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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.strategy.cache.name;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.UUID;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import org.apache.logging.log4j.LogManager;
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import org.apache.logging.log4j.Logger;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.common.UTF8;
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import eu.etaxonomy.cdm.model.agent.Team;
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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.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.strategy.cache.TagEnum;
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import eu.etaxonomy.cdm.strategy.cache.TaggedText;
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import eu.etaxonomy.cdm.strategy.cache.TaggedTextBuilder;
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import eu.etaxonomy.cdm.strategy.cache.agent.TeamDefaultCacheStrategy;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImplRegExBase;
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/**
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* This class is a default implementation for the INonViralNameCacheStrategy<T extends NonViralName>
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* interface.<BR>
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* The method implements a cache strategy for botanical names so no method has to be overwritten by
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* a subclass for botanic names.
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* Where differing from this default botanic name strategy other subclasses should overwrite the
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* existing methods, e.g. a CacheStrategy for zoological names should overwrite getAuthorAndExAuthor
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* @author a.mueller
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*/
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public class TaxonNameDefaultCacheStrategy
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extends NameCacheStrategyBase
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implements INonViralNameCacheStrategy {
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private static final Logger logger = LogManager.getLogger();
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private static final long serialVersionUID = -6577757501563212669L;
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final static UUID uuid = UUID.fromString("1cdda0d1-d5bc-480f-bf08-40a510a2f223");
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protected String nameAuthorSeperator = " ";
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protected String basionymStart = "(";
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protected String basionymEnd = ")";
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protected String exAuthorSeperator = " ex ";
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private static String NOTHO = "notho";
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private CharSequence basionymAuthorCombinationAuthorSeperator = " ";
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private String zooAuthorYearSeperator = ", ";
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private Integer etAlPosition;
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private String cultivarStart = "'";
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private String cultivarEnd = "'";
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@Override
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public UUID getUuid(){
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return uuid;
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}
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// ************************** FACTORY ******************************/
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public static TaxonNameDefaultCacheStrategy NewInstance(){
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return new TaxonNameDefaultCacheStrategy();
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}
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// ************ CONSTRUCTOR *******************/
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protected TaxonNameDefaultCacheStrategy(){
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super();
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}
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/* **************** GETTER / SETTER **************************************/
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@Override
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public Integer getEtAlPosition() {
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return etAlPosition;
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}
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@Override
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public void setEtAlPosition(Integer etAlPosition) {
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this.etAlPosition = etAlPosition;
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}
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/**
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* String that separates the NameCache part from the AuthorCache part
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* @return
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*/
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public String getNameAuthorSeperator() {
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return nameAuthorSeperator;
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}
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public void setNameAuthorSeperator(String nameAuthorSeperator) {
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this.nameAuthorSeperator = nameAuthorSeperator;
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}
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/**
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* String the basionym author part starts with e.g. '('.
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* This should correspond with the {@link TaxonNameDefaultCacheStrategy#getBasionymEnd() basionymEnd} attribute
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* @return
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*/
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public String getBasionymStart() {
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return basionymStart;
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}
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public void setBasionymStart(String basionymStart) {
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this.basionymStart = basionymStart;
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}
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/**
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* String the basionym author part ends with e.g. ')'.
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* This should correspond with the {@link TaxonNameDefaultCacheStrategy#getBasionymStart() basionymStart} attribute
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* @return
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*/
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public String getBasionymEnd() {
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return basionymEnd;
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}
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public void setBasionymEnd(String basionymEnd) {
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this.basionymEnd = basionymEnd;
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}
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/**
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* String to separate ex author from author.
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*/
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public String getExAuthorSeperator() {
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return exAuthorSeperator;
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}
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public void setExAuthorSeperator(String exAuthorSeperator) {
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this.exAuthorSeperator = exAuthorSeperator;
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}
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/**
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* String that separates the basionym/original_combination author part from the combination author part
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*/
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public CharSequence getBasionymAuthorCombinationAuthorSeperator() {
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return basionymAuthorCombinationAuthorSeperator;
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}
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public void setBasionymAuthorCombinationAuthorSeperator( CharSequence basionymAuthorCombinationAuthorSeperator) {
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this.basionymAuthorCombinationAuthorSeperator = basionymAuthorCombinationAuthorSeperator;
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}
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public String getZooAuthorYearSeperator() {
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return zooAuthorYearSeperator;
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}
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public void setZooAuthorYearSeperator(String authorYearSeperator) {
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this.zooAuthorYearSeperator = authorYearSeperator;
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}
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// ******************* Authorship ******************************/
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@Override
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public String getAuthorshipCache(TaxonName taxonName) {
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if (taxonName == null){
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return null;
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}else if (taxonName.isViral()){
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return null;
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}else if(taxonName.isProtectedAuthorshipCache() == true) {
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//cache protected
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return taxonName.getAuthorshipCache();
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}else{
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return getNonCacheAuthorshipCache(taxonName);
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}
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}
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/**
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* Returns the authorshipcache string for the atomized authorship fields. Does not use the authorship field.
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* @throws NullPointerException if nonViralName is null.
