|
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.model.taxon;
|
|
11
|
|
|
12
|
|
|
13
|
import eu.etaxonomy.cdm.model.common.IRelated;
|
|
14
|
import eu.etaxonomy.cdm.model.common.RelationshipBase;
|
|
15
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
|
16
|
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
|
|
17
|
import eu.etaxonomy.cdm.model.name.NameRelationship;
|
|
18
|
import eu.etaxonomy.cdm.model.name.NameRelationshipType;
|
|
19
|
import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
|
|
20
|
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
|
|
21
|
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
|
|
22
|
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
23
|
import eu.etaxonomy.cdm.model.name.TypeDesignationStatus;
|
|
24
|
import eu.etaxonomy.cdm.model.occurrence.Specimen;
|
|
25
|
import eu.etaxonomy.cdm.model.reference.ReferenceBase;
|
|
26
|
|
|
27
|
import org.apache.log4j.Logger;
|
|
28
|
import org.hibernate.annotations.Cascade;
|
|
29
|
import org.hibernate.annotations.CascadeType;
|
|
30
|
|
|
31
|
import java.lang.reflect.Method;
|
|
32
|
import java.util.*;
|
|
33
|
|
|
34
|
import javax.persistence.*;
|
|
35
|
import javax.xml.bind.annotation.XmlAccessType;
|
|
36
|
import javax.xml.bind.annotation.XmlAccessorType;
|
|
37
|
import javax.xml.bind.annotation.XmlElement;
|
|
38
|
import javax.xml.bind.annotation.XmlElementWrapper;
|
|
39
|
import javax.xml.bind.annotation.XmlIDREF;
|
|
40
|
import javax.xml.bind.annotation.XmlRootElement;
|
|
41
|
import javax.xml.bind.annotation.XmlSchemaType;
|
|
42
|
import javax.xml.bind.annotation.XmlTransient;
|
|
43
|
import javax.xml.bind.annotation.XmlType;
|
|
44
|
|
|
45
|
/**
|
|
46
|
* The class for "accepted/correct" {@link TaxonBase taxa} (only these taxa according to
|
|
47
|
* the opinion of the {@link reference.ReferenceBase reference} can build a taxonomic tree).
|
|
48
|
* An {@link java.lang.Iterable interface} is supported to iterate through taxonomic children.<BR>
|
|
49
|
* Splitting taxa in "accepted/correct" and {@link Synonym "synonyms"} makes it easier to handle
|
|
50
|
* particular relationships between ("accepted/correct") taxa on the one hand
|
|
51
|
* and between ("synonym") taxa and ("accepted/correct") taxa on the other.
|
|
52
|
*
|
|
53
|
* @author m.doering
|
|
54
|
* @version 1.0
|
|
55
|
* @created 08-Nov-2007 13:06:56
|
|
56
|
*/
|
|
57
|
@XmlAccessorType(XmlAccessType.FIELD)
|
|
58
|
@XmlType(name = "Taxon", propOrder = {
|
|
59
|
"taxonomicParentCache",
|
|
60
|
"taxonomicChildrenCount",
|
|
61
|
"synonymRelations",
|
|
62
|
"relationsFromThisTaxon",
|
|
63
|
"relationsToThisTaxon",
|
|
64
|
"descriptions"
|
|
65
|
})
|
|
66
|
@XmlRootElement(name = "Taxon")
|
|
67
|
@Entity
|
|
68
|
public class Taxon extends TaxonBase implements Iterable<Taxon>, IRelated<RelationshipBase>{
|
|
69
|
|
|
70
|
static Logger logger = Logger.getLogger(Taxon.class);
|
|
71
|
|
|
72
|
@XmlElementWrapper(name = "Descriptions")
|
|
73
|
@XmlElement(name = "Description")
|
|
74
|
private Set<TaxonDescription> descriptions = new HashSet<TaxonDescription>();
|
|
75
|
|
|
76
|
// all related synonyms
|
|
77
|
@XmlElementWrapper(name = "SynonymRelations")
|
|
78
|
@XmlElement(name = "SynonymRelationship")
|
|
79
|
private Set<SynonymRelationship> synonymRelations = new HashSet<SynonymRelationship>();
|
|
80
|
|
|
81
|
// all taxa relations with rel.fromTaxon==this
|
|
82
|
@XmlElementWrapper(name = "RelationsFromThisTaxon")
|
|
83
|
@XmlElement(name = "FromThisTaxonRelationship")
|
|
84
|
private Set<TaxonRelationship> relationsFromThisTaxon = new HashSet<TaxonRelationship>();
|
|
85
|
|
|
86
|
// all taxa relations with rel.toTaxon==this
|
|
87
|
@XmlElementWrapper(name = "RelationsToThisTaxon")
|
|
88
|
@XmlElement(name = "ToThisTaxonRelationship")
|
|
89
|
private Set<TaxonRelationship> relationsToThisTaxon = new HashSet<TaxonRelationship>();
|
|
90
|
|
|
91
|
// shortcut to the taxonomicIncluded (parent) taxon. Managed by the taxonRelations setter
|
|
92
|
@XmlElement(name = "TaxonomicParentCache")
|
|
93
|
@XmlIDREF
|
|
94
|
@XmlSchemaType(name = "IDREF")
|
|
95
|
private Taxon taxonomicParentCache;
|
|
96
|
|
|
97
|
//cached number of taxonomic children
|
|
98
|
@XmlElement(name = "TaxonomicChildrenCount")
|
|
99
|
private int taxonomicChildrenCount;
|
|
100
|
|
|
101
|
private static Method methodDescriptionSetTaxon;
|
|
102
|
|
|
103
|
|
|
104
|
// ************* CONSTRUCTORS *************/
|
|
105
|
|
|
106
|
//TODO should be private, but still produces Spring init errors
|
|
107
|
@Deprecated
|
|
108
|
public Taxon(){
|
|
109
|
}
|
|
110
|
|
|
111
|
/**
|
|
112
|
* Class constructor: creates a new (accepted/correct) taxon instance with
|
|
113
|
* the {@link name.TaxonNameBase taxon name} used and the {@link reference.ReferenceBase reference}
|
|
114
|
* using it.
|
|
115
|
*
|
|
116
|
* @param taxonNameBase the taxon name used
|
|
117
|
* @param sec the reference using the taxon name
|
|
118
|
* @see TaxonBase#TaxonBase(TaxonNameBase, ReferenceBase)
|
|
119
|
*/
|
|
120
|
public Taxon(TaxonNameBase taxonNameBase, ReferenceBase sec){
|
|
121
|
super(taxonNameBase, sec);
|
|
122
|
}
|
|
123
|
|
|
124
|
//********* METHODS **************************************/
|
|
125
|
|
|
126
|
/**
|
|
127
|
* Creates a new (accepted/correct) taxon instance with
|
|
128
|
* the {@link name.TaxonNameBase taxon name} used and the {@link reference.ReferenceBase reference}
|
|
129
|
* using it.
|
|
130
|
*
|
|
131
|
* @param taxonNameBase the taxon name used
|
|
132
|
* @param sec the reference using the taxon name
|
|
133
|
* @see #Taxon(TaxonNameBase, ReferenceBase)
|
|
134
|
*/
|
|
135
|
public static Taxon NewInstance(TaxonNameBase taxonNameBase, ReferenceBase sec){
|
|
136
|
Taxon result = new Taxon(taxonNameBase, sec);
|
|
137
|
return result;
|
|
138
|
}
|
|
139
|
|
|
140
|
|
|
141
|
/**
|
|
142
|
* Returns the set of {@link description.TaxonDescription taxon descriptions}
|
|
143
|
* concerning <i>this</i> taxon.
|
|
144
|
*
|
|
145
|
* @see #removeDescription(TaxonDescription)
|
|
146
|
* @see #addDescription(TaxonDescription)
|
|
147
|
* @see description.TaxonDescription#getTaxon()
|
|
148
|
*/
|
|
149
|
@OneToMany(mappedBy="taxon", fetch= FetchType.LAZY)
|
|
150
|
@Cascade({CascadeType.SAVE_UPDATE})
|
|
151
|
public Set<TaxonDescription> getDescriptions() {
|
|
152
|
return descriptions;
|
|
153
|
}
|
|
154
|
/**
|
|
155
|
* @see #getDescriptions()
|
|
156
|
*/
|
|
157
|
protected void setDescriptions(Set<TaxonDescription> descriptions) {
|
|
158
|
this.descriptions = descriptions;
|
|
159
|
}
|
|
160
|
/**
|
|
161
|
* Adds a new {@link description.TaxonDescription taxon description} to the set
|
|
162
|
* of taxon descriptions assigned to <i>this</i> (accepted/correct) taxon.
|
|
163
|
* Due to bidirectionality the content of the {@link description.TaxonDescription#getTaxon() taxon attribute} of the
|
|
164
|
* taxon description itself will be replaced with <i>this</i> taxon. The taxon
|
|
165
|
* description will also be removed from the set of taxon descriptions
|
|
166
|
* assigned to its previous taxon.
|
|
167
|
*
|
|
168
|
* @param description the taxon description to be added for <i>this</i> taxon
|
|
169
|
* @see #getDescriptions()
|
|
170
|
* @see #removeDescription(TaxonDescription)
|
|
171
|
* @see description.TaxonDescription#getTaxon()
|
|
172
|
*/
|
|
173
|
public void addDescription(TaxonDescription description) {
|
|
174
|
initMethods();
|
|
175
|
if (description.getTaxon() != null){
|
|
176
|
description.getTaxon().removeDescription(description);
|
|
177
|
}
|
|
178
|
//description.setTaxon(this) for not visible method
|
|
179
|
this.invokeSetMethod(methodDescriptionSetTaxon, description);
|
|
180
|
descriptions.add(description);
|
|
181
|
|
|
182
|
}
|
|
183
|
/**
|
|
184
|
* Removes one element from the set of {@link description.TaxonDescription taxon descriptions} assigned
|
|
185
|
* to <i>this</i> (accepted/correct) taxon. Due to bidirectionality the content of
|
|
186
|
* the {@link description.TaxonDescription#getTaxon() taxon attribute} of the taxon description
|
|
187
|
* itself will be set to "null".
