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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.name;
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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.XmlType;
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import eu.etaxonomy.cdm.model.common.OrderedTermBase;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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import org.apache.log4j.Logger;
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import org.hibernate.envers.Audited;
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import java.util.*;
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import javax.persistence.*;
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/**
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* The class representing the taxonomical ranks (like "Family", "Genus" or
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* "Species") used for {@link TaxonNameBase taxon names} across all {@link NomenclaturalCode nomenclatural codes}
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* for bacteria (ICNB), viruses (ICVCN), plants and fungi (ICBN),
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* cultivars (ICNCP) and animals (ICZN).
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* <P>
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* A standard (ordered) list of taxonomical rank 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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* list by creating new instances of additional taxonomical ranks if needed.
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* <P>
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* This class corresponds to: <ul>
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* <li> TaxonRankTerm according to the TDWG ontology
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* <li> TaxonomicRankEnum according to the TCS
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* <li> Rank according to the ABCD schema
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* </ul>
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*
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* @author m.doering
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* @version 1.0
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* @created 08-Nov-2007 13:06:46
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "Rank")
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@Entity
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@Audited
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public class Rank extends OrderedTermBase<Rank> {
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private static final Logger logger = Logger.getLogger(Rank.class);
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private static final UUID uuidEmpire = UUID.fromString("ac470211-1586-4b24-95ca-1038050b618d");
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private static final UUID uuidDomain = UUID.fromString("ffca6ec8-8b88-417b-a6a0-f7c992aac19b");
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private static final UUID uuidSuperkingdom = UUID.fromString("64223610-7625-4cfd-83ad-b797bf7f0edd");
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private static final UUID uuidKingdom = UUID.fromString("fbe7109d-66b3-498c-a697-c6c49c686162");
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private static final UUID uuidSubkingdom = UUID.fromString("a71bd9d8-f3ab-4083-afb5-d89315d71655");
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private static final UUID uuidInfrakingdom = UUID.fromString("1e37930c-86cf-44f6-90fd-7822928df260");
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private static final UUID uuidSuperphylum = UUID.fromString("0d0cecb1-e254-4607-b210-6801e7ecbb04");
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private static final UUID uuidPhylum = UUID.fromString("773430d2-76b4-438c-b817-97a543a33287");
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private static final UUID uuidSubphylum = UUID.fromString("23a9b6ff-9408-49c9-bd9e-7a2ca5ab4725");
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private static final UUID uuidInfraphylum = UUID.fromString("1701de3a-7693-42a5-a2d3-42697f944190");
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private static final UUID uuidSuperdivision = UUID.fromString("a735a48f-4fc8-49a7-ae0c-6a984f658131");
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private static final UUID uuidDivision = UUID.fromString("7e56f5cc-123a-4fd1-8cbb-6fd80358b581");
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private static final UUID uuidSubdivision = UUID.fromString("931c840f-7a6b-4d76-ad38-bfdd77d7b2e8");
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private static final UUID uuidInfradivision = UUID.fromString("c0ede273-be52-4dee-b411-66ee08d30c94");
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private static final UUID uuidSuperclass = UUID.fromString("e65b4e1a-21ec-428d-9b9f-e87721ab967c");
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private static final UUID uuidClass = UUID.fromString("f23d14c4-1d34-4ee6-8b4e-eee2eb9a3daf");
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private static final UUID uuidSubclass = UUID.fromString("8cb26733-e2f5-46cb-ab5c-f99254f877aa");
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private static final UUID uuidInfraclass = UUID.fromString("ad23cfda-879a-4021-8629-c54d27caf717");
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private static final UUID uuidSuperorder = UUID.fromString("c8c67a22-301a-4219-b882-4a49121232ff");
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private static final UUID uuidOrder = UUID.fromString("b0785a65-c1c1-4eb4-88c7-dbd3df5aaad1");
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private static final UUID uuidSuborder = UUID.fromString("768ad378-fa85-42ab-b668-763225832f57");
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private static final UUID uuidInfraorder = UUID.fromString("84099182-a6f5-47d7-8586-33c9e9955a10");
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private static final UUID uuidSuperfamily = UUID.fromString("2cfa510a-dcea-4a03-b66a-b1528f9b0796");
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private static final UUID uuidFamily = UUID.fromString("af5f2481-3192-403f-ae65-7c957a0f02b6");
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private static final UUID uuidSubfamily = UUID.fromString("862526ee-7592-4760-a23a-4ff3641541c5");
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private static final UUID uuidInfrafamily = UUID.fromString("c3f2e3bb-6eef-4a26-9fb7-b14f4c8c5e4f");
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private static final UUID uuidSupertribe = UUID.fromString("11e94828-8c61-499b-87d6-1de35ce2c51c");
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private static final UUID uuidTribe = UUID.fromString("4aa6890b-0363-4899-8d7c-ee0cb78e6166");
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private static final UUID uuidSubtribe = UUID.fromString("ae41ecc5-5165-4126-9d24-79939ae5d822");
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private static final UUID uuidInfratribe = UUID.fromString("1ec02e8f-f2b7-4c65-af9f-b436b34c79a3");
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private static final UUID uuidSupragenericTaxon = UUID.fromString("1fdc0b93-c354-441a-8406-091e0303ff5c");
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private static final UUID uuidGenus = UUID.fromString("1b11c34c-48a8-4efa-98d5-84f7f66ef43a");
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private static final UUID uuidSubgenus = UUID.fromString("78786e16-2a70-48af-a608-494023b91904");
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private static final UUID uuidInfragenus = UUID.fromString("a9972969-82cd-4d54-b693-a096422f13fa");
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private static final UUID uuidSection = UUID.fromString("3edff68f-8527-49b5-bf91-7e4398bb975c");
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private static final UUID uuidSubsection = UUID.fromString("d20f5b61-d463-4448-8f8a-c1ff1f262f59");
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private static final UUID uuidSeries = UUID.fromString("d7381ecf-48f8-429b-9c54-f461656978cd");
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private static final UUID uuidSubseries = UUID.fromString("80c9a263-f4db-4a13-b6c2-b7fec1aa1200");
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private static final UUID uuidSpeciesAggregate = UUID.fromString("1ecae058-4217-4f75-9c27-6d8ba099ac7a");
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private static final UUID uuidInfragenericTaxon = UUID.fromString("41bcc6ac-37d3-4fd4-bb80-3cc5b04298b9");
