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.description;
|
11
|
|
12
|
|
13
|
import java.util.HashMap;
|
14
|
import java.util.HashSet;
|
15
|
import java.util.List;
|
16
|
import java.util.Map;
|
17
|
import java.util.Set;
|
18
|
import java.util.UUID;
|
19
|
|
20
|
import javax.persistence.Entity;
|
21
|
import javax.persistence.FetchType;
|
22
|
import javax.persistence.JoinTable;
|
23
|
import javax.persistence.ManyToMany;
|
24
|
import javax.persistence.OneToMany;
|
25
|
import javax.xml.bind.annotation.XmlAccessType;
|
26
|
import javax.xml.bind.annotation.XmlAccessorType;
|
27
|
import javax.xml.bind.annotation.XmlElement;
|
28
|
import javax.xml.bind.annotation.XmlElementWrapper;
|
29
|
import javax.xml.bind.annotation.XmlIDREF;
|
30
|
import javax.xml.bind.annotation.XmlRootElement;
|
31
|
import javax.xml.bind.annotation.XmlSchemaType;
|
32
|
import javax.xml.bind.annotation.XmlType;
|
33
|
|
34
|
import org.apache.log4j.Logger;
|
35
|
import org.hibernate.envers.Audited;
|
36
|
import org.hibernate.search.annotations.Indexed;
|
37
|
|
38
|
import eu.etaxonomy.cdm.model.common.DefinedTerm;
|
39
|
import eu.etaxonomy.cdm.model.common.DefinedTermBase;
|
40
|
import eu.etaxonomy.cdm.model.common.Language;
|
41
|
import eu.etaxonomy.cdm.model.common.TermType;
|
42
|
import eu.etaxonomy.cdm.model.common.TermVocabulary;
|
43
|
import eu.etaxonomy.cdm.model.name.BotanicalName;
|
44
|
import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
|
45
|
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
|
46
|
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
47
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
48
|
|
49
|
/**
|
50
|
* The class for individual properties (also designed as character, type or
|
51
|
* category) of observed phenomena able to be described or measured. It also
|
52
|
* covers categories of informations on {@link TaxonNameBase taxon names} not
|
53
|
* taken in account in {@link NomenclaturalCode nomenclature}.<BR>
|
54
|
* Descriptions require features in order to be structured and disaggregated
|
55
|
* in {@link DescriptionElementBase description elements}.<BR>
|
56
|
* Experts do not use the word feature for the actual description
|
57
|
* but only for the property itself. Therefore naming this class FeatureType
|
58
|
* would have leaded to confusion.
|
59
|
* <P>
|
60
|
* Since features are {@link DefinedTermBase defined terms} they have a hierarchical
|
61
|
* structure that allows to specify ("kind of") or generalize
|
62
|
* ("generalization of") features. "Kind of" / "generalization of" relations
|
63
|
* are bidirectional (a feature F1 is a "Kind of" a feature F2 if and only
|
64
|
* if the feature F2 is a "generalization of" the feature F1. This hierarchical
|
65
|
* structure has nothing in common with {@link FeatureTree feature trees} used for determination.
|
66
|
* <P>
|
67
|
* A standard set of feature instances will be automatically
|
68
|
* created as the project starts. But this class allows to extend this standard
|
69
|
* set by creating new instances of additional features if needed.<BR>
|
70
|
* <P>
|
71
|
* This class corresponds to DescriptionsSectionType according to the SDD
|
72
|
* schema.
|
73
|
*
|
74
|
* @author m.doering
|
75
|
* @created 08-Nov-2007 13:06:24
|
76
|
*/
|
77
|
@XmlAccessorType(XmlAccessType.PROPERTY)
|
78
|
@XmlType(name="Feature", factoryMethod="NewInstance", propOrder = {
|
79
|
"kindOf",
|
80
|
"generalizationOf",
|
81
|
"partOf",
|
82
|
"includes",
|
83
|
"supportsTextData",
|
84
|
"supportsQuantitativeData",
|
85
|
"supportsDistribution",
|
86
|
"supportsIndividualAssociation",
|
87
|
"supportsTaxonInteraction",
|
88
|
"supportsCommonTaxonName",
|
89
|
"supportsCategoricalData",
|
90
|
"recommendedModifierEnumeration",
|
91
|
"recommendedStatisticalMeasures",
|
92
|
"supportedCategoricalEnumerations",
|
93
|
"recommendedMeasurementUnits"
|
94
|
})
|
95
|
@XmlRootElement(name = "Feature")
|
96
|
@Entity
|
97
|
@Indexed(index = "eu.etaxonomy.cdm.model.common.DefinedTermBase")
|
98
|
@Audited
|
99
|
public class Feature extends DefinedTermBase<Feature> {
|
100
|
private static final long serialVersionUID = 6754598791831848704L;
|
101
|
private static final Logger logger = Logger.getLogger(Feature.class);
|
102
|
|
103
|
protected static Map<UUID, Feature> termMap = null;
|
104
|
|
105
|
private boolean supportsTextData = true; //by default text data should be always supported
|
106
|
|
107
|
private boolean supportsQuantitativeData;
|
108
|
|
109
|
private boolean supportsDistribution;
|
110
|
|
111
|
private boolean supportsIndividualAssociation;
|
112
|
|
113
|
private boolean supportsTaxonInteraction;
|
114
|
|
115
|
private boolean supportsCategoricalData;
|
116
|
|
117
|
private boolean supportsCommonTaxonName;
|
118
|
|
119
|
/*
|
120
|
* FIXME Should this be Many-To-Many or do we expect each Feature to have its own unique modifier enums?
|
121
|
*/
|
122
|
@OneToMany(fetch = FetchType.LAZY)
|
123
|
@JoinTable(name="DefinedTermBase_RecommendedModifierEnumeration")
|
124
|
private final Set<TermVocabulary<DefinedTerm>> recommendedModifierEnumeration = new HashSet<TermVocabulary<DefinedTerm>>();
|
125
|
|
126
|
|
127
|
@ManyToMany(fetch = FetchType.LAZY)
|
128
|
@JoinTable(name="DefinedTermBase_StatisticalMeasure")
|
129
|
private final Set<StatisticalMeasure> recommendedStatisticalMeasures = new HashSet<StatisticalMeasure>();
|
130
|
|
131
|
/*
|
132
|
* FIXME Should this be Many-To-Many or do we expect each Feature to have its own unique state enums?
