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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 java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.UUID;
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import javax.persistence.Entity;
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import javax.persistence.Transient;
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import javax.validation.constraints.NotNull;
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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.XmlAttribute;
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import javax.xml.bind.annotation.XmlType;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.hibernate.annotations.Type;
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import org.hibernate.envers.Audited;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.OrderedTermBase;
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import eu.etaxonomy.cdm.model.common.Representation;
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import eu.etaxonomy.cdm.model.common.TermType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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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 TaxonName 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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* @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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//@Indexed disabled to reduce clutter in indexes, since this type is not used by any search
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//@Indexed(index = "eu.etaxonomy.cdm.model.common.DefinedTermBase")
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@Audited
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public class Rank extends OrderedTermBase<Rank> {
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private static final long serialVersionUID = -8648081681348758485L;
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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 uuidSectionZoology = UUID.fromString("691d371e-10d7-43f0-93db-3d7fa1a62c54");
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private static final UUID uuidSubsectionZoology = UUID.fromString("0ed32d28-adc4-4303-a9ca-68e2acd67e33");
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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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public 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 uuidSectionBotany = UUID.fromString("3edff68f-8527-49b5-bf91-7e4398bb975c");
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private static final UUID uuidSubsectionBotany = 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 uuidSpeciesGroup = UUID.fromString("d1988a11-292b-46fa-8fb7-bc64ea6d8fc6");
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public static final UUID uuidInfragenericTaxon = UUID.fromString("41bcc6ac-37d3-4fd4-bb80-3cc5b04298b9");
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public 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 uuidNatio = UUID.fromString("965f2f38-7f97-4270-ab5a-1999bf050a22");
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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 uuidProles = UUID.fromString("8810d1ba-6a34-4ae3-a355-919ccd1cd1a5");
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private static final UUID uuidRace = UUID.fromString("196dee39-cfd8-4460-8bf0-88b83da27f62");
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private static final UUID uuidSublusus = UUID.fromString("1fafa596-a8e7-4e62-a378-3cc8cb3627ca");
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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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public 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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//additional (not yet in csv files, but used in single databases)
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//https://dev.e-taxonomy.eu/redmine/issues/7285
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public static final UUID uuidCohort = UUID.fromString("3e4dc2fa-79e8-4ee7-b7d8-4c02a18fe555"); //edaphobase
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public static final UUID uuidHyporder = UUID.fromString("2a1bdf1f-80fc-4846-b4d7-edcbf664f270"); //edaphobase
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private static Map<String, UUID> idInVocMap = null;
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private static Map<String, UUID> labelMap = null;
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protected static Map<UUID, Rank> termMap = null;
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//*********************** Factory methods ********************************************/
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// /**
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// * Creates a new empty rank.
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// *
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// * @see #NewInstance(String, String, String)
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// */
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// private static Rank NewInstance(){
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// return new Rank();
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// }
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/**
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* Creates an additional rank with a description (in the {@link Language#DEFAULT() default language}),
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* 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 #NewInstance()
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*/
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public static Rank NewInstance(RankClass rankClass, String term, String label, String labelAbbrev){
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return new Rank(rankClass, term, label, labelAbbrev);
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}
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/**
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* The {@link RankClass rank class} of a rank. It is usually needed for correct formatting of a
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* rank by using e.g. isSupraGeneric(). Prior to v3.3 this was computed by comparison of ranks.
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*/
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@XmlAttribute(name ="RankClass")
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@NotNull
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@Type(type = "eu.etaxonomy.cdm.hibernate.EnumUserType",
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parameters = {@org.hibernate.annotations.Parameter(name="enumClass", value="eu.etaxonomy.cdm.model.name.RankClass")}
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)
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@Audited
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private RankClass rankClass;
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//********************************** Constructor *********************************/
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//for hibernate use only
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@Deprecated
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protected Rank() {
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super(TermType.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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protected Rank(RankClass rankClass, String term, String label, String labelAbbrev) {
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super(TermType.Rank, term, label, labelAbbrev);
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this.rankClass = rankClass;
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}
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//********* METHODS **************************************/
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.model.common.DefinedTermBase#resetTerms()
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*/
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@Override
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public void resetTerms(){
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termMap = null;
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}
