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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.Iterator;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.Representation;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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/**
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* This class is a default implementation for the INonViralNameCacheStrategy<T extends NonViralName> interface.
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* The method actually 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 BotanicNameCacheStrategy other subclasses should overwrite the existing methods
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* 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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/**
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* @author AM
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*
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* @param <T>
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*/
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public class NonViralNameDefaultCacheStrategy<T extends NonViralName> extends NameCacheStrategyBase<T> implements INonViralNameCacheStrategy<T> {
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private static final Logger logger = Logger.getLogger(NonViralNameDefaultCacheStrategy.class);
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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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protected CharSequence BasionymAuthorCombinationAuthorSeperator = " ";
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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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/**
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* Factory method
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* @return NonViralNameDefaultCacheStrategy A new instance of NonViralNameDefaultCacheStrategy
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*/
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public static NonViralNameDefaultCacheStrategy NewInstance(){
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return new NonViralNameDefaultCacheStrategy();
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}
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/**
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* Constructor
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*/
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protected NonViralNameDefaultCacheStrategy(){
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super();
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}
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/* **************** GETTER / SETTER **************************************/
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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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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 NonViralNameDefaultCacheStrategy#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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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 NonViralNameDefaultCacheStrategy#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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BasionymEnd = basionymEnd;
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}
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/**
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* String to seperate ex author from author.
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* @return
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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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ExAuthorSeperator = exAuthorSeperator;
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}
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/**
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* String that seperates the basionym/original_combination author part from the combination author part
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* @return
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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(
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CharSequence basionymAuthorCombinationAuthorSeperator) {
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BasionymAuthorCombinationAuthorSeperator = basionymAuthorCombinationAuthorSeperator;
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}
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//** *****************************************************************************************/
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.strategy.INameCacheStrategy#getNameCache()
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*/
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@Override
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public String getTitleCache(T nonViralName) {
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if (nonViralName == null){
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return null;
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}
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if (nonViralName.isProtectedTitleCache()){
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return nonViralName.getTitleCache();
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}
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String result = "";
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//Autonym
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if (isAutonym(nonViralName)){
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String speciesPart = getSpeciesNameCache(nonViralName);
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//TODO should this include basionym authors and ex authors
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INomenclaturalAuthor author = nonViralName.getCombinationAuthorTeam();
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String authorPart = "";
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if (author != null){
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authorPart = CdmUtils.Nz(author.getNomenclaturalTitle());
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}
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INomenclaturalAuthor basAuthor = nonViralName.getBasionymAuthorTeam();
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String basAuthorPart = "";
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if (basAuthor != null){
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basAuthorPart = CdmUtils.Nz(basAuthor.getNomenclaturalTitle());
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}
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if (! "".equals(basAuthorPart)){
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authorPart = "("+ basAuthorPart +")" + authorPart;
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}
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String infraSpeciesPart = (CdmUtils.Nz(nonViralName.getInfraSpecificEpithet()));
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String infraSpeciesSeparator = "";
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if (nonViralName.getRank() == null || !nonViralName.getRank().isInfraSpecific()){
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//TODO handle exception
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logger.warn("Rank for autonym does not exist or is not lower than species !!");
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}else{
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infraSpeciesSeparator = nonViralName.getRank().getAbbreviation();
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}
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result = CdmUtils.concat(" ", new String[]{speciesPart, authorPart, infraSpeciesSeparator, infraSpeciesPart});
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result = result.trim().replace("null", "");
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}else{ //not Autonym
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String nameCache = nonViralName.getNameCache(); //OLD: CdmUtils.Nz(getNameCache(nonViralName));
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if (nameIncludesAuthorship(nonViralName)){
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String authorCache = CdmUtils.Nz(getAuthorshipCache(nonViralName));
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result = CdmUtils.concat(NameAuthorSeperator, nameCache, authorCache);
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}else{
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result = nameCache;
