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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.taxon;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.UUID;
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import javax.persistence.Entity;
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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.XmlRootElement;
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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 eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
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import eu.etaxonomy.cdm.model.common.TermType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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/**
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* The class representing categories of {@link TaxonRelationship taxon relationships}
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* (like "is congruent to" or "is misapplied name for").
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* <P>
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* A standard (ordered) list of taxon relationship type instances will be
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* automatically created as the project starts. But this class allows to extend
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* this standard list by creating new instances of additional taxon
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* relationship types if needed.
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* <P>
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* This class corresponds in part to: <ul>
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* <li> TaxonRelationshipTerm according to the TDWG ontology
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* <li> RelationshipType according to the TCS
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* </ul>
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*
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* @author m.doering
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* @created 08-Nov-2007 13:06:17
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "TaxonRelationshipType")
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@XmlRootElement(name = "TaxonRelationshipType")
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@Entity
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//@Indexed disabled to reduce clutter in indexes, since this type is not used by any search
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//@Indexed(index = "eu.etaxonomy.cdm.model.common.DefinedTermBase")
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@Audited
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public class TaxonRelationshipType extends RelationshipTermBase<TaxonRelationshipType> {
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private static final long serialVersionUID = 6575652105931691670L;
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(TaxonRelationshipType.class);
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protected static Map<UUID, TaxonRelationshipType> termMap = null;
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@Deprecated //will be removed in future versions. Use Classification/TaxonNode instead
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private static final UUID uuidTaxonomicallyIncludedIn = UUID.fromString("d13fecdf-eb44-4dd7-9244-26679c05df1c");
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private static final UUID uuidMisappliedNameFor = UUID.fromString("1ed87175-59dd-437e-959e-0d71583d8417");
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private static final UUID uuidInvalidDesignationFor = UUID.fromString("605b1d01-f2b1-4544-b2e0-6f08def3d6ed");
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private static final UUID uuidContradiction = UUID.fromString("a8f03491-2ad6-4fae-a04c-2a4c117a2e9b");
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private static final UUID uuidCongruentTo = UUID.fromString("60974c98-64ab-4574-bb5c-c110f6db634d");
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private static final UUID uuidIncludes = UUID.fromString("0501c385-cab1-4fbe-b945-fc747419bb13");
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private static final UUID uuidOverlaps = UUID.fromString("2046a0fd-4fd6-45a1-b707-2b91547f3ec7");
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private static final UUID uuidExcludes = UUID.fromString("4535a63c-4a3f-4d69-9350-7bf02e2c23be");
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private static final UUID uuidDoesNotExclude = UUID.fromString("0e5099bb-87c0-400e-abdc-bcfed5b5eece");
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private static final UUID uuidDoesNotOverlap = UUID.fromString("ecd2382b-3d94-4169-9dd2-2c4ea1d24605");
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private static final UUID uuidNotIncludedIn = UUID.fromString("89dffa4e-e004-4d42-b0d1-ae1827529e43");
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private static final UUID uuidNotCongruentTo = UUID.fromString("6c16c33b-cfc5-4a00-92bd-a9f9e448f389");
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private static final UUID uuidCongruentToOrIncludes = UUID.fromString("b55cb3a2-6e20-4ca3-95bc-12b59d3235b0");
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private static final UUID uuidIncludedInOrIncludes = UUID.fromString("c3ed5089-6779-4051-bb24-f5ea0eca80d5");
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private static final UUID uuidCongruentIncludedInOrIncludes = UUID.fromString("0170cd83-93ad-43c2-9ad1-7ac879300e2f");
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private static final UUID uuidCongruentToOrOverlaps = UUID.fromString("78355cfa-5200-432f-8e00-82b97afad0ed");
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private static final UUID uuidIncludesOrOverlaps = UUID.fromString("f1ec567b-3c73-436b-8625-b4fd53588abb");
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private static final UUID uuidCongruentToOrIncludesOrOverlaps = UUID.fromString("2d923b1a-6c0f-414c-ac9b-bbc502e18078");
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private static final UUID uuidIncludedInOrIncludesOrOverlaps = UUID.fromString("43466aa9-e431-4f37-8bca-febfd9f63716");
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private static final UUID uuidCongruentToOrExcludes = UUID.fromString("758e6cf3-05a0-49ed-9496-d8c4a9fd02ae");
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private static final UUID uuidIncludesOrExcludes = UUID.fromString("6ee440bc-fd3d-4da2-ad85-906d35a94731");
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private static final UUID uuidCongruentToOrIncludesOrExcludes = UUID.fromString("d5c6953d-aa53-46f8-aafc-ebc6428ad5d0");
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private static final UUID uuidIncludedInOrIncludesOrExcludes = UUID.fromString("43d8492c-8bd5-4f38-a633-f1ad910a34dd");
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private static final UUID uuidOverlapsOrExcludes = UUID.fromString("623ecdeb-ff1f-471d-a8dc-0d75b2fe8d94");
