|
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.name;
|
|
11
|
|
|
12
|
|
|
13
|
import java.util.HashMap;
|
|
14
|
import java.util.List;
|
|
15
|
import java.util.Map;
|
|
16
|
import java.util.UUID;
|
|
17
|
|
|
18
|
import javax.persistence.Entity;
|
|
19
|
import javax.persistence.Transient;
|
|
20
|
import javax.xml.bind.annotation.XmlAccessType;
|
|
21
|
import javax.xml.bind.annotation.XmlAccessorType;
|
|
22
|
import javax.xml.bind.annotation.XmlType;
|
|
23
|
|
|
24
|
import org.apache.commons.lang.StringUtils;
|
|
25
|
import org.apache.log4j.Logger;
|
|
26
|
import org.hibernate.envers.Audited;
|
|
27
|
|
|
28
|
import eu.etaxonomy.cdm.model.common.DefinedTermBase;
|
|
29
|
import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
|
|
30
|
import eu.etaxonomy.cdm.model.common.TermType;
|
|
31
|
import eu.etaxonomy.cdm.model.common.TermVocabulary;
|
|
32
|
|
|
33
|
/**
|
|
34
|
* The class representing the categories of {@link NameRelationship taxon name relationships} between
|
|
35
|
* two {@link TaxonNameBase taxon names}. These name relationship types are
|
|
36
|
* based on the concrete {@link NomenclaturalCode nomenclatural code} governing
|
|
37
|
* the taxon names involved in the name relationship or on decisions taken by
|
|
38
|
* the competent authorities; they do not depend on the use made of these
|
|
39
|
* taxon names in a particular reference or in a particular taxonomic treatment.
|
|
40
|
* Most relationships are to be understood as 'is .... of': for instance
|
|
41
|
* <i>Linum radiola</i> L. is a replaced synonym of <i>Radiola linoides</i> Roth or
|
|
42
|
* <i>Astragalus rhizanthus</i> Boiss. is a later homonym of
|
|
43
|
* <i>Astragalus rhizanthus</i> Royle.
|
|
44
|
* <P>
|
|
45
|
* A standard (ordered) list of name relationship type instances will be
|
|
46
|
* automatically created as the project starts. But this class allows to extend
|
|
47
|
* this standard list by creating new instances of additional name relationship
|
|
48
|
* types if needed.
|
|
49
|
* <P>
|
|
50
|
* This class corresponds partially to: <ul>
|
|
51
|
* <li> TaxonRelationshipTerm and NomenclaturalNoteTypeTerm according to the TDWG ontology
|
|
52
|
* <li> RelationshipType and NomenclaturalNoteType according to the TCS
|
|
53
|
* </ul>
|
|
54
|
*
|
|
55
|
* @author m.doering
|
|
56
|
* @created 08-Nov-2007 13:06:38
|
|
57
|
*/
|
|
58
|
@XmlAccessorType(XmlAccessType.FIELD)
|
|
59
|
@XmlType(name = "NameRelationshipType")
|
|
60
|
@Entity
|
|
61
|
//@Indexed disabled to reduce clutter in indexes, since this type is not used by any search
|
|
62
|
//@Indexed(index = "eu.etaxonomy.cdm.model.common.DefinedTermBase")
|
|
63
|
@Audited
|
|
64
|
public class NameRelationshipType extends RelationshipTermBase<NameRelationshipType> {
|
|
65
|
private static final long serialVersionUID = 8504916205254159334L;
|
|
66
|
|
|
67
|
static Logger logger = Logger.getLogger(NameRelationshipType.class);
|
|
68
|
|
|
69
|
private static final UUID uuidOrthographicVariant = UUID.fromString("eeaea868-c4c1-497f-b9fe-52c9fc4aca53");
|
|
70
|
private static final UUID uuidMisspelling = UUID.fromString("c6f9afcb-8287-4a2b-a6f6-4da3a073d5de");
|
|
71
|
private static final UUID uuidEmendation = UUID.fromString("6e23ad45-3f2a-462b-ad87-d2389cd6e26c");
|
|
72
|
private static final UUID uuidLaterHomonym = UUID.fromString("80f06f65-58e0-4209-b811-cb40ad7220a6");
|
|
73
|
private static final UUID uuidTreatedAsLaterHomonym = UUID.fromString("2990a884-3302-4c8b-90b2-dfd31aaa2778");
|
|
74
|
private static final UUID uuidAlternativeName = UUID.fromString("049c6358-1094-4765-9fae-c9972a0e7780");
|
|
75
|
private static final UUID uuidBasionym = UUID.fromString("25792738-98de-4762-bac1-8c156faded4a");
|
|
76
|
