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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.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.JoinTable;
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import javax.persistence.ManyToMany;
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import javax.persistence.OneToMany;
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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.envers.Audited;
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import org.hibernate.search.annotations.Indexed;
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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.TermVocabulary;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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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.TaxonNameBase;
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import eu.etaxonomy.cdm.model.occurrence.Specimen;
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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 TaxonNameBase 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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* @version 1.0
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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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})
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@XmlRootElement(name = "Feature")
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@Entity
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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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private static Feature IMAGE;
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private static Feature CULTIVATION;
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private static Feature CONSERVATION;
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private static Feature USES;
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private static Feature ADDITIONAL_PUBLICATION;
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private static Feature CITATION;
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private static Feature OCCURRENCE;
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private static Feature PHENOLOGY;
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private static Feature COMMON_NAME;
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private static Feature PROTOLOG;
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private static Feature INTRODUCTION;
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private static Feature DIAGNOSIS;
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private static Feature ETYMOLOGY;
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private static Feature MATERIALS_METHODS;
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private static Feature MATERIALS_EXAMINED;
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private static Feature KEY;
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private static Feature BIOLOGY_ECOLOGY;
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private static Feature ECOLOGY;
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private static Feature DISCUSSION;
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private static Feature DISTRIBUTION;
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private static Feature DESCRIPTION;
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private static Feature UNKNOWN;
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@XmlElement(name = "SupportsTextData")
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private boolean supportsTextData;
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@XmlElement(name = "SupportsQuantitativeData")
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private boolean supportsQuantitativeData;
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@XmlElement(name = "SupportsDistribution")
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private boolean supportsDistribution;
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@XmlElement(name = "SupportsIndividualAssociation")
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private boolean supportsIndividualAssociation;
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@XmlElement(name = "SupportsTaxonInteraction")
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private boolean supportsTaxonInteraction;
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@XmlElement(name = "SupportsCategoricalData")
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private boolean supportsCategoricalData;
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/*
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* FIXME Should this be Many-To-Many or do we expect each Feature to have its own unique modifier enums?
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*/
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@XmlElementWrapper(name = "RecommendedModifierEnumerations")
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@XmlElement(name = "RecommendedModifierEnumeration")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@OneToMany(fetch = FetchType.LAZY)
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@JoinTable(name="DefinedTermBase_RecommendedModifierEnumeration")
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private Set<TermVocabulary<Modifier>> recommendedModifierEnumeration = new HashSet<TermVocabulary<Modifier>>();
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@XmlElementWrapper(name = "RecommendedStatisticalMeasures")
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@XmlElement(name = "RecommendedStatisticalMeasure")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToMany(fetch = FetchType.LAZY)
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@JoinTable(name="DefinedTermBase_StatisticalMeasure")
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private Set<StatisticalMeasure> recommendedStatisticalMeasures = new HashSet<StatisticalMeasure>();
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/*
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* FIXME Should this be Many-To-Many or do we expect each Feature to have its own unique state enums?
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*/
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@XmlElementWrapper(name = "SupportedCategoricalEnumerations")
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@XmlElement(name = "SupportedCategoricalEnumeration")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@OneToMany(fetch = FetchType.LAZY)
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@JoinTable(name="DefinedTermBase_SupportedCategoricalEnumeration")
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private Set<TermVocabulary<State>> supportedCategoricalEnumerations = new HashSet<TermVocabulary<State>>();
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@XmlElement(name = "SupportsCommonTaxonName")
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private boolean supportsCommonTaxonName;
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@XmlElementWrapper(name = "RecommendedMeasurementUnits")
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@XmlElement(name = "RecommendedMeasurementUnit")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToMany(fetch = FetchType.LAZY)
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@JoinTable(name="DefinedTermBase_MeasurementUnit")
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private Set<MeasurementUnit> recommendedMeasurementUnits = new HashSet<MeasurementUnit>();
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/* ***************** CONSTRUCTOR AND FACTORY METHODS **********************************/
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/**
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* Class constructor: creates a new empty feature instance.
