import java.io.Serializable;
import java.util.Comparator;
-import java.util.HashSet;
-import java.util.Set;
import org.apache.log4j.Logger;
-import eu.etaxonomy.cdm.compare.taxon.TaxonComparator;
-import eu.etaxonomy.cdm.model.name.NameRelationship;
-import eu.etaxonomy.cdm.model.name.NameRelationshipType;
-import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
-import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
-import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.compare.taxon.HomotypicGroupTaxonComparator;
import eu.etaxonomy.cdm.model.name.TaxonName;
-import eu.etaxonomy.cdm.model.reference.Reference;
-import eu.etaxonomy.cdm.model.taxon.TaxonBase;
/**
* This class orders synonyms of a homotypic group,
*/
public class HomotypicalGroupNameComparator implements Comparator<TaxonName>, Serializable{
+ private static final long serialVersionUID = 2306033011970230866L;
+ @SuppressWarnings("unused")
private static final Logger logger = Logger.getLogger(HomotypicalGroupNameComparator.class);
+ private HomotypicGroupTaxonComparator taxonComparator;
- private final TaxonName firstNameInGroup;
- private boolean includeRanks = false;
+ public HomotypicalGroupNameComparator(TaxonName firstNameInGroup, boolean includeRanks) {
+ taxonComparator = new HomotypicGroupTaxonComparator(firstNameInGroup, includeRanks);
+ }
- /**
- * @param firstNameInGroup
- */
- public HomotypicalGroupNameComparator(@SuppressWarnings("rawtypes") TaxonName firstNameInGroup, boolean includeRanks) {
- super();
- this.firstNameInGroup = firstNameInGroup;
- this.includeRanks = includeRanks;
- }
-
-
- /**
- *
- * @see TaxonComparator#compare(TaxonBase, TaxonBase)
- * @see java.lang.String#compareTo(String)
- * @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
- */
- @Override
- public int compare(
- @SuppressWarnings("rawtypes") TaxonName taxonName1,
- @SuppressWarnings("rawtypes") TaxonName taxonName2) {
-
-
- if (logger.isDebugEnabled()){logger.debug(taxonName1.getTitleCache() +" : "+ taxonName2.getTitleCache());}
-
-
- int compareStatus = compareStatus(taxonName1, taxonName2);
- if (compareStatus != 0){
- return compareStatus;
- }
-
- //not same homotypical group -
- //NOTE: this comparator should usually not be used
- // for comparing names of different homotypical groups.
- // The following is only to have a defined compare behavior
- // which follows the contract of Comparator#compare.
- if (taxonName1 == null ||
- taxonName2 == null ||
- ! taxonName1.getHomotypicalGroup().equals(taxonName2.getHomotypicalGroup())){
-
- String compareString1 =
- taxonName1.getHomotypicalGroup().getUuid().toString() ;
- String compareString2 =
- taxonName2.getHomotypicalGroup().getUuid().toString() ;
- int result = compareString1.compareTo(compareString2);
- return result;
- }
-
- //same homotypical group ...
- //one taxon is first in group
- if (taxonName1.equals(firstNameInGroup)){
- return -1;
- }else if (taxonName2.equals(firstNameInGroup)){
- return 1;
- }
-
-
-
- TaxonName basionym1 = getPreferredInBasionymGroup(taxonName1);
- TaxonName basionym2 = getPreferredInBasionymGroup(taxonName2);
-
- int compareResult;
- if (basionym1.equals(basionym2)){
- //both names belong to same basionym sub-group
- compareResult = handleSameBasionym(basionym1, taxonName1, taxonName2);
- }else{
- compareResult = compareBasionyms(basionym1, basionym2);
- }
-
- return compareResult;
- }
-
-
- /**
- * Compare 2 names which have the same basionym.
- * The names must not be equal to each other but may be equal
- * to the basionym.
- * @param basionym the basionym
- * @param name1 first name to compare
- * @param name2 second name to compare
- * @return compare value according to the {@link Comparator#compare(Object, Object)} contract.