private static final UUID uuidReplacedSynonym = UUID.fromString("71c67c38-d162-445b-b0c2-7aba56106696");
|
|
77
|
private static final UUID uuidConservedAgainst = UUID.fromString("e6439f95-bcac-4ebb-a8b5-69fa5ce79e6a");
|
|
78
|
private static final UUID uuidValidatedByName = UUID.fromString("a176c9ad-b4c2-4c57-addd-90373f8270eb");
|
|
79
|
private static final UUID uuidLaterValidatedByName = UUID.fromString("a25ee4c1-863a-4dab-9499-290bf9b89639");
|
|
80
|
private static final UUID uuidBlockingNameFor = UUID.fromString("1dab357f-2e12-4511-97a4-e5153589e6a6");
|
|
81
|
private static final UUID uuidLaterIsonym = UUID.fromString("29ab238d-598d-45b9-addd-003cf39ccc3e");
|
|
82
|
private static final UUID uuidOriginalSpellingFor = UUID.fromString("264d2be4-e378-4168-9760-a9512ffbddc4");
|
|
83
|
|
|
84
|
|
|
85
|
public static NameRelationshipType NewInstance(String term, String label, String labelAbbrev, boolean symmetric, boolean transitive) {
|
|
86
|
return new NameRelationshipType(term, label, labelAbbrev, symmetric, transitive);
|
|
87
|
}
|
|
88
|
|
|
89
|
|
|
90
|
protected static Map<UUID, NameRelationshipType> termMap = null;
|
|
91
|
|
|
92
|
protected static NameRelationshipType findTermByUuid(UUID uuid){
|
|
93
|
if (termMap == null || termMap.isEmpty()){
|
|
94
|
return getTermByClassAndUUID(NameRelationshipType.class, uuid);
|
|
95
|
} else {
|
|
96
|
return termMap.get(uuid);
|
|
97
|
}
|
|
98
|
}
|
|
99
|
|
|
100
|
|
|
101
|
//********************************** Constructor *********************************/
|
|
102
|
|
|
103
|
//for hibernate use only
|
|
104
|
@Deprecated
|
|
105
|
protected NameRelationshipType() {
|
|
106
|
super(TermType.NameRelationshipType);
|
|
107
|
}
|
|
108
|
|
|
109
|
/**
|
|
110
|
* Class constructor: creates an additional name relationship type
|
|
111
|
* instance with a description, a label, a label abbreviation and the flags
|
|
112
|
* indicating whether <i>this</i> new name relationship type is symmetric and/or
|
|
113
|
* transitive.
|
|
114
|
*
|
|
115
|
* @param term the string (in the default language) describing the
|
|
116
|
* new name relationship type to be created
|
|
117
|
* @param label the string identifying the new name relationship
|
|
118
|
* type to be created
|
|
119
|
* @param labelAbbrev the string identifying (in abbreviated form) the
|
|
120
|
* new name relationship type to be created
|
|
121
|
* @param symmetric the boolean indicating whether the new name
|
|
122
|
* relationship type to be created is symmetric
|
|
123
|
* @param transitive the boolean indicating whether the new name
|
|
124
|
* relationship type to be created is transitive
|
|
125
|
* @see #NameRelationshipType()
|
|
126
|
*/
|
|
127
|
private NameRelationshipType(String term, String label, String labelAbbrev, boolean symmetric, boolean transitive) {
|
|
128
|
super(TermType.NameRelationshipType, term, label, labelAbbrev, symmetric, transitive);
|
|
129
|
}
|
|
130
|
|
|
131
|
|
|
132
|
|
|
133
|
//************************** METHODS ********************************
|
|
134
|
|
|
135
|
/* (non-Javadoc)
|
|
136
|
* @see eu.etaxonomy.cdm.model.common.DefinedTermBase#resetTerms()
|
|
137
|
*/
|
|
138
|
@Override
|
|
139
|
public void resetTerms(){
|
|
140
|
termMap = null;
|
|
141
|
}
|
|
142
|
|
|
143
|
// TODO this method should be moved to consistency proof classes
|
|
144
|
/**
|
|
145
|
* Returns the boolean value indicating whether the nomenclatural status
|
|
146
|
* type of the {@link eu.etaxonomy.cdm.model.common.RelationshipBase#getRelatedFrom() first taxon name}
|
|
147
|
* involved in a name relationship with <i>this</i> name relationship type should
|
|
148
|
* be "invalid" (true) or not (false). Returns false if <i>this</i> name
|
|
149
|
* relationship status type is null.