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*
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* @see #Feature(String, String, String)
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*/
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public Feature() {
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super();
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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(term, label, labelAbbrev);
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}
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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 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 #readCsvLine(List, Language)
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* @see #NewInstance()
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*/
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public static Feature NewInstance(String term, String label, String labelAbbrev){
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return new Feature(term, label, labelAbbrev);
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}
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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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public boolean supportsQuantitativeData() {
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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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public boolean supportsTextData() {
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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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public boolean supportsDistribution() {
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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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public boolean supportsIndividualAssociation() {
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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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public boolean supportsTaxonInteraction() {
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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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public boolean supportsCommonTaxonName() {
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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;
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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 CategoricalData categorical data}
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* (true) or not (false).
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*
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* @return the boolean value of the supportsCategoricalData flag
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*/
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public boolean supportsCategoricalData() {
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return supportsCategoricalData;
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}
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/**
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* @see #supportsCategoricalData()
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*/
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public void setSupportsCategoricalData(boolean supportsCategoricalData) {
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this.supportsCategoricalData = supportsCategoricalData;
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}
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/**
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* Returns the set of {@link TermVocabulary term vocabularies} containing the
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* {@link Modifier modifiers} recommended to be used for {@link DescriptionElementBase description elements}
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* with <i>this</i> feature.
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*
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*/
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public Set<TermVocabulary<Modifier>> getRecommendedModifierEnumeration() {
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return recommendedModifierEnumeration;
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}
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/**
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* Adds a {@link TermVocabulary term vocabulary} (with {@link Modifier modifiers}) to the set of
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* {@link #getRecommendedModifierEnumeration() recommended modifier vocabularies} assigned
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* to <i>this</i> feature.
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*
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* @param recommendedModifierEnumeration the term vocabulary to be added
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* @see #getRecommendedModifierEnumeration()
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*/
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public void addRecommendedModifierEnumeration(
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TermVocabulary<Modifier> recommendedModifierEnumeration) {
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this.recommendedModifierEnumeration.add(recommendedModifierEnumeration);
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}
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/**
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* Removes one element from the set of {@link #getRecommendedModifierEnumeration() recommended modifier vocabularies}
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* assigned to <i>this</i> feature.
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*
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* @param recommendedModifierEnumeration the term vocabulary which should be removed
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* @see #getRecommendedModifierEnumeration()
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* @see #addRecommendedModifierEnumeration(TermVocabulary)
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*/
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public void removeRecommendedModifierEnumeration(
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TermVocabulary<Modifier> recommendedModifierEnumeration) {
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this.recommendedModifierEnumeration.remove(recommendedModifierEnumeration);
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}
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/**
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* Returns the set of {@link StatisticalMeasure statistical measures} recommended to be used
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* in case of {@link QuantitativeData quantitative data} with <i>this</i> feature.
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*/
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public Set<StatisticalMeasure> getRecommendedStatisticalMeasures() {
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return recommendedStatisticalMeasures;
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}
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/**
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* Adds a {@link StatisticalMeasure statistical measure} to the set of
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* {@link #getRecommendedStatisticalMeasures() recommended statistical measures} assigned
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* to <i>this</i> feature.
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*
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* @param recommendedStatisticalMeasure the statistical measure to be added
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* @see #getRecommendedStatisticalMeasures()
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*/
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public void addRecommendedStatisticalMeasure(
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StatisticalMeasure recommendedStatisticalMeasure) {
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this.recommendedStatisticalMeasures.add(recommendedStatisticalMeasure);
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}
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/**
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* Removes one element from the set of {@link #getRecommendedStatisticalMeasures() recommended statistical measures}
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* assigned to <i>this</i> feature.