- */
- private int handleSameBasionym(TaxonName basionym,
- TaxonName name1,
- TaxonName name2) {
-
- if (basionym.equals(name1)){
- return -1;
- }else if (basionym.equals(name2)){
- return 1;
- }else{
- return this.compare(name1, name2, false);
- }
-
- }
-
- /**
- * @param basionym1
- * @param basionym2
- * @return
- */
- private int compareBasionyms(TaxonName basionym1Orig, TaxonName basionym2Orig) {
- //one taxon is first in group
- TaxonName basionym1 = getFirstNameInGroup(basionym1Orig);
- TaxonName basionym2 = getFirstNameInGroup(basionym2Orig);
-
- //handle accepted taxon case
- if (basionym1.equals(firstNameInGroup)){
- return -1;
- }else if (basionym2.equals(firstNameInGroup)){
- return 1;
- }
-
- //handle replaced synonyms
- boolean basio2IsReplacedSynForBasio1 = getReplacedSynonymClosure(basionym1).contains(basionym2);
- boolean basio1IsReplacedSynForBasio2 = getReplacedSynonymClosure(basionym2).contains(basionym1);
-
- if (basio2IsReplacedSynForBasio1 && !basio1IsReplacedSynForBasio2){
- return 1;
- }else if (basio1IsReplacedSynForBasio2 && !basio2IsReplacedSynForBasio1){
- return -1;
- }
-
- //compare by date, nom. illeg., rank and alphabetically
- return this.compare(basionym1, basionym2, false);
-
- }
-
- /**
- * @param basionym
- * @return
- */
- private TaxonName getFirstNameInGroup(TaxonName basionym) {
- for (NameRelationship nameRel : basionym.getRelationsFromThisName()){
- if (nameRel.getType() != null && nameRel.getType().equals(NameRelationshipType.BASIONYM())){
- if (nameRel.getToName().equals(firstNameInGroup)){
- return firstNameInGroup;
- }
- }
- }
- return basionym;
- }
-
- /**
- * @param basionym1
- * @return
- */
- @SuppressWarnings("rawtypes")
- private Set<TaxonName> getReplacedSynonymClosure(TaxonName name) {
- Set<TaxonName> set = name.getReplacedSynonyms();
- if (set.isEmpty()){
- return set;
- }
- Set<TaxonName> result = new HashSet<TaxonName>();
- for (TaxonName replSyn : set){
- boolean notYetContained = result.add(replSyn);
- if (notYetContained){
- result.addAll(replSyn.getReplacedSynonyms());
- }
- }
- return result;
- }
-
- /**
- * @param name
- * @return
- */
- private TaxonName getPreferredInBasionymGroup(TaxonName name) {
- Set<TaxonName> candidates = new HashSet<>();
- //get all final basionyms, except for those being part of a basionym circle
- for (TaxonName candidate : name.getBasionyms()){
- if (candidate != null
- && candidate.getHomotypicalGroup().equals(name.getHomotypicalGroup())
- && !hasBasionymCircle(candidate, null)){
- candidate = getPreferredInBasionymGroup(candidate);
- candidates.add(candidate);
- }
- }
-
- if (candidates.isEmpty()){
- return name;
- }else if (candidates.size() == 1){
- return candidates.iterator().next();
- }else{
- TaxonName result = candidates.iterator().next();
- candidates.remove(result);
- for(TaxonName candidate : candidates){
- if (this.compare(result, candidate) > 0){
- result = candidate;
- }
- }
- return result;
- }
- }
-
- /**
- * @param candidate
- * @return
- */
- private boolean hasBasionymCircle(TaxonName name, Set<TaxonName> existing) {
- if (existing == null){
- existing = new HashSet<>();
- }
- if (existing.contains(name)){
- return true;
- }else{
- Set<TaxonName> basionyms = name.getBasionyms();
- if (basionyms.isEmpty()){
- return false;
- }
- existing.add(name);
- for (TaxonName basionym : basionyms){
- if (hasBasionymCircle(basionym, existing)){
- return true;
- }
- }
- return false;
- }
- }
-
-
- // /**
- // * @param homotypicalGroup
- // * @return
- // */
- // private TaxonBase<?> getFirstInHomotypicalGroup(HomotypicalGroup homotypicalGroup, Collection<TaxonBase<?>> existing) {
-// List<TaxonBase<?>> candidates = new ArrayList<TaxonBase<?>>();
-// for (TaxonBase<?> candidate : existing){
-// if (homotypicalGroup.getTypifiedNames().contains(candidate.getName())){
-// candidates.add(candidate);
-// }
-// }
-// Collections.sort(candidates, this);
-// return candidates.isEmpty() ? null : candidates.get(0);
- // }
-
- /**
- * @param taxonName
- * @param taxonName2
- * @param statusCompareWeight
- * @return
- */
- protected int compareStatus(TaxonName taxonName, TaxonName taxonName2) {
- int statusCompareWeight = 0;
- statusCompareWeight += computeStatusCompareWeight(taxonName);
- statusCompareWeight -= computeStatusCompareWeight(taxonName2);
- return statusCompareWeight;
- }
-
- /**
- * @param taxonBase1
- * @param statusCompareWeight
- * @return
- */
- private int computeStatusCompareWeight(TaxonName taxonName) {
- //NOTE: this represented an ordered list for different types of invalid designation status.