|
|
188
|
*
|
|
189
|
* @param description the taxon description which should be removed
|
|
190
|
* @see #getDescriptions()
|
|
191
|
* @see #addDescription(TaxonDescription)
|
|
192
|
* @see description.TaxonDescription#getTaxon()
|
|
193
|
*/
|
|
194
|
public void removeDescription(TaxonDescription description) {
|
|
195
|
initMethods();
|
|
196
|
//description.setTaxon(null) for not visible method
|
|
197
|
this.invokeSetMethodWithNull(methodDescriptionSetTaxon, description);
|
|
198
|
descriptions.remove(description);
|
|
199
|
}
|
|
200
|
|
|
201
|
private void initMethods(){
|
|
202
|
if (methodDescriptionSetTaxon == null){
|
|
203
|
try {
|
|
204
|
methodDescriptionSetTaxon = TaxonDescription.class.getDeclaredMethod("setTaxon", Taxon.class);
|
|
205
|
methodDescriptionSetTaxon.setAccessible(true);
|
|
206
|
} catch (Exception e) {
|
|
207
|
e.printStackTrace();
|
|
208
|
//TODO handle exception
|
|
209
|
}
|
|
210
|
}
|
|
211
|
}
|
|
212
|
|
|
213
|
|
|
214
|
/**
|
|
215
|
* Returns the set of all {@link SynonymRelationship synonym relationships}
|
|
216
|
* in which <i>this</i> ("accepted/correct") taxon is involved. <i>This</i> taxon can only
|
|
217
|
* be the target of these synonym relationships.
|
|
218
|
*
|
|
219
|
* @see #addSynonymRelation(SynonymRelationship)
|
|
220
|
* @see #removeSynonymRelation(SynonymRelationship)
|
|
221
|
* @see #getSynonyms()
|
|
222
|
*/
|
|
223
|
@OneToMany(mappedBy="relatedTo", fetch=FetchType.LAZY)
|
|
224
|
@Cascade({CascadeType.SAVE_UPDATE})
|
|
225
|
public Set<SynonymRelationship> getSynonymRelations() {
|
|
226
|
return synonymRelations;
|
|
227
|
}
|
|
228
|
/**
|
|
229
|
* @see #getSynonymRelations()
|
|
230
|
* @see #addSynonymRelation(SynonymRelationship)
|
|
231
|
*/
|
|
232
|
protected void setSynonymRelations(Set<SynonymRelationship> synonymRelations) {
|
|
233
|
this.synonymRelations = synonymRelations;
|
|
234
|
}
|
|
235
|
/**
|
|
236
|
* Adds an existing {@link SynonymRelationship synonym relationship} to the set of
|
|
237
|
* {@link #getSynonymRelations() synonym relationships} assigned to <i>this</i> taxon. If
|
|
238
|
* the target of the synonym relationship does not match with <i>this</i> taxon
|
|
239
|
* no addition will be carried out.
|
|
240
|
*
|
|
241
|
* @param synonymRelation the synonym relationship to be added to <i>this</i> taxon's
|
|
242
|
* synonym relationships set
|
|
243
|
* @see #getSynonymRelations()
|
|
244
|
* @see #addSynonym(Synonym, SynonymRelationshipType)
|
|
245
|
* @see #addSynonym(Synonym, SynonymRelationshipType, ReferenceBase, String)
|
|
246
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType)
|
|
247
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType, ReferenceBase, String)
|
|
248
|
*/
|
|
249
|
protected void addSynonymRelation(SynonymRelationship synonymRelation) {
|
|
250
|
this.synonymRelations.add(synonymRelation);
|
|
251
|
}
|
|
252
|
/**
|
|
253
|
* Removes one element from the set of {@link SynonymRelationship synonym relationships} assigned
|
|
254
|
* to <i>this</i> (accepted/correct) taxon. Due to bidirectionality the given
|
|
255
|
* synonym relationship will also be removed from the set of synonym
|
|
256
|
* relationships assigned to the {@link Synonym#getSynonymRelations() synonym} involved in the
|
|
257
|
* relationship. Furthermore the content of
|
|
258
|
* the {@link SynonymRelationship#getAcceptedTaxon() accepted taxon attribute} and of the
|
|
259
|
* {@link SynonymRelationship#getSynonym() synonym attribute} within the synonym relationship
|
|
260
|
* itself will be set to "null".
|
|
261
|
*
|
|
262
|
* @param synonymRelation the synonym relationship which should be deleted
|
|
263
|
* @see #getSynonymRelations()
|
|
264
|
* @see #addSynonymRelation(SynonymRelationship)
|
|
265
|
* @see #removeSynonym(Synonym)
|
|
266
|
*/
|
|
267
|
public void removeSynonymRelation(SynonymRelationship synonymRelation) {
|
|
268
|
synonymRelation.setAcceptedTaxon(null);
|
|
269
|
Synonym synonym = synonymRelation.getSynonym();
|
|
270
|
if (synonym != null){
|
|
271
|
synonymRelation.setSynonym(null);
|
|
272
|
synonym.removeSynonymRelation(synonymRelation);
|
|
273
|
}
|
|
274
|
this.synonymRelations.remove(synonymRelation);
|
|
275
|
}
|
|
276
|
|
|
277
|
|
|
278
|
/**
|
|
279
|
* Returns the set of all {@link TaxonRelationship taxon relationships}
|
|
280
|
* between two taxa in which <i>this</i> taxon is involved as a source.
|
|
281
|
*
|
|
282
|
* @see #getRelationsToThisTaxon()
|
|
283
|
* @see #getTaxonRelations()
|
|
284
|
*/
|
|
285
|
@OneToMany(mappedBy="relatedFrom", fetch=FetchType.LAZY)
|
|
286
|
@Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE_ORPHAN})
|
|
287
|
public Set<TaxonRelationship> getRelationsFromThisTaxon() {
|
|
288
|
return relationsFromThisTaxon;
|
|
289
|
}
|
|
290
|
/**
|
|
291
|
* @see #getRelationsFromThisTaxon()
|
|
292
|
*/
|
|
293
|
protected void setRelationsFromThisTaxon(
|
|
294
|
Set<TaxonRelationship> relationsFromThisTaxon) {
|
|
295
|
this.relationsFromThisTaxon = relationsFromThisTaxon;
|
|
296
|
}
|
|
297
|
|
|
298
|
|
|
299
|
/**
|
|
300
|
* Returns the set of all {@link TaxonRelationship taxon relationships}
|
|
301
|
* between two taxa in which <i>this</i> taxon is involved as a target.
|
|
302
|
*
|
|
303
|
* @see #getRelationsFromThisTaxon()
|
|
304
|
* @see #getTaxonRelations()
|
|
305
|
*/
|
|
306
|
@OneToMany(mappedBy="relatedTo", fetch=FetchType.LAZY)
|
|
307
|
@Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE_ORPHAN})
|
|
308
|
public Set<TaxonRelationship> getRelationsToThisTaxon() {
|
|
309
|
return relationsToThisTaxon;
|
|
310
|
}
|
|
311
|
/**
|
|
312
|
* @see #getRelationsToThisTaxon()
|
|
313
|
*/
|
|
314
|
protected void setRelationsToThisTaxon(Set<TaxonRelationship> relationsToThisTaxon) {
|
|
315
|
this.relationsToThisTaxon = relationsToThisTaxon;
|
|
316
|
}
|
|
317
|
|
|
318
|
@ManyToOne
|
|
319
|
// used by hibernate only...
|
|
320
|
private Taxon getTaxonomicParentCache() {
|
|
321
|
return taxonomicParentCache;
|
|
322
|
}
|
|
323
|
private void setTaxonomicParentCache(Taxon taxonomicParent) {
|
|
324
|
this.taxonomicParentCache = taxonomicParent;
|
|
325
|
}
|
|
326
|
|
|
327
|
/**
|
|
328
|
* Returns the set of all {@link TaxonRelationship taxon relationships}
|
|
329
|
* between two taxa in which <i>this</i> taxon is involved either as a source or
|
|
330
|
* as a target.
|
|
331
|
*
|
|
332
|
* @see #getRelationsFromThisTaxon()
|
|
333
|
* @see #getRelationsToThisTaxon()
|
|
334
|
*/
|
|
335
|
@Transient
|
|
336
|
public Set<TaxonRelationship> getTaxonRelations() {
|
|
337
|
Set<TaxonRelationship> rels = new HashSet<TaxonRelationship>();
|
|
338
|
rels.addAll(getRelationsToThisTaxon());
|
|
339
|
rels.addAll(getRelationsFromThisTaxon());
|
|
340
|
return rels;
|
|
341
|
}
|
|
342
|
/**
|
|
343
|
* Removes one {@link TaxonRelationship taxon relationship} from one of both sets of
|
|
344
|
* {@link #getTaxonRelations() taxon relationships} in which <i>this</i> taxon is involved
|
|
345
|
* either as a {@link #getRelationsFromThisTaxon() source} or as a {@link #getRelationsToThisTaxon() target}.
|
|
346
|
* The taxon relationship will also be removed from one of both sets
|
|
347
|
* belonging to the second taxon involved. Furthermore the inherited RelatedFrom and
|
|
348
|
* RelatedTo attributes of the given taxon relationship will be nullified.<P>
|
|
349
|
* If the taxon relationship concerns the taxonomic tree possible
|
|
350
|
* modifications of the {@link #getTaxonomicParent() parent taxon} or of the number of
|
|
351
|
* {@link #getTaxonomicChildrenCount() childrens} will be stored.