|
133
|
*/
|
134
|
@OneToMany(fetch = FetchType.LAZY)
|
135
|
@JoinTable(name="DefinedTermBase_SupportedCategoricalEnumeration")
|
136
|
private final Set<TermVocabulary<State>> supportedCategoricalEnumerations = new HashSet<TermVocabulary<State>>();
|
137
|
|
138
|
|
139
|
@ManyToMany(fetch = FetchType.LAZY)
|
140
|
@JoinTable(name="DefinedTermBase_MeasurementUnit")
|
141
|
private final Set<MeasurementUnit> recommendedMeasurementUnits = new HashSet<MeasurementUnit>();
|
142
|
|
143
|
/* ***************** CONSTRUCTOR AND FACTORY METHODS **********************************/
|
144
|
|
145
|
//for hibernate use only
|
146
|
@Deprecated
|
147
|
protected Feature() {
|
148
|
super(TermType.Feature);
|
149
|
}
|
150
|
|
151
|
/**
|
152
|
* Class constructor: creates a new feature instance with a description (in the {@link Language#DEFAULT() default language}),
|
153
|
* a label and a label abbreviation.
|
154
|
*
|
155
|
* @param term the string (in the default language) describing the
|
156
|
* new feature to be created
|
157
|
* @param label the string identifying the new feature to be created
|
158
|
* @param labelAbbrev the string identifying (in abbreviated form) the
|
159
|
* new feature to be created
|
160
|
* @see #Feature()
|
161
|
*/
|
162
|
protected Feature(String term, String label, String labelAbbrev) {
|
163
|
super(TermType.Feature, term, label, labelAbbrev);
|
164
|
}
|
165
|
|
166
|
/**
|
167
|
* Creates a new empty feature instance.
|
168
|
*
|
169
|
* @see #NewInstance(String, String, String)
|
170
|
*/
|
171
|
public static Feature NewInstance() {
|
172
|
return new Feature();
|
173
|
}
|
174
|
|
175
|
/**
|
176
|
* Creates a new feature instance with a description (in the {@link Language#DEFAULT() default language}),
|
177
|
* a label and a label abbreviation.
|
178
|
*
|
179
|
* @param term the string (in the default language) describing the
|
180
|
* new feature to be created
|
181
|
* @param label the string identifying the new feature to be created
|
182
|
* @param labelAbbrev the string identifying (in abbreviated form) the
|
183
|
* new feature to be created
|
184
|
* @see #readCsvLine(List, Language)
|
185
|
* @see #NewInstance()
|
186
|
*/
|
187
|
public static Feature NewInstance(String term, String label, String labelAbbrev){
|
188
|
return new Feature(term, label, labelAbbrev);
|
189
|
}
|
190
|
|
191
|
/* *************************************************************************************/
|
192
|
|
193
|
|
194
|
/* (non-Javadoc)
|
195
|
* @see eu.etaxonomy.cdm.model.common.DefinedTermBase#resetTerms()
|
196
|
*/
|
197
|
@Override
|
198
|
public void resetTerms(){
|
199
|
termMap = null;
|
200
|
}
|
201
|
|
202
|
|
203
|
/**
|
204
|
* Returns the boolean value of the flag indicating whether <i>this</i>
|
205
|
* feature can be described with {@link QuantitativeData quantitative data} (true)
|
206
|
* or not (false). If this flag is set <i>this</i> feature can only apply to
|
207
|
* {@link TaxonDescription taxon descriptions} or {@link SpecimenDescription specimen descriptions}.
|
208
|
*
|
209
|
* @return the boolean value of the supportsQuantitativeData flag
|
210
|
*/
|
211
|
@XmlElement(name = "SupportsQuantitativeData")
|
212
|
public boolean isSupportsQuantitativeData() {
|
213
|
return supportsQuantitativeData;
|
214
|
}
|
215
|
|
216
|
/**
|
217
|
* @see #isSupportsQuantitativeData()
|
218
|
*/
|
219
|
public void setSupportsQuantitativeData(boolean supportsQuantitativeData) {
|
220
|
this.supportsQuantitativeData = supportsQuantitativeData;
|
221
|
}
|
222
|
|
223
|
/**
|
224
|
* Returns the boolean value of the flag indicating whether <i>this</i>
|
225
|
* feature can be described with {@link TextData text data} (true)
|
226
|
* or not (false).
|
227
|
*
|
228
|
* @return the boolean value of the supportsTextData flag
|
229
|
*/
|
230
|
@XmlElement(name = "SupportsTextData")
|
231
|
public boolean isSupportsTextData() {
|
232
|
return supportsTextData;
|
233
|
}
|
234
|
|
235
|
/**
|
236
|
* @see #isSupportsTextData()
|
237
|
*/
|
238
|
public void setSupportsTextData(boolean supportsTextData) {
|
239
|
this.supportsTextData = supportsTextData;
|
240
|
}
|
241
|
|
242
|
/**
|
243
|
* Returns the boolean value of the flag indicating whether <i>this</i>
|
244
|
* feature can be described with {@link Distribution distribution} objects
|
245
|
* (true) or not (false). This flag is set if and only if <i>this</i> feature
|
246
|
* is the {@link #DISTRIBUTION() distribution feature}.
|
247
|
*
|
248
|
* @return the boolean value of the supportsDistribution flag
|
249
|
*/
|
250
|
@XmlElement(name = "SupportsDistribution")
|
251
|
public boolean isSupportsDistribution() {
|
252
|
return supportsDistribution;
|
253
|
}
|
254
|
|
255
|
/**
|
256
|
* @see #isSupportsDistribution()
|
257
|
*/
|
258
|
public void setSupportsDistribution(boolean supportsDistribution) {
|
259
|
this.supportsDistribution = supportsDistribution;
|
260
|
}
|
261
|
|
262
|
/**
|
263
|
* Returns the boolean value of the flag indicating whether <i>this</i>
|
264
|
* feature can be described with {@link IndividualsAssociation individuals associations}
|
265
|
* (true) or not (false).
