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package eu.etaxonomy.cdm.io.tcs;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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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.TypeDesignationStatus;
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import eu.etaxonomy.cdm.model.reference.Book;
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import eu.etaxonomy.cdm.model.reference.Journal;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.reference.WebPage;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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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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public final class TcsTransformer {
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private static final Logger logger = Logger.getLogger(TcsTransformer.class);
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//TypeDesignation
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public static TypeDesignationStatus typeStatusId2TypeStatus (int typeStatusId) throws UnknownCdmTypeException{
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switch (typeStatusId){
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case 1: return TypeDesignationStatus.HOLOTYPE();
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case 2: return TypeDesignationStatus.LECTOTYPE();
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case 3: return TypeDesignationStatus.NEOTYPE();
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case 4: return TypeDesignationStatus.EPITYPE();
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case 5: return TypeDesignationStatus.ISOLECTOTYPE();
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case 6: return TypeDesignationStatus.ISONEOTYPE();
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case 7: return TypeDesignationStatus.ISOTYPE();
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case 8: return TypeDesignationStatus.PARANEOTYPE();
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case 9: return TypeDesignationStatus.PARATYPE();
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case 10: return TypeDesignationStatus.SECOND_STEP_LECTOTYPE();
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case 11: return TypeDesignationStatus.SECOND_STEP_NEOTYPE();
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case 12: return TypeDesignationStatus.SYNTYPE();
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case 21: return TypeDesignationStatus.ICONOTYPE();
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case 22: return TypeDesignationStatus.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 tcsVariety = tcsRoot + "Variety";
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String tcsSubVariety = tcsRoot + "Sub-Variety";
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String tcsForm = tcsRoot + "Form";
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String tcsSubSpecies = tcsRoot + "Subspecies";
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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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}else if (tcsVariety.equals(strRank)){return Rank.VARIETY();
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}else if (tcsSubVariety.equals(strRank)){return Rank.SUBVARIETY();
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}else if (tcsSubSpecies.equals(strRank)){return Rank.SUBSPECIES();
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}else if (tcsForm.equals(strRank)){return Rank.FORM();
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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 NomenclaturalCode nomCodeString2NomCode (String nomCode) throws UnknownCdmTypeException{
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String tcsRoot = "http://rs.tdwg.org/ontology/voc/TaxonName#";
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String tcsICBN = tcsRoot + "ICBN";
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String tcsICZN = tcsRoot + "ICZN";
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String tcsICNCP = tcsRoot + "ICNCP";
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String tcsBacteriological = tcsRoot + "BACTERIOLOGICAL";
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String tcsViral = tcsRoot + "VIRAL";
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if (nomCode == null){ return null;
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}else if (tcsICBN.equals(nomCode)){return NomenclaturalCode.ICBN();
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}else if (tcsICZN.equals(nomCode)){return NomenclaturalCode.ICZN();
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}else if (tcsICNCP.equals(nomCode)){return NomenclaturalCode.ICNCP();
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}else if (tcsBacteriological.equals(nomCode)){return NomenclaturalCode.ICNB();
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}else if (tcsViral.equals(nomCode)){return NomenclaturalCode.ICVCN();
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}
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else {
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throw new UnknownCdmTypeException("Unknown Nomenclatural Code " + nomCode);
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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-Rank by the tcs rank
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*/
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public static ReferenceBase pubTypeStr2PubType (String strPubType) throws UnknownCdmTypeException{
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String tcsRoot = "http://rs.tdwg.org/ontology/voc/PublicationCitation#";
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String tcsBook = tcsRoot + "Book";
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String tcsJournal = tcsRoot + "Journal";
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String tcsWebPage = tcsRoot + "WebPage";
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String tcsCommunication = tcsRoot + "Communication";
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String tcsBookSeries = tcsRoot + "BookSeries";
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if (strPubType == null){return null;
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}else if (tcsBook.equals(strPubType)){return Book.NewInstance();
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}else if (tcsJournal.equals(strPubType)){return Journal.NewInstance();
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}else if (tcsWebPage.equals(strPubType)){return WebPage.NewInstance();
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}
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else {
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throw new UnknownCdmTypeException("Unknown publication type " + strPubType);
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}
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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 SynonymRelationshipType.SYNONYM_OF();
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}else if (hasSynonym.equals(tcsRelationshipCategory)){/*isReverse = true; */ return SynonymRelationshipType.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.DOESNOTOVERLAP();
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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.CONGRUENTTO();
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}else if (isNotCongruentTo.equals(tcsRelationshipCategory)){return TaxonRelationshipType.NOTCONGRUENTTO();
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}else if (isNotIncludedIn.equals(tcsRelationshipCategory)){return TaxonRelationshipType.NOTINCLUDEDIN();
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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.NOTINCLUDEDIN();
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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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