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9479da48
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Andreas Müller
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/**
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* Copyright (C) 2007 EDIT
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8ba55ff3
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Patric Plitzner
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* European Distributed Institute of Taxonomy
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9479da48
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Andreas Müller
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* http://www.e-taxonomy.eu
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8ba55ff3
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Patric Plitzner
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*
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9479da48
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Andreas Müller
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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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892efc69
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Andreas Kohlbecker
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import java.util.HashMap;
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14 |
6b8f5129
|
Andreas Müller
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import java.util.HashSet;
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15 |
1016f650
|
Andreas Müller
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import java.util.List;
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16 |
f6765014
|
ben.clark
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import java.util.Map;
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6b8f5129
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Andreas Müller
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import java.util.Set;
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import java.util.UUID;
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de3e2329
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Andreas Müller
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6b8f5129
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Andreas Müller
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import javax.persistence.Entity;
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f6765014
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ben.clark
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import javax.persistence.FetchType;
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c5e86e43
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a.babadshanjan
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import javax.persistence.JoinTable;
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import javax.persistence.ManyToMany;
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6b8f5129
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Andreas Müller
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import javax.persistence.OneToMany;
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4393fcb0
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a.babadshanjan
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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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6b8f5129
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Andreas Müller
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import javax.xml.bind.annotation.XmlType;
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9479da48
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Andreas Müller
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6b8f5129
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Andreas Müller
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import org.apache.log4j.Logger;
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ee91bcd9
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ben.clark
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import org.hibernate.envers.Audited;
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fd7ee7b1
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ben.clark
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import org.hibernate.search.annotations.Indexed;
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9479da48
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Andreas Müller
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533cbb43
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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6b8f5129
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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1016f650
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.Language;
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533cbb43
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.TermType;
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6b8f5129
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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4daf2f37
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m.geoffroy
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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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8ba55ff3
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Patric Plitzner
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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.taxon.Taxon;
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9479da48
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Andreas Müller
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/**
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4daf2f37
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m.geoffroy
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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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8ba55ff3
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Patric Plitzner
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* Descriptions require features in order to be structured and disaggregated
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4daf2f37
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m.geoffroy
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* in {@link DescriptionElementBase description elements}.<BR>
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b22e4839
|
m.geoffroy
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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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4daf2f37
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m.geoffroy
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* would have leaded to confusion.
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* <P>
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509b132a
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m.geoffroy
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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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8ba55ff3
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Patric Plitzner
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* <P>
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4daf2f37
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m.geoffroy
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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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8ba55ff3
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Patric Plitzner
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*
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9479da48
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Andreas Müller
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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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c9866164
|
ben.clark
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@XmlAccessorType(XmlAccessType.PROPERTY)
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4393fcb0
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a.babadshanjan
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@XmlType(name="Feature", factoryMethod="NewInstance", propOrder = {
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c9866164
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ben.clark
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"kindOf",
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"generalizationOf",
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"partOf",
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"includes",
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4393fcb0
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a.babadshanjan
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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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3190e7d8
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ben.clark
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"supportsCategoricalData",
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4393fcb0
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a.babadshanjan
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"recommendedModifierEnumeration",
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"recommendedStatisticalMeasures",
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52931327
|
h.fradin
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"supportedCategoricalEnumerations",
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"recommendedMeasurementUnits"
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4393fcb0
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a.babadshanjan
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})
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@XmlRootElement(name = "Feature")
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9479da48
|
Andreas Müller
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@Entity
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fd7ee7b1
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ben.clark
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@Indexed(index = "eu.etaxonomy.cdm.model.common.DefinedTermBase")
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ee91bcd9
|
ben.clark
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@Audited
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03abbcde
|
Andreas Müller
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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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8ba55ff3
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Patric Plitzner
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protected static Map<UUID, Feature> termMap = null;
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9479da48
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Andreas Müller
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05f4da4e
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Andreas Müller
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private boolean supportsTextData = true; //by default text data should be always supported
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8ba55ff3
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Patric Plitzner
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1016f650
|
Andreas Müller
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private boolean supportsQuantitativeData;
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8ba55ff3
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Patric Plitzner
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9479da48
|
Andreas Müller
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private boolean supportsDistribution;
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8ba55ff3
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Patric Plitzner
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9479da48
|
Andreas Müller
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private boolean supportsIndividualAssociation;
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8ba55ff3
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Patric Plitzner
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9479da48
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Andreas Müller
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private boolean supportsTaxonInteraction;
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8ba55ff3
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Patric Plitzner
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b2231758
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h.fradin
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private boolean supportsCategoricalData;
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8ba55ff3
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Patric Plitzner
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private boolean supportsCommonTaxonName;
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ee91bcd9
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ben.clark
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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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@OneToMany(fetch = FetchType.LAZY)
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@JoinTable(name="DefinedTermBase_RecommendedModifierEnumeration")
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8ba55ff3
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Patric Plitzner
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private final Set<TermVocabulary<DefinedTerm>> recommendedModifierEnumeration = new HashSet<TermVocabulary<DefinedTerm>>();
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ee91bcd9
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ben.clark
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@ManyToMany(fetch = FetchType.LAZY)
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@JoinTable(name="DefinedTermBase_StatisticalMeasure")
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8ba55ff3
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Patric Plitzner
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private final Set<StatisticalMeasure> recommendedStatisticalMeasures = new HashSet<StatisticalMeasure>();
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ee91bcd9
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ben.clark
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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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@OneToMany(fetch = FetchType.LAZY)
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@JoinTable(name="DefinedTermBase_SupportedCategoricalEnumeration")
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8ba55ff3
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Patric Plitzner
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private final Set<TermVocabulary<State>> supportedCategoricalEnumerations = new HashSet<TermVocabulary<State>>();
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17a0cbe8
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ben.clark
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52931327
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h.fradin
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@ManyToMany(fetch = FetchType.LAZY)
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@JoinTable(name="DefinedTermBase_MeasurementUnit")
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8ba55ff3
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Patric Plitzner
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private final Set<MeasurementUnit> recommendedMeasurementUnits = new HashSet<MeasurementUnit>();
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d80a0479
|
Andreas Müller
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/* ***************** CONSTRUCTOR AND FACTORY METHODS **********************************/
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8ba55ff3
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Patric Plitzner
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9e3239f6
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Andreas Müller
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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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d80a0479
|
Andreas Müller
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}
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8ba55ff3
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Patric Plitzner
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/**
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4daf2f37
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m.geoffroy
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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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8ba55ff3
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Patric Plitzner
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*
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4daf2f37
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m.geoffroy
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* @param term the string (in the default language) describing the
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156 |
8ba55ff3
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Patric Plitzner
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* new feature to be created
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157 |
4daf2f37
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m.geoffroy
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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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162 |
41b23b4e
|
Andreas Müller
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protected Feature(String term, String label, String labelAbbrev) {
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163 |
533cbb43
|
Andreas Müller
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super(TermType.Feature, term, label, labelAbbrev);
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9479da48
|
Andreas Müller
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}
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8ba55ff3
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Patric Plitzner
|
/**
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167 |
4daf2f37
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m.geoffroy
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* Creates a new empty feature instance.
