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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.model.description;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import javax.persistence.Entity;
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import javax.persistence.FetchType;
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import javax.persistence.JoinColumn;
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import javax.persistence.JoinTable;
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import javax.persistence.ManyToMany;
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import javax.persistence.OneToMany;
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import javax.persistence.Transient;
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import javax.xml.bind.annotation.XmlAccessType;
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import javax.xml.bind.annotation.XmlAccessorType;
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import javax.xml.bind.annotation.XmlElement;
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import javax.xml.bind.annotation.XmlElementWrapper;
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import javax.xml.bind.annotation.XmlIDREF;
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import javax.xml.bind.annotation.XmlRootElement;
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import javax.xml.bind.annotation.XmlSchemaType;
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import javax.xml.bind.annotation.XmlType;
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import org.apache.log4j.Logger;
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import org.hibernate.annotations.Cascade;
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import org.hibernate.annotations.CascadeType;
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import org.hibernate.envers.Audited;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.Representation;
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import eu.etaxonomy.cdm.model.common.TermType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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/**
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* The class for individual properties (also designed as character, type or
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* category) of observed phenomena able to be described or measured. It also
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* covers categories of informations on {@link TaxonName taxon names} not
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* taken in account in {@link NomenclaturalCode nomenclature}.<BR>
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* Descriptions require features in order to be structured and disaggregated
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* in {@link DescriptionElementBase description elements}.<BR>
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* Experts do not use the word feature for the actual description
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* but only for the property itself. Therefore naming this class FeatureType
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* would have leaded to confusion.
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* <P>
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* Since features are {@link DefinedTermBase defined terms} they have a hierarchical
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* structure that allows to specify ("kind of") or generalize
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* ("generalization of") features. "Kind of" / "generalization of" relations
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* are bidirectional (a feature F1 is a "Kind of" a feature F2 if and only
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* if the feature F2 is a "generalization of" the feature F1. This hierarchical
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* structure has nothing in common with {@link FeatureTree feature trees} used for determination.
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* <P>
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* A standard set of feature instances will be automatically
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* created as the project starts. But this class allows to extend this standard
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* set by creating new instances of additional features if needed.<BR>
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* <P>
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* This class corresponds to DescriptionsSectionType according to the SDD
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* schema.
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*
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* @author m.doering
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* @created 08-Nov-2007 13:06:24
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*/
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@XmlAccessorType(XmlAccessType.PROPERTY)
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@XmlType(name="Feature", factoryMethod="NewInstance", propOrder = {
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"kindOf",
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"generalizationOf",
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"partOf",
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"includes",
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"supportsTextData",
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"supportsQuantitativeData",
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"supportsDistribution",
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"supportsIndividualAssociation",
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"supportsTaxonInteraction",
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"supportsCommonTaxonName",
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"supportsCategoricalData",
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"recommendedModifierEnumeration",
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"recommendedStatisticalMeasures",
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"supportedCategoricalEnumerations",
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"recommendedMeasurementUnits",
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"inverseRepresentations"
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})
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@XmlRootElement(name = "Feature")
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@Entity
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//@Indexed disabled to reduce clutter in indexes, since this type is not used by any search
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//@Indexed(index = "eu.etaxonomy.cdm.model.common.DefinedTermBase")
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@Audited
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public class Feature extends DefinedTermBase<Feature> {
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private static final long serialVersionUID = 6754598791831848704L;
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private static final Logger logger = Logger.getLogger(Feature.class);
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protected static Map<UUID, Feature> termMap = null;
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private boolean supportsTextData = true; //by default text data should be always supported
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private boolean supportsQuantitativeData;
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private boolean supportsDistribution;
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private boolean supportsIndividualAssociation;
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private boolean supportsTaxonInteraction;
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private boolean supportsCategoricalData;
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private boolean supportsCommonTaxonName;
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/* for M:M see #4843 */
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@ManyToMany(fetch = FetchType.LAZY)
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@JoinTable(name="DefinedTermBase_RecommendedModifierEnumeration")
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private final Set<TermVocabulary<DefinedTerm>> recommendedModifierEnumeration = new HashSet<>();
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@ManyToMany(fetch = FetchType.LAZY)
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@JoinTable(name="DefinedTermBase_StatisticalMeasure")
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private final Set<StatisticalMeasure> recommendedStatisticalMeasures = new HashSet<>();
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/* for M:M see #4843 */
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@ManyToMany(fetch = FetchType.LAZY)
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@JoinTable(name="DefinedTermBase_SupportedCategoricalEnumeration")
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private final Set<TermVocabulary<State>> supportedCategoricalEnumerations = new HashSet<>();
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@ManyToMany(fetch = FetchType.LAZY)
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@JoinTable(name="DefinedTermBase_MeasurementUnit")
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private final Set<MeasurementUnit> recommendedMeasurementUnits = new HashSet<>();
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//copy from RelationshipTermBase
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@XmlElementWrapper(name = "InverseRepresentations")
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@XmlElement(name = "Representation")
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@OneToMany(fetch = FetchType.LAZY, orphanRemoval=true)
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@JoinTable(name="TermBase_inverseRepresentation",
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joinColumns=@JoinColumn(name="term_id")
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)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
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// @IndexedEmbedded(depth = 2)