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* @param taxonName
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* @return
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*/
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protected String getNonCacheAuthorshipCache(TaxonName nonViralName){
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if (nonViralName.getNameType().isZoological()){
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return this.getZoologicalNonCacheAuthorshipCache(nonViralName);
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}else{
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String result = "";
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TeamOrPersonBase<?> combinationAuthor = nonViralName.getCombinationAuthorship();
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TeamOrPersonBase<?> exCombinationAuthor = nonViralName.getExCombinationAuthorship();
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TeamOrPersonBase<?> basionymAuthor = nonViralName.getBasionymAuthorship();
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TeamOrPersonBase<?> exBasionymAuthor = nonViralName.getExBasionymAuthorship();
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if (isCultivar(nonViralName) ){
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exCombinationAuthor = null;
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basionymAuthor = null;
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exBasionymAuthor = null;
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}
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String basionymPart = "";
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String authorPart = "";
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//basionym
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if (basionymAuthor != null || exBasionymAuthor != null){
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basionymPart = basionymStart + getAuthorAndExAuthor(basionymAuthor, exBasionymAuthor) + basionymEnd;
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}
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if (combinationAuthor != null || exCombinationAuthor != null){
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authorPart = getAuthorAndExAuthor(combinationAuthor, exCombinationAuthor);
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}
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result = CdmUtils.concat(basionymAuthorCombinationAuthorSeperator, basionymPart, authorPart);
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// if ("".equals(result)){
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// result = null;
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// }
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return result;
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}
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}
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private boolean isCultivar(TaxonName name) {
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return name.isCultivar() || isNotBlank(name.getCultivarEpithet()) || isNotBlank(name.getCultivarGroupEpithet());
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}
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protected String getZoologicalNonCacheAuthorshipCache(TaxonName nonViralName) {
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if (nonViralName == null){
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return null;
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}
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String result = "";
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TeamOrPersonBase<?> combinationAuthor = nonViralName.getCombinationAuthorship();
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TeamOrPersonBase<?> exCombinationAuthor = nonViralName.getExCombinationAuthorship();
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TeamOrPersonBase<?> basionymAuthor = nonViralName.getBasionymAuthorship();
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TeamOrPersonBase<?> exBasionymAuthor = nonViralName.getExBasionymAuthorship();
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Integer publicationYear = nonViralName.getPublicationYear();
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Integer originalPublicationYear = nonViralName.getOriginalPublicationYear();
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String basionymPart = "";
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String authorPart = "";
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//basionym
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if (basionymAuthor != null || exBasionymAuthor != null || originalPublicationYear != null ){
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String authorAndEx = getAuthorAndExAuthor(basionymAuthor, exBasionymAuthor);
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String originalPublicationYearString = originalPublicationYear == null ? null : String.valueOf(originalPublicationYear);
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String authorAndExAndYear = CdmUtils.concat(zooAuthorYearSeperator, authorAndEx, originalPublicationYearString );
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basionymPart = basionymStart + authorAndExAndYear + basionymEnd;
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}
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if (combinationAuthor != null || exCombinationAuthor != null){
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String authorAndEx = getAuthorAndExAuthor(combinationAuthor, exCombinationAuthor);
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String publicationYearString = publicationYear == null ? null : String.valueOf(publicationYear);
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authorPart = CdmUtils.concat(zooAuthorYearSeperator, authorAndEx, publicationYearString);
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}
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result = CdmUtils.concat(basionymAuthorCombinationAuthorSeperator, basionymPart, authorPart);
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if (result == null){
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result = "";
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}
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return result;
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}
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/**
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* Returns the AuthorCache part for a combination of an author and an ex author. This applies on
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* combination authors as well as on basionym/orginal combination authors.
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* The correct order is exAuthor ex author though some botanist do not know about and do it the
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* other way round. (see 46.4-46.6 ICBN (Vienna Code, 2006))
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*/
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protected String getAuthorAndExAuthor(TeamOrPersonBase<?> author, TeamOrPersonBase<?> exAuthor){
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String authorString = "";
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String exAuthorString = "";
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if (author != null){
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authorString = getNomAuthorTitle(author);
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}
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if (exAuthor != null){
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exAuthorString = getNomAuthorTitle(exAuthor);
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exAuthorString += exAuthorSeperator;
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}
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String result = exAuthorString + authorString;
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return result;
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}
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private String getNomAuthorTitle(TeamOrPersonBase<?> author) {
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if (!author.isInstanceOf(Team.class) || this.getEtAlPosition() == null || this.getEtAlPosition() < 2) {
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return CdmUtils.Nz(author.getNomenclaturalTitleCache());
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}else {
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Team team = CdmBase.deproxy(author, Team.class);
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TeamDefaultCacheStrategy formatter = TeamDefaultCacheStrategy.NewInstanceNomEtAl(this.getEtAlPosition());
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return formatter.getNomenclaturalTitleCache(team);
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}
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}
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/**
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* Checks if the given name should include the author in it's cached version.<BR>
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* This is usually the case but not for <i>species aggregates</i>.