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private static final UUID uuidSpecies = UUID.fromString("b301f787-f319-4ccc-a10f-b4ed3b99a86d");
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private static final UUID uuidSubspecificAggregate = UUID.fromString("72c248b9-027d-4402-b375-dd4f0850c9ad");
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private static final UUID uuidSubspecies = UUID.fromString("462a7819-8b00-4190-8313-88b5be81fad5");
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private static final UUID uuidInfraspecies = UUID.fromString("f28ebc9e-bd50-4194-9af1-42f5cb971a2c");
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private static final UUID uuidVariety = UUID.fromString("d5feb6a5-af5c-45ef-9878-bb4f36aaf490");
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private static final UUID uuidBioVariety = UUID.fromString("a3a364cb-1a92-43fc-a717-3c44980a0991");
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private static final UUID uuidPathoVariety = UUID.fromString("2f4f4303-a099-47e3-9048-d749d735423b");
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private static final UUID uuidSubvariety = UUID.fromString("9a83862a-7aee-480c-a98d-4bceaf8712ca");
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private static final UUID uuidSubsubvariety = UUID.fromString("bff22f84-553a-4429-a4e7-c4b3796c3a18");
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private static final UUID uuidConvar = UUID.fromString("2cc740c9-cebb-43c8-9b06-1bef79e6a56a");
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private static final UUID uuidForm = UUID.fromString("0461281e-458a-47b9-8d41-19a3d39356d5");
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private static final UUID uuidSpecialForm = UUID.fromString("bed20aee-2f5a-4635-9c02-eff06246d067");
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private static final UUID uuidSubform = UUID.fromString("47cfc5b0-0fb7-4ceb-b61d-e1dd8de8b569");
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private static final UUID uuidSubsubform = UUID.fromString("1c8ac389-4349-4ae0-87be-7239f6635068");
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private static final UUID uuidInfraspecificTaxon = UUID.fromString("eb75c27d-e154-4570-9d96-227b2df60474");
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private static final UUID uuidCandidate = UUID.fromString("ead9a1f5-dfd4-4de2-9121-70a47accb10b");
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private static final UUID uuidDenominationClass = UUID.fromString("49bdf74a-2170-40ed-8be2-887a0db517bf");
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private static final UUID uuidGrex = UUID.fromString("08dcb4ff-ac58-48a3-93af-efb3d836ac84");
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private static final UUID uuidGraftChimaera = UUID.fromString("6b4063bc-f934-4796-9bf3-0ef3aea5c1cb");
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private static final UUID uuidCultivarGroup = UUID.fromString("d763e7d3-e7de-4bb1-9d75-225ca6948659");
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private static final UUID uuidCultivar = UUID.fromString("5e98415b-dc6e-440b-95d6-ea33dbb39ad0");
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private static final UUID uuidUnknownRank = UUID.fromString("5c4d6755-2cf6-44ca-9220-cccf8881700b");
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private static Rank UNKNOWN_RANK;
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private static Rank CULTIVAR;
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private static Rank CULTIVARGROUP;
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private static Rank GRAFTCHIMAERA;
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private static Rank GREX;
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private static Rank DENOMINATIONCLASS;
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private static Rank CANDIDATE;
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private static Rank INFRASPECIFICTAXON;
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private static Rank SUBSUBFORM;
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private static Rank SUBFORM;
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private static Rank SPECIALFORM;
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private static Rank FORM;
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private static Rank CONVAR;
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private static Rank SUBSUBVARIETY;
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private static Rank SUBVARIETY;
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private static Rank PATHOVARIETY;
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private static Rank BIOVARIETY;
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private static Rank VARIETY;
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private static Rank INFRASPECIES;
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private static Rank SUBSPECIES;
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private static Rank SUBSPECIFICAGGREGATE;
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private static Rank SPECIES;
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private static Rank INFRAGENERICTAXON;
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private static Rank SPECIESAGGREGATE;
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private static Rank SUBSERIES;
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private static Rank SERIES;
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private static Rank SUBSECTION;
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private static Rank SECTION;
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private static Rank INFRAGENUS;
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private static Rank SUBGENUS;
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private static Rank GENUS;
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private static Rank SUPRAGENERICTAXON;
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private static Rank INFRATRIBE;
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private static Rank SUBTRIBE;
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private static Rank TRIBE;
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private static Rank SUPERTRIBE;
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private static Rank INFRAFAMILY;
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private static Rank SUBFAMILY;
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private static Rank FAMILY;
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private static Rank SUPERFAMILY;
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private static Rank INFRAORDER;
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private static Rank SUBORDER;
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private static Rank ORDER;
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private static Rank SUPERORDER;
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private static Rank INFRACLASS;
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private static Rank SUBCLASS;
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private static Rank CLASS;
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private static Rank SUPERCLASS;
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private static Rank INFRADIVISION;
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private static Rank SUBDIVISION;
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private static Rank DIVISION;
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private static Rank SUPERDIVISION;
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private static Rank INFRAPHYLUM;
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private static Rank SUBPHYLUM;
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private static Rank PHYLUM;
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private static Rank SUPERPHYLUM;
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private static Rank INFRAKINGDOM;
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private static Rank SUBKINGDOM;
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private static Rank KINGDOM;
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private static Rank SUPERKINGDOM;
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private static Rank DOMAIN;
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private static Rank EMPIRE;
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// ************* CONSTRUCTORS *************/
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/**
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* Class constructor: creates a new empty rank instance.