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private static final UUID uuidCongruentToOrOverlapsOrExcludes = UUID.fromString("6fabef72-5264-44f1-bfc0-8e2e141375f2");
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private static final UUID uuidIncludesOrOverlapsOrExcludes = UUID.fromString("b7153c89-cc6c-4f8c-bf74-216f10feac46");
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private static final UUID uuidAllRelationships = UUID.fromString("831fcd88-e5c9-49e0-b06e-bbb67d1c05c9");
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private static final UUID uuidUnclear = UUID.fromString("4c48ba25-c1d0-4bdd-9260-c1fa2e42a5d3");
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private static final UUID uuidNotYetWorkedOn = UUID.fromString("8d47e59a-790d-428f-8060-01d443519166");
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public static TaxonRelationshipType NewInstance(String term, String label, String labelAbbrev, boolean symmetric, boolean transitive) {
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return new TaxonRelationshipType(term, label, labelAbbrev, symmetric, transitive);
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}
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//********************************** CONSTRUCTOR *********************************/
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//for hibernate use only
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@Deprecated
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protected TaxonRelationshipType() {
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super(TermType.TaxonRelationshipType);
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}
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/**
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* Class constructor: creates an additional taxon relationship type
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* instance with a description (in the {@link eu.etaxonomy.cdm.model.common.Language#DEFAULT() default language}), a label,
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* a label abbreviation and the flags indicating whether this new taxon
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* relationship type is symmetric and/or transitive.
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*
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* @param term the string (in the default language) describing the
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* new taxon relationship type to be created
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* @param label the string identifying the new taxon relationship
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* type to be created
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* @param labelAbbrev the string identifying (in abbreviated form) the
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* new taxon relationship type to be created
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* @param symmetric the boolean indicating whether the new taxon
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* relationship type to be created is symmetric
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* @param transitive the boolean indicating whether the new taxon
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* relationship type to be created is transitive
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* @see #TaxonRelationshipType()
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*/
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private TaxonRelationshipType(String term, String label, String labelAbbrev, boolean symmetric, boolean transitive) {
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super(TermType.TaxonRelationshipType, term, label, labelAbbrev, symmetric, transitive);
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}
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//************************** METHODS ********************************
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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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protected static TaxonRelationshipType getTermByUuid(UUID uuid){
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if (termMap == null || termMap.isEmpty()){
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return getTermByClassAndUUID(TaxonRelationshipType.class, uuid);
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} else {
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return termMap.get(uuid);
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}
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}
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/**
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* Returns true, if this relationship type is not a <i>misapplied name for<i>
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* and also no <i>taxonomically included in</i> relationship.<BR>
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* It assumes that all other relationships are concept relationships.
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* @return
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*/
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public boolean isConceptRelationship(){
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if (this.equals(MISAPPLIED_NAME_FOR())){
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return false;
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}else if (this.equals(INVALID_DESIGNATION_FOR())){
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return false;
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}else if (this.equals(TAXONOMICALLY_INCLUDED_IN())){
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return false;
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}
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return true;
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}
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/**
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* Returns the taxon relationship type "is taxonomically included in". This
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* indicates that the {@link TaxonRelationship#getFromTaxon() source taxon}
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* in such a {@link TaxonRelationship taxon relationship} has the target {@link Taxon taxon}
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* as immediate next higher parent within the classification. Generally
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* the {@link Taxon#getSec() concept reference} of both taxa are the same
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* except if the concept reference follows the taxonomical opinion of
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* another reference.<BR>
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* This type is neither symmetric nor transitive.