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*
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* @param recommendedStatisticalMeasure the statistical measure which should be removed
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* @see #getRecommendedStatisticalMeasures()
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428
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* @see #addRecommendedStatisticalMeasure(StatisticalMeasure)
|
429
|
*/
|
430
|
public void removeRecommendedStatisticalMeasure(
|
431
|
StatisticalMeasure recommendedStatisticalMeasure) {
|
432
|
this.recommendedStatisticalMeasures.remove(recommendedStatisticalMeasure);
|
433
|
}
|
434
|
|
435
|
/**
|
436
|
* Returns the set of {@link StatisticalMeasure statistical measures} recommended to be used
|
437
|
* in case of {@link QuantitativeData quantitative data} with <i>this</i> feature.
|
438
|
*/
|
439
|
public Set<MeasurementUnit> getRecommendedMeasurementUnits() {
|
440
|
return recommendedMeasurementUnits;
|
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 addRecommendedMeasurementUnit(
|
452
|
MeasurementUnit recommendedMeasurementUnit) {
|
453
|
this.recommendedMeasurementUnits.add(recommendedMeasurementUnit);
|
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 removeRecommendedMeasurementUnit(
|
464
|
MeasurementUnit recommendedMeasurementUnit) {
|
465
|
this.recommendedMeasurementUnits.remove(recommendedMeasurementUnit);
|
466
|
}
|
467
|
|
468
|
/**
|
469
|
* Returns the set of {@link TermVocabulary term vocabularies} containing the list of
|
470
|
* possible {@link State states} to be used in {@link CategoricalData categorical data}
|
471
|
* with <i>this</i> feature.
|
472
|
*
|
473
|
*/
|
474
|
public Set<TermVocabulary<State>> getSupportedCategoricalEnumerations() {
|
475
|
return supportedCategoricalEnumerations;
|
476
|
}
|
477
|
|
478
|
/**
|
479
|
* Adds a {@link TermVocabulary term vocabulary} to the set of
|
480
|
* {@link #getSupportedCategoricalEnumerations() supported state vocabularies} assigned
|
481
|
* to <i>this</i> feature.
|
482
|
*
|
483
|
* @param supportedCategoricalEnumeration the term vocabulary which should be removed
|
484
|
* @see #getSupportedCategoricalEnumerations()
|
485
|
*/
|
486
|
public void addSupportedCategoricalEnumeration(
|
487
|
TermVocabulary<State> supportedCategoricalEnumeration) {
|
488
|
this.supportedCategoricalEnumerations.add(supportedCategoricalEnumeration);
|
489
|
}
|
490
|
/**
|
491
|
* Removes one element from the set of {@link #getSupportedCategoricalEnumerations() supported state vocabularies}
|
492
|
* assigned to <i>this</i> feature.
|
493
|
*
|
494
|
* @param supportedCategoricalEnumeration the term vocabulary which should be removed
|
495
|
* @see #getSupportedCategoricalEnumerations()
|
496
|
* @see #addSupportedCategoricalEnumeration(TermVocabulary)
|
497
|
*/
|
498
|
public void removeSupportedCategoricalEnumeration(
|
499
|
TermVocabulary<State> supportedCategoricalEnumeration) {
|
500
|
this.supportedCategoricalEnumerations.remove(supportedCategoricalEnumeration);
|
501
|
}
|
502
|
|
503
|
@XmlElement(name = "KindOf", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
504
|
@XmlIDREF
|
505
|
@XmlSchemaType(name = "IDREF")
|
506
|
public Feature getKindOf(){
|
507
|
return super.getKindOf();
|
508
|
}
|
509
|
|
510
|
public void setKindOf(Feature kindOf){
|
511
|
super.setKindOf(kindOf);
|
512
|
}
|
513
|
|
514
|