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private Set<Representation> inverseRepresentations = new HashSet<>();
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private static final UUID uuidUnknown = UUID.fromString("910307f1-dc3c-452c-a6dd-af5ac7cd365c");
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public static final UUID uuidDescription = UUID.fromString("9087cdcd-8b08-4082-a1de-34c9ba9fb493");
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private static final UUID uuidDistribution = UUID.fromString("9fc9d10c-ba50-49ee-b174-ce83fc3f80c6");
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private static final UUID uuidDistributionGeneral = UUID.fromString("fd8c64f0-6ea5-44b0-9f70-e95833d6076e");
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private static final UUID uuidEcology = UUID.fromString("aa923827-d333-4cf5-9a5f-438ae0a4746b");
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private static final UUID uuidHabitat = UUID.fromString("fb16929f-bc9c-456f-9d40-dec987b36438");
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private static final UUID uuidHabitatAndEcology = UUID.fromString("9fdc4663-4d56-47d0-90b5-c0bf251bafbb");
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private static final UUID uuidChromosomeNumber = UUID.fromString("6f677e98-d8d5-4bc5-80bf-affdb7e3945a");
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private static final UUID uuidBiologyEcology = UUID.fromString("9832e24f-b670-43b4-ac7c-20a7261a1d8c");
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private static final UUID uuidKey = UUID.fromString("a677f827-22b9-4205-bb37-11cb48dd9106");
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private static final UUID uuidMaterialsExamined = UUID.fromString("7c0c7571-a864-47c1-891d-01f59000dae1");
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private static final UUID uuidMaterialsMethods = UUID.fromString("1e87d9c3-0844-4a03-9686-773e2ccb3ab6");
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private static final UUID uuidEtymology = UUID.fromString("dd653d48-355c-4aec-a4e7-724f6eb29f8d");
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private static final UUID uuidDiagnosis = UUID.fromString("d43d8501-ceab-4caa-9e51-e87138528fac");
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private static final UUID uuidProtologue = UUID.fromString("71b356c5-1e3f-4f5d-9b0f-c2cf8ae7779f");
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public static final UUID uuidCommonName = UUID.fromString("fc810911-51f0-4a46-ab97-6562fe263ae5");
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private static final UUID uuidPhenology = UUID.fromString("a7786d3e-7c58-4141-8416-346d4c80c4a2");
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private static final UUID uuidOccurrence = UUID.fromString("5deff505-1a32-4817-9a74-50e6936fd630");
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private static final UUID uuidCitation = UUID.fromString("99b2842f-9aa7-42fa-bd5f-7285311e0101");
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private static final UUID uuidAdditionalPublication = UUID.fromString("2c355c16-cb04-4858-92bf-8da8d56dea95");
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public static final UUID uuidUses = UUID.fromString("e5374d39-b210-47c7-bec1-bee05b5f1cb6");
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private static final UUID uuidConservation = UUID.fromString("4518fc20-2492-47de-b345-777d2b83c9cf");
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private static final UUID uuidCultivation = UUID.fromString("e28965b2-a367-48c5-b954-8afc8ac2c69b");
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private static final UUID uuidIntroduction = UUID.fromString("e75255ca-8ff4-4905-baad-f842927fe1d3");
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private static final UUID uuidDiscussion = UUID.fromString("d3c4cbb6-0025-4322-886b-cd0156753a25");
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public static final UUID uuidImage = UUID.fromString("84193b2c-327f-4cce-90ef-c8da18fd5bb5");
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private static final UUID uuidAnatomy = UUID.fromString("94213b2c-e67a-4d37-25ef-e8d316edfba1");
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private static final UUID uuidHostPlant = UUID.fromString("6e9de1d5-05f0-40d5-8786-2fe30d0d894d");
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private static final UUID uuidPathogenAgent = UUID.fromString("002d05f2-fd72-49f1-ba4d-196cf09240b5");
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private static final UUID uuidIndividualsAssociation = UUID.fromString("e2308f37-ddc5-447d-b483-5e2171dd85fd");
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public static final UUID uuidSpecimen = UUID.fromString("8200e050-d5fd-4cac-8a76-4b47afb13809");
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private static final UUID uuidObservation = UUID.fromString("f59e747d-0b4f-4bf7-b69a-cbd50bc78595");
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private static final UUID uuidStatus = UUID.fromString("86d40635-2a63-4ad6-be75-9faa4a6a57fb");
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private static final UUID uuidSystematics = UUID.fromString("bd9aca17-cd0e-4418-a3a1-1a4b80dbc162");
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private static final UUID uuidUseRecord = UUID.fromString("8125a59d-b4d5-4485-89ea-67306297b599");
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private static final UUID uuidNotes = UUID.fromString("b5780b45-6439-4f3c-9818-d89d26d36eb2");
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public static final UUID uuidLifeform = UUID.fromString("db9228d3-8bbf-4460-abfe-0b1326c82f8e");
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/* ***************** CONSTRUCTOR AND FACTORY METHODS **********************************/
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/**
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* Creates a new empty feature instance.
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*
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* @see #NewInstance(String, String, String)
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*/
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public static Feature NewInstance() {
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return new Feature();
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}
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/**
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* Creates a new feature instance with a description (in the {@link Language#DEFAULT() default language}),
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* a label and a label abbreviation.
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*
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* @param description the string (in the default language) describing the
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* new feature to be created
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* @param label the string identifying the new feature to be created
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* @param labelAbbrev the string identifying (in abbreviated form) the
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* new feature to be created
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* @see #readCsvLine(List, Language)
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* @see #NewInstance()
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*/
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public static Feature NewInstance(String description, String label, String labelAbbrev){
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return new Feature(description, label, labelAbbrev);
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}
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//for hibernate use only
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@Deprecated
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protected Feature() {
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super(TermType.Feature);
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}
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/**
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* Class constructor: creates a new feature instance with a description (in the {@link Language#DEFAULT() default language}),
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* a label and a label abbreviation.
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*
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* @param term the string (in the default language) describing the
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* new feature to be created
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* @param label the string identifying the new feature to be created
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* @param labelAbbrev the string identifying (in abbreviated form) the
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* new feature to be created
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* @see #Feature()
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*/
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protected Feature(String term, String label, String labelAbbrev) {
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super(TermType.Feature, term, label, labelAbbrev);
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}
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/* *************************************************************************************/
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@Override
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public void resetTerms(){
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termMap = null;
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}
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/**
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* Returns the boolean value of the flag indicating whether <i>this</i>
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* feature can be described with {@link QuantitativeData quantitative data} (true)
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* or not (false). If this flag is set <i>this</i> feature can only apply to
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* {@link TaxonDescription taxon descriptions} or {@link SpecimenDescription specimen descriptions}.
