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/**
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* Copyright (C) 2017 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.io.Serializable;
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import java.util.Comparator;
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import java.util.HashSet;
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import java.util.Set;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonComparator;
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/**
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* This class orders synonyms of a homotypic group,
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* first by
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* <ul>
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* <li>Basionym groups (the basionym and all names derived from this basionym)
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* should be kept together in a subgroup</li>
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* <li>The order of the subgroups is defined by the ordering of their
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* basionyms (according to the following ordering)</li>
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* <li>If a name is illegitimate or not does play a role for ordering</li>
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* <li>Names with publication year should always come first</li>
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* <li>Names with no publication year are sorted by rank</li>
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* <li>Names with no publication year and equal rank are sorted alphabetically</li>
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* <li>If 2 names have a replaced synonym relationship the replaced synonym comes first,
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* the replacement name comes later as this reflects the order of publication</li>
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* </ul>
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*
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* Details on ordering are explained at http://dev.e-taxonomy.eu/trac/ticket/3338<BR>
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*
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* @author k.luther
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* @date 20.03.2017
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*
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*/
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public class HomotypicalGroupNameComparator implements Comparator<TaxonName>, Serializable{
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private static final Logger logger = Logger.getLogger(HomotypicalGroupNameComparator.class);
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private final TaxonName firstNameInGroup;
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private boolean includeRanks = false;
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/**
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* @param firstNameInGroup
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*/
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public HomotypicalGroupNameComparator(@SuppressWarnings("rawtypes") TaxonName firstNameInGroup, boolean includeRanks) {
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super();
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this.firstNameInGroup = firstNameInGroup;
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this.includeRanks = includeRanks;
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}
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/**
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*
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* @see TaxonComparator#compare(TaxonBase, TaxonBase)
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* @see java.lang.String#compareTo(String)
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* @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
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*/
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@Override
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public int compare(
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@SuppressWarnings("rawtypes") TaxonName taxonName1,
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@SuppressWarnings("rawtypes") TaxonName taxonName2) {
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if (logger.isDebugEnabled()){logger.debug(taxonName1.getTitleCache() +" : "+ taxonName2.getTitleCache());}
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int compareStatus = compareStatus(taxonName1, taxonName2);
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if (compareStatus != 0){
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return compareStatus;
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}
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//not same homotypical group -
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//NOTE: this comparator should usually not be used
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// for comparing names of different homotypical groups.
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// The following is only to have a defined compare behavior
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// which follows the contract of Comparator#compare.
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if (taxonName1 == null ||
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taxonName2 == null ||
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! taxonName1.getHomotypicalGroup().equals(taxonName2.getHomotypicalGroup())){
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String compareString1 =
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taxonName1.getHomotypicalGroup().getUuid().toString() ;
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String compareString2 =
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taxonName2.getHomotypicalGroup().getUuid().toString() ;
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int result = compareString1.compareTo(compareString2);
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return result;
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}
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//same homotypical group ...
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//one taxon is first in group
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if (taxonName1.equals(firstNameInGroup)){
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return -1;
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}else if (taxonName2.equals(firstNameInGroup)){
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return 1;
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}
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TaxonName basionym1 = getPreferredInBasionymGroup(taxonName1);
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TaxonName basionym2 = getPreferredInBasionymGroup(taxonName2);
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int compareResult;
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if (basionym1.equals(basionym2)){
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//both names belong to same basionym sub-group
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compareResult = handleSameBasionym(basionym1, taxonName1, taxonName2);
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}else{
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compareResult = compareBasionyms(basionym1, basionym2);
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}
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return compareResult;
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}
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/**
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* Compare 2 names which have the same basionym.
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* The names must not be equal to each other but may be equal
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* to the basionym.
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* @param basionym the basionym
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* @param name1 first name to compare
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* @param name2 second name to compare
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* @return compare value according to the {@link Comparator#compare(Object, Object)} contract.