|
|
352
|
*
|
|
353
|
* @param rel the taxon relationship which should be removed from one
|
|
354
|
* of both sets
|
|
355
|
* @see #getTaxonRelations()
|
|
356
|
* @see #getTaxonomicParent()
|
|
357
|
* @see #getTaxonomicChildrenCount()
|
|
358
|
* @see common.RelationshipBase#getRelatedFrom()
|
|
359
|
* @see common.RelationshipBase#getRelatedTo()
|
|
360
|
*
|
|
361
|
*/
|
|
362
|
public void removeTaxonRelation(TaxonRelationship rel) {
|
|
363
|
logger.warn("remove TaxonRelation"); //for testing only
|
|
364
|
this.relationsToThisTaxon.remove(rel);
|
|
365
|
this.relationsFromThisTaxon.remove(rel);
|
|
366
|
Taxon fromTaxon = rel.getFromTaxon();
|
|
367
|
Taxon toTaxon = rel.getToTaxon();
|
|
368
|
// check if this removes the taxonomical parent. If so, also remove shortcut to the higher taxon
|
|
369
|
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) ){
|
|
370
|
if (fromTaxon != null && fromTaxon.equals(this)){
|
|
371
|
this.setTaxonomicParentCache(null);
|
|
372
|
}else if (toTaxon != null && toTaxon.equals(this)){
|
|
373
|
this.setTaxonomicChildrenCount(computeTaxonomicChildrenCount());
|
|
374
|
}
|
|
375
|
}
|
|
376
|
//delete Relationship from other related Taxon
|
|
377
|
if (fromTaxon != null && fromTaxon != this){
|
|
378
|
rel.setToTaxon(null); //remove this Taxon from relationship
|
|
379
|
fromTaxon.removeTaxonRelation(rel);
|
|
380
|
}
|
|
381
|
if (toTaxon != null && toTaxon != this){
|
|
382
|
rel.setFromTaxon(null); //remove this Taxon from relationship
|
|
383
|
toTaxon.removeTaxonRelation(rel);
|
|
384
|
}
|
|
385
|
}
|
|
386
|
|
|
387
|
/**
|
|
388
|
* Adds an existing {@link TaxonRelationship taxon relationship} either to the set of
|
|
389
|
* {@link #getRelationsToThisTaxon() taxon relationships to <i>this</i> taxon} or to the set of
|
|
390
|
* {@link #getRelationsFromThisTaxon() taxon relationships from <i>this</i> taxon}. If neither the
|
|
391
|
* source nor the target of the taxon relationship match with <i>this</i> taxon
|
|
392
|
* no addition will be carried out. The taxon relationship will also be
|
|
393
|
* added to the second taxon involved in the given relationship.<P>
|
|
394
|
* If the taxon relationship concerns the taxonomic tree possible
|
|
395
|
* modifications of the {@link #getTaxonomicParent() parent taxon} or of the number of
|
|
396
|
* {@link #getTaxonomicChildrenCount() childrens} will be stored.
|
|
397
|
*
|
|
398
|
* @param rel the taxon relationship to be added to one of <i>this</i> taxon's taxon relationships sets
|
|
399
|
* @see #addTaxonRelation(Taxon, TaxonRelationshipType, ReferenceBase, String)
|
|
400
|
* @see #getTaxonRelations()
|
|
401
|
* @see #getRelationsFromThisTaxon()
|
|
402
|
* @see #getRelationsToThisTaxon()
|
|
403
|
* @see #getTaxonomicParent()
|
|
404
|
* @see #getTaxonomicChildrenCount()
|
|
405
|
*/
|
|
406
|
public void addTaxonRelation(TaxonRelationship rel) {
|
|
407
|
if (rel!=null && rel.getType()!=null && !getTaxonRelations().contains(rel) ){
|
|
408
|
Taxon toTaxon=rel.getToTaxon();
|
|
409
|
Taxon fromTaxon=rel.getFromTaxon();
|
|
410
|
if ( this.equals(toTaxon) || this.equals(fromTaxon) ){
|
|
411
|
if (this.equals(fromTaxon)){
|
|
412
|
relationsFromThisTaxon.add(rel);
|
|
413
|
// also add relation to other taxon object
|
|
414
|
if (toTaxon!=null){
|
|
415
|
toTaxon.addTaxonRelation(rel);
|
|
416
|
}
|
|
417
|
// check if this sets the taxonomical parent. If so, remember a shortcut to this taxon
|
|
418
|
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) && toTaxon!=null ){
|
|
419
|
this.setTaxonomicParentCache(toTaxon);
|
|
420
|
}
|
|
421
|
}else if (this.equals(toTaxon)){
|
|
422
|
relationsToThisTaxon.add(rel);
|
|
423
|
// also add relation to other taxon object
|
|
424
|
if (fromTaxon!=null){
|
|
425
|
fromTaxon.addTaxonRelation(rel);
|
|
426
|
}
|
|
427
|
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) && fromTaxon!=null ){
|
|
428
|
this.taxonomicChildrenCount++;
|
|
429
|
}
|
|
430
|
|
|
431
|
}
|
|
432
|
}
|
|
433
|
}
|
|
434
|
}
|
|
435
|
|
|
436
|
/* (non-Javadoc)
|
|
437
|
* @see eu.etaxonomy.cdm.model.common.IRelated#addRelationship(eu.etaxonomy.cdm.model.common.RelationshipBase)
|
|
438
|
*/
|
|
439
|
@Deprecated //for inner use by RelationshipBase only
|
|
440
|
public void addRelationship(RelationshipBase rel){
|
|
441
|
if (rel instanceof TaxonRelationship){
|
|
442
|
addTaxonRelation((TaxonRelationship)rel);
|
|
443
|
}else if (rel instanceof SynonymRelationship){
|
|
444
|
addSynonymRelation((SynonymRelationship)rel);
|
|
445
|
}else{
|
|
446
|
throw new ClassCastException("Wrong Relationsship type for Taxon.addRelationship");
|
|
447
|
}
|
|
448
|
}
|
|
449
|
|
|
450
|
/**
|
|
451
|
* Creates a new {@link TaxonRelationship taxon relationship} instance where <i>this</i> taxon
|
|
452
|
* plays the source role and adds it to the set of
|
|
453
|
* {@link #getRelationsFromThisTaxon() "taxon relationships from"} belonging to <i>this</i> taxon.
|
|
454
|
* The taxon relationship will also be added to the set of taxon
|
|
455
|
* relationships to the second taxon involved in the created relationship.<P>
|
|
456
|
* If the taxon relationship concerns the taxonomic tree possible
|
|
457
|
* modifications of the {@link #getTaxonomicParent() parent taxon} or of the number of
|
|
458
|
* {@link #getTaxonomicChildrenCount() childrens} will be stored.
|
|
459
|
*
|
|
460
|
* @param toTaxon the taxon which plays the target role in the new taxon relationship
|
|
461
|
* @param type the taxon relationship type for the new taxon relationship
|
|
462
|
* @param citation the reference source for the new taxon relationship
|
|
463
|
* @param microcitation the string with the details describing the exact localisation within the reference
|
|
464
|
* @see #addTaxonRelation(TaxonRelationship)
|
|
465
|
* @see #getTaxonRelations()
|
|
466
|
* @see #getRelationsFromThisTaxon()
|
|
467
|
* @see #getRelationsToThisTaxon()
|
|
468
|
* @see #getTaxonomicParent()
|
|
469
|
* @see #getTaxonomicChildrenCount()
|
|
470
|
*/
|
|
471
|
public void addTaxonRelation(Taxon toTaxon, TaxonRelationshipType type, ReferenceBase citation, String microcitation) {
|
|
472
|
TaxonRelationship rel = new TaxonRelationship(this, toTaxon, type, citation, microcitation);
|
|
473
|
}
|
|
474
|
/**
|
|
475
|
* Creates a new {@link TaxonRelationship taxon relationship} (with {@link TaxonRelationshipType taxon relationship type}
|
|
476
|
* "misapplied name for") instance where <i>this</i> taxon plays the target role
|
|
477
|
* and adds it to the set of {@link #getRelationsToThisTaxon() taxon relationships to <i>this</i> taxon}.
|
|
478
|
* The taxon relationship will also be added to the set of taxon
|
|
479
|
* relationships to the other (misapplied name) taxon involved in the created relationship.
|
|
480
|
*
|
|
481
|
* @param misappliedNameTaxon the taxon which plays the target role in the new taxon relationship
|
|
482
|
* @param citation the reference source for the new taxon relationship
|
|
483
|
* @param microcitation the string with the details describing the exact localisation within the reference
|
|
484
|
* @see #getMisappliedNames()
|
|
485
|
* @see #addTaxonRelation(Taxon, TaxonRelationshipType, ReferenceBase, String)
|
|
486
|
* @see #addTaxonRelation(TaxonRelationship)
|
|
487
|
* @see #getTaxonRelations()
|
|
488
|
* @see #getRelationsFromThisTaxon()
|
|
489
|
* @see #getRelationsToThisTaxon()
|
|
490
|
*/
|
|
491
|
public void addMisappliedName(Taxon misappliedNameTaxon, ReferenceBase citation, String microcitation) {
|
|
492
|
misappliedNameTaxon.addTaxonRelation(this, TaxonRelationshipType.MISAPPLIEDNAMEFOR(), citation, microcitation);
|
|
493
|
}
|
|
494
|
|
|
495
|
|
|
496
|
/**
|
|
497
|
* Creates a new {@link TaxonRelationship taxon relationship} (with {@link TaxonRelationshipType taxon relationship type}
|
|
498
|
* "taxonomically included in") instance where <i>this</i> taxon plays the target
|
|
499
|
* role (parent) and adds it to the set of
|
|
500
|
* {@link #getRelationsToThisTaxon() "taxon relationships to"} belonging to <i>this</i> taxon.
|
|
501
|
* The taxon relationship will also be added to the set of
|
|
502
|
* {@link #getRelationsFromThisTaxon() "taxon relationships from"} belonging to the second taxon
|
|
503
|
* (child) involved in the created relationship.<P>
|
|
504
|
* Since the taxon relationship concerns the modifications
|
|
505
|
* of the number of {@link #getTaxonomicChildrenCount() childrens} for <i>this</i> taxon and
|
|
506
|
* of the {@link #getTaxonomicParent() parent taxon} for the child taxon will be stored.
|
|
507
|
* The {@link name.Rank rank} of the taxon name used as a parent taxon must be higher
|
|
508
|
* than the rank of the taxon name used as a child taxon.