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* @deprecated will be removed in version 3.0
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*/
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@Deprecated
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public static final TaxonRelationshipType TAXONOMICALLY_INCLUDED_IN(){
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return getTermByUuid(uuidTaxonomicallyIncludedIn);
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}
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/**
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* Returns the taxon relationship type "is misapplied name for". This
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* indicates that the {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} of the {@link TaxonRelationship#getFromTaxon() source taxon}
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* in such a {@link TaxonRelationship taxon relationship} has been erroneously used by
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* the {@link TaxonBase#getSec() concept reference} to denominate the same real taxon
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* as the one meant by the target {@link Taxon taxon}.<BR>
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* This type is neither symmetric nor transitive.
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*/
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public static final TaxonRelationshipType MISAPPLIED_NAME_FOR(){
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return getTermByUuid(uuidMisappliedNameFor);
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}
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/**
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* Returns the taxon relationship type "is invalid designation for". This
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* indicates that the {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon name} of the {@link TaxonRelationship#getFromTaxon() source taxon}
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* in such a {@link TaxonRelationship taxon relationship} has
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* {@link eu.etaxonomy.cdm.model.name.NomenclaturalStatusType#isInvalidType() not been validly published} but was intended to denominate
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* a real taxon which is the same as the one meant by the target {@link Taxon taxon}.<BR>
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* According to the nomenclature codes a not validly published taxon name is
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* not a taxon name at all.<BR>
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* This type is neither symmetric nor transitive.
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*/
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public static final TaxonRelationshipType INVALID_DESIGNATION_FOR(){
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return getTermByUuid(uuidInvalidDesignationFor);
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}
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/**
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* Returns the (concept) taxon relationship type "is impossible"
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* (contradiction). This is a concept relationship type which means that the
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* circumscriptions (the set of organisms/specimens that belong to a {@link Taxon taxon}
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* according to the -maybe implicit- opinion of the {@link TaxonBase#getSec() concept reference})
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* of both taxa involved in such a {@link TaxonRelationship taxon relationship} are
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* beeing compared. In a concept relationship the concept references of the
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* involved taxa must be distinct. <BR>
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* The "is impossible" (contradiction) taxon relationship type arises
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* logically if two or more incompatible (concept) taxon relationships
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* between the two taxa already exist (for instance with the types
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* "is congruent to" and "excludes").<BR>
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* This type is symmetric but not transitive.
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*/
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public static final TaxonRelationshipType CONTRADICTION(){
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return getTermByUuid(uuidContradiction);
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}
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/**
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* Returns the (concept) taxon relationship type "is congruent to".
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* This is a concept relationship type which means that the circumscriptions
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* (the set of organisms/specimens that belong to a {@link Taxon taxon} according
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* to the -maybe implicit- opinion of the {@link TaxonBase#getSec() concept reference})
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* of both taxa involved in such a {@link TaxonRelationship taxon relationship} are
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* beeing compared. In a concept relationship the concept references of the
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* involved taxa must be distinct. <BR>
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* The "is congruent to" taxon relationship type indicates that the
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* circumscriptions of both taxa involved in the taxon relationship are
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* identical.<BR>
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* This type is symmetric and transitive.
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*/
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public static final TaxonRelationshipType CONGRUENT_TO(){
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return getTermByUuid(uuidCongruentTo);
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}
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/**
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* Returns the (concept) taxon relationship type "includes".
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* This is a concept relationship type which means that the circumscriptions
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* (the set of organisms/specimens that belong to a {@link Taxon taxon} according
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* to the -maybe implicit- opinion of the {@link TaxonBase#getSec() concept reference})
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* of both taxa involved in such a {@link TaxonRelationship taxon relationship} are
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* beeing compared. In a concept relationship the concept references of the
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* involved taxa must be distinct. <BR>
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* The "includes" taxon relationship type indicates that each element
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* belonging to the circumscription of the target taxon involved in the
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* taxon relationship belongs to the circumscription of the source taxon,
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* but that some elements belonging to the circumscription of the source
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* taxon do not belong to the circumscription of the target taxon.<BR>
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* This type is not symmetric but transitive.