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8ba55ff3
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Patric Plitzner
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*
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4daf2f37
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m.geoffroy
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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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174 |
8ba55ff3
|
Patric Plitzner
|
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/**
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176 |
4daf2f37
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m.geoffroy
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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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8ba55ff3
|
Patric Plitzner
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*
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4daf2f37
|
m.geoffroy
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* @param term the string (in the default language) describing the
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180 |
8ba55ff3
|
Patric Plitzner
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* new feature to be created
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181 |
4daf2f37
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m.geoffroy
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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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d80a0479
|
Andreas Müller
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/* *************************************************************************************/
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8ba55ff3
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Patric Plitzner
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8cc82a87
|
Andreas Müller
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.DefinedTermBase#resetTerms()
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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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8ba55ff3
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Patric Plitzner
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4daf2f37
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m.geoffroy
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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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8ba55ff3
|
Patric Plitzner
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*
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4daf2f37
|
m.geoffroy
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* @return the boolean value of the supportsQuantitativeData flag
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*/
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17a0cbe8
|
ben.clark
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@XmlElement(name = "SupportsQuantitativeData")
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public boolean isSupportsQuantitativeData() {
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213 |
9479da48
|
Andreas Müller
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return supportsQuantitativeData;
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}
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4daf2f37
|
m.geoffroy
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/**
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217 |
8ba55ff3
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Patric Plitzner
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* @see #isSupportsQuantitativeData()
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218 |
4daf2f37
|
m.geoffroy
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*/
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219 |
9479da48
|
Andreas Müller
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public void setSupportsQuantitativeData(boolean supportsQuantitativeData) {
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this.supportsQuantitativeData = supportsQuantitativeData;
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}
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4daf2f37
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m.geoffroy
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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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227 |
8ba55ff3
|
Patric Plitzner
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*
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228 |
4daf2f37
|
m.geoffroy
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* @return the boolean value of the supportsTextData flag
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*/
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230 |
17a0cbe8
|
ben.clark
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@XmlElement(name = "SupportsTextData")
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public boolean isSupportsTextData() {
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232 |
9479da48
|
Andreas Müller
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return supportsTextData;
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}
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235 |
4daf2f37
|
m.geoffroy
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/**
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236 |
8ba55ff3
|
Patric Plitzner
|
* @see #isSupportsTextData()
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237 |
4daf2f37
|
m.geoffroy
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*/
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238 |
9479da48
|
Andreas Müller
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public void setSupportsTextData(boolean supportsTextData) {
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this.supportsTextData = supportsTextData;
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}
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242 |
4daf2f37
|
m.geoffroy
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/**
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* Returns the boolean value of the flag indicating whether <i>this</i>
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244 |
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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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247 |
8ba55ff3
|
Patric Plitzner
|
*
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248 |
4daf2f37
|
m.geoffroy
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* @return the boolean value of the supportsDistribution flag
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249 |
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*/
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250 |
17a0cbe8
|
ben.clark
|
@XmlElement(name = "SupportsDistribution")
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public boolean isSupportsDistribution() {
|
252 |
9479da48
|
Andreas Müller
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return supportsDistribution;
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}
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254 |
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255 |
4daf2f37
|
m.geoffroy
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/**
|
256 |
8ba55ff3
|
Patric Plitzner
|
* @see #isSupportsDistribution()
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257 |
4daf2f37
|
m.geoffroy
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*/
|
258 |
9479da48
|
Andreas Müller
|
public void setSupportsDistribution(boolean supportsDistribution) {
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this.supportsDistribution = supportsDistribution;
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}
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262 |
4daf2f37
|
m.geoffroy
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/**
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* Returns the boolean value of the flag indicating whether <i>this</i>
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264 |
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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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266 |
8ba55ff3
|
Patric Plitzner
|
*
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267 |
4daf2f37
|
m.geoffroy
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* @return the boolean value of the supportsIndividualAssociation flag
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*/
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269 |
17a0cbe8
|
ben.clark
|
@XmlElement(name = "SupportsIndividualAssociation")
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270 |
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public boolean isSupportsIndividualAssociation() {
|
271 |
9479da48
|
Andreas Müller
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return supportsIndividualAssociation;
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}
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273 |
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274 |
4daf2f37
|
m.geoffroy
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/**
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275 |
8ba55ff3
|
Patric Plitzner
|
* @see #isSupportsIndividualAssociation()
|
276 |
4daf2f37
|
m.geoffroy
|
*/
|
277 |
9479da48
|
Andreas Müller
|
public void setSupportsIndividualAssociation(
|
278 |
|
|
boolean supportsIndividualAssociation) {
|
279 |
|
|
this.supportsIndividualAssociation = supportsIndividualAssociation;
|
280 |
|
|
}
|
281 |
|
|
|
282 |
4daf2f37
|
m.geoffroy
|
/**
|
283 |
|
|
* Returns the boolean value of the flag indicating whether <i>this</i>
|
284 |
|
|
* feature can be described with {@link TaxonInteraction taxon interactions}
|
285 |
|
|
* (true) or not (false).
|
286 |
8ba55ff3
|
Patric Plitzner
|
*
|
287 |
4daf2f37
|
m.geoffroy
|
* @return the boolean value of the supportsTaxonInteraction flag
|
288 |
|
|
*/
|
289 |
17a0cbe8
|
ben.clark
|
@XmlElement(name = "SupportsTaxonInteraction")
|
290 |
|
|
public boolean isSupportsTaxonInteraction() {
|
291 |
9479da48
|
Andreas Müller
|
return supportsTaxonInteraction;
|
292 |
|
|
}
|
293 |
|
|
|
294 |
4daf2f37
|
m.geoffroy
|
/**
|
295 |
8ba55ff3
|
Patric Plitzner
|
* @see #isSupportsTaxonInteraction()
|
296 |
4daf2f37
|
m.geoffroy
|
*/
|
297 |
9479da48
|
Andreas Müller
|
public void setSupportsTaxonInteraction(boolean supportsTaxonInteraction) {
|
298 |
|
|
this.supportsTaxonInteraction = supportsTaxonInteraction;
|
299 |
|
|
}
|
300 |
|
|
|
301 |
4daf2f37
|
m.geoffroy
|
/**
|
302 |
|
|
* Returns the boolean value of the flag indicating whether <i>this</i>
|
303 |
|
|
* feature can be described with {@link CommonTaxonName common names}
|
304 |
|
|
* (true) or not (false). This flag is set if and only if <i>this</i> feature
|
305 |
|
|
* is the {@link #COMMON_NAME() common name feature}.
|
306 |
8ba55ff3
|
Patric Plitzner
|
*
|
307 |
4daf2f37
|
m.geoffroy
|
* @return the boolean value of the supportsCommonTaxonName flag
|
308 |
|
|
*/
|
309 |
17a0cbe8
|
ben.clark
|
@XmlElement(name = "SupportsCommonTaxonName")
|
310 |
|
|
public boolean isSupportsCommonTaxonName() {
|
311 |
9479da48
|
Andreas Müller
|
return supportsCommonTaxonName;
|
312 |
|
|
}
|
313 |
|
|
|
314 |
4daf2f37
|
m.geoffroy
|
/**
|
315 |
8ba55ff3
|
Patric Plitzner
|
* @see #isSupportsTaxonInteraction()
|
316 |
4daf2f37
|
m.geoffroy
|
*/
|
317 |
9479da48
|
Andreas Müller
|
public void setSupportsCommonTaxonName(boolean supportsCommonTaxonName) {
|
318 |
|
|
this.supportsCommonTaxonName = supportsCommonTaxonName;
|
319 |
|
|
}
|
320 |
|
|
|
321 |
b2231758
|
h.fradin
|
/**
|
322 |
|
|
* Returns the boolean value of the flag indicating whether <i>this</i>
|
323 |
|
|
* feature can be described with {@link CategoricalData categorical data}
|
324 |
|
|
* (true) or not (false).