|
|
150
|
*
|
|
151
|
* @see #isLegitimateType()
|
|
152
|
* @see #isIllegitimateType()
|
|
153
|
* @see NomenclaturalStatusType#isInvalidType()
|
|
154
|
* @see eu.etaxonomy.cdm.model.common.RelationshipBase#getRelatedFrom()
|
|
155
|
*/
|
|
156
|
@Transient
|
|
157
|
public boolean isInvalidType(){
|
|
158
|
if (this.equals(VALIDATED_BY_NAME()) ||
|
|
159
|
this.equals(LATER_VALIDATED_BY_NAME())
|
|
160
|
){
|
|
161
|
return true;
|
|
162
|
}else{
|
|
163
|
return false;
|
|
164
|
}
|
|
165
|
}
|
|
166
|
|
|
167
|
// TODO this method should be moved to consistency proof classes
|
|
168
|
/**
|
|
169
|
* Returns the boolean value indicating whether the nomenclatural status
|
|
170
|
* type of the {@link eu.etaxonomy.cdm.model.common.RelationshipBase#getRelatedFrom() first taxon name}
|
|
171
|
* involved in a name relationship with <i>this</i> name relationship type should
|
|
172
|
* be "legitimate" (true) or not (false). Returns false if <i>this</i> name
|
|
173
|
* relationship status type is null.
|
|
174
|
*
|
|
175
|
* @see #isInvalidType()
|
|
176
|
* @see #isIllegitimateType()
|
|
177
|
* @see NomenclaturalStatusType#isLegitimateType()
|
|
178
|
* @see eu.etaxonomy.cdm.model.common.RelationshipBase#getRelatedFrom()
|
|
179
|
*/
|
|
180
|
@Transient
|
|
181
|
public boolean isLegitimateType(){
|
|
182
|
if (this.equals(BASIONYM()) ||
|
|
183
|
this.equals(REPLACED_SYNONYM()) ||
|
|
184
|
this.equals(ALTERNATIVE_NAME()) ||
|
|
185
|
this.equals(CONSERVED_AGAINST())
|
|
186
|
){
|
|
187
|
return true;
|
|
188
|
}else{
|
|
189
|
return false;
|
|
190
|
}
|
|
191
|
}
|
|
192
|
|
|
193
|
// TODO this method should be moved to consistency proof classes
|
|
194
|
/**
|
|
195
|
* Returns the boolean value indicating whether the nomenclatural status
|
|
196
|
* type of the {@link eu.etaxonomy.cdm.model.common.RelationshipBase#getRelatedFrom() first taxon name}
|
|
197
|
* involved in a name relationship with <i>this</i> name relationship type should
|
|
198
|
* be "illegitimate" (true) or not (false). Returns false if <i>this</i> name
|
|
199
|
* relationship status type is null.
|
|
200
|
*
|
|
201
|
* @see #isInvalidType()
|
|
202
|
* @see #isLegitimateType()
|
|
203
|
* @see NomenclaturalStatusType#isIllegitimateType()
|
|
204
|
* @see eu.etaxonomy.cdm.model.common.RelationshipBase#getRelatedFrom()
|
|
205
|
*/
|
|
206
|
@Transient
|
|
207
|
public boolean isIllegitimateType(){
|
|
208
|
//TODO: implement isX method. Maybe as persistent class attribute?