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*/
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public static final TaxonRelationshipType INCLUDES(){
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return getTermByUuid(uuidIncludes);
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}
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/**
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* Returns the (concept) taxon relationship type "overlaps".
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* This is a concept relationship type which means that the circumscriptions
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* (the set of organisms/specimens that belong to a {@link Taxon taxon} according
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* to the -maybe implicit- opinion of the {@link TaxonBase#getSec() concept reference})
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* of both taxa involved in such a {@link TaxonRelationship taxon relationship} are
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* beeing compared. In a concept relationship the concept references of the
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* involved taxa must be distinct. <BR>
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* The "overlaps" taxon relationship type indicates that both
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* circumscriptions have common elements but that some elements belonging
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* to the circumscription of the source taxon do not belong to the
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* circumscription of the target taxon and vice-versa.<BR>
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* This type is symmetric but not transitive.
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*/
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public static final TaxonRelationshipType OVERLAPS(){
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return getTermByUuid(uuidOverlaps);
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}
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/**
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* Returns the (concept) taxon relationship type "excludes".
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* This is a concept relationship type which means that the circumscriptions
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* (the set of organisms/specimens that belong to a {@link Taxon taxon} according
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* to the -maybe implicit- opinion of the {@link TaxonBase#getSec() concept reference})
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* of both taxa involved in such a {@link TaxonRelationship taxon relationship} are
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* beeing compared. In a concept relationship the concept references of the
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* involved taxa must be distinct. <BR>
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* The "excludes" taxon relationship type indicates that both
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* circumscriptions have no common elements.<BR>
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* This type is symmetric but not transitive.
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*/
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public static final TaxonRelationshipType EXCLUDES(){
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return getTermByUuid(uuidExcludes);
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}
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/**
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* Returns the (concept) taxon relationship type "does not exclude".
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301
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* This is a concept relationship type which means that the circumscriptions
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302
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* (the set of organisms/specimens that belong to a {@link Taxon taxon} according
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303
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* to the -maybe implicit- opinion of the {@link TaxonBase#getSec() concept reference})
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304
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* of both taxa involved in such a {@link TaxonRelationship taxon relationship} are
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305
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* beeing compared. In a concept relationship the concept references of the
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306
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* involved taxa must be distinct. <BR>
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307
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* The "does not exclude" taxon relationship type indicates that both
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308
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* circumscriptions have common elements. This type is a generalisation of
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309
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* {@link #CONGRUENT_TO() "is congruent to"}, {@link #INCLUDES() "includes"} and {@link #OVERLAPS() "overlaps"}.<BR>
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310
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* This type is symmetric but not transitive.
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311
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*
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312
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* @see #EXCLUDES()
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313
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*/
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314
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public static final TaxonRelationshipType DOES_NOT_EXCLUDE(){
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315
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return getTermByUuid(uuidDoesNotExclude);
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316
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}
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317
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/**
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318
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* Returns the (concept) taxon relationship type "does not overlap".
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319
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* This is a concept relationship type which means that the circumscriptions
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320
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* (the set of organisms/specimens that belong to a {@link Taxon taxon} according
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321
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* to the -maybe implicit- opinion of the {@link TaxonBase#getSec() concept reference})
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322
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* of both taxa involved in such a {@link TaxonRelationship taxon relationship} are
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323
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* beeing compared. In a concept relationship the concept references of the
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324
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* involved taxa must be distinct. <BR>
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325
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* The "does not overlap" taxon relationship type is a generalisation of
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326
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* {@link #CONGRUENT_TO() "is congruent to"}, {@link #INCLUDES() "includes"} and {@link #EXCLUDES() "excludes"}.<BR>
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327
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* This type is symmetric but not transitive.
