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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.description;
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import java.text.ParseException;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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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.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.XmlRootElement;
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import javax.xml.bind.annotation.XmlType;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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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.Language;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.model.term.OrderedTermBase;
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import eu.etaxonomy.cdm.model.term.TermType;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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/**
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* This class represents terms describing the {@link AbsenceTerm absence}
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* (like "extinct") or the {@link PresenceTerm presence} (like "cultivated") of a
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* {@link Taxon taxon} in an {@link NamedArea area}. These terms are only
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* used for {@link Distribution distributions}.
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*
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* The current implementation includes multiple qualities of distribution status:<BR><BR>
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*
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* 1. Degree of "presence": present, presence questionable, reported in error, absent, ...<BR>
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* 2. Nativeness/naturalization/...: native, alien (introduced), naturalized, cultivated, invasive, ... <BR>
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* <BR>
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* There might be further qualities like adventive(unwanted)<->introduced(wanted - for cultivation)
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* <BR>
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* For an interesting discussion of these status see Pyšek & al.: Alien plants in checklists and floras;
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* Taxon 53(1), Feb. 2004: 131-143 <BR>
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*
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* Pyšek et al. distinguises<BR>
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* native - alien<BR>
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* alien => cultivated-outside cultivation<BR>
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* outside cultivation=>casual - naturalized<BR>
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* naturalized => non invasive - invasive<BR>
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* invasive => not harmful - transformers - weeds
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*
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* @see https://dev.e-taxonomy.eu/redmine/issues/6000
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*
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* @author m.doering
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* @since 08-Nov-2007 13:06:44
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* @author a.mueller
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "PresenceAbsenceTerm")
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@XmlRootElement(name = "PresenceAbsenceTerm")
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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.term.DefinedTermBase")
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@Audited
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public class PresenceAbsenceTerm extends OrderedTermBase<PresenceAbsenceTerm> {
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private static final long serialVersionUID = 1036807546935584396L;
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private static final Logger logger = LogManager.getLogger(PresenceAbsenceTerm.class);
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//presence base
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public static final UUID uuidPresent = UUID.fromString("cef81d25-501c-48d8-bbea-542ec50de2c2");
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private static final UUID uuidPresentDoubfully = UUID.fromString("75a60279-a4c2-4f53-bc57-466028a4b3db");
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//presence
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public static final UUID uuidNative = UUID.fromString("ddeac4f2-d8fa-43b8-ad7e-ca13abdd32c7");
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private static final UUID uuidNativeDoubtfullyNative = UUID.fromString("310373bf-7df4-4d02-8cb3-bcc7448805fc");
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public static final UUID uuidCultivated = UUID.fromString("9eb99fe6-59e2-4445-8e6a-478365bd0fa9");
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public static final UUID uuidIntroduced = UUID.fromString("643cf9d1-a5f1-4622-9837-82ef961e880b");
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private static final UUID uuidIntroducedDoubtfullyIntroduced = UUID.fromString("0c54761e-4887-4788-9dfa-7190c88746e3");
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public static final UUID uuidIntroducedUncertainDegreeNaturalisation = UUID.fromString("da159544-b0dd-4599-a9c9-640826af8c17");
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public static final UUID uuidIntroducedAdventitious = UUID.fromString("42946bd6-9c22-45ad-a910-7427e8f60bfd");
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public static final UUID uuidNaturalised = UUID.fromString("e191e89a-a751-4b0c-b883-7f1de70915c9");
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private static final UUID uuidIntroducedCultiated = UUID.fromString("fac8c347-8262-44a1-b0a4-db4de451c021");
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private static final UUID uuidEndemic = UUID.fromString("c3ee7048-15b7-4be1-b687-9ce9c1a669d6");
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private static final UUID uuidNotEndemic = UUID.fromString("2fda5393-7423-4076-814c-1fa7678d7d33");
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private static final UUID uuidUnknownEndemism = UUID.fromString("094aa2e4-8048-4086-aca1-2d671a05a86e");
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// private static final UUID uuidNa=UUID.fromString("4e04990a-66fe-4fdf-856c-f40772fbcf0a");
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//invasive
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private static final UUID uuidInvasive = UUID.fromString("dc536e3d-a753-4bbe-a386-dd8aff35c234");
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private static final UUID uuidNonInvasive = UUID.fromString("1b025e8b-901a-42e8-9739-119b410c6f03");
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//presents questionable
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public static final UUID uuidNativePresenceQuestionable = UUID.fromString("925662c1-bb10-459a-8c53-da5a738ac770");