|
|
209
|
//TODO: RejectedInFavour,
|
|
210
|
if (this.equals(LATER_HOMONYM()) ||
|
|
211
|
this.equals(TREATED_AS_LATER_HOMONYM())
|
|
212
|
){
|
|
213
|
return true;
|
|
214
|
}else{
|
|
215
|
return false;
|
|
216
|
}
|
|
217
|
}
|
|
218
|
|
|
219
|
@Transient
|
|
220
|
public boolean isBasionymRelation(){
|
|
221
|
if (BASIONYM() == null){
|
|
222
|
throw new IllegalStateException("NameRelationships have not been initialized yet. Please initialize DefinedTerms first");
|
|
223
|
}
|
|
224
|
return this.equals(BASIONYM());
|
|
225
|
}
|
|
226
|
|
|
227
|
@Transient
|
|
228
|
public boolean isReplacedSynonymRelation(){
|
|
229
|
if (REPLACED_SYNONYM() == null){
|
|
230
|
throw new IllegalStateException("NameRelationships have not been initialized yet. Please initialize DefinedTerms first");
|
|
231
|
}
|
|
232
|
return this.equals(REPLACED_SYNONYM());
|
|
233
|
}
|
|
234
|
|
|
235
|
|
|
236
|
/**
|
|
237
|
* Returns the "orthographic variant" name relationship type. The first
|
|
238
|
* {@link TaxonNameBase taxon name} involved in such a relationship is an
|
|
239
|
* orthographic variant of the second taxon name. The two {@link TaxonNameBase taxon names}
|
|
240
|
* involved in such a relationship must have the same {@link NonViralName#getAuthorshipCache() authorship}
|
|
241
|
* and {@link Rank rank}, belong to the same {@link HomotypicalGroup homotypical group} and their name parts
|
|
242
|
* must be almost identical (so one usually does not differentiate them).<BR>
|
|
243
|
* For instance <i>Angelica silvestris</i> L. is an orthographic variant of
|
|
244
|
* <i>Angelica sylvestris</i> L.<BR>
|
|
245
|
* This type is symmetric and transitive but usually orthographic variant relationships should be organized
|
|
246
|
* in a star schema with the correct variant in the middle and other variants pointing to it.
|
|
247
|
* @see #ORIGINAL_SPELLING()()
|
|
248
|
*/
|
|
249
|
public static final NameRelationshipType ORTHOGRAPHIC_VARIANT(){
|
|
250
|
return findTermByUuid(uuidOrthographicVariant);
|
|
251
|
}
|
|
252
|
|
|
253
|
/**
|
|
254
|
* Returns the {@link TaxonNameBase taxon name} as it is spelled in the original
|
|
255
|
* publication of the given name. The first (left) name in the relationship takes the role
|
|
256
|
* of the original spelling whereas the second (right) name takes the role of the
|
|
257
|
* current/correct spelling.<BR>
|
|
258
|
* Original spelling is a specialization of {@link #ORTHOGRAPHIC_VARIANT()}.
|
|
259
|
* <BR>
|
|
260
|
* @see #ORTHOGRAPHIC_VARIANT()
|
|
261
|
* @see #MISSPELLING()
|
|
262
|
*/
|
|
263
|
public static final NameRelationshipType ORIGINAL_SPELLING(){
|
|
264
|
return findTermByUuid(uuidOriginalSpellingFor);
|
|
265
|
}
|
|
266
|
|
|
267
|
/**
|
|
268
|
* Returns the "misspelling" name relationship type. The first
|
|
269
|
* {@link TaxonNameBase taxon name} involved in such a relationship is a
|
|
270
|
* misspelling of the second taxon name. The two {@link TaxonNameBase taxon names}
|
|
271
|
* involved in such a relationship must have the same {@link NonViralName#getAuthorshipCache() authorship}
|
|
272
|
* and {@link Rank rank}, belong to the same {@link HomotypicalGroup homotypical group} and their name parts
|
|
273
|
* must be almost identical (so one usually does not differentiate them).<BR>
|
|
274
|
* For instance <i>Anhelica silvestris</i> L. is a misspelling of
|
|
275
|
* <i>Angelica silvestris</i> L.<BR>
|
|
276
|
* A misspelling is always accicentally (not on purpose). Therefore misspellings are a
|
|
277
|
* subset of {@link #ORTHOGRAPHIC_VARIANT orthographic variants} and are complementary to
|
|
278
|
* emendations. A misspelling is always an {@link #ORTHOGRAPHIC_VARIANT orthographic variant}, too.