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328
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*
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329
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* @see #OVERLAPS()
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330
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*/
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331
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public static final TaxonRelationshipType DOES_NOT_OVERLAP(){
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332
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return getTermByUuid(uuidDoesNotOverlap);
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333
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}
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334
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/**
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335
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* Returns the (concept) taxon relationship type "is not included in".
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336
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* This is a concept relationship type which means that the circumscriptions
|
|
337
|
* (the set of organisms/specimens that belong to a {@link Taxon taxon} according
|
|
338
|
* to the -maybe implicit- opinion of the {@link TaxonBase#getSec() concept reference})
|
|
339
|
* of both taxa involved in such a {@link TaxonRelationship taxon relationship} are
|
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340
|
* beeing compared. In a concept relationship the concept references of the
|
|
341
|
* involved taxa must be distinct. <BR>
|
|
342
|
* The "is not included in" taxon relationship type indicates that at least
|
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343
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* one element belonging to the circumscription of the source taxon involved
|
|
344
|
* in the taxon relationship does not belong to the circumscription of the
|
|
345
|
* target taxon. <BR>
|
|
346
|
* This type is neither symmetric nor transitive.
|
|
347
|
*
|
|
348
|
* @see #INCLUDES()
|
|
349
|
*/
|
|
350
|
public static final TaxonRelationshipType NOT_INCLUDED_IN(){
|
|
351
|
return getTermByUuid(uuidNotIncludedIn);
|
|
352
|
}
|
|
353
|
/**
|
|
354
|
* Returns the (concept) taxon relationship type "is not congruent to".
|
|
355
|
* This is a concept relationship type which means that the circumscriptions
|
|
356
|
* (the set of organisms/specimens that belong to a {@link Taxon taxon} according
|
|
357
|
* to the -maybe implicit- opinion of the {@link TaxonBase#getSec() concept reference})
|
|
358
|
* of both taxa involved in such a {@link TaxonRelationship taxon relationship} are
|
|
359
|
* beeing compared. In a concept relationship the concept references of the
|
|
360
|
* involved taxa must be distinct. <BR>
|
|
361
|
* The "is not congruent to" taxon relationship type indicates that at least
|
|
362
|
* one element belonging to one of both circumscriptions does not belong to
|
|
363
|
* the other circumscription. This type is a generalisation of
|
|
364
|
* {@link #INCLUDES() "includes"}, {@link #OVERLAPS() "overlaps"} and {@link #EXCLUDES() "excludes"}.<BR>
|
|
365
|
* This type is symmetric but not transitive.
|
|
366
|
*
|
|
367
|
* @see #CONGRUENT_TO()
|
|
368
|
*/
|
|
369
|
public static final TaxonRelationshipType NOT_CONGRUENT_TO(){
|
|
370
|
return getTermByUuid(uuidNotCongruentTo);
|
|
371
|
}
|
|
372
|
|
|
373
|
public static final TaxonRelationshipType CONGRUENT_OR_INCLUDES(){