|
266
|
*
|
267
|
* @return the boolean value of the supportsIndividualAssociation flag
|
268
|
*/
|
269
|
@XmlElement(name = "SupportsIndividualAssociation")
|
270
|
public boolean isSupportsIndividualAssociation() {
|
271
|
return supportsIndividualAssociation;
|
272
|
}
|
273
|
|
274
|
/**
|
275
|
* @see #isSupportsIndividualAssociation()
|
276
|
*/
|
277
|
public void setSupportsIndividualAssociation(
|
278
|
boolean supportsIndividualAssociation) {
|
279
|
this.supportsIndividualAssociation = supportsIndividualAssociation;
|
280
|
}
|
281
|
|
282
|
/**
|
283
|
* Returns the boolean value of the flag indicating whether <i>this</i>
|
284
|
* feature can be described with {@link TaxonInteraction taxon interactions}
|
285
|
* (true) or not (false).
|
286
|
*
|
287
|
* @return the boolean value of the supportsTaxonInteraction flag
|
288
|
*/
|
289
|
@XmlElement(name = "SupportsTaxonInteraction")
|
290
|
public boolean isSupportsTaxonInteraction() {
|
291
|
return supportsTaxonInteraction;
|
292
|
}
|
293
|
|
294
|
/**
|
295
|
* @see #isSupportsTaxonInteraction()
|
296
|
*/
|
297
|
public void setSupportsTaxonInteraction(boolean supportsTaxonInteraction) {
|
298
|
this.supportsTaxonInteraction = supportsTaxonInteraction;
|
299
|
}
|
300
|
|
301
|
/**
|
302
|
* Returns the boolean value of the flag indicating whether <i>this</i>
|
303
|
* feature can be described with {@link CommonTaxonName common names}
|
304
|
* (true) or not (false). This flag is set if and only if <i>this</i> feature
|
305
|
* is the {@link #COMMON_NAME() common name feature}.
|
306
|
*
|
307
|
* @return the boolean value of the supportsCommonTaxonName flag
|
308
|
*/
|
309
|
@XmlElement(name = "SupportsCommonTaxonName")
|
310
|
public boolean isSupportsCommonTaxonName() {
|
311
|
return supportsCommonTaxonName;
|
312
|
}
|
313
|
|
314
|
/**
|
315
|
* @see #isSupportsTaxonInteraction()
|
316
|
*/
|
317
|
public void setSupportsCommonTaxonName(boolean supportsCommonTaxonName) {
|
318
|
this.supportsCommonTaxonName = supportsCommonTaxonName;
|
319
|
}
|
320
|
|
321
|
/**
|
322
|
* Returns the boolean value of the flag indicating whether <i>this</i>
|
323
|
* feature can be described with {@link CategoricalData categorical data}
|
324
|
* (true) or not (false).
|
325
|
*
|
326
|
* @return the boolean value of the supportsCategoricalData flag
|
327
|
*/
|
328
|
@XmlElement(name = "SupportsCategoricalData")
|
329
|
public boolean isSupportsCategoricalData() {
|
330
|
return supportsCategoricalData;
|
331
|
}
|
332
|
|
333
|
/**
|
334
|
* @see #supportsCategoricalData()
|
335
|
*/
|
336
|
public void setSupportsCategoricalData(boolean supportsCategoricalData) {
|
337
|
this.supportsCategoricalData = supportsCategoricalData;
|
338
|
}
|
339
|
|
340
|
|
341
|
/**
|
342
|
* Returns the set of {@link TermVocabulary term vocabularies} containing the
|
343
|
* {@link Modifier modifiers} recommended to be used for {@link DescriptionElementBase description elements}
|
344
|
* with <i>this</i> feature.
|
345
|
*
|
346
|
*/
|
347
|
@XmlElementWrapper(name = "RecommendedModifierEnumerations")
|
348
|
@XmlElement(name = "RecommendedModifierEnumeration")
|
349
|
@XmlIDREF
|
350
|
@XmlSchemaType(name = "IDREF")
|
351
|
public Set<TermVocabulary<DefinedTerm>> getRecommendedModifierEnumeration() {
|
352
|
return recommendedModifierEnumeration;
|
353
|
}
|
354
|
|
355
|
/**
|
356
|
* Adds a {@link TermVocabulary term vocabulary} (with {@link Modifier modifiers}) to the set of
|
357
|
* {@link #getRecommendedModifierEnumeration() recommended modifier vocabularies} assigned
|
358
|
* to <i>this</i> feature.
|
359
|
*
|
360
|
* @param recommendedModifierEnumeration the term vocabulary to be added
|
361
|
* @see #getRecommendedModifierEnumeration()
|
362
|
*/
|
363
|
public void addRecommendedModifierEnumeration(
|
364
|
TermVocabulary<DefinedTerm> recommendedModifierEnumeration) {
|
365
|
this.recommendedModifierEnumeration.add(recommendedModifierEnumeration);
|
366
|
}
|
367
|
/**
|
368
|
* Removes one element from the set of {@link #getRecommendedModifierEnumeration() recommended modifier vocabularies}
|
369
|
* assigned to <i>this</i> feature.
|
370
|
*
|
371
|
* @param recommendedModifierEnumeration the term vocabulary which should be removed
|
372
|
* @see #getRecommendedModifierEnumeration()
|
373
|
* @see #addRecommendedModifierEnumeration(TermVocabulary)
|
374
|
*/
|
375
|
public void removeRecommendedModifierEnumeration(
|
376
|
TermVocabulary<DefinedTerm> recommendedModifierEnumeration) {
|
377
|
this.recommendedModifierEnumeration.remove(recommendedModifierEnumeration);
|
378
|
}
|
379
|
|
380
|
/**
|
381
|
* Returns the set of {@link StatisticalMeasure statistical measures} recommended to be used
|
382
|
* in case of {@link QuantitativeData quantitative data} with <i>this</i> feature.