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*
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* @return the boolean value of the supportsQuantitativeData flag
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*/
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@XmlElement(name = "SupportsQuantitativeData")
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public boolean isSupportsQuantitativeData() {
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return supportsQuantitativeData;
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}
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/**
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* @see #isSupportsQuantitativeData()
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*/
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public void setSupportsQuantitativeData(boolean supportsQuantitativeData) {
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this.supportsQuantitativeData = supportsQuantitativeData;
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}
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/**
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* Returns the boolean value of the flag indicating whether <i>this</i>
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* feature can be described with {@link TextData text data} (true)
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* or not (false).
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*
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* @return the boolean value of the supportsTextData flag
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*/
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@XmlElement(name = "SupportsTextData")
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public boolean isSupportsTextData() {
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return supportsTextData;
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}
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/**
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* @see #isSupportsTextData()
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*/
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public void setSupportsTextData(boolean supportsTextData) {
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this.supportsTextData = supportsTextData;
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}
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/**
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* Returns the boolean value of the flag indicating whether <i>this</i>
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* feature can be described with {@link Distribution distribution} objects
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* (true) or not (false). This flag is set if and only if <i>this</i> feature
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* is the {@link #DISTRIBUTION() distribution feature}.
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*
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* @return the boolean value of the supportsDistribution flag
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*/
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@XmlElement(name = "SupportsDistribution")
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public boolean isSupportsDistribution() {
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return supportsDistribution;
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}
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/**
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* @see #isSupportsDistribution()
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*/
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public void setSupportsDistribution(boolean supportsDistribution) {
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this.supportsDistribution = supportsDistribution;
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}
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/**
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* Returns the boolean value of the flag indicating whether <i>this</i>
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* feature can be described with {@link IndividualsAssociation individuals associations}
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* (true) or not (false).
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*
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* @return the boolean value of the supportsIndividualAssociation flag
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*/
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@XmlElement(name = "SupportsIndividualAssociation")
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public boolean isSupportsIndividualAssociation() {
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return supportsIndividualAssociation;
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}
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/**
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* @see #isSupportsIndividualAssociation()
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*/
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public void setSupportsIndividualAssociation(
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boolean supportsIndividualAssociation) {
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this.supportsIndividualAssociation = supportsIndividualAssociation;
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}
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/**
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* Returns the boolean value of the flag indicating whether <i>this</i>
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* feature can be described with {@link TaxonInteraction taxon interactions}
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* (true) or not (false).
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*
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* @return the boolean value of the supportsTaxonInteraction flag
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*/
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@XmlElement(name = "SupportsTaxonInteraction")
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public boolean isSupportsTaxonInteraction() {
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return supportsTaxonInteraction;
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}
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/**
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* @see #isSupportsTaxonInteraction()
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*/
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public void setSupportsTaxonInteraction(boolean supportsTaxonInteraction) {
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this.supportsTaxonInteraction = supportsTaxonInteraction;
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}
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/**
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* Returns the boolean value of the flag indicating whether <i>this</i>
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* feature can be described with {@link CommonTaxonName common names}
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* (true) or not (false). This flag is set if and only if <i>this</i> feature
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* is the {@link #COMMON_NAME() common name feature}.
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*
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* @return the boolean value of the supportsCommonTaxonName flag
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*/
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@XmlElement(name = "SupportsCommonTaxonName")
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public boolean isSupportsCommonTaxonName() {
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return supportsCommonTaxonName;
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}
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/**
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* @see #isSupportsTaxonInteraction()
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*/
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public void setSupportsCommonTaxonName(boolean supportsCommonTaxonName) {
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this.supportsCommonTaxonName = supportsCommonTaxonName;
|
370
|
}
|
371
|
|
372
|
/**
|
373
|
* Returns the boolean value of the flag indicating whether <i>this</i>
|
374
|
* feature can be described with {@link CategoricalData categorical data}
|
375
|
* (true) or not (false).
|
376
|
*
|
377
|
* @return the boolean value of the supportsCategoricalData flag
|
378
|
*/
|
379
|
@XmlElement(name = "SupportsCategoricalData")
|
380
|
public boolean isSupportsCategoricalData() {
|
381
|
return supportsCategoricalData;
|
382
|
}
|
383
|
|
384
|
/**
|
385
|
* @see #supportsCategoricalData()
|
386
|
*/
|
387
|
public void setSupportsCategoricalData(boolean supportsCategoricalData) {
|
388
|
this.supportsCategoricalData = supportsCategoricalData;
|
389
|
}
|
390
|
|
391
|
|
392
|
/**
|
393
|
* Returns the set of {@link TermVocabulary term vocabularies} containing the
|
394
|
* {@link Modifier modifiers} recommended to be used for {@link DescriptionElementBase description elements}
|
395
|
* with <i>this</i> feature.
|
396
|
*
|
397
|
*/
|
398
|
@XmlElementWrapper(name = "RecommendedModifierEnumerations")
|
399
|
@XmlElement(name = "RecommendedModifierEnumeration")
|
400
|
@XmlIDREF
|
401
|
@XmlSchemaType(name = "IDREF")
|
402
|
public Set<TermVocabulary<DefinedTerm>> getRecommendedModifierEnumeration() {
|
403
|
return recommendedModifierEnumeration;
|
404
|
}
|
405
|
|
406
|
/**
|
407
|
* Adds a {@link TermVocabulary term vocabulary} (with {@link Modifier modifiers}) to the set of
|
408
|
* {@link #getRecommendedModifierEnumeration() recommended modifier vocabularies} assigned
|
409
|
* to <i>this</i> feature.
|
410
|
*
|
411
|
* @param recommendedModifierEnumeration the term vocabulary to be added
|
412
|
* @see #getRecommendedModifierEnumeration()
|
413
|
*/
|
414
|
public void addRecommendedModifierEnumeration(
|
415
|
TermVocabulary<DefinedTerm> recommendedModifierEnumeration) {
|
416
|
this.recommendedModifierEnumeration.add(recommendedModifierEnumeration);
|
417
|
}
|
418
|
/**
|
419
|
* Removes one element from the set of {@link #getRecommendedModifierEnumeration() recommended modifier vocabularies}
|
420
|
* assigned to <i>this</i> feature.
