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
|
import java.math.BigDecimal;
|
13
|
import java.util.HashSet;
|
14
|
import java.util.Set;
|
15
|
|
16
|
import javax.persistence.Column;
|
17
|
import javax.persistence.Entity;
|
18
|
import javax.persistence.FetchType;
|
19
|
import javax.persistence.ManyToOne;
|
20
|
import javax.persistence.OneToMany;
|
21
|
import javax.persistence.Transient;
|
22
|
import javax.xml.bind.annotation.XmlAccessType;
|
23
|
import javax.xml.bind.annotation.XmlAccessorType;
|
24
|
import javax.xml.bind.annotation.XmlElement;
|
25
|
import javax.xml.bind.annotation.XmlElementWrapper;
|
26
|
import javax.xml.bind.annotation.XmlIDREF;
|
27
|
import javax.xml.bind.annotation.XmlRootElement;
|
28
|
import javax.xml.bind.annotation.XmlSchemaType;
|
29
|
import javax.xml.bind.annotation.XmlType;
|
30
|
|
31
|
import org.apache.log4j.Logger;
|
32
|
import org.hibernate.annotations.Cascade;
|
33
|
import org.hibernate.annotations.CascadeType;
|
34
|
import org.hibernate.envers.Audited;
|
35
|
import org.hibernate.search.annotations.Indexed;
|
36
|
import org.hibernate.validator.constraints.NotEmpty;
|
37
|
|
38
|
import eu.etaxonomy.cdm.model.common.DefinedTerm;
|
39
|
import eu.etaxonomy.cdm.validation.Level2;
|
40
|
|
41
|
/**
|
42
|
* This class represents information pieces expressed in numerical data
|
43
|
* (in opposition to {@link CategoricalData categorical data} on one side and to literal data on
|
44
|
* the other side). Only {@link TaxonDescription taxon descriptions} and
|
45
|
* {@link SpecimenDescription specimen descriptions} may contain quantitative data.<BR>
|
46
|
* The "length of leaves" {@link Feature feature} for instance can be measured in inches.
|
47
|
* If the length of leaves of a particular tree is described as
|
48
|
* "typically between 3 and 5 inches" and "at the utmost 8 inches" then three
|
49
|
* {@link StatisticalMeasurementValue statistical measurement value} instances
|
50
|
* must be assigned to an instance of the present class
|
51
|
* (with the {@link MeasurementUnit measurement unit} set to "inch"):<ul>
|
52
|
* <li> the first one with the value "3" and the {@link StatisticalMeasure statistical measure}
|
53
|
* "typical lower boundary",
|
54
|
* <li> the second one with the value "5" and the statistical measure
|
55
|
* "typical upper boundary"
|
56
|
* <li> the third one with the value "8" and the statistical measure "maximum"
|
57
|
* </ul>
|
58
|
* <P>
|
59
|
* This class corresponds partially to CodedDescriptionType according to
|
60
|
* the SDD schema.
|
61
|
*
|
62
|
* @author m.doering
|
63
|
* @version 1.0
|
64
|
* @created 08-Nov-2007 13:06:46
|
65
|
*/
|
66
|
@XmlAccessorType(XmlAccessType.FIELD)
|
67
|
@XmlType(name = "QuantitativeData", propOrder = {
|
68
|
"unit",
|
69
|
"statisticalValues",
|
70
|
"unknownData"
|
71
|
})
|
72
|
@XmlRootElement(name = "QuantitativeData")
|
73
|
@Entity
|
74
|
@Indexed(index = "eu.etaxonomy.cdm.model.description.DescriptionElementBase")
|
75
|
@Audited
|
76
|
public class QuantitativeData extends DescriptionElementBase implements Cloneable {
|
77
|
private static final long serialVersionUID = -2755806455420051488L;
|
78
|
|
79
|
private static final Logger logger = Logger.getLogger(QuantitativeData.class);
|
80
|
|
81
|
@XmlElement(name = "MeasurementUnit")
|
82
|
@XmlIDREF
|
83
|
@XmlSchemaType(name = "IDREF")
|
84
|
@ManyToOne(fetch = FetchType.LAZY)
|
85
|
private MeasurementUnit unit;
|
86
|
|
87
|
@XmlElementWrapper(name = "StatisticalValues")
|
88
|
@XmlElement(name = "StatisticalValue")
|
89
|
@OneToMany(fetch = FetchType.LAZY, orphanRemoval=true)
|
90
|
@Cascade({ CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
|
91
|
@NotEmpty(groups = Level2.class)
|
92
|
private Set<StatisticalMeasurementValue> statisticalValues = new HashSet<StatisticalMeasurementValue>();
|
93
|
|
94
|
//see #4471
|
95
|
// @Column(precision = 20, scale = 10)
|
96
|
// private BigDecimal minimum;
|
97
|
//
|
98
|
// @Column(precision = 20, scale = 10)
|
99
|
// private BigDecimal maximum;
|
100
|
//
|
101
|
// @Column(precision = 20, scale = 10)
|
102
|
// private BigDecimal average;
|
103
|
//
|
104
|
// @Column(precision = 16, scale = 8)
|
105
|
// private BigDecimal variance;
|
106
|
//
|
107
|
// @Column(precision = 16, scale = 8)
|
108
|
// private BigDecimal standardDeviation;
|
109
|
//
|
110
|
// @Column(precision = 20, scale = 10)
|
111
|
// private BigDecimal singleValue;
|
112
|
//
|
113
|
// private Integer sampleSize;
|
114
|
|
115
|
@XmlElement(name = "UnknownData")
|
116
|
private Boolean unknownData = false;
|
117
|
|
118
|
|
119
|
// ******************************** FACTORY METHOD *******************************/
|
120
|
|
121
|
/**
|
122
|
* Creates a new empty quantitative data instance.
