|
1
|
/**
|
|
2
|
* Copyright (C) 2007 EDIT
|
|
3
|
* European Distributed Institute of Taxonomy
|
|
4
|
* http://www.e-taxonomy.eu
|
|
5
|
*
|
|
6
|
* The contents of this file are subject to the Mozilla Public License Version 1.1
|
|
7
|
* See LICENSE.TXT at the top of this package for the full license terms.
|
|
8
|
*/
|
|
9
|
|
|
10
|
package eu.etaxonomy.cdm.compare.taxon;
|
|
11
|
|
|
12
|
import java.util.Comparator;
|
|
13
|
import java.util.HashSet;
|
|
14
|
import java.util.Set;
|
|
15
|
|
|
16
|
import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
|
|
17
|
|
|
18
|
import eu.etaxonomy.cdm.model.name.NameRelationship;
|
|
19
|
import eu.etaxonomy.cdm.model.name.NameRelationshipType;
|
|
20
|
import eu.etaxonomy.cdm.model.name.TaxonName;
|
|
21
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
|
22
|
|
|
23
|
/**
|
|
24
|
* This class orders synonyms of a homotypic group,
|
|
25
|
* first by
|
|
26
|
* <ul>
|
|
27
|
* <li>Basionym groups (the basionym and all names derived from this basionym)
|
|
28
|
* should be kept together in a subgroup</li>
|
|
29
|
* <li>The order of the subgroups is defined by the ordering of their
|
|
30
|
* basionyms (according to the following ordering)</li>
|
|
31
|
* <li>If a name is illegitimate or not does play a role for ordering</li>
|
|
32
|
* <li>Names with publication year should always come first</li>
|
|
33
|
* <li>Names with no publication year are sorted by rank</li>
|
|
34
|
* <li>Names with no publication year and equal rank are sorted alphabetically</li>
|
|
35
|
* <li>If 2 names have a replaced synonym relationship the replaced synonym comes first,
|
|
36
|
* the replacement name comes later as this reflects the order of publication</li>
|
|
37
|
* </ul>
|
|
38
|
*
|
|
39
|
* Details on ordering are explained at https://dev.e-taxonomy.eu/redmine/issues/3338<BR>
|
|
40
|
*
|
|
41
|
* @author a.mueller
|
|
42
|
* @since 02.03.2016
|
|
43
|
*/
|
|
44
|
public class HomotypicGroupTaxonComparator extends TaxonComparator {
|
|
45
|
|
|
46
|
private static final long serialVersionUID = -5088210641256430878L;
|
|
47
|
private static final Logger logger = LogManager.getLogger(HomotypicGroupTaxonComparator.class);
|
|
48
|
|
|
49
|
private final TaxonBase<?> firstTaxonInGroup;
|
|
50
|
private final TaxonName firstNameInGroup;
|
|
51
|
|
|
52
|
public HomotypicGroupTaxonComparator(@SuppressWarnings("rawtypes") TaxonBase firstTaxonInGroup) {
|
|
53
|
super(true);
|
|
54
|
this.firstTaxonInGroup = firstTaxonInGroup;
|
|
55
|
this.firstNameInGroup = firstTaxonInGroup == null ? null: firstTaxonInGroup.getName();
|
|
56
|
}
|
|
57
|
|
|
58
|
public HomotypicGroupTaxonComparator(@SuppressWarnings("rawtypes") TaxonBase firstTaxonInGroup, boolean includeRanks) {
|
|
59
|
super(includeRanks);
|
|
60
|
this.firstTaxonInGroup = firstTaxonInGroup;
|
|
61
|
this.firstNameInGroup = firstTaxonInGroup == null ? null: firstTaxonInGroup.getName();
|
|
62
|
}
|
|
63
|
|
|
64
|
public HomotypicGroupTaxonComparator(TaxonName firstNameInGroup, boolean includeRanks) {
|
|
65
|
super(includeRanks);
|
|
66
|
firstTaxonInGroup = null;
|
|
67
|
this.firstNameInGroup = firstNameInGroup;
|
|
68
|
}
|
|
69
|
|
|
70
|
/**
|
|
71
|
*
|
|
72
|
* @see TaxonComparator#compare(TaxonBase, TaxonBase)
|
|
73
|
* @see java.lang.String#compareTo(String)
|
|
74
|
* @see java.util.Comparator#compare(java.lang.Object, java.lang.Object)
|
|
75
|
*/
|
|
76
|
@Override
|
|
77
|
public int compare(
|
|
78
|
@SuppressWarnings("rawtypes") TaxonBase taxonBase1,
|
|
79
|
@SuppressWarnings("rawtypes") TaxonBase taxonBase2) {
|
|
80
|
|
|
81
|
TaxonName name1 = taxonBase1.getName();
|
|
82
|
TaxonName name2 = taxonBase2.getName();
|
|
83
|
|
|
84
|
return compareNames(name1, name2, taxonBase1, taxonBase2);
|
|
85
|
}
|
|
86
|
|
|
87
|
public int compareNames(TaxonName name1, TaxonName name2, TaxonBase<?> taxonBase1, TaxonBase<?> taxonBase2) {
|
|
88
|
if (logger.isDebugEnabled()){logger.debug(name1.getTitleCache() +" : "+ name2.getTitleCache());}
|
|
89
|
if (name1 == null && taxonBase1 == null ||
|
|
90
|
name2 == null && taxonBase2 == null){
|
|
91
|
throw new IllegalArgumentException("There should always be either a name or a taxon to be compared");
|
|
92
|
}
|
|
93
|
|
|
94
|
int compareStatus = compareStatus(name1, name2);
|
|
95
|
if (compareStatus != 0){
|
|
96
|
return compareStatus;
|
|
97
|
}
|
|
98
|
|
|
99
|
//not same homotypical group -
|
|
100
|
//NOTE: this comparator should usually not be used
|
|
101
|
// for comparing names of different homotypical groups.