|
383
|
*/
|
384
|
@XmlElementWrapper(name = "RecommendedStatisticalMeasures")
|
385
|
@XmlElement(name = "RecommendedStatisticalMeasure")
|
386
|
@XmlIDREF
|
387
|
@XmlSchemaType(name = "IDREF")
|
388
|
public Set<StatisticalMeasure> getRecommendedStatisticalMeasures() {
|
389
|
return recommendedStatisticalMeasures;
|
390
|
}
|
391
|
|
392
|
/**
|
393
|
* Adds a {@link StatisticalMeasure statistical measure} to the set of
|
394
|
* {@link #getRecommendedStatisticalMeasures() recommended statistical measures} assigned
|
395
|
* to <i>this</i> feature.
|
396
|
*
|
397
|
* @param recommendedStatisticalMeasure the statistical measure to be added
|
398
|
* @see #getRecommendedStatisticalMeasures()
|
399
|
*/
|
400
|
public void addRecommendedStatisticalMeasure(
|
401
|
StatisticalMeasure recommendedStatisticalMeasure) {
|
402
|
this.recommendedStatisticalMeasures.add(recommendedStatisticalMeasure);
|
403
|
}
|
404
|
/**
|
405
|
* Removes one element from the set of {@link #getRecommendedStatisticalMeasures() recommended statistical measures}
|
406
|
* assigned to <i>this</i> feature.
|
407
|
*
|
408
|
* @param recommendedStatisticalMeasure the statistical measure which should be removed
|
409
|
* @see #getRecommendedStatisticalMeasures()
|
410
|
* @see #addRecommendedStatisticalMeasure(StatisticalMeasure)
|
411
|
*/
|
412
|
public void removeRecommendedStatisticalMeasure(
|
413
|
StatisticalMeasure recommendedStatisticalMeasure) {
|
414
|
this.recommendedStatisticalMeasures.remove(recommendedStatisticalMeasure);
|
415
|
}
|
416
|
|
417
|
/**
|
418
|
* Returns the set of {@link StatisticalMeasure statistical measures} recommended to be used
|
419
|
* in case of {@link QuantitativeData quantitative data} with <i>this</i> feature.
|
420
|
*/
|
421
|
@XmlElementWrapper(name = "RecommendedMeasurementUnits")
|
422
|
@XmlElement(name = "RecommendedMeasurementUnit")
|
423
|
@XmlIDREF
|
424
|
@XmlSchemaType(name = "IDREF")
|
425
|
public Set<MeasurementUnit> getRecommendedMeasurementUnits() {
|
426
|
return recommendedMeasurementUnits;
|
427
|
}
|
428
|
|
429
|
/**
|
430
|
* Adds a {@link StatisticalMeasure statistical measure} to the set of
|
431
|
* {@link #getRecommendedStatisticalMeasures() recommended statistical measures} assigned
|
432
|
* to <i>this</i> feature.
|
433
|
*
|
434
|
* @param recommendedStatisticalMeasure the statistical measure to be added
|
435
|
* @see #getRecommendedStatisticalMeasures()
|
436
|
*/
|
437
|
public void addRecommendedMeasurementUnit(
|
438
|
MeasurementUnit recommendedMeasurementUnit) {
|
439
|
this.recommendedMeasurementUnits.add(recommendedMeasurementUnit);
|
440
|
}
|
441
|
/**
|
442
|
* Removes one element from the set of {@link #getRecommendedStatisticalMeasures() recommended statistical measures}
|
443
|
* assigned to <i>this</i> feature.
|
444
|
*
|
445
|
* @param recommendedStatisticalMeasure the statistical measure which should be removed
|
446
|
* @see #getRecommendedStatisticalMeasures()
|
447
|
* @see #addRecommendedStatisticalMeasure(StatisticalMeasure)
|
448
|
*/
|
449
|
public void removeRecommendedMeasurementUnit(
|
450
|
MeasurementUnit recommendedMeasurementUnit) {
|
451
|
this.recommendedMeasurementUnits.remove(recommendedMeasurementUnit);
|
452
|
}
|
453
|
|
454
|
/**
|
455
|
* Returns the set of {@link TermVocabulary term vocabularies} containing the list of
|
456
|
* possible {@link State states} to be used in {@link CategoricalData categorical data}
|
457
|
* with <i>this</i> feature.
|
458
|
*
|
459
|
*/
|
460
|
@XmlElementWrapper(name = "SupportedCategoricalEnumerations")
|
461
|
@XmlElement(name = "SupportedCategoricalEnumeration")
|
462
|
@XmlIDREF
|
463
|
@XmlSchemaType(name = "IDREF")
|
464
|
public Set<TermVocabulary<State>> getSupportedCategoricalEnumerations() {
|
465
|
return supportedCategoricalEnumerations;
|
466
|
}
|
467
|
|
468
|
/**
|
469
|
* Adds a {@link TermVocabulary term vocabulary} to the set of
|
470
|
* {@link #getSupportedCategoricalEnumerations() supported state vocabularies} assigned
|
471
|
* to <i>this</i> feature.
|
472
|
*
|
473
|
* @param supportedCategoricalEnumeration the term vocabulary which should be removed
|
474
|
* @see #getSupportedCategoricalEnumerations()
|
475
|
*/
|
476
|
public void addSupportedCategoricalEnumeration(
|
477
|
TermVocabulary<State> supportedCategoricalEnumeration) {
|
478
|
this.supportedCategoricalEnumerations.add(supportedCategoricalEnumeration);
|
479
|
}
|
480
|
/**
|
481
|
* Removes one element from the set of {@link #getSupportedCategoricalEnumerations() supported state vocabularies}
|
482
|
* assigned to <i>this</i> feature.