|
325 |
8ba55ff3
|
Patric Plitzner
|
*
|
326 |
b2231758
|
h.fradin
|
* @return the boolean value of the supportsCategoricalData flag
|
327 |
|
|
*/
|
328 |
17a0cbe8
|
ben.clark
|
@XmlElement(name = "SupportsCategoricalData")
|
329 |
|
|
public boolean isSupportsCategoricalData() {
|
330 |
b2231758
|
h.fradin
|
return supportsCategoricalData;
|
331 |
|
|
}
|
332 |
|
|
|
333 |
|
|
/**
|
334 |
8ba55ff3
|
Patric Plitzner
|
* @see #supportsCategoricalData()
|
335 |
b2231758
|
h.fradin
|
*/
|
336 |
|
|
public void setSupportsCategoricalData(boolean supportsCategoricalData) {
|
337 |
|
|
this.supportsCategoricalData = supportsCategoricalData;
|
338 |
|
|
}
|
339 |
|
|
|
340 |
8ba55ff3
|
Patric Plitzner
|
|
341 |
4daf2f37
|
m.geoffroy
|
/**
|
342 |
|
|
* Returns the set of {@link TermVocabulary term vocabularies} containing the
|
343 |
|
|
* {@link Modifier modifiers} recommended to be used for {@link DescriptionElementBase description elements}
|
344 |
|
|
* with <i>this</i> feature.
|
345 |
8ba55ff3
|
Patric Plitzner
|
*
|
346 |
4daf2f37
|
m.geoffroy
|
*/
|
347 |
17a0cbe8
|
ben.clark
|
@XmlElementWrapper(name = "RecommendedModifierEnumerations")
|
348 |
|
|
@XmlElement(name = "RecommendedModifierEnumeration")
|
349 |
|
|
@XmlIDREF
|
350 |
|
|
@XmlSchemaType(name = "IDREF")
|
351 |
533cbb43
|
Andreas Müller
|
public Set<TermVocabulary<DefinedTerm>> getRecommendedModifierEnumeration() {
|
352 |
9479da48
|
Andreas Müller
|
return recommendedModifierEnumeration;
|
353 |
|
|
}
|
354 |
|
|
|
355 |
4daf2f37
|
m.geoffroy
|
/**
|
356 |
|
|
* Adds a {@link TermVocabulary term vocabulary} (with {@link Modifier modifiers}) to the set of
|
357 |
|
|
* {@link #getRecommendedModifierEnumeration() recommended modifier vocabularies} assigned
|
358 |
|
|
* to <i>this</i> feature.
|
359 |
8ba55ff3
|
Patric Plitzner
|
*
|
360 |
4daf2f37
|
m.geoffroy
|
* @param recommendedModifierEnumeration the term vocabulary to be added
|
361 |
|
|
* @see #getRecommendedModifierEnumeration()
|
362 |
|
|
*/
|
363 |
9479da48
|
Andreas Müller
|
public void addRecommendedModifierEnumeration(
|
364 |
533cbb43
|
Andreas Müller
|
TermVocabulary<DefinedTerm> recommendedModifierEnumeration) {
|
365 |
9479da48
|
Andreas Müller
|
this.recommendedModifierEnumeration.add(recommendedModifierEnumeration);
|
366 |
|
|
}
|
367 |
8ba55ff3
|
Patric Plitzner
|
/**
|
368 |
4daf2f37
|
m.geoffroy
|
* Removes one element from the set of {@link #getRecommendedModifierEnumeration() recommended modifier vocabularies}
|
369 |
|
|
* assigned to <i>this</i> feature.
|
370 |
|
|
*
|
371 |
|
|
* @param recommendedModifierEnumeration the term vocabulary which should be removed
|
372 |
|
|
* @see #getRecommendedModifierEnumeration()
|
373 |
|
|
* @see #addRecommendedModifierEnumeration(TermVocabulary)
|
374 |
|
|
*/
|
375 |
9479da48
|
Andreas Müller
|
public void removeRecommendedModifierEnumeration(
|
376 |
533cbb43
|
Andreas Müller
|
TermVocabulary<DefinedTerm> recommendedModifierEnumeration) {
|
377 |
9479da48
|
Andreas Müller
|
this.recommendedModifierEnumeration.remove(recommendedModifierEnumeration);
|
378 |
|
|
}
|
379 |
|
|
|
380 |
4daf2f37
|
m.geoffroy
|
/**
|
381 |
|
|
* Returns the set of {@link StatisticalMeasure statistical measures} recommended to be used
|
382 |
|
|
* in case of {@link QuantitativeData quantitative data} with <i>this</i> feature.
|
383 |
|
|
*/
|
384 |
17a0cbe8
|
ben.clark
|
@XmlElementWrapper(name = "RecommendedStatisticalMeasures")
|
385 |
|
|
@XmlElement(name = "RecommendedStatisticalMeasure")
|
386 |
|
|
@XmlIDREF
|
387 |
|
|
@XmlSchemaType(name = "IDREF")
|
388 |
9479da48
|
Andreas Müller
|
public Set<StatisticalMeasure> getRecommendedStatisticalMeasures() {
|
389 |
|
|
return recommendedStatisticalMeasures;
|
390 |
|
|
}
|
391 |
|
|
|
392 |
4daf2f37
|
m.geoffroy
|
/**
|
393 |
|
|
* Adds a {@link StatisticalMeasure statistical measure} to the set of
|
394 |
|
|
* {@link #getRecommendedStatisticalMeasures() recommended statistical measures} assigned
|
395 |
|
|
* to <i>this</i> feature.
|
396 |
8ba55ff3
|
Patric Plitzner
|
*
|
397 |
4daf2f37
|
m.geoffroy
|
* @param recommendedStatisticalMeasure the statistical measure to be added
|
398 |
|
|
* @see #getRecommendedStatisticalMeasures()
|
399 |
|
|
*/
|
400 |
9479da48
|
Andreas Müller
|
public void addRecommendedStatisticalMeasure(
|
401 |
|
|
StatisticalMeasure recommendedStatisticalMeasure) {
|
402 |
|
|
this.recommendedStatisticalMeasures.add(recommendedStatisticalMeasure);
|
403 |
|
|
}
|
404 |
8ba55ff3
|
Patric Plitzner
|
/**
|
405 |
4daf2f37
|
m.geoffroy
|
* Removes one element from the set of {@link #getRecommendedStatisticalMeasures() recommended statistical measures}
|
406 |
|
|
* assigned to <i>this</i> feature.
|
407 |
|
|
*
|
408 |
|
|
* @param recommendedStatisticalMeasure the statistical measure which should be removed
|
409 |
|
|
* @see #getRecommendedStatisticalMeasures()
|
410 |
|
|
* @see #addRecommendedStatisticalMeasure(StatisticalMeasure)
|
411 |
|
|
*/
|
412 |
9479da48
|
Andreas Müller
|
public void removeRecommendedStatisticalMeasure(
|
413 |
|
|
StatisticalMeasure recommendedStatisticalMeasure) {
|
414 |
|
|
this.recommendedStatisticalMeasures.remove(recommendedStatisticalMeasure);
|
415 |
|
|
}
|
416 |
|
|
|
417 |
52931327
|
h.fradin
|
/**
|
418 |
|
|
* Returns the set of {@link StatisticalMeasure statistical measures} recommended to be used
|
419 |
|
|
* in case of {@link QuantitativeData quantitative data} with <i>this</i> feature.
|
420 |
|
|
*/
|
421 |
17a0cbe8
|
ben.clark
|
@XmlElementWrapper(name = "RecommendedMeasurementUnits")
|
422 |
|
|
@XmlElement(name = "RecommendedMeasurementUnit")
|
423 |
|
|
@XmlIDREF
|
424 |
|
|
@XmlSchemaType(name = "IDREF")
|
425 |
52931327
|
h.fradin
|
public Set<MeasurementUnit> getRecommendedMeasurementUnits() {
|
426 |
|
|
return recommendedMeasurementUnits;
|
427 |
|
|
}
|
428 |
|
|
|
429 |
|
|
/**
|
430 |
|
|
* Adds a {@link StatisticalMeasure statistical measure} to the set of
|
431 |
|
|
* {@link #getRecommendedStatisticalMeasures() recommended statistical measures} assigned
|
432 |
|
|
* to <i>this</i> feature.