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* @param nonViralName
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* @return
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*/
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protected boolean nameIncludesAuthorship(INonViralName nonViralName){
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Rank rank = nonViralName.getRank();
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if (rank != null && rank.isSpeciesAggregate()){
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return false;
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}else{
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return true;
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}
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}
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// ************* TAGGED NAME ***************************************/
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@Override
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protected List<TaggedText> doGetTaggedTitle(TaxonName taxonName) {
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List<TaggedText> tags = new ArrayList<>();
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if (taxonName.getNameType().isViral()){
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String acronym = taxonName.getAcronym();
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if (isNotBlank(taxonName.getAcronym())){
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//this is not according to the code
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tags.add(new TaggedText(TagEnum.name, acronym));
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}
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return tags;
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}else if (taxonName.isHybridFormula()){
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//hybrid formula
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String hybridSeparator = NonViralNameParserImplRegExBase.hybridSign;
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boolean isFirst = true;
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List<HybridRelationship> rels = taxonName.getOrderedChildRelationships();
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for (HybridRelationship rel: rels){
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if (! isFirst){
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tags.add(new TaggedText(TagEnum.hybridSign, hybridSeparator));
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}
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isFirst = false;
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tags.addAll(getTaggedTitle(rel.getParentName()));
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}
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return tags;
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}else if (taxonName.isAutonym()){
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//Autonym
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tags.addAll(handleTaggedAutonym(taxonName, true));
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}else{ //not Autonym
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List<TaggedText> nameTags = getTaggedName(taxonName);
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tags.addAll(nameTags);
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String authorCache = getAuthorshipCache(taxonName);
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if (isNotBlank(authorCache)){
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tags.add(new TaggedText(TagEnum.authors, authorCache));
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}
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}
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return tags;
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}
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/**
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* Returns the tag list of the name part (without author and reference).
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* @param taxonName
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* @return
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*/
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@Override
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public List<TaggedText> getTaggedName(TaxonName taxonName) {
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if (taxonName == null){
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return null;
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}else if (taxonName.isViral()){
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return null;
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}
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List<TaggedText> tags = new ArrayList<>();
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Rank rank = taxonName.getRank();
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348
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if (taxonName.isProtectedNameCache()){
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tags.add(new TaggedText(TagEnum.name, taxonName.getNameCache()));
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}else if (taxonName.isHybridFormula()){
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//hybrid formula
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//TODO graft-chimera (see also cultivars)
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String hybridSeparator = NonViralNameParserImplRegExBase.hybridSign;
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boolean isFirst = true;
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List<HybridRelationship> rels = taxonName.getOrderedChildRelationships();
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357
|
for (HybridRelationship rel: rels){
|
|
358
|
if (! isFirst){
|
|
359
|
tags.add(new TaggedText(TagEnum.hybridSign, hybridSeparator));
|
|
360
|
}
|
|
361
|
isFirst = false;
|
|
362
|
tags.addAll(getTaggedName(rel.getParentName()));