|
|
374
|
return getTermByUuid(uuidCongruentToOrIncludes);
|
|
375
|
}
|
|
376
|
public static final TaxonRelationshipType INCLUDED_OR_INCLUDES(){
|
|
377
|
return getTermByUuid(uuidIncludedInOrIncludes);
|
|
378
|
}
|
|
379
|
public static final TaxonRelationshipType CONGRUENT_OR_INCLUDED_OR_INCLUDES(){
|
|
380
|
return getTermByUuid(uuidCongruentIncludedInOrIncludes);
|
|
381
|
}
|
|
382
|
public static final TaxonRelationshipType CONGRUENT_OR_OVERLAPS(){
|
|
383
|
return getTermByUuid(uuidCongruentToOrOverlaps);
|
|
384
|
}
|
|
385
|
|
|
386
|
public static final TaxonRelationshipType INCLUDES_OR_OVERLAPS(){
|
|
387
|
return getTermByUuid(uuidIncludesOrOverlaps);
|
|
388
|
}
|
|
389
|
|
|
390
|
public static final TaxonRelationshipType CONGRUENT_OR_INCLUDES_OR_EXCLUDES(){
|
|
391
|
return getTermByUuid(uuidCongruentToOrIncludesOrExcludes);
|
|
392
|
}
|
|
393
|
|
|
394
|
public static final TaxonRelationshipType INCLUDES_OR_EXCLUDES(){
|
|
395
|
return getTermByUuid(uuidIncludesOrExcludes);
|
|
396
|
}
|
|
397
|
|
|
398
|
public static final TaxonRelationshipType CONGRUENT_OR_EXCLUDES(){
|
|
399
|
return getTermByUuid(uuidCongruentToOrExcludes);
|
|
400
|
}
|
|
401
|
|
|
402
|
public static final TaxonRelationshipType INCLUDED_OR_INCLUDES_OR_OVERLAPS(){
|
|
403
|
return getTermByUuid(uuidIncludedInOrIncludesOrOverlaps);
|
|
404
|
}
|
|
405
|
|
|
406
|
public static final TaxonRelationshipType CONGRUENT_OR_INCLUDES_OR_OVERLAPS(){
|
|
407
|
return getTermByUuid(uuidCongruentToOrIncludesOrOverlaps);
|
|
408
|
}
|
|
409
|
|
|
410
|
public static final TaxonRelationshipType INCLUDES_OR_OVERLAPS_OR_EXCLUDES(){
|
|
411
|
return getTermByUuid(uuidIncludesOrOverlapsOrExcludes);
|
|
412
|
}
|
|
413
|
|
|
414
|
public static final TaxonRelationshipType CONGRUENT_OR_OVERLAPS_OR_EXCLUDES(){
|
|
415
|
return getTermByUuid(uuidCongruentToOrOverlapsOrExcludes);
|
|
416
|
}
|
|
417
|
|
|
418
|
public static final TaxonRelationshipType OVERLAPS_OR_EXCLUDES(){
|
|
419
|
return getTermByUuid(uuidOverlapsOrExcludes);
|
|
420
|
}
|
|
421
|
|
|
422
|
public static final TaxonRelationshipType INCLUDED_OR_INCLUDES_OR_EXCLUDES(){
|
|
423
|
return getTermByUuid(uuidIncludedInOrIncludesOrExcludes);
|
|
424
|
}
|
|
425
|
|
|
426
|
public static final TaxonRelationshipType UNCLEAR(){
|
|
427
|
return getTermByUuid(uuidUnclear);
|
|
428
|
}
|
|
429
|
|
|
430
|
public static final TaxonRelationshipType NOT_YET_WORKED_ON(){
|
|
431
|
return getTermByUuid(uuidNotYetWorkedOn);
|
|
432
|
}
|
|
433
|
|
|
434
|
|
|
435
|
@Override
|
|
436
|
protected void setDefaultTerms(TermVocabulary<TaxonRelationshipType> termVocabulary) {
|
|
437
|
termMap = new HashMap<UUID, TaxonRelationshipType>();
|
|
438
|
for (TaxonRelationshipType term : termVocabulary.getTerms()){
|
|
439
|
termMap.put(term.getUuid(), term);
|
|
440
|
}
|
|
441
|
}
|
|
442
|
|
|
443
|
//TODO ohter relationshipTypes
|
|
444
|
|
|
445
|
public static final TaxonRelationshipType ALL_RELATIONSHIPS(){
|
|
446
|
return getTermByUuid(uuidAllRelationships);
|
|
447
|
}
|
|
448
|
|
|
449
|
@Override
|
|
450
|
public TaxonRelationshipType readCsvLine(Class<TaxonRelationshipType> termClass, List<String> csvLine, Map<UUID,DefinedTermBase> terms, boolean abbrevAsId) {
|
|
451
|
TaxonRelationshipType newInstance = super.readCsvLine(termClass, csvLine, terms, abbrevAsId);
|
|
452
|
|
|
453
|
newInstance.setSymbol(newInstance.getIdInVocabulary());
|
|
454
|
String inverseLabelAbbrev = csvLine.get(7).trim();
|
|
455
|
newInstance.setInverseSymbol(inverseLabelAbbrev);
|
|
456
|
return newInstance;
|
|
457
|
}
|
|
458
|
}
|