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*
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* @see #Rank(String, String, String)
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*/
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public Rank() {
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}
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/**
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* Class constructor: creates an additional rank instance with a description
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* (in the {@link eu.etaxonomy.cdm.model.common.Language#DEFAULT() default language}), a label and a label abbreviation.
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*
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* @param term the string (in the default language) describing the
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* new rank to be created
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* @param label the string identifying the new rank to be created
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* @param labelAbbrev the string identifying (in abbreviated form) the
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* new rank to be created
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* @see #Rank()
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*/
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public Rank(String term, String label, String labelAbbrev) {
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super(term, label, labelAbbrev);
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}
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//********* METHODS **************************************/
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public static final Rank EMPIRE(){
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return EMPIRE;
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}
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public static final Rank DOMAIN(){
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return DOMAIN;
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}
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public static final Rank SUPERKINGDOM(){
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return SUPERKINGDOM;
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}
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public static final Rank KINGDOM(){
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return KINGDOM;
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}
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public static final Rank SUBKINGDOM(){
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return SUBKINGDOM;
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}
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public static final Rank INFRAKINGDOM(){
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return INFRAKINGDOM;
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}
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public static final Rank SUPERPHYLUM(){
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return SUPERPHYLUM;
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}
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public static final Rank PHYLUM(){
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return PHYLUM;
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}
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public static final Rank SUBPHYLUM(){
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return SUBPHYLUM;
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}
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public static final Rank INFRAPHYLUM(){
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return INFRAPHYLUM;
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}
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public static final Rank SUPERDIVISION(){
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return SUPERDIVISION;
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}
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public static final Rank DIVISION(){
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return DIVISION;
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}
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public static final Rank SUBDIVISION(){
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return SUBDIVISION;
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}
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public static final Rank INFRADIVISION(){
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return INFRADIVISION;
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}
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public static final Rank SUPERCLASS(){
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return SUPERCLASS;
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}
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public static final Rank CLASS(){
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return CLASS;
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}
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public static final Rank SUBCLASS(){
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return SUBCLASS;
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}
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public static final Rank INFRACLASS(){
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return INFRACLASS;
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}
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public static final Rank SUPERORDER(){
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return SUPERORDER;
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}
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public static final Rank ORDER(){
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return ORDER;
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}
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public static final Rank SUBORDER(){
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return SUBORDER;
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}
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public static final Rank INFRAORDER(){
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return INFRAORDER;
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}
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public static final Rank SUPERFAMILY(){
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return SUPERFAMILY;
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}
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public static final Rank FAMILY(){
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return FAMILY;
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}
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public static final Rank SUBFAMILY(){
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return SUBFAMILY;
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}
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public static final Rank INFRAFAMILY(){
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return INFRAFAMILY;
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}
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public static final Rank SUPERTRIBE(){
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return SUPERTRIBE;
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}
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public static final Rank TRIBE(){
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return TRIBE;
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288
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}
|
|
289
|
public static final Rank SUBTRIBE(){
|
|
290
|
return SUBTRIBE;
|
|
291
|
}
|
|
292
|
public static final Rank INFRATRIBE(){
|
|
293
|
return INFRATRIBE;
|
|
294
|
}
|
|
295
|
public static final Rank SUPRAGENERICTAXON(){
|
|
296
|
return SUPRAGENERICTAXON;
|
|
297
|
}
|
|
298
|
public static final Rank GENUS(){
|
|
299
|
return GENUS;
|
|
300
|
}
|
|
301
|
public static final Rank SUBGENUS(){
|
|
302
|
return SUBGENUS;
|
|
303
|
}
|
|
304
|
public static final Rank INFRAGENUS(){
|
|
305
|
return INFRAGENUS;
|
|
306
|
}
|
|
307
|
public static final Rank SECTION(){
|
|
308
|
return SECTION;
|
|
309
|
}
|
|
310
|
public static final Rank SUBSECTION(){
|
|
311
|
return SUBSECTION;
|
|
312
|
}
|
|
313
|
public static final Rank SERIES(){
|
|
314
|
return SERIES;
|
|
315
|
}
|
|
316
|
public static final Rank SUBSERIES(){
|
|
317
|
return SUBSERIES;
|
|
318
|
}
|
|
319
|
public static final Rank SPECIESAGGREGATE(){
|
|
320
|
return SPECIESAGGREGATE;
|
|
321
|
}
|
|
322
|
public static final Rank INFRAGENERICTAXON(){
|
|
323
|
return INFRAGENERICTAXON;
|
|
324
|
}
|
|
325
|
public static final Rank SPECIES(){
|
|
326
|
return SPECIES;
|
|
327
|
}
|
|
328
|
public static final Rank SUBSPECIFICAGGREGATE(){
|
|
329
|
return SUBSPECIFICAGGREGATE;
|
|
330
|
}
|
|
331
|
public static final Rank SUBSPECIES(){
|
|
332
|
return SUBSPECIES;
|
|
333
|
}
|
|
334
|
public static final Rank INFRASPECIES(){
|
|
335
|
return INFRASPECIES;
|
|
336
|
}
|
|
337
|
public static final Rank VARIETY(){
|
|
338
|
return VARIETY;
|
|
339
|
}
|
|
340
|
public static final Rank BIOVARIETY(){
|
|
341
|
return BIOVARIETY;
|
|
342
|
}
|
|
343
|
public static final Rank PATHOVARIETY(){
|
|
344
|
return PATHOVARIETY;
|
|
345
|
}
|
|
346
|
public static final Rank SUBVARIETY(){
|
|
347
|
return SUBVARIETY;
|
|
348
|
}
|
|
349
|
public static final Rank SUBSUBVARIETY(){
|
|
350
|
return SUBSUBVARIETY;
|
|
351
|
}
|
|
352
|
public static final Rank CONVAR(){
|
|
353
|
return CONVAR;
|
|
354
|
}
|
|
355
|
public static final Rank FORM(){
|
|
356
|
return FORM;
|
|
357
|
}
|
|
358
|
public static final Rank SPECIALFORM(){
|
|
359
|
return SPECIALFORM;
|
|
360
|
}
|
|
361
|
public static final Rank SUBFORM(){
|
|
362
|
return SUBFORM;
|
|
363
|
}
|
|
364
|
public static final Rank SUBSUBFORM(){
|
|
365
|
return SUBSUBFORM;
|
|
366
|
}
|
|
367
|
public static final Rank INFRASPECIFICTAXON(){
|
|
368
|
return INFRASPECIFICTAXON;
|
|
369
|
}
|
|
370
|
public static final Rank CANDIDATE(){
|
|
371
|
return CANDIDATE;
|
|
372
|
}
|
|
373
|
public static final Rank DENOMINATIONCLASS(){
|
|
374
|
return DENOMINATIONCLASS;
|
|
375
|
}
|
|
376
|
public static final Rank GREX(){
|
|
377
|
return GREX;
|
|
378
|
}
|
|
379
|
public static final Rank GRAFTCHIMAERA(){
|
|
380
|
return GRAFTCHIMAERA;
|
|
381
|
}
|
|
382
|
public static final Rank CULTIVARGROUP(){
|
|
383
|
return CULTIVARGROUP;
|
|
384
|
}
|
|
385
|
public static final Rank CULTIVAR(){
|
|
386
|
return CULTIVAR;
|
|
387
|
}
|
|
388
|
public static final Rank UNKNOWN_RANK(){
|
|
389
|
return UNKNOWN_RANK;
|
|
390
|
}
|
|
391
|
|
|
392
|
/**
|
|
393
|
* Returns the boolean value indicating whether <i>this</i> rank is higher than
|
|
394
|
* the genus rank (true) or not (false). Returns false if <i>this</i> rank is null.