|
421
|
*
|
422
|
* @param recommendedModifierEnumeration the term vocabulary which should be removed
|
423
|
* @see #getRecommendedModifierEnumeration()
|
424
|
* @see #addRecommendedModifierEnumeration(TermVocabulary)
|
425
|
*/
|
426
|
public void removeRecommendedModifierEnumeration(
|
427
|
TermVocabulary<DefinedTerm> recommendedModifierEnumeration) {
|
428
|
this.recommendedModifierEnumeration.remove(recommendedModifierEnumeration);
|
429
|
}
|
430
|
|
431
|
/**
|
432
|
* Returns the set of {@link StatisticalMeasure statistical measures} recommended to be used
|
433
|
* in case of {@link QuantitativeData quantitative data} with <i>this</i> feature.
|
434
|
*/
|
435
|
@XmlElementWrapper(name = "RecommendedStatisticalMeasures")
|
436
|
@XmlElement(name = "RecommendedStatisticalMeasure")
|
437
|
@XmlIDREF
|
438
|
@XmlSchemaType(name = "IDREF")
|
439
|
public Set<StatisticalMeasure> getRecommendedStatisticalMeasures() {
|
440
|
return recommendedStatisticalMeasures;
|
441
|
}
|
442
|
|
443
|
/**
|
444
|
* Adds a {@link StatisticalMeasure statistical measure} to the set of
|
445
|
* {@link #getRecommendedStatisticalMeasures() recommended statistical measures} assigned
|
446
|
* to <i>this</i> feature.
|
447
|
*
|
448
|
* @param recommendedStatisticalMeasure the statistical measure to be added
|
449
|
* @see #getRecommendedStatisticalMeasures()
|
450
|
*/
|
451
|
public void addRecommendedStatisticalMeasure(
|
452
|
StatisticalMeasure recommendedStatisticalMeasure) {
|
453
|
this.recommendedStatisticalMeasures.add(recommendedStatisticalMeasure);
|
454
|
}
|
455
|
/**
|
456
|
* Removes one element from the set of {@link #getRecommendedStatisticalMeasures() recommended statistical measures}
|
457
|
* assigned to <i>this</i> feature.
|
458
|
*
|
459
|
* @param recommendedStatisticalMeasure the statistical measure which should be removed
|
460
|
* @see #getRecommendedStatisticalMeasures()
|
461
|
* @see #addRecommendedStatisticalMeasure(StatisticalMeasure)
|
462
|
*/
|
463
|
public void removeRecommendedStatisticalMeasure(
|
464
|
StatisticalMeasure recommendedStatisticalMeasure) {
|
465
|
this.recommendedStatisticalMeasures.remove(recommendedStatisticalMeasure);
|
466
|
}
|
467
|
|
468
|
/**
|
469
|
* Returns the set of {@link StatisticalMeasure statistical measures} recommended to be used
|
470
|
* in case of {@link QuantitativeData quantitative data} with <i>this</i> feature.
|
471
|
*/
|
472
|
@XmlElementWrapper(name = "RecommendedMeasurementUnits")
|
473
|
@XmlElement(name = "RecommendedMeasurementUnit")
|
474
|
@XmlIDREF
|
475
|
@XmlSchemaType(name = "IDREF")
|
476
|
public Set<MeasurementUnit> getRecommendedMeasurementUnits() {
|
477
|
return recommendedMeasurementUnits;
|
478
|
}
|
479
|
|
480
|
/**
|
481
|
* Adds a {@link StatisticalMeasure statistical measure} to the set of
|
482
|
* {@link #getRecommendedStatisticalMeasures() recommended statistical measures} assigned
|
483
|
* to <i>this</i> feature.
|
484
|
*
|
485
|
* @param recommendedStatisticalMeasure the statistical measure to be added
|
486
|
* @see #getRecommendedStatisticalMeasures()
|
487
|
*/
|
488
|
public void addRecommendedMeasurementUnit(
|
489
|
MeasurementUnit recommendedMeasurementUnit) {
|
490
|
this.recommendedMeasurementUnits.add(recommendedMeasurementUnit);
|
491
|
}
|
492
|
/**
|
493
|
* Removes one element from the set of {@link #getRecommendedStatisticalMeasures() recommended statistical measures}
|
494
|
* assigned to <i>this</i> feature.
|
495
|
*
|
496
|
* @param recommendedStatisticalMeasure the statistical measure which should be removed
|
497
|
* @see #getRecommendedStatisticalMeasures()
|
498
|
* @see #addRecommendedStatisticalMeasure(StatisticalMeasure)
|
499
|
*/
|
500
|
public void removeRecommendedMeasurementUnit(
|
501
|
MeasurementUnit recommendedMeasurementUnit) {
|
502
|
this.recommendedMeasurementUnits.remove(recommendedMeasurementUnit);
|
503
|
}
|
504
|
|
505
|
/**
|
506
|
* Returns the set of {@link TermVocabulary term vocabularies} containing the list of
|
507
|
* possible {@link State states} to be used in {@link CategoricalData categorical data}
|
508
|
* with <i>this</i> feature.
|
509
|
*
|
510
|
*/
|
511
|
@XmlElementWrapper(name = "SupportedCategoricalEnumerations")
|
512
|
@XmlElement(name = "SupportedCategoricalEnumeration")
|
513
|
@XmlIDREF
|
514
|
@XmlSchemaType(name = "IDREF")
|
515
|
public Set<TermVocabulary<State>> getSupportedCategoricalEnumerations() {
|
516
|
return supportedCategoricalEnumerations;
|
517
|
}
|
518
|
|
519
|
/**
|
520
|
* Adds a {@link TermVocabulary term vocabulary} to the set of
|
521
|
* {@link #getSupportedCategoricalEnumerations() supported state vocabularies} assigned
|
522
|
* to <i>this</i> feature.
