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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.Map;
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import javax.persistence.Entity;
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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.XmlElement;
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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.log4j.Logger;
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import org.hibernate.envers.Audited;
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import org.hibernate.search.annotations.Indexed;
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import org.springframework.beans.factory.annotation.Configurable;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
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import eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy;
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import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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/**
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* The taxon name class for plants and fungi.
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* <P>
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* This class corresponds to: NameBotanical according to the ABCD schema.
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*
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* @author m.doering
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* @version 1.0
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* @created 08-Nov-2007 13:06:15
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "BotanicalName", propOrder = {
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"anamorphic"
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})
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@XmlRootElement(name = "BotanicalName")
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@Entity
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@Indexed(index = "eu.etaxonomy.cdm.model.name.TaxonNameBase")
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@Audited
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@Configurable
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public class BotanicalName extends NonViralName<BotanicalName> implements Cloneable /*, IMergable*/ {
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private static final long serialVersionUID = 6818651572463497727L;
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(BotanicalName.class);
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//Only for fungi: to indicate that the type of the name is asexual or not
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@XmlElement(name ="IsAnamorphic")
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private boolean anamorphic;
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static private INonViralNameParser<?> nameParser = new NonViralNameParserImpl();
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// ************* CONSTRUCTORS *************/
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//needed by hibernate
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/**
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* Class constructor: creates a new botanical taxon name instance
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* only containing the {@link eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy default cache strategy}.
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*
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* @see #BotanicalName(Rank, HomotypicalGroup)
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* @see #BotanicalName(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
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* @see eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy
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*/
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protected BotanicalName(){
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super();
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this.cacheStrategy = BotanicNameDefaultCacheStrategy.NewInstance();
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}
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/**
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* Class constructor: creates a new botanical taxon name instance
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* only containing its {@link Rank rank},
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* its {@link HomotypicalGroup homotypical group} and
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* the {@link eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy default cache strategy}.
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* The new botanical taxon name instance will be also added to the set of
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* botanical taxon names belonging to this homotypical group.
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*
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* @param rank the rank to be assigned to <i>this</i> botanical taxon name
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* @param homotypicalGroup the homotypical group to which <i>this</i> botanical taxon name belongs
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* @see #BotanicalName()
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* @see #BotanicalName(Rank, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
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* @see eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy
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*/
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protected BotanicalName(Rank rank, HomotypicalGroup homotypicalGroup) {
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super(rank, homotypicalGroup);
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this.cacheStrategy = BotanicNameDefaultCacheStrategy.NewInstance();
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}
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/**
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* Class constructor: creates a new botanical taxon name instance
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* containing its {@link Rank rank},
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* its {@link HomotypicalGroup homotypical group},
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* its scientific name components, its {@link eu.etaxonomy.cdm.model.agent.TeamOrPersonBase author(team)},
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* its {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} and
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* the {@link eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy default cache strategy}.
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* The new botanical taxon name instance will be also added to the set of
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* botanical taxon names belonging to this homotypical group.
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*
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* @param rank the rank to be assigned to <i>this</i> botanical taxon name
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* @param genusOrUninomial the string for <i>this</i> botanical taxon name
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* if its rank is genus or higher or for the genus part
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* if its rank is lower than genus
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* @param infraGenericEpithet the string for the first epithet of
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* <i>this</i> botanical taxon name if its rank is lower than genus
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* and higher than species aggregate
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* @param specificEpithet the string for the first epithet of
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* <i>this</i> botanical taxon name if its rank is species aggregate or lower
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* @param infraSpecificEpithet the string for the second epithet of
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* <i>this</i> botanical taxon name if its rank is lower than species
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* @param combinationAuthorship the author or the team who published <i>this</i> botanical taxon name
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* @param nomenclaturalReference the nomenclatural reference where <i>this</i> botanical taxon name was published
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* @param nomenclMicroRef the string with the details for precise location within the nomenclatural reference
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* @param homotypicalGroup the homotypical group to which <i>this</i> botanical taxon name belongs
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* @see #BotanicalName()
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* @see #BotanicalName(Rank, HomotypicalGroup)
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* @see #NewInstance(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
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* @see eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy
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* @see eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy
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* @see eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
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*/
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protected BotanicalName(Rank rank, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, TeamOrPersonBase combinationAuthorship, INomenclaturalReference nomenclaturalReference, String nomenclMicroRef, HomotypicalGroup homotypicalGroup) {
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super(rank, genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet, combinationAuthorship, nomenclaturalReference, nomenclMicroRef, homotypicalGroup);
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this.cacheStrategy = BotanicNameDefaultCacheStrategy.NewInstance();
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}
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//********* METHODS **************************************/
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/**
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* Creates a new botanical taxon name instance
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* only containing its {@link Rank rank} and
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* the {@link eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy default cache strategy}.
