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
|
|
14
|
|
15
|
import java.util.HashMap;
|
16
|
import java.util.Map;
|
17
|
import java.util.UUID;
|
18
|
|
19
|
import javax.persistence.Entity;
|
20
|
import javax.persistence.Transient;
|
21
|
import javax.xml.bind.annotation.XmlAccessType;
|
22
|
import javax.xml.bind.annotation.XmlAccessorType;
|
23
|
import javax.xml.bind.annotation.XmlType;
|
24
|
|
25
|
import org.apache.log4j.Logger;
|
26
|
import org.hibernate.envers.Audited;
|
27
|
|
28
|
import eu.etaxonomy.cdm.model.common.TermType;
|
29
|
import eu.etaxonomy.cdm.model.common.TermVocabulary;
|
30
|
|
31
|
/**
|
32
|
* The class representing status (categories) of {@link SpecimenTypeDesignation specimen type designations}
|
33
|
* for a {@link TaxonName taxon name} or a set of them. Within this set {@link NameRelationshipType#BASIONYM() basionyms}
|
34
|
* or {@link NameRelationshipType#REPLACED_SYNONYM() replaced synonyms}, in case of reclassifications,
|
35
|
* will be here referred as "type-bringing" taxon names.
|
36
|
* <P>
|
37
|
* The different status indicate whether the {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimens} used as types
|
38
|
* in a designation are duplicates, replacements, related specimens etc.
|
39
|
* <P>
|
40
|
* A standard (ordered) list of type designation status instances will be
|
41
|
* automatically created as the project starts. But this class allows to extend
|
42
|
* this standard list by creating new instances of additional type designation
|
43
|
* status if needed.
|
44
|
* <P>
|
45
|
* This class corresponds to: <ul>
|
46
|
* <li> NomencalturalTypeTypeTerm according to the TDWG ontology
|
47
|
* <li> NomenclaturalTypeStatusOfUnitsEnum according to the TCS
|
48
|
* </ul>
|
49
|
*
|
50
|
* @author m.doering
|
51
|
* @created 08-Nov-2007 13:07:00
|
52
|
*/
|
53
|
@XmlAccessorType(XmlAccessType.FIELD)
|
54
|
@XmlType(name = "SpecimenTypeDesignationStatus")
|
55
|
@Entity
|
56
|
//@Indexed disabled to reduce clutter in indexes, since this type is not used by any search
|
57
|
//@Indexed(index = "eu.etaxonomy.cdm.model.common.DefinedTermBase")
|
58
|
@Audited
|
59
|
public class SpecimenTypeDesignationStatus extends TypeDesignationStatusBase<SpecimenTypeDesignationStatus> {
|
60
|
private static final long serialVersionUID = -7918261741824966182L;
|
61
|
@SuppressWarnings("unused")
|
62
|
private static final Logger logger = Logger.getLogger(SpecimenTypeDesignationStatus.class);
|
63
|
|
64
|
protected static Map<UUID, SpecimenTypeDesignationStatus> termMap = null;
|
65
|
|
66
|
private static final UUID uuidType = UUID.fromString("7194020b-a326-4b47-9bfe-9f31a30aba7f");
|
67
|
private static final UUID uuidHolotype = UUID.fromString("a407dbc7-e60c-46ff-be11-eddf4c5a970d");
|
68
|
private static final UUID uuidLectotype = UUID.fromString("05002d46-083e-4b27-8731-2e7c28a8825c");
|
69
|
private static final UUID uuidNeotype = UUID.fromString("26e13359-8f77-4e40-a85a-56c01782fce0");
|
70
|
private static final UUID uuidEpitype = UUID.fromString("989a2715-71d5-4fbe-aa9a-db9168353744");
|
71
|
private static final UUID uuidIsolectotype = UUID.fromString("7a1a8a53-78f4-4fc0-89f7-782e94992d08");
|
72
|
private static final UUID uuidIsoneotype = UUID.fromString("7afc2f4f-f70a-4aa5-80a5-87764f746bde");
|
73
|
private static final UUID uuidIsotype = UUID.fromString("93ef8257-0a08-47bb-9b36-542417ae7560");
|
74
|
private static final UUID uuidParaneotype = UUID.fromString("0c39e2a5-2fe0-4d4f-819a-f609b5340339");
|
75
|
private static final UUID uuidParatype = UUID.fromString("eb7df2e5-d9a7-479d-970c-c6f2b0a761d7");
|
76
|