|
523
|
*
|
524
|
* @param supportedCategoricalEnumeration the term vocabulary which should be removed
|
525
|
* @see #getSupportedCategoricalEnumerations()
|
526
|
*/
|
527
|
public void addSupportedCategoricalEnumeration(
|
528
|
TermVocabulary<State> supportedCategoricalEnumeration) {
|
529
|
this.supportedCategoricalEnumerations.add(supportedCategoricalEnumeration);
|
530
|
}
|
531
|
/**
|
532
|
* Removes one element from the set of {@link #getSupportedCategoricalEnumerations() supported state vocabularies}
|
533
|
* assigned to <i>this</i> feature.
|
534
|
*
|
535
|
* @param supportedCategoricalEnumeration the term vocabulary which should be removed
|
536
|
* @see #getSupportedCategoricalEnumerations()
|
537
|
* @see #addSupportedCategoricalEnumeration(TermVocabulary)
|
538
|
*/
|
539
|
public void removeSupportedCategoricalEnumeration(
|
540
|
TermVocabulary<State> supportedCategoricalEnumeration) {
|
541
|
this.supportedCategoricalEnumerations.remove(supportedCategoricalEnumeration);
|
542
|
}
|
543
|
|
544
|
@XmlElement(name = "KindOf", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
545
|
@XmlIDREF
|
546
|
@XmlSchemaType(name = "IDREF")
|
547
|
@Override
|
548
|
public Feature getKindOf(){
|
549
|
return super.getKindOf();
|
550
|
}
|
551
|
|
552
|
@Override
|
553
|
public void setKindOf(Feature kindOf){
|
554
|
super.setKindOf(kindOf);
|
555
|
}
|
556
|
|
557
|
@Override
|
558
|
@XmlElement(name = "PartOf", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
559
|
@XmlIDREF
|
560
|
@XmlSchemaType(name = "IDREF")
|
561
|
public Feature getPartOf(){
|
562
|
return super.getPartOf();
|
563
|
}
|
564
|
|
565
|
@Override
|
566
|
public void setPartOf(Feature partOf){
|
567
|
super.setPartOf(partOf);
|
568
|
}
|
569
|
|
570
|
@Override
|
571
|
@XmlElementWrapper(name = "Generalizations", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
572
|
@XmlElement(name = "GeneralizationOf", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
573
|
@XmlIDREF
|
574
|
@XmlSchemaType(name = "IDREF")
|
575
|
public Set<Feature> getGeneralizationOf(){
|
576
|
return super.getGeneralizationOf();
|
577
|
}
|
578
|
|
579
|
@Override
|
580
|
protected void setGeneralizationOf(Set<Feature> value){
|
581
|
super.setGeneralizationOf(value);
|
582
|
}
|
583
|
|
584
|
@Override
|
585
|
@XmlElementWrapper(name = "Includes", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
586
|
@XmlElement(name = "Include", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
587
|
@XmlIDREF
|
588
|
@XmlSchemaType(name = "IDREF")
|
589
|
public Set<Feature> getIncludes(){
|
590
|
return super.getIncludes();
|
591
|
}
|
592
|
|
593
|
@Override
|
594
|
protected void setIncludes(Set<Feature> includes) {
|
595
|
super.setIncludes(includes);
|
596
|
}
|
597
|
|
598
|
// ***************** Invers Label *****************************************/
|
599
|
|
600
|
public Set<Representation> getInverseRepresentations() {
|
601
|
return inverseRepresentations;
|
602
|
}
|
603
|
public void addInverseRepresentation(Representation inverseRepresentation) {
|
604
|
this.inverseRepresentations.add(inverseRepresentation);
|
605
|
}
|
606
|
public void removeInverseRepresentation(Representation inverseRepresentation) {
|
607
|
this.inverseRepresentations.remove(inverseRepresentation);
|
608
|
}
|
609
|
/*
|
610
|
* Inverse representation convenience methods similar to TermBase.xxx
|
611
|
* @see eu.etaxonomy.cdm.model.common.TermBase#getLabel()
|
612
|
*/
|
613
|
@Transient
|
614
|
public String getInverseLabel() {
|
615
|
if(getInverseLabel(Language.DEFAULT()) != null){
|
616
|
return this.getInverseRepresentation(Language.DEFAULT()).getLabel();
|
617
|
}else{
|
618
|
for (Representation r : inverseRepresentations){
|
619
|
return r.getLabel();
|
620
|
}
|
621
|
}
|
622
|
return super.getUuid().toString();
|
623
|
}
|
624
|
public String getInverseLabel(Language lang) {
|
625
|
Representation r = this.getInverseRepresentation(lang);
|
626
|
if(r==null){
|
627
|
return null;
|
628
|
}else{
|
629
|
return r.getLabel();
|
630
|
}
|
631
|
}
|
632
|
public Representation getInverseRepresentation(Language lang) {
|
633
|
Representation result = null;
|
634
|
for (Representation repr : this.getInverseRepresentations()){
|
635
|
if (lang.equals(repr.getLanguage())){
|
636
|
result = repr;
|
637
|
}
|
638
|
}
|
639
|
return result;
|
640
|
}
|
641
|
// ****************** END INVERS REPRESENTATION **************************/
|
642
|
|
643
|
/**
|
644
|
* Creates and returns a new feature instance on the basis of a given string
|
645
|
* list (containing an UUID, an URI, a label and a description) and a given
|
646
|
* {@link Language language} to be associated with the description. Furthermore
|
647
|
* the flags concerning the supported subclasses of {@link DescriptionElementBase description elements}
|
648
|
* are set according to a particular string belonging to the given
|
649
|
* string list.<BR>
|
650
|
* This method overrides the readCsvLine method from {@link DefinedTermBase#readCsvLine(List, Language) DefinedTermBase}.