@XmlElement(name = "PartOf", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
515
|
@XmlIDREF
|
516
|
@XmlSchemaType(name = "IDREF")
|
517
|
public Feature getPartOf(){
|
518
|
return super.getPartOf();
|
519
|
}
|
520
|
|
521
|
public void setPartOf(Feature partOf){
|
522
|
super.setPartOf(partOf);
|
523
|
}
|
524
|
|
525
|
@XmlElementWrapper(name = "Generalizations", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
526
|
@XmlElement(name = "GeneralizationOf", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
527
|
@XmlIDREF
|
528
|
@XmlSchemaType(name = "IDREF")
|
529
|
public Set<Feature> getGeneralizationOf(){
|
530
|
return super.getGeneralizationOf();
|
531
|
}
|
532
|
|
533
|
protected void setGeneralizationOf(Set<Feature> value){
|
534
|
super.setGeneralizationOf(value);
|
535
|
}
|
536
|
|
537
|
@XmlElementWrapper(name = "Includes", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
538
|
@XmlElement(name = "Include", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
539
|
@XmlIDREF
|
540
|
@XmlSchemaType(name = "IDREF")
|
541
|
public Set<Feature> getIncludes(){
|
542
|
return super.getIncludes();
|
543
|
}
|
544
|
|
545
|
protected void setIncludes(Set<Feature> includes) {
|
546
|
super.setIncludes(includes);
|
547
|
}
|
548
|
|
549
|
private static final UUID uuidUnknown = UUID.fromString("910307f1-dc3c-452c-a6dd-af5ac7cd365c");
|
550
|
private static final UUID uuidDescription = UUID.fromString("9087cdcd-8b08-4082-a1de-34c9ba9fb493");
|
551
|
private static final UUID uuidDistribution = UUID.fromString("9fc9d10c-ba50-49ee-b174-ce83fc3f80c6");
|
552
|
private static final UUID uuidEcology = UUID.fromString("aa923827-d333-4cf5-9a5f-438ae0a4746b");
|
553
|
private static final UUID uuidBiologyEcology = UUID.fromString("9832e24f-b670-43b4-ac7c-20a7261a1d8c");
|
554
|
private static final UUID uuidKey = UUID.fromString("a677f827-22b9-4205-bb37-11cb48dd9106");
|
555
|
private static final UUID uuidMaterialsExamined = UUID.fromString("7c0c7571-a864-47c1-891d-01f59000dae1");
|
556
|
private static final UUID uuidMaterialsMethods = UUID.fromString("1e87d9c3-0844-4a03-9686-773e2ccb3ab6");
|
557
|
private static final UUID uuidEtymology = UUID.fromString("dd653d48-355c-4aec-a4e7-724f6eb29f8d");
|
558
|
private static final UUID uuidDiagnosis = UUID.fromString("d43d8501-ceab-4caa-9e51-e87138528fac");
|
559
|
private static final UUID uuidProtolog = UUID.fromString("7f1fd111-fc52-49f0-9e75-d0097f576b2d");
|
560
|
private static final UUID uuidCommonName = UUID.fromString("fc810911-51f0-4a46-ab97-6562fe263ae5");
|
561
|
private static final UUID uuidPhenology = UUID.fromString("a7786d3e-7c58-4141-8416-346d4c80c4a2");
|
562
|
private static final UUID uuidOccurrence = UUID.fromString("5deff505-1a32-4817-9a74-50e6936fd630");
|
563
|
private static final UUID uuidCitation = UUID.fromString("99b2842f-9aa7-42fa-bd5f-7285311e0101");
|
564
|
private static final UUID uuidAdditionalPublication = UUID.fromString("cb2eab09-6d9d-4e43-8ad2-873f23400930");
|
565
|
private static final UUID uuidUses = UUID.fromString("e5374d39-b210-47c7-bec1-bee05b5f1cb6");
|
566
|
private static final UUID uuidConservation = UUID.fromString("4518fc20-2492-47de-b345-777d2b83c9cf");
|
567
|
private static final UUID uuidCultivation = UUID.fromString("e28965b2-a367-48c5-b954-8afc8ac2c69b");
|
568
|
private static final UUID uuidIntroduction = UUID.fromString("e75255ca-8ff4-4905-baad-f842927fe1d3");
|
569
|