|
433 |
8ba55ff3
|
Patric Plitzner
|
*
|
434 |
52931327
|
h.fradin
|
* @param recommendedStatisticalMeasure the statistical measure to be added
|
435 |
|
|
* @see #getRecommendedStatisticalMeasures()
|
436 |
|
|
*/
|
437 |
|
|
public void addRecommendedMeasurementUnit(
|
438 |
|
|
MeasurementUnit recommendedMeasurementUnit) {
|
439 |
|
|
this.recommendedMeasurementUnits.add(recommendedMeasurementUnit);
|
440 |
|
|
}
|
441 |
8ba55ff3
|
Patric Plitzner
|
/**
|
442 |
52931327
|
h.fradin
|
* Removes one element from the set of {@link #getRecommendedStatisticalMeasures() recommended statistical measures}
|
443 |
|
|
* assigned to <i>this</i> feature.
|
444 |
|
|
*
|
445 |
|
|
* @param recommendedStatisticalMeasure the statistical measure which should be removed
|
446 |
|
|
* @see #getRecommendedStatisticalMeasures()
|
447 |
|
|
* @see #addRecommendedStatisticalMeasure(StatisticalMeasure)
|
448 |
|
|
*/
|
449 |
|
|
public void removeRecommendedMeasurementUnit(
|
450 |
|
|
MeasurementUnit recommendedMeasurementUnit) {
|
451 |
|
|
this.recommendedMeasurementUnits.remove(recommendedMeasurementUnit);
|
452 |
|
|
}
|
453 |
8ba55ff3
|
Patric Plitzner
|
|
454 |
4daf2f37
|
m.geoffroy
|
/**
|
455 |
|
|
* Returns the set of {@link TermVocabulary term vocabularies} containing the list of
|
456 |
|
|
* possible {@link State states} to be used in {@link CategoricalData categorical data}
|
457 |
|
|
* with <i>this</i> feature.
|
458 |
8ba55ff3
|
Patric Plitzner
|
*
|
459 |
4daf2f37
|
m.geoffroy
|
*/
|
460 |
17a0cbe8
|
ben.clark
|
@XmlElementWrapper(name = "SupportedCategoricalEnumerations")
|
461 |
|
|
@XmlElement(name = "SupportedCategoricalEnumeration")
|
462 |
|
|
@XmlIDREF
|
463 |
|
|
@XmlSchemaType(name = "IDREF")
|
464 |
f6765014
|
ben.clark
|
public Set<TermVocabulary<State>> getSupportedCategoricalEnumerations() {
|
465 |
9479da48
|
Andreas Müller
|
return supportedCategoricalEnumerations;
|
466 |
|
|
}
|
467 |
|
|
|
468 |
4daf2f37
|
m.geoffroy
|
/**
|
469 |
|
|
* Adds a {@link TermVocabulary term vocabulary} to the set of
|
470 |
|
|
* {@link #getSupportedCategoricalEnumerations() supported state vocabularies} assigned
|
471 |
|
|
* to <i>this</i> feature.
|
472 |
8ba55ff3
|
Patric Plitzner
|
*
|
473 |
4daf2f37
|
m.geoffroy
|
* @param supportedCategoricalEnumeration the term vocabulary which should be removed
|
474 |
|
|
* @see #getSupportedCategoricalEnumerations()
|
475 |
|
|
*/
|
476 |
9479da48
|
Andreas Müller
|
public void addSupportedCategoricalEnumeration(
|
477 |
f6765014
|
ben.clark
|
TermVocabulary<State> supportedCategoricalEnumeration) {
|
478 |
9479da48
|
Andreas Müller
|
this.supportedCategoricalEnumerations.add(supportedCategoricalEnumeration);
|
479 |
|
|
}
|
480 |
8ba55ff3
|
Patric Plitzner
|
/**
|
481 |
4daf2f37
|
m.geoffroy
|
* Removes one element from the set of {@link #getSupportedCategoricalEnumerations() supported state vocabularies}
|
482 |
|
|
* assigned to <i>this</i> feature.
|
483 |
|
|
*
|
484 |
|
|
* @param supportedCategoricalEnumeration the term vocabulary which should be removed
|
485 |
|
|
* @see #getSupportedCategoricalEnumerations()
|
486 |
|
|
* @see #addSupportedCategoricalEnumeration(TermVocabulary)
|
487 |
|
|
*/
|
488 |
9479da48
|
Andreas Müller
|
public void removeSupportedCategoricalEnumeration(
|
489 |
f6765014
|
ben.clark
|
TermVocabulary<State> supportedCategoricalEnumeration) {
|
490 |
9479da48
|
Andreas Müller
|
this.supportedCategoricalEnumerations.remove(supportedCategoricalEnumeration);
|
491 |
|
|
}
|
492 |
8ba55ff3
|
Patric Plitzner
|
|
493 |
c9866164
|
ben.clark
|
@XmlElement(name = "KindOf", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
494 |
|
|
@XmlIDREF
|
495 |
|
|
@XmlSchemaType(name = "IDREF")
|
496 |
17a0cbe8
|
ben.clark
|
@Override
|
497 |
c9866164
|
ben.clark
|
public Feature getKindOf(){
|
498 |
|
|
return super.getKindOf();
|
499 |
|
|
}
|
500 |
|
|
|
501 |
8ba55ff3
|
Patric Plitzner
|
@Override
|
502 |
|
|
public void setKindOf(Feature kindOf){
|
503 |
c9866164
|
ben.clark
|
super.setKindOf(kindOf);
|
504 |
|
|
}
|
505 |
8ba55ff3
|
Patric Plitzner
|
|
506 |
|
|
@Override
|
507 |
|
|
@XmlElement(name = "PartOf", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
508 |
c9866164
|
ben.clark
|
@XmlIDREF
|
509 |
|
|
@XmlSchemaType(name = "IDREF")
|
510 |
|
|
public Feature getPartOf(){
|
511 |
|
|
return super.getPartOf();
|
512 |
|
|
}
|
513 |
8ba55ff3
|
Patric Plitzner
|
|
514 |
|
|
@Override
|
515 |
|
|
public void setPartOf(Feature partOf){
|
516 |
c9866164
|
ben.clark
|
super.setPartOf(partOf);
|
517 |
|
|
}
|
518 |
8ba55ff3
|
Patric Plitzner
|
|
519 |
|
|
@Override
|
520 |
|
|
@XmlElementWrapper(name = "Generalizations", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
521 |
c9866164
|
ben.clark
|
@XmlElement(name = "GeneralizationOf", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
522 |
|
|
@XmlIDREF
|
523 |
|
|
@XmlSchemaType(name = "IDREF")
|
524 |
|
|
public Set<Feature> getGeneralizationOf(){
|
525 |
|
|
return super.getGeneralizationOf();
|
526 |
|
|
}
|
527 |
8ba55ff3
|
Patric Plitzner
|
|
528 |
|
|
@Override
|
529 |
|
|
protected void setGeneralizationOf(Set<Feature> value){
|
530 |
c9866164
|
ben.clark
|
super.setGeneralizationOf(value);
|
531 |
|
|
}
|
532 |
8ba55ff3
|
Patric Plitzner
|
|
533 |
|
|
@Override
|
534 |
|
|
@XmlElementWrapper(name = "Includes", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
535 |
c9866164
|
ben.clark
|
@XmlElement(name = "Include", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
536 |
|
|
@XmlIDREF
|
537 |
|
|
@XmlSchemaType(name = "IDREF")
|
538 |
|
|
public Set<Feature> getIncludes(){
|
539 |
|
|
return super.getIncludes();
|
540 |
|
|
}
|
541 |
8ba55ff3
|
Patric Plitzner
|
|
542 |
|
|
@Override
|
543 |
|
|
protected void setIncludes(Set<Feature> includes) {
|
544 |
c9866164
|
ben.clark
|
super.setIncludes(includes);
|
545 |
|
|
}
|
546 |
8ba55ff3
|
Patric Plitzner
|
|
547 |
a8113d09