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}
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}
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return result;
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}
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protected boolean nameIncludesAuthorship(NonViralName 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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@Override
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public String getFullTitleCache(T nonViralName) {
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//null
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if (nonViralName == null){
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return null;
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}
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//full title cache
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if (nonViralName.isProtectedFullTitleCache() == true) {
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return nonViralName.getFullTitleCache();
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}
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String result = "";
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//title cache
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String titleCache = nonViralName.getTitleCache(); // OLD: getTitleCache(nonViralName);
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String microReference = nonViralName.getNomenclaturalMicroReference();
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INomenclaturalReference ref = nonViralName.getNomenclaturalReference();
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String referenceBaseCache = null;
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if (ref != null){
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INomenclaturalReference nomenclaturalReference = HibernateProxyHelper.deproxy(ref, INomenclaturalReference.class);
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nomenclaturalReference.setCacheStrategy(nomenclaturalReference.getType().getCacheStrategy());
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referenceBaseCache = nomenclaturalReference.getNomenclaturalCitation(microReference);
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}
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//make nomenclatural status
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String ncStatusCache = "";
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Set<NomenclaturalStatus> ncStati = nonViralName.getStatus();
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Iterator<NomenclaturalStatus> iterator = ncStati.iterator();
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while (iterator.hasNext()) {
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NomenclaturalStatus ncStatus = (NomenclaturalStatus)iterator.next();
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// since the NewInstance method of nomencatural status allows null as parameter
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// we have to check for null values here
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String suffix = "not defined";
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if(ncStatus.getType() != null){
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NomenclaturalStatusType statusType = ncStatus.getType();
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Language lang = Language.LATIN();
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Representation repr = statusType.getRepresentation(lang);
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if (repr != null){
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suffix = repr.getAbbreviatedLabel();
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}else{
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String message = "No latin representation available for nom. status. " + statusType.getTitleCache();
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logger.warn(message);
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throw new IllegalStateException(message);
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}
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}else if(ncStatus.getRuleConsidered() != null && ! ncStatus.getRuleConsidered().equals("")){
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suffix = ncStatus.getRuleConsidered();
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}
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ncStatusCache = ", " + suffix;
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}
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String refConcat = " ";
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if (referenceBaseCache != null && ! referenceBaseCache.trim().startsWith("in ")){
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refConcat = ", ";
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}
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result = CdmUtils.concat(refConcat, titleCache, referenceBaseCache);
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result = CdmUtils.concat("", result, ncStatusCache);
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return result;
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}
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/**
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* Generates and returns the "name cache" (only scientific name without author teams and year).
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* @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy#getNameCache(eu.etaxonomy.cdm.model.name.TaxonNameBase)
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*/
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public String getNameCache(T 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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Rank rank = nonViralName.getRank();
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if (nonViralName.isProtectedNameCache()){
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result = nonViralName.getNameCache();
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}else if (rank == null){
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result = getRanklessNameCache(nonViralName);
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}else if (rank.isInfraSpecific()){
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result = getInfraSpeciesNameCache(nonViralName);
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}else if (rank.isSpecies()){
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result = getSpeciesNameCache(nonViralName);
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}else if (rank.isInfraGeneric()){
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result = getInfraGenusNameCache(nonViralName);
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}else if (rank.isGenus()){
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result = getGenusOrUninomialNameCache(nonViralName);
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}else if (rank.isSupraGeneric()){
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result = getGenusOrUninomialNameCache(nonViralName);
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}else{
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logger.warn("Name Strategy for Name (UUID: " + nonViralName.getUuid() + ") not yet implemented");
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result = "";
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}
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return result;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy#getAuthorCache(eu.etaxonomy.cdm.model.name.NonViralName)
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*/
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public String getAuthorshipCache(T nonViralName) {
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if (nonViralName == null){
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return null;
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}
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//cache protected
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if (nonViralName.isProtectedAuthorshipCache() == true) {
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return nonViralName.getAuthorshipCache();
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}
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return getNonCacheAuthorshipCache(nonViralName);
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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 authorshipfield.
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* @throws NullPointerException if nonViralName is null.