|
|
509
|
*
|
|
510
|
* @param child the taxon which plays the source role (child) in the new taxon relationship
|
|
511
|
* @param citation the reference source for the new taxon relationship
|
|
512
|
* @param microcitation the string with the details describing the exact localisation within the reference
|
|
513
|
* @see #setTaxonomicParent(Taxon, ReferenceBase, String)
|
|
514
|
* @see #addTaxonRelation(Taxon, TaxonRelationshipType, ReferenceBase, String)
|
|
515
|
* @see #addTaxonRelation(TaxonRelationship)
|
|
516
|
* @see #getTaxonRelations()
|
|
517
|
* @see #getRelationsFromThisTaxon()
|
|
518
|
* @see #getRelationsToThisTaxon()
|
|
519
|
* @see #getTaxonomicParent()
|
|
520
|
* @see #getTaxonomicChildrenCount()
|
|
521
|
*/
|
|
522
|
@Transient
|
|
523
|
public void addTaxonomicChild(Taxon child, ReferenceBase citation, String microcitation){
|
|
524
|
if (child == null){
|
|
525
|
throw new NullPointerException("Child Taxon is 'null'");
|
|
526
|
}else{
|
|
527
|
child.setTaxonomicParent(this, citation, microcitation);
|
|
528
|
}
|
|
529
|
}
|
|
530
|
/**
|
|
531
|
* Removes one {@link TaxonRelationship taxon relationship} with {@link TaxonRelationshipType taxon relationship type}
|
|
532
|
* "taxonomically included in" and with the given child taxon playing the
|
|
533
|
* source role from the set of {@link #getRelationsToThisTaxon() "taxon relationships to"} belonging
|
|
534
|
* to <i>this</i> taxon. The taxon relationship will also be removed from the set
|
|
535
|
* of {@link #getRelationsFromThisTaxon() "taxon relationships from"} belonging to the child taxon.
|
|
536
|
* Furthermore the inherited RelatedFrom and RelatedTo attributes of the
|
|
537
|
* taxon relationship will be nullified.<P>
|
|
538
|
* Since the taxon relationship concerns the taxonomic tree modifications
|
|
539
|
* of the number of {@link #getTaxonomicChildrenCount() childrens} for <i>this</i> taxon and
|
|
540
|
* of the {@link #getTaxonomicParent() parent taxon} for the child taxon will be stored.
|
|
541
|
*
|
|
542
|
* @param child the taxon playing the source role in the relationship to be removed
|
|
543
|
* @see #removeTaxonRelation(TaxonRelationship)
|
|
544
|
* @see #getRelationsToThisTaxon()
|
|
545
|
* @see #getRelationsFromThisTaxon()
|
|
546
|
* @see #getTaxonomicParent()
|
|
547
|
* @see #getTaxonomicChildrenCount()
|
|
548
|
* @see common.RelationshipBase#getRelatedFrom()
|
|
549
|
* @see common.RelationshipBase#getRelatedTo()
|
|
550
|
*
|
|
551
|
*/
|
|
552
|
@Transient
|
|
553
|
public void removeTaxonomicChild(Taxon child){
|
|
554
|
Set<TaxonRelationship> taxRels = this.getTaxonRelations();
|
|
555
|
for (TaxonRelationship taxRel : taxRels ){
|
|
556
|
if (taxRel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) && taxRel.getFromTaxon().equals(child)){
|
|
557
|
this.removeTaxonRelation(taxRel);
|
|
558
|
}
|
|
559
|
}
|
|
560
|
}
|
|
561
|
|
|
562
|
/**
|
|
563
|
* Returns the taxon which is the next higher taxon (parent) of <i>this</i> taxon
|
|
564
|
* within the taxonomic tree and which is stored in the
|
|
565
|
* TaxonomicParentCache attribute. Each taxon can have only one parent taxon.
|
|
566
|
* The child taxon and the parent taxon play the source respectively the
|
|
567
|
* target role in one {@link TaxonRelationship taxon relationship} with
|
|
568
|
* {@link TaxonRelationshipType taxon relationship type} "taxonomically included in".
|
|
569
|
* The {@link name.Rank rank} of the taxon name used as a parent taxon must be higher
|
|
570
|
* than the rank of the taxon name used as a child taxon.
|
|
571
|
*
|
|
572
|
* @see #setTaxonomicParent(Taxon, ReferenceBase, String)
|
|
573
|
* @see #getTaxonomicChildren()
|
|
574
|
* @see #getTaxonomicChildrenCount()
|
|
575
|
* @see #getRelationsFromThisTaxon()
|
|
576
|
*/
|
|
577
|
@Transient
|
|
578
|
public Taxon getTaxonomicParent() {
|
|
579
|
return getTaxonomicParentCache();
|
|
580
|
}
|
|
581
|
/**
|
|
582
|
* Replaces both the taxonomic parent cache with the given new parent taxon
|
|
583
|
* and the corresponding taxon relationship with a new {@link TaxonRelationship taxon relationship}
|
|
584
|
* (with {@link TaxonRelationshipType taxon relationship type} "taxonomically included in") instance.
|
|
585
|
* In the new taxon relationship <i>this</i> taxon plays the source role (child).
|
|
586
|
* This method creates and adds the new taxon relationship to the set of
|
|
587
|
* {@link #getRelationsFromThisTaxon() "taxon relationships from"} belonging to <i>this</i> taxon.
|
|
588
|
* The taxon relationship will also be added to the set of
|
|
589
|
* {@link #getRelationsToThisTaxon() "taxon relationships to"} belonging to the second taxon
|
|
590
|
* (parent) involved in the new relationship.<P>
|
|
591
|
* Since the taxon relationship concerns the taxonomic tree modifications
|
|
592
|
* of the {@link #getTaxonomicParent() parent taxon} for <i>this</i> taxon and of the number of
|
|
593
|
* {@link #getTaxonomicChildrenCount() childrens} for the child taxon will be stored.
|
|
594
|
*
|
|
595
|
* @param newParent the taxon which plays the target role (parent) in the new taxon relationship
|
|
596
|
* @param citation the reference source for the new taxon relationship
|
|
597
|
* @param microcitation the string with the details describing the exact localisation within the reference
|
|
598
|
* @see #removeTaxonRelation(TaxonRelationship)
|
|
599
|
* @see #getTaxonomicParent()
|
|
600
|
* @see #addTaxonRelation(Taxon, TaxonRelationshipType, ReferenceBase, String)
|
|
601
|
* @see #addTaxonRelation(TaxonRelationship)
|
|
602
|
* @see #getTaxonRelations()
|
|
603
|
* @see #getRelationsFromThisTaxon()
|
|
604
|
* @see #getRelationsToThisTaxon()
|
|
605
|
* @see #getTaxonomicChildrenCount()
|
|
606
|
*/
|
|
607
|
public void setTaxonomicParent(Taxon newParent, ReferenceBase citation, String microcitation){
|
|
608
|
//remove previously existing parent relationship!!!
|
|
609
|
Taxon oldParent = this.getTaxonomicParent();
|
|
610
|
Set<TaxonRelationship> taxRels = this.getTaxonRelations();
|
|
611
|
for (TaxonRelationship taxRel : taxRels ){
|
|
612
|
if (taxRel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN()) && taxRel.getToTaxon().equals(oldParent)){
|
|
613
|
this.removeTaxonRelation(taxRel);
|
|
614
|
}
|
|
615
|
}
|
|
616
|
//add new parent
|
|
617
|
if (newParent != null){
|
|
618
|
addTaxonRelation(newParent, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),citation,microcitation);
|
|
619
|
}
|
|
620
|
}
|
|
621
|
|
|
622
|
/**
|
|
623
|
* Returns the set of taxa which have <i>this</i> taxon as next higher taxon
|
|
624
|
* (parent) within the taxonomic tree. Each taxon can have several child
|
|
625
|
* taxa. The child taxon and the parent taxon play the source respectively
|
|
626
|
* the target role in one {@link TaxonRelationship taxon relationship} with
|
|
627
|
* {@link TaxonRelationshipType taxon relationship type} "taxonomically included in".
|
|
628
|
* The {@link name.Rank rank} of the taxon name used as a parent taxon must be higher
|
|
629
|
* than the rank of the taxon name used as a child taxon.
|
|
630
|
*
|
|
631
|
* @see #getTaxonomicParent()
|
|
632
|
* @see #addTaxonomicChild(Taxon, ReferenceBase, String)
|
|
633
|
* @see #getTaxonomicChildrenCount()
|
|
634
|
* @see #getRelationsToThisTaxon()
|
|
635
|
*/
|
|
636
|
@Transient
|
|
637
|
public Set<Taxon> getTaxonomicChildren() {
|
|
638
|
Set<Taxon> taxa = new HashSet<Taxon>();
|
|
639
|
Set<TaxonRelationship> rels = this.getRelationsToThisTaxon();
|
|
640
|
for (TaxonRelationship rel: rels){
|
|
641
|
TaxonRelationshipType tt = rel.getType();
|
|
642
|
TaxonRelationshipType incl = TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();
|
|
643
|
if (tt.equals(incl)){
|
|
644
|
taxa.add(rel.getFromTaxon());
|
|
645
|
}
|
|
646
|
}
|
|
647
|
return taxa;
|
|
648
|
}
|
|
649
|
|
|
650
|
/**
|
|
651
|
* Returns the number of taxa which have <i>this</i> taxon as next higher taxon
|
|
652
|
* (parent) within the taxonomic tree and the number of which is stored in
|
|
653
|
* the TaxonomicChildrenCount attribute. Each taxon can have several child
|
|
654
|
* taxa. The child taxon and the parent taxon play the source respectively
|
|
655
|
* the target role in one {@link TaxonRelationship taxon relationship} with
|
|
656
|
* {@link TaxonRelationshipType taxon relationship type} "taxonomically included in".
|
|
657
|
* The {@link name.Rank rank} of the taxon name used as a parent taxon must be higher
|
|
658
|
* than the rank of the taxon name used as a child taxon.
|
|
659
|
*
|
|
660
|
* @see #getTaxonomicChildren()
|
|
661
|
* @see #getRelationsToThisTaxon()
|
|
662
|
*/
|
|
663
|
public int getTaxonomicChildrenCount(){
|
|
664
|
return taxonomicChildrenCount;
|
|
665
|
}
|
|
666
|
|
|
667
|
|
|
668
|
/**
|
|
669
|
* @see #getTaxonomicChildrenCount()
|
|
670
|
*/
|
|
671
|
private void setTaxonomicChildrenCount(int taxonomicChildrenCount) {
|
|
672
|
this.taxonomicChildrenCount = taxonomicChildrenCount;
|
|
673
|
}
|
|
674
|
|
|
675
|
/**
|
|
676
|
* Returns the boolean value indicating whether <i>this</i> taxon has at least one
|
|
677
|
* taxonomic child taxon within the taxonomic tree (true) or not (false).