|
|
279
|
* This type is symmetric and transitive but usually the misspelling relationships should be organized
|
|
280
|
* in a star schema with the correct variant in the middle and the misspellings pointing to it.
|
|
281
|
* @see #ORTHOGRAPHIC_VARIANT()
|
|
282
|
* @see #ORIGINAL_SPELLING()
|
|
283
|
*/
|
|
284
|
public static final NameRelationshipType MISSPELLING(){
|
|
285
|
return findTermByUuid(uuidMisspelling);
|
|
286
|
}
|
|
287
|
/**
|
|
288
|
* Returns the "emendation" name relationship type. The first
|
|
289
|
* {@link TaxonNameBase taxon name} involved in such a relationship is a
|
|
290
|
* misspelling of the second taxon name. The two {@link TaxonNameBase taxon names}
|
|
291
|
* involved in such a relationship must have the same {@link NonViralName#getAuthorshipCache() authorship}
|
|
292
|
* and {@link Rank rank}, belong to the same {@link HomotypicalGroup homotypical group} and their name parts
|
|
293
|
* must be almost identical (so one usually does not differentiate them).<BR>
|
|
294
|
* For instance <i>Angelica silvestris</i> L. is a emendation of
|
|
295
|
* <i>Angelica sylvestris</i> L.<BR>
|
|
296
|
* The name corrected by an emendation has originally been used on purpose (not accidentially)
|
|
297
|
* Therefore emendations are a subset of {@link #ORTHOGRAPHIC_VARIANT orthographic variants} and are
|
|
298
|
* complementary to {@link #MISSPELLING missepllings}. An emendation is always an
|
|
299
|
* {@link #ORTHOGRAPHIC_VARIANT orthographic variant}, too.<BR>
|
|
300
|
* This type is symmetric and transitive but usually the misspelling relationships should be organized
|
|
301
|
* in a star schema with the correct variant in the middle and the misspellings pointing to it.
|
|
302
|
*/
|
|
303
|
public static final NameRelationshipType EMENDATION(){
|
|
304
|
return findTermByUuid(uuidEmendation);
|
|
305
|
}
|
|
306
|
/**
|
|
307
|
* Returns the "later homonym" name relationship type. The first
|
|
308
|
* {@link TaxonNameBase taxon name} involved in such a relationship should
|
|
309
|
* have been published after the second taxon name. The two {@link TaxonNameBase taxon names}
|
|
310
|
* involved in such a relationship must belong to different
|
|
311
|
* {@link HomotypicalGroup homotypical groups}, have in general different
|
|
312
|
* {@link NonViralName#getAuthorshipCache() authorship} and their name parts (excluding infraspecific
|
|
313
|
* {@link Rank ranks}) must be (almost) identical, so one could be mistaken for
|
|
314
|
* the other one. The first taxon name is "illegitimate" and the second one
|
|
315
|
* is "legitimate" (this corresponds to "invalid" and "valid" in case of
|
|
316
|
* {@link ZoologicalName zoological names}).<BR>
|
|
317
|
* For instance <i>Astragalus rhizanthus</i> Boiss. is a later homonym of
|
|
318
|
* <i>Astragalus rhizanthus</i> Royle.<BR>
|
|
319
|
* This type is not symmetric but transitive.
|
|
320
|
*
|
|
321
|
* @see NomenclaturalStatusType#isIllegitimateType()
|
|
322
|
* @see NomenclaturalStatusType#isLegitimateType()
|
|
323
|
*/
|
|
324
|
public static final NameRelationshipType LATER_HOMONYM(){
|
|
325
|
return findTermByUuid(uuidLaterHomonym);
|
|
326
|
}
|
|
327
|
|
|
328
|
|
|
329
|
/**
|
|
330
|
* Returns the "treated as later homonym" name relationship type. The first
|
|
331
|
* {@link TaxonNameBase taxon name} involved in such a relationship is
|
|
332
|
* treated as an homonym although it has been published before the second
|
|
333
|
* taxon name. The two taxon names involved must belong to different
|
|
334
|
* {@link HomotypicalGroup homotypical groups} and their name parts (excluding
|
|
335
|
* {@link Rank#isInfraSpecific() infraspecific ranks} and {@link NonViralName#getAuthorshipCache() authorship}) must be
|
|
336
|
* almost identical (so one could be mistaken for the other). The first
|
|
337
|
* taxon name is "illegitimate" and the second one is "legitimate" (this
|
|
338
|
* corresponds to "invalid" and "valid" in case of {@link ZoologicalName zoological names}).<BR>
|
|
339
|
* This type is not symmetric but transitive.