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*
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* @param rank the rank to be assigned to <i>this</i> botanical taxon name
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* @see #BotanicalName(Rank, HomotypicalGroup)
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* @see #NewInstance(Rank, HomotypicalGroup)
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* @see #NewInstance(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
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* @see eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy
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*/
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public static BotanicalName NewInstance(Rank rank){
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return new BotanicalName(rank, null);
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}
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/**
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* Creates a new botanical taxon name instance
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* only containing its {@link Rank rank},
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* its {@link HomotypicalGroup homotypical group} and
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* the {@link eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy default cache strategy}.
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* The new botanical taxon name instance will be also added to the set of
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* botanical taxon names belonging to this homotypical group.
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*
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* @param rank the rank to be assigned to <i>this</i> botanical taxon name
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* @param homotypicalGroup the homotypical group to which <i>this</i> botanical taxon name belongs
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* @see #NewInstance(Rank)
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* @see #NewInstance(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
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* @see #BotanicalName(Rank, HomotypicalGroup)
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* @see eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy
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*/
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public static BotanicalName NewInstance(Rank rank, HomotypicalGroup homotypicalGroup){
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return new BotanicalName(rank, homotypicalGroup);
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}
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/**
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* Creates a new botanical taxon name instance
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* containing its {@link Rank rank},
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* its {@link HomotypicalGroup homotypical group},
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* its scientific name components, its {@link eu.etaxonomy.cdm.model.agent.TeamOrPersonBase author(team)},
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* its {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} and
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* the {@link eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy default cache strategy}.
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* The new botanical taxon name instance will be also added to the set of
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* botanical taxon names belonging to this homotypical group.
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*
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* @param rank the rank to be assigned to <i>this</i> botanical taxon name
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* @param genusOrUninomial the string for <i>this</i> botanical taxon name
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* if its rank is genus or higher or for the genus part
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* if its rank is lower than genus
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* @param infraGenericEpithet the string for the first epithet of
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* <i>this</i> botanical taxon name if its rank is lower than genus
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* and higher than species aggregate
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* @param specificEpithet the string for the first epithet of
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* <i>this</i> botanical taxon name if its rank is species aggregate or lower
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* @param infraSpecificEpithet the string for the second epithet of
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* <i>this</i> botanical taxon name if its rank is lower than species
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* @param combinationAuthorship the author or the team who published <i>this</i> botanical taxon name
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* @param nomenclaturalReference the nomenclatural reference where <i>this</i> botanical taxon name was published
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* @param nomenclMicroRef the string with the details for precise location within the nomenclatural reference
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* @param homotypicalGroup the homotypical group to which <i>this</i> botanical taxon name belongs
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* @see #NewInstance(Rank)
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* @see #NewInstance(Rank, HomotypicalGroup)
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* @see ZoologicalName#ZoologicalName(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
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* @see eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy
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*/
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public static BotanicalName NewInstance(Rank rank, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, TeamOrPersonBase combinationAuthorship, INomenclaturalReference nomenclaturalReference, String nomenclMicroRef, HomotypicalGroup homotypicalGroup) {
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return new BotanicalName(rank, genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet, combinationAuthorship, nomenclaturalReference, nomenclMicroRef, homotypicalGroup);
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}
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/**
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* Returns a botanical taxon name based on parsing a string representing
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* all elements (according to the ICBN) of a botanical taxon name (where
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* the scientific name is an uninomial) including authorship but without
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* nomenclatural reference. If the {@link Rank rank} is not "Genus" it should be
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* set afterwards with the {@link TaxonNameBase#setRank(Rank) setRank} methode.
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*
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* @param fullNameString the string to be parsed
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* @return the new botanical taxon name
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*/
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public static BotanicalName PARSED_NAME(String fullNameString){
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return PARSED_NAME(fullNameString, Rank.GENUS());
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}
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/**
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* Returns a botanical taxon name based on parsing a string representing
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* all elements (according to the ICBN) of a botanical taxon name including
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* authorship but without nomenclatural reference. The parsing result
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* depends on the given rank of the botanical taxon name to be created.
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*
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* @param fullNameString the string to be parsed
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* @param rank the rank of the taxon name
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* @return the new botanical taxon name
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*/
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public static BotanicalName PARSED_NAME(String fullNameString, Rank rank){
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if (nameParser == null){
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nameParser = new NonViralNameParserImpl();
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}
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return (BotanicalName)nameParser.parseFullName(fullNameString, NomenclaturalCode.ICNAFP, rank);
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}
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/**
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* Returns a botanical taxon name based on parsing a string representing
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* all elements (according to the ICBN) of a botanical taxon name (where
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* the scientific name is an uninomial) including authorship and
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* nomenclatural reference. Eventually a new {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference}
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* instance will also be created. If the {@link Rank rank} is not "Genus" it should be
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* set afterwards with the {@link TaxonNameBase#setRank(Rank) setRank} methode.