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* @param nonViralName
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* @return
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*/
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protected String getNonCacheAuthorshipCache(T nonViralName){
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String result = "";
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INomenclaturalAuthor combinationAuthor = nonViralName.getCombinationAuthorTeam();
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INomenclaturalAuthor exCombinationAuthor = nonViralName.getExCombinationAuthorTeam();
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INomenclaturalAuthor basionymAuthor = nonViralName.getBasionymAuthorTeam();
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INomenclaturalAuthor exBasionymAuthor = nonViralName.getExBasionymAuthorTeam();
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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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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 combination authors
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* as well as on basionym/orginal combination authors.
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* @param author the author
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* @param exAuthor the ex-author
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* @return
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*/
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protected String getAuthorAndExAuthor(INomenclaturalAuthor author, INomenclaturalAuthor exAuthor){
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String result = "";
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String authorString = "";
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String exAuthorString = "";
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if (author != null){
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authorString = CdmUtils.Nz(author.getNomenclaturalTitle());
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}
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if (exAuthor != null){
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370
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exAuthorString = CdmUtils.Nz(exAuthor.getNomenclaturalTitle());
|
|
371
|
}
|
|
372
|
if (exAuthorString.length() > 0 ){
|
|
373
|
exAuthorString = exAuthorString + ExAuthorSeperator;
|
|
374
|
}
|
|
375
|
result = exAuthorString + authorString;
|
|
376
|
return result;
|
|
377
|
|
|
378
|
}
|
|
379
|
|
|
380
|
|
|
381
|
/* (non-Javadoc)
|
|
382
|
* @see eu.etaxonomy.cdm.strategy.INameCacheStrategy#getTaggedName(eu.etaxonomy.cdm.model.common.CdmBase)
|
|
383
|
*/
|
|
384
|
@Override
|
|
385
|
public List<Object> getTaggedName(T nonViralName) {
|
|
386
|
List<Object> tags = new ArrayList<Object>();
|
|
387
|
if (nonViralName.getGenusOrUninomial() == null){
|
|
388
|
tags.add(nonViralName.getNameCache());
|
|
389
|
}else{
|
|
390
|
tags.add(nonViralName.getGenusOrUninomial());
|
|
391
|
}
|
|
392
|
if (nonViralName.isSpecies() || nonViralName.isInfraSpecific()){
|
|
393
|
tags.add(nonViralName.getSpecificEpithet());
|
|
394
|
}
|
|
395
|
|
|
396
|
// No autonym
|
|
397
|
if (nonViralName.isInfraSpecific() && ! nonViralName.getSpecificEpithet().equals(nonViralName.getInfraSpecificEpithet())){
|
|
398
|
tags.add(nonViralName.getRank());
|
|
399
|
tags.add(nonViralName.getInfraSpecificEpithet());
|
|
400
|
}
|
|
401
|
|
|
402
|
if (nonViralName.isInfraGeneric()){
|
|
403
|
//TODO choose right strategy or generic approach?