|
123
|
*/
|
124
|
public static QuantitativeData NewInstance(){
|
125
|
return new QuantitativeData();
|
126
|
}
|
127
|
|
128
|
// ******************************** FACTORY METHOD *******************************/
|
129
|
|
130
|
/**
|
131
|
* Creates a new empty quantitative data instance.
|
132
|
*/
|
133
|
public static QuantitativeData NewInstance(Feature feature){
|
134
|
return new QuantitativeData(feature);
|
135
|
}
|
136
|
|
137
|
|
138
|
// ******************************** CONSTRUCTOR *******************************/
|
139
|
|
140
|
/**
|
141
|
* Class constructor: creates a new empty quantitative data instance.
|
142
|
*/
|
143
|
protected QuantitativeData(){
|
144
|
super(null);
|
145
|
}
|
146
|
|
147
|
/**
|
148
|
* Class constructor: creates a new empty quantitative data instance.
|
149
|
*/
|
150
|
protected QuantitativeData(Feature feature){
|
151
|
super(feature);
|
152
|
}
|
153
|
|
154
|
|
155
|
// ******************************** GETTER /SETTER *******************************/
|
156
|
|
157
|
|
158
|
/**
|
159
|
* Returns the set of {@link StatisticalMeasurementValue statistical measurement values} describing
|
160
|
* the {@link Feature feature} corresponding to <i>this</i> quantitative data.
|
161
|
*/
|
162
|
public Set<StatisticalMeasurementValue> getStatisticalValues() {
|
163
|
return statisticalValues;
|
164
|
}
|
165
|
|
166
|
protected void setStatisticalValues(Set<StatisticalMeasurementValue> statisticalValues) {
|
167
|
this.statisticalValues = statisticalValues;
|
168
|
}
|
169
|
/**
|
170
|
* Adds a {@link StatisticalMeasurementValue statistical measurement value} to the set of
|
171
|
* {@link #getStatisticalValues() statistical measurement values} describing
|
172
|
* the {@link Feature feature} corresponding to <i>this</i> quantitative data.
|
173
|
*
|
174
|
* @param statisticalValue the statistical measurement value to be added to
|
175
|
* <i>this</i> quantitative data
|
176
|
* @see #getStatisticalValues()
|
177
|
*/
|
178
|
public void addStatisticalValue(StatisticalMeasurementValue statisticalValue) {
|
179
|
this.statisticalValues.add(statisticalValue);
|
180
|
}
|
181
|
/**
|
182
|
* Removes one element from the set of {@link #getStatisticalValues() statistical measurement values}
|
183
|
* describing the {@link Feature feature} corresponding to <i>this</i> quantitative data.
|
184
|
*
|
185
|
* @param statisticalValue the statistical measurement value which should be removed
|
186
|
* @see #getStatisticalValues()
|
187
|
* @see #addStatisticalValue(StatisticalMeasurementValue)
|
188
|
*/
|
189
|
public void removeStatisticalValue(StatisticalMeasurementValue statisticalValue) {
|
190
|
this.statisticalValues.remove(statisticalValue);
|
191
|
}
|
192
|
|
193
|
|
194
|
/**
|
195
|
* Returns the {@link MeasurementUnit measurement unit} used in <i>this</i>
|
196
|
* quantitative data.