private static final UUID uuidSecondStepLectotype = UUID.fromString("01d91053-7004-4984-aa0d-9f4de59d6205");
|
77
|
private static final UUID uuidSecondStepNeotype = UUID.fromString("8d2fed1f-242e-4bcf-bbd7-e85133e479dc");
|
78
|
private static final UUID uuidSyntype = UUID.fromString("f3b60bdb-4638-4ca9-a0c7-36e77d8459bb");
|
79
|
private static final UUID uuidParalectotype = UUID.fromString("7244bc51-14d8-41a6-9524-7dc5303bba29");
|
80
|
private static final UUID uuidIsoepitype = UUID.fromString("95b90696-e103-4bc0-b60b-c594983fb566");
|
81
|
private static final UUID uuidIconotype = UUID.fromString("643513d0-32f5-46ba-840b-d9b9caf8160f");
|
82
|
private static final UUID uuidPhototype = UUID.fromString("b7807acc-f559-474e-ad4a-e7a41e085e34");
|
83
|
private static final UUID uuidUnspecified = UUID.fromString("230fd762-b143-49de-ac2e-744bcc48a63b");
|
84
|
private static final UUID uuidOriginalMaterial = UUID.fromString("49c96cae-6be6-401e-9b36-1bc12d9dc8f9");
|
85
|
private static final UUID uuidIsosyntype = UUID.fromString("052a5ff0-8e9a-4355-b24f-5e4bb6071f44");
|
86
|
private static final UUID uuidIsoparatype = UUID.fromString("497137f3-b614-4183-8a22-97fcd6e2bdd8");
|
87
|
|
88
|
//********************************** Constructor *********************************/
|
89
|
|
90
|
//for hibernate use only
|
91
|
@Deprecated
|
92
|
protected SpecimenTypeDesignationStatus() {
|
93
|
super(TermType.SpecimenTypeDesignationStatus);
|
94
|
}
|
95
|
|
96
|
|
97
|
/**
|
98
|
* Class constructor: creates an additional type designation status instance
|
99
|
* with a description (in the {@link eu.etaxonomy.cdm.model.common.Language#DEFAULT() default language}), a label
|
100
|
* and a label abbreviation.
|
101
|
*
|
102
|
* @param term the string (in the default language) describing the
|
103
|
* new type designation status to be created
|
104
|
* @param label the string identifying the new type designation
|
105
|
* status to be created
|
106
|
* @param labelAbbrev the string identifying (in abbreviated form) the
|
107
|
* new type designation status to be created
|
108
|
* @see #TypeDesignationStatus()
|
109
|
*/
|
110
|
private SpecimenTypeDesignationStatus(String term, String label, String labelAbbrev) {
|
111
|
super(TermType.SpecimenTypeDesignationStatus, term, label, labelAbbrev);
|
112
|
}
|
113
|
|
114
|
//************************** METHODS ********************************
|
115
|
|
116
|
/* (non-Javadoc)
|
117
|
* @see eu.etaxonomy.cdm.model.common.DefinedTermBase#resetTerms()
|
118
|
*/
|
119
|
@Override
|
120
|
public void resetTerms(){
|
121
|
termMap = null;
|
122
|
}
|
123
|
|
124
|
|
125
|
protected static SpecimenTypeDesignationStatus findTermByUuid(UUID uuid){
|
126
|
if (termMap == null || termMap.isEmpty()){
|
127
|
return getTermByClassAndUUID(SpecimenTypeDesignationStatus.class, uuid);
|
128
|
} else {
|
129
|
return termMap.get(uuid);
|
130
|
}
|
131
|
}
|
132
|
|
133
|
|
134
|
/**
|
135
|
* Returns the boolean value indicating whether <i>this</i> type designation
|
136
|
* status is itself "lectotype" or a kind of "lectotype" (true) or not
|
137
|
* (false). Returns false if <i>this</i> type designation status is null.<BR>
|
138
|
* A lectotype is a {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or illustration} designated as the
|
139
|
* nomenclatural type, when no holotype was indicated at the time of
|
140
|
* publication of the "type-bringing" {@link TaxonName taxon name}, when the
|
141
|
* holotype is found to be assigned to taxon names belonging to more than
|
142
|
* one {@link HomotypicalGroup homotypical group}, or as long as it is missing.