|
|
678
|
*
|
|
679
|
* @see #getTaxonomicChildrenCount()
|
|
680
|
* @see #getTaxonomicChildren()
|
|
681
|
*/
|
|
682
|
@Transient
|
|
683
|
public boolean hasTaxonomicChildren(){
|
|
684
|
return this.taxonomicChildrenCount > 0;
|
|
685
|
}
|
|
686
|
|
|
687
|
@Transient
|
|
688
|
private int computeTaxonomicChildrenCount(){
|
|
689
|
int count = 0;
|
|
690
|
for (TaxonRelationship rel: this.getRelationsToThisTaxon()){
|
|
691
|
if (rel.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())){
|
|
692
|
count++;
|
|
693
|
}
|
|
694
|
}
|
|
695
|
return count;
|
|
696
|
}
|
|
697
|
|
|
698
|
/**
|
|
699
|
* Returns the boolean value indicating whether <i>this</i> taxon has at least one
|
|
700
|
* {@link Synoynm synonym} (true) or not (false). If true the {@link #getSynonymRelations() set of synonym relationships}
|
|
701
|
* belonging to <i>this</i> ("accepted/correct") taxon is not empty .
|
|
702
|
*
|
|
703
|
* @see #getSynonymRelations()
|
|
704
|
* @see #getSynonyms()
|
|
705
|
* @see #getSynonymNames()
|
|
706
|
* @see #removeSynonym(Synonym)
|
|
707
|
* @see SynonymRelationship
|
|
708
|
*/
|
|
709
|
@Transient
|
|
710
|
public boolean hasSynonyms(){
|
|
711
|
return this.getSynonymRelations().size() > 0;
|
|
712
|
}
|
|
713
|
|
|
714
|
|
|
715
|
/**
|
|
716
|
* Returns the boolean value indicating whether <i>this</i> taxon is at least
|
|
717
|
* involved in one {@link #getTaxonRelations() taxon relationship} between
|
|
718
|
* two taxa (true), either as a source or as a target, or not (false).
|
|
719
|
*
|
|
720
|
* @see #getTaxonRelations()
|
|
721
|
* @see #getRelationsToThisTaxon()
|
|
722
|
* @see #getRelationsFromThisTaxon()
|
|
723
|
* @see #removeTaxonRelation(TaxonRelationship)
|
|
724
|
* @see TaxonRelationship
|
|
725
|
*/
|
|
726
|
@Transient
|
|
727
|
public boolean hasTaxonRelationships(){
|
|
728
|
return this.getTaxonRelations().size() > 0;
|
|
729
|
}
|
|
730
|
|
|
731
|
/*
|
|
732
|
* MISAPPLIED NAMES
|
|
733
|
*/
|
|
734
|
/**
|
|
735
|
* Returns the set of taxa playing the source role in {@link TaxonRelationship taxon relationships}
|
|
736
|
* (with {@link TaxonRelationshipType taxon relationship type} "misapplied name for") where
|
|
737
|
* <i>this</i> taxon plays the target role. A misapplied name is a taxon the
|
|
738
|
* {@link name.TaxonNameBase taxon name} of which has been erroneously used
|
|
739
|
* by the {@link TaxonBase#getSec() taxon reference} to denominate the same real taxon
|
|
740
|
* as the one meant by <i>this</i> ("accepted/correct") taxon.
|
|
741
|
*
|
|
742
|
* @see #getTaxonRelations()
|
|
743
|
* @see #getRelationsToThisTaxon()
|
|
744
|
* @see #addMisappliedName(Taxon, ReferenceBase, String)
|
|
745
|
*/
|
|
746
|
@Transient
|
|
747
|
public Set<Taxon> getMisappliedNames(){
|
|
748
|
Set<Taxon> taxa = new HashSet<Taxon>();
|
|
749
|
Set<TaxonRelationship> rels = this.getRelationsToThisTaxon();
|
|
750
|
for (TaxonRelationship rel: rels){
|
|
751
|
TaxonRelationshipType tt = rel.getType();
|
|
752
|
TaxonRelationshipType incl = TaxonRelationshipType.MISAPPLIEDNAMEFOR();
|
|
753
|
if (tt.equals(incl)){
|
|
754
|
taxa.add(rel.getFromTaxon());
|
|
755
|
}
|
|
756
|
}
|
|
757
|
return taxa;
|
|
758
|
}
|
|
759
|
|
|
760
|
|
|
761
|
/*
|
|
762
|
* DEALING WITH SYNONYMS
|
|
763
|
*/
|
|
764
|
/**
|
|
765
|
* Returns the set of all {@link Synonym synonyms} of <i>this</i> ("accepted/correct") taxon.
|
|
766
|
* Each synonym is the source and <i>this</i> taxon is the target of a {@link SynonymRelationship synonym relationship}
|
|
767
|
* belonging to the {@link #getSynonymRelations() set of synonym relationships} assigned to <i>this</i> taxon.
|
|
768
|
* For a particular synonym and for a particular ("accepted/correct") taxon
|
|
769
|
* there can be several synonym relationships (if two or more
|
|
770
|
* {@link SynonymRelationshipType synonym relationship types} - for instance
|
|
771
|
* "pro parte synonym of" and "is homotypic synonym of" - must be combined).
|
|
772
|
*
|
|
773
|
* @see #getSynonymsSortedByType()
|
|
774
|
* @see #getSynonymNames()
|
|
775
|
* @see #getSynonymRelations()
|
|
776
|
* @see #addSynonym(Synonym, SynonymRelationshipType)
|
|
777
|
* @see #addSynonym(Synonym, SynonymRelationshipType, ReferenceBase, String)
|
|
778
|
* @see #removeSynonymRelation(SynonymRelationship)
|
|
779
|
* @see #removeSynonym(Synonym)
|
|
780
|
*/
|
|
781
|
@Transient
|
|
782
|
public Set<Synonym> getSynonyms(){
|
|
783
|
Set<Synonym> syns = new HashSet<Synonym>();
|
|
784
|
for (SynonymRelationship rel: this.getSynonymRelations()){
|
|
785
|
syns.add(rel.getSynonym());
|
|
786
|
}
|
|
787
|
return syns;
|
|
788
|
}
|
|
789
|
/**
|
|
790
|
* Returns the set of all {@link Synonym synonyms} of <i>this</i> ("accepted/correct") taxon
|
|
791
|
* sorted by the different {@link SynonymRelationshipType categories of synonym relationships}.
|
|
792
|
* Each synonym is the source and <i>this</i> taxon is the target of a {@link SynonymRelationship synonym relationship}
|
|
793
|
* belonging to the {@link #getSynonymRelations() set of synonym relationships} assigned to <i>this</i> taxon.
|
|
794
|
*
|
|
795
|
* @see #getSynonyms()
|
|
796
|
* @see #getSynonymNames()
|
|
797
|
* @see #getSynonymRelations()
|
|
798
|
* @see #addSynonym(Synonym, SynonymRelationshipType)
|
|
799
|
* @see #addSynonym(Synonym, SynonymRelationshipType, ReferenceBase, String)
|
|
800
|
* @see #removeSynonymRelation(SynonymRelationship)
|
|
801
|
* @see #removeSynonym(Synonym)
|
|
802
|
*/
|
|
803
|
@Transient
|
|
804
|
public Set<Synonym> getSynonymsSortedByType(){
|
|
805
|
// FIXME: need to sort synonyms according to type!!!
|
|
806
|
logger.warn("getSynonymsSortedByType() not yet implemented");
|
|
807
|
return getSynonyms();
|
|
808
|
}
|
|
809
|
/**
|
|
810
|
* Returns the set of all {@link name.TaxonNameBase taxon names} used as {@link Synonym synonyms}
|
|
811
|
* of <i>this</i> ("accepted/correct") taxon. Each synonym is the source and
|
|
812
|
* <i>this</i> taxon is the target of a {@link SynonymRelationship synonym relationship} belonging
|
|
813
|
* to the {@link #getSynonymRelations() set of synonym relationships} assigned to <i>this</i> taxon.
|
|
814
|
*
|
|
815
|
* @see #getSynonyms()
|
|
816
|
* @see #getSynonymsSortedByType()
|
|
817
|
* @see #getSynonymRelations()
|
|
818
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType)
|
|
819
|
* @see #addSynonym(Synonym, SynonymRelationshipType, ReferenceBase, String)
|
|
820
|
* @see #removeSynonymRelation(SynonymRelationship)
|
|
821
|
* @see #removeSynonym(Synonym)
|
|
822
|
*/
|
|
823
|
@Transient
|
|
824
|
public Set<TaxonNameBase> getSynonymNames(){
|
|
825
|
Set<TaxonNameBase> names = new HashSet<TaxonNameBase>();
|
|
826
|
for (SynonymRelationship rel: this.getSynonymRelations()){
|
|
827
|
names.add(rel.getSynonym().getName());
|
|
828
|
}
|
|
829
|
return names;
|
|
830
|
}
|
|
831
|
/**
|
|
832
|
* Creates a new {@link SynonymRelationship synonym relationship} (with the given {@link Synonym synonym}
|
|
833
|
* and with the given {@link SynonymRelationshipType synonym relationship type}), returns it and adds it
|
|
834
|
* to the set of {@link #getSynonymRelations() synonym relationships} assigned to <i>this</i> taxon.
|
|
835
|
* The new synonym relationship will also be added to the set of
|
|
836
|
* {@link Synonym#getSynonymRelations() synonym relationships} belonging to the synonym
|
|
837
|
* involved in this synonym relationship.<BR>
|
|
838
|
* The returned synonym relationship allows to add further information to it.