private static final UUID uuidDiscussion = UUID.fromString("d3c4cbb6-0025-4322-886b-cd0156753a25");
|
570
|
private static final UUID uuidImage = UUID.fromString("84193b2c-327f-4cce-90ef-c8da18fd5bb5");
|
571
|
|
572
|
|
573
|
// private static final UUID uuidDistribution = UUID.fromString("");
|
574
|
// private static final UUID uuidDistribution = UUID.fromString("");
|
575
|
// private static final UUID uuidDistribution = UUID.fromString("");
|
576
|
|
577
|
// "86bd920d-f8c5-48b9-af1d-03f63c31de5c",,"Abstract","Abstract"
|
578
|
// "489bf358-b78a-45e2-a691-f9f3f10446ce",,"Synopsis","Synopsis"
|
579
|
// "89d3b005-9876-4923-89d9-60eb75b9583b",,"Multiple","Multiple"
|
580
|
// "555a46bc-211a-476f-a022-c472970d6f8b",,"Acknowledgments","Acknowledgments"
|
581
|
|
582
|
|
583
|
/**
|
584
|
* Creates and returns a new feature instance on the basis of a given string
|
585
|
* list (containing an UUID, an URI, a label and a description) and a given
|
586
|
* {@link Language language} to be associated with the description. Furthermore
|
587
|
* the flags concerning the supported subclasses of {@link DescriptionElementBase description elements}
|
588
|
* are set according to a particular string belonging to the given
|
589
|
* string list.<BR>
|
590
|
* This method overrides the readCsvLine method from {@link DefinedTermBase#readCsvLine(List, Language) DefinedTermBase}.
|
591
|
*
|
592
|
* @param csvLine the string list with elementary information for attributes
|
593
|
* @param lang the language in which the description has been formulated
|
594
|
* @see #NewInstance(String, String, String)
|
595
|
*/
|
596
|
@Override
|
597
|
public Feature readCsvLine(Class<Feature> termClass, List<String> csvLine, Map<UUID,DefinedTermBase> terms) {
|
598
|
Feature newInstance = super.readCsvLine(termClass, csvLine, terms);
|
599
|
String text = (String)csvLine.get(4);
|
600
|
if (text != null && text.length() >= 6){
|
601
|
if ("1".equals(text.substring(0, 1))){newInstance.setSupportsTextData(true);};
|
602
|
if ("1".equals(text.substring(1, 2))){newInstance.setSupportsQuantitativeData(true);};
|
603
|
if ("1".equals(text.substring(2, 3))){newInstance.setSupportsDistribution(true);};
|
604
|
if ("1".equals(text.substring(3, 4))){newInstance.setSupportsIndividualAssociation(true);};
|
605
|
if ("1".equals(text.substring(4, 5))){newInstance.setSupportsTaxonInteraction(true);};
|
606
|
if ("1".equals(text.substring(5, 6))){newInstance.setSupportsCommonTaxonName(true);};
|
607
|
// if ("1".equals(text.substring(6, 7))){newInstance.setSupportsCategoricalData(true);};
|
608
|
}
|
609
|
return newInstance;
|
610
|
}
|
611
|
|
612
|
/**
|
613
|
* Returns the "unknown" feature. This feature allows to store values of
|
614
|
* {@link DescriptionElementBase description elements} even if it is momentarily
|
615
|
* not known what they mean.
|
616
|
*/
|
617
|
public static final Feature UNKNOWN(){
|
618
|
return UNKNOWN;
|
619
|
}
|
620
|
|
621
|
/**
|
622
|
* Returns the "description" feature. This feature allows to handle global
|
623
|
* {@link DescriptionElementBase description elements} for a global {@link DescriptionBase description}.<BR>
|
624
|
* The "description" feature is the highest level feature.
|
625
|
*/
|
626
|
public static final Feature DESCRIPTION(){
|
627
|
return DESCRIPTION;
|
628
|
}
|
629
|
|
630
|
/**
|
631
|
* Returns the "distribution" feature. This feature allows to handle only
|
632
|
* {@link Distribution distributions}.