|
483
|
*
|
484
|
* @param supportedCategoricalEnumeration the term vocabulary which should be removed
|
485
|
* @see #getSupportedCategoricalEnumerations()
|
486
|
* @see #addSupportedCategoricalEnumeration(TermVocabulary)
|
487
|
*/
|
488
|
public void removeSupportedCategoricalEnumeration(
|
489
|
TermVocabulary<State> supportedCategoricalEnumeration) {
|
490
|
this.supportedCategoricalEnumerations.remove(supportedCategoricalEnumeration);
|
491
|
}
|
492
|
|
493
|
@XmlElement(name = "KindOf", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
494
|
@XmlIDREF
|
495
|
@XmlSchemaType(name = "IDREF")
|
496
|
@Override
|
497
|
public Feature getKindOf(){
|
498
|
return super.getKindOf();
|
499
|
}
|
500
|
|
501
|
@Override
|
502
|
public void setKindOf(Feature kindOf){
|
503
|
super.setKindOf(kindOf);
|
504
|
}
|
505
|
|
506
|
@Override
|
507
|
@XmlElement(name = "PartOf", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
508
|
@XmlIDREF
|
509
|
@XmlSchemaType(name = "IDREF")
|
510
|
public Feature getPartOf(){
|
511
|
return super.getPartOf();
|
512
|
}
|
513
|
|
514
|
@Override
|
515
|
public void setPartOf(Feature partOf){
|
516
|
super.setPartOf(partOf);
|
517
|
}
|
518
|
|
519
|
@Override
|
520
|
@XmlElementWrapper(name = "Generalizations", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
521
|
@XmlElement(name = "GeneralizationOf", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
522
|
@XmlIDREF
|
523
|
@XmlSchemaType(name = "IDREF")
|
524
|
public Set<Feature> getGeneralizationOf(){
|
525
|
return super.getGeneralizationOf();
|
526
|
}
|
527
|
|
528
|
@Override
|
529
|
protected void setGeneralizationOf(Set<Feature> value){
|
530
|
super.setGeneralizationOf(value);
|
531
|
}
|
532
|
|
533
|
@Override
|
534
|
@XmlElementWrapper(name = "Includes", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
535
|
@XmlElement(name = "Include", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
536
|
@XmlIDREF
|
537
|
@XmlSchemaType(name = "IDREF")
|
538
|
public Set<Feature> getIncludes(){
|
539
|
return super.getIncludes();
|
540
|
}
|
541
|
|
542
|
@Override
|
543
|
protected void setIncludes(Set<Feature> includes) {
|
544
|
super.setIncludes(includes);
|
545
|
}
|
546
|
|
547
|
private static final UUID uuidUnknown = UUID.fromString("910307f1-dc3c-452c-a6dd-af5ac7cd365c");
|
548
|
private static final UUID uuidDescription = UUID.fromString("9087cdcd-8b08-4082-a1de-34c9ba9fb493");
|
549
|
private static final UUID uuidDistribution = UUID.fromString("9fc9d10c-ba50-49ee-b174-ce83fc3f80c6");
|
550
|
private static final UUID uuidEcology = UUID.fromString("aa923827-d333-4cf5-9a5f-438ae0a4746b");
|
551
|
private static final UUID uuidHabitat = UUID.fromString("fb16929f-bc9c-456f-9d40-dec987b36438");
|
552
|
private static final UUID uuidHabitatAndEcology = UUID.fromString("9fdc4663-4d56-47d0-90b5-c0bf251bafbb");
|
553
|
private static final UUID uuidChromosomeNumber = UUID.fromString("6f677e98-d8d5-4bc5-80bf-affdb7e3945a");
|
554
|
|
555
|
private static final UUID uuidBiologyEcology = UUID.fromString("9832e24f-b670-43b4-ac7c-20a7261a1d8c");
|
556
|
private static final UUID uuidKey = UUID.fromString("a677f827-22b9-4205-bb37-11cb48dd9106");
|
557
|
private static final UUID uuidMaterialsExamined = UUID.fromString("7c0c7571-a864-47c1-891d-01f59000dae1");
|
558
|
private static final UUID uuidMaterialsMethods = UUID.fromString("1e87d9c3-0844-4a03-9686-773e2ccb3ab6");
|
559
|
private static final UUID uuidEtymology = UUID.fromString("dd653d48-355c-4aec-a4e7-724f6eb29f8d");
|
560
|
private static final UUID uuidDiagnosis = UUID.fromString("d43d8501-ceab-4caa-9e51-e87138528fac");
|
561
|
private static final UUID uuidProtologue = UUID.fromString("71b356c5-1e3f-4f5d-9b0f-c2cf8ae7779f");
|
562
|
private static final UUID uuidCommonName = UUID.fromString("fc810911-51f0-4a46-ab97-6562fe263ae5");
|
563
|
private static final UUID uuidPhenology = UUID.fromString("a7786d3e-7c58-4141-8416-346d4c80c4a2");
|
564
|
private static final UUID uuidOccurrence = UUID.fromString("5deff505-1a32-4817-9a74-50e6936fd630");
|
565
|
private static final UUID uuidCitation = UUID.fromString("99b2842f-9aa7-42fa-bd5f-7285311e0101");
|
566
|
private static final UUID uuidAdditionalPublication = UUID.fromString("2c355c16-cb04-4858-92bf-8da8d56dea95");
|
567
|
private static final UUID uuidUses = UUID.fromString("e5374d39-b210-47c7-bec1-bee05b5f1cb6");
|
568
|
private static final UUID uuidConservation = UUID.fromString("4518fc20-2492-47de-b345-777d2b83c9cf");
|
569
|
private static final UUID uuidCultivation = UUID.fromString("e28965b2-a367-48c5-b954-8afc8ac2c69b");
|
570
|
private static final UUID uuidIntroduction = UUID.fromString("e75255ca-8ff4-4905-baad-f842927fe1d3");
|
571
|
private static final UUID uuidDiscussion = UUID.fromString("d3c4cbb6-0025-4322-886b-cd0156753a25");
|
572
|
private static final UUID uuidImage = UUID.fromString("84193b2c-327f-4cce-90ef-c8da18fd5bb5");
|
573
|
private static final UUID uuidAnatomy = UUID.fromString("94213b2c-e67a-4d37-25ef-e8d316edfba1");
|
574
|
private static final UUID uuidHostPlant = UUID.fromString("6e9de1d5-05f0-40d5-8786-2fe30d0d894d");
|
575
|
private static final UUID uuidPathogenAgent = UUID.fromString("002d05f2-fd72-49f1-ba4d-196cf09240b5");
|
576
|
private static final UUID uuidIndividualsAssociation = UUID.fromString("e2308f37-ddc5-447d-b483-5e2171dd85fd");
|
577
|
private static final UUID uuidSpecimen = UUID.fromString("8200e050-d5fd-4cac-8a76-4b47afb13809");
|
578
|
private static final UUID uuidObservation = UUID.fromString("f59e747d-0b4f-4bf7-b69a-cbd50bc78595");
|
579
|
private static final UUID uuidStatus = UUID.fromString("86d40635-2a63-4ad6-be75-9faa4a6a57fb");
|
580
|
private static final UUID uuidSystematics = UUID.fromString("bd9aca17-cd0e-4418-a3a1-1a4b80dbc162");
|
581
|
private static final UUID uuidUseRecord = UUID.fromString("8125a59d-b4d5-4485-89ea-67306297b599");
|
582
|
|
583
|
/**
|
584
|
* Creates and returns a new feature instance on the basis of a given string
|
585
|
* list (containing an UUID, an URI, a label and a description) and a given
|
586
|
* {@link Language language} to be associated with the description. Furthermore
|
587
|
* the flags concerning the supported subclasses of {@link DescriptionElementBase description elements}
|
588
|
* are set according to a particular string belonging to the given
|
589
|
* string list.<BR>
|
590
|
* This method overrides the readCsvLine method from {@link DefinedTermBase#readCsvLine(List, Language) DefinedTermBase}.