|
|
340
|
*
|
|
341
|
* @see #LATER_HOMONYM()
|
|
342
|
* @see NomenclaturalStatusType#isIllegitimateType()
|
|
343
|
* @see NomenclaturalStatusType#isLegitimateType()
|
|
344
|
*/
|
|
345
|
public static final NameRelationshipType TREATED_AS_LATER_HOMONYM(){
|
|
346
|
return findTermByUuid(uuidTreatedAsLaterHomonym);
|
|
347
|
}
|
|
348
|
|
|
349
|
/**
|
|
350
|
* Returns the "later isonym" name relationship type where the first
|
|
351
|
* {@link TaxonNameBase taxon name} involved has been published after the second taxon name.<BR>
|
|
352
|
* In contrast to the {@link #LATER_HOMONYM() later homonym} relationship the two
|
|
353
|
* {@link TaxonNameBase taxon names} involved have the type(s) so they belong to the
|
|
354
|
* same {@link HomotypicalGroup homotypical groups}. As later homonyms they have in general
|
|
355
|
* different {@link NonViralName#getAuthorshipCache() authorship} and their name parts
|
|
356
|
* must be (almost) identical, so one could be mistaken for the other one.<BR>
|
|
357
|
* Later isonyms are validly published names but with a wrong citation. So there are rather errors
|
|
358
|
* then independent names.<BR>
|
|
359
|
* Isonyms are handled in Article 6, Note 2 of the ICNAFP (Melbourne Code):
|
|
360
|
* <code>When the same name, based on the same type, has been published independently at different
|
|
361
|
* times perhaps by different authors, then only the earliest of these �isonyms� has
|
|
362
|
* nomenclatural status. The name is always to be cited from its original
|
|
363
|
* place of valid publication, and later isonyms may be disregarded (but see Art. 14.15).</code>
|
|
364
|
* <BR><BR>
|
|
365
|
* See discussion at: <a href=http://dev.e-taxonomy.eu/trac/ticket/2901>#2901</a>
|
|
366
|
*
|
|
367
|
*/
|
|
368
|
public static final NameRelationshipType LATER_ISONYM(){
|
|
369
|
return findTermByUuid(uuidLaterIsonym);
|
|
370
|
}
|
|
371
|
|
|
372
|
/**
|
|
373
|
* Returns the "alternative name" name relationship type. Both {@link TaxonNameBase taxon names}
|
|
374
|
* involved in such a relationship are family names. The first one is a
|
|
375
|
* classical name long in use, in some cases, even before 1753 and is considered as
|
|
376
|
* {@link NomenclaturalStatusType#VALID() valid} and also {@link NomenclaturalStatusType#isLegitimateType() legitimate}
|
|
377
|
* although it does not follow the rules for family names (see Article 18 of
|
|
378
|
* the ICBN). An alternative name is typified by the type of the name
|
|
379
|
* it is alternative to (so both must belong to the same
|
|
380
|
* {@link HomotypicalGroup homotypical group}).<BR>
|
|
381
|
* For instance <i>Cruciferae</i> Adans is an alternative name to
|
|
382
|
* <i>Brassicaceae</i> Lindl.<BR>
|
|
383
|
* This type is neither symmetric nor transitive.
|
|
384
|
*/
|
|
385
|
public static final NameRelationshipType ALTERNATIVE_NAME(){
|
|
386
|
return findTermByUuid(uuidAlternativeName);
|
|
387
|
}
|
|
388
|
/**
|
|
389
|
* Returns the "basionym" name relationship type. The first {@link TaxonNameBase taxon name}
|
|
390
|
* involved in such a relationship is the "basionym" of the second taxon
|
|
391
|
* name. Both taxon names belong to the same {@link HomotypicalGroup homotypical group}).