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protected static Rank getTermByUuid(UUID uuid){
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if (termMap == null || termMap.isEmpty()){
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return getTermByClassAndUUID(Rank.class, uuid);
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} else {
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return termMap.get(uuid);
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}
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}
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public static final Rank EMPIRE(){
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return getTermByUuid(uuidEmpire);
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}
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public static final Rank DOMAIN(){
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return getTermByUuid(uuidDomain);
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}
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public static final Rank SUPERKINGDOM(){
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return getTermByUuid(uuidSuperkingdom);
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}
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public static final Rank KINGDOM(){
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return getTermByUuid(uuidKingdom);
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}
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public static final Rank SUBKINGDOM(){
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return getTermByUuid(uuidSubkingdom);
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}
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public static final Rank INFRAKINGDOM(){
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return getTermByUuid(uuidInfrakingdom);
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}
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public static final Rank SUPERPHYLUM(){
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return getTermByUuid(uuidSuperphylum);
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}
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public static final Rank PHYLUM(){
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return getTermByUuid(uuidPhylum);
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}
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public static final Rank SUBPHYLUM(){
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return getTermByUuid(uuidSubphylum);
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}
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263
|
public static final Rank INFRAPHYLUM(){
|
|
264
|
return getTermByUuid(uuidInfraphylum);
|
|
265
|
}
|
|
266
|
public static final Rank SUPERDIVISION(){
|
|
267
|
return getTermByUuid(uuidSuperdivision);
|
|
268
|
}
|
|
269
|
public static final Rank DIVISION(){
|
|
270
|
return getTermByUuid(uuidDivision);
|
|
271
|
}
|
|
272
|
public static final Rank SUBDIVISION(){
|
|
273
|
return getTermByUuid(uuidSubdivision);
|
|
274
|
}
|
|
275
|
public static final Rank INFRADIVISION(){
|
|
276
|
return getTermByUuid(uuidInfradivision);
|
|
277
|
}
|
|
278
|
public static final Rank SUPERCLASS(){
|
|
279
|
return getTermByUuid(uuidSuperclass);
|
|
280
|
}
|
|
281
|
public static final Rank CLASS(){
|
|
282
|
return getTermByUuid(uuidClass);
|
|
283
|
}
|
|
284
|
public static final Rank SUBCLASS(){
|
|
285
|
return getTermByUuid(uuidSubclass);
|
|
286
|
}
|
|
287
|
public static final Rank INFRACLASS(){
|
|
288
|
return getTermByUuid(uuidInfraclass);
|
|
289
|
}
|
|
290
|
public static final Rank SUPERORDER(){
|
|
291
|
return getTermByUuid(uuidSuperorder);
|
|
292
|
}
|
|
293
|
public static final Rank ORDER(){
|
|
294
|
return getTermByUuid(uuidOrder);
|
|
295
|
}
|
|
296
|
public static final Rank SUBORDER(){
|
|
297
|
return getTermByUuid(uuidSuborder);
|
|
298
|
}
|
|
299
|
public static final Rank INFRAORDER(){
|
|
300
|
return getTermByUuid(uuidInfraorder);
|
|
301
|
}
|
|
302
|
public static final Rank SUPERFAMILY(){
|
|
303
|
return getTermByUuid(uuidSuperfamily);
|
|
304
|
}
|
|
305
|
public static final Rank FAMILY(){
|
|
306
|
return getTermByUuid(uuidFamily);
|
|
307
|
}
|
|
308
|
public static final Rank SUBFAMILY(){
|
|
309
|
return getTermByUuid(uuidSubfamily);
|
|
310
|
}
|
|
311
|
public static final Rank INFRAFAMILY(){
|
|
312
|
return getTermByUuid(uuidInfrafamily);
|
|
313
|
}
|
|
314
|
public static final Rank SUPERTRIBE(){
|
|
315
|
return getTermByUuid(uuidSupertribe);
|
|
316
|
}
|
|
317
|
public static final Rank TRIBE(){
|
|
318
|
return getTermByUuid(uuidTribe);
|
|
319
|
}
|
|
320
|
public static final Rank SUBTRIBE(){
|
|
321
|
return getTermByUuid(uuidSubtribe);
|
|
322
|
}
|
|
323
|
public static final Rank INFRATRIBE(){
|
|
324
|
return getTermByUuid(uuidInfratribe);
|
|
325
|
}
|
|
326
|
public static final Rank SUPRAGENERICTAXON(){
|
|
327
|
return getTermByUuid(uuidSupragenericTaxon);
|
|
328
|
}
|
|
329
|
public static final Rank GENUS(){
|
|
330
|
return getTermByUuid(uuidGenus);
|
|
331
|
}
|
|
332
|
public static final Rank SUBGENUS(){
|
|
333
|
return getTermByUuid(uuidSubgenus);
|
|
334
|
}
|
|
335
|
public static final Rank INFRAGENUS(){
|
|
336
|
return getTermByUuid(uuidInfragenus);
|
|
337
|
}
|
|
338
|
public static final Rank SECTION_BOTANY(){
|
|
339
|
return getTermByUuid(uuidSectionBotany);
|
|
340
|
}
|
|
341
|
public static final Rank SUBSECTION_BOTANY(){
|
|
342
|
return getTermByUuid(uuidSubsectionBotany);
|
|
343
|
}
|
|
344
|
public static final Rank SECTION_ZOOLOGY(){
|
|
345
|
return getTermByUuid(uuidSectionZoology);
|
|
346
|
}
|
|
347
|
public static final Rank SUBSECTION_ZOOLOGY(){
|
|
348
|
return getTermByUuid(uuidSubsectionZoology);
|
|
349
|
}
|
|
350
|
public static final Rank SERIES(){
|
|
351
|
return getTermByUuid(uuidSeries);
|
|
352
|
}
|
|
353
|
public static final Rank SUBSERIES(){
|
|
354
|
return getTermByUuid(uuidSubseries);
|
|
355
|
}
|
|
356
|
public static final Rank SPECIESAGGREGATE(){
|
|
357
|
return getTermByUuid(uuidSpeciesAggregate);
|
|
358
|
}
|
|
359
|
public static final Rank SPECIESGROUP(){
|
|
360
|
return getTermByUuid(uuidSpeciesGroup);
|
|
361
|
}
|
|
362
|
/**
|
|
363
|
* 'Unranked infrageneric'. An infrageneric rank which is on purpose not further defined.
|
|
364
|
* This sometimes holds for names from the 19th century.
|
|
365
|
*/
|
|
366
|
public static final Rank INFRAGENERICTAXON(){
|
|
367
|
return getTermByUuid(uuidInfragenericTaxon);
|
|
368
|
}
|
|
369
|
public static final Rank SPECIES(){
|
|
370
|
return getTermByUuid(uuidSpecies);
|
|
371
|
}
|
|
372
|
public static final Rank SUBSPECIFICAGGREGATE(){
|
|
373
|
return getTermByUuid(uuidSubspecificAggregate);
|
|
374
|
}
|
|
375
|
public static final Rank SUBSPECIES(){
|
|
376
|
return getTermByUuid(uuidSubspecies);
|
|
377
|
}
|
|
378
|
public static final Rank INFRASPECIES(){
|
|
379
|
return getTermByUuid(uuidInfraspecies);
|
|
380
|
}
|
|
381
|
public static final Rank VARIETY(){
|
|
382
|
return getTermByUuid(uuidVariety);
|
|
383
|
}
|
|
384
|
public static final Rank BIOVARIETY(){
|
|
385
|
return getTermByUuid(uuidBioVariety);
|
|
386
|
}
|
|
387
|
public static final Rank PATHOVARIETY(){
|
|
388
|
return getTermByUuid(uuidPathoVariety);
|
|
389
|
}
|
|
390
|
public static final Rank SUBVARIETY(){
|
|
391
|
return getTermByUuid(uuidSubvariety);
|
|
392
|
}
|
|
393
|
public static final Rank SUBSUBVARIETY(){
|
|
394
|
return getTermByUuid(uuidSubsubvariety );
|
|
395
|
}
|
|
396
|
public static final Rank PROLES(){
|
|
397
|
return getTermByUuid(uuidProles);
|
|
398
|
}
|
|
399
|
public static final Rank RACE(){
|
|
400
|
return getTermByUuid(uuidRace);
|
|
401
|
}
|
|
402
|
public static final Rank SUBLUSUS(){
|
|
403
|
return getTermByUuid(uuidSublusus);
|
|
404
|
}
|
|
405
|
|
|
406
|
public static final Rank CONVAR(){
|
|
407
|
return getTermByUuid(uuidConvar);
|
|
408
|
}
|
|
409
|
public static final Rank FORM(){
|
|
410
|
return getTermByUuid(uuidForm);
|
|
411
|
}
|
|
412
|
public static final Rank SPECIALFORM(){
|
|
413
|
return getTermByUuid(uuidSpecialForm);
|
|
414
|
}
|
|
415
|
public static final Rank SUBFORM(){
|
|
416
|
return getTermByUuid(uuidSubform);
|
|
417
|
}
|
|
418
|
public static final Rank SUBSUBFORM(){
|
|
419
|
return getTermByUuid(uuidSubsubform);
|
|
420
|
}
|
|
421
|
/**
|
|
422
|
* 'Unranked infraspecific'. An infraspecific rank which is on purpose not further defined.