|
|
395
|
*
|
|
396
|
* @see #isGenus()
|
|
397
|
* @see #isInfraGeneric()
|
|
398
|
* @see #isSpecies()
|
|
399
|
* @see #isInfraSpecific()
|
|
400
|
*/
|
|
401
|
@Transient
|
|
402
|
public boolean isSupraGeneric(){
|
|
403
|
return (this.isHigher(Rank.GENUS()));
|
|
404
|
}
|
|
405
|
|
|
406
|
/**
|
|
407
|
* Returns the boolean value indicating whether <i>this</i> rank is the genus rank
|
|
408
|
* (true) or not (false). Returns false if <i>this</i> rank is null.
|
|
409
|
*
|
|
410
|
* @see #isSupraGeneric()
|
|
411
|
* @see #isInfraGeneric()
|
|
412
|
* @see #isSpecies()
|
|
413
|
* @see #isInfraSpecific()
|
|
414
|
*/
|
|
415
|
@Transient
|
|
416
|
public boolean isGenus(){
|
|
417
|
return (this.equals(Rank.GENUS()));
|
|
418
|
}
|
|
419
|
|
|
420
|
/**
|
|
421
|
* Returns the boolean value indicating whether <i>this</i> rank is higher than the
|
|
422
|
* species rank and lower than the genus rank (true) or not (false).
|
|
423
|
* Returns false if <i>this</i> rank is null.
|
|
424
|
*
|
|
425
|
* @see #isSupraGeneric()
|
|
426
|
* @see #isGenus()
|
|
427
|
* @see #isSpecies()
|
|
428
|
* @see #isInfraSpecific()
|
|
429
|
*/
|
|
430
|
@Transient
|
|
431
|
public boolean isInfraGeneric(){
|
|
432
|
return (this.isLower(Rank.GENUS()) && this.isHigher(Rank.SPECIES()));
|
|
433
|
}
|
|
434
|
|
|
435
|
/**
|
|
436
|
* Returns the boolean value indicating whether <i>this</i> rank is the species
|
|
437
|
* rank (true) or not (false). Returns false if <i>this</i> rank is null.
|
|
438
|
*
|
|
439
|
* @see #isSupraGeneric()
|
|
440
|
* @see #isGenus()
|
|
441
|
* @see #isInfraGeneric()
|
|
442
|
* @see #isInfraSpecific()
|
|
443
|
*/
|
|
444
|
@Transient
|
|
445
|
public boolean isSpecies(){
|
|
446
|
return (this.equals(Rank.SPECIES()));
|
|
447
|
}
|
|
448
|
|
|
449
|
/**
|
|
450
|
* Returns the boolean value indicating whether <i>this</i> rank is lower than the
|
|
451
|
* species rank (true) or not (false). Returns false if <i>this</i> rank is null.
|
|
452
|
*
|
|
453
|
* @see #isSupraGeneric()
|
|
454
|
* @see #isGenus()
|
|
455
|
* @see #isInfraGeneric()
|
|
456
|
* @see #isSpecies()
|
|
457
|
*/
|
|
458
|
@Transient
|
|
459
|
public boolean isInfraSpecific(){
|
|
460
|
return (this.isLower(Rank.SPECIES()));
|
|
461
|
}
|
|
462
|
|
|
463
|
|
|
464
|
/**
|
|
465
|
* Returns the rank identified through a name (abbreviated or not).
|
|
466
|
* Preliminary implementation for BotanicalNameParser.
|
|
467
|
*
|
|
468
|
* @param strRank the string identifying the rank
|
|
469
|
* @return the rank
|
|
470
|
*/
|
|
471
|
public static Rank getRankByNameOrAbbreviation(String strRank)
|
|
472
|
throws UnknownCdmTypeException{
|
|
473
|
return getRankByNameOrAbbreviation(strRank, false);
|
|
474
|
}
|
|
475
|
|
|
476
|
// TODO
|
|
477
|
// Preliminary implementation for BotanicalNameParser.
|
|
478
|
// not yet complete
|
|
479
|
/**
|
|
480
|
* Returns the rank identified through a name (abbreviated or not).
|
|
481
|
* Preliminary implementation for BotanicalNameParser.