|
143
|
*
|
144
|
* @see #LECTOTYPE()
|
145
|
* @see #HOLOTYPE()
|
146
|
* @see eu.etaxonomy.cdm.model.common.DefinedTermBase#getKindOf()
|
147
|
*/
|
148
|
@Transient
|
149
|
public boolean isLectotype(){
|
150
|
if (this.equals(LECTOTYPE()) ||
|
151
|
this.equals(ISOLECTOTYPE()) ||
|
152
|
this.equals(SECOND_STEP_LECTOTYPE()) ||
|
153
|
this.equals(PARALECTOTYPE()) ){
|
154
|
return true;
|
155
|
}else{
|
156
|
return false;
|
157
|
}
|
158
|
}
|
159
|
|
160
|
/**
|
161
|
* Returns the "unknown" designation status. One may choose this status to indicate that the type
|
162
|
* designation is not
|
163
|
*
|
164
|
*/
|
165
|
public static final SpecimenTypeDesignationStatus TYPE(){
|
166
|
return findTermByUuid(uuidType);
|
167
|
}
|
168
|
|
169
|
/**
|
170
|
* Returns the "holotype" designation status. A holotype of a
|
171
|
* set of names is the one {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or illustration}
|
172
|
* designated as the nomenclatural type by the {@link NonViralName#getCombinationAuthorship() author} of the
|
173
|
* "type-bringing" {@link TaxonName taxon name} (or by the author of a later validated
|
174
|
* "invalid" taxon name).
|
175
|
*
|
176
|
* @see NameRelationshipType#VALIDATED_BY_NAME()
|
177
|
*/
|
178
|
public static final SpecimenTypeDesignationStatus HOLOTYPE(){
|
179
|
return findTermByUuid(uuidHolotype);
|
180
|
}
|
181
|
|
182
|
/**
|
183
|
* Returns the "lectotype" designation status. A lectotype is a
|
184
|
* {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or illustration} designated as the nomenclatural type,
|
185
|
* when no holotype was indicated at the time of publication of the
|
186
|
* "type-bringing" {@link TaxonName taxon name}, when the
|
187
|
* holotype is found to to be assigned to taxon names belonging to more than one
|
188
|
* {@link HomotypicalGroup homotypical group}, or as long as it is missing.
|
189
|
*
|
190
|
* @see #HOLOTYPE()
|
191
|
*/
|
192
|
public static final SpecimenTypeDesignationStatus LECTOTYPE(){
|
193
|
return findTermByUuid(uuidLectotype);
|
194
|
}
|
195
|
|
196
|
/**
|
197
|
* Returns the "neotype" designation status. A neotype is a
|
198
|
* {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or illustration} selected to serve as nomenclatural type
|
199
|
* as long as all of the material on which the "type-bringing" {@link TaxonName taxon name} was based
|
200
|
* is missing.
|
201
|
*
|
202
|
* @see #HOLOTYPE()
|
203
|
*/
|
204
|
public static final SpecimenTypeDesignationStatus NEOTYPE(){
|
205
|
return findTermByUuid(uuidNeotype);
|
206
|
}
|
207
|
|
208
|
/**
|
209
|
* Returns the "epitype" designation status. An epitype is a
|
210
|
* {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or illustration} selected to serve as an interpretative type
|
211
|
* when the holotype, lectotype or previously designated neotype, or all
|
212
|
* original material associated with the {@link NomenclaturalStatusType#VALID() validly} published "type-bringing"
|
213
|
* {@link TaxonName taxon name}, is demonstrably ambiguous and cannot be critically
|
214
|
* identified for purposes of the precise application of the taxon name.
|
215
|
* When an epitype is designated, the holotype, lectotype or neotype that
|
216
|
* the epitype supports must be explicitly cited.
|
217
|
*
|
218
|
* @see #HOLOTYPE()
|
219
|
* @see #LECTOTYPE()
|
220
|
* @see #NEOTYPE()
|
221
|
*/
|
222
|
public static final SpecimenTypeDesignationStatus EPITYPE(){
|
223
|
return findTermByUuid(uuidEpitype);
|
224
|
}
|
225
|
|
226
|
/**
|
227
|
* Returns the "isotype" designation status. </BR>An isotype is any duplicate of
|
228
|
* the holotype; it is always a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}.