|
651
|
*
|
652
|
* @param csvLine the string list with elementary information for attributes
|
653
|
* @param lang the language in which the description has been formulated
|
654
|
* @see #NewInstance(String, String, String)
|
655
|
*/
|
656
|
@Override
|
657
|
public Feature readCsvLine(Class<Feature> termClass, List<String> csvLine, Map<UUID,DefinedTermBase> terms, boolean abbrevAsId) {
|
658
|
Feature newInstance = super.readCsvLine(termClass, csvLine, terms, abbrevAsId);
|
659
|
String text = csvLine.get(4);
|
660
|
if (text != null && text.length() >= 6){
|
661
|
if ("1".equals(text.substring(0, 1))){newInstance.setSupportsTextData(true);}
|
662
|
if ("1".equals(text.substring(1, 2))){newInstance.setSupportsQuantitativeData(true);}
|
663
|
if ("1".equals(text.substring(2, 3))){newInstance.setSupportsDistribution(true);}
|
664
|
if ("1".equals(text.substring(3, 4))){newInstance.setSupportsIndividualAssociation(true);}
|
665
|
if ("1".equals(text.substring(4, 5))){newInstance.setSupportsTaxonInteraction(true);}
|
666
|
if ("1".equals(text.substring(5, 6))){newInstance.setSupportsCommonTaxonName(true);}
|
667
|
if (text.length() > 6 && "1".equals(text.substring(6, 7))){newInstance.setSupportsCategoricalData(true);}
|
668
|
//there is no abbreviated label for features yet, if there is one in future we need to increment the index for supportXXX form 4 to 5
|
669
|
newInstance.getRepresentation(Language.DEFAULT()).setAbbreviatedLabel(null);
|
670
|
}
|
671
|
return newInstance;
|
672
|
}
|
673
|
|
674
|
//******************************* STATIC METHODS *****************************************
|
675
|
|
676
|
protected static Feature getTermByUuid(UUID uuid){
|
677
|
if (termMap == null || termMap.isEmpty()){
|
678
|
return getTermByClassAndUUID(Feature.class, uuid);
|
679
|
} else {
|
680
|
return termMap.get(uuid);
|
681
|
}
|
682
|
}
|
683
|
|
684
|
/**
|
685
|
* Returns the "unknown" feature. This feature allows to store values of
|
686
|
* {@link DescriptionElementBase description elements} even if it is momentarily
|
687
|
* not known what they mean.
|
688
|
*/
|
689
|
public static final Feature UNKNOWN(){
|
690
|
return getTermByUuid(uuidUnknown);
|
691
|
}
|
692
|
|
693
|
/**
|
694
|
* Returns the "description" feature. This feature allows to handle global
|
695
|
* {@link DescriptionElementBase description elements} for a global {@link DescriptionBase description}.<BR>
|
696
|
* The "description" feature is the highest level feature.
|
697
|
*/
|
698
|
public static final Feature DESCRIPTION(){
|
699
|
return getTermByUuid(uuidDescription);
|
700
|
}
|
701
|
|
702
|
/**
|
703
|
* Returns the "distribution" feature. This feature allows to handle only
|
704
|
* {@link Distribution distributions}.
|
705
|
*
|
706
|
* @see #isSupportsDistribution()
|
707
|
*/
|
708
|
public static final Feature DISTRIBUTION(){
|
709
|
return getTermByUuid(uuidDistribution);
|
710
|
}
|
711
|
|
712
|
/**
|
713
|
* Returns the feature for general text-based
|
714
|
* distributions
|
715
|
*/
|
716
|
public static final Feature DISTRIBUTION_GENERAL(){
|
717
|
return getTermByUuid(uuidDistributionGeneral);
|
718
|
}
|
719
|
|
720
|
/**
|
721
|
* Returns the "discussion" feature. This feature can only be described
|
722
|
* with {@link TextData text data}.
|
723
|
*
|
724
|
* @see #isSupportsTextData()
|
725
|
*/
|
726
|
public static final Feature DISCUSSION(){
|
727
|
return getTermByUuid(uuidDiscussion);
|
728
|
}
|
729
|
|
730
|
/**
|
731
|
* Returns the "ecology" feature. This feature only applies
|
732
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
733
|
* The "ecology" feature generalizes all other possible features concerning
|
734
|
* ecological matters.
|
735
|
*/
|
736
|
public static final Feature ECOLOGY(){
|
737
|
return getTermByUuid(uuidEcology);
|
738
|
}
|
739
|
|
740
|
/**
|
741
|
* Returns the "habitat" feature. This feature only applies
|
742
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
743
|
* The "habitat" feature generalizes all other possible features concerning
|
744
|
* habitat matters.
|
745
|
*/
|
746
|
public static final Feature HABITAT(){
|
747
|
return getTermByUuid(uuidHabitat);
|
748
|
}
|
749
|
|
750
|
|
751
|
/**
|
752
|
* Returns the "habitat & ecology" feature. This feature only applies
|
753
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
754
|
* The "habitat & ecology" feature generalizes all other possible features concerning
|
755
|
* habitat and ecology matters.
|
756
|
*/
|
757
|
public static final Feature HABITAT_ECOLOGY(){
|
758
|
return getTermByUuid(uuidHabitatAndEcology);
|
759
|
}
|
760
|
|
761
|
/**
|
762
|
* Returns the "biology_ecology" feature. This feature only applies
|
763
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
764
|
* The "biology_ecology" feature generalizes all possible features concerning
|
765
|
* biological aspects of ecological matters.
|
766
|
*
|
767
|
* @see #ECOLOGY()
|
768
|
*/
|
769
|
public static final Feature BIOLOGY_ECOLOGY(){
|
770
|
return getTermByUuid(uuidBiologyEcology);
|
771
|
}
|
772
|
|
773
|
/**
|
774
|
* Returns the "chromosome number" feature. This feature only applies
|
775
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
776
|
*/
|
777
|
public static final Feature CHROMOSOME_NUMBER(){
|
778
|
return getTermByUuid(uuidChromosomeNumber);
|
779
|
}
|
780
|
|
781
|
|
782
|
/**
|
783
|
* Returns the "key" feature. This feature is the "upper" feature generalizing
|
784
|
* all features being used within an identification key.