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*/
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private int handleSameBasionym(TaxonName basionym,
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TaxonName name1,
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TaxonName name2) {
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if (basionym.equals(name1)){
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return -1;
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}else if (basionym.equals(name2)){
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return 1;
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}else{
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this.compare(name1, name2, false);
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}
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return 0;
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}
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/**
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* @param basionym1
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* @param basionym2
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* @return
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*/
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private int compareBasionyms(TaxonName basionym1Orig, TaxonName basionym2Orig) {
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//one taxon is first in group
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TaxonName basionym1 = getFirstNameInGroup(basionym1Orig);
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TaxonName basionym2 = getFirstNameInGroup(basionym2Orig);
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//handle accepted taxon case
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if (basionym1.equals(firstNameInGroup)){
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return -1;
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}else if (basionym2.equals(firstNameInGroup)){
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return 1;
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}
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//handle replaced synonyms
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boolean basio2IsReplacedSynForBasio1 = getReplacedSynonymClosure(basionym1).contains(basionym2);
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boolean basio1IsReplacedSynForBasio2 = getReplacedSynonymClosure(basionym2).contains(basionym1);
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if (basio2IsReplacedSynForBasio1 && !basio1IsReplacedSynForBasio2){
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return 1;
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}else if (basio1IsReplacedSynForBasio2 && !basio2IsReplacedSynForBasio1){
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return -1;
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}
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//compare by date, nom. illeg., rank and alphabetically
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return this.compare(basionym1, basionym2, false);
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}
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/**
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* @param basionym
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* @return
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*/
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private TaxonName getFirstNameInGroup(TaxonName basionym) {
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for (NameRelationship nameRel : basionym.getRelationsFromThisName()){
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if (nameRel.getType() != null && nameRel.getType().equals(NameRelationshipType.BASIONYM())){
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if (nameRel.getToName().equals(firstNameInGroup)){
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return firstNameInGroup;
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}
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}
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}
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return basionym;
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}
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/**
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* @param basionym1
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* @return
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*/
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@SuppressWarnings("rawtypes")
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private Set<TaxonName> getReplacedSynonymClosure(TaxonName name) {
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Set<TaxonName> set = name.getReplacedSynonyms();
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if (set.isEmpty()){
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return set;
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}
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Set<TaxonName> result = new HashSet<TaxonName>();
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for (TaxonName replSyn : set){
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boolean notYetContained = result.add(replSyn);
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if (notYetContained){
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result.addAll(replSyn.getReplacedSynonyms());
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}
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}
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return result;
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}
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/**
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* @param name
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* @return
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*/
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private TaxonName getPreferredInBasionymGroup(TaxonName name) {
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Set<TaxonName> candidates = new HashSet<>();
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//get all final basionyms, except for those being part of a basionym circle
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for (TaxonName candidate : name.getBasionyms()){
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if (candidate != null
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&& candidate.getHomotypicalGroup().equals(name.getHomotypicalGroup())
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&& !hasBasionymCircle(candidate, null)){
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candidate = getPreferredInBasionymGroup(candidate);
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candidates.add(candidate);
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}
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}
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if (candidates.isEmpty()){
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return name;
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}else if (candidates.size() == 1){
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return candidates.iterator().next();
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}else{
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TaxonName result = candidates.iterator().next();
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candidates.remove(result);
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for(TaxonName candidate : candidates){
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if (this.compare(result, candidate) > 0){
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result = candidate;
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}
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}
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return result;
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}
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}
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/**
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* @param candidate
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* @return
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*/
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private boolean hasBasionymCircle(TaxonName name, Set<TaxonName> existing) {
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if (existing == null){
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existing = new HashSet<>();
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}
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if (existing.contains(name)){
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return true;
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}else{
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Set<TaxonName> basionyms = name.getBasionyms();
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if (basionyms.isEmpty()){
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return false;
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}
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existing.add(name);
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for (TaxonName basionym : basionyms){
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if (hasBasionymCircle(basionym, existing)){
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return true;
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}
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}
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return false;
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}
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}
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// /**
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// * @param homotypicalGroup
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// * @return
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// */
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// private TaxonBase<?> getFirstInHomotypicalGroup(HomotypicalGroup homotypicalGroup, Collection<TaxonBase<?>> existing) {
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// List<TaxonBase<?>> candidates = new ArrayList<TaxonBase<?>>();
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// for (TaxonBase<?> candidate : existing){
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// if (homotypicalGroup.getTypifiedNames().contains(candidate.getName())){
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// candidates.add(candidate);
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// }
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// }
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// Collections.sort(candidates, this);
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// return candidates.isEmpty() ? null : candidates.get(0);
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// }
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/**
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* @param taxonName
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* @param taxonName2
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* @param statusCompareWeight
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* @return
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*/
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protected int compareStatus(TaxonName taxonName, TaxonName taxonName2) {
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int statusCompareWeight = 0;
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statusCompareWeight += computeStatusCompareWeight(taxonName);
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statusCompareWeight -= computeStatusCompareWeight(taxonName2);
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return statusCompareWeight;
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}
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/**
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* @param taxonBase1
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* @param statusCompareWeight
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* @return
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*/
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private int computeStatusCompareWeight(TaxonName taxonName) {
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int result = 0;
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if (taxonName == null || taxonName.getStatus() == null){
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return 0;
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}
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Set<NomenclaturalStatus> status1 = taxonName.getStatus();
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for (NomenclaturalStatus nomStatus1 : status1){
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NomenclaturalStatusType type = nomStatus1.getType();
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if (type != null && type.isInvalidType()){
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if(type.equals(NomenclaturalStatusType.PROVISIONAL())){
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result += 1;
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}else if (type.equals(NomenclaturalStatusType.INVALID())){
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result += 2;
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}else if(type.equals(NomenclaturalStatusType.COMBINATION_INVALID())){
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result += 2;
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}else if (type.equals(NomenclaturalStatusType.OPUS_UTIQUE_OPPR())){
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result += 2;
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}else if(type.equals(NomenclaturalStatusType.NUDUM())){
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result += 3;
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}
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result += 1;
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}
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}
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return result;
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}
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/**
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*
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* @param name1
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* @param name2
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* @param includeNomIlleg if true and if both names have no date or same date, the only
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* name having nom. illeg. state is handled as if the name was published later than the name
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* without status nom. illeg.