|
591
|
*
|
592
|
* @param csvLine the string list with elementary information for attributes
|
593
|
* @param lang the language in which the description has been formulated
|
594
|
* @see #NewInstance(String, String, String)
|
595
|
*/
|
596
|
@Override
|
597
|
public Feature readCsvLine(Class<Feature> termClass, List<String> csvLine, Map<UUID,DefinedTermBase> terms, boolean abbrevAsId) {
|
598
|
Feature newInstance = super.readCsvLine(termClass, csvLine, terms, abbrevAsId);
|
599
|
String text = csvLine.get(4);
|
600
|
if (text != null && text.length() >= 6){
|
601
|
if ("1".equals(text.substring(0, 1))){newInstance.setSupportsTextData(true);};
|
602
|
if ("1".equals(text.substring(1, 2))){newInstance.setSupportsQuantitativeData(true);};
|
603
|
if ("1".equals(text.substring(2, 3))){newInstance.setSupportsDistribution(true);};
|
604
|
if ("1".equals(text.substring(3, 4))){newInstance.setSupportsIndividualAssociation(true);};
|
605
|
if ("1".equals(text.substring(4, 5))){newInstance.setSupportsTaxonInteraction(true);};
|
606
|
if ("1".equals(text.substring(5, 6))){newInstance.setSupportsCommonTaxonName(true);};
|
607
|
// if ("1".equals(text.substring(6, 7))){newInstance.setSupportsCategoricalData(true);};
|
608
|
//there is no abbreviated label for features yet, if there is one in future we need to increment the index for supportXXX form 4 to 5
|
609
|
newInstance.getRepresentation(Language.DEFAULT()).setAbbreviatedLabel(null);
|
610
|
}
|
611
|
return newInstance;
|
612
|
}
|
613
|
|
614
|
//******************************* STATIC METHODS *****************************************
|
615
|
|
616
|
protected static Feature getTermByUuid(UUID uuid){
|
617
|
if (termMap == null){
|
618
|
return null; //better return null then initialize the termMap in an unwanted way
|
619
|
//example for an unwanted initialization: before initializing spring you may use a static method of this class.
|
620
|
//This would result in an default terminitialization instead of a database based
|
621
|
// term initialization
|
622
|
|
623
|
// DefaultTermInitializer vocabularyStore = new DefaultTermInitializer();
|
624
|
// vocabularyStore.initialize();
|
625
|
}
|
626
|
return termMap.get(uuid);
|
627
|
}
|
628
|
|
629
|
/**
|
630
|
* Returns the "unknown" feature. This feature allows to store values of
|
631
|
* {@link DescriptionElementBase description elements} even if it is momentarily
|
632
|
* not known what they mean.
|
633
|
*/
|
634
|
public static final Feature UNKNOWN(){
|
635
|
return getTermByUuid(uuidUnknown);
|
636
|
}
|
637
|
|
638
|
/**
|
639
|
* Returns the "description" feature. This feature allows to handle global
|
640
|
* {@link DescriptionElementBase description elements} for a global {@link DescriptionBase description}.<BR>
|
641
|
* The "description" feature is the highest level feature.
|
642
|
*/
|
643
|
public static final Feature DESCRIPTION(){
|
644
|
return getTermByUuid(uuidDescription);
|
645
|
}
|
646
|
|
647
|
/**
|
648
|
* Returns the "distribution" feature. This feature allows to handle only
|
649
|
* {@link Distribution distributions}.
|
650
|
*
|
651
|
* @see #isSupportsDistribution()
|
652
|
*/
|
653
|
public static final Feature DISTRIBUTION(){
|
654
|
return getTermByUuid(uuidDistribution);
|
655
|
}
|
656
|
|
657
|
/**
|
658
|
* Returns the "discussion" feature. This feature can only be described
|
659
|
* with {@link TextData text data}.
|
660
|
*
|
661
|
* @see #isSupportsTextData()
|
662
|
*/
|
663
|
public static final Feature DISCUSSION(){
|
664
|
return getTermByUuid(uuidDiscussion);
|
665
|
}
|
666
|
|
667
|
/**
|
668
|
* Returns the "ecology" feature. This feature only applies
|
669
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
670
|
* The "ecology" feature generalizes all other possible features concerning
|
671
|
* ecological matters.
|
672
|
*/
|
673
|
public static final Feature ECOLOGY(){
|
674
|
return getTermByUuid(uuidEcology);
|
675
|
}
|
676
|
|
677
|
/**
|
678
|
* Returns the "habitat" feature. This feature only applies
|
679
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
680
|
* The "habitat" feature generalizes all other possible features concerning
|
681
|
* habitat matters.