|
|
363
|
}
|
|
364
|
return tags;
|
|
365
|
|
|
366
|
}else if (rank == null){
|
|
367
|
tags = getRanklessTaggedNameCache(taxonName, true);
|
|
368
|
}else if (rank.isCultivar()){
|
|
369
|
tags = getCultivarTaggedNameCache(taxonName);
|
|
370
|
}else if (rank.isInfraSpecific()){
|
|
371
|
tags = getInfraSpeciesTaggedNameCache(taxonName);
|
|
372
|
}else if (rank.isSpecies() || isAggregateWithAuthorship(taxonName, rank) ){ //exception see #4288
|
|
373
|
tags = getSpeciesTaggedNameCache(taxonName, true);
|
|
374
|
}else if (rank.isInfraGeneric()){
|
|
375
|
tags = getInfraGenusTaggedNameCache(taxonName, true);
|
|
376
|
}else if (rank.isGenus()){
|
|
377
|
tags = getGenusOrUninomialTaggedNameCache(taxonName, true);
|
|
378
|
}else if (rank.isSupraGeneric()){
|
|
379
|
tags = getGenusOrUninomialTaggedNameCache(taxonName, true);
|
|
380
|
}else{
|
|
381
|
tags = getRanklessTaggedNameCache(taxonName, true);
|
|
382
|
logger.warn("Rank does not belong to a rank class: " + rank.getTitleCache() + ". Used rankless nameCache for name " + taxonName.getUuid());
|
|
383
|
}
|
|
384
|
//TODO handle appended phrase here instead of different places, check first if this is true for all
|
|
385
|
//cases
|
|
386
|
|
|
387
|
return tags;
|
|
388
|
}
|
|
389
|
|
|
390
|
//***************************** PRIVATES ***************************************/
|
|
391
|
|
|
392
|
private List<TaggedText> getCultivarTaggedNameCache(TaxonName taxonName) {
|
|
393
|
List<TaggedText> scientificNameTags;
|
|
394
|
TaggedTextBuilder builder = TaggedTextBuilder.NewInstance();
|
|
395
|
if (isNotBlank(taxonName.getInfraSpecificEpithet())){
|
|
396
|
scientificNameTags = getInfraSpeciesTaggedNameCache(taxonName, false, false);
|
|
397
|
} else if (isNotBlank(taxonName.getSpecificEpithet())){
|
|
398
|
scientificNameTags = getSpeciesTaggedNameCache(taxonName, false);
|
|
399
|
} else if (isNotBlank(taxonName.getInfraGenericEpithet())){
|
|
400
|
scientificNameTags = getInfraGenusTaggedNameCache(taxonName, false);
|
|
401
|
} else /*if (isNotBlank(taxonName.getGenusOrUninomial())) */{
|
|
402
|
scientificNameTags = getGenusOrUninomialTaggedNameCache(taxonName, false);
|
|
403
|
}
|
|
404
|
|
|
405
|
UUID rankUuid = taxonName.getRank().getUuid();
|
|
406
|
boolean rankIsHandled = true;
|
|
407
|
String cultivarStr = null;
|
|
408
|
String groupStr = taxonName.getCultivarGroupEpithet();
|
|
409
|
if (rankUuid.equals(Rank.uuidCultivar)){
|
|
410
|
cultivarStr = surroundedCultivarEpithet(taxonName.getCultivarEpithet());
|
|
411
|
if (isNotBlank(cultivarStr) && isNotBlank(groupStr)){
|
|
412
|
groupStr = surroundGroupWithBracket(groupStr);
|
|
413
|
}
|
|
414
|
cultivarStr = CdmUtils.concat(" ", groupStr, cultivarStr);
|
|
415
|
}else if (rankUuid.equals(Rank.uuidCultivarGroup)){
|
|
416
|
cultivarStr = CdmUtils.concat(" ", groupStr, checkHasGroupEpithet(groupStr)? null: "Group");
|
|
417
|
}else if (rankUuid.equals(Rank.uuidGrexICNCP)){
|
|
418
|
cultivarStr = CdmUtils.concat(" ", groupStr, checkHasGrexEpithet(groupStr)? null: "grex");
|
|
419
|
}else{
|
|
420
|
rankIsHandled = false;
|
|
421
|
}
|
|
422
|
if (rankIsHandled){
|
|
423
|
builder.addAll(scientificNameTags);
|
|
424
|
}else if (rankUuid.equals(Rank.uuidGraftChimaera)){
|
|
425
|
//TODO not yet fully implemented
|
|
426
|
cultivarStr = "+ " + CdmUtils.concat(" ", taxonName.getGenusOrUninomial(), surroundedCultivarEpithet(taxonName.getCultivarEpithet()));
|
|
427
|
}else if (rankUuid.equals(Rank.uuidDenominationClass)){
|
|
428
|
//TODO dummy implementation
|
|
429
|
cultivarStr = CdmUtils.concat(" ", taxonName.getGenusOrUninomial(), surroundedCultivarEpithet(taxonName.getCultivarEpithet()));
|
|
430
|
} else { //(!rankIsHandled)
|
|
431
|
throw new IllegalStateException("Unsupported rank " + taxonName.getRank().getTitleCache() + " for cultivar.");
|
|
432
|
}
|
|
433
|
if (isNotBlank(cultivarStr)){
|
|
434
|
builder.add(TagEnum.cultivar, cultivarStr);
|
|
435
|
}
|
|
436
|
|
|
437
|
List<TaggedText> tags = builder.getTaggedText();
|
|
438
|
addAppendedTaggedPhrase(tags, taxonName, true);
|
|
439
|
return tags;
|
|
440
|
}
|
|
441
|
|
|
442
|
private String surroundGroupWithBracket(String groupStr) {
|
|
443
|
if (groupStr.matches(NonViralNameParserImplRegExBase.grex + "$")){
|
|
444
|
return groupStr;
|
|
445
|
}else if (groupStr.matches(".*" + NonViralNameParserImplRegExBase.grex + ".+")){
|
|
446
|
Matcher matcher = Pattern.compile(NonViralNameParserImplRegExBase.grex + "\\s*" ).matcher(groupStr);
|
|
447
|
matcher.find();
|
|
448
|
return groupStr.substring(0, matcher.end()) + "("+ groupStr.substring(matcher.end())+ ")";
|
|
449
|
}else{
|
|
450
|
return "("+ groupStr + ")";
|
|
451
|
}
|
|
452
|
}
|
|
453
|
|
|
454
|
private boolean checkHasGroupEpithet(String group) {
|
|
455
|
|
|
456
|
String[] splits = group == null? new String[0]: group.split("\\s+");
|
|
457
|
if (splits.length <= 1){
|
|
458
|
return false;
|
|
459
|
}else if (splits[0].matches(NonViralNameParserImplRegExBase.group)
|
|
460
|
|| splits[splits.length-1].matches(NonViralNameParserImplRegExBase.group)){
|
|
461
|
return true;
|
|
462
|
}else{
|
|
463
|
return false;
|
|
464
|
}
|
|
465
|
}
|
|
466
|
|
|
467
|
private boolean checkHasGrexEpithet(String grex) {
|
|
468
|
String[] splits = grex == null? new String[0]: grex.split("\\s+");
|
|
469
|
if (splits.length <= 1){
|
|
470
|
return false;
|
|
471
|
}else if (splits[splits.length-1].matches(NonViralNameParserImplRegExBase.grex)){
|
|
472
|
return true;
|
|
473
|
}else{
|
|
474
|
return false;
|
|
475
|
}
|
|
476
|
}
|
|
477
|
|
|
478
|
private String surroundedCultivarEpithet(String cultivarEpi) {
|
|
479
|
return cultivarStart + CdmUtils.Nz(cultivarEpi) + cultivarEnd;
|
|
480
|
}
|
|
481
|
|
|
482
|
private boolean isAggregateWithAuthorship(TaxonName nonViralName, Rank rank) {
|
|
483
|
if (rank == null){
|
|
484
|
return false;
|
|
485
|
}else{
|
|
486
|
return rank.isSpeciesAggregate() && ( isNotBlank(nonViralName.getAuthorshipCache()) || nonViralName.getNomenclaturalReference() != null );
|
|
487
|
}
|
|
488
|
}
|
|
489
|
|
|
490
|
/**
|
|
491
|
* Returns the tag list for an autonym taxon.