|
|
839
|
*
|
|
840
|
* @param synonym the synonym involved in the relationship to be created
|
|
841
|
* and added to <i>this</i> taxon's synonym relationships set
|
|
842
|
* @param synonymType the synonym relationship category of the synonym
|
|
843
|
* relationship to be added
|
|
844
|
* @return the created synonym relationship
|
|
845
|
* @see #addSynonymRelation(SynonymRelationship)
|
|
846
|
* @see #addSynonym(Synonym, SynonymRelationshipType, ReferenceBase, String)
|
|
847
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType)
|
|
848
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType, ReferenceBase, String)
|
|
849
|
* @see #addHomotypicSynonym(Synonym, ReferenceBase, String)
|
|
850
|
* @see #addHomotypicSynonymName(TaxonNameBase, ReferenceBase, String)
|
|
851
|
* @see #addHeterotypicSynonymName(TaxonNameBase)
|
|
852
|
* @see #addHeterotypicSynonymName(TaxonNameBase, HomotypicalGroup, ReferenceBase, String)
|
|
853
|
* @see #getSynonymRelations()
|
|
854
|
* @see #removeSynonym(Synonym)
|
|
855
|
* @see Synonym#getSynonymRelations()
|
|
856
|
*/
|
|
857
|
public SynonymRelationship addSynonym(Synonym synonym, SynonymRelationshipType synonymType){
|
|
858
|
return addSynonym(synonym, synonymType, null, null);
|
|
859
|
}
|
|
860
|
/**
|
|
861
|
* Creates a new {@link SynonymRelationship synonym relationship} (with the given {@link Synonym synonym},
|
|
862
|
* with the given {@link SynonymRelationshipType synonym relationship type} and with the
|
|
863
|
* {@link reference.ReferenceBase reference source} on which the relationship assertion is based),
|
|
864
|
* returns it and adds it to the set of {@link #getSynonymRelations() synonym relationships}
|
|
865
|
* assigned to <i>this</i> taxon. The new synonym relationship will also be
|
|
866
|
* added to the set of {@link Synonym#getSynonymRelations() synonym relationships} belonging to the synonym
|
|
867
|
* involved in this synonym relationship.<BR>
|
|
868
|
* The returned synonym relationship allows to add further information to it.
|
|
869
|
*
|
|
870
|
* @param synonym the synonym involved in the relationship to be created
|
|
871
|
* and added to <i>this</i> taxon's synonym relationships set
|
|
872
|
* @param synonymType the synonym relationship category of the synonym
|
|
873
|
* relationship to be added
|
|
874
|
* @param citation the reference source for the new synonym relationship
|
|
875
|
* @param microcitation the string with the details describing the exact localisation within the reference
|
|
876
|
* @return the created synonym relationship
|
|
877
|
* @see #addSynonymRelation(SynonymRelationship)
|
|
878
|
* @see #addSynonym(Synonym, SynonymRelationshipType, ReferenceBase, String)
|
|
879
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType)
|
|
880
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType, ReferenceBase, String)
|
|
881
|
* @see #addHomotypicSynonym(Synonym, ReferenceBase, String)
|
|
882
|
* @see #addHomotypicSynonymName(TaxonNameBase, ReferenceBase, String)
|
|
883
|
* @see #addHeterotypicSynonymName(TaxonNameBase)
|
|
884
|
* @see #addHeterotypicSynonymName(TaxonNameBase, HomotypicalGroup, ReferenceBase, String)
|
|
885
|
* @see #getSynonymRelations()
|
|
886
|
* @see #removeSynonym(Synonym)
|
|
887
|
* @see Synonym#getSynonymRelations()
|
|
888
|
*/
|
|
889
|
public SynonymRelationship addSynonym(Synonym synonym, SynonymRelationshipType synonymType, ReferenceBase citation, String citationMicroReference){
|
|
890
|
SynonymRelationship synonymRelationship = new SynonymRelationship(synonym, this, synonymType, citation, citationMicroReference);
|
|
891
|
return synonymRelationship;
|
|
892
|
}
|
|
893
|
|
|
894
|
/**
|
|
895
|
* Creates a new {@link Synonym synonym} (with the given {@link name.TaxonNameBase taxon name}),
|
|
896
|
* a new {@link SynonymRelationship synonym relationship} (with the new synonym and with the given
|
|
897
|
* {@link SynonymRelationshipType synonym relationship type}), returns the relationship and adds it
|
|
898
|
* to the set of {@link #getSynonymRelations() synonym relationships} assigned to <i>this</i> taxon.
|
|
899
|
* The new synonym will have the same {@link TaxonBase#getSec() concept reference}
|
|
900
|
* as <i>this</i> taxon. The new synonym relationship will also be added to
|
|
901
|
* the set of {@link Synonym#getSynonymRelations() synonym relationships} belonging
|
|
902
|
* to the created synonym.<BR>
|
|
903
|
* The returned synonym relationship allows to add further information to it.
|
|
904
|
*
|
|
905
|
* @param synonymName the taxon name to be used as a synonym to be added
|
|
906
|
* to <i>this</i> taxon's set of synonyms
|
|
907
|
* @param synonymType the synonym relationship category of the synonym
|
|
908
|
* relationship to be added
|
|
909
|
* @return the created synonym relationship
|
|
910
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType, ReferenceBase, String)
|
|
911
|
* @see #addSynonym(Synonym, SynonymRelationshipType)
|
|
912
|
* @see #addSynonym(Synonym, SynonymRelationshipType, ReferenceBase, String)
|
|
913
|
* @see #addSynonymRelation(SynonymRelationship)
|
|
914
|
* @see #addHomotypicSynonym(Synonym, ReferenceBase, String)
|
|
915
|
* @see #addHomotypicSynonymName(TaxonNameBase, ReferenceBase, String)
|
|
916
|
* @see #addHeterotypicSynonymName(TaxonNameBase)
|
|
917
|
* @see #addHeterotypicSynonymName(TaxonNameBase, HomotypicalGroup, ReferenceBase, String)
|
|
918
|
* @see #getSynonymRelations()
|
|
919
|
* @see #removeSynonym(Synonym)
|
|
920
|
* @see Synonym#getSynonymRelations()
|
|
921
|
*/
|
|
922
|
public SynonymRelationship addSynonymName(TaxonNameBase synonymName, SynonymRelationshipType synonymType){
|
|
923
|
return addSynonymName(synonymName, synonymType, null, null);
|
|
924
|
}
|
|
925
|
/**
|
|
926
|
* Creates a new {@link Synonym synonym} (with the given {@link name.TaxonNameBase taxon name}),
|
|
927
|
* a new {@link SynonymRelationship synonym relationship} (with the new synonym, with the given
|
|
928
|
* {@link SynonymRelationshipType synonym relationship type} and with the {@link reference.ReferenceBase reference source}
|
|
929
|
* on which the relationship assertion is based), returns the relationship
|
|
930
|
* and adds it to the set of {@link #getSynonymRelations() synonym relationships} assigned
|
|
931
|
* to <i>this</i> taxon. The new synonym will have the same {@link TaxonBase#getSec() concept reference}
|
|
932
|
* as <i>this</i> taxon. The new synonym relationship will also be added to
|
|
933
|
* the set of {@link Synonym#getSynonymRelations() synonym relationships} belonging
|
|
934
|
* to the created synonym.<BR>
|
|
935
|
* The returned synonym relationship allows to add further information to it.
|
|
936
|
*
|
|
937
|
* @param synonymName the taxon name to be used as a synonym to be added
|
|
938
|
* to <i>this</i> taxon's set of synonyms
|
|
939
|
* @param synonymType the synonym relationship category of the synonym
|
|
940
|
* relationship to be added
|
|
941
|
* @param citation the reference source for the new synonym relationship
|
|
942
|
* @param microcitation the string with the details describing the exact localisation within the reference
|
|
943
|
* @return the created synonym relationship
|
|
944
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType, ReferenceBase, String)
|
|
945
|
* @see #addSynonym(Synonym, SynonymRelationshipType)
|
|
946
|
* @see #addSynonym(Synonym, SynonymRelationshipType, ReferenceBase, String)
|
|
947
|
* @see #addSynonymRelation(SynonymRelationship)
|
|
948
|
* @see #addHomotypicSynonym(Synonym, ReferenceBase, String)
|
|
949
|
* @see #addHomotypicSynonymName(TaxonNameBase, ReferenceBase, String)
|
|
950
|
* @see #addHeterotypicSynonymName(TaxonNameBase)
|
|
951
|
* @see #addHeterotypicSynonymName(TaxonNameBase, HomotypicalGroup, ReferenceBase, String)
|
|
952
|
* @see #getSynonymRelations()
|
|
953
|
* @see #removeSynonym(Synonym)
|
|
954
|
* @see Synonym#getSynonymRelations()
|
|
955
|
*/
|
|
956
|
public SynonymRelationship addSynonymName(TaxonNameBase synonymName, SynonymRelationshipType synonymType, ReferenceBase citation, String citationMicroReference){
|
|
957
|
Synonym synonym = Synonym.NewInstance(synonymName, this.getSec());
|
|
958
|
return addSynonym(synonym, synonymType, citation, citationMicroReference);
|
|
959
|
}
|
|
960
|
|
|
961
|
|
|
962
|
/**
|
|
963
|
* Creates a new {@link Synonym synonym} (with the given {@link name.TaxonNameBase taxon name}),
|
|
964
|
* a new {@link SynonymRelationship synonym relationship} (with the new synonym and with the
|
|
965
|
* {@link SynonymRelationshipType#HETEROTYPIC_SYNONYM_OF() "is heterotypic synonym of" relationship type}),
|
|
966
|
* returns the relationship and adds it to the set of
|
|
967
|
* {@link #getSynonymRelations() synonym relationships} assigned to <i>this</i> taxon.
|
|
968
|
* The new synonym will have the same {@link TaxonBase#getSec() concept reference}
|
|
969
|
* as <i>this</i> taxon. The new synonym relationship will also be added to
|
|
970
|
* the set of {@link Synonym#getSynonymRelations() synonym relationships} belonging
|
|
971
|
* to the created synonym.<BR>
|
|
972
|
* The returned synonym relationship allows to add further information to it.