- // but not clear were this order came from, it is partly mentioned
- //in #5794, it is unclear if it fits to the longer list mentioned in #9272
- //With #9272 and finally #9566 we decided to handle all invalid status with same weight
- if (taxonName != null && taxonName.isInvalid()){
- return 1;
- }else{
- return 0;
- }
- }
- /**
- *
- * @param name1
- * @param name2
- * @param includeNomIlleg if true and if both names have no date or same date, the only
- * name having nom. illeg. state is handled as if the name was published later than the name
- * without status nom. illeg.
- * @return
- */
- protected int compare(TaxonName name1, TaxonName name2, boolean includeNomIlleg) {
- int result;
-
- //dates
- Integer intDate1 = getIntegerDate(name1);
- Integer intDate2 = getIntegerDate(name2);
-
- if (intDate1 == null && intDate2 == null){
- result = 0;
- }else if (intDate1 == null){
- return 1;
- }else if (intDate2 == null){
- return -1;
- }else{
- result = intDate1.compareTo(intDate2);
- }
-
- //nom. illeg.
- if (result == 0 && includeNomIlleg){
- result = compareNomIlleg(name1, name2);
- if (result != 0){
- return result;
- }
- }
-
- if (result == 0 && includeRanks){
- Rank rank1 = name1 == null? null : name1.getRank();
- Rank rank2 = name2 == null? null : name2.getRank();
-
- if (rank1 == null && rank2 == null){
- result = 0;
- }else if (rank1 == null){
- return 1;
- }else if (rank2 == null){
- return -1;
- }else{
- //for some strange reason compareTo for ranks returns 1 if rank2 is lower. So we add minus (-)
- result = - rank1.compareTo(rank2);
- }
- }
-
- if (result == 0 && name1 != null && name2 != null){
- result = name1.compareToName(name2);
- if (result != 0){
- return result;
- }
- }
- return result;
- }
-
- private Integer getIntegerDate(TaxonName name){
- Integer result;
-
- if (name == null){
- result = null;
- }else{
- if (name.isZoological()){
- result = name.getPublicationYear();
- }else{
- Reference ref = name.getNomenclaturalReference();
- if (ref == null){
- result = null;
- }else{
- if (ref.getDatePublished() == null){
- Reference inRef = ref.getInReference();
- if (inRef == null){
- result = null;
- }else{
- if (inRef.getDatePublished() == null){
- result = null;
- }else{
- result = ref.getInReference().getDatePublished().getStartYear();
- }
- }
- }else{
- result = ref.getDatePublished().getStartYear();
- }
- }
- }
- }
-
- return result;
- }
-
- protected int compareNomIlleg(TaxonName taxonName1, TaxonName taxonName2) {
- int isNomIlleg1 = isNomIlleg(taxonName1);
- int isNomIlleg2 = isNomIlleg(taxonName2);
- return isNomIlleg1 - isNomIlleg2;
- }
-
- private int isNomIlleg(TaxonName taxonName) {
- if (taxonName == null || taxonName.getStatus() == null){
- return 0;
- }
- Set<NomenclaturalStatus> status = taxonName.getStatus();
- for (NomenclaturalStatus nomStatus : status){
- if (nomStatus.getType() != null){
- if (nomStatus.getType().equals(NomenclaturalStatusType.ILLEGITIMATE())){
- return 1;
- }
- }
- }
- return 0;
- }
-
-}
+ @Override
+ public int compare(TaxonName taxonName1, TaxonName taxonName2) {
+ return taxonComparator.compareNames(taxonName1, taxonName2, null, null);
+ }
+}
\ No newline at end of file
BGBM BDI Projects / cdmlib.git / blobdiff