|
|
492
|
*
|
|
493
|
* @see NonViralName#isAutonym()
|
|
494
|
* @see BotanicalName#isAutonym()
|
|
495
|
* @param nonViralName
|
|
496
|
* @return
|
|
497
|
*/
|
|
498
|
private List<TaggedText> handleTaggedAutonym(TaxonName nonViralName, boolean addAppended) {
|
|
499
|
List<TaggedText> tags = null;
|
|
500
|
if (nonViralName.isInfraSpecific()){
|
|
501
|
//species part
|
|
502
|
tags = getSpeciesTaggedNameCache(nonViralName, addAppended);
|
|
503
|
|
|
504
|
//author
|
|
505
|
String authorCache = getAuthorshipCache(nonViralName);
|
|
506
|
if (isNotBlank(authorCache)){
|
|
507
|
tags.add(new TaggedText(TagEnum.authors, authorCache));
|
|
508
|
}
|
|
509
|
|
|
510
|
//infra species marker
|
|
511
|
if (nonViralName.getRank() == null || !nonViralName.getRank().isInfraSpecific()){
|
|
512
|
//TODO handle exception
|
|
513
|
logger.warn("Rank for autonym does not exist or is not lower than species !!");
|
|
514
|
}else{
|
|
515
|
String infraSpeciesMarker = nonViralName.getRank().getAbbreviation();
|
|
516
|
if (nonViralName.isTrinomHybrid()){
|
|
517
|
infraSpeciesMarker = CdmUtils.concat("", NOTHO, infraSpeciesMarker);
|
|
518
|
}
|
|
519
|
if (isNotBlank(infraSpeciesMarker)){
|
|
520
|
tags.add(new TaggedText(TagEnum.rank, infraSpeciesMarker));
|
|
521
|
}
|
|
522
|
}
|
|
523
|
|
|
524
|
//infra species
|
|
525
|
String infraSpeciesPart = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet()).trim();
|
|
526
|
if (isNotBlank(infraSpeciesPart)){
|
|
527
|
tags.add(new TaggedText(TagEnum.name, infraSpeciesPart));
|
|
528
|
}
|
|
529
|
|
|
530
|
} else if (nonViralName.isInfraGeneric()){
|
|
531
|
//genus part
|
|
532
|
tags =getGenusOrUninomialTaggedNameCache(nonViralName, addAppended);
|
|
533
|
|
|
534
|
//author
|
|
535
|
String authorCache = getAuthorshipCache(nonViralName);
|
|
536
|
if (isNotBlank(authorCache)){
|
|
537
|
tags.add(new TaggedText(TagEnum.authors, authorCache));
|
|
538
|
}
|
|
539
|
|
|
540
|
//infra species marker
|
|
541
|
if (nonViralName.getRank() == null || !nonViralName.getRank().isInfraGeneric()){
|
|
542
|
//TODO handle exception
|
|
543
|
logger.warn("Rank for autonym does not exist or is not lower than species !!");
|
|
544
|
}else{
|
|
545
|
Rank rank = nonViralName.getRank();
|
|
546
|
String infraGenericMarker = rank.getAbbreviation();
|
|
547
|
if (rank.equals(Rank.SECTION_BOTANY()) || rank.equals(Rank.SUBSECTION_BOTANY())){
|
|
548
|
infraGenericMarker = infraGenericMarker.replace("(bot.)", "");
|
|
549
|
}
|
|
550
|
if (isNotBlank(infraGenericMarker)){
|
|
551
|
tags.add(new TaggedText(TagEnum.rank, infraGenericMarker));
|
|
552
|
}
|
|
553
|
}
|
|
554
|
|
|
555
|
//infra genus
|
|
556
|
String infraGenericPart = CdmUtils.Nz(nonViralName.getInfraGenericEpithet()).trim();
|
|
557
|
if (isNotBlank(infraGenericPart)){
|
|
558
|
tags.add(new TaggedText(TagEnum.name, infraGenericPart));
|
|
559
|
}
|
|
560
|
}
|
|
561
|
|
|
562
|
return tags;
|
|
563
|
}
|
|
564
|
|
|
565
|
|
|
566
|
|
|
567
|
/**
|
|
568
|
* Returns the tag list for rankless taxa.