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private static final UUID uuidCultivatedPresenceQuestionable = UUID.fromString("4f31bfc8-3058-4d83-aea5-3a1fe9773f9f");
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private static final UUID uuidIntroducedPresenceQuestionable = UUID.fromString("83eb0aa0-1a45-495a-a3ca-bf6958b74366");
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private static final UUID uuidEndedmicPresenceQuestionable = UUID.fromString("5f954f08-267a-4928-b073-12328f74c187");
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//intr. naturalized questionable
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private static final UUID uuidNaturalisedPresenceQuestionable = UUID.fromString("9e0b413b-5a68-4e5b-91f2-227b4f832466");
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//natur. invasive questionable
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private static final UUID uuidInvasivePresenceQuestionable = UUID.fromString("ac429d5f-e8ad-49ae-a41c-e4779b58b96a");
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//natur. non-invasive questionable
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private static final UUID uuidNonInvasivePresenceQuestionable = UUID.fromString("11f56e2f-c16c-4b3d-a870-bb5d3b20e624");
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//absence
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private static final UUID uuidAbsence=UUID.fromString("59709861-f7d9-41f9-bb21-92559cedd598");
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private static final UUID uuidReportedInError = UUID.fromString("38604788-cf05-4607-b155-86db456f7680");
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public static final UUID uuidNativeError = UUID.fromString("61cee840-801e-41d8-bead-015ad866c2f1");
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private static final UUID uuidIntroducedReportedError = UUID.fromString("aeec2947-2700-4623-8e32-9e3a430569d1");
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private static final UUID uuidCultivatedReportedError = UUID.fromString("9d4d3431-177a-4abe-8e4b-1558573169d6");
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private static final UUID uuidNativeFormerlyNative = UUID.fromString("5c397f7b-59ef-4c11-a33c-45691ceda91b");
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private static final UUID uuidNativeDoubtfullyNativeReportedError = UUID.fromString("71b72e24-c2b6-44a5-bdab-39f083bf0f06");
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private static final UUID uuidIntroducedFormerlyIntroduced = UUID.fromString("b74dc30b-ee93-496d-8c00-4d00abae1ec7");
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private static final UUID uuidEndemicReportedError = UUID.fromString("679b215d-c231-4ee2-ae12-3ffc3dd528ad");
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private static final UUID uuidNaturalisedReportedError = UUID.fromString("8d918a37-3add-4e1c-a233-c37dbee209aa");
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private static final UUID uuidCasualPresenceQuestionable = UUID.fromString("73f75493-1185-4a3e-af1e-9a1f2e8dadb7");
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private static final UUID uuidCasualReportedError = UUID.fromString("9b910b7b-43e3-4260-961c-6063b11cb7dc");
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//undefined
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public static final UUID uuidUndefined = UUID.fromString("bdb46487-01f8-451d-bf7b-d3e0fd44938e");
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protected static Map<UUID, PresenceAbsenceTerm> termMap = null;
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private String defaultColor = "000000";
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@XmlAttribute(name = "absenceTerm")
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private boolean absenceTerm = false;
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//********* METHODS **************************************/
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/**
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* Creates a new empty presence term.
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*
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* @see #NewInstance(String, String, String)
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*/
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public static PresenceAbsenceTerm NewInstance(){
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return new PresenceAbsenceTerm();
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}
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/**
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* Creates a new presence term 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 presence term to be created
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* @param label the string identifying the new presence term to be created
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* @param labelAbbrev the string identifying (in abbreviated form) the
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* new presence term to be created
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* @see #NewInstance()
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*/
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public static PresenceAbsenceTerm NewPresenceInstance(String term, String label, String labelAbbrev){
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return new PresenceAbsenceTerm(term, label, labelAbbrev, false);
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}
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/**
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* Creates a new absence term 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 presence term to be created
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* @param label the string identifying the new presence term to be created
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* @param labelAbbrev the string identifying (in abbreviated form) the
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* new presence term to be created
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* @see #NewInstance()
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*/
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public static PresenceAbsenceTerm NewAbsenceInstance(String term, String label, String labelAbbrev){
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return new PresenceAbsenceTerm(term, label, labelAbbrev, true);
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}
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//********************************** Constructor *******************************************************************/
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//for hibernate use only
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@Deprecated
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protected PresenceAbsenceTerm() {
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super(TermType.PresenceAbsenceTerm);
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}
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/**
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* Class constructor: creates a new presence or absence term with a description