|
682
|
*/
|
683
|
public static final Feature HABITAT(){
|
684
|
return getTermByUuid(uuidHabitat);
|
685
|
}
|
686
|
|
687
|
|
688
|
/**
|
689
|
* Returns the "habitat & ecology" feature. This feature only applies
|
690
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
691
|
* The "habitat & ecology" feature generalizes all other possible features concerning
|
692
|
* habitat and ecology matters.
|
693
|
*/
|
694
|
public static final Feature HABITAT_ECOLOGY(){
|
695
|
return getTermByUuid(uuidHabitatAndEcology);
|
696
|
}
|
697
|
|
698
|
/**
|
699
|
* Returns the "biology_ecology" feature. This feature only applies
|
700
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
701
|
* The "biology_ecology" feature generalizes all possible features concerning
|
702
|
* biological aspects of ecological matters.
|
703
|
*
|
704
|
* @see #ECOLOGY()
|
705
|
*/
|
706
|
public static final Feature BIOLOGY_ECOLOGY(){
|
707
|
return getTermByUuid(uuidBiologyEcology);
|
708
|
}
|
709
|
|
710
|
/**
|
711
|
* Returns the "chromosome number" feature. This feature only applies
|
712
|
* to {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.<BR>
|
713
|
*/
|
714
|
public static final Feature CHROMOSOME_NUMBER(){
|
715
|
return getTermByUuid(uuidChromosomeNumber);
|
716
|
}
|
717
|
|
718
|
|
719
|
/**
|
720
|
* Returns the "key" feature. This feature is the "upper" feature generalizing
|
721
|
* all features being used within an identification key.
|
722
|
*/
|
723
|
public static final Feature KEY(){
|
724
|
return getTermByUuid(uuidKey);
|
725
|
}
|
726
|
|
727
|
|
728
|
/**
|
729
|
* Returns the "materials_examined" feature. This feature can only be described
|
730
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}
|
731
|
* mentioning which material has been examined in order to accomplish
|
732
|
* the description. This feature applies only to
|
733
|
* {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.
|
734
|
*/
|
735
|
public static final Feature MATERIALS_EXAMINED(){
|
736
|
return getTermByUuid(uuidMaterialsExamined);
|
737
|
}
|
738
|
|
739
|
/**
|
740
|
* Returns the "materials_methods" feature. This feature can only be described
|
741
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}
|
742
|
* mentioning which methods have been adopted to analyze the material in
|
743
|
* order to accomplish the description. This feature applies only to
|
744
|
* {@link SpecimenDescription specimen descriptions} or to {@link TaxonDescription taxon descriptions}.
|
745
|
*/
|
746
|
public static final Feature MATERIALS_METHODS(){
|
747
|
return getTermByUuid(uuidMaterialsMethods);
|
748
|
}
|
749
|
|
750
|
/**
|
751
|
* Returns the "etymology" feature. This feature can only be described
|
752
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}
|
753
|
* giving some information about the history of the taxon name. This feature applies only to
|
754
|
* {@link TaxonNameDescription taxon name descriptions}.
|
755
|
*/
|
756
|
public static final Feature ETYMOLOGY(){
|
757
|
return getTermByUuid(uuidEtymology);
|
758
|
}
|
759
|
|
760
|
/**
|
761
|
* Returns the "diagnosis" feature. This feature can only be described
|
762
|
* with {@link TextData text data} or eventually with {@link CategoricalData categorical data}.
|
763
|
* This feature applies only to {@link SpecimenDescription specimen descriptions} or to
|
764
|
* {@link TaxonDescription taxon descriptions}.
|
765
|
*/
|
766
|
public static final Feature DIAGNOSIS(){
|
767
|
return getTermByUuid(uuidDiagnosis);
|
768
|
}
|
769
|
|
770
|
|
771
|
/**
|
772
|
* Returns the "introduction" feature. This feature can only be described
|
773
|
* with {@link TextData text data}.
|
774
|
*
|
775
|
* @see #isSupportsTextData()
|
776
|
*/
|
777
|
public static final Feature INTRODUCTION(){
|
778
|
return getTermByUuid(uuidIntroduction);
|
779
|
}
|
780
|
|
781
|
/**
|
782
|
* Returns the "protologue" feature. This feature can only be described
|
783
|
* with {@link TextData text data} reproducing the content of the protologue
|
784
|
* (or some information about it) of the taxon name. This feature applies only to
|
785
|
* {@link TaxonNameDescription taxon name descriptions}.
|
786
|
*
|
787
|
* @see #isSupportsTextData()
|
788
|
*/
|
789
|
public static final Feature PROTOLOGUE(){
|
790
|
return getTermByUuid(uuidProtologue);
|
791
|
}
|
792
|
|
793
|
/**
|
794
|
* Returns the "common_name" feature. This feature allows to handle only
|
795
|
* {@link CommonTaxonName common names}.
|
796
|
*
|
797
|
* @see #isSupportsCommonTaxonName()
|
798
|
*/
|
799
|
public static final Feature COMMON_NAME(){
|
800
|
return getTermByUuid(uuidCommonName);
|
801
|
}
|
802
|
|
803
|
/**
|
804
|
* Returns the "phenology" feature. This feature can only be described
|
805
|
* with {@link CategoricalData categorical data} or eventually with {@link TextData text data}
|
806
|
* containing information time about recurring natural phenomena.
|
807
|
* This feature only applies to {@link TaxonDescription taxon descriptions}.<BR>
|
808
|
* The "phenology" feature generalizes all other possible features
|
809
|
* concerning time information about particular natural phenomena
|
810
|
* (such as "first flight of butterflies").
|
811
|
*/
|
812
|
public static final Feature PHENOLOGY(){
|
813
|
return getTermByUuid(uuidPhenology);
|
814
|
}
|
815
|
|
816
|
/**
|
817
|
* Returns the "occurrence" feature.
|
818
|
*/
|
819
|
public static final Feature OCCURRENCE(){
|
820
|
return getTermByUuid(uuidOccurrence);
|
821
|
}
|
822
|
|
823
|
/**
|
824
|
* Returns the "anatomy" feature.