|
|
569
|
* @param nonViralName
|
|
570
|
* @return
|
|
571
|
*/
|
|
572
|
protected List<TaggedText> getRanklessTaggedNameCache(INonViralName nonViralName, boolean addAppended){
|
|
573
|
List<TaggedText> tags = getUninomialTaggedPart(nonViralName);
|
|
574
|
String speciesEpi = CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim();
|
|
575
|
if (isNotBlank(speciesEpi)){
|
|
576
|
tags.add(new TaggedText(TagEnum.name, speciesEpi));
|
|
577
|
}
|
|
578
|
|
|
579
|
String infraSpeciesEpi = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet());
|
|
580
|
if (isNotBlank(infraSpeciesEpi)){
|
|
581
|
if (nonViralName.isTrinomHybrid()){
|
|
582
|
tags.add(new TaggedText(TagEnum.rank, NOTHO));
|
|
583
|
}
|
|
584
|
tags.add(new TaggedText(TagEnum.name, infraSpeciesEpi));
|
|
585
|
}
|
|
586
|
|
|
587
|
//result += " (rankless)";
|
|
588
|
addAppendedTaggedPhrase(tags, nonViralName, addAppended);
|
|
589
|
return tags;
|
|
590
|
}
|
|
591
|
|
|
592
|
/**
|
|
593
|
* Returns the tag list for the first epithet (including a hybrid sign if required).
|
|
594
|
* @param nonViralName
|
|
595
|
* @return
|
|
596
|
*/
|
|
597
|
private List<TaggedText> getUninomialTaggedPart(INonViralName nonViralName) {
|
|
598
|
List<TaggedText> tags = new ArrayList<>();
|
|
599
|
|
|
600
|
if (nonViralName.isMonomHybrid()){
|
|
601
|
addHybridPrefix(tags);
|
|
602
|
}
|
|
603
|
|
|
604
|
String uninomial = CdmUtils.Nz(nonViralName.getGenusOrUninomial()).trim();
|
|
605
|
if (isNotBlank(uninomial)){
|
|
606
|
tags.add(new TaggedText(TagEnum.name, uninomial));
|
|
607
|
}
|
|
608
|
|
|
609
|
return tags;
|
|
610
|
}
|
|
611
|
|
|
612
|
/**
|
|
613
|
* Returns the tag list for an genus or higher taxon.
|
|
614
|
*
|
|
615
|
* @param nonViralName
|
|
616
|
* @return
|
|
617
|
*/
|
|
618
|
protected List<TaggedText> getGenusOrUninomialTaggedNameCache(INonViralName nonViralName, boolean addAppended){
|
|
619
|
List<TaggedText> tags = getUninomialTaggedPart(nonViralName);
|
|
620
|
addAppendedTaggedPhrase(tags, nonViralName, addAppended);
|
|
621
|
return tags;
|
|
622
|
}
|
|
623
|
|
|
624
|
/**
|
|
625
|
* Returns the tag list for an infrageneric taxon (including species aggregates).
|
|
626
|
*
|
|
627
|
* @see #getSpeciesAggregateTaggedCache(NonViralName)
|
|
628
|
* @param nonViralName
|
|
629
|
* @return
|
|
630
|
*/
|
|
631
|
protected List<TaggedText> getInfraGenusTaggedNameCache(INonViralName nonViralName, boolean addAppended){
|
|
632
|
Rank rank = nonViralName.getRank();
|
|
633
|
if (rank != null && rank.isSpeciesAggregate() && isBlank(nonViralName.getAuthorshipCache())){
|
|
634
|
return getSpeciesAggregateTaggedCache(nonViralName, addAppended);
|
|
635
|
}
|
|
636
|
|
|
637
|
//genus
|
|
638
|
List<TaggedText> tags = getUninomialTaggedPart(nonViralName);
|
|
639
|
|
|
640
|
//marker
|
|
641
|
String infraGenericMarker;
|
|
642
|
if (rank != null){
|
|
643
|
try {
|
|
644
|
infraGenericMarker = rank.getInfraGenericMarker();
|
|
645
|
if (rank.equals(Rank.SECTION_BOTANY()) || rank.equals(Rank.SUBSECTION_BOTANY())){
|
|
646
|
infraGenericMarker = infraGenericMarker.replace("(bot.)", "");
|
|
647
|
}
|
|
648
|
} catch (UnknownCdmTypeException e) {
|
|
649
|
infraGenericMarker = "'unhandled infrageneric rank'";
|
|
650
|
}
|
|
651
|
}else{
|
|
652
|
infraGenericMarker = "'undefined infrageneric rank'";
|
|
653
|
}
|
|
654
|
String infraGenEpi = CdmUtils.Nz(nonViralName.getInfraGenericEpithet()).trim();
|
|
655
|
if (nonViralName.isBinomHybrid()){
|
|
656
|
infraGenericMarker = CdmUtils.concat("", NOTHO, infraGenericMarker);
|
|
657
|
}
|
|
658
|
|
|
659
|
addInfraGenericPart(nonViralName, tags, infraGenericMarker, infraGenEpi);
|
|
660
|
|
|
661
|
addAppendedTaggedPhrase(tags, nonViralName, addAppended);
|
|
662
|
return tags;
|
|
663
|
}
|
|
664
|
|
|
665
|
|
|
666
|
/**
|
|
667
|
* Default implementation for the infrageneric part of a name.