|
|
482
|
*
|
|
483
|
* @param strRank the string identifying the rank
|
|
484
|
* @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
|
|
485
|
* unknown or not yet implemented
|
|
486
|
* @return the rank
|
|
487
|
*/
|
|
488
|
public static Rank getRankByNameOrAbbreviation(String strRank, boolean useUnknown)
|
|
489
|
throws UnknownCdmTypeException{
|
|
490
|
try {
|
|
491
|
return getRankByAbbreviation(strRank);
|
|
492
|
} catch (UnknownCdmTypeException e) {
|
|
493
|
return getRankByName(strRank, useUnknown);
|
|
494
|
}
|
|
495
|
}
|
|
496
|
|
|
497
|
|
|
498
|
/**
|
|
499
|
* Returns the rank identified through an abbreviated name.
|
|
500
|
* Preliminary implementation for BotanicalNameParser.
|
|
501
|
*
|
|
502
|
* @param abbrev the string for the name abbreviation
|
|
503
|
* @return the rank
|
|
504
|
*/
|
|
505
|
public static Rank getRankByAbbreviation(String abbrev)
|
|
506
|
throws UnknownCdmTypeException{
|
|
507
|
return getRankByAbbreviation(abbrev, false);
|
|
508
|
}
|
|
509
|
|
|
510
|
// TODO
|
|
511
|
// Preliminary implementation for BotanicalNameParser.
|
|
512
|
// not yet complete
|
|
513
|
/**
|
|
514
|
* Returns the rank identified through an abbreviated name.
|
|
515
|
* Preliminary implementation for BotanicalNameParser.
|
|
516
|
*
|
|
517
|
* @param abbrev the string for the name abbreviation
|
|
518
|
* @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
|
|
519
|
* unknown or not yet implemented
|
|
520
|
* @return the rank
|
|
521
|
*/
|
|
522
|
public static Rank getRankByAbbreviation(String abbrev, boolean useUnknown)
|
|
523
|
throws UnknownCdmTypeException{
|
|
524
|
if (abbrev == null){ throw new NullPointerException("abbrev is 'null' in getRankByAbbreviation");
|
|
525
|
}else if (abbrev.equalsIgnoreCase("reg.")){ return Rank.KINGDOM();
|
|
526
|
}else if (abbrev.equalsIgnoreCase("subreg.")){ return Rank.SUBKINGDOM();
|
|
527
|
}else if (abbrev.equalsIgnoreCase("phyl.")){return Rank.PHYLUM();
|
|
528
|
}else if (abbrev.equalsIgnoreCase("subphyl.")) { return Rank.SUBPHYLUM();
|
|
529
|
}else if (abbrev.equalsIgnoreCase("div.")) { return Rank.DIVISION();
|
|
530
|
}else if (abbrev.equalsIgnoreCase("subdiv.")) { return Rank.SUBDIVISION();
|
|
531
|
}else if (abbrev.equalsIgnoreCase("cl.")) { return Rank.CLASS();
|
|
532
|
}else if (abbrev.equalsIgnoreCase("subcl.")) { return Rank.SUBCLASS();
|
|
533
|
}else if (abbrev.equalsIgnoreCase("superor.")) { return Rank.SUPERORDER();
|
|
534
|
}else if (abbrev.equalsIgnoreCase("ordo")) { return Rank.ORDER();
|
|
535
|
}else if (abbrev.equalsIgnoreCase("subor.")) { return Rank.SUBORDER();
|
|
536
|
}else if (abbrev.equalsIgnoreCase("fam.")) { return Rank.FAMILY();
|
|
537
|
}else if (abbrev.equalsIgnoreCase("subfam.")) { return Rank.SUBFAMILY();
|
|
538
|
}else if (abbrev.equalsIgnoreCase("trib.")) { return Rank.TRIBE();
|
|
539
|
}else if (abbrev.equalsIgnoreCase("subtrib.")) { return Rank.SUBTRIBE();
|
|
540
|
}else if (abbrev.equalsIgnoreCase("gen.")) { return Rank.GENUS();
|
|
541
|
}else if (abbrev.equalsIgnoreCase("subg.")) { return Rank.SUBGENUS();
|
|
542
|
}else if (abbrev.equalsIgnoreCase("sect.")) { return Rank.SECTION();
|
|
543
|
}else if (abbrev.equalsIgnoreCase("subsect.")) { return Rank.SUBSECTION();
|
|
544
|
}else if (abbrev.equalsIgnoreCase("ser.")) { return Rank.SERIES();
|
|
545
|
}else if (abbrev.equalsIgnoreCase("subser.")) { return Rank.SUBSERIES();
|
|
546
|
}else if (abbrev.equalsIgnoreCase("aggr.")) { return Rank.SPECIESAGGREGATE();
|
|
547
|
//TODO
|
|
548
|
//}else if (abbrev.equalsIgnoreCase("group")) { return Rank.SPECIESGROUP();
|
|
549
|
}else if (abbrev.equalsIgnoreCase("sp.")) { return Rank.SPECIES();
|
|
550
|
}else if (abbrev.equalsIgnoreCase("subsp.")) { return Rank.SUBSPECIES();
|
|
551
|
}else if (abbrev.equalsIgnoreCase("convar.")) { return Rank.CONVAR();
|
|
552
|
}else if (abbrev.equalsIgnoreCase("var.")) { return Rank.VARIETY();
|
|
553
|
}else if (abbrev.equalsIgnoreCase("subvar.")) { return Rank.SUBVARIETY();
|
|
554
|
}else if (abbrev.equalsIgnoreCase("f.")) { return Rank.FORM();
|
|
555
|
}else if (abbrev.equalsIgnoreCase("subf.")) { return Rank.SUBFORM();
|
|
556
|
//TODO
|
|
557
|
//}else if (abbrev.equalsIgnoreCase("f.spec.")) { return Rank.FORMA_SPEC();
|
|
558
|
}else if (abbrev.equalsIgnoreCase("t.infgen.")) { return Rank.INFRAGENERICTAXON();
|
|
559
|
}else if (abbrev.equalsIgnoreCase("t.infr.")) { return Rank.INFRASPECIFICTAXON();
|
|
560
|
}else {
|
|
561
|
if (abbrev == null){
|
|
562
|
abbrev = "(null)";
|
|
563
|
}
|
|
564
|
if (useUnknown){
|
|
565
|
logger.info("Unknown rank name: " + abbrev+". Rank 'UNKNOWN_RANK' created instead");
|
|
566
|
return Rank.UNKNOWN_RANK();
|
|
567
|
}else{
|
|
568
|
if (abbrev == null){
|
|
569
|
abbrev = "(null)";
|
|
570
|
}
|
|
571
|
throw new UnknownCdmTypeException("Unknown rank abbreviation: " + abbrev);
|
|
572
|
}
|
|
573
|
}
|
|
574
|
}
|
|
575
|
|
|
576
|
// TODO
|
|
577
|
// Preliminary implementation for BotanicalNameParser.