|
785
|
*/
|
786
|
public static final Feature KEY(){
|
787
|
return getTermByUuid(uuidKey);
|
788
|
}
|
789
|
|
790
|
|
791
|
/**
|
792
|
* Returns the "materials_examined" feature. This feature can only be described
|
793
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}
|
794
|
* mentioning which material has been examined in order to accomplish
|
795
|
* the description. This feature applies only to
|
796
|
* {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.
|
797
|
*/
|
798
|
public static final Feature MATERIALS_EXAMINED(){
|
799
|
return getTermByUuid(uuidMaterialsExamined);
|
800
|
}
|
801
|
|
802
|
/**
|
803
|
* Returns the "materials_methods" feature. This feature can only be described
|
804
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}
|
805
|
* mentioning which methods have been adopted to analyze the material in
|
806
|
* order to accomplish the description. This feature applies only to
|
807
|
* {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.
|
808
|
*/
|
809
|
public static final Feature MATERIALS_METHODS(){
|
810
|
return getTermByUuid(uuidMaterialsMethods);
|
811
|
}
|
812
|
|
813
|
/**
|
814
|
* Returns the "etymology" feature. This feature can only be described
|
815
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}
|
816
|
* giving some information about the history of the taxon name. This feature applies only to
|
817
|
* {@link TaxonNameDescription taxon name descriptions}.
|
818
|
*/
|
819
|
public static final Feature ETYMOLOGY(){
|
820
|
return getTermByUuid(uuidEtymology);
|
821
|
}
|
822
|
|
823
|
/**
|
824
|
* Returns the "diagnosis" feature. This feature can only be described
|
825
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}.
|
826
|
* This feature applies only to {@link SpecimenDescription specimen descriptions} or to
|
827
|
* {@link TaxonDescription taxon descriptions}.
|
828
|
*/
|
829
|
public static final Feature DIAGNOSIS(){
|
830
|
return getTermByUuid(uuidDiagnosis);
|
831
|
}
|
832
|
|
833
|
|
834
|
/**
|
835
|
* Returns the "introduction" feature. This feature can only be described
|
836
|
* with {@link TextData text data}.
|
837
|
*
|
838
|
* @see #isSupportsTextData()
|
839
|
*/
|
840
|
public static final Feature INTRODUCTION(){
|
841
|
return getTermByUuid(uuidIntroduction);
|
842
|
}
|
843
|
|
844
|
/**
|
845
|
* Returns the "protologue" feature. This feature can only be described
|
846
|
* with {@link TextData text data} reproducing the content of the protologue
|
847
|
* (or some information about it) of the taxon name. This feature applies only to
|
848
|
* {@link TaxonNameDescription taxon name descriptions}.
|
849
|
*
|
850
|
* @see #isSupportsTextData()
|
851
|
*/
|
852
|
public static final Feature PROTOLOGUE(){
|
853
|
return getTermByUuid(uuidProtologue);
|
854
|
}
|
855
|
|
856
|
/**
|
857
|
* Returns the "common_name" feature. This feature allows to handle only
|
858
|
* {@link CommonTaxonName common names}.
|
859
|
*
|
860
|
* @see #isSupportsCommonTaxonName()
|
861
|
*/
|
862
|
public static final Feature COMMON_NAME(){
|
863
|
return getTermByUuid(uuidCommonName);
|
864
|
}
|
865
|
|
866
|
/**
|
867
|
* Returns the "phenology" feature. This feature can only be described
|
868
|
* with {@link CategoricalData categorical data} or eventually with {@link TextData text data}
|
869
|
* containing information time about recurring natural phenomena.
|
870
|
* This feature only applies to {@link TaxonDescription taxon descriptions}.<BR>
|
871
|
* The "phenology" feature generalizes all other possible features
|
872
|
* concerning time information about particular natural phenomena
|
873
|
* (such as "first flight of butterflies").
|
874
|
*/
|
875
|
public static final Feature PHENOLOGY(){
|
876
|
return getTermByUuid(uuidPhenology);
|
877
|
}
|
878
|
|
879
|
/**
|
880
|
* Returns the "occurrence" feature.
|
881
|
*/
|
882
|
public static final Feature OCCURRENCE(){
|
883
|
return getTermByUuid(uuidOccurrence);
|
884
|
}
|
885
|
|
886
|
/**
|
887
|
* Returns the "anatomy" feature.
|
888
|
*/
|
889
|
public static final Feature ANATOMY(){
|
890
|
return getTermByUuid(uuidAnatomy);
|
891
|
}
|
892
|
/**
|
893
|
* Returns the "hostplant" feature.
|
894
|
*/
|
895
|
public static final Feature HOSTPLANT(){
|
896
|
return getTermByUuid(uuidHostPlant);
|
897
|
}
|
898
|
/**
|
899
|
* Returns the "pathogen agent" feature.
|
900
|
*/
|
901
|
public static final Feature PATHOGEN_AGENT(){
|
902
|
return getTermByUuid(uuidPathogenAgent);
|
903
|
}
|
904
|
|
905
|
/**
|
906
|
* Returns the "citation" feature. This feature can only be described
|
907
|
* with {@link TextData text data}.
|
908
|
*
|
909
|
* @see #isSupportsTextData()
|
910
|
*/
|
911
|
public static final Feature CITATION(){
|
912
|
return getTermByUuid(uuidCitation);
|
913
|
}
|
914
|
|
915
|
/**
|
916
|
* Returns the "additional_publication" feature. This feature can only be
|
917
|
* described with {@link TextData text data} with information about a
|
918
|
* publication where a {@link TaxonName taxon name} has also been published
|
919
|
* but which is not the {@link TaxonName#getNomenclaturalReference() nomenclatural reference}.