|
|
668
|
* This is usually the infrageneric marker and the infrageneric epitheton. But may be
|
|
669
|
* implemented differently e.g. for zoological names the infrageneric epitheton
|
|
670
|
* may be surrounded by brackets and the marker left out.
|
|
671
|
* @param nonViralName
|
|
672
|
* @param tags
|
|
673
|
* @param infraGenericMarker
|
|
674
|
*/
|
|
675
|
protected void addInfraGenericPart(
|
|
676
|
@SuppressWarnings("unused") INonViralName name,
|
|
677
|
List<TaggedText> tags,
|
|
678
|
String infraGenericMarker,
|
|
679
|
String infraGenEpi) {
|
|
680
|
//add marker
|
|
681
|
tags.add(new TaggedText(TagEnum.rank, infraGenericMarker));
|
|
682
|
|
|
683
|
//add epitheton
|
|
684
|
if (isNotBlank(infraGenEpi)){
|
|
685
|
tags.add(new TaggedText(TagEnum.name, infraGenEpi));
|
|
686
|
}
|
|
687
|
}
|
|
688
|
|
|
689
|
/**
|
|
690
|
* Returns the tag list for a species aggregate (or similar) taxon.<BR>
|
|
691
|
* Possible ranks for a <i>species aggregate</i> are "aggr.", "species group", ...
|
|
692
|
* @param nonViralName
|
|
693
|
* @return
|
|
694
|
*/
|
|
695
|
protected List<TaggedText> getSpeciesAggregateTaggedCache(INonViralName nonViralName, boolean addAppended){
|
|
696
|
if (! isBlank(nonViralName.getAuthorshipCache())){
|
|
697
|
List<TaggedText> result = getSpeciesTaggedNameCache(nonViralName, addAppended);
|
|
698
|
return result;
|
|
699
|
}
|
|
700
|
|
|
701
|
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName);
|
|
702
|
|
|
703
|
addSpeciesAggregateTaggedEpithet(tags, nonViralName);
|
|
704
|
addAppendedTaggedPhrase(tags, nonViralName, addAppended);
|
|
705
|
return tags;
|
|
706
|
}
|
|
707
|
|
|
708
|
/**
|
|
709
|
* Adds the aggregate tag to the tag list.
|
|
710
|
*/
|
|
711
|
private void addSpeciesAggregateTaggedEpithet(List<TaggedText> tags, INonViralName nonViralName) {
|
|
712
|
String marker;
|
|
713
|
try {
|
|
714
|
marker = nonViralName.getRank().getInfraGenericMarker();
|
|
715
|
} catch (UnknownCdmTypeException e) {
|
|
716
|
marker = "'unknown aggregat type'";
|
|
717
|
}
|
|
718
|
if (isNotBlank(marker)){
|
|
719
|
tags.add(new TaggedText(TagEnum.rank, marker));
|
|
720
|
}
|
|
721
|
}
|
|
722
|
|
|
723
|
/**
|
|
724
|
* Returns the tag list for a species taxon.
|
|
725
|
*/
|
|
726
|
protected List<TaggedText> getSpeciesTaggedNameCache(INonViralName nonViralName, boolean addAppended){
|
|
727
|
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName);
|
|
728
|
addAppendedTaggedPhrase(tags, nonViralName, addAppended);
|
|
729
|
return tags;
|
|
730
|
}
|
|
731
|
|
|
732
|
protected List<TaggedText> getInfraSpeciesTaggedNameCache(TaxonName name){
|
|
733
|
if (name.getNameType().isZoological()){
|
|
734
|
boolean includeMarker = includeInfraSpecificMarkerForZooNames(name);
|
|
735
|
return getInfraSpeciesTaggedNameCache(name, includeMarker, true);
|
|
736
|
}else{
|
|
737
|
return getInfraSpeciesTaggedNameCache(name, true, true);
|
|
738
|
}
|
|
739
|
}
|
|
740
|
|
|
741
|
protected boolean includeInfraSpecificMarkerForZooNames(TaxonName name){
|
|
742
|
return ! (name.isAutonym()); //only exclude marker if autonym, see also ZooNameNoMarkerCacheStrategy
|
|
743
|
}
|
|
744
|
|
|
745
|
/**
|
|
746
|
* Creates the tag list for an infraspecific taxon. If include is true the result will contain
|
|
747
|
* the infraspecific marker (e.g. "var.")
|
|
748
|
* @param nonViralName
|
|
749
|
* @param includeMarker
|
|
750
|
* @return
|
|
751
|
*/
|
|
752
|
protected List<TaggedText> getInfraSpeciesTaggedNameCache(INonViralName nonViralName,
|
|
753
|
boolean includeMarker, boolean addAppended){
|
|
754
|
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName);
|
|
755
|
if (includeMarker || nonViralName.isTrinomHybrid()){
|
|
756
|
String rankAbbrev = nonViralName.getRank()==null? "" : CdmUtils.Nz(nonViralName.getRank().getAbbreviation()).trim();
|
|
757
|
String marker = rankAbbrev.replace("null", ""); //TODO really needed?