|
825
|
*/
|
826
|
public static final Feature ANATOMY(){
|
827
|
return getTermByUuid(uuidAnatomy);
|
828
|
}
|
829
|
/**
|
830
|
* Returns the "hostplant" feature.
|
831
|
*/
|
832
|
public static final Feature HOSTPLANT(){
|
833
|
return getTermByUuid(uuidHostPlant);
|
834
|
}
|
835
|
/**
|
836
|
* Returns the "pathogen agent" feature.
|
837
|
*/
|
838
|
public static final Feature PATHOGEN_AGENT(){
|
839
|
return getTermByUuid(uuidPathogenAgent);
|
840
|
}
|
841
|
|
842
|
/**
|
843
|
* Returns the "citation" feature. This feature can only be described
|
844
|
* with {@link TextData text data}.
|
845
|
*
|
846
|
* @see #isSupportsTextData()
|
847
|
*/
|
848
|
public static final Feature CITATION(){
|
849
|
return getTermByUuid(uuidCitation);
|
850
|
}
|
851
|
|
852
|
/**
|
853
|
* Returns the "additional_publication" feature. This feature can only be
|
854
|
* described with {@link TextData text data} with information about a
|
855
|
* publication where a {@link TaxonNameBase taxon name} has also been published
|
856
|
* but which is not the {@link TaxonNameBase#getNomenclaturalReference() nomenclatural reference}.
|
857
|
* This feature applies only to {@link TaxonNameDescription taxon name descriptions}.
|
858
|
*
|
859
|
* @see #isSupportsTextData()
|
860
|
*/
|
861
|
public static final Feature ADDITIONAL_PUBLICATION(){
|
862
|
return getTermByUuid(uuidAdditionalPublication);
|
863
|
}
|
864
|
|
865
|
|
866
|
/**
|
867
|
* Returns the "uses" feature. This feature only applies
|
868
|
* to {@link TaxonDescription taxon descriptions}.<BR>
|
869
|
* The "uses" feature generalizes all other possible features concerning
|
870
|
* particular uses (for instance "industrial use of seeds").
|
871
|
*/
|
872
|
public static final Feature USES(){
|
873
|
return getTermByUuid(uuidUses);
|
874
|
}
|
875
|
|
876
|
public static final Feature USERECORD(){
|
877
|
return getTermByUuid(uuidUseRecord);
|
878
|
}
|
879
|
|
880
|
|
881
|
/**
|
882
|
* Returns the "conservation" feature. This feature only applies
|
883
|
* to {@link SpecimenDescription specimen descriptions} and generalizes
|
884
|
* methods and conditions for the conservation of {@link Specimen specimens}.<BR>
|
885
|
*/
|
886
|
public static final Feature CONSERVATION(){
|
887
|
return getTermByUuid(uuidConservation);
|
888
|
}
|
889
|
|
890
|
|
891
|
/**
|
892
|
* Returns the "cultivation" feature.
|
893
|
*/
|
894
|
public static final Feature CULTIVATION(){
|
895
|
return getTermByUuid(uuidCultivation);
|
896
|
}
|
897
|
|
898
|
|
899
|
/**
|
900
|
* Returns the "image" feature.
|
901
|
*/
|
902
|
public static final Feature IMAGE(){
|
903
|
return getTermByUuid(uuidImage);
|
904
|
}
|
905
|
|
906
|
/**
|
907
|
* Returns the "individuals association" feature.
|
908
|
*/
|
909
|
public static final Feature INDIVIDUALS_ASSOCIATION(){
|
910
|
Feature individuals_association = getTermByUuid(uuidIndividualsAssociation);
|
911
|
Set<Feature> generalizationOf = new HashSet<Feature>();
|
912
|
generalizationOf.add(SPECIMEN());
|
913
|
generalizationOf.add(OBSERVATION());
|
914
|
individuals_association.setGeneralizationOf(generalizationOf);
|
915
|
return individuals_association;
|
916
|
|
917
|
}
|
918
|
|
919
|
public static final Feature SPECIMEN(){
|
920
|
return getTermByUuid(uuidSpecimen);
|
921
|
}
|
922
|
|
923
|
public static final Feature OBSERVATION(){
|
924
|
return getTermByUuid(uuidObservation);
|
925
|
}
|
926
|
|
927
|
/**
|
928
|
* The status of a taxon. Usually the status should be determined within a {@link Distribution distribution}.
|
929
|
* If this is not possible for some reason (e.g. the area is not well defined) the status feature
|
930
|
* may be used.
|
931
|
* @return
|
932
|
*/
|
933
|
public static final Feature STATUS(){
|
934
|
return getTermByUuid(uuidStatus);
|
935
|
}
|
936
|
|
937
|
public static final Feature SYSTEMATICS(){
|
938
|
return getTermByUuid(uuidSystematics);
|
939
|
}
|
940
|
|
941
|
/**
|
942
|
* Returns the "hybrid_parent" feature. This feature can only be used
|
943
|
* by {@link TaxonInteraction taxon interactions}.<BR>
|
944
|
* <P>
|
945
|
* Note: It must be distinguished between hybrid relationships as
|
946
|
* relevant nomenclatural relationships between {@link BotanicalName plant names}
|
947
|
* on the one side and the biological relation between two {@link Taxon taxa}
|
948
|
* as it is here the case on the other one.
|
949
|
*
|
950
|
* @see #isSupportsTaxonInteraction()
|
951
|
* @see HybridRelationshipType
|
952
|
*/
|
953
|
public static final Feature HYBRID_PARENT(){
|
954
|
//TODO
|
955
|
logger.warn("HYBRID_PARENT not yet implemented");
|
956
|
return null;
|
957
|
}
|
958
|
|
959
|
@Override
|
960
|
protected void setDefaultTerms(TermVocabulary<Feature> termVocabulary) {
|
961
|
if (termMap == null){ //needed because there are multiple feature vocabularies
|
962
|
termMap = new HashMap<UUID, Feature>();
|
963
|
}
|
964
|
for (Feature term : termVocabulary.getTerms()){
|
965
|
termMap.put(term.getUuid(), term);
|
966
|
}
|
967
|
}
|
968
|
|
969
|
}
|