|
|
102
|
// The following is only to have a defined compare behavior
|
|
103
|
// which follows the contract of Comparator#compare.
|
|
104
|
if (name1 == null ||
|
|
105
|
name2 == null ||
|
|
106
|
! name1.getHomotypicalGroup().equals(name2.getHomotypicalGroup())){
|
|
107
|
|
|
108
|
String compareString1 = name1 != null ?
|
|
109
|
name1.getHomotypicalGroup().getUuid().toString() :
|
|
110
|
taxonBase1.getUuid().toString();
|
|
111
|
String compareString2 = name2 != null ?
|
|
112
|
name2.getHomotypicalGroup().getUuid().toString() :
|
|
113
|
taxonBase2.getUuid().toString();
|
|
114
|
int result = compareString1.compareTo(compareString2);
|
|
115
|
return result;
|
|
116
|
}
|
|
117
|
|
|
118
|
//same homotypical group ...
|
|
119
|
//one taxon is first in group
|
|
120
|
if (isFirstInGroup(taxonBase1, name1)){
|
|
121
|
return -1;
|
|
122
|
}else if (taxonBase2 != null && taxonBase2.equals(firstTaxonInGroup)){
|
|
123
|
return 1;
|
|
124
|
}
|
|
125
|
|
|
126
|
//same name => compare on taxon level
|
|
127
|
if (name1.equals(name2)){
|
|
128
|
return super.compare(taxonBase1, taxonBase2); //if name is the same compare on taxon level
|
|
129
|
}
|
|
130
|
|
|
131
|
TaxonName basionym1 = getPreferredInBasionymGroup(name1);
|
|
132
|
TaxonName basionym2 = getPreferredInBasionymGroup(name2);
|
|
133
|
|
|
134
|
int compareResult;
|
|
135
|
if (basionym1.equals(basionym2)){
|
|
136
|
//both names belong to same basionym sub-group
|
|
137
|
compareResult = handleSameBasionym(basionym1, name1, name2);
|
|
138
|
}else{
|
|
139
|
compareResult = compareBasionyms(basionym1, basionym2);
|
|
140
|
}
|
|
141
|
|
|
142
|
if (compareResult != 0){
|
|
143
|
// if (logger.isDebugEnabled()){logger.debug(": " + compareResult);}
|
|
144
|
return compareResult;
|
|
145
|
}else{
|
|
146
|
//names are uncomparable on name level (except for uuid, id, etc.)
|
|
147
|
int result = super.compare(taxonBase1, taxonBase2);
|
|
148
|
if (logger.isDebugEnabled()){logger.debug(": = " + result);}
|
|
149
|
return result;
|
|
150
|
}
|
|
151
|
}
|
|
152
|
|
|
153
|
private boolean isFirstInGroup(TaxonBase<?> taxonBase, TaxonName name) {
|
|
154
|
if (taxonBase != null){
|
|
155
|
return taxonBase.equals(firstTaxonInGroup);
|
|
156
|
}else{
|
|
157
|
return name.equals(firstNameInGroup);
|
|
158
|
}
|
|
159
|
}
|
|
160
|
|
|
161
|
/**
|
|
162
|
* Compare 2 names which have the same basionym.
|
|
163
|
* The names must not be equal to each other but may be equal
|
|
164
|
* to the basionym.
|
|
165
|
*
|
|
166
|
* @param basionym the basionym
|
|
167
|
* @param name1 first name to compare
|
|
168
|
* @param name2 second name to compare
|
|
169
|
* @return compare value according to the {@link Comparator#compare(Object, Object)} contract.