|
Andreas Müller
|
private static final UUID uuidUnknown = UUID.fromString("910307f1-dc3c-452c-a6dd-af5ac7cd365c");
|
548 |
de3e2329
|
Andreas Müller
|
private static final UUID uuidDescription = UUID.fromString("9087cdcd-8b08-4082-a1de-34c9ba9fb493");
|
549 |
|
|
private static final UUID uuidDistribution = UUID.fromString("9fc9d10c-ba50-49ee-b174-ce83fc3f80c6");
|
550 |
|
|
private static final UUID uuidEcology = UUID.fromString("aa923827-d333-4cf5-9a5f-438ae0a4746b");
|
551 |
95742cf8
|
Andreas Müller
|
private static final UUID uuidHabitat = UUID.fromString("fb16929f-bc9c-456f-9d40-dec987b36438");
|
552 |
|
|
private static final UUID uuidHabitatAndEcology = UUID.fromString("9fdc4663-4d56-47d0-90b5-c0bf251bafbb");
|
553 |
|
|
private static final UUID uuidChromosomeNumber = UUID.fromString("6f677e98-d8d5-4bc5-80bf-affdb7e3945a");
|
554 |
8ba55ff3
|
Patric Plitzner
|
|
555 |
de3e2329
|
Andreas Müller
|
private static final UUID uuidBiologyEcology = UUID.fromString("9832e24f-b670-43b4-ac7c-20a7261a1d8c");
|
556 |
|
|
private static final UUID uuidKey = UUID.fromString("a677f827-22b9-4205-bb37-11cb48dd9106");
|
557 |
|
|
private static final UUID uuidMaterialsExamined = UUID.fromString("7c0c7571-a864-47c1-891d-01f59000dae1");
|
558 |
|
|
private static final UUID uuidMaterialsMethods = UUID.fromString("1e87d9c3-0844-4a03-9686-773e2ccb3ab6");
|
559 |
|
|
private static final UUID uuidEtymology = UUID.fromString("dd653d48-355c-4aec-a4e7-724f6eb29f8d");
|
560 |
|
|
private static final UUID uuidDiagnosis = UUID.fromString("d43d8501-ceab-4caa-9e51-e87138528fac");
|
561 |
892efc69
|
Andreas Kohlbecker
|
private static final UUID uuidProtologue = UUID.fromString("71b356c5-1e3f-4f5d-9b0f-c2cf8ae7779f");
|
562 |
dfa65fb3
|
Andreas Müller
|
private static final UUID uuidCommonName = UUID.fromString("fc810911-51f0-4a46-ab97-6562fe263ae5");
|
563 |
6b8f5129
|
Andreas Müller
|
private static final UUID uuidPhenology = UUID.fromString("a7786d3e-7c58-4141-8416-346d4c80c4a2");
|
564 |
|
|
private static final UUID uuidOccurrence = UUID.fromString("5deff505-1a32-4817-9a74-50e6936fd630");
|
565 |
|
|
private static final UUID uuidCitation = UUID.fromString("99b2842f-9aa7-42fa-bd5f-7285311e0101");
|
566 |
892efc69
|
Andreas Kohlbecker
|
private static final UUID uuidAdditionalPublication = UUID.fromString("2c355c16-cb04-4858-92bf-8da8d56dea95");
|
567 |
dc115dfc
|
Andreas Müller
|
private static final UUID uuidUses = UUID.fromString("e5374d39-b210-47c7-bec1-bee05b5f1cb6");
|
568 |
|
|
private static final UUID uuidConservation = UUID.fromString("4518fc20-2492-47de-b345-777d2b83c9cf");
|
569 |
|
|
private static final UUID uuidCultivation = UUID.fromString("e28965b2-a367-48c5-b954-8afc8ac2c69b");
|
570 |
|
|
private static final UUID uuidIntroduction = UUID.fromString("e75255ca-8ff4-4905-baad-f842927fe1d3");
|
571 |
|
|
private static final UUID uuidDiscussion = UUID.fromString("d3c4cbb6-0025-4322-886b-cd0156753a25");
|
572 |
6986dfa3
|
Andreas Müller
|
private static final UUID uuidImage = UUID.fromString("84193b2c-327f-4cce-90ef-c8da18fd5bb5");
|
573 |
459f7cf1
|
Andreas Müller
|
private static final UUID uuidAnatomy = UUID.fromString("94213b2c-e67a-4d37-25ef-e8d316edfba1");
|
574 |
7ac2e775
|
Katja Luther
|
private static final UUID uuidHostPlant = UUID.fromString("6e9de1d5-05f0-40d5-8786-2fe30d0d894d");
|
575 |
|
|
private static final UUID uuidPathogenAgent = UUID.fromString("002d05f2-fd72-49f1-ba4d-196cf09240b5");
|
576 |
1412a4c4
|
Katja Luther
|
private static final UUID uuidIndividualsAssociation = UUID.fromString("e2308f37-ddc5-447d-b483-5e2171dd85fd");
|
577 |
7ddf740a
|
Katja Luther
|
private static final UUID uuidSpecimen = UUID.fromString("8200e050-d5fd-4cac-8a76-4b47afb13809");
|
578 |
|
|
private static final UUID uuidObservation = UUID.fromString("f59e747d-0b4f-4bf7-b69a-cbd50bc78595");
|
579 |
ca8ee70a
|
Andreas Müller
|
private static final UUID uuidStatus = UUID.fromString("86d40635-2a63-4ad6-be75-9faa4a6a57fb");
|
580 |
|
|
private static final UUID uuidSystematics = UUID.fromString("bd9aca17-cd0e-4418-a3a1-1a4b80dbc162");
|
581 |
df13735b
|
a.theys
|
private static final UUID uuidUseRecord = UUID.fromString("8125a59d-b4d5-4485-89ea-67306297b599");
|
582 |
8ba55ff3
|
Patric Plitzner
|
|
583 |
|
|
/**
|
584 |
4daf2f37
|
m.geoffroy
|
* 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 |
1016f650
|
Andreas Müller
|
@Override
|
597 |
9e3239f6
|
Andreas Müller
|
public Feature readCsvLine(Class<Feature> termClass, List<String> csvLine, Map<UUID,DefinedTermBase> terms, boolean abbrevAsId) {
|
598 |
8ba55ff3
|
Patric Plitzner
|
Feature newInstance = super.readCsvLine(termClass, csvLine, terms, abbrevAsId);
|
599 |
|
|
String text = csvLine.get(4);
|
600 |
1016f650
|
Andreas Müller
|
if (text != null && text.length() >= 6){
|
601 |
f6765014
|
ben.clark
|
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 |
b2231758
|
h.fradin
|
// if ("1".equals(text.substring(6, 7))){newInstance.setSupportsCategoricalData(true);};
|
608 |
892efc69
|
Andreas Kohlbecker
|
//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
|
609 |
|
|
newInstance.getRepresentation(Language.DEFAULT()).setAbbreviatedLabel(null);
|
610 |
1016f650
|
Andreas Müller
|
}
|
611 |
f6765014
|
ben.clark
|
return newInstance;
|
612 |
de3e2329
|
Andreas Müller
|
}
|
613 |
8ba55ff3
|
Patric Plitzner
|
|
614 |
892efc69
|
Andreas Kohlbecker
|
//******************************* STATIC METHODS *****************************************
|
615 |
8ba55ff3
|
Patric Plitzner
|
|
616 |
892efc69
|
Andreas Kohlbecker
|
protected static Feature getTermByUuid(UUID uuid){
|
617 |
|
|
if (termMap == null){
|
618 |
8ba55ff3
|
Patric Plitzner
|
return null; //better return null then initialize the termMap in an unwanted way
|
619 |
892efc69
|
Andreas Kohlbecker
|
//example for an unwanted initialization: before initializing spring you may use a static method of this class.