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*
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* @param fullNameAndReferenceString the string to be parsed
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* @return the new botanical taxon name
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*/
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public static BotanicalName PARSED_REFERENCE(String fullNameAndReferenceString){
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return PARSED_REFERENCE(fullNameAndReferenceString, Rank.GENUS());
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}
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/**
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* Returns a botanical taxon name based on parsing a string representing
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* all elements (according to the ICBN) of a botanical taxon name including
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* authorship and nomenclatural reference. The parsing result depends on
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* the given rank of the botanical taxon name to be created.
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* Eventually a new {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference}
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* instance will also be created.
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*
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* @param fullNameAndReferenceString the string to be parsed
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* @param rank the rank of the taxon name
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* @return the new botanical taxon name
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*/
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public static BotanicalName PARSED_REFERENCE(String fullNameAndReferenceString, Rank rank){
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if (nameParser == null){
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nameParser = new NonViralNameParserImpl();
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}
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return (BotanicalName)nameParser.parseReferencedName(fullNameAndReferenceString, NomenclaturalCode.ICNAFP, rank);
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}
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//***********************
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private static Map<String, java.lang.reflect.Field> allFields = null;
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@Override
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protected Map<String, java.lang.reflect.Field> getAllFields(){
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if (allFields == null){
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allFields = CdmUtils.getAllFields(this.getClass(), CdmBase.class, false, false, false, true);
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}
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return allFields;
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}
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//*************************
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/**
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* Returns the boolean value of the flag indicating whether the specimen
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* type of <i>this</i> botanical taxon name for a fungus is asexual (true) or not
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* (false). This applies only in case of fungi. The Article 59 of the ICBN
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* permits mycologists to give asexually reproducing fungi (anamorphs)
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* separate names from their sexual states (teleomorphs).
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*
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* @return the boolean value of the isAnamorphic flag
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*/
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public boolean isAnamorphic(){
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return this.anamorphic;
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}
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/**
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* @see #isAnamorphic()
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*/
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public void setAnamorphic(boolean anamorphic){
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this.anamorphic = anamorphic;
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}
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/**
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* Returns the {@link NomenclaturalCode nomenclatural code} that governs
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* the construction of <i>this</i> botanical taxon name, that is the
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* International Code of Botanical Nomenclature. This method overrides
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* the getNomenclaturalCode method from {@link NonViralName NonViralName}.
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*
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* @return the nomenclatural code for plants
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* @see NonViralName#isCodeCompliant()
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* @see TaxonNameBase#getHasProblem()
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*/
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@Override
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312
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public NomenclaturalCode getNomenclaturalCode(){
|
|
313
|
return NomenclaturalCode.ICNAFP;
|
|
314
|
}
|
|
315
|
|
|
316
|
|
|
317
|
/**
|
|
318
|
* Checks if this name is an autonym.<BR>
|
|
319
|
* An autonym is a taxon name that has equal specific and infra specific epithets.<BR>
|
|
320
|
* {@link http://ibot.sav.sk/icbn/frameset/0010Ch2Sec1a006.htm#6.8. Vienna Code §6.8}
|
|
321
|
* or a taxon name that has equal generic and infrageneric epithets (A22.2)
|
|
322
|
* @return true, if name has Rank, Rank is below species and species epithet equals infraSpeciesEpithtet, else false
|
|
323
|
*/
|
|
324
|
@Override
|
|
325
|
public boolean isAutonym(){
|
|
326
|
if (this.getRank() != null && this.getSpecificEpithet() != null && this.getInfraSpecificEpithet() != null &&
|
|
327
|
this.isInfraSpecific() && this.getSpecificEpithet().trim().equals(this.getInfraSpecificEpithet().trim())){
|
|
328
|
return true;
|
|
329
|
}else if (this.getRank() != null && this.getGenusOrUninomial() != null && this.getInfraGenericEpithet() != null &&
|
|
330
|
this.isInfraGeneric() && this.getGenusOrUninomial().trim().equals(this.getInfraGenericEpithet().trim())){
|
|
331
|
return true;
|
|
332
|
}else{
|
|
333
|
return false;
|
|
334
|
}
|
|
335
|
}
|
|
336
|
|
|
337
|
//*********************** CLONE ********************************************************/
|
|
338
|
|
|
339
|
/**
|
|
340
|
* Clones <i>this</i> botanical name. This is a shortcut that enables to create
|
|
341
|
* a new instance that differs only slightly from <i>this</i> botanical name by
|
|
342
|
* modifying only some of the attributes.
|
|
343
|
*
|
|
344
|
* @see eu.etaxonomy.cdm.model.name.NonViralName#clone()
|
|
345
|
* @see java.lang.Object#clone()
|
|
346
|
*/
|
|
347
|
@Override
|
|
348
|
public Object clone() {
|
|
349
|
BotanicalName result = (BotanicalName)super.clone();
|
|
350
|
//no changes to: title, authorTeam, hasProblem, nomenclaturallyRelevant, uri
|
|
351
|
return result;
|
|
352
|
}
|
|
353
|
|
|
354
|
|
|
355
|
}
|