|
|
758
|
if (nonViralName.isTrinomHybrid()){
|
|
759
|
marker = CdmUtils.concat("", NOTHO, marker);
|
|
760
|
}
|
|
761
|
if (isNotBlank(marker)){
|
|
762
|
tags.add(new TaggedText(TagEnum.rank, marker));
|
|
763
|
}
|
|
764
|
|
|
765
|
}
|
|
766
|
String infrSpecEpi = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet());
|
|
767
|
|
|
768
|
infrSpecEpi = infrSpecEpi.trim().replace("null", "");
|
|
769
|
|
|
770
|
if (isNotBlank(infrSpecEpi)){
|
|
771
|
tags.add(new TaggedText(TagEnum.name, infrSpecEpi));
|
|
772
|
}
|
|
773
|
|
|
774
|
addAppendedTaggedPhrase(tags, nonViralName, addAppended);
|
|
775
|
return tags;
|
|
776
|
}
|
|
777
|
|
|
778
|
|
|
779
|
/**
|
|
780
|
* Adds a tag for the hybrid sign and an empty separator to avoid trailing whitespaces.
|
|
781
|
* @param tags
|
|
782
|
*/
|
|
783
|
private void addHybridPrefix(List<TaggedText> tags) {
|
|
784
|
tags.add(new TaggedText(TagEnum.hybridSign, NonViralNameParserImplRegExBase.hybridSign));
|
|
785
|
tags.add(new TaggedText(TagEnum.separator, "")); //no whitespace separator
|
|
786
|
}
|
|
787
|
|
|
788
|
/**
|
|
789
|
* Creates the tag list for the genus and species part.
|
|
790
|
* @param nonViralName
|
|
791
|
* @return
|
|
792
|
*/
|
|
793
|
private List<TaggedText> getGenusAndSpeciesTaggedPart(INonViralName nonViralName) {
|
|
794
|
//Uninomial
|
|
795
|
List<TaggedText> tags = getUninomialTaggedPart(nonViralName);
|
|
796
|
|
|
797
|
//InfraGenericEpi
|
|
798
|
boolean hasInfraGenericEpi = isNotBlank(nonViralName.getInfraGenericEpithet());
|
|
799
|
if (hasInfraGenericEpi){
|
|
800
|
String infrGenEpi = nonViralName.getInfraGenericEpithet().trim();
|
|
801
|
if (nonViralName.isBinomHybrid()){
|
|
802
|
//maybe not correct but not really expected to happen
|
|
803
|
infrGenEpi = UTF8.HYBRID + infrGenEpi;
|
|
804
|
}
|
|
805
|
infrGenEpi = "(" + infrGenEpi + ")";
|
|
806
|
tags.add(new TaggedText(TagEnum.name, infrGenEpi));
|
|
807
|
}
|
|
808
|
|
|
809
|
//Species Epi
|
|
810
|
String specEpi = CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim();
|
|
811
|
if (! hasInfraGenericEpi && nonViralName.isBinomHybrid() ||
|
|
812
|
hasInfraGenericEpi && nonViralName.isTrinomHybrid()){
|
|
813
|
addHybridPrefix(tags);
|
|
814
|
}
|
|
815
|
if (isNotBlank(specEpi)){
|
|
816
|
tags.add(new TaggedText(TagEnum.name, specEpi));
|
|
817
|
}
|
|
818
|
return tags;
|
|
819
|
}
|
|
820
|
|
|
821
|
/**
|
|
822
|
* Adds the tag for the appended phrase if an appended phrase exists
|
|
823
|
* @param tags
|
|
824
|
* @param nonViralName
|
|
825
|
* @param addAppended
|
|
826
|
*/
|
|
827
|
protected void addAppendedTaggedPhrase(List<TaggedText> tags, INonViralName nonViralName, boolean addAppended){
|
|
828
|
if (!addAppended){
|
|
829
|
return;
|
|
830
|
}
|
|
831
|
String appendedPhrase = nonViralName ==null ? null : nonViralName.getAppendedPhrase();
|
|
832
|
if (isNotBlank(appendedPhrase)){
|
|
833
|
tags.add(new TaggedText(TagEnum.name, appendedPhrase));
|
|
834
|
}
|
|
835
|
}
|
|
836
|
|
|
837
|
@Override
|
|
838
|
public String getLastEpithet(TaxonName taxonName) {
|
|
839
|
Rank rank = taxonName.getRank();
|
|
840
|
//TODO potential NPE / used?
|
|
841
|
if(rank.isGenus() || rank.isSupraGeneric()) {
|
|
842
|
return taxonName.getGenusOrUninomial();
|
|
843
|
} else if(rank.isInfraGeneric()) {
|
|
844
|
return taxonName.getInfraGenericEpithet();
|
|
845
|
} else if(rank.isSpecies()) {
|
|
846
|
return taxonName.getSpecificEpithet();
|
|
847
|
} else {
|
|
848
|
return taxonName.getInfraSpecificEpithet();
|
|
849
|
}
|
|
850
|
}
|
|
851
|
}
|