|
|
170
|
*/
|
|
171
|
private int handleSameBasionym(TaxonName basionym,
|
|
172
|
TaxonName name1,
|
|
173
|
TaxonName name2) {
|
|
174
|
|
|
175
|
if (basionym.equals(name1)){
|
|
176
|
return -1;
|
|
177
|
}else if (basionym.equals(name2)){
|
|
178
|
return 1;
|
|
179
|
}else{
|
|
180
|
return super.compare(name1, name2, false);
|
|
181
|
}
|
|
182
|
|
|
183
|
}
|
|
184
|
|
|
185
|
private int compareBasionyms(TaxonName basionym1Orig, TaxonName basionym2Orig) {
|
|
186
|
//one taxon is first in group
|
|
187
|
TaxonName basionym1 = getFirstNameInGroup(basionym1Orig);
|
|
188
|
TaxonName basionym2 = getFirstNameInGroup(basionym2Orig);
|
|
189
|
|
|
190
|
//handle accepted taxon case
|
|
191
|
if (basionym1.equals(firstNameInGroup)){
|
|
192
|
return -1;
|
|
193
|
}else if (basionym2.equals(firstNameInGroup)){
|
|
194
|
return 1;
|
|
195
|
}
|
|
196
|
|
|
197
|
//handle replaced synonyms
|
|
198
|
boolean basio2IsReplacedSynForBasio1 = getReplacedSynonymClosure(basionym1).contains(basionym2);
|
|
199
|
boolean basio1IsReplacedSynForBasio2 = getReplacedSynonymClosure(basionym2).contains(basionym1);
|
|
200
|
|
|
201
|
if (basio2IsReplacedSynForBasio1 && !basio1IsReplacedSynForBasio2){
|
|
202
|
return 1;
|
|
203
|
}else if (basio1IsReplacedSynForBasio2 && !basio2IsReplacedSynForBasio1){
|
|
204
|
return -1;
|
|
205
|
}
|
|
206
|
|
|
207
|
//compare by date, nom. illeg., rank and alphabetically
|
|
208
|
return super.compare(basionym1, basionym2, true);
|
|
209
|
}
|
|
210
|
|
|
211
|
private TaxonName getFirstNameInGroup(TaxonName basionym) {
|
|
212
|
for (NameRelationship nameRel : basionym.getRelationsFromThisName()){
|
|
213
|
if (nameRel.getType() != null && nameRel.getType().equals(NameRelationshipType.BASIONYM())){
|
|
214
|
if (nameRel.getToName().equals(firstNameInGroup)){
|
|
215
|
return firstNameInGroup;
|
|
216
|
}
|
|
217
|
}
|
|
218
|
}
|
|
219
|
return basionym;
|
|
220
|
}
|
|
221
|
|
|
222
|
private Set<TaxonName> getReplacedSynonymClosure(TaxonName name) {
|
|
223
|
Set<TaxonName> set = name.getReplacedSynonyms();
|
|
224
|
if (set.isEmpty()){
|
|
225
|
return set;
|
|
226
|
}
|
|
227
|
Set<TaxonName> result = new HashSet<>();
|
|
228
|
for (TaxonName replSyn : set){
|
|
229
|
boolean notYetContained = result.add(replSyn);
|
|
230
|
if (notYetContained){
|
|
231
|
result.addAll(replSyn.getReplacedSynonyms());
|
|
232
|
}
|
|
233
|
}
|
|
234
|
return result;
|
|
235
|
}
|
|
236
|
|
|
237
|
private TaxonName getPreferredInBasionymGroup(TaxonName name) {
|
|
238
|
Set<TaxonName> candidates = new HashSet<>();
|
|
239
|
//get all final basionyms, except for those being part of a basionym circle
|
|
240
|
for (TaxonName candidate : name.getBasionyms()){
|
|
241
|
if (candidate != null
|
|
242
|
&& candidate.getHomotypicalGroup().equals(name.getHomotypicalGroup())
|
|
243
|
&& !hasBasionymCircle(candidate, null)){
|
|
244
|
candidate = getPreferredInBasionymGroup(candidate);
|
|
245
|
candidates.add(candidate);
|
|
246
|
}
|
|
247
|
}
|
|
248
|
|
|
249
|
if (candidates.isEmpty()){
|
|
250
|
return name;
|
|
251
|
}else if (candidates.size() == 1){
|
|
252
|
return candidates.iterator().next();
|
|
253
|
}else{
|
|
254
|
TaxonName result = candidates.iterator().next();
|
|
255
|
candidates.remove(result);
|
|
256
|
for (TaxonName candidate : candidates){
|
|
257
|
if (super.compare(result, candidate, false) > 0){
|
|
258
|
result = candidate;
|
|
259
|
}
|
|
260
|
}
|
|
261
|
return result;
|
|
262
|
}
|
|
263
|
}
|
|
264
|
|
|
265
|
private boolean hasBasionymCircle(TaxonName name, Set<TaxonName> existing) {
|
|
266
|
if (existing == null){
|
|
267
|
existing = new HashSet<>();
|
|
268
|
}
|
|
269
|
if (existing.contains(name)){
|
|
270
|
return true;
|
|
271
|
}else{
|
|
272
|
Set<TaxonName> basionyms = name.getBasionyms();
|
|
273
|
if (basionyms.isEmpty()){
|
|
274
|
return false;
|
|
275
|
}
|
|
276
|
existing.add(name);
|
|
277
|
for (TaxonName basionym : basionyms){
|
|
278
|
if (hasBasionymCircle(basionym, existing)){
|
|
279
|
return true;
|
|
280
|
}
|
|
281
|
}
|
|
282
|
return false;
|
|
283
|
}
|
|
284
|
}
|
|
285
|
}
|