|
|
423
|
* This sometimes holds for names from the 19th century.
|
|
424
|
*/
|
|
425
|
public static final Rank INFRASPECIFICTAXON(){
|
|
426
|
return getTermByUuid(uuidInfraspecificTaxon);
|
|
427
|
}
|
|
428
|
public static final Rank CANDIDATE(){
|
|
429
|
return getTermByUuid(uuidCandidate);
|
|
430
|
}
|
|
431
|
public static final Rank DENOMINATIONCLASS(){
|
|
432
|
return getTermByUuid(uuidDenominationClass);
|
|
433
|
}
|
|
434
|
public static final Rank GREX(){
|
|
435
|
return getTermByUuid(uuidGrex);
|
|
436
|
}
|
|
437
|
public static final Rank GRAFTCHIMAERA(){
|
|
438
|
return getTermByUuid(uuidGraftChimaera);
|
|
439
|
}
|
|
440
|
public static final Rank CULTIVARGROUP(){
|
|
441
|
return getTermByUuid(uuidCultivarGroup);
|
|
442
|
}
|
|
443
|
public static final Rank CULTIVAR(){
|
|
444
|
return getTermByUuid(uuidCultivar);
|
|
445
|
}
|
|
446
|
public static final Rank UNKNOWN_RANK(){
|
|
447
|
return getTermByUuid(uuidUnknownRank);
|
|
448
|
}
|
|
449
|
public static final Rank NATIO(){
|
|
450
|
return getTermByUuid(uuidNatio);
|
|
451
|
}
|
|
452
|
/**
|
|
453
|
* @see #INFRASPECIFICTAXON()
|
|
454
|
*/
|
|
455
|
public static final Rank UNRANKED_INFRASPECIFIC(){
|
|
456
|
return getTermByUuid(uuidInfraspecificTaxon);
|
|
457
|
}
|
|
458
|
/**
|
|
459
|
* @see #INFRAGENERICTAXON()
|
|
460
|
*/
|
|
461
|
public static final Rank UNRANKED_INFRAGENERIC(){
|
|
462
|
return getTermByUuid(uuidInfragenericTaxon);
|
|
463
|
}
|
|
464
|
|
|
465
|
// ************************ GETTER / SETTER **********************************/
|
|
466
|
|
|
467
|
public RankClass getRankClass() {
|
|
468
|
return rankClass;
|
|
469
|
}
|
|
470
|
|
|
471
|
public void setRankClass(RankClass rankClass) {
|
|
472
|
this.rankClass = rankClass;
|
|
473
|
}
|
|
474
|
|
|
475
|
// ******************************** METHODS ***************************************/
|
|
476
|
|
|
477
|
/**
|
|
478
|
* Returns the boolean value indicating whether <i>this</i> rank is higher than
|
|
479
|
* the genus rank (true) or not (false). Returns false if <i>this</i> rank is null.
|
|
480
|
*
|
|
481
|
* @see #isGenus()
|
|
482
|
* @see #isInfraGeneric()
|
|
483
|
* @see #isSpecies()
|
|
484
|
* @see #isInfraSpecific()
|
|
485
|
*/
|
|
486
|
@Transient
|
|
487
|
public boolean isSupraGeneric(){
|
|
488
|
return this.rankClass.equals(RankClass.Suprageneric); // (this.isHigher(Rank.GENUS()));
|
|
489
|
}
|
|
490
|
|
|
491
|
/**
|
|
492
|
* Returns the boolean value indicating whether <i>this</i> rank is the genus rank
|
|
493
|
* (true) or not (false). Returns false if <i>this</i> rank is null.
|
|
494
|
*
|
|
495
|
* @see #isSupraGeneric()
|
|
496
|
* @see #isInfraGeneric()
|
|
497
|
* @see #isSpecies()
|
|
498
|
* @see #isInfraSpecific()
|
|
499
|
*/
|
|
500
|
@Transient
|
|
501
|
public boolean isGenus(){
|
|
502
|
return this.rankClass.equals(RankClass.Genus); // (this.equals(Rank.GENUS()));
|
|
503
|
}
|
|
504
|
|
|
505
|
/**
|
|
506
|
* Returns the boolean value indicating whether <i>this</i> rank is higher than the
|
|
507
|
* species rank and lower than the genus rank (true) or not (false). Species groups or
|
|
508
|
* aggregates are also handled as infrageneric ranks.
|
|
509
|
* Returns false if <i>this</i> rank is null.
|
|
510
|
*
|
|
511
|
* @see #isSupraGeneric()
|
|
512
|
* @see #isGenus()
|
|
513
|
* @see #isInfraGenericButNotSpeciesGroup()
|
|
514
|
* @see #isSpeciesAggregate()
|
|
515
|
* @see #isSpecies()
|
|
516
|
* @see #isInfraSpecific()
|
|
517
|
*/
|
|
518
|
@Transient
|
|
519
|
public boolean isInfraGeneric(){
|
|
520
|
return this.rankClass.equals(RankClass.Infrageneric) || this.rankClass.equals(RankClass.SpeciesGroup) ; //(this.isLower(Rank.GENUS()) && this.isHigher(Rank.SPECIES()));
|
|
521
|
}
|
|
522
|
|
|
523
|
/**
|
|
524
|
* Returns the boolean value indicating whether <i>this</i> rank is higher than the
|
|
525
|
* species aggregate/group rank and lower than the genus rank (true) or not (false).
|
|
526
|
* Returns false if <i>this</i> rank is null.