|
633
|
*
|
634
|
* @see #isSupportsDistribution()
|
635
|
*/
|
636
|
public static final Feature DISTRIBUTION(){
|
637
|
return DISTRIBUTION;
|
638
|
}
|
639
|
|
640
|
/**
|
641
|
* Returns the "discussion" feature. This feature can only be described
|
642
|
* with {@link TextData text data}.
|
643
|
*
|
644
|
* @see #isSupportsTextData()
|
645
|
*/
|
646
|
public static final Feature DISCUSSION(){
|
647
|
return DISCUSSION;
|
648
|
}
|
649
|
|
650
|
/**
|
651
|
* Returns the "ecology" feature. This feature only applies
|
652
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
653
|
* The "ecology" feature generalizes all other possible features concerning
|
654
|
* ecological matters.
|
655
|
*/
|
656
|
public static final Feature ECOLOGY(){
|
657
|
return ECOLOGY;
|
658
|
}
|
659
|
|
660
|
/**
|
661
|
* Returns the "biology_ecology" feature. This feature only applies
|
662
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
663
|
* The "biology_ecology" feature generalizes all possible features concerning
|
664
|
* biological aspects of ecological matters.
|
665
|
*
|
666
|
* @see #ECOLOGY()
|
667
|
*/
|
668
|
public static final Feature BIOLOGY_ECOLOGY(){
|
669
|
return BIOLOGY_ECOLOGY;
|
670
|
}
|
671
|
|
672
|
/**
|
673
|
* Returns the "key" feature. This feature is the "upper" feature generalizing
|
674
|
* all features being used within an identification key.
|
675
|
*/
|
676
|
public static final Feature KEY(){
|
677
|
return KEY;
|
678
|
}
|
679
|
|
680
|
|
681
|
/**
|
682
|
* Returns the "materials_examined" feature. This feature can only be described
|
683
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}
|
684
|
* mentioning which material has been examined in order to accomplish
|
685
|
* the description. This feature applies only to
|
686
|
* {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.
|
687
|
*/
|
688
|
public static final Feature MATERIALS_EXAMINED(){
|
689
|
return MATERIALS_EXAMINED;
|
690
|
}
|
691
|
|
692
|
/**
|
693
|
* Returns the "materials_methods" feature. This feature can only be described
|
694
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}
|
695
|
* mentioning which methods have been adopted to analyze the material in
|
696
|
* order to accomplish the description. This feature applies only to
|
697
|
* {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.
|
698
|
*/
|
699
|
public static final Feature MATERIALS_METHODS(){
|
700
|
return MATERIALS_METHODS;
|
701
|
}
|
702
|
|
703
|
/**
|
704
|
* Returns the "etymology" feature. This feature can only be described
|
705
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}
|
706
|
* giving some information about the history of the taxon name. This feature applies only to
|
707
|
* {@link TaxonNameDescription taxon name descriptions}.
|
708
|
*/
|
709
|
public static final Feature ETYMOLOGY(){
|
710
|
return ETYMOLOGY;
|
711
|
}
|
712
|
|
713
|
/**
|
714
|
* Returns the "diagnosis" feature. This feature can only be described
|
715
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}.
|
716
|
* This feature applies only to {@link SpecimenDescription specimen descriptions} or to
|
717
|
* {@link TaxonDescription taxon descriptions}.
|
718
|
*/
|
719
|
public static final Feature DIAGNOSIS(){
|
720
|
return DIAGNOSIS;
|
721
|
}
|
722
|
|
723
|
|
724
|
/**
|
725
|
* Returns the "introduction" feature. This feature can only be described
|
726
|
* with {@link TextData text data}.