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* (in the {@link 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 presence or absence term to be created
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* @param label the string identifying the new presence or absence term to be created
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* @param labelAbbrev the string identifying (in abbreviated form) the
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* new presence or absence term to be created
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* @param isAbsenceTerm boolean value indicating if this term represents an absence or not
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* @see #PresenceAbsenceTermBase()
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*/
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protected PresenceAbsenceTerm(String term, String label, String labelAbbrev, boolean isAbsenceTerm) {
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super(TermType.PresenceAbsenceTerm, term, label, labelAbbrev);
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this.setAbsenceTerm(isAbsenceTerm);
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}
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//******************************* STATIC METHODS *****************************************
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protected static PresenceAbsenceTerm getTermByUuid(UUID uuid){
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if (termMap == null || termMap.isEmpty()){
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return getTermByClassAndUUID(PresenceAbsenceTerm.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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//TODO read from label(abbrevs) like in TDWGArea
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public static PresenceAbsenceTerm getPresenceAbsenceTermByAbbreviation(String abbrev) {
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if (abbrev == null) { throw new NullPointerException("abbrev is 'null' in getPresenceTermByAbbreviation");
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} else if (abbrev.equalsIgnoreCase("c")) { return PresenceAbsenceTerm.CULTIVATED();
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} else if (abbrev.equalsIgnoreCase("e")) { return PresenceAbsenceTerm.ENDEMIC_FOR_THE_RELEVANT_AREA();
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} else if (abbrev.equalsIgnoreCase("i")) { return PresenceAbsenceTerm.INTRODUCED();
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} else if (abbrev.equalsIgnoreCase("ia")) { return PresenceAbsenceTerm.CASUAL();
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} else if (abbrev.equalsIgnoreCase("ic")) { return PresenceAbsenceTerm.INTRODUCED_CULTIVATED();
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} else if (abbrev.equalsIgnoreCase("id")) { return PresenceAbsenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED();
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} else if (abbrev.equalsIgnoreCase("in")) { return PresenceAbsenceTerm.NATURALISED();
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} else if (abbrev.equalsIgnoreCase("ip")) { return PresenceAbsenceTerm.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION();
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} else if (abbrev.equalsIgnoreCase("iq")) { return PresenceAbsenceTerm.INTRODUCED_PRESENCE_QUESTIONABLE();
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} else if (abbrev.equalsIgnoreCase("n")) { return PresenceAbsenceTerm.NATIVE();
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} else if (abbrev.equalsIgnoreCase("nd")) { return PresenceAbsenceTerm.NATIVE_DOUBTFULLY_NATIVE();
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} else if (abbrev.equalsIgnoreCase("nq")) { return PresenceAbsenceTerm.NATIVE_PRESENCE_QUESTIONABLE();
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} else if (abbrev.equalsIgnoreCase("p")) { return PresenceAbsenceTerm.PRESENT();
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} else if (abbrev.equalsIgnoreCase("na")) { return PresenceAbsenceTerm.NATURALISED();
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} else if (abbrev.equalsIgnoreCase("iv")) { return PresenceAbsenceTerm.INVASIVE();
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//absence
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} else if (abbrev.equalsIgnoreCase("cf")) { return PresenceAbsenceTerm.CULTIVATED_REPORTED_IN_ERROR();
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} else if (abbrev.equalsIgnoreCase("if")) { return PresenceAbsenceTerm.INTRODUCED_REPORTED_IN_ERROR();
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} else if (abbrev.equalsIgnoreCase("nf")) { return PresenceAbsenceTerm.NATIVE_REPORTED_IN_ERROR();
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} else if (abbrev.equalsIgnoreCase("ne")) { return PresenceAbsenceTerm.NATIVE_FORMERLY_NATIVE();
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} else if (abbrev.equalsIgnoreCase("ie")) { return PresenceAbsenceTerm.INTRODUCED_FORMERLY_INTRODUCED();
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} else {
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logger.warn("Unknown presence or absence status term abbreviation: " + abbrev);
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return null;
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}
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}
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/**
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* The taxon is endemic for the given area.
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* @see #PRESENT()
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* @see #NATIVE()
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* @see #ENDEMIC_DOUBTFULLY_PRESENT()
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* @see #ENDEMIC_REPORTED_IN_ERROR()
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*/
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public static final PresenceAbsenceTerm ENDEMIC_FOR_THE_RELEVANT_AREA(){
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return getTermByUuid(uuidEndemic);
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}
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/**
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* The taxon is present but not endemic for the given area.
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* @see #PRESENT()
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* @see #NATIVE()
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* @see #ENDEMIC_FOR_THE_RELEVANT_AREA()
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* @see #ENDEMIC_DOUBTFULLY_PRESENT()
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* @see #ENDEMIC_REPORTED_IN_ERROR()
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*/
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public static final PresenceAbsenceTerm NOT_ENDEMIC_FOR_THE_RELEVANT_AREA(){
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return getTermByUuid(uuidNotEndemic);
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}
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/**
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* The taxon is present but with unknown endemism for the given area.