|
|
578
|
// not yet complete
|
|
579
|
/**
|
|
580
|
* Returns the rank identified through a name.
|
|
581
|
* Preliminary implementation for BotanicalNameParser.
|
|
582
|
*
|
|
583
|
* @param rankName the string for the name of the rank
|
|
584
|
* @return the rank
|
|
585
|
*/
|
|
586
|
public static Rank getRankByName(String rankName)throws UnknownCdmTypeException{
|
|
587
|
return getRankByName(rankName, false);
|
|
588
|
}
|
|
589
|
|
|
590
|
|
|
591
|
/**
|
|
592
|
* Returns the rank identified through a name.
|
|
593
|
* Preliminary implementation for BotanicalNameParser.
|
|
594
|
*
|
|
595
|
* @param rankName the string for the name of the rank
|
|
596
|
* @param useUnknown if true the rank UNKNOWN_RANK is returned if the rank name is
|
|
597
|
* unknown or not yet implemented
|
|
598
|
* @return the rank
|
|
599
|
*/
|
|
600
|
public static Rank getRankByName(String rankName, boolean useUnknown)
|
|
601
|
throws UnknownCdmTypeException{
|
|
602
|
if (rankName.equalsIgnoreCase("Regnum")){ return Rank.KINGDOM();
|
|
603
|
}else if (rankName.equalsIgnoreCase("Subregnum")){ return Rank.SUBKINGDOM();
|
|
604
|
}else if (rankName.equalsIgnoreCase("Phylum")){ return Rank.PHYLUM();
|
|
605
|
}else if (rankName.equalsIgnoreCase("subphylum")){ return Rank.SUBPHYLUM();
|
|
606
|
}else if (rankName.equalsIgnoreCase("Divisio")){ return Rank.DIVISION();
|
|
607
|
}else if (rankName.equalsIgnoreCase("Subdivisio")){ return Rank.SUBDIVISION();
|
|
608
|
}else if (rankName.equalsIgnoreCase("Classis")){ return Rank.CLASS();
|
|
609
|
}else if (rankName.equalsIgnoreCase("Subclassis")){ return Rank.SUBCLASS();
|
|
610
|
}else if (rankName.equalsIgnoreCase("Superordo")){ return Rank.SUPERORDER();
|
|
611
|
}else if (rankName.equalsIgnoreCase("Ordo")){ return Rank.ORDER();
|
|
612
|
}else if (rankName.equalsIgnoreCase("Subordo")){ return Rank.SUBORDER();
|
|
613
|
}else if (rankName.equalsIgnoreCase("Familia")){ return Rank.FAMILY();
|
|
614
|
}else if (rankName.equalsIgnoreCase("Subfamilia")){ return Rank.SUBFAMILY();
|
|
615
|
}else if (rankName.equalsIgnoreCase("Tribus")){ return Rank.TRIBE();
|
|
616
|
}else if (rankName.equalsIgnoreCase("Subtribus")){ return Rank.SUBTRIBE();
|
|
617
|
}else if (rankName.equalsIgnoreCase("Genus")){ return Rank.GENUS();
|
|
618
|
}else if (rankName.equalsIgnoreCase("Subgenus")){ return Rank.SUBGENUS();
|
|
619
|
}else if (rankName.equalsIgnoreCase("Sectio")){ return Rank.SECTION();
|
|
620
|
}else if (rankName.equalsIgnoreCase("Subsectio")){ return Rank.SUBSECTION();
|
|
621
|
}else if (rankName.equalsIgnoreCase("Series")){ return Rank.SERIES();
|
|
622
|
}else if (rankName.equalsIgnoreCase("Subseries")){ return Rank.SUBSERIES();
|
|
623
|
}else if (rankName.equalsIgnoreCase("Aggregate")){ return Rank.SPECIESAGGREGATE();
|
|
624
|
//TODO
|
|
625
|
//}else if (rankName.equalsIgnoreCase("Speciesgroup")){ return Rank.SPECIESGROUP();
|
|
626
|
}else if (rankName.equalsIgnoreCase("Species")){ return Rank.SPECIES();
|
|
627
|
}else if (rankName.equalsIgnoreCase("Subspecies")){ return Rank.SUBSPECIES();
|
|
628
|
}else if (rankName.equalsIgnoreCase("Convarietas")){ return Rank.CONVAR();
|
|
629
|
}else if (rankName.equalsIgnoreCase("Varietas")){ return Rank.VARIETY();
|
|
630
|
}else if (rankName.equalsIgnoreCase("Subvarietas")){ return Rank.SUBVARIETY();
|
|
631
|
}else if (rankName.equalsIgnoreCase("Forma")){ return Rank.FORM();
|
|
632
|
}else if (rankName.equalsIgnoreCase("Subforma")){ return Rank.SUBFORM();
|
|
633
|
}else if (rankName.equalsIgnoreCase("Forma spec.")){ return Rank.SPECIALFORM();
|
|
634
|
}else if (rankName.equalsIgnoreCase("tax.infragen.")){ return Rank.INFRAGENERICTAXON();
|
|
635
|
}else if (rankName.equalsIgnoreCase("tax.infrasp.")){ return Rank.INFRASPECIFICTAXON();
|
|
636
|
// old ranks
|
|
637
|
}else if (rankName.equalsIgnoreCase("proles")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
|
|
638
|
}else if (rankName.equalsIgnoreCase("race")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
|
|
639
|
}else if (rankName.equalsIgnoreCase("taxon")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
|
|
640
|
}else if (rankName.equalsIgnoreCase("sublusus")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
|
|
641
|
|
|
642
|
}else{
|
|
643
|
if (rankName == null){
|
|
644
|
rankName = "(null)";
|
|
645
|
}
|
|
646
|
if (useUnknown){
|
|
647
|
logger.info("Unknown rank name: " + rankName+". Rank 'UNKNOWN_RANK' created instead");
|
|
648
|
return Rank.UNKNOWN_RANK();
|
|
649
|
}else{
|
|
650
|
if (rankName == null){
|
|
651
|
rankName = "(null)";
|
|
652
|
}
|
|
653
|
throw new UnknownCdmTypeException("Unknown rank name: " + rankName);
|
|
654
|
}
|
|
655
|
}
|
|
656
|
}
|
|
657
|
|
|
658
|
//TODO
|
|
659
|
//dummy implementation for BerlinModelImport
|
|
660
|
// not yet complete
|
|
661
|
/**
|
|
662
|
* Returns the abbreviated rank name for <i>this</i> rank according to the
|
|
663
|
* Berlin Model. Preliminary implementation for BerlinModelImport.
