Revision 82ca4447
Added by Andreas Müller over 7 years ago
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/HomotypicGroupTaxonComparator.java | ||
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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 alphabetically</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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* @param firstNameInGroup |
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*/ |
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public HomotypicGroupTaxonComparator(@SuppressWarnings("rawtypes") TaxonBase firstTaxonInGroup) {
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super(true); |
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this.firstTaxonInGroup = firstTaxonInGroup; |
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this.firstNameInGroup = firstTaxonInGroup == null ? null: firstTaxonInGroup.getName(); |
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} |
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/** |
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* @param firstNameInGroup |
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*/ |
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public HomotypicGroupTaxonComparator(@SuppressWarnings("rawtypes") TaxonBase firstTaxonInGroup, boolean includeRanks) {
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super(includeRanks); |
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this.firstTaxonInGroup = firstTaxonInGroup; |
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this.firstNameInGroup = firstTaxonInGroup == null ? null: firstTaxonInGroup.getName(); |
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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 homotypcial groups.
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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 (name1 == null || |
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name2 == null || |
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! name1.getHomotypicalGroup().equals(name2.getHomotypicalGroup())){
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// |
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// HomotypicalGroup hg1 = name1.getHomotypicalGroup(); |
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// HomotypicalGroup hg2 = name2.getHomotypicalGroup(); |
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String compareString1 = name1 != null ? |
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// getFirstNameInHomotypicalGroup(name1) |
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name1.getHomotypicalGroup().getUuid().toString() : |
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taxonBase1.getUuid().toString(); |
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String compareString2 = name2 != null ? |
| cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/taxon/TaxonComparator.java | ||
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| 18 | 18 |
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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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@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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result = intDate1.compareTo(intDate2); |
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} |
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if (result == 0){
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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; |
| cdmlib-model/src/test/java/eu/etaxonomy/cdm/model/taxon/HomotypicGroupTaxonComparatorTest.java | ||
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private List<TaxonBase<?>> list; |
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private Taxon taxon1; |
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private Synonym synonym1; |
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private Synonym synonym2; |
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private Synonym synonym3; |
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|
| ... | ... | |
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public void testCompare_BasionymGroupsSomeWithYears() {
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//2 basionym groups, 1 new combination with year (botName2) and 1 basionym with year (botName5) |
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//The later should come first according to the rules, though alphabetically behing
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//The later should come first according to the rules, though alphabetically being |
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//basionym botName4 |
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botName2.setNomenclaturalReference(ref2); |
| ... | ... | |
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Assert.assertEquals(botName3, list.get(3).getName()); |
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} |
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@Test |
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public void testCompare_BasionymGroupsWithRanks1() {
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botName2.setRank(Rank.VARIETY()); |
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botName2.setInfraSpecificEpithet("varbbbb");
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botName3.setRank(Rank.VARIETY()); |
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botName3.setInfraSpecificEpithet("subspccc");
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botName4.setRank(Rank.SUBSPECIES()); |
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botName4.setInfraSpecificEpithet("subspddd");
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HomotypicalGroup homotypicalGroup = botName2.getHomotypicalGroup(); |
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taxon1.addHeterotypicSynonymName(botName3); |
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taxon1.addHeterotypicSynonymName(botName5, homotypicalGroup, null, null); |
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botName3.addBasionym(botName5); |
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synonym2 = taxon1.addHeterotypicSynonymName(botName2).getSynonym(); |
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taxon1.addHeterotypicSynonymName(botName4, homotypicalGroup, null, null); |
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botName2.addBasionym(botName4); |
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list.addAll(taxon1.getSynonyms()); |
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Collections.sort(list, new HomotypicGroupTaxonComparator(null)); |
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Assert.assertEquals("basionym with rank species should comes first", botName5, list.get(0).getName());
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Assert.assertEquals(botName3, list.get(1).getName()); |
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Assert.assertEquals(botName4, list.get(2).getName()); |
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Assert.assertEquals(botName2, list.get(3).getName()); |
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//add replaced synonym relation between basionyms |
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botName5.addReplacedSynonym(botName4, null, null, null); |
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Collections.sort(list, new HomotypicGroupTaxonComparator(null)); |
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Assert.assertEquals("basionym of second group should come first now as it is the replaced synonym",
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botName4, list.get(0).getName()); |
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Assert.assertEquals(botName2, list.get(1).getName()); |
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Assert.assertEquals("replacement name should come after replaced synonym but first in basionym group",
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botName5, list.get(2).getName()); |
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Assert.assertEquals(botName3, list.get(3).getName()); |
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} |
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@Test |
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public void testCompare_BasionymGroupsWithRanks2() {
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botName2.setRank(Rank.VARIETY()); |
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botName2.setInfraSpecificEpithet("varbbbb");
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botName3.setRank(Rank.VARIETY()); |
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botName3.setInfraSpecificEpithet("subspccc");
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botName4.setRank(Rank.SUBSPECIES()); |
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botName4.setInfraSpecificEpithet("subspddd");
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botName5.setRank(Rank.VARIETY()); |
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botName5.setInfraSpecificEpithet("vareee");
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HomotypicalGroup homotypicalGroup = botName2.getHomotypicalGroup(); |
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taxon1.addHeterotypicSynonymName(botName3); |
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taxon1.addHeterotypicSynonymName(botName5, homotypicalGroup, null, null); |
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botName3.addBasionym(botName5); |
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synonym2 = taxon1.addHeterotypicSynonymName(botName2).getSynonym(); |
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taxon1.addHeterotypicSynonymName(botName4, homotypicalGroup, null, null); |
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botName2.addBasionym(botName5); |
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botName4.addBasionym(botName5); |
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list.addAll(taxon1.getSynonyms()); |
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Collections.sort(list, new HomotypicGroupTaxonComparator(null)); |
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Assert.assertEquals("basionym should comes first", botName5, list.get(0).getName());
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Assert.assertEquals("subspecies should come next", botName4, list.get(1).getName());
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Assert.assertEquals("variety with b should come next", botName2, list.get(2).getName());
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Assert.assertEquals("variety with c should come last", botName3, list.get(3).getName());
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} |
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@Test |
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public void testCompare_NoCircularProblems() {
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|
Also available in: Unified diff
Include rank comparison in HomotypicGroupTaxonComparator #3338