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* @see #PRESENT()
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* @see #NATIVE()
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* @see #ENDEMIC_FOR_THE_RELEVANT_AREA()
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* @see #ENDEMIC_DOUBTFULLY_PRESENT()
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* @see #ENDEMIC_REPORTED_IN_ERROR()
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* @see #NOT_ENDEMIC_FOR_THE_RELEVANT_AREA()
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*/
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public static final PresenceAbsenceTerm ENDEMISM_UNKNOWN(){
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286
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return getTermByUuid(uuidUnknownEndemism);
|
|
287
|
}
|
|
288
|
|
|
289
|
/**
|
|
290
|
* The taxon is endemic for the given area but doubtfully present.
|
|
291
|
* @see #ENDEMIC_FOR_THE_RELEVANT_AREA()
|
|
292
|
* @see #ENDEMIC_REPORTED_IN_ERROR()
|
|
293
|
* @see #PRESENT_DOUBTFULLY()
|
|
294
|
* @see #NATIVE_PRESENCE_QUESTIONABLE()
|
|
295
|
*/
|
|
296
|
public static final PresenceAbsenceTerm ENDEMIC_DOUBTFULLY_PRESENT(){
|
|
297
|
return getTermByUuid(uuidEndedmicPresenceQuestionable);
|
|
298
|
}
|
|
299
|
|
|
300
|
/**
|
|
301
|
* The taxon if it exists is endemic for the given area but was only
|
|
302
|
* erroneously reported.
|
|
303
|
* So it either does not exist or it is unclear where it was originally found.
|
|
304
|
* @see #ENDEMIC_FOR_THE_RELEVANT_AREA()
|
|
305
|
* @see #ENDEMIC_DOUBTFULLY_PRESENT()
|
|
306
|
* @see #REPORTED_IN_ERROR()
|
|
307
|
* @see #NATIVE_REPORTED_IN_ERROR()
|
|
308
|
*/
|
|
309
|
public static final PresenceAbsenceTerm ENDEMIC_REPORTED_IN_ERROR(){
|
|
310
|
return getTermByUuid(uuidEndemicReportedError);
|
|
311
|
}
|
|
312
|
|
|
313
|
|
|
314
|
/**
|
|
315
|
* The taxon is present in the given area. No information given about
|
|
316
|
* nativeness/establishment means.
|
|
317
|
*
|
|
318
|
* @see #PRESENT_DOUBTFULLY()
|
|
319
|
* @see #ABSENT()
|
|
320
|
*/
|
|
321
|
public static final PresenceAbsenceTerm PRESENT(){
|
|
322
|
return getTermByUuid(uuidPresent);
|
|
323
|
}
|
|
324
|
|
|
325
|
/**
|
|
326
|
* Presence of the taxon in the given area is doubtful. No information given about
|
|
327
|
* nativeness/establishment means.
|
|
328
|
*
|
|
329
|
* @see #PRESENT()
|
|
330
|
* @see #ABSENT()
|
|
331
|
*/
|
|
332
|
public static final PresenceAbsenceTerm PRESENT_DOUBTFULLY(){
|
|
333
|
return getTermByUuid(uuidPresentDoubfully);
|
|
334
|
}
|
|
335
|
|
|
336
|
/**
|
|
337
|
* The taxon is not native but cultivated.
|
|
338
|
*
|
|
339
|
* @see #CULTIVATED_PRESENCE_QUESTIONABLE()
|
|
340
|
* @see #CULTIVATED_REPORTED_IN_ERROR()
|
|
341
|
*/
|
|
342
|
public static final PresenceAbsenceTerm CULTIVATED(){
|
|
343
|
return getTermByUuid(uuidCultivated);
|
|
344
|
}
|
|
345
|
|
|
346
|
/**
|
|
347
|
* The taxon is cultivated but presence is questionable.
|
|
348
|
*
|
|
349
|
* @see #CULTIVATED()
|
|
350
|
* @see #CULTIVATED_REPORTED_IN_ERROR()
|
|
351
|
*/
|
|
352
|
public static final PresenceAbsenceTerm CULTIVATED_PRESENCE_QUESTIONABLE(){
|
|
353
|
return getTermByUuid(uuidCultivatedPresenceQuestionable);
|
|
354
|
}
|
|
355
|
|
|
356
|
/**
|
|
357
|
* The taxon is erroneously reported as cultivated.