|
620 |
|
|
//This would result in an default terminitialization instead of a database based
|
621 |
|
|
// term initialization
|
622 |
8ba55ff3
|
Patric Plitzner
|
|
623 |
892efc69
|
Andreas Kohlbecker
|
// DefaultTermInitializer vocabularyStore = new DefaultTermInitializer();
|
624 |
8ba55ff3
|
Patric Plitzner
|
// vocabularyStore.initialize();
|
625 |
892efc69
|
Andreas Kohlbecker
|
}
|
626 |
8ba55ff3
|
Patric Plitzner
|
return termMap.get(uuid);
|
627 |
892efc69
|
Andreas Kohlbecker
|
}
|
628 |
8ba55ff3
|
Patric Plitzner
|
|
629 |
4daf2f37
|
m.geoffroy
|
/**
|
630 |
|
|
* Returns the "unknown" feature. This feature allows to store values of
|
631 |
|
|
* {@link DescriptionElementBase description elements} even if it is momentarily
|
632 |
|
|
* not known what they mean.
|
633 |
|
|
*/
|
634 |
a8113d09
|
Andreas Müller
|
public static final Feature UNKNOWN(){
|
635 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidUnknown);
|
636 |
a8113d09
|
Andreas Müller
|
}
|
637 |
8ba55ff3
|
Patric Plitzner
|
|
638 |
4daf2f37
|
m.geoffroy
|
/**
|
639 |
|
|
* Returns the "description" feature. This feature allows to handle global
|
640 |
|
|
* {@link DescriptionElementBase description elements} for a global {@link DescriptionBase description}.<BR>
|
641 |
8ba55ff3
|
Patric Plitzner
|
* The "description" feature is the highest level feature.
|
642 |
4daf2f37
|
m.geoffroy
|
*/
|
643 |
de3e2329
|
Andreas Müller
|
public static final Feature DESCRIPTION(){
|
644 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidDescription);
|
645 |
de3e2329
|
Andreas Müller
|
}
|
646 |
|
|
|
647 |
4daf2f37
|
m.geoffroy
|
/**
|
648 |
|
|
* Returns the "distribution" feature. This feature allows to handle only
|
649 |
|
|
* {@link Distribution distributions}.
|
650 |
8ba55ff3
|
Patric Plitzner
|
*
|
651 |
4daf2f37
|
m.geoffroy
|
* @see #isSupportsDistribution()
|
652 |
|
|
*/
|
653 |
ea2896ba
|
m.geoffroy
|
public static final Feature DISTRIBUTION(){
|
654 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidDistribution);
|
655 |
9479da48
|
Andreas Müller
|
}
|
656 |
|
|
|
657 |
4daf2f37
|
m.geoffroy
|
/**
|
658 |
|
|
* Returns the "discussion" feature. This feature can only be described
|
659 |
|
|
* with {@link TextData text data}.
|
660 |
8ba55ff3
|
Patric Plitzner
|
*
|
661 |
4daf2f37
|
m.geoffroy
|
* @see #isSupportsTextData()
|
662 |
|
|
*/
|
663 |
dc115dfc
|
Andreas Müller
|
public static final Feature DISCUSSION(){
|
664 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidDiscussion);
|
665 |
dc115dfc
|
Andreas Müller
|
}
|
666 |
8ba55ff3
|
Patric Plitzner
|
|
667 |
4daf2f37
|
m.geoffroy
|
/**
|
668 |
|
|
* Returns the "ecology" feature. This feature only applies
|
669 |
|
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
670 |
|
|
* The "ecology" feature generalizes all other possible features concerning
|
671 |
|
|
* ecological matters.
|
672 |
|
|
*/
|
673 |
de3e2329
|
Andreas Müller
|
public static final Feature ECOLOGY(){
|
674 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidEcology);
|
675 |
95742cf8
|
Andreas Müller
|
}
|
676 |
8ba55ff3
|
Patric Plitzner
|
|
677 |
95742cf8
|
Andreas Müller
|
/**
|
678 |
|
|
* Returns the "habitat" feature. This feature only applies
|
679 |
|
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
680 |
|
|
* The "habitat" feature generalizes all other possible features concerning
|
681 |
|
|
* habitat matters.
|
682 |
|
|
*/
|
683 |
|
|
public static final Feature HABITAT(){
|
684 |
|
|
return getTermByUuid(uuidHabitat);
|
685 |
|
|
}
|
686 |
|
|
|
687 |
8ba55ff3
|
Patric Plitzner
|
|
688 |
95742cf8
|
Andreas Müller
|
/**
|
689 |
|
|
* Returns the "habitat & ecology" feature. This feature only applies
|
690 |
|
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
691 |
|
|
* The "habitat & ecology" feature generalizes all other possible features concerning
|
692 |
|
|
* habitat and ecology matters.
|
693 |
|
|
*/
|
694 |
|
|
public static final Feature HABITAT_ECOLOGY(){
|
695 |
|
|
return getTermByUuid(uuidHabitatAndEcology);
|
696 |
|
|
}
|
697 |
|
|
|
698 |
4daf2f37
|
m.geoffroy
|
/**
|
699 |
|
|
* Returns the "biology_ecology" feature. This feature only applies
|
700 |
|
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
701 |
|
|
* The "biology_ecology" feature generalizes all possible features concerning
|
702 |
|
|
* biological aspects of ecological matters.
|
703 |
8ba55ff3
|
Patric Plitzner
|
*
|
704 |
4daf2f37
|
m.geoffroy
|
* @see #ECOLOGY()
|
705 |
|
|
*/
|
706 |
de3e2329
|
Andreas Müller
|
public static final Feature BIOLOGY_ECOLOGY(){
|
707 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidBiologyEcology);
|
708 |
de3e2329
|
Andreas Müller
|
}
|
709 |
95742cf8
|
Andreas Müller
|
|
710 |
|
|
/**
|
711 |
|
|
* Returns the "chromosome number" feature. This feature only applies
|
712 |
|
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
713 |
|
|
*/
|
714 |
|
|
public static final Feature CHROMOSOME_NUMBER(){
|
715 |
|
|
return getTermByUuid(uuidChromosomeNumber);
|
716 |
|
|
}
|
717 |
|
|
|
718 |
8ba55ff3
|
Patric Plitzner
|
|
719 |
4daf2f37
|
m.geoffroy
|
/**
|
720 |
|
|
* Returns the "key" feature. This feature is the "upper" feature generalizing
|
721 |
|
|
* all features being used within an identification key.
|
722 |
|
|
*/
|
723 |
de3e2329
|
Andreas Müller
|
public static final Feature KEY(){
|
724 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidKey);
|
725 |
8ba55ff3
|
Patric Plitzner
|
}
|
726 |
|
|
|
727 |
|
|
|
728 |
4daf2f37
|
m.geoffroy
|
/**
|
729 |
|
|
* Returns the "materials_examined" feature. This feature can only be described
|
730 |
|
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}
|
731 |
|
|
* mentioning which material has been examined in order to accomplish
|
732 |
|
|
* the description. This feature applies only to
|
733 |
|
|
* {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.