|
229
|
*
|
230
|
* @see #HOLOTYPE()
|
231
|
*/
|
232
|
public static final SpecimenTypeDesignationStatus ISOTYPE(){
|
233
|
return findTermByUuid(uuidIsotype);
|
234
|
}
|
235
|
|
236
|
/**
|
237
|
* Returns the "syntype" designation status. </BR>A syntype is any one of two or
|
238
|
* more {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimens} cited in the {@link TaxonName#getNomenclaturalReference() protologue} of the
|
239
|
* "type-bringing" {@link TaxonName taxon name} when no holotype was designated,
|
240
|
* or any one of two or more specimens simultaneously designated as types.
|
241
|
*
|
242
|
* @see #HOLOTYPE()
|
243
|
*/
|
244
|
public static final SpecimenTypeDesignationStatus SYNTYPE(){
|
245
|
return findTermByUuid(uuidSyntype);
|
246
|
}
|
247
|
|
248
|
/**
|
249
|
* Returns the "isosyntype" designation status. </BR>An isosyntype is any
|
250
|
* {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen} cited in the
|
251
|
* protologue of the type-bringing {@link TaxonName taxon name} which is
|
252
|
* a duplicate of a {@link eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus#SYNTYPE() syntype}.
|
253
|
* See also article 9.10 of the ICBN
|
254
|
*
|
255
|
* @see #HOLOTYPE()
|
256
|
*/
|
257
|
public static final SpecimenTypeDesignationStatus ISOSYNTYPE(){
|
258
|
return findTermByUuid(uuidIsosyntype);
|
259
|
}
|
260
|
|
261
|
/**
|
262
|
* Returns the "paratype" designation status. </BR>A paratype is a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}
|
263
|
* cited in the {@link TaxonName#getNomenclaturalReference() protologue} of the "type-bringing"
|
264
|
* {@link TaxonName taxon name} that is neither the holotype nor an isotype,
|
265
|
* nor one of the syntypes if two or more specimens were simultaneously
|
266
|
* designated as types.
|
267
|
*
|
268
|
* @see #HOLOTYPE()
|
269
|
* @see #ISOTYPE()
|
270
|
* @see #SYNTYPE()
|
271
|
*/
|
272
|
public static final SpecimenTypeDesignationStatus PARATYPE(){
|
273
|
return findTermByUuid(uuidParatype);
|
274
|
}
|
275
|
|
276
|
/**
|
277
|
* Returns the "isolectotype" designation status. </BR>
|
278
|
* An isolectotype is any
|
279
|
* duplicate of the lectotype; it is always a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}.
|
280
|
*
|
281
|
* @see #LECTOTYPE()
|
282
|
*/
|
283
|
public static final SpecimenTypeDesignationStatus ISOLECTOTYPE(){
|
284
|
return findTermByUuid(uuidIsolectotype);
|
285
|
}
|
286
|
|
287
|
/**
|
288
|
* Returns the "isoneotype" designation status. </BR>
|
289
|
* An isoneotype is any
|
290
|
* duplicate of the neotype; it is always a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}.
|
291
|
*
|
292
|
* @see #NEOTYPE()
|
293
|
*/
|
294
|
public static final SpecimenTypeDesignationStatus ISONEOTYPE(){
|
295
|
return findTermByUuid(uuidIsoneotype);
|
296
|
}
|
297
|
|
298
|
/**
|
299
|
* Returns the "isoparatype" designation status. </BR>
|
300
|
* An isoparatype is any
|
301
|
* duplicate of a paratype; it is always a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}.
|
302
|
*
|
303
|
* @see #PARATYPE()
|
304
|
* @see #ISOTYPE()
|
305
|
*/
|
306
|
public static final SpecimenTypeDesignationStatus ISOPARATYPE(){
|
307
|
return findTermByUuid(uuidIsoparatype);
|
308
|
}
|
309
|
|
310
|
/**
|
311
|
* Returns the "paraneotype" designation status. </BR>
|
312
|
* A paraneotype is a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen},
|
313
|
* cited when selecting a neotype, other than the neotype itself. Also
|
314
|
* called "neoparatype" in zoology.
|
315
|
*
|
316
|
* @see #NEOTYPE()
|
317
|
*/
|
318
|
public static final SpecimenTypeDesignationStatus PARANEOTYPE(){
|
319
|
return findTermByUuid(uuidParaneotype);
|
320
|
}
|
321
|
|
322
|
/**
|
323
|
* Returns the "second step lectotype" designation status. </BR>
|
324
|
* A second step lectotype is a {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or illustration}, designated as lectotype
|
325
|
* in order to substitute another already existing lectotype.