|
|
392
|
* The basionym is the epithet-bringing taxon name (first taxon name
|
|
393
|
* ever validly published given to the same {@link Rank#isInfraGeneric() infrageneric}
|
|
394
|
* taxon, the epithet of which is the same as in the second taxon name
|
|
395
|
* originated through a reclassification).<BR>
|
|
396
|
* According to the ICBN the author of the basionym must be mentioned in the
|
|
397
|
* later taxon name (by placing it in parentheses before the authority of
|
|
398
|
* the new combination). For instance <i>Pinus abies</i> L. is the basionym of
|
|
399
|
* <i>Picea abies</i> (L.) H. Karst.<BR>
|
|
400
|
* This type is neither symmetric nor transitive.
|
|
401
|
*/
|
|
402
|
public static final NameRelationshipType BASIONYM(){
|
|
403
|
return findTermByUuid(uuidBasionym);
|
|
404
|
}
|
|
405
|
/**
|
|
406
|
* Returns the "replaced synonym" name relationship type. The first
|
|
407
|
* {@link TaxonNameBase taxon name} involved in such a relationship is the
|
|
408
|
* "replaced synonym" of the second taxon name. Both taxon names belong to
|
|
409
|
* the same {@link HomotypicalGroup homotypical group}. The replaced synonym is the
|
|
410
|
* first taxon name ever validly published given to the same
|
|
411
|
* {@link Rank#isInfraGeneric() infrageneric} taxon that is either itself a
|
|
412
|
* "later homonym" or the epithet of which could not be used in the new
|
|
413
|
* taxon name originated through a reclassification. A new epithet must be
|
|
414
|
* proposed if the use of the original epithet leads to an already existing
|
|
415
|
* taxon name (for another taxon) or in botany to autonyms (since the ICBN
|
|
416
|
* does not allow such names where epithet and genus name are the same).<BR>
|
|
417
|
* For instance <i>Spartium biflorum</i> Desf. is the replaced synonym of
|
|
418
|
* of <i>Cytisus fontanesii</i> Spach ("novum" taxon name) because at the time
|
|
419
|
* of reclassification a taxon name <i>Cytisus biflorum</i> had been already
|
|
420
|
* published by L'H�r.<BR>
|
|
421
|
* This type is neither symmetric nor transitive.
|
|
422
|
*
|
|
423
|
* @see #BASIONYM()
|
|
424
|
* @see #LATER_HOMONYM()
|
|
425
|
* @see NomenclaturalStatusType#NOVUM()
|
|
426
|
*/
|
|
427
|
public static final NameRelationshipType REPLACED_SYNONYM(){
|
|
428
|
return findTermByUuid(uuidReplacedSynonym);
|
|
429
|
}
|
|
430
|
/**
|
|
431
|
* Returns the "conserved against" name relationship type. Both {@link TaxonNameBase taxon names}
|
|
432
|
* involved in such a relationship belong to the same {@link HomotypicalGroup homotypical group}.
|
|
433
|
* Competent authorities decided, regardless of the general
|
|
434
|
* nomenclatural rules, to handle the first one as the "legitimate"
|
|
435
|
* one and the second taxon name as "illegitimate" (this corresponds to
|
|
436
|
* "valid" and "invalid" in case of {@link ZoologicalName zoological names}).<BR>
|
|
437
|
* For instance <i>Cephaloziella</i> (Spruce) Schiffn. is conserved against
|
|
438
|
* <i>Dichiton</i> Mont.<BR>
|
|
439
|
* This type is neither symmetric nor transitive.
|
|
440
|
*
|
|
441
|
* @see NomenclaturalStatusType#CONSERVED()
|
|
442
|
* @see NomenclaturalStatusType#REJECTED()
|
|
443
|
* @see NomenclaturalStatusType#isLegitimateType()
|
|
444
|
* @see NomenclaturalStatusType#isIllegitimateType()
|
|
445
|
*/
|
|
446
|
public static final NameRelationshipType CONSERVED_AGAINST(){
|
|
447
|
return findTermByUuid(uuidConservedAgainst);
|
|
448
|
}
|
|
449
|
/**
|
|
450
|
* Returns the "validated by name" name relationship type. The two
|
|
451
|
* {@link TaxonNameBase taxon names} involved in such a relationship were published
|
|
452
|
* in order to define the same taxonomical group but the first
|
|
453
|
* (earlier) taxon name was invalidly published whereas the second (later)
|
|
454
|
* taxon name is the one which was validly published for the first time.<BR>
|
|
455
|
* This type is neither symmetric nor transitive.