|
|
527
|
*
|
|
528
|
* @see #isSupraGeneric()
|
|
529
|
* @see #isGenus()
|
|
530
|
* @see #isInfraGeneric()
|
|
531
|
* @see #isSpeciesAggregate()
|
|
532
|
* @see #isSpecies()
|
|
533
|
* @see #isInfraSpecific()
|
|
534
|
*/
|
|
535
|
@Transient
|
|
536
|
public boolean isInfraGenericButNotSpeciesGroup(){
|
|
537
|
return this.rankClass.equals(RankClass.Infrageneric) ;
|
|
538
|
}
|
|
539
|
|
|
540
|
/**
|
|
541
|
* Returns true if this rank indicates a rank that aggregates species
|
|
542
|
* like species aggregates or species groups, false otherwise.
|
|
543
|
* @return
|
|
544
|
*/
|
|
545
|
@Transient
|
|
546
|
public boolean isSpeciesAggregate(){
|
|
547
|
return this.rankClass.equals(RankClass.SpeciesGroup); //(this.equals(Rank.SPECIESAGGREGATE()) || (this.isLower(Rank.SPECIESAGGREGATE()) && this.isHigher(Rank.SPECIES())));
|
|
548
|
}
|
|
549
|
|
|
550
|
/**
|
|
551
|
* Returns the boolean value indicating whether <i>this</i> rank is the species
|
|
552
|
* rank (true) or not (false). Returns false if <i>this</i> rank is null.
|
|
553
|
*
|
|
554
|
* @see #isSupraGeneric()
|
|
555
|
* @see #isGenus()
|
|
556
|
* @see #isInfraGeneric()
|
|
557
|
* @see #isInfraSpecific()
|
|
558
|
*/
|
|
559
|
@Transient
|
|
560
|
public boolean isSpecies(){
|
|
561
|
return this.rankClass.equals(RankClass.Species); //(this.equals(Rank.SPECIES()));
|
|
562
|
}
|
|
563
|
|
|
564
|
/**
|
|
565
|
* Returns the boolean value indicating whether <i>this</i> rank is lower than the
|
|
566
|
* species rank (true) or not (false). Returns false if <i>this</i> rank is null.
|
|
567
|
*
|
|
568
|
* @see #isSupraGeneric()
|
|
569
|
* @see #isGenus()
|
|
570
|
* @see #isInfraGeneric()
|
|
571
|
* @see #isSpecies()
|
|
572
|
*/
|
|
573
|
@Transient
|
|
574
|
public boolean isInfraSpecific(){
|
|
575
|
return this.rankClass.equals(RankClass.Infraspecific); // (this.isLower(Rank.SPECIES()));
|
|
576
|
}
|
|
577
|
|
|
578
|
|
|
579
|
/**
|
|
580
|
* Returns the rank identified through a label or the identifier within the vocabulary
|
|
581
|
* Preliminary implementation for BotanicalNameParser.
|
|
582
|
*
|
|
583
|
* @param strRank the string identifying the rank
|
|
584
|
* @return the rank
|
|
585
|
*/
|
|
586
|
public static Rank getRankByNameOrIdInVoc(String strRank) throws UnknownCdmTypeException{
|
|
587
|
return getRankByNameOrIdInVoc(strRank, false);
|
|
588
|
}
|
|
589
|
|
|
590
|
/**
|
|
591
|
* Returns the rank identified through a label or the identifier within the vocabulary
|
|
592
|
* for a given nomenclatural code.
|
|
593
|
* Preliminary implementation for BotanicalNameParser.
|
|
594
|
*
|
|
595
|
* @param strRank the string identifying the rank
|
|
596
|
* @param nc the nomenclatural code
|
|
597
|
* @return the rank
|
|
598
|
*/
|
|
599
|
public static Rank getRankByNameOrIdInVoc(String strRank, NomenclaturalCode nc) throws UnknownCdmTypeException{
|
|
600
|
return getRankByNameOrIdInVoc(strRank, nc, false);
|
|
601
|
}
|
|
602
|
|
|
603
|
// TODO
|
|
604
|
// Preliminary implementation for BotanicalNameParser.
|
|
605
|
// not yet complete
|
|
606
|
/**
|
|
607
|
* Returns the rank identified through a label or the identifier within the vocabulary.
|
|
608
|
* Preliminary implementation for BotanicalNameParser.
|
|
609
|
*
|
|
610
|
* @param strRank the string identifying the rank
|
|
611
|
* @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
|
|
612
|
* unknown or not yet implemented
|
|
613
|
* @return the rank
|
|
614
|
*/
|
|
615
|
public static Rank getRankByNameOrIdInVoc(String strRank, boolean useUnknown) throws UnknownCdmTypeException{
|
|
616
|
try {
|
|
617
|
return getRankByIdInVoc(strRank);
|
|
618
|
} catch (UnknownCdmTypeException e) {
|
|
619
|
return getRankByName(strRank, useUnknown);
|
|
620
|
}
|
|
621
|
}
|
|
622
|
|
|
623
|
// TODO
|
|
624
|
// Preliminary implementation for BotanicalNameParser.
|
|
625
|
// not yet complete
|
|
626
|
/**
|
|
627
|
* Returns the rank identified through a label or the identifier within the vocabulary.
|
|
628
|
* Preliminary implementation for BotanicalNameParser.
|
|
629
|
*
|
|
630
|
* @param strRank the string identifying the rank
|
|
631
|
* @param nc the nomenclatural code
|
|
632
|
* @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
|
|
633
|
* unknown or not yet implemented
|
|
634
|
* @return the rank
|
|
635
|
*/
|
|
636
|
public static Rank getRankByNameOrIdInVoc(String strRank, NomenclaturalCode nc, boolean useUnknown)
|
|
637
|
throws UnknownCdmTypeException{
|
|
638
|
try {
|
|
639
|
return getRankByIdInVoc(strRank, nc);
|
|
640
|
} catch (UnknownCdmTypeException e) {
|
|
641
|
return getRankByName(strRank, nc, useUnknown);
|
|
642
|
}
|
|
643
|
}
|
|
644
|
|
|
645
|
/**
|
|
646
|
* Returns the rank identified through the vocabulary identifier.
|
|
647
|
* Preliminary implementation for BotanicalNameParser.<BR>
|
|
648
|
* Note: For abbrev = "[unranked]" the result is undefined.