|
|
358
|
*
|
|
359
|
* @see #CULTIVATED()
|
|
360
|
* @see #CULTIVATED_REPORTED_IN_ERROR()
|
|
361
|
*/
|
|
362
|
public static final PresenceAbsenceTerm CULTIVATED_REPORTED_IN_ERROR(){
|
|
363
|
return getTermByUuid(uuidCultivatedReportedError);
|
|
364
|
}
|
|
365
|
|
|
366
|
|
|
367
|
public static final PresenceAbsenceTerm INTRODUCED(){
|
|
368
|
return getTermByUuid(uuidIntroduced);
|
|
369
|
}
|
|
370
|
|
|
371
|
/**
|
|
372
|
* Casual alien or introduced: adventive (casual)
|
|
373
|
*
|
|
374
|
* @see #CASUAL_REPORTED_IN_ERROR()
|
|
375
|
* @see #CASUAL_PRESENCE_QUESTIONABLE()
|
|
376
|
* @see #INTRODUCED_ADVENTITIOUS()
|
|
377
|
*/
|
|
378
|
public static final PresenceAbsenceTerm CASUAL(){
|
|
379
|
return getTermByUuid(uuidIntroducedAdventitious);
|
|
380
|
}
|
|
381
|
/**
|
|
382
|
* Casual alien, presence questionable
|
|
383
|
*
|
|
384
|
* @see #CASUAL()
|
|
385
|
* @see #CASUAL_REPORTED_IN_ERROR()
|
|
386
|
* @see #PRESENT_DOUBTFULLY()
|
|
387
|
*/
|
|
388
|
public static final PresenceAbsenceTerm CASUAL_PRESENCE_QUESTIONABLE(){
|
|
389
|
return getTermByUuid(uuidCasualPresenceQuestionable);
|
|
390
|
}
|
|
391
|
/**
|
|
392
|
* Casual alien, reported in error
|
|
393
|
*
|
|
394
|
* @see #CASUAL()
|
|
395
|
* @see #CASUAL_PRESENCE_QUESTIONABLE()
|
|
396
|
* @see #REPORTED_IN_ERROR()
|
|
397
|
*/
|
|
398
|
public static final PresenceAbsenceTerm CASUAL_REPORTED_IN_ERROR(){
|
|
399
|
return getTermByUuid(uuidCasualReportedError);
|
|
400
|
}
|
|
401
|
|
|
402
|
|
|
403
|
/**
|
|
404
|
* This term is of questional value. Introduced often is handled as opposite
|
|
405
|
* of adventitious/adventive and describes how the alien species came
|
|
406
|
* - on purpose for cultivation (introduced) or not (adventive).
|
|
407
|
* Adventitious or better adventive is often a synonym for casual which might
|
|
408
|
* be the better term here.
|
|
409
|
*
|
|
410
|
* @deprecated better use {@link #CASUAL()}, which has the same result (same semantics, but more precise)
|
|
411
|
*/
|
|
412
|
@Deprecated
|
|
413
|
public static final PresenceAbsenceTerm INTRODUCED_ADVENTITIOUS(){
|
|
414
|
return getTermByUuid(uuidIntroducedAdventitious);
|
|
415
|
}
|
|
416
|
|
|
417
|
public static final PresenceAbsenceTerm INTRODUCED_CULTIVATED(){
|
|
418
|
return getTermByUuid(uuidIntroducedCultiated);
|
|
419
|
}
|
|
420
|
|
|
421
|
public static final PresenceAbsenceTerm INTRODUCED_DOUBTFULLY_INTRODUCED(){
|
|
422
|
return getTermByUuid(uuidIntroducedDoubtfullyIntroduced);
|
|
423
|
}
|
|
424
|
|
|
425
|
|
|
426
|
public static final PresenceAbsenceTerm INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION(){
|
|
427
|
return getTermByUuid(uuidIntroducedUncertainDegreeNaturalisation);
|
|
428
|
}
|
|
429
|
|
|
430
|
public static final PresenceAbsenceTerm INTRODUCED_PRESENCE_QUESTIONABLE(){
|
|
431
|
return getTermByUuid(uuidIntroducedPresenceQuestionable);
|
|
432
|
}
|
|
433
|
|
|
434
|
public static final PresenceAbsenceTerm INTRODUCED_FORMERLY_INTRODUCED(){
|
|
435
|
return getTermByUuid(uuidIntroducedFormerlyIntroduced);
|
|
436
|
}
|
|
437
|
|
|
438
|
public static final PresenceAbsenceTerm INTRODUCED_REPORTED_IN_ERROR(){
|
|
439
|
return getTermByUuid(uuidIntroducedReportedError);
|
|
440
|
}
|
|
441
|
|
|
442
|
/**
|
|
443
|
* Use native if the taxon is native in the according area. Native and indigenous
|
|
444
|
* have the same meaning. Native might be problematic because the abbreviation
|
|
445
|
* N is already used for naturalised.
|
|
446
|
*
|
|
447
|
* @see #NATIVE_DOUBTFULLY_NATIVE()
|
|
448
|
* @see #NATIVE_PRESENCE_QUESTIONABLE()
|
|
449
|
* @see #NATIVE_REPORTED_IN_ERROR()
|
|
450
|
*/
|
|
451
|
public static final PresenceAbsenceTerm NATIVE(){
|
|
452
|
return getTermByUuid(uuidNative);
|
|
453
|
}
|
|
454
|
|
|
455
|
/**
|
|
456
|
* Same as {@link #NATIVE()} but presence is questionable
|
|
457
|
* @see #NATIVE()
|
|
458
|
* @see #NATIVE_DOUBTFULLY_NATIVE()
|
|
459
|
* @see #NATIVE_REPORTED_IN_ERROR()
|
|
460
|
*/
|
|
461
|
public static final PresenceAbsenceTerm NATIVE_PRESENCE_QUESTIONABLE(){
|
|
462
|
return getTermByUuid(uuidNativePresenceQuestionable);
|
|
463
|
}
|
|
464
|
|
|
465
|
/**
|
|
466
|
* The taxon was formerly native, but is extinct now in the given area.