|
|
973
|
*
|
|
974
|
* @param synonymName the taxon name to be used as an heterotypic synonym
|
|
975
|
* to be added to <i>this</i> taxon's set of synonyms
|
|
976
|
* @return the created synonym relationship
|
|
977
|
* @see #addHeterotypicSynonymName(TaxonNameBase, HomotypicalGroup, ReferenceBase, String)
|
|
978
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType)
|
|
979
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType, ReferenceBase, String)
|
|
980
|
* @see #addSynonym(Synonym, SynonymRelationshipType)
|
|
981
|
* @see #addSynonym(Synonym, SynonymRelationshipType, ReferenceBase, String)
|
|
982
|
* @see #addSynonymRelation(SynonymRelationship)
|
|
983
|
* @see #addHomotypicSynonym(Synonym, ReferenceBase, String)
|
|
984
|
* @see #addHomotypicSynonymName(TaxonNameBase, ReferenceBase, String)
|
|
985
|
* @see #getSynonymRelations()
|
|
986
|
* @see #removeSynonym(Synonym)
|
|
987
|
* @see Synonym#getSynonymRelations()
|
|
988
|
*/
|
|
989
|
public SynonymRelationship addHeterotypicSynonymName(TaxonNameBase synonymName){
|
|
990
|
return addHeterotypicSynonymName(synonymName, null, null, null);
|
|
991
|
}
|
|
992
|
|
|
993
|
|
|
994
|
/**
|
|
995
|
* Creates a new {@link Synonym synonym} (with the given {@link name.TaxonNameBase taxon name}),
|
|
996
|
* a new {@link SynonymRelationship synonym relationship} (with the new synonym, with the
|
|
997
|
* {@link SynonymRelationshipType#HETEROTYPIC_SYNONYM_OF() "is heterotypic synonym of" relationship type}
|
|
998
|
* and with the {@link reference.ReferenceBase reference source}
|
|
999
|
* on which the relationship assertion is based), returns the relationship
|
|
1000
|
* and adds it to the set of {@link #getSynonymRelations() synonym relationships} assigned
|
|
1001
|
* to <i>this</i> taxon. The new synonym will have the same {@link TaxonBase#getSec() concept reference}
|
|
1002
|
* as <i>this</i> taxon. Furthermore the new synonym relationship will be
|
|
1003
|
* added to the set of {@link Synonym#getSynonymRelations() synonym relationships} belonging
|
|
1004
|
* to the created synonym and the taxon name used as synonym will be added
|
|
1005
|
* to the given {@link name.HomotypicalGroup homotypical group}.<BR>
|
|
1006
|
* The returned synonym relationship allows to add further information to it.
|
|
1007
|
*
|
|
1008
|
* @param synonymName the taxon name to be used as an heterotypic synonym
|
|
1009
|
* to be added to <i>this</i> taxon's set of synonyms
|
|
1010
|
* @param homotypicalGroup the homotypical group to which the taxon name
|
|
1011
|
* of the synonym will be added
|
|
1012
|
* @param citation the reference source for the new synonym relationship
|
|
1013
|
* @param microcitation the string with the details describing the exact localisation
|
|
1014
|
* within the reference
|
|
1015
|
* @return the created synonym relationship
|
|
1016
|
* @see #addHeterotypicSynonymName(TaxonNameBase)
|
|
1017
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType, ReferenceBase, String)
|
|
1018
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType)
|
|
1019
|
* @see #addSynonym(Synonym, SynonymRelationshipType)
|
|
1020
|
* @see #addSynonym(Synonym, SynonymRelationshipType, ReferenceBase, String)
|
|
1021
|
* @see #addSynonymRelation(SynonymRelationship)
|
|
1022
|
* @see #addHomotypicSynonym(Synonym, ReferenceBase, String)
|
|
1023
|
* @see #addHomotypicSynonymName(TaxonNameBase, ReferenceBase, String)
|
|
1024
|
* @see #getSynonymRelations()
|
|
1025
|
* @see #removeSynonym(Synonym)
|
|
1026
|
* @see Synonym#getSynonymRelations()
|
|
1027
|
*/
|
|
1028
|
public SynonymRelationship addHeterotypicSynonymName(TaxonNameBase synonymName, HomotypicalGroup homotypicalGroup, ReferenceBase citation, String microCitation){
|
|
1029
|
Synonym synonym = Synonym.NewInstance(synonymName, this.getSec());
|
|
1030
|
if (homotypicalGroup != null){
|
|
1031
|
homotypicalGroup.addTypifiedName(synonymName);
|
|
1032
|
}
|
|
1033
|
return addSynonym(synonym, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), citation, microCitation);
|
|
1034
|
}
|
|
1035
|
|
|
1036
|
/**
|
|
1037
|
* Creates a new {@link Synonym synonym} (with the given {@link name.TaxonNameBase taxon name}),
|
|
1038
|
* a new {@link SynonymRelationship synonym relationship} (with the new synonym, with the
|
|
1039
|
* {@link SynonymRelationshipType#HOMOTYPIC_SYNONYM_OF() "is homotypic synonym of" relationship type})
|
|
1040
|
* and with the {@link reference.ReferenceBase reference source}
|
|
1041
|
* on which the relationship assertion is based), returns the relationship
|
|
1042
|
* and adds it to the set of {@link #getSynonymRelations() synonym relationships} assigned
|
|
1043
|
* to <i>this</i> taxon. The new synonym will have the same {@link TaxonBase#getSec() concept reference}
|
|
1044
|
* as <i>this</i> taxon. Furthermore the new synonym relationship will be
|
|
1045
|
* added to the set of {@link Synonym#getSynonymRelations() synonym relationships} belonging
|
|
1046
|
* to the created synonym and the taxon name used as synonym will be added
|
|
1047
|
* to the same {@link name.HomotypicalGroup homotypical group} to which the taxon name
|
|
1048
|
* of <i>this</i> taxon belongs.<BR>
|
|
1049
|
* The returned synonym relationship allows to add further information to it.
|
|
1050
|
*
|
|
1051
|
* @param synonymName the taxon name to be used as an homotypic synonym
|
|
1052
|
* to be added to <i>this</i> taxon's set of synonyms
|
|
1053
|
* @param citation the reference source for the new synonym relationship
|
|
1054
|
* @param microcitation the string with the details describing the exact localisation
|
|
1055
|
* within the reference
|
|
1056
|
* @return the created synonym relationship
|
|
1057
|
* @see #addHomotypicSynonym(Synonym, ReferenceBase, String)
|
|
1058
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType, ReferenceBase, String)
|
|
1059
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType)
|
|
1060
|
* @see #addSynonym(Synonym, SynonymRelationshipType)
|
|
1061
|
* @see #addSynonym(Synonym, SynonymRelationshipType, ReferenceBase, String)
|
|
1062
|
* @see #addSynonymRelation(SynonymRelationship)
|
|
1063
|
* @see #addHeterotypicSynonymName(TaxonNameBase)
|
|
1064
|
* @see #addHeterotypicSynonymName(TaxonNameBase, HomotypicalGroup, ReferenceBase, String)
|
|
1065
|
* @see #getSynonymRelations()
|
|
1066
|
* @see #removeSynonym(Synonym)
|
|
1067
|
* @see Synonym#getSynonymRelations()
|
|
1068
|
*/
|
|
1069
|
public SynonymRelationship addHomotypicSynonymName(TaxonNameBase synonymName, ReferenceBase citation, String microCitation){
|
|
1070
|
Synonym synonym = Synonym.NewInstance(synonymName, this.getSec());
|
|
1071
|
return addHomotypicSynonym(synonym, citation, microCitation);
|
|
1072
|
}
|
|
1073
|
|
|
1074
|
/**
|
|
1075
|
* Creates a new {@link SynonymRelationship synonym relationship} (with the given {@link Synonym synonym},
|
|
1076
|
* with the {@link SynonymRelationshipType#HOMOTYPIC_SYNONYM_OF() "is homotypic synonym of" relationship type}
|
|
1077
|
* and with the {@link reference.ReferenceBase reference source} on which the relationship
|
|
1078
|
* assertion is based), returns it and adds it to the set of
|
|
1079
|
* {@link #getSynonymRelations() synonym relationships} assigned to <i>this</i> taxon.
|
|
1080
|
* Furthermore the new synonym relationship will be added to the set of
|
|
1081
|
* {@link Synonym#getSynonymRelations() synonym relationships} belonging to the synonym
|
|
1082
|
* involved in this synonym relationship and the {@link name.TaxonNameBase taxon name}
|
|
1083
|
* used as synonym will be added to the same {@link name.HomotypicalGroup homotypical group}
|
|
1084
|
* to which the taxon name of <i>this</i> taxon belongs.<BR>
|
|
1085
|
* The returned synonym relationship allows to add further information to it.
|
|
1086
|
*
|
|
1087
|
* @param synonym the synonym involved in the "is homotypic synonym of" relationship to be created
|
|
1088
|
* and added to <i>this</i> taxon's synonym relationships set
|
|
1089
|
* @param citation the reference source for the new synonym relationship
|
|
1090
|
* @param microcitation the string with the details describing the exact localisation within the reference
|
|
1091
|
* @return the created synonym relationship
|
|
1092
|
* @see #addHomotypicSynonymName(TaxonNameBase, ReferenceBase, String)
|
|
1093
|
* @see #addSynonym(Synonym, SynonymRelationshipType)
|
|
1094
|
* @see #addSynonym(Synonym, SynonymRelationshipType, ReferenceBase, String)
|
|
1095
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType, ReferenceBase, String)
|
|
1096
|
* @see #addSynonymName(TaxonNameBase, SynonymRelationshipType)
|
|
1097
|
* @see #addSynonymRelation(SynonymRelationship)
|
|
1098
|
* @see #addHeterotypicSynonymName(TaxonNameBase)
|
|
1099
|
* @see #addHeterotypicSynonymName(TaxonNameBase, HomotypicalGroup, ReferenceBase, String)
|
|
1100
|
* @see #getSynonymRelations()
|
|
1101
|
* @see #removeSynonym(Synonym)
|
|
1102
|
* @see Synonym#getSynonymRelations()
|
|
1103
|
*/
|
|
1104
|
public SynonymRelationship addHomotypicSynonym(Synonym synonym, ReferenceBase citation, String microCitation){
|
|
1105
|
if (this.getName() != null){
|
|
1106
|
this.getName().getHomotypicalGroup().addTypifiedName(synonym.getName());
|
|
1107
|
}
|
|
1108
|
SynonymRelationship synRel = addSynonym(synonym, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF(), citation, microCitation);
|
|
1109
|
return synRel;
|
|
1110
|
}
|
|
1111
|
|
|
1112
|
/**
|
|
1113
|
* Removes the element(s) from the set of {@link SynonymRelationship synonym relationships}
|
|
1114
|
* assigned to <i>this</i> ("accepted/correct") taxon in which the given synonym is involved.
|
|
1115
|
* Due to bidirectionality the same synonym relationships will also be
|
|
1116
|
* removed from the set of synonym relationships assigned to the
|
|
1117
|
* {@link Synonym#getSynonymRelations() synonym} involved in the relationship. Furthermore the content of
|
|
1118
|
* the {@link SynonymRelationship#getAcceptedTaxon() accepted taxon attribute} and of the
|
|
1119
|
* {@link SynonymRelationship#getSynonym() synonym attribute} within the synonym relationships
|
|
1120
|
* themselves will be set to "null".