|
|
649
|
* It maybe the infrageneric unranked or the infraspecific unranked.
|
|
650
|
* You need to define by context which one is correct.
|
|
651
|
*
|
|
652
|
* @param abbrev the string for the name abbreviation
|
|
653
|
* @return the rank
|
|
654
|
*/
|
|
655
|
public static Rank getRankByIdInVoc(String abbrev) throws UnknownCdmTypeException{
|
|
656
|
return getRankByIdInVoc(abbrev, false);
|
|
657
|
}
|
|
658
|
|
|
659
|
/**
|
|
660
|
* Returns the rank identified through an abbreviated name for a given nomenclatural code.
|
|
661
|
* See also {@link #getRankByIdInVoc(String, boolean)}
|
|
662
|
*
|
|
663
|
* @param abbrev the string for the name abbreviation
|
|
664
|
* @param nc the nomenclatural code
|
|
665
|
* @return the rank
|
|
666
|
*/
|
|
667
|
public static Rank getRankByIdInVoc(String abbrev, NomenclaturalCode nc) throws UnknownCdmTypeException{
|
|
668
|
return getRankByIdInVoc(abbrev, nc, false);
|
|
669
|
}
|
|
670
|
|
|
671
|
// TODO
|
|
672
|
// Preliminary implementation for BotanicalNameParser.
|
|
673
|
// not yet complete
|
|
674
|
/**
|
|
675
|
* Returns the rank identified through an abbreviated representation.
|
|
676
|
* At the moment it uses the English abbreviations (being Latin because
|
|
677
|
* we do not have Latin representations yet.
|
|
678
|
* TODO
|
|
679
|
* If no according abbreviation is available it throws either an UnknownCdmTypeException
|
|
680
|
* or an #Rank.UNKNOWN() object depending on the useUnknown flag.
|
|
681
|
*
|
|
682
|
* @param idInVoc the string for the name abbreviation
|
|
683
|
* @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
|
|
684
|
* unknown or not yet existent
|
|
685
|
* @return the rank
|
|
686
|
*/
|
|
687
|
public static Rank getRankByIdInVoc(String idInVoc, boolean useUnknown) throws UnknownCdmTypeException{
|
|
688
|
Rank result = null;
|
|
689
|
if (idInVoc == null){
|
|
690
|
throw new NullPointerException("idInVoc is NULL in getRankByIdInVoc");
|
|
691
|
}
|
|
692
|
if (StringUtils.isBlank(idInVoc)){
|
|
693
|
//handle empty idInVoc as unknown
|
|
694
|
idInVoc = "oijas34\u0155";
|
|
695
|
}
|
|
696
|
if (idInVocMap == null){
|
|
697
|
return null;
|
|
698
|
}
|
|
699
|
idInVoc = normalizeSectionAndSubsection(idInVoc);
|
|
700
|
idInVoc = normalizeSubgen(idInVoc);
|
|
701
|
idInVoc = normalizeSpecialForm(idInVoc);
|
|
702
|
idInVoc = normalizeSsp(idInVoc);
|
|
703
|
idInVoc = normalizeForma(idInVoc);
|
|
704
|
UUID uuid = idInVocMap.get(idInVoc);
|
|
705
|
if (uuid != null ){
|
|
706
|
result = getTermByUuid(uuid);
|
|
707
|
}
|
|
708
|
if (result != null){
|
|
709
|
return result;
|
|
710
|
}else {
|
|
711
|
if (idInVoc == null){
|
|
712
|
idInVoc = "(null)";
|
|
713
|
}
|
|
714
|
if (useUnknown){
|
|
715
|
logger.info("Unknown rank name: " + idInVoc + ". Rank 'UNKNOWN_RANK' created instead");
|
|
716
|
return Rank.UNKNOWN_RANK();
|
|
717
|
}else{
|
|
718
|
throw new UnknownCdmTypeException("Unknown rank abbreviation: " + idInVoc);
|
|
719
|
}
|
|
720
|
}
|
|
721
|
}
|
|
722
|
|
|
723
|
private static String normalizeSectionAndSubsection(String idInVoc) {
|
|
724
|
if (idInVoc.equals("sect.")){
|
|
725
|
return "sect.(bot.)";
|
|
726
|
}else if (idInVoc.equals("subsect.")){
|
|
727
|
return "subsect.(bot.)";
|
|
728
|
}
|
|
729
|
return idInVoc;
|
|
730
|
}
|
|
731
|
|
|
732
|
private static String normalizeSubgen(String idInVoc) {
|
|
733
|
if (idInVoc.equals("subgen.")){
|
|
734
|
return "subg.";
|
|
735
|
}
|
|
736
|
return idInVoc;
|
|
737
|
}
|
|
738
|
|
|
739
|
private static String normalizeSpecialForm(String idInVoc) {
|
|
740
|
if (idInVoc.equals("f.sp.") || idInVoc.equals("f. sp.")){
|
|
741
|
return "f.spec.";
|
|
742
|
}
|
|
743
|
return idInVoc;
|
|
744
|
}
|
|
745
|
|
|
746
|
private static String normalizeForma(String idInVoc) {
|
|
747
|
if (idInVoc.equals("forma")){
|
|
748
|
return "f.";
|
|
749
|
}
|
|
750
|
return idInVoc;
|
|
751
|
}
|
|
752
|
|
|
753
|
private static String normalizeSsp(String idInVoc) {
|
|
754
|
if (idInVoc.equals("ssp.") && !idInVocMap.containsKey("ssp.") && idInVocMap.containsKey("subsp.")){
|
|
755
|
return "subsp.";
|
|
756
|
}
|
|
757
|
return idInVoc;
|
|
758
|
}
|
|
759
|
|
|
760
|
// TODO
|
|
761
|
// Preliminary implementation to cover Botany and Zoology.
|
|
762
|
/**
|
|
763
|
* Returns the rank identified through an abbreviated name for a given nomenclatural code.
|
|
764
|
* Preliminary implementation for ICBN and ICZN.