|
920
|
* This feature applies only to {@link TaxonNameDescription taxon name descriptions}.
|
921
|
*
|
922
|
* @see #isSupportsTextData()
|
923
|
*/
|
924
|
public static final Feature ADDITIONAL_PUBLICATION(){
|
925
|
return getTermByUuid(uuidAdditionalPublication);
|
926
|
}
|
927
|
|
928
|
|
929
|
/**
|
930
|
* Returns the "uses" feature. This feature only applies
|
931
|
* to {@link TaxonDescription taxon descriptions}.<BR>
|
932
|
* The "uses" feature generalizes all other possible features concerning
|
933
|
* particular uses (for instance "industrial use of seeds").
|
934
|
*/
|
935
|
public static final Feature USES(){
|
936
|
return getTermByUuid(uuidUses);
|
937
|
}
|
938
|
|
939
|
public static final Feature USERECORD(){
|
940
|
return getTermByUuid(uuidUseRecord);
|
941
|
}
|
942
|
|
943
|
/**
|
944
|
* Returns the "notes" feature. Used for
|
945
|
* taxonomic notes.
|
946
|
*/
|
947
|
public static final Feature NOTES(){
|
948
|
return getTermByUuid(uuidNotes);
|
949
|
}
|
950
|
|
951
|
/**
|
952
|
* Returns the "conservation" feature. This feature only applies
|
953
|
* to {@link SpecimenDescription specimen descriptions} and generalizes
|
954
|
* methods and conditions for the conservation of {@link Specimen specimens}.<BR>
|
955
|
*/
|
956
|
public static final Feature CONSERVATION(){
|
957
|
return getTermByUuid(uuidConservation);
|
958
|
}
|
959
|
|
960
|
|
961
|
/**
|
962
|
* Returns the "cultivation" feature.
|
963
|
*/
|
964
|
public static final Feature CULTIVATION(){
|
965
|
return getTermByUuid(uuidCultivation);
|
966
|
}
|
967
|
|
968
|
|
969
|
/**
|
970
|
* Returns the "image" feature.
|
971
|
*/
|
972
|
public static final Feature IMAGE(){
|
973
|
return getTermByUuid(uuidImage);
|
974
|
}
|
975
|
|
976
|
/**
|
977
|
* Returns the "individuals association" feature.
|
978
|
*/
|
979
|
public static final Feature INDIVIDUALS_ASSOCIATION(){
|
980
|
Feature individuals_association = getTermByUuid(uuidIndividualsAssociation);
|
981
|
Set<Feature> generalizationOf = new HashSet<Feature>();
|
982
|
generalizationOf.add(SPECIMEN());
|
983
|
generalizationOf.add(OBSERVATION());
|
984
|
individuals_association.setGeneralizationOf(generalizationOf);
|
985
|
return individuals_association;
|
986
|
|
987
|
}
|
988
|
|
989
|
public static final Feature SPECIMEN(){
|
990
|
return getTermByUuid(uuidSpecimen);
|
991
|
}
|
992
|
|
993
|
public static final Feature OBSERVATION(){
|
994
|
return getTermByUuid(uuidObservation);
|
995
|
}
|
996
|
|
997
|
/**
|
998
|
* The status of a taxon. Usually the status should be determined within a {@link Distribution distribution}.
|
999
|
* If this is not possible for some reason (e.g. the area is not well defined) the status feature
|
1000
|
* may be used.
|
1001
|
* @return
|
1002
|
*/
|
1003
|
public static final Feature STATUS(){
|
1004
|
return getTermByUuid(uuidStatus);
|
1005
|
}
|
1006
|
|
1007
|
public static final Feature SYSTEMATICS(){
|
1008
|
return getTermByUuid(uuidSystematics);
|
1009
|
}
|
1010
|
|
1011
|
public static final Feature LIFEFORM(){
|
1012
|
return getTermByUuid(uuidLifeform);
|
1013
|
}
|
1014
|
|
1015
|
/**
|
1016
|
* Returns the "hybrid_parent" feature. This feature can only be used
|
1017
|
* by {@link TaxonInteraction taxon interactions}.<BR>
|
1018
|
* <P>
|
1019
|
* Note: It must be distinguished between hybrid relationships as
|
1020
|
* relevant nomenclatural relationships between {@link BotanicalName plant names}
|
1021
|
* on the one side and the biological relation between two {@link Taxon taxa}
|
1022
|
* as it is here the case on the other one.
|
1023
|
*
|
1024
|
* @see #isSupportsTaxonInteraction()
|
1025
|
* @see HybridRelationshipType
|
1026
|
*/
|
1027
|
public static final Feature HYBRID_PARENT(){
|
1028
|
//TODO
|
1029
|
logger.warn("HYBRID_PARENT not yet implemented");
|
1030
|
return null;
|
1031
|
}
|
1032
|
|
1033
|
@Override
|
1034
|
protected void setDefaultTerms(TermVocabulary<Feature> termVocabulary) {
|
1035
|
if (termMap == null){ //needed because there are multiple feature vocabularies
|
1036
|
termMap = new HashMap<UUID, Feature>();
|
1037
|
}
|
1038
|
for (Feature term : termVocabulary.getTerms()){
|
1039
|
termMap.put(term.getUuid(), term);
|
1040
|
}
|
1041
|
}
|
1042
|
|
1043
|
//*********************************** CLONE *********************************************************/
|
1044
|
|
1045
|
@Override
|
1046
|
public Object clone() {
|
1047
|
Feature result = (Feature)super.clone();
|
1048
|
|
1049
|
result.inverseRepresentations = new HashSet<Representation>();
|
1050
|
for (Representation rep: this.inverseRepresentations){
|
1051
|
result.addInverseRepresentation((Representation)rep.clone());
|
1052
|
}
|
1053
|
|
1054
|
//no changes to: symmetric, transitiv
|
1055
|
return result;
|
1056
|
}
|
1057
|
|
1058
|
}
|