|
734 |
|
|
*/
|
735 |
de3e2329
|
Andreas Müller
|
public static final Feature MATERIALS_EXAMINED(){
|
736 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidMaterialsExamined);
|
737 |
de3e2329
|
Andreas Müller
|
}
|
738 |
8ba55ff3
|
Patric Plitzner
|
|
739 |
4daf2f37
|
m.geoffroy
|
/**
|
740 |
|
|
* Returns the "materials_methods" feature. This feature can only be described
|
741 |
|
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}
|
742 |
|
|
* mentioning which methods have been adopted to analyze the material in
|
743 |
|
|
* order to accomplish the description. This feature applies only to
|
744 |
|
|
* {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.
|
745 |
|
|
*/
|
746 |
de3e2329
|
Andreas Müller
|
public static final Feature MATERIALS_METHODS(){
|
747 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidMaterialsMethods);
|
748 |
de3e2329
|
Andreas Müller
|
}
|
749 |
8ba55ff3
|
Patric Plitzner
|
|
750 |
4daf2f37
|
m.geoffroy
|
/**
|
751 |
|
|
* Returns the "etymology" feature. This feature can only be described
|
752 |
|
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}
|
753 |
|
|
* giving some information about the history of the taxon name. This feature applies only to
|
754 |
|
|
* {@link TaxonNameDescription taxon name descriptions}.
|
755 |
|
|
*/
|
756 |
de3e2329
|
Andreas Müller
|
public static final Feature ETYMOLOGY(){
|
757 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidEtymology);
|
758 |
de3e2329
|
Andreas Müller
|
}
|
759 |
8ba55ff3
|
Patric Plitzner
|
|
760 |
4daf2f37
|
m.geoffroy
|
/**
|
761 |
|
|
* Returns the "diagnosis" feature. This feature can only be described
|
762 |
|
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}.
|
763 |
|
|
* This feature applies only to {@link SpecimenDescription specimen descriptions} or to
|
764 |
|
|
* {@link TaxonDescription taxon descriptions}.
|
765 |
|
|
*/
|
766 |
de3e2329
|
Andreas Müller
|
public static final Feature DIAGNOSIS(){
|
767 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidDiagnosis);
|
768 |
de3e2329
|
Andreas Müller
|
}
|
769 |
dc115dfc
|
Andreas Müller
|
|
770 |
8ba55ff3
|
Patric Plitzner
|
|
771 |
4daf2f37
|
m.geoffroy
|
/**
|
772 |
|
|
* Returns the "introduction" feature. This feature can only be described
|
773 |
|
|
* with {@link TextData text data}.
|
774 |
8ba55ff3
|
Patric Plitzner
|
*
|
775 |
4daf2f37
|
m.geoffroy
|
* @see #isSupportsTextData()
|
776 |
|
|
*/
|
777 |
dc115dfc
|
Andreas Müller
|
public static final Feature INTRODUCTION(){
|
778 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidIntroduction);
|
779 |
dc115dfc
|
Andreas Müller
|
}
|
780 |
|
|
|
781 |
4daf2f37
|
m.geoffroy
|
/**
|
782 |
|
|
* Returns the "protologue" feature. This feature can only be described
|
783 |
8ba55ff3
|
Patric Plitzner
|
* with {@link TextData text data} reproducing the content of the protologue
|
784 |
4daf2f37
|
m.geoffroy
|
* (or some information about it) of the taxon name. This feature applies only to
|
785 |
|
|
* {@link TaxonNameDescription taxon name descriptions}.
|
786 |
8ba55ff3
|
Patric Plitzner
|
*
|
787 |
4daf2f37
|
m.geoffroy
|
* @see #isSupportsTextData()
|
788 |
04bf71a9
|
Katja Luther
|
*/
|
789 |
892efc69
|
Andreas Kohlbecker
|
public static final Feature PROTOLOGUE(){
|
790 |
|
|
return getTermByUuid(uuidProtologue);
|
791 |
76f719a7
|
Andreas Müller
|
}
|
792 |
8ba55ff3
|
Patric Plitzner
|
|
793 |
4daf2f37
|
m.geoffroy
|
/**
|
794 |
|
|
* Returns the "common_name" feature. This feature allows to handle only
|
795 |
|
|
* {@link CommonTaxonName common names}.
|
796 |
8ba55ff3
|
Patric Plitzner
|
*
|
797 |
4daf2f37
|
m.geoffroy
|
* @see #isSupportsCommonTaxonName()
|
798 |
|
|
*/
|
799 |
dfa65fb3
|
Andreas Müller
|
public static final Feature COMMON_NAME(){
|
800 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidCommonName);
|
801 |
dfa65fb3
|
Andreas Müller
|
}
|
802 |
8ba55ff3
|
Patric Plitzner
|
|
803 |
4daf2f37
|
m.geoffroy
|
/**
|
804 |
|
|
* Returns the "phenology" feature. This feature can only be described
|
805 |
|
|
* with {@link CategoricalData categorical data} or eventually with {@link TextData text data}
|
806 |
|
|
* containing information time about recurring natural phenomena.
|
807 |
|
|
* This feature only applies to {@link TaxonDescription taxon descriptions}.<BR>
|
808 |
|
|
* The "phenology" feature generalizes all other possible features
|
809 |
|
|
* concerning time information about particular natural phenomena
|
810 |
|
|
* (such as "first flight of butterflies").
|
811 |
|
|
*/
|
812 |
6b8f5129
|
Andreas Müller
|
public static final Feature PHENOLOGY(){
|
813 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidPhenology);
|
814 |
6b8f5129
|
Andreas Müller
|
}
|
815 |
de3e2329
|
Andreas Müller
|
|
816 |
4daf2f37
|
m.geoffroy
|
/**
|
817 |
|
|
* Returns the "occurrence" feature.
|
818 |
|
|
*/
|
819 |
6b8f5129
|
Andreas Müller
|
public static final Feature OCCURRENCE(){
|
820 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidOccurrence);
|
821 |
6b8f5129
|
Andreas Müller
|
}
|
822 |
459f7cf1
|
Andreas Müller
|
|
823 |
|
|
/**
|
824 |
|
|
* Returns the "anatomy" feature.
|
825 |
|
|
*/
|
826 |
|
|
public static final Feature ANATOMY(){
|
827 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidAnatomy);
|
828 |
459f7cf1
|
Andreas Müller
|
}
|
829 |
7ac2e775
|
Katja Luther
|
/**
|
830 |
|
|
* Returns the "hostplant" feature.
|
831 |
|
|
*/
|
832 |
|
|
public static final Feature HOSTPLANT(){
|
833 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidHostPlant);
|
834 |
7ac2e775
|
Katja Luther
|
}
|
835 |
|
|
/**
|
836 |
|
|
* Returns the "pathogen agent" feature.
|
837 |
|
|
*/
|
838 |
|
|
public static final Feature PATHOGEN_AGENT(){
|
839 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidPathogenAgent);
|
840 |
7ac2e775
|
Katja Luther
|
}
|
841 |
|
|
|
842 |
4daf2f37
|
m.geoffroy
|
/**
|
843 |
|
|
* Returns the "citation" feature. This feature can only be described
|
844 |
|
|
* with {@link TextData text data}.
|
845 |
8ba55ff3
|
Patric Plitzner
|
*
|
846 |
4daf2f37
|
m.geoffroy
|
* @see #isSupportsTextData()
|
847 |
|
|
*/
|
848 |
6b8f5129
|
Andreas Müller
|
public static final Feature CITATION(){
|
849 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidCitation);
|
850 |
6b8f5129
|
Andreas Müller
|
}
|
851 |
8ba55ff3
|
Patric Plitzner
|
|
852 |
4daf2f37
|
m.geoffroy
|
/**
|
853 |
|
|
* Returns the "additional_publication" feature. This feature can only be
|
854 |
|
|
* described with {@link TextData text data} with information about a
|
855 |
|
|
* publication where a {@link TaxonNameBase taxon name} has also been published
|
856 |
|
|
* but which is not the {@link TaxonNameBase#getNomenclaturalReference() nomenclatural reference}.