|
|
1121
|
*
|
|
1122
|
* @param synonym the synonym involved in the synonym relationship which should be deleted
|
|
1123
|
* @see #getSynonymRelations()
|
|
1124
|
* @see #addSynonym(Synonym, SynonymRelationshipType)
|
|
1125
|
* @see #addSynonym(Synonym, SynonymRelationshipType, ReferenceBase, String)
|
|
1126
|
* @see #removeSynonymRelation(SynonymRelationship)
|
|
1127
|
*/
|
|
1128
|
public void removeSynonym(Synonym synonym){
|
|
1129
|
Set<SynonymRelationship> synonymRelationships = new HashSet<SynonymRelationship>();
|
|
1130
|
synonymRelationships.addAll(this.getSynonymRelations());
|
|
1131
|
for(SynonymRelationship synonymRelationship : synonymRelationships){
|
|
1132
|
if (synonymRelationship.getAcceptedTaxon().equals(this) && synonymRelationship.getSynonym().equals(synonym)){
|
|
1133
|
this.removeSynonymRelation(synonymRelationship);
|
|
1134
|
}
|
|
1135
|
}
|
|
1136
|
}
|
|
1137
|
|
|
1138
|
|
|
1139
|
|
|
1140
|
/**
|
|
1141
|
* Returns an {@link java.lang.Iterable#iterator() iterator} over the set of taxa which
|
|
1142
|
* are {@link #getTaxonomicChildren() taxonomic children} of <i>this</i> taxon.
|
|
1143
|
*
|
|
1144
|
* @see #getTaxonomicChildren()
|
|
1145
|
* @see java.lang.Iterable#iterator()
|
|
1146
|
*/
|
|
1147
|
public Iterator<Taxon> iterator() {
|
|
1148
|
return new TaxonIterator(this.getTaxonomicChildren());
|
|
1149
|
}
|
|
1150
|
/**
|
|
1151
|
* inner iterator class for the iterable interface
|
|
1152
|
* @author m.doering
|
|
1153
|
*
|
|
1154
|
*/
|
|
1155
|
private class TaxonIterator implements Iterator<Taxon> {
|
|
1156
|
private Taxon[] items;
|
|
1157
|
private int i= 0;
|
|
1158
|
public TaxonIterator(Set<Taxon> items) {
|
|
1159
|
// check for null being passed in etc.
|
|
1160
|
this.items= items.toArray(new Taxon[0]);
|
|
1161
|
}
|
|
1162
|
// interface implementation
|
|
1163
|
public boolean hasNext() { return i < items.length; }
|
|
1164
|
public Taxon next() { return items[i++]; }
|
|
1165
|
public void remove() { throw new UnsupportedOperationException(); }
|
|
1166
|
}
|
|
1167
|
|
|
1168
|
/**
|
|
1169
|
* Retrieves the ordered list (depending on the date of publication) of
|
|
1170
|
* homotypic {@link Synonym synonyms} (according to the same {@link reference.ReferenceBase reference}
|
|
1171
|
* as for <i>this</i> taxon) under the condition that the {@link name.TaxonNameBase taxon names}
|
|
1172
|
* of these synonyms and the taxon name of <i>this</i> taxon belong to the
|
|
1173
|
* same {@link name.HomotypicalGroup homotypical group}.
|
|
1174
|
*
|
|
1175
|
* @return the ordered list of homotypic synonyms
|
|
1176
|
* @see #getHomotypicSynonymsByHomotypicRelationship()
|
|
1177
|
* @see #getSynonyms()
|
|
1178
|
* @see #getHomotypicSynonymyGroups()
|
|
1179
|
* @see name.HomotypicalGroup
|
|
1180
|
* @see name.HomotypicalGroup#getSynonymsInGroup(ReferenceBase)
|
|
1181
|
*/
|
|
1182
|
@Transient
|
|
1183
|
public List<Synonym> getHomotypicSynonymsByHomotypicGroup(){
|
|
1184
|
if (this.getHomotypicGroup() == null){
|
|
1185
|
return null;
|
|
1186
|
}else{
|
|
1187
|
return this.getHomotypicGroup().getSynonymsInGroup(this.getSec());
|
|
1188
|
}
|
|
1189
|
}
|
|
1190
|
|
|
1191
|
/**
|
|
1192
|
* Retrieves the ordered list (depending on the date of publication) of
|
|
1193
|
* homotypic {@link Synonym synonyms} (according to the same {@link reference.ReferenceBase reference}
|
|
1194
|
* as for <i>this</i> taxon) under the condition that these synonyms and
|
|
1195
|
* <i>this</i> taxon are involved in {@link SynonymRelationship synonym relationships} with an
|
|
1196
|
* "is homotypic synonym of" {@link SynonymRelationshipType#HOMOTYPIC_SYNONYM_OF() synonym relationship type}.
|
|
1197
|
*
|
|
1198
|
* @return the ordered list of homotypic synonyms
|
|
1199
|
* @see #getHomotypicSynonymsByHomotypicGroup()
|
|
1200
|
* @see #getSynonyms()
|
|
1201
|
* @see #getHomotypicSynonymyGroups()
|
|
1202
|
* @see SynonymRelationshipType
|
|
1203
|
*/
|
|
1204
|
@Transient
|
|
1205
|
public List<Synonym> getHomotypicSynonymsByHomotypicRelationship(){
|
|
1206
|
Set<SynonymRelationship> synonymRelations = this.getSynonymRelations();
|
|
1207
|
List<Synonym> result = new ArrayList<Synonym>();
|
|
1208
|
for(SynonymRelationship synonymRelation : synonymRelations) {
|
|
1209
|
if(synonymRelation.getType().equals(SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF())){
|
|
1210
|
result.add(synonymRelation.getSynonym());
|
|
1211
|
}
|
|
1212
|
}
|
|
1213
|
return result;
|
|
1214
|
}
|
|
1215
|
|
|
1216
|
/**
|
|
1217
|
* Returns the ordered list of all {@link name.HomotypicalGroup homotypical groups} {@link Synonym synonyms} of
|
|
1218
|
* <i>this</i> taxon belongs to. {@link name.TaxonNameBase Taxon names} of homotypic synonyms
|
|
1219
|
* belong to the same homotypical group as the taxon name of <i>this</i>
|
|
1220
|
* taxon. Taxon names of heterotypic synonyms belong to at least one other
|
|
1221
|
* homotypical group. <BR>
|
|
1222
|
* The list returned is ordered according to the date of publication of the
|
|
1223
|
* first published name within each homotypical group.
|
|
1224
|
*
|
|
1225
|
* @see #getHeterotypicSynonymyGroups()
|
|
1226
|
* @see #getSynonyms()
|
|
1227
|
* @see name.HomotypicalGroup
|
|
1228
|
*/
|
|
1229
|
@Transient
|
|
1230
|
public List<HomotypicalGroup> getHomotypicSynonymyGroups(){
|
|
1231
|
List<HomotypicalGroup> result = new ArrayList<HomotypicalGroup>();
|
|
1232
|
result.add(this.getHomotypicGroup());
|
|
1233
|
for (TaxonNameBase taxonNameBase :this.getSynonymNames()){
|
|
1234
|
if (!result.contains(taxonNameBase.getHomotypicalGroup())){
|
|
1235
|
result.add(taxonNameBase.getHomotypicalGroup());
|
|
1236
|
}
|
|
1237
|
}
|
|
1238
|
// TODO: sort list according to date of first published name within each group
|
|
1239
|
return result;
|
|
1240
|
}
|
|
1241
|
|
|
1242
|
/**
|
|
1243
|
* Returns the List of all homotypic groups heterotypic synonyms of this taxon belongs too.
|
|
1244
|
* This does not include the homotypic group of <i>this</i> taxon.
|
|
1245
|
* @return
|
|
1246
|
*/
|
|
1247
|
/**
|
|
1248
|
* Returns the ordered list of all {@link name.HomotypicalGroup homotypical groups} heterotypic
|
|
1249
|
* {@link Synonym synonyms} of <i>this</i> taxon belongs to.
|
|
1250
|
* {@link name.TaxonNameBase Taxon names} of heterotypic synonyms belong to at least
|
|
1251
|
* one homotypical group which cannot be the homotypical group to which the
|
|
1252
|
* taxon name of <i>this</i> taxon belongs. This method returns the same
|
|
1253
|
* list as the {@link #getHomotypicSynonymyGroups() getHomotypicSynonymyGroups} method
|
|
1254
|
* but the homotypical group to which the taxon name of <i>this</i> taxon
|
|
1255
|
* belongs.<BR>
|
|
1256
|
* The list returned is ordered according to the date of publication of the
|
|
1257
|
* first published name within each homotypical group.
|
|
1258
|
*
|
|
1259
|
* @see #getHeterotypicSynonymyGroups()
|
|
1260
|
* @see #getSynonyms()
|
|
1261
|
* @see SynonymRelationshipType#HETEROTYPIC_SYNONYM_OF()
|
|
1262
|
* @see name.HomotypicalGroup
|
|
1263
|
*/
|
|
1264
|
@Transient
|
|
1265
|
public List<HomotypicalGroup> getHeterotypicSynonymyGroups(){
|
|
1266
|
List<HomotypicalGroup> list = getHomotypicSynonymyGroups();
|
|
1267
|
list.remove(this.getHomotypicGroup());
|
|
1268
|
//sort
|
|
1269
|
Map<Synonym, HomotypicalGroup> map = new HashMap<Synonym, HomotypicalGroup>();
|
|
1270
|
for (HomotypicalGroup homoGroup: list){
|
|
1271
|
List<Synonym> synonymList = homoGroup.getSynonymsInGroup(getSec());
|
|
1272
|
if (synonymList.size() > 0){
|
|
1273
|
map.put(synonymList.get(0), homoGroup);
|
|
1274
|
}
|
|
1275
|
}
|
|
1276
|
List<Synonym> keyList = new ArrayList<Synonym>();
|
|
1277
|
keyList.addAll(map.keySet());
|
|
1278
|
Collections.sort(keyList, new TaxonComparator());
|
|
1279
|
|
|
1280
|
List<HomotypicalGroup> result = new ArrayList<HomotypicalGroup>();
|
|
1281
|
for(Synonym synonym: keyList){
|
|
1282
|
result.add(map.get(synonym));
|
|
1283
|
}
|
|
1284
|
//sort end
|
|
1285
|
return result;
|
|
1286
|
}
|
|
1287
|
|
|
1288
|
}
|