|
|
404
|
// --- strategy 1 ---
|
|
405
|
|
|
406
|
if (nonViralName.getRank().isSpeciesAggregate()){
|
|
407
|
tags.add(getSpeciesAggregateEpithet(nonViralName));
|
|
408
|
}else{
|
|
409
|
tags.add(nonViralName.getRank());
|
|
410
|
tags.add(nonViralName.getInfraGenericEpithet());
|
|
411
|
}
|
|
412
|
// --- strategy 2 ---
|
|
413
|
// tags.add('('+nvn.getInfraGenericEpithet()+')');
|
|
414
|
}
|
|
415
|
Team authorTeam = Team.NewInstance();
|
|
416
|
authorTeam.setProtectedTitleCache(true);
|
|
417
|
authorTeam.setTitleCache(nonViralName.getAuthorshipCache(), true);
|
|
418
|
tags.add(authorTeam);
|
|
419
|
|
|
420
|
// Name is an autonym. Rank and infraspecific eitheton follow the author
|
|
421
|
if (nonViralName.isInfraSpecific() && nonViralName.getSpecificEpithet().equals(nonViralName.getInfraSpecificEpithet())){
|
|
422
|
tags.add(nonViralName.getRank());
|
|
423
|
tags.add(nonViralName.getInfraSpecificEpithet());
|
|
424
|
}
|
|
425
|
|
|
426
|
if(! "".equals(nonViralName.getAppendedPhrase())&& (nonViralName.getAppendedPhrase() != null)){
|
|
427
|
tags.add(nonViralName.getAppendedPhrase());
|
|
428
|
}
|
|
429
|
|
|
430
|
return tags;
|
|
431
|
}
|
|
432
|
|
|
433
|
|
|
434
|
//***************************** PRIVATES ***************************************/
|
|
435
|
|
|
436
|
protected String getRanklessNameCache(NonViralName nonViralName){
|
|
437
|
String result = "";
|
|
438
|
result = (result + (nonViralName.getGenusOrUninomial())).trim().replace("null", "");
|
|
439
|
result += " " + (CdmUtils.Nz(nonViralName.getSpecificEpithet())).trim();
|
|
440
|
result += " " + (CdmUtils.Nz(nonViralName.getInfraSpecificEpithet())).trim();
|
|
441
|
result = result.trim().replace("null", "");
|
|
442
|
//result += " (rankless)";
|
|
443
|
result = addAppendedPhrase(result, nonViralName);
|
|
444
|
return result;
|
|
445
|
}
|
|
446
|
|
|
447
|
|
|
448
|
protected String getGenusOrUninomialNameCache(NonViralName nonViralName){
|
|
449
|
String result;
|
|
450
|
result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
|
|
451
|
result = addAppendedPhrase(result, nonViralName).trim();
|
|
452
|
return result;
|
|
453
|
}
|
|
454
|
|
|
455
|
protected String getInfraGenusNameCache(NonViralName nonViralName){
|
|
456
|
String result;
|
|
457
|
Rank rank = nonViralName.getRank();
|
|
458
|
if (rank.isSpeciesAggregate()){
|
|
459
|
return getSpeciesAggregateCache(nonViralName);
|
|
460
|
}
|
|
461
|
String infraGenericMarker = "'unhandled infrageneric rank'";
|
|
462
|
if (rank != null){
|
|
463
|
try {
|
|
464
|
infraGenericMarker = rank.getInfraGenericMarker();
|
|
465
|
} catch (UnknownCdmTypeException e) {
|
|
466
|
infraGenericMarker = "'unhandled infrageneric rank'";
|
|
467
|
}
|
|
468
|
}
|
|
469
|
result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
|
|
470
|
result += " " + infraGenericMarker + " " + (CdmUtils.Nz(nonViralName.getInfraGenericEpithet())).trim().replace("null", "");
|
|
471
|
result = addAppendedPhrase(result, nonViralName).trim();
|
|
472
|
return result;
|
|
473
|
}
|
|
474
|
|
|
475
|
// aggr.|agg.|group
|
|
476
|
protected String getSpeciesAggregateCache(NonViralName nonViralName){
|
|
477
|
String result;
|
|
478
|
result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
|
|
479
|
|
|
480
|
result += " "+getSpeciesAggregateEpithet(nonViralName);
|
|
481
|
/*result += " " + CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim().replace("null", "");
|
|
482
|
String marker;
|
|
483
|
try {
|
|
484
|
marker = nonViralName.getRank().getInfraGenericMarker();
|
|
485
|
} catch (UnknownCdmTypeException e) {
|
|
486
|
marker = "'unknown aggregat type'";
|
|
487
|
}
|
|
488
|
result += " " + marker;*/