|
727
|
*
|
728
|
* @see #isSupportsTextData()
|
729
|
*/
|
730
|
public static final Feature INTRODUCTION(){
|
731
|
return INTRODUCTION;
|
732
|
}
|
733
|
|
734
|
/**
|
735
|
* Returns the "protologue" feature. This feature can only be described
|
736
|
* with {@link TextData text data} reproducing the content of the protologue
|
737
|
* (or some information about it) of the taxon name. This feature applies only to
|
738
|
* {@link TaxonNameDescription taxon name descriptions}.
|
739
|
*
|
740
|
* @see #isSupportsTextData()
|
741
|
*/
|
742
|
public static final Feature PROTOLOG(){
|
743
|
return PROTOLOG;
|
744
|
}
|
745
|
/**
|
746
|
* Returns the "common_name" feature. This feature allows to handle only
|
747
|
* {@link CommonTaxonName common names}.
|
748
|
*
|
749
|
* @see #isSupportsCommonTaxonName()
|
750
|
*/
|
751
|
public static final Feature COMMON_NAME(){
|
752
|
return COMMON_NAME;
|
753
|
}
|
754
|
|
755
|
/**
|
756
|
* Returns the "phenology" feature. This feature can only be described
|
757
|
* with {@link CategoricalData categorical data} or eventually with {@link TextData text data}
|
758
|
* containing information time about recurring natural phenomena.
|
759
|
* This feature only applies to {@link TaxonDescription taxon descriptions}.<BR>
|
760
|
* The "phenology" feature generalizes all other possible features
|
761
|
* concerning time information about particular natural phenomena
|
762
|
* (such as "first flight of butterflies").
|
763
|
*/
|
764
|
public static final Feature PHENOLOGY(){
|
765
|
return PHENOLOGY;
|
766
|
}
|
767
|
|
768
|
/**
|
769
|
* Returns the "occurrence" feature.
|
770
|
*/
|
771
|
public static final Feature OCCURRENCE(){
|
772
|
return OCCURRENCE;
|
773
|
}
|
774
|
|
775
|
/**
|
776
|
* Returns the "citation" feature. This feature can only be described
|
777
|
* with {@link TextData text data}.
|
778
|
*
|
779
|
* @see #isSupportsTextData()
|
780
|
*/
|
781
|
public static final Feature CITATION(){
|
782
|
return CITATION;
|
783
|
}
|
784
|
|
785
|
/**
|
786
|
* Returns the "additional_publication" feature. This feature can only be
|
787
|
* described with {@link TextData text data} with information about a
|
788
|
* publication where a {@link TaxonNameBase taxon name} has also been published
|
789
|
* but which is not the {@link TaxonNameBase#getNomenclaturalReference() nomenclatural reference}.
|
790
|
* This feature applies only to {@link TaxonNameDescription taxon name descriptions}.
|
791
|
*
|
792
|
* @see #isSupportsTextData()
|
793
|
*/
|
794
|
public static final Feature ADDITIONAL_PUBLICATION(){
|
795
|
return ADDITIONAL_PUBLICATION;
|
796
|
}
|
797
|
|
798
|
|
799
|
/**
|
800
|
* Returns the "uses" feature. This feature only applies
|
801
|
* to {@link TaxonDescription taxon descriptions}.<BR>
|
802
|
* The "uses" feature generalizes all other possible features concerning
|
803
|
* particular uses (for instance "industrial use of seeds").
|
804
|
*/
|
805
|
public static final Feature USES(){
|
806
|
return USES;
|
807
|
}
|
808
|
|
809
|
|
810
|
/**
|
811
|
* Returns the "conservation" feature. This feature only applies
|
812
|
* to {@link SpecimenDescription specimen descriptions} and generalizes
|
813
|
* methods and conditions for the conservation of {@link Specimen specimens}.<BR>
|
814
|
*/
|
815
|
public static final Feature CONSERVATION(){
|
816
|
return CONSERVATION;
|
817
|
}
|
818
|
|
819
|
|
820
|
/**
|
821
|
* Returns the "cultivation" feature.
|
822
|
*/
|
823
|
public static final Feature CULTIVATION(){
|
824
|
return CULTIVATION;
|
825
|
}
|
826
|
|
827
|
|
828
|
/**
|
829
|
* Returns the "cultivation" feature.