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* @return
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*/
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protected int compare(TaxonName name1, TaxonName name2, boolean includeNomIlleg) {
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int result;
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//dates
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Integer intDate1 = getIntegerDate(name1);
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Integer intDate2 = getIntegerDate(name2);
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if (intDate1 == null && intDate2 == null){
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result = 0;
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}else if (intDate1 == null){
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return 1;
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}else if (intDate2 == null){
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return -1;
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}else{
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result = intDate1.compareTo(intDate2);
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}
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//nom. illeg.
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if (result == 0 && includeNomIlleg){
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result = compareNomIlleg(name1, name2);
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if (result != 0){
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return result;
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}
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}
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if (result == 0 && includeRanks){
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Rank rank1 = name1 == null? null : name1.getRank();
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Rank rank2 = name2 == null? null : name2.getRank();
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if (rank1 == null && rank2 == null){
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result = 0;
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}else if (rank1 == null){
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return 1;
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}else if (rank2 == null){
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return -1;
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}else{
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//for some strange reason compareTo for ranks returns 1 if rank2 is lower. So we add minus (-)
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result = - rank1.compareTo(rank2);
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}
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}
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if (result == 0 && name1 != null && name2 != null){
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|
result = name1.compareToName(name2);
|
|
382
|
if (result != 0){
|
|
383
|
return result;
|
|
384
|
}
|
|
385
|
}
|
|
386
|
return result;
|
|
387
|
}
|
|
388
|
|
|
389
|
private Integer getIntegerDate(TaxonName name){
|
|
390
|
Integer result;
|
|
391
|
|
|
392
|
if (name == null){
|
|
393
|
result = null;
|
|
394
|
}else{
|
|
395
|
if (name.isZoological()){
|
|
396
|
result = name.getPublicationYear();
|
|
397
|
}else{
|
|
398
|
Reference ref = (Reference) name.getNomenclaturalReference();
|
|
399
|
if (ref == null){
|
|
400
|
result = null;
|
|
401
|
}else{
|
|
402
|
if (ref.getDatePublished() == null){
|
|
403
|
Reference inRef = ref.getInReference();
|
|
404
|
if (inRef == null){
|
|
405
|
result = null;
|
|
406
|
}else{
|
|
407
|
if (inRef.getDatePublished() == null){
|
|
408
|
result = null;
|
|
409
|
}else{
|
|
410
|
result = ref.getInReference().getDatePublished().getStartYear();
|
|
411
|
}
|
|
412
|
}
|
|
413
|
}else{
|
|
414
|
result = ref.getDatePublished().getStartYear();
|
|
415
|
}
|
|
416
|
}
|
|
417
|
}
|
|
418
|
}
|
|
419
|
|
|
420
|
return result;
|
|
421
|
}
|
|
422
|
|
|
423
|
protected int compareNomIlleg(TaxonName taxonName1, TaxonName taxonName2) {
|
|
424
|
int isNomIlleg1 = isNomIlleg(taxonName1);
|
|
425
|
int isNomIlleg2 = isNomIlleg(taxonName2);
|
|
426
|
return isNomIlleg1 - isNomIlleg2;
|
|
427
|
}
|
|
428
|
|
|
429
|
private int isNomIlleg(TaxonName taxonName) {
|
|
430
|
if (taxonName == null || taxonName.getStatus() == null){
|
|
431
|
return 0;
|
|
432
|
}
|
|
433
|
Set<NomenclaturalStatus> status = taxonName.getStatus();
|
|
434
|
for (NomenclaturalStatus nomStatus : status){
|
|
435
|
if (nomStatus.getType() != null){
|
|
436
|
if (nomStatus.getType().equals(NomenclaturalStatusType.ILLEGITIMATE())){
|
|
437
|
return 1;
|
|
438
|
}
|
|
439
|
}
|
|
440
|
}
|
|
441
|
return 0;
|
|
442
|
}
|
|
443
|
|
|
444
|
}
|