|
|
467
|
*
|
|
468
|
* @see #NATIVE()
|
|
469
|
* @see #ABSENT()
|
|
470
|
*/
|
|
471
|
public static final PresenceAbsenceTerm NATIVE_FORMERLY_NATIVE(){
|
|
472
|
return getTermByUuid(uuidNativeFormerlyNative);
|
|
473
|
}
|
|
474
|
|
|
475
|
/**
|
|
476
|
* Same as {@link #NATIVE()} but presence was reported in error, so
|
|
477
|
* finally it is not native.
|
|
478
|
* @see #NATIVE()
|
|
479
|
* @see #NATIVE_PRESENCE_QUESTIONABLE()
|
|
480
|
* @see #NATIVE_DOUBTFULLY_NATIVE()
|
|
481
|
*/
|
|
482
|
public static final PresenceAbsenceTerm NATIVE_REPORTED_IN_ERROR(){
|
|
483
|
return getTermByUuid(uuidNativeError );
|
|
484
|
}
|
|
485
|
|
|
486
|
/**
|
|
487
|
* Same as {@link #NATIVE()} but the nativeness is doubtful, while presence
|
|
488
|
* is NOT questionable
|
|
489
|
* @see #NATIVE()
|
|
490
|
* @see #NATIVE_PRESENCE_QUESTIONABLE()
|
|
491
|
* @see #NATIVE_REPORTED_IN_ERROR()
|
|
492
|
*/
|
|
493
|
public static final PresenceAbsenceTerm NATIVE_DOUBTFULLY_NATIVE(){
|
|
494
|
return getTermByUuid(uuidNativeDoubtfullyNative);
|
|
495
|
}
|
|
496
|
|
|
497
|
/**
|
|
498
|
* Same as {@link #NATIVE()} but the nativeness is doubtful, while presence
|
|
499
|
* is NOT questionable
|
|
500
|
* @see #NATIVE_DOUBTFULLY_NATIVE()
|
|
501
|
* @see #NATIVE()
|
|
502
|
* @see #NATIVE_PRESENCE_QUESTIONABLE()
|
|
503
|
*/
|
|
504
|
public static final PresenceAbsenceTerm NATIVE_DOUBTFULLY_NATIVE_REPORTED_IN_ERROR(){
|
|
505
|
return getTermByUuid(uuidNativeDoubtfullyNativeReportedError);
|
|
506
|
}
|
|
507
|
|
|
508
|
|
|
509
|
/**
|
|
510
|
* Naturalized (or introduced: naturalized). Further distinction can be made by
|
|
511
|
* distinguishing invasive / non-invasive
|
|
512
|
* @see #NATURALISED_PRESENCE_QUESTIONABLE()
|
|
513
|
* @see #NATURALISED_REPORTED_IN_ERROR()
|
|
514
|
* @see #INVASIVE()
|
|
515
|
* @see #NON_INVASIVE
|
|
516
|
*/
|
|
517
|
public static final PresenceAbsenceTerm NATURALISED(){
|
|
518
|
return getTermByUuid(uuidNaturalised);
|
|
519
|
}
|
|
520
|
|
|
521
|
/**
|
|
522
|
*
|
|
523
|
* @see #NATURALISED()
|
|
524
|
*/
|
|
525
|
public static final PresenceAbsenceTerm NATURALISED_PRESENCE_QUESTIONABLE(){
|
|
526
|
return getTermByUuid(uuidNaturalisedPresenceQuestionable);
|
|
527
|
}
|
|
528
|
|
|
529
|
public static final PresenceAbsenceTerm NATURALISED_REPORTED_IN_ERROR(){
|
|
530
|
return getTermByUuid(uuidNaturalisedReportedError);
|
|
531
|
}
|
|
532
|
|
|
533
|
/**
|
|
534
|
* Naturalized invasive. <BR>
|
|
535
|
* The taxon is present but not native in the given area. Additionally
|
|
536
|
* it is spreading fast.
|
|
537
|
*
|
|
538
|
* @see #INVASIVE_PRESENCE_QUESTIONABLE()
|
|
539
|
* @see #NON_INVASIVE()
|
|
540
|
* @see #NON_INVASIVE_PRESENCE_QUESTIONABLE()
|
|
541
|
*/
|
|
542
|
public static final PresenceAbsenceTerm INVASIVE(){
|
|
543
|
return getTermByUuid(uuidInvasive);
|
|
544
|
}
|
|
545
|
/**
|
|
546
|
* Invasive, presence questionable.