|
326
|
*
|
327
|
* @see #LECTOTYPE()
|
328
|
*/
|
329
|
public static final SpecimenTypeDesignationStatus SECOND_STEP_LECTOTYPE(){
|
330
|
return findTermByUuid(uuidSecondStepLectotype);
|
331
|
}
|
332
|
|
333
|
/**
|
334
|
* Returns the "second step neotype" designation status. </BR>
|
335
|
* A second step neotype is a {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit specimen or illustration}, designated as neotype
|
336
|
* in order to substitute another already existing neotype.
|
337
|
*
|
338
|
* @see #LECTOTYPE()
|
339
|
*/
|
340
|
public static final SpecimenTypeDesignationStatus SECOND_STEP_NEOTYPE(){
|
341
|
return findTermByUuid(uuidSecondStepNeotype);
|
342
|
}
|
343
|
|
344
|
/**
|
345
|
* Returns the "paralectotype" designation status. </BR>
|
346
|
* A paralectotype is a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}, cited when designating a lectotype, other than
|
347
|
* the lectotype itself. Also called "lectoparatype" in zoology.
|
348
|
*
|
349
|
* @see #LECTOTYPE()
|
350
|
*/
|
351
|
public static final SpecimenTypeDesignationStatus PARALECTOTYPE(){
|
352
|
return findTermByUuid(uuidParalectotype);
|
353
|
}
|
354
|
|
355
|
/**
|
356
|
* Returns the "isoepitype" designation status. An isoepitype is any
|
357
|
* duplicate of the epitype; it is always a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}.
|
358
|
*
|
359
|
* @see #EPITYPE()
|
360
|
*/
|
361
|
public static final SpecimenTypeDesignationStatus ISOEPITYPE(){
|
362
|
return findTermByUuid(uuidIsoepitype);
|
363
|
}
|
364
|
|
365
|
/**
|
366
|
* Returns the "iconotype" designation status. An iconotype is a holotype or
|
367
|
* a lectotype that is a {@link eu.etaxonomy.cdm.model.occurrence.DerivedUnit drawing}
|
368
|
* and not a {@link eu.etaxonomy.cdm.model.occurrence.Specimen specimen}.
|
369
|
* "Iconotype" does not have type status according to the ICBN.
|
370
|
*
|
371
|
* @see #HOLOTYPE()
|
372
|
* @see #LECTOTYPE()
|
373
|
*/
|
374
|
public static final SpecimenTypeDesignationStatus ICONOTYPE(){
|
375
|
return findTermByUuid(uuidIconotype);
|
376
|
}
|
377
|
|
378
|
/**
|
379
|
* Returns the "unspecific" type designation status. Used if from literature where it is not
|
380
|
* clear if it refers to another publication not cited or if it is a new designation.
|
381
|
*
|
382
|
*/
|
383
|
public static final SpecimenTypeDesignationStatus UNSPECIFIC(){
|
384
|
return findTermByUuid(uuidUnspecified);
|
385
|
}
|
386
|
|
387
|
/**
|
388
|
* Returns the "original material" type designation status.
|
389
|
* Botanical term for material from which a lectotype can be designated.
|
390
|
* "Original material" does not have type status according to the ICBN.
|
391
|
*
|
392
|
*/
|
393
|
public static final SpecimenTypeDesignationStatus ORIGINAL_MATERIAL(){
|
394
|
return findTermByUuid(uuidOriginalMaterial);
|
395
|
}
|
396
|
|
397
|
|
398
|
/**
|
399
|
* Returns the "phototype" type designation status.
|
400
|
* "Phototype" does not have type status according to the ICBN.
|
401
|
*
|
402
|
*/
|
403
|
public static final SpecimenTypeDesignationStatus PHOTOTYPE(){
|
404
|
return findTermByUuid(uuidPhototype);
|
405
|
}
|
406
|
|
407
|
@Override
|
408
|
protected void setDefaultTerms(TermVocabulary<SpecimenTypeDesignationStatus> termVocabulary) {
|
409
|
termMap = new HashMap<UUID, SpecimenTypeDesignationStatus>();
|
410
|
for (SpecimenTypeDesignationStatus term : termVocabulary.getTerms()){
|
411
|
termMap.put(term.getUuid(), term);
|
412
|
}
|
413
|
|
414
|
}
|
415
|
|
416
|
}
|