|
830
|
*/
|
831
|
public static final Feature IMAGE(){
|
832
|
return IMAGE;
|
833
|
}
|
834
|
|
835
|
/**
|
836
|
* Returns the "hybrid_parent" feature. This feature can only be used
|
837
|
* by {@link TaxonInteraction taxon interactions}.<BR>
|
838
|
* <P>
|
839
|
* Note: It must be distinguished between hybrid relationships as
|
840
|
* relevant nomenclatural relationships between {@link BotanicalName plant names}
|
841
|
* on the one side and the biological relation between two {@link Taxon taxa}
|
842
|
* as it is here the case on the other one.
|
843
|
*
|
844
|
* @see #isSupportsTaxonInteraction()
|
845
|
* @see HybridRelationshipType
|
846
|
*/
|
847
|
public static final Feature HYBRID_PARENT(){
|
848
|
//TODO
|
849
|
logger.warn("HYBRID_PARENT not yet implemented");
|
850
|
return null;
|
851
|
}
|
852
|
|
853
|
@Override
|
854
|
protected void setDefaultTerms(TermVocabulary<Feature> termVocabulary) {
|
855
|
Feature.ADDITIONAL_PUBLICATION = termVocabulary.findTermByUuid(Feature.uuidAdditionalPublication);
|
856
|
Feature.BIOLOGY_ECOLOGY = termVocabulary.findTermByUuid(Feature.uuidBiologyEcology);
|
857
|
Feature.CITATION = termVocabulary.findTermByUuid(Feature.uuidCitation);
|
858
|
Feature.COMMON_NAME = termVocabulary.findTermByUuid(Feature.uuidCommonName);
|
859
|
Feature.CONSERVATION = termVocabulary.findTermByUuid(Feature.uuidConservation);
|
860
|
Feature.CULTIVATION = termVocabulary.findTermByUuid(Feature.uuidCultivation);
|
861
|
Feature.DESCRIPTION = termVocabulary.findTermByUuid(Feature.uuidDescription);
|
862
|
Feature.DIAGNOSIS = termVocabulary.findTermByUuid(Feature.uuidDiagnosis);
|
863
|
Feature.DISCUSSION = termVocabulary.findTermByUuid(Feature.uuidDiscussion);
|
864
|
Feature.DISTRIBUTION = termVocabulary.findTermByUuid(Feature.uuidDistribution);
|
865
|
Feature.ECOLOGY = termVocabulary.findTermByUuid(Feature.uuidEcology);
|
866
|
Feature.ETYMOLOGY = termVocabulary.findTermByUuid(Feature.uuidEtymology);
|
867
|
Feature.IMAGE = termVocabulary.findTermByUuid(Feature.uuidImage);
|
868
|
Feature.INTRODUCTION = termVocabulary.findTermByUuid(Feature.uuidIntroduction);
|
869
|
Feature.KEY = termVocabulary.findTermByUuid(Feature.uuidKey);
|
870
|
Feature.MATERIALS_EXAMINED = termVocabulary.findTermByUuid(Feature.uuidMaterialsExamined);
|
871
|
Feature.MATERIALS_METHODS = termVocabulary.findTermByUuid(Feature.uuidMaterialsMethods);
|
872
|
Feature.OCCURRENCE = termVocabulary.findTermByUuid(Feature.uuidOccurrence);
|
873
|
Feature.PHENOLOGY = termVocabulary.findTermByUuid(Feature.uuidPhenology);
|
874
|
Feature.PROTOLOG = termVocabulary.findTermByUuid(Feature.uuidProtolog);
|
875
|
Feature.UNKNOWN = termVocabulary.findTermByUuid(Feature.uuidUnknown);
|
876
|
Feature.USES = termVocabulary.findTermByUuid(Feature.uuidUses);
|
877
|
}
|
878
|
|
879
|
|
880
|
}
|