|
857 |
|
|
* This feature applies only to {@link TaxonNameDescription taxon name descriptions}.
|
858 |
8ba55ff3
|
Patric Plitzner
|
*
|
859 |
4daf2f37
|
m.geoffroy
|
* @see #isSupportsTextData()
|
860 |
754001bc
|
Katja Luther
|
*/
|
861 |
22b75e84
|
Andreas Müller
|
public static final Feature ADDITIONAL_PUBLICATION(){
|
862 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidAdditionalPublication);
|
863 |
22b75e84
|
Andreas Müller
|
}
|
864 |
8ba55ff3
|
Patric Plitzner
|
|
865 |
|
|
|
866 |
4daf2f37
|
m.geoffroy
|
/**
|
867 |
|
|
* Returns the "uses" feature. This feature only applies
|
868 |
|
|
* to {@link TaxonDescription taxon descriptions}.<BR>
|
869 |
|
|
* The "uses" feature generalizes all other possible features concerning
|
870 |
|
|
* particular uses (for instance "industrial use of seeds").
|
871 |
|
|
*/
|
872 |
dc115dfc
|
Andreas Müller
|
public static final Feature USES(){
|
873 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidUses);
|
874 |
dc115dfc
|
Andreas Müller
|
}
|
875 |
8ba55ff3
|
Patric Plitzner
|
|
876 |
df13735b
|
a.theys
|
public static final Feature USERECORD(){
|
877 |
|
|
return getTermByUuid(uuidUseRecord);
|
878 |
|
|
}
|
879 |
8ba55ff3
|
Patric Plitzner
|
|
880 |
|
|
|
881 |
4daf2f37
|
m.geoffroy
|
/**
|
882 |
|
|
* Returns the "conservation" feature. This feature only applies
|
883 |
|
|
* to {@link SpecimenDescription specimen descriptions} and generalizes
|
884 |
|
|
* methods and conditions for the conservation of {@link Specimen specimens}.<BR>
|
885 |
|
|
*/
|
886 |
dc115dfc
|
Andreas Müller
|
public static final Feature CONSERVATION(){
|
887 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidConservation);
|
888 |
dc115dfc
|
Andreas Müller
|
}
|
889 |
8ba55ff3
|
Patric Plitzner
|
|
890 |
|
|
|
891 |
4daf2f37
|
m.geoffroy
|
/**
|
892 |
|
|
* Returns the "cultivation" feature.
|
893 |
|
|
*/
|
894 |
dc115dfc
|
Andreas Müller
|
public static final Feature CULTIVATION(){
|
895 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidCultivation);
|
896 |
dc115dfc
|
Andreas Müller
|
}
|
897 |
8ba55ff3
|
Patric Plitzner
|
|
898 |
|
|
|
899 |
6986dfa3
|
Andreas Müller
|
/**
|
900 |
892efc69
|
Andreas Kohlbecker
|
* Returns the "image" feature.
|
901 |
6986dfa3
|
Andreas Müller
|
*/
|
902 |
|
|
public static final Feature IMAGE(){
|
903 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidImage);
|
904 |
6986dfa3
|
Andreas Müller
|
}
|
905 |
8ba55ff3
|
Patric Plitzner
|
|
906 |
1412a4c4
|
Katja Luther
|
/**
|
907 |
|
|
* Returns the "individuals association" feature.
|
908 |
|
|
*/
|
909 |
|
|
public static final Feature INDIVIDUALS_ASSOCIATION(){
|
910 |
892efc69
|
Andreas Kohlbecker
|
Feature individuals_association = getTermByUuid(uuidIndividualsAssociation);
|
911 |
064e68ad
|
Katja Luther
|
Set<Feature> generalizationOf = new HashSet<Feature>();
|
912 |
|
|
generalizationOf.add(SPECIMEN());
|
913 |
|
|
generalizationOf.add(OBSERVATION());
|
914 |
|
|
individuals_association.setGeneralizationOf(generalizationOf);
|
915 |
|
|
return individuals_association;
|
916 |
8ba55ff3
|
Patric Plitzner
|
|
917 |
1412a4c4
|
Katja Luther
|
}
|
918 |
8ba55ff3
|
Patric Plitzner
|
|
919 |
7ddf740a
|
Katja Luther
|
public static final Feature SPECIMEN(){
|
920 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidSpecimen);
|
921 |
7ddf740a
|
Katja Luther
|
}
|
922 |
8ba55ff3
|
Patric Plitzner
|
|
923 |
7ddf740a
|
Katja Luther
|
public static final Feature OBSERVATION(){
|
924 |
892efc69
|
Andreas Kohlbecker
|
return getTermByUuid(uuidObservation);
|
925 |
7ddf740a
|
Katja Luther
|
}
|
926 |
ca8ee70a
|
Andreas Müller
|
|
927 |
|
|
/**
|
928 |
|
|
* The status of a taxon. Usually the status should be determined within a {@link Distribution distribution}.
|
929 |
|
|
* If this is not possible for some reason (e.g. the area is not well defined) the status feature
|
930 |
|
|
* may be used.
|
931 |
|
|
* @return
|
932 |
|
|
*/
|
933 |
|
|
public static final Feature STATUS(){
|
934 |
|
|
return getTermByUuid(uuidStatus);
|
935 |
|
|
}
|
936 |
|
|
|
937 |
|
|
public static final Feature SYSTEMATICS(){
|
938 |
|
|
return getTermByUuid(uuidSystematics);
|
939 |
|
|
}
|
940 |
8ba55ff3
|
Patric Plitzner
|
|
941 |
4daf2f37
|
m.geoffroy
|
/**
|
942 |
|
|
* Returns the "hybrid_parent" feature. This feature can only be used
|
943 |
|
|
* by {@link TaxonInteraction taxon interactions}.<BR>
|
944 |
|
|
* <P>
|
945 |
|
|
* Note: It must be distinguished between hybrid relationships as
|
946 |
|
|
* relevant nomenclatural relationships between {@link BotanicalName plant names}
|
947 |
|
|
* on the one side and the biological relation between two {@link Taxon taxa}
|
948 |
8ba55ff3
|
Patric Plitzner
|
* as it is here the case on the other one.
|
949 |
|
|
*
|
950 |
4daf2f37
|
m.geoffroy
|
* @see #isSupportsTaxonInteraction()
|
951 |
|
|
* @see HybridRelationshipType
|
952 |
|
|
*/
|
953 |
ea2896ba
|
m.geoffroy
|
public static final Feature HYBRID_PARENT(){
|
954 |
46170dab
|
Andreas Müller
|
//TODO
|
955 |
|
|
logger.warn("HYBRID_PARENT not yet implemented");
|
956 |
9479da48
|
Andreas Müller
|
return null;
|
957 |
|
|
}
|
958 |
|
|
|
959 |
f6765014
|
ben.clark
|
@Override
|
960 |
|
|
protected void setDefaultTerms(TermVocabulary<Feature> termVocabulary) {
|
961 |
892efc69
|
Andreas Kohlbecker
|
if (termMap == null){ //needed because there are multiple feature vocabularies
|
962 |
|
|
termMap = new HashMap<UUID, Feature>();
|
963 |
|
|
}
|
964 |
|
|
for (Feature term : termVocabulary.getTerms()){
|
965 |
8ba55ff3
|
Patric Plitzner
|
termMap.put(term.getUuid(), term);
|
966 |
892efc69
|
Andreas Kohlbecker
|
}
|
967 |
f6765014
|
ben.clark
|
}
|
968 |
|
|
|
969 |
9479da48
|
Andreas Müller
|
}
|