|
|
489
|
result = addAppendedPhrase(result, nonViralName).trim();
|
|
490
|
return result;
|
|
491
|
}
|
|
492
|
|
|
493
|
private String getSpeciesAggregateEpithet(NonViralName nonViralName) {
|
|
494
|
String result;
|
|
495
|
|
|
496
|
result = CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim().replace("null", "");
|
|
497
|
String marker;
|
|
498
|
try {
|
|
499
|
marker = nonViralName.getRank().getInfraGenericMarker();
|
|
500
|
} catch (UnknownCdmTypeException e) {
|
|
501
|
marker = "'unknown aggregat type'";
|
|
502
|
}
|
|
503
|
result += " " + marker;
|
|
504
|
|
|
505
|
return result;
|
|
506
|
}
|
|
507
|
|
|
508
|
protected String getSpeciesNameCache(NonViralName nonViralName){
|
|
509
|
String result;
|
|
510
|
result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
|
|
511
|
result += " " + CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim().replace("null", "");
|
|
512
|
result = addAppendedPhrase(result, nonViralName).trim();
|
|
513
|
result = result.replace("\\s\\", " ");
|
|
514
|
return result;
|
|
515
|
}
|
|
516
|
|
|
517
|
|
|
518
|
protected String getInfraSpeciesNameCache(NonViralName nonViralName){
|
|
519
|
return getInfraSpeciesNameCache(nonViralName, true);
|
|
520
|
}
|
|
521
|
|
|
522
|
protected String getInfraSpeciesNameCache(NonViralName nonViralName, boolean includeMarker){
|
|
523
|
String result;
|
|
524
|
result = CdmUtils.Nz(nonViralName.getGenusOrUninomial());
|
|
525
|
result += " " + (CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim()).replace("null", "");
|
|
526
|
if (includeMarker){
|
|
527
|
result += " " + (nonViralName.getRank().getAbbreviation()).trim().replace("null", "");
|
|
528
|
}
|
|
529
|
result += " " + (CdmUtils.Nz(nonViralName.getInfraSpecificEpithet())).trim().replace("null", "");
|
|
530
|
result = addAppendedPhrase(result, nonViralName).trim();
|
|
531
|
return result;
|
|
532
|
}
|
|
533
|
|
|
534
|
|
|
535
|
|
|
536
|
/**
|
|
537
|
* @param name
|
|
538
|
* @return true, if name has Rank, Rank is below species and species epithet equals infraSpeciesEpithtet, else false
|
|
539
|
*/
|
|
540
|
protected boolean isAutonym(NonViralName nonViralName){
|
|
541
|
if (nonViralName != null && nonViralName.getRank() != null && nonViralName.getSpecificEpithet() != null && nonViralName.getInfraSpecificEpithet() != null &&
|
|
542
|
nonViralName.getRank().isInfraSpecific() && nonViralName.getSpecificEpithet().trim().equals(nonViralName.getInfraSpecificEpithet().trim())){
|
|
543
|
return true;
|
|
544
|
}else{
|
|
545
|
return false;
|
|
546
|
}
|
|
547
|
}
|
|
548
|
|
|
549
|
protected String addAppendedPhrase(String resultString, NonViralName nonViralName){
|
|
550
|
String appendedPhrase = nonViralName ==null ? null : nonViralName.getAppendedPhrase();
|
|
551
|
if (resultString == null){
|
|
552
|
return appendedPhrase;
|
|
553
|
}else if(appendedPhrase == null || "".equals(appendedPhrase.trim())) {
|
|
554
|
return resultString;
|
|
555
|
}else if ("".equals(resultString)){
|
|
556
|
return resultString + appendedPhrase;
|
|
557
|
}else {
|
|
558
|
return resultString + " " + appendedPhrase;
|
|
559
|
}
|
|
560
|
}
|
|
561
|
|
|
562
|
|
|
563
|
public String getLastEpithet(T taxonNameBase) {
|
|
564
|
Rank rank = taxonNameBase.getRank();
|
|
565
|
if(rank.isGenus() || rank.isSupraGeneric()) {
|
|
566
|
return taxonNameBase.getGenusOrUninomial();
|
|
567
|
} else if(rank.isInfraGeneric()) {
|
|
568
|
return taxonNameBase.getInfraGenericEpithet();
|
|
569
|
} else if(rank.isSpecies()) {
|
|
570
|
return taxonNameBase.getSpecificEpithet();
|
|
571
|
} else {
|
|
572
|
return taxonNameBase.getInfraSpecificEpithet();
|
|
573
|
}
|
|
574
|
}
|
|
575
|
}
|