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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.io.taxonx;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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/**
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* @author a.mueller
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* @since 29.07.2008
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* @version 1.0
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*/
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public final class TaxonXTransformer {
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@SuppressWarnings("unused")
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private static final Logger logger = LogManager.getLogger(TaxonXTransformer.class);
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//Facts
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public static int FACT_DESCRIPTION = 1;
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public static int FACT_GROWTH_FORM = 2;
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public static int FACT_HARDINESS = 3;
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public static int FACT_ECOLOGY = 4;
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public static int FACT_PHENOLOGY = 5;
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public static int FACT_KARYOLOGY = 6;
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public static int FACT_ILLUSTRATION = 7;
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public static int FACT_IDENTIFICATION = 8;
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public static int FACT_OBSERVATION = 9;
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public static int FACT_DISTIRBUTION_EM = 10;
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public static int FACT_DISTIRBUTION_WORLD = 11;
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//TypeDesignation
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public static SpecimenTypeDesignationStatus typeStatusId2TypeStatus (int typeStatusId) throws UnknownCdmTypeException{
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switch (typeStatusId){
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case 1: return SpecimenTypeDesignationStatus.HOLOTYPE();
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case 2: return SpecimenTypeDesignationStatus.LECTOTYPE();
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case 3: return SpecimenTypeDesignationStatus.NEOTYPE();
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case 4: return SpecimenTypeDesignationStatus.EPITYPE();
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case 5: return SpecimenTypeDesignationStatus.ISOLECTOTYPE();
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case 6: return SpecimenTypeDesignationStatus.ISONEOTYPE();
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case 7: return SpecimenTypeDesignationStatus.ISOTYPE();
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case 8: return SpecimenTypeDesignationStatus.PARANEOTYPE();
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case 9: return SpecimenTypeDesignationStatus.PARATYPE();
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case 10: return SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE();
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case 11: return SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE();
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case 12: return SpecimenTypeDesignationStatus.SYNTYPE();
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case 21: return SpecimenTypeDesignationStatus.ICONOTYPE();
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case 22: return SpecimenTypeDesignationStatus.PHOTOTYPE();
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default: {
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throw new UnknownCdmTypeException("Unknown TypeDesignationStatus (id=" + Integer.valueOf(typeStatusId).toString() + ")");
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}
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}
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}
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/** Creates an cdm-Rank by the tcs rank
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*/
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public static Rank rankString2Rank (String strRank) throws UnknownCdmTypeException{
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String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonRank#";
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String tcsGenus = tcsRoot + "Genus";
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String tcsSpecies = tcsRoot + "Species";
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// String tcsGenus = tcsRoot + "Genus";
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if (strRank == null){return null;
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}else if (tcsGenus.equals(strRank)){return Rank.GENUS();
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}else if (tcsSpecies.equals(strRank)){return Rank.SPECIES();
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}
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else {
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throw new UnknownCdmTypeException("Unknown Rank " + strRank);
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}
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}
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/** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
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*/
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public static Feature descriptionType2feature (String descriptionType) throws UnknownCdmTypeException{
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if (descriptionType == null){ return null;
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// }else if ("abstract".equals(descriptionType)){return Feature.XX();
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// }else if ("acknowledgments".equals(descriptionType)){return Feature.ICZN();
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}else if ("biology_ecology".equals(descriptionType)){return Feature.BIOLOGY_ECOLOGY();
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}else if ("description".equals(descriptionType)){return Feature.DESCRIPTION();
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}else if ("cultivation".equals(descriptionType)){return Feature.CULTIVATION();
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}else if ("conservation".equals(descriptionType)){return Feature.CONSERVATION();
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}else if ("diagnosis".equals(descriptionType)){return Feature.DIAGNOSIS();
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}else if ("Description".equals(descriptionType)){return Feature.DESCRIPTION();
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}else if ("discussion".equals(descriptionType)){return Feature.DISCUSSION();
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}else if ("distribution".equals(descriptionType)){return Feature.DISTRIBUTION();
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}else if ("etymology".equals(descriptionType)){return Feature.ETYMOLOGY();
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}else if ("key".equals(descriptionType)){return Feature.KEY();
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}else if ("introduction".equals(descriptionType)){return Feature.INTRODUCTION();
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}else if ("materials_examined".equals(descriptionType)){return Feature.MATERIALS_EXAMINED();
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}else if ("materials_methods".equals(descriptionType)){return Feature.MATERIALS_METHODS();
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// }else if ("multiple".equals(descriptionType)){return Feature.multi;
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// }else if ("synopsis".equals(descriptionType)){return Feature.synopsis;
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}else if ("uses".equals(descriptionType)){return Feature.USES();
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}else if ("vernacular".equals(descriptionType)){return Feature.COMMON_NAME();
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}else if ("anatomy".equals(descriptionType)){return Feature.ANATOMY();
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}else {
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throw new UnknownCdmTypeException("Unknown Description Type: " + descriptionType);
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}
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}
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public static boolean isReverseRelationshipCategory (String tcsRelationshipCategory){
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String str = tcsRelationshipCategory.replace("http://rs.tdwg.org/ontology/voc/TaxonConcept#", "");
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if ("HasSynonym".equalsIgnoreCase(str)
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|| "IsParentTaxonOf".equalsIgnoreCase(str)
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|| "IsIncludedIn".equalsIgnoreCase(str)
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|| "DoesNotInclude".equalsIgnoreCase(str)
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){
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return true;
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}
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return false;
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}
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/** Creates an cdm-RelationshipTermBase by the tcsRelationshipCategory
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*/
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public static RelationshipTermBase tcsRelationshipCategory2Relationship (String tcsRelationshipCategory) throws UnknownCdmTypeException{
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String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonConcept#";
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String doesNotInclude = tcsRoot + "DoesNotInclude";
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String doesNotOverlap = tcsRoot + "DoesNotOverlap";
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String excludes = tcsRoot + "Excludes";
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String hasSynonym = tcsRoot + "HasSynonym";
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String hasVernacular = tcsRoot + "HasVernacular";
