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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.model.taxon;
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import java.io.Serializable;
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import java.util.Comparator;
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import java.util.Set;
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import org.apache.log4j.Logger;
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import org.joda.time.DateTime;
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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.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.ZoologicalName;
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import eu.etaxonomy.cdm.model.reference.Reference;
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/**
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* This class makes available a method to compare two {@link TaxonBase taxa} by
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* comparing the publication dates of the corresponding
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* {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon names}.
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*
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* @author a.mueller
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* @created 11.06.2008
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*/
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public class TaxonComparator implements Comparator<TaxonBase>, Serializable {
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private static final long serialVersionUID = -1433623743189043446L;
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(TaxonComparator.class);
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private boolean includeRanks = false;
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/**
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* @param includeRanks
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*/
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public TaxonComparator() {
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super();
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}
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/**
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* @param includeRanks
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*/
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public TaxonComparator(boolean includeRanks) {
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super();
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this.includeRanks = includeRanks;
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}
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/**
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* Returns an integer generated by comparing first the nomenclatural status and then the
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* {@link eu.etaxonomy.cdm.model.name.INomenclaturalReference#getYear() publication years}
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* of both {@link eu.etaxonomy.cdm.model.name.TaxonNameBase taxon names}
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* used in the given {@link TaxonBase taxa}.
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* If 1 name has status of type nom. inval. or nom. nudum the name is put to the end of a
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* list (returns +1 for a status in taxon1 and -1 for a status in taxon2). If both do have
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* no status or the same status, the publication date is taken for comparison.
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* Nom. nudum is handled as more "severe" status then nom.inval.
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*
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* Returns a negative value if the publication year corresponding to the
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* first given taxon precedes the publication year corresponding to the
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* second given taxon. Returns a positive value if the contrary is true and
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* 0 if both publication years and the date, when they are created, are identical.
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* In case one of the publication
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* years is "null" and the other is not, the "empty" publication year will
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* be considered to be always preceded by the "not null" publication year.
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* If both publication years are "null" the creation date is used for the comparison
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*
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*
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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") TaxonBase taxonBase1,
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@SuppressWarnings("rawtypes") TaxonBase taxonBase2) {
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int result;
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if (taxonBase1.equals(taxonBase2)){
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return 0;
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}
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TaxonNameBase<?,?> name1 = taxonBase1.getName();
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TaxonNameBase<?,?> name2 = taxonBase2.getName();
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//set to end if a taxon has nomenclatural status "nom. inval." or "nom. nud."
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int statusCompareWeight = compareStatus(name1, name2);
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if (statusCompareWeight != 0){
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return Integer.signum(statusCompareWeight);
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}
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//TODO discuss if we should also include nom. illeg. here on taxon level comparison
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result = compare(name1, name2, false);
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if (result == 0){
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DateTime date11 = taxonBase1.getCreated();
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DateTime date12 = taxonBase2.getCreated();
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if (date11 == null && date12 == null) {
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result = 0;
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}else if (date11 == null) {
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return 1;
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}else if (date12 == null) {
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return -1;
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}else{
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result = date11.compareTo(date12);
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}
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}
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if (result == 0){
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//the Comparator contract
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return taxonBase1.getUuid().compareTo(taxonBase1.getUuid());
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}else{
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return result;
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}
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}
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/**
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* @param taxonNameBase
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* @param taxonNameBase2
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* @param statusCompareWeight
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* @return
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*/
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protected int compareStatus(TaxonNameBase<?,?> taxonNameBase, TaxonNameBase<?,?> taxonNameBase2) {
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int statusCompareWeight = 0;
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statusCompareWeight += computeStatusCompareWeight(taxonNameBase);
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statusCompareWeight -= computeStatusCompareWeight(taxonNameBase2);
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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(TaxonNameBase<?,?> taxonNameBase) {
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int result = 0;
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if (taxonNameBase == null || taxonNameBase.getStatus() == null){
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return 0;
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}
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Set<NomenclaturalStatus> status1 = taxonNameBase.getStatus();
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for (NomenclaturalStatus nomStatus1 : status1){
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if (nomStatus1.getType() != null){
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if (nomStatus1.getType().equals(NomenclaturalStatusType.INVALID())){
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result += 1;
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}else if(nomStatus1.getType().equals(NomenclaturalStatusType.NUDUM())){
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result += 2;
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}
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}
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}
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return result;
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}
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protected int compareNomIlleg(TaxonNameBase<?,?> taxonNameBase1, TaxonNameBase<?,?> taxonNameBase2) {
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int isNomIlleg1 = isNomIlleg(taxonNameBase1);
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int isNomIlleg2 = isNomIlleg(taxonNameBase2);
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return isNomIlleg1 - isNomIlleg2;
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}
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private int isNomIlleg(TaxonNameBase<?,?> taxonNameBase) {
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if (taxonNameBase == null || taxonNameBase.getStatus() == null){
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return 0;
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}
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Set<NomenclaturalStatus> status = taxonNameBase.getStatus();
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for (NomenclaturalStatus nomStatus : status){
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if (nomStatus.getType() != null){
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if (nomStatus.getType().equals(NomenclaturalStatusType.ILLEGITIMATE())){
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return 1;
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}
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}
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}
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return 0;
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}
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private Integer getIntegerDate(TaxonNameBase<?,?> name){
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Integer result;
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if (name == null){
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result = null;
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}else{
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if (name instanceof ZoologicalName){
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result = (((ZoologicalName)name).getPublicationYear());
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}else{
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Reference<?> ref = (Reference<?>) name.getNomenclaturalReference();
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if (ref == null){
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result = null;
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}else{
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if (ref.getDatePublished() == null){
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Reference<?> inRef = ref.getInReference();
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if (inRef == null){
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result = null;
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}else{
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if (inRef.getDatePublished() == null){
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result = null;
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}else{
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result = ref.getInReference().getDatePublished().getStartYear();
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}
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}
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}else{
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result = ref.getDatePublished().getStartYear();
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}
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}
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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(TaxonNameBase<?,?> name1, TaxonNameBase<?,?> 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.compareTo(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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return result;
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}
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}
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