|
|
547
|
*
|
|
548
|
* @see #INVASIVE()
|
|
549
|
* @see #NON_INVASIVE()
|
|
550
|
* @see #NON_INVASIVE_PRESENCE_QUESTIONABLE()
|
|
551
|
*/
|
|
552
|
public static final PresenceAbsenceTerm INVASIVE_PRESENCE_QUESTIONABLE(){
|
|
553
|
return getTermByUuid(uuidInvasivePresenceQuestionable);
|
|
554
|
}
|
|
555
|
/**
|
|
556
|
* The taxon is present but not native in the given area (naturalized).
|
|
557
|
* Additionally it is spreading not so fast.
|
|
558
|
*
|
|
559
|
* @see #INVASIVE()
|
|
560
|
* @see #INVASIVE_PRESENCE_QUESTIONABLE()
|
|
561
|
* @see #NON_INVASIVE_PRESENCE_QUESTIONABLE()
|
|
562
|
*/
|
|
563
|
public static final PresenceAbsenceTerm NON_INVASIVE(){
|
|
564
|
return getTermByUuid(uuidNonInvasive);
|
|
565
|
}
|
|
566
|
/**
|
|
567
|
* The taxon is questionable present and not native in the given area (naturalized).
|
|
568
|
* Additionally it is spreading not so fast
|
|
569
|
*
|
|
570
|
* @see #NON_INVASIVE()
|
|
571
|
* @see #INVASIVE()
|
|
572
|
* @see #INVASIVE_PRESENCE_QUESTIONABLE()
|
|
573
|
*/
|
|
574
|
public static final PresenceAbsenceTerm NON_INVASIVE_PRESENCE_QUESTIONABLE(){
|
|
575
|
return getTermByUuid(uuidNonInvasivePresenceQuestionable);
|
|
576
|
}
|
|
577
|
|
|
578
|
|
|
579
|
/**
|
|
580
|
* @see #PRESENT()
|
|
581
|
* @see #REPORTED_IN_ERROR()
|
|
582
|
*/
|
|
583
|
public static final PresenceAbsenceTerm ABSENT(){
|
|
584
|
return getTermByUuid(uuidAbsence);
|
|
585
|
}
|
|
586
|
|
|
587
|
/**
|
|
588
|
* The taxon is {@link #ABSENT() absent} in the given area
|
|
589
|
* but was erroneously reported as present.
|
|
590
|
*
|
|
591
|
* @see #ABSENT()
|
|
592
|
* @see #NATIVE_REPORTED_IN_ERROR()
|
|
593
|
* @see #INTRODUCED_REPORTED_IN_ERROR()
|
|
594
|
*/
|
|
595
|
public static final PresenceAbsenceTerm REPORTED_IN_ERROR(){
|
|
596
|
return getTermByUuid(uuidReportedInError);
|
|
597
|
}
|
|
598
|
|
|
599
|
/**
|
|
600
|
* The status of the taxon in the given area is not defined
|
|
601
|
* for whatever reason.
|
|
602
|
*/
|
|
603
|
public static final PresenceAbsenceTerm UNDEFINED(){
|
|
604
|
return getTermByUuid(uuidUndefined);
|
|
605
|
}
|
|
606
|
|
|
607
|
|
|
608
|
//******************************** METHODS ****************************/
|
|
609
|
|
|
610
|
@Override
|
|
611
|
public void resetTerms(){
|
|
612
|
termMap = null;
|
|
613
|
}
|
|
614
|
|
|
615
|
@Override
|
|
616
|
protected void setDefaultTerms(TermVocabulary<PresenceAbsenceTerm> termVocabulary) {
|
|
617
|
termMap = new HashMap<>();
|
|
618
|
for (PresenceAbsenceTerm term : termVocabulary.getTerms()){
|
|
619
|
termMap.put(term.getUuid(), term);
|
|
620
|
}
|
|
621
|
}
|
|
622
|
|
|
623
|
@Override
|
|
624
|
public PresenceAbsenceTerm readCsvLine(Class<PresenceAbsenceTerm> termClass, List<String> csvLine, TermType termType,
|
|
625
|
Map<UUID,DefinedTermBase> terms, boolean abbrevAsId){
|
|
626
|
PresenceAbsenceTerm newInstance = super.readCsvLine(termClass, csvLine, termType, terms, abbrevAsId);
|
|
627
|
String abbreviatedLabel = csvLine.get(4);
|
|
628
|
// String uuid = (String)csvLine.get(0);
|
|
629
|
// map.put(abbreviatedLabel, UUID.fromString(uuid));
|
|
630
|
String symbol = csvLine.get(5);
|
|
631
|
newInstance.setSymbol(symbol);
|
|
632
|
String color = csvLine.get(6);
|
|
633
|
try {
|
|
634
|
newInstance.setDefaultColor(color);
|
|
635
|
} catch (ParseException e) {
|
|
636
|
throw new RuntimeException(e);
|
|
637
|
}
|
|
638
|
boolean isAbsence = csvLine.get(7).equals("1") ? true : false;
|
|
639
|