|
|
664
|
*
|
|
665
|
* @return the abbreviation string for <i>this</i> rank
|
|
666
|
*/
|
|
667
|
public String getAbbreviation(){
|
|
668
|
if (this.equals(Rank.ORDER()) ){return "ordo";}
|
|
669
|
if (this.equals(Rank.FAMILY()) ){return "fam.";}
|
|
670
|
else if (this.equals(Rank.SUBFAMILY()) ){return "subfam.";}
|
|
671
|
else if (this.equals(Rank.TRIBE()) ){return "trib.";}
|
|
672
|
else if (this.equals(Rank.SUBTRIBE()) ){return "subtrib.";}
|
|
673
|
else if (this.equals(Rank.GENUS()) ){return "gen.";}
|
|
674
|
else if (this.equals(Rank.SUBGENUS()) ){return "subg.";}
|
|
675
|
else if (this.equals(Rank.SECTION()) ){return "sect.";}
|
|
676
|
else if (this.equals(Rank.SUBSECTION()) ){return "subsect.";}
|
|
677
|
else if (this.equals(Rank.SERIES()) ){return "ser.";}
|
|
678
|
//else if (this.equals(Rank.AGGREGATE()) ){return "aggr.";}
|
|
679
|
else if (this.equals(Rank.SPECIES()) ){return "sp.";}
|
|
680
|
else if (this.equals(Rank.SUBSPECIES()) ){return "subsp.";}
|
|
681
|
else if (this.equals(Rank.VARIETY()) ){return "var.";}
|
|
682
|
else if (this.equals(Rank.CONVAR()) ){return "convar.";}
|
|
683
|
else if (this.equals(Rank.SUBVARIETY()) ){return "subvar.";}
|
|
684
|
else if (this.equals(Rank.FORM()) ){return "f.";}
|
|
685
|
else if (this.equals(Rank.SPECIALFORM()) ){return "f.spec.";}
|
|
686
|
else if (this.equals(Rank.INFRAGENERICTAXON()) ){return "t.infgen.";}
|
|
687
|
else if (this.equals(Rank.INFRASPECIFICTAXON()) ){return "t.infr.";}
|
|
688
|
else {
|
|
689
|
logger.warn("Abbreviation for this Rank " + this.toString() + " not yet implemented");
|
|
690
|
return "xxx.";
|
|
691
|
}
|
|
692
|
}
|
|
693
|
|
|
694
|
@Override
|
|
695
|
protected void setDefaultTerms(TermVocabulary<Rank> termVocabulary) {
|
|
696
|
Rank.BIOVARIETY = termVocabulary.findTermByUuid(Rank.uuidBioVariety);
|
|
697
|
Rank.CANDIDATE = termVocabulary.findTermByUuid(Rank.uuidCandidate);
|
|
698
|
Rank.CLASS = termVocabulary.findTermByUuid(Rank.uuidClass);
|
|
699
|
Rank.CONVAR = termVocabulary.findTermByUuid(Rank.uuidConvar);
|
|
700
|
Rank.CULTIVAR = termVocabulary.findTermByUuid(Rank.uuidCultivar);
|
|
701
|
Rank.CULTIVARGROUP = termVocabulary.findTermByUuid(Rank.uuidCultivarGroup);
|
|
702
|
Rank.DENOMINATIONCLASS = termVocabulary.findTermByUuid(Rank.uuidDenominationClass);
|
|
703
|
Rank.DIVISION = termVocabulary.findTermByUuid(Rank.uuidDivision);
|
|
704
|
Rank.DOMAIN = termVocabulary.findTermByUuid(Rank.uuidDomain);
|
|
705
|
Rank.EMPIRE = termVocabulary.findTermByUuid(Rank.uuidEmpire);
|
|
706
|
Rank.FAMILY = termVocabulary.findTermByUuid(Rank.uuidFamily);
|
|
707
|
Rank.FORM = termVocabulary.findTermByUuid(Rank.uuidForm);
|
|
708
|
Rank.GENUS = termVocabulary.findTermByUuid(Rank.uuidGenus);
|
|
709
|
Rank.GRAFTCHIMAERA = termVocabulary.findTermByUuid(Rank.uuidGraftChimaera);
|
|
710
|
Rank.GREX = termVocabulary.findTermByUuid(Rank.uuidGrex);
|
|
711
|
Rank.INFRACLASS = termVocabulary.findTermByUuid(Rank.uuidInfraclass);
|
|
712
|
Rank.INFRADIVISION = termVocabulary.findTermByUuid(Rank.uuidInfradivision);
|
|
713
|
Rank.INFRAFAMILY = termVocabulary.findTermByUuid(Rank.uuidInfrafamily);
|
|
714
|
Rank.INFRAGENERICTAXON = termVocabulary.findTermByUuid(Rank.uuidInfragenericTaxon);
|
|
715
|
Rank.INFRAGENUS = termVocabulary.findTermByUuid(Rank.uuidInfragenus);
|
|
716
|