|
|
456
|
*
|
|
457
|
* @see NomenclaturalStatusType#isInvalidType()
|
|
458
|
* @see NomenclaturalStatusType#VALID()
|
|
459
|
*/
|
|
460
|
public static final NameRelationshipType VALIDATED_BY_NAME(){
|
|
461
|
return findTermByUuid(uuidValidatedByName);
|
|
462
|
}
|
|
463
|
/**
|
|
464
|
* Returns the "later validated by name" name relationship type. The two
|
|
465
|
* {@link TaxonNameBase taxon names} involved in such a relationship were published
|
|
466
|
* in order to define the same taxonomical group but the first
|
|
467
|
* (earlier) taxon name was invalidly published whereas the second (later)
|
|
468
|
* taxon name is the one which was validly published for the first time.<BR>
|
|
469
|
* This type is neither symmetric nor transitive.
|
|
470
|
*
|
|
471
|
* @see NomenclaturalStatusType#isInvalidType()
|
|
472
|
* @see NomenclaturalStatusType#VALID()
|
|
473
|
*/
|
|
474
|
public static final NameRelationshipType LATER_VALIDATED_BY_NAME(){
|
|
475
|
return findTermByUuid(uuidLaterValidatedByName);
|
|
476
|
}
|
|
477
|
/**
|
|
478
|
* Returns the "blocking name" name relationship type. The first
|
|
479
|
* {@link TaxonNameBase taxon name} involved in such a relationship is the
|
|
480
|
* "blocking name" for the second taxon name. Both taxon names belong to
|
|
481
|
* different {@link HomotypicalGroup homotypical groups}). The blocking taxon name is the
|
|
482
|
* {@link Rank#isInfraGeneric() infrageneric} taxon name, already published at the time of
|
|
483
|
* reclassification, which makes illegitim (because of homonymy) the use of
|
|
484
|
* the epithet in the second taxon name originated through a reclassification.
|
|
485
|
* Therefore a "replaced synonym" name relationship arises.<BR>
|
|
486
|
* For instance <i>Cytisus biflorum</i> L'H�r. is the blocking name for
|
|
487
|
* <i>Cytisus fontanesii</i> Spach ("novum" taxon name) when reclassifying
|
|
488
|
* <i>Spartium biflorum</i> Desf. from <i>Spartium</i> to <i>Cytisus</i>.<BR>
|
|
489
|
* This type is neither symmetric nor transitive.
|
|
490
|
*
|
|
491
|
* @see #REPLACED_SYNONYM()
|
|
492
|
* @see #LATER_HOMONYM()
|
|
493
|
* @see NomenclaturalStatusType#NOVUM()
|
|
494
|
*/
|
|
495
|
public static final NameRelationshipType BLOCKING_NAME_FOR(){
|
|
496
|
return findTermByUuid(uuidBlockingNameFor);
|
|
497
|
}
|
|
498
|
|
|
499
|
@Override
|
|
500
|
protected void setDefaultTerms(TermVocabulary<NameRelationshipType> termVocabulary) {
|
|
501
|
termMap = new HashMap<UUID, NameRelationshipType>();
|
|
502
|
for (NameRelationshipType term : termVocabulary.getTerms()){
|
|
503
|
termMap.put(term.getUuid(), term);
|
|
504
|
}
|
|
505
|
}
|
|
506
|
|
|
507
|
@Override
|
|
508
|
public NameRelationshipType readCsvLine(Class<NameRelationshipType> termClass, List<String> csvLine, Map<UUID,DefinedTermBase> terms, boolean abbrevAsId) {
|
|
509
|
NameRelationshipType result = super.readCsvLine(termClass, csvLine, terms, abbrevAsId);
|
|
510
|
String kindOfString = csvLine.get(10).trim();
|
|
511
|
if (StringUtils.isNotBlank(kindOfString)){
|
|
512
|
UUID uuidKindOf = UUID.fromString(kindOfString);
|
|
513
|
DefinedTermBase<?> kindOf = terms.get(uuidKindOf);
|
|
514
|
result.setKindOf((NameRelationshipType)kindOf);
|
|
515
|
}
|
|
516
|
return result;
|
|
517
|
}
|
|
518
|
}
|