newInstance.setAbsenceTerm(isAbsence);
|
|
640
|
|
|
641
|
newInstance.getRepresentation(Language.DEFAULT()).setAbbreviatedLabel(abbreviatedLabel);
|
|
642
|
return newInstance;
|
|
643
|
}
|
|
644
|
|
|
645
|
/**
|
|
646
|
* @return the defaultColor
|
|
647
|
*/
|
|
648
|
public String getDefaultColor() {
|
|
649
|
return defaultColor;
|
|
650
|
}
|
|
651
|
|
|
652
|
/**
|
|
653
|
* @param defaultColor the defaultColor to set
|
|
654
|
* @throws ParseException
|
|
655
|
*/
|
|
656
|
//TODO make format checking a hibernate validation rule
|
|
657
|
public void setDefaultColor(String defaultColor) throws ParseException {
|
|
658
|
String regEx = "[0-9a-fA-F]{6}";
|
|
659
|
if (StringUtils.isEmpty(defaultColor)){
|
|
660
|
this.defaultColor = null;
|
|
661
|
}else if (StringUtils.isEmpty(defaultColor) || defaultColor.matches(regEx)){
|
|
662
|
this.defaultColor = defaultColor;
|
|
663
|
}else{
|
|
664
|
throw new java.text.ParseException("Default color is not of correct format. Required is 'FFFFFF'", -1);
|
|
665
|
}
|
|
666
|
}
|
|
667
|
|
|
668
|
/**
|
|
669
|
* Includes presence/absence compare instead of pure uuid compare
|
|
670
|
*/
|
|
671
|
@Override
|
|
672
|
protected int compareVocabularies(PresenceAbsenceTerm thatTerm) {
|
|
673
|
UUID thisVocUuid = this.vocabulary == null? null:this.vocabulary.getUuid();
|
|
674
|
UUID thatVocUuid = thatTerm.getVocabulary() == null? null:thatTerm.getVocabulary().getUuid();
|
|
675
|
int vocCompare = CdmUtils.nullSafeCompareTo(thisVocUuid, thatVocUuid);
|
|
676
|
if (vocCompare != 0 && thatTerm.isAbsenceTerm() != this.isAbsenceTerm() ){
|
|
677
|
if (thatTerm.isAbsenceTerm()){
|
|
678
|
return 1;
|
|
679
|
}else{
|
|
680
|
return -1;
|
|
681
|
}
|
|
682
|
}
|
|
683
|
return vocCompare;
|
|
684
|
}
|
|
685
|
|
|
686
|
/**
|
|
687
|
* {@inheritDoc}
|
|
688
|
*
|
|
689
|
* For {@link PresenceAbsenceTerm} there is an additional rule that before comparing vocabulary uuid
|
|
690
|
* presence terms are preferred to absence terms.
|
|
691
|
*/
|
|
692
|
@Override
|
|
693
|
public int compareTo(PresenceAbsenceTerm presenceAbsenceTerm) {
|
|
694
|
return performCompareTo(presenceAbsenceTerm, true);
|
|
695
|
}
|
|
696
|
|
|
697
|
public boolean isAbsenceTerm() {
|
|
698
|
return absenceTerm;
|
|
699
|
}
|
|
700
|
|
|
701
|
public void setAbsenceTerm(boolean isAbsenceTerm) {
|
|
702
|
this.absenceTerm = isAbsenceTerm;
|
|
703
|
}
|
|
704
|
|
|
705
|
@Transient
|
|
706
|
private Set<UUID> isAnyIntroduced;
|
|
707
|
public boolean isAnyIntroduced() {
|
|
708
|
if (isAnyIntroduced == null){
|
|
709
|
isAnyIntroduced = new HashSet<>(Arrays.asList(new UUID[]{
|
|
710
|
uuidCasualPresenceQuestionable, uuidCasualReportedError,
|
|
711
|
uuidCultivated, uuidCultivatedPresenceQuestionable, uuidCultivatedReportedError,
|
|
712
|
uuidIntroduced, uuidIntroducedCultiated, uuidIntroducedDoubtfullyIntroduced,
|
|
713
|
uuidIntroducedFormerlyIntroduced, uuidIntroducedPresenceQuestionable,
|
|
714
|
uuidIntroducedReportedError, uuidIntroducedUncertainDegreeNaturalisation,
|
|
715
|
uuidIntroducedAdventitious,
|
|
716
|
uuidInvasive, uuidInvasivePresenceQuestionable,
|
|
717
|
uuidNaturalised, uuidNaturalisedPresenceQuestionable, uuidNaturalisedReportedError,
|
|
718
|
uuidIntroducedUncertainDegreeNaturalisation,
|
|
719
|
uuidInvasive, uuidInvasivePresenceQuestionable, uuidNonInvasive, uuidNonInvasivePresenceQuestionable
|
|
720
|
}));
|
|
721
|
}
|
|
722
|
return isAnyIntroduced.contains(uuid);
|
|
723
|
}
|
|
724
|
}
|