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String includes = tcsRoot + "Includes";
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String isAmbiregnalOf = tcsRoot + "IsAmbiregnalOf";
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String isAnamorphOf = tcsRoot + "IsAnamorphOf";
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String isChildTaxonOf = tcsRoot + "IsChildTaxonOf";
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String isCongruentTo = tcsRoot + "IsCongruentTo";
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String isFemaleParentOf = tcsRoot + "IsFemaleParentOf";
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String isFirstParentOf = tcsRoot + "IsFirstParentOf";
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String isHybridChildOf = tcsRoot + "IsHybridChildOf";
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String isHybridParentOf = tcsRoot + "IsHybridParentOf";
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String isIncludedIn = tcsRoot + "IsIncludedIn";
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String isMaleParentOf = tcsRoot + "IsMaleParentOf";
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String isNotCongruentTo = tcsRoot + "IsNotCongruentTo";
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String isNotIncludedIn = tcsRoot + "IsNotIncludedIn";
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String isParentTaxonOf = tcsRoot + "IsParentTaxonOf";
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String isSecondParentOf = tcsRoot + "IsSecondParentOf";
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String isSynonymFor = tcsRoot + "IsSynonymFor";
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String isTeleomorphOf = tcsRoot + "IsTeleomorphOf";
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String isVernacularFor = tcsRoot + "IsVernacularFor";
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String overlaps = tcsRoot + "Overlaps";
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if (tcsRelationshipCategory == null){ return null;
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//Synonym relationships
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}else if (isSynonymFor.equals(tcsRelationshipCategory)){return SynonymType.SYNONYM_OF();
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}else if (hasSynonym.equals(tcsRelationshipCategory)){/*isReverse = true; */ return SynonymType.SYNONYM_OF();
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//Taxon relationships
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}else if (isChildTaxonOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();
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}else if (isParentTaxonOf.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();
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//concept relationships
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}else if (doesNotOverlap.equals(tcsRelationshipCategory)){return TaxonRelationshipType.DOES_NOT_OVERLAP();
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}else if (excludes.equals(tcsRelationshipCategory)){return TaxonRelationshipType.EXCLUDES();
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}else if (includes.equals(tcsRelationshipCategory)){return TaxonRelationshipType.INCLUDES();
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}else if (isCongruentTo.equals(tcsRelationshipCategory)){return TaxonRelationshipType.CONGRUENT_TO();
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}else if (isNotCongruentTo.equals(tcsRelationshipCategory)){return TaxonRelationshipType.NOT_CONGRUENT_TO();
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}else if (isNotIncludedIn.equals(tcsRelationshipCategory)){return TaxonRelationshipType.NOT_INCLUDED_IN();
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}else if (overlaps.equals(tcsRelationshipCategory)){return TaxonRelationshipType.OVERLAPS();
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//reverse concept relationships
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}else if (isIncludedIn.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.INCLUDES();
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}else if (doesNotInclude.equals(tcsRelationshipCategory)){/*isReverse = true; */ return TaxonRelationshipType.NOT_INCLUDED_IN();
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//TODO
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// }else if (hasVernacular.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isAmbiregnalOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isAnamorphOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isFemaleParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isFirstParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isHybridChildOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isHybridParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isMaleParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isSecondParentOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isTeleomorphOf.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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// }else if (isVernacularFor.equals(tcsRelationshipCategory)){return TaxonRelationshipType.X;
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}else {
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throw new UnknownCdmTypeException("Unknown RelationshipCategory " + tcsRelationshipCategory);
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}
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}
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/** Creates an cdm-NomenclaturalCode by the tcs NomenclaturalCode
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*/
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public static NomenclaturalStatusType nomStatusString2NomStatus (String nomStatus) throws UnknownCdmTypeException{
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if (nomStatus == null){ return null;
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}else if ("Valid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.VALID();
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}else if ("Alternative".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
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}else if ("nom. altern.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ALTERNATIVE();
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}else if ("Ambiguous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.AMBIGUOUS();
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}else if ("Doubtful".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.DOUBTFUL();
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}else if ("Confusum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONFUSUM();
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}else if ("Illegitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
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}else if ("nom. illeg.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ILLEGITIMATE();
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}else if ("Superfluous".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
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}else if ("nom. superfl.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SUPERFLUOUS();
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}else if ("Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
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}else if ("nom. rej.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED();
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}else if ("Utique Rejected".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED();
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}else if ("Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED_PROP();
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}else if ("Orthography Conserved Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP();
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}else if ("Legitimate".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.LEGITIMATE();
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}else if ("Novum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
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}else if ("nom. nov.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NOVUM();
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}else if ("Utique Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.UTIQUE_REJECTED_PROP();
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}else if ("Orthography Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED();
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}else if ("Rejected Prop".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.REJECTED_PROP();
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}else if ("Conserved".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
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}else if ("nom. cons.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.CONSERVED();
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}else if ("Sanctioned".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.SANCTIONED();
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}else if ("Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
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}else if ("nom. inval.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.INVALID();
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}else if ("Nudum".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
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}else if ("nom. nud.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.NUDUM();
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}else if ("Combination Invalid".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.COMBINATION_INVALID();
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}else if ("Provisional".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
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}else if ("nom. provis.".equalsIgnoreCase(nomStatus)){return NomenclaturalStatusType.PROVISIONAL();
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}
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else {
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throw new UnknownCdmTypeException("Unknown Nomenclatural status type " + nomStatus);
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}
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}
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}
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