Rank.INFRAKINGDOM = termVocabulary.findTermByUuid(Rank.uuidInfrakingdom);
|
|
717
|
Rank.INFRAORDER = termVocabulary.findTermByUuid(Rank.uuidInfraorder);
|
|
718
|
Rank.INFRAPHYLUM = termVocabulary.findTermByUuid(Rank.uuidInfraphylum);
|
|
719
|
Rank.INFRASPECIES = termVocabulary.findTermByUuid(Rank.uuidInfraspecies);
|
|
720
|
Rank.INFRASPECIFICTAXON = termVocabulary.findTermByUuid(Rank.uuidInfraspecificTaxon);
|
|
721
|
Rank.INFRATRIBE = termVocabulary.findTermByUuid(Rank.uuidInfratribe);
|
|
722
|
Rank.KINGDOM = termVocabulary.findTermByUuid(Rank.uuidKingdom);
|
|
723
|
Rank.ORDER = termVocabulary.findTermByUuid(Rank.uuidOrder);
|
|
724
|
Rank.PATHOVARIETY = termVocabulary.findTermByUuid(Rank.uuidPathoVariety);
|
|
725
|
Rank.PHYLUM = termVocabulary.findTermByUuid(Rank.uuidPhylum);
|
|
726
|
Rank.SECTION = termVocabulary.findTermByUuid(Rank.uuidSection);
|
|
727
|
Rank.SERIES = termVocabulary.findTermByUuid(Rank.uuidSeries);
|
|
728
|
Rank.SPECIALFORM = termVocabulary.findTermByUuid(Rank.uuidSpecialForm);
|
|
729
|
Rank.SPECIES = termVocabulary.findTermByUuid(Rank.uuidSpecies);
|
|
730
|
Rank.SPECIESAGGREGATE = termVocabulary.findTermByUuid(Rank.uuidSpeciesAggregate);
|
|
731
|
Rank.SUBCLASS = termVocabulary.findTermByUuid(Rank.uuidSubclass);
|
|
732
|
Rank.SUBDIVISION = termVocabulary.findTermByUuid(Rank.uuidSubdivision);
|
|
733
|
Rank.SUBFAMILY = termVocabulary.findTermByUuid(Rank.uuidSubfamily);
|
|
734
|
Rank.SUBFORM = termVocabulary.findTermByUuid(Rank.uuidSubform);
|
|
735
|
Rank.SUBGENUS = termVocabulary.findTermByUuid(Rank.uuidSubgenus);
|
|
736
|
Rank.SUBKINGDOM = termVocabulary.findTermByUuid(Rank.uuidSubkingdom);
|
|
737
|
Rank.SUBORDER = termVocabulary.findTermByUuid(Rank.uuidSuborder);
|
|
738
|
Rank.SUBPHYLUM = termVocabulary.findTermByUuid(Rank.uuidSubphylum);
|
|
739
|
Rank.SUBSECTION = termVocabulary.findTermByUuid(Rank.uuidSubsection);
|
|
740
|
Rank.SUBSERIES = termVocabulary.findTermByUuid(Rank.uuidSubseries);
|
|
741
|
Rank.SUBSPECIES = termVocabulary.findTermByUuid(Rank.uuidSubspecies);
|
|
742
|
Rank.SUBSPECIFICAGGREGATE = termVocabulary.findTermByUuid(Rank.uuidSubspecificAggregate);
|
|
743
|
Rank.SUBSUBFORM = termVocabulary.findTermByUuid(Rank.uuidSubsubform);
|
|
744
|
Rank.SUBSUBVARIETY = termVocabulary.findTermByUuid(Rank.uuidSubsubvariety);
|
|
745
|
Rank.SUBTRIBE = termVocabulary.findTermByUuid(Rank.uuidSubtribe);
|
|
746
|
Rank.SUBVARIETY = termVocabulary.findTermByUuid(Rank.uuidSubvariety);
|
|
747
|
Rank.SUPERCLASS = termVocabulary.findTermByUuid(Rank.uuidSuperclass);
|
|
748
|
Rank.SUPERDIVISION = termVocabulary.findTermByUuid(Rank.uuidSuperdivision);
|
|
749
|
Rank.SUPERFAMILY = termVocabulary.findTermByUuid(Rank.uuidSuperfamily);
|
|
750
|
Rank.SUPERKINGDOM = termVocabulary.findTermByUuid(Rank.uuidSuperkingdom);
|
|
751
|
Rank.SUPERORDER = termVocabulary.findTermByUuid(Rank.uuidSuperorder);
|
|
752
|
Rank.SUPERPHYLUM = termVocabulary.findTermByUuid(Rank.uuidSuperphylum);
|
|
753
|
Rank.SUPERTRIBE = termVocabulary.findTermByUuid(Rank.uuidSupertribe);
|
|
754
|
Rank.SUPRAGENERICTAXON = termVocabulary.findTermByUuid(Rank.uuidSupragenericTaxon);
|
|
755
|
Rank.TRIBE = termVocabulary.findTermByUuid(Rank.uuidTribe);
|
|
756
|
Rank.UNKNOWN_RANK = termVocabulary.findTermByUuid(Rank.uuidUnknownRank);
|
|
757
|
Rank.VARIETY = termVocabulary.findTermByUuid(Rank.uuidVariety);
|
|
758
|
}
|
|
759
|
}
|