|
|
765
|
* See also {@link #getRankByIdInVoc(String, boolean)}
|
|
766
|
|
|
767
|
*
|
|
768
|
* @param abbrev the string for the name abbreviation
|
|
769
|
* @param nc the nomenclatural code
|
|
770
|
* @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
|
|
771
|
* unknown or not yet implemented
|
|
772
|
* @return the rank
|
|
773
|
*/
|
|
774
|
public static Rank getRankByIdInVoc(String abbrev, NomenclaturalCode nc, boolean useUnknown)
|
|
775
|
throws UnknownCdmTypeException{
|
|
776
|
|
|
777
|
if (nc != null && nc.equals(NomenclaturalCode.ICZN)) {
|
|
778
|
if (abbrev != null){
|
|
779
|
if (abbrev.equalsIgnoreCase("sect.")) {
|
|
780
|
return Rank.SECTION_ZOOLOGY();
|
|
781
|
} else if (abbrev.equalsIgnoreCase("subsect.")) {
|
|
782
|
return Rank.SUBSECTION_ZOOLOGY();
|
|
783
|
}
|
|
784
|
}
|
|
785
|
}else if (nc != null && nc.equals(NomenclaturalCode.ICNAFP)) {
|
|
786
|
if (abbrev != null){
|
|
787
|
if (abbrev.equalsIgnoreCase("sect.")) {
|
|
788
|
return Rank.SECTION_BOTANY();
|
|
789
|
} else if (abbrev.equalsIgnoreCase("subsect.")) {
|
|
790
|
return Rank.SUBSECTION_BOTANY();
|
|
791
|
}
|
|
792
|
}
|
|
793
|
}
|
|
794
|
return getRankByIdInVoc(abbrev, useUnknown);
|
|
795
|
}
|
|
796
|
|
|
797
|
// TODO
|
|
798
|
// Preliminary implementation for BotanicalNameParser.
|
|
799
|
// not yet complete
|
|
800
|
/**
|
|
801
|
* Returns the rank identified through a name.
|
|
802
|
* Preliminary implementation for BotanicalNameParser.
|
|
803
|
*
|
|
804
|
* @param rankName the string for the name of the rank
|
|
805
|
* @return the rank
|
|
806
|
*/
|
|
807
|
public static Rank getRankByName(String rankName) throws UnknownCdmTypeException{
|
|
808
|
return getRankByName(rankName, false);
|
|
809
|
}
|
|
810
|
|
|
811
|
|
|
812
|
// TODO
|
|
813
|
// Preliminary implementation for ICBN and ICZN.
|
|
814
|
// not yet complete
|
|
815
|
/**
|
|
816
|
* Returns the rank identified through a name for a given nomenclatural code.
|
|
817
|
* Preliminary implementation for ICBN and ICZN.
|
|
818
|
*
|
|
819
|
* @param rankName the string for the name of the rank
|
|
820
|
* @param nc the nomenclatural code
|
|
821
|
* @return the rank
|
|
822
|
*/
|
|
823
|
public static Rank getRankByName(String rankName, NomenclaturalCode nc) throws UnknownCdmTypeException{
|
|
824
|
return getRankByName(rankName, nc, false);
|
|
825
|
}
|
|
826
|
|
|
827
|
/**
|
|
828
|
* Returns the rank identified through a name.
|
|
829
|
* Preliminary implementation for BotanicalNameParser.
|
|
830
|
* TODO At the moment we do not have Latin representations yet.
|
|
831
|
*
|
|
832
|
* @param rankName the string for the name of the rank
|
|
833
|
* @param useUnknown if true the rank UNKNOWN_RANK is returned if the rank name is
|
|
834
|
* unknown or not yet implemented
|
|
835
|
* @return the rank
|
|
836
|
*/
|
|
837
|
public static Rank getRankByName(String rankName, boolean useUnknown)
|
|
838
|
throws UnknownCdmTypeException{
|
|
839
|
if (rankName.equalsIgnoreCase("Regnum")){ return Rank.KINGDOM();
|
|
840
|
}else if (rankName.equalsIgnoreCase("Subregnum")){ return Rank.SUBKINGDOM();
|
|
841
|
}else if (rankName.equalsIgnoreCase("Phylum")){ return Rank.PHYLUM();
|
|
842
|
}else if (rankName.equalsIgnoreCase("Subphylum")){ return Rank.SUBPHYLUM();
|
|
843
|
}else if (rankName.equalsIgnoreCase("Divisio")){ return Rank.DIVISION();
|
|
844
|
}else if (rankName.equalsIgnoreCase("Subdivisio")){ return Rank.SUBDIVISION();
|
|
845
|
}else if (rankName.equalsIgnoreCase("Classis")){ return Rank.CLASS();
|
|
846
|
}else if (rankName.equalsIgnoreCase("Subclassis")){ return Rank.SUBCLASS();
|
|
847
|
}else if (rankName.equalsIgnoreCase("Superordo")){ return Rank.SUPERORDER();
|
|
848
|
}else if (rankName.equalsIgnoreCase("Ordo")){ return Rank.ORDER();
|
|
849
|
}else if (rankName.equalsIgnoreCase("Subordo")){ return Rank.SUBORDER();
|
|
850
|
}else if (rankName.equalsIgnoreCase("Familia")){ return Rank.FAMILY();
|
|
851
|
}else if (rankName.equalsIgnoreCase("Subfamilia")){ return Rank.SUBFAMILY();
|
|
852
|
}else if (rankName.equalsIgnoreCase("Tribus")){ return Rank.TRIBE();
|
|
853
|
}else if (rankName.equalsIgnoreCase("Subtribus")){ return Rank.SUBTRIBE();
|
|
854
|
}else if (rankName.equalsIgnoreCase("Genus")){ return Rank.GENUS();
|
|
855
|
}else if (rankName.equalsIgnoreCase("Subgenus")){ return Rank.SUBGENUS();
|
|
856
|
}else if (rankName.equalsIgnoreCase("Sectio")){ return Rank.SECTION_BOTANY();
|
|
857
|
}else if (rankName.equalsIgnoreCase("Subsectio")){ return Rank.SUBSECTION_BOTANY();
|
|
858
|
}else if (rankName.equalsIgnoreCase("Series")){ return Rank.SERIES();
|
|
859
|
}else if (rankName.equalsIgnoreCase("Subseries")){ return Rank.SUBSERIES();
|
|
860
|
}else if (rankName.equalsIgnoreCase("Aggregate")){ return Rank.SPECIESAGGREGATE();
|
|
861
|
}else if (rankName.equalsIgnoreCase("Speciesgroup")){ return Rank.SPECIESGROUP();
|
|
862
|
}else if (rankName.equalsIgnoreCase("Species")){ return Rank.SPECIES();
|
|
863
|
