738      *     {@link Set<RelationshipBase> }
 739      *
 740      */
 741     public Set<RelationshipBase> getRelationships() {
 742         return relationships;
 743     }
 744
 745     /**
 746      * Sets the value of the relationships property.
 747      *
 748      * @param value
 749      *     allowed object is
 750      *     {@link Set<RelationshipBase> }
 751      *
 752      */
 753     public void setRelationships(Set<RelationshipBase> value) {
 754         this.relationships = value;
 755     }
 756
 757     /**
 758      * Adds the relationship in value to the relationships property list.
 759      *
 760      * @param value
 761      *     allowed object is
 762      *     {@link Collection<RelationshipBase> }
 763      *
 764      */
 765     public void addRelationships(Collection<? extends RelationshipBase> value) {
 766         for (RelationshipBase relationship: value) {
 767                 this.relationships.add(relationship);
 768         }
 769     }
 770
 771     /**
 772      * Adds the media in value to the media property list.
 773      *
 774      * @param value
 775      *     allowed object is
 776      *     {@link Collection<VersionableEntity> }
 777      *
 778      */
 779     public <T extends VersionableEntity> void addMedia(Collection<T> value) {
 780         for (T medium: value) {
 781                 this.media.add(medium);
 782         }
 783     }
 784
 785     /**
 786      * Gets the value of the  property.
 787      *
 788      * @return
 789      *     possible object is
 790      *     {@link List<ReferencedEntityBase> }
 791      *
 792      */
 793     public List<VersionableEntity> getMedia() {
 794         return media;
 795     }
 796
 797     /**
 798      * Sets the value of the referencedEntities property.
 799      *
 800      * @param value
 801      *     allowed object is
 802      *     {@link List<ReferencedEntityBase> }
 803      *
 804      */
 805     public void setMedia(List<? extends VersionableEntity> value) {
 806         this.media = new ArrayList<VersionableEntity>();
 807         media.addAll(value);
 808     }
 809
 810     /**
 811      * Gets the value of the synonyms property.
 812      *
 813      * @return
 814      *     possible object is
 815      *     {@link List<Synonym> }
 816      *
 817      */
 818     public List<HomotypicalGroup> getHomotypicalGroups() {
 819         return homotypicalGroups;
 820     }
 821
 822     /**
 823      * Sets the value of the synonyms property.
 824      *
 825      * @param value
 826      *     allowed object is
 827      *     {@link List<Synonym> }
 828      *
 829      */
 830     public void setHomotypicalGroups(List<HomotypicalGroup> value) {
 831         this.homotypicalGroups = value;
 832     }
 833
 834 }