}else if (rankName.equalsIgnoreCase("Subspecies")){ return Rank.SUBSPECIES();
|
|
864
|
}else if (rankName.equalsIgnoreCase("Convarietas")){ return Rank.CONVAR();
|
|
865
|
}else if (rankName.equalsIgnoreCase("Varietas")){ return Rank.VARIETY();
|
|
866
|
}else if (rankName.equalsIgnoreCase("Subvarietas")){ return Rank.SUBVARIETY();
|
|
867
|
}else if (rankName.equalsIgnoreCase("Forma")){ return Rank.FORM();
|
|
868
|
}else if (rankName.equalsIgnoreCase("Subforma")){ return Rank.SUBFORM();
|
|
869
|
}else if (rankName.equalsIgnoreCase("Forma spec.")){ return Rank.SPECIALFORM();
|
|
870
|
}else if (rankName.equalsIgnoreCase("tax.infragen.")){ return Rank.INFRAGENERICTAXON();
|
|
871
|
}else if (rankName.equalsIgnoreCase("tax.infrasp.")){ return Rank.INFRASPECIFICTAXON();
|
|
872
|
// old ranks
|
|
873
|
}else if (rankName.equalsIgnoreCase("proles")){ return Rank.PROLES();
|
|
874
|
}else if (rankName.equalsIgnoreCase("race")){ return Rank.RACE();
|
|
875
|
}else if (rankName.equalsIgnoreCase("sublusus")){ return Rank.SUBLUSUS();
|
|
876
|
|
|
877
|
}else if (rankName.equalsIgnoreCase("taxon")){ return Rank.INFRASPECIFICTAXON(); //to create the name put 'taxon' and the infraspeciesepi to the field unnamed namephrase
|
|
878
|
|
|
879
|
}else{
|
|
880
|
if (rankName == null){
|
|
881
|
rankName = "(null)"; //see NPE above
|
|
882
|
}
|
|
883
|
if (useUnknown){
|
|
884
|
if (logger.isInfoEnabled()){logger.info("Unknown rank name: " + rankName+". Rank 'UNKNOWN_RANK' created instead");}
|
|
885
|
return Rank.UNKNOWN_RANK();
|
|
886
|
}else{
|
|
887
|
throw new UnknownCdmTypeException("Unknown rank name: " + rankName);
|
|
888
|
}
|
|
889
|
}
|
|
890
|
}
|
|
891
|
|
|
892
|
/**
|
|
893
|
* Defines the rank according to the English name.
|
|
894
|
* @param rankName English rank name.
|
|
895
|
* @param nc Defines the handling of the section and subsection ranks. These are in different orders depending on the
|
|
896
|
* nomenclatural code.
|
|
897
|
* @param useUnknown if true, the "Unknown" rank is returned as a placeholder.
|
|
898
|
* @return
|
|
899
|
* @throws UnknownCdmTypeException never thrown if useUnknown is true
|
|
900
|
*/
|
|
901
|
public static Rank getRankByEnglishName(String rankName, NomenclaturalCode nc, boolean useUnknown) throws UnknownCdmTypeException{
|
|
902
|
Rank result = null;
|
|
903
|
if (rankName == null){
|
|
904
|
throw new NullPointerException("Abbrev is NULL in getRankByAbbreviation");
|
|
905
|
}
|
|
906
|
if (labelMap == null){
|
|
907
|
return null;
|
|
908
|
}
|
|
909
|
//handle section and subsection (not unique representations)
|
|
910
|
if (rankName.equalsIgnoreCase("Section")){
|
|
911
|
if (nc != null && nc.equals(NomenclaturalCode.ICZN)){ return Rank.SECTION_ZOOLOGY();
|
|
912
|
}else if (nc != null && nc.equals(NomenclaturalCode.ICNAFP)){return Rank.SECTION_BOTANY();
|
|
913
|
}else{
|
|
914
|
String errorWarning = "Section is only defined for ICZN and ICNAFP at the moment but here needed for " + ((nc == null)? "(null)": nc.toString());
|
|
915
|
logger.warn(errorWarning);
|
|
916
|
throw new UnknownCdmTypeException (errorWarning);
|
|
917
|
}
|
|
918
|
}else if (rankName.equalsIgnoreCase("Subsection")){
|
|
919
|
if (nc != null && nc.equals(NomenclaturalCode.ICZN)){ return Rank.SUBSECTION_ZOOLOGY();
|
|
920
|
}else if (nc != null && nc.equals(NomenclaturalCode.ICNAFP)){ return Rank.SUBSECTION_BOTANY();
|
|
921
|
}else{
|
|
922
|
String errorWarning = "Subsection is only defined for ICZN and ICBN at the moment but here needed for " + ((nc == null)? "(null)": nc.toString());
|
|
923
|
logger.warn(errorWarning);
|
|
924
|
throw new UnknownCdmTypeException (errorWarning);
|
|
925
|
}
|
|
926
|
}
|
|
927
|
|
|
928
|
rankName = rankName.toLowerCase();
|
|
929
|
|
|
930
|
UUID uuid = labelMap.get(rankName);
|
|
931
|
if (uuid != null ){
|
|
932
|
result = getTermByUuid(uuid);
|
|
933
|
}
|
|
934
|
if (result != null){
|
|
935
|
return result;
|
|
936
|
}else {
|
|
937
|
if (rankName == null){
|
|
938
|
rankName = "(null)";
|
|
939
|
}
|
|
940
|
if (useUnknown){
|
|
941
|
if (logger.isInfoEnabled()){logger.info("Unknown rank name: " + rankName + ". Rank 'UNKNOWN_RANK' created instead");}
|
|
942
|
return Rank.UNKNOWN_RANK();
|
|
943
|
}else{
|
|
944
|
throw new UnknownCdmTypeException("Unknown rank: " + rankName);
|
|
945
|
}
|
|
946
|
}
|
|
947
|
}
|
|
948
|
|
|
949
|
|
|
950
|
public static Rank getRankByName(String rankName, NomenclaturalCode nc, boolean useUnknown)
|
|
951
|
throws UnknownCdmTypeException {
|
|
952
|
|
|
953
|
if (nc.equals(NomenclaturalCode.ICZN)) {
|
|
954
|
if (rankName.equalsIgnoreCase("Sectio")) { return Rank.SECTION_ZOOLOGY();
|
|
955
|
}else if (rankName.equalsIgnoreCase("Subsectio")) { return Rank.SUBSECTION_ZOOLOGY();
|
|
956
|
}
|
|
957
|
}
|
|
958
|
return getRankByName(rankName, useUnknown);
|
|
959
|
}
|
|
960
|
|
|
961
|
/**
|
|
962
|
* Returns the abbreviated rank name for <i>this</i> rank according to the English representation
|
|
963
|
* abbreviated label.
|
|
964
|
* TODO Needs to be changed to Latin as soon as Latin representations are available.
|
|
965
|
*
|
|
966
|
* @return the abbreviation string for <i>this</i> rank
|
|
967
|
*/
|
|
968
|
public String getAbbreviation(){
|
|
969
|
Language language = Language.getLanguageFromUuid(Language.uuidEnglish);
|
|
970
|
String result = this.getRepresentation(language).getAbbreviatedLabel();
|
|
971
|
if (result== null) {
|
|
972
|
logger.warn("Abbreviation for rank " + this.toString() + " not yet implemented");
|
|
973
|
return "no abbreviation available.";
|
|
974
|
}else{
|
|
975
|
return result;
|
|
976
|
}
|
|
977
|
}
|
|
978
|
|
|
979
|
@Transient
|
|
980
|
public String getInfraGenericMarker() throws UnknownCdmTypeException{
|
|
981
|
String result = null;
|
|
982
|
if (! this.isInfraGeneric()){
|
|
983
|
throw new IllegalStateException("An infrageneric marker is only available for an infrageneric rank but was asked for rank: " + this.toString());
|
|
984
|
}else{
|
|
985
|
result = this.getAbbreviation();
|
|
986
|
}
|
|
987
|
if (result == null){
|
|
988
|
throw new UnknownCdmTypeException("Abbreviation for rank unknown: " + this.toString());
|
|
989
|
}
|
|
990
|
return result;
|
|
991
|
}
|
|
992
|
|
|
993
|
|
|
994
|
|
|
995
|
@Override
|
|
996
|
public Rank readCsvLine(Class<Rank> termClass, List<String> csvLine, Map<UUID, DefinedTermBase> terms, boolean abbrevAsId) {
|
|
997
|
Rank rank = super.readCsvLine(termClass, csvLine, terms, abbrevAsId);
|
|
998
|
RankClass rankClass = RankClass.getByKey(csvLine.get(5));
|
|
999
|
assert rankClass != null: "XXXXXXXXXXXXXXXXXXXXX Rank class must not be null: " + csvLine ;
|
|
1000
|
rank.setRankClass(rankClass);
|
|
1001
|
return rank;
|
|
1002
|
}
|
|
1003
|
|
|
1004
|
@Override
|
|
1005
|
protected void setDefaultTerms(TermVocabulary<Rank> termVocabulary) {
|
|
1006
|
termMap = new HashMap<UUID, Rank>();
|
|
1007
|
for (Rank term : termVocabulary.getTerms()){
|
|
1008
|
termMap.put(term.getUuid(), term);
|
|
1009
|
addRank(term);
|
|
1010
|
}
|
|
1011
|
}
|
|
1012
|
|
|
1013
|
// FIXME:Remoting This is a ugly hack and need to be removed
|
|
1014
|
// once the static initialisation is refactored
|
|
1015
|
public static void initDefaultTerms() {
|
|
1016
|
TermVocabulary<Rank> vocabulary = getTermByUuid(uuidKingdom).getVocabulary();
|
|
1017
|
if(idInVocMap != null) {
|
|
1018
|
idInVocMap.clear();
|
|
1019
|
}
|
|
1020
|
(new Rank()).setDefaultTerms(vocabulary);
|
|
1021
|
}
|
|
1022
|
|
|
1023
|
/**
|
|
1024
|
* @param term
|
|
1025
|
*/
|
|
1026
|
private void addRank(Rank rank) {
|
|
1027
|
if (rank == null){
|
|
1028
|
logger.warn("rank is NULL");
|
|
1029
|
return;
|
|
1030
|
}
|
|
1031
|
if (rank.getUuid().equals(uuidSectionZoology) || rank.getUuid().equals(uuidSubsectionZoology )){
|
|
1032
|
//sect./subsect. is used for botanical sections, see also #getRankByAbbreviation(String, NomenclaturalCode, boolean)
|
|
1033
|
return;
|
|
1034
|
}
|
|
1035
|
Language lang = Language.DEFAULT(); //TODO should be Latin but at the moment we have only English representations
|
|
1036
|
Representation representation = rank.getRepresentation(lang);
|
|
1037
|
String abbrevLabel = representation.getAbbreviatedLabel();
|
|
1038
|
String label = representation.getLabel();
|
|
1039
|
|
|
1040
|
//initialize maps
|
|
1041
|
if (idInVocMap == null){
|
|
1042
|
idInVocMap = new HashMap<String, UUID>();
|
|
1043
|
}
|
|
1044
|
if (labelMap == null){
|
|
1045
|
labelMap = new HashMap<String, UUID>();
|
|
1046
|
}
|
|
1047
|
labelMap.put(label.toLowerCase(), rank.getUuid());
|
|
1048
|
//add to map
|
|
1049
|
if (StringUtils.isBlank(abbrevLabel)){
|
|
1050
|
if (logger.isDebugEnabled()){logger.info("Abbreviated label for rank is NULL or empty.Can't add rank to abbrevLabel map: " + CdmUtils.Nz(rank.getLabel()));}
|
|
1051
|
}else{
|
|
1052
|
idInVocMap.put(abbrevLabel, rank.getUuid());
|
|
1053
|
}
|
|
1054
|
}
|
|
1055
|
|
|
1056
|
|
|
1057
|
/**
|
|
1058
|
* It is necessary to skip the vocabulary check, otherwise we would have
|
|
1059
|
* problems in some CacheStrategies, due to uninitialized Vocabularies.
|
|
1060
|
*
|
|
1061
|
* @see eu.etaxonomy.cdm.model.common.OrderedTermBase#compareTo(eu.etaxonomy.cdm.model.common.OrderedTermBase)
|
|
1062
|
*/
|
|
1063
|
@Override
|
|
1064
|
public int compareTo(Rank orderedTerm) {
|
|
1065
|
return performCompareTo(orderedTerm, true);
|
|
1066
|
}
|
|
1067
|
|
|
1068
|
}
|