|
197
|
*/
|
198
|
public MeasurementUnit getUnit(){
|
199
|
return this.unit;
|
200
|
}
|
201
|
/**
|
202
|
* @see #getUnit()
|
203
|
*/
|
204
|
public void setUnit(MeasurementUnit unit){
|
205
|
this.unit = unit;
|
206
|
}
|
207
|
|
208
|
// ******************************** TRANSIENT METHODS *******************************/
|
209
|
|
210
|
|
211
|
/**
|
212
|
* Returns the numerical value of the one {@link StatisticalMeasurementValue statistical measurement value}
|
213
|
* with the corresponding {@link StatisticalMeasure statistical measure} "minimum" and
|
214
|
* belonging to <i>this</i> quantitative data. Returns <code>null</code> if no such
|
215
|
* statistical measurement value instance exists.
|
216
|
*/
|
217
|
@Transient
|
218
|
public Float getMin(){
|
219
|
return getSpecificStatisticalValue(StatisticalMeasure.MIN());
|
220
|
}
|
221
|
|
222
|
/**
|
223
|
* Returns the numerical value of the one {@link StatisticalMeasurementValue statistical measurement value}
|
224
|
* with the corresponding {@link StatisticalMeasure statistical measure} "maximum" and
|
225
|
* belonging to <i>this</i> quantitative data. Returns <code>null</code> if no such
|
226
|
* statistical measurement value instance exists.
|
227
|
*/
|
228
|
@Transient
|
229
|
public Float getMax(){
|
230
|
return getSpecificStatisticalValue(StatisticalMeasure.MAX());
|
231
|
}
|
232
|
|
233
|
/**
|
234
|
* Returns the numerical value of the one {@link StatisticalMeasurementValue statistical measurement value}
|
235
|
* with the corresponding {@link StatisticalMeasure statistical measure}
|
236
|
* "typical lower boundary" and belonging to <i>this</i> quantitative data.
|
237
|
* Returns <code>null</code> if no such statistical measurement value instance exists.
|
238
|
*/
|
239
|
@Transient
|
240
|
public Float getTypicalLowerBoundary(){
|
241
|
return getSpecificStatisticalValue(StatisticalMeasure.TYPICAL_LOWER_BOUNDARY());
|
242
|
}
|
243
|
|
244
|
/**
|
245
|
* Returns the numerical value of the one {@link StatisticalMeasurementValue statistical measurement value}
|
246
|
* with the corresponding {@link StatisticalMeasure statistical measure}
|
247
|
* "average" and belonging to <i>this</i> quantitative data.
|
248
|
* Returns <code>null</code> if no such statistical measurement value instance exists.
|
249
|
*/
|
250
|
@Transient
|
251
|
public Float getAverage(){
|
252
|
return getSpecificStatisticalValue(StatisticalMeasure.AVERAGE());
|
253
|
}
|
254
|
|
255
|
/**
|
256
|
* Returns the numerical value of the one {@link StatisticalMeasurementValue statistical measurement value}
|
257
|
* with the corresponding {@link StatisticalMeasure statistical measure}
|
258
|
* "standard deviation" and belonging to <i>this</i> quantitative data.
|
259
|
* Returns <code>null</code> if no such statistical measurement value instance exists.
|
260
|
*/
|
261
|
@Transient
|
262
|
public Float getStandardDeviation(){
|
263
|
return getSpecificStatisticalValue(StatisticalMeasure.STANDARD_DEVIATION());
|
264
|
}
|
265
|
|
266
|
/**
|
267
|
* Returns the numerical value of the one {@link StatisticalMeasurementValue statistical measurement value}
|
268
|
* with the corresponding {@link StatisticalMeasure statistical measure}
|
269
|
* "sample size" and belonging to <i>this</i> quantitative data.
|
270
|
* Returns <code>null</code> if no such statistical measurement value instance exists.
|
271
|
*/
|
272
|
@Transient
|
273
|
public Float getSampleSize(){
|
274
|
return getSpecificStatisticalValue(StatisticalMeasure.SAMPLE_SIZE());
|
275
|
}
|
276
|
|
277
|
/**
|
278
|
* Returns the numerical value of the one {@link StatisticalMeasurementValue statistical measurement value}
|
279
|
* with the corresponding {@link StatisticalMeasure statistical measure}
|
280
|
* "typical upper boundary" and belonging to <i>this</i> quantitative data.
|
281
|
* Returns <code>null</code> if no such statistical measurement value instance exists.
|
282
|
*/
|
283
|
@Transient
|
284
|
public Float getTypicalUpperBoundary(){
|
285
|
return getSpecificStatisticalValue(StatisticalMeasure.TYPICAL_UPPER_BOUNDARY());
|
286
|
}
|
287
|
|
288
|
/**
|
289
|
* Returns the statistical value of type <code>type</code>.
|
290
|
* If no such value exists <code>null</code> is returned. If multiple such
|
291
|
* values exist an arbitrary one is returned.
|
292
|
* @param type
|
293
|
* @return the value
|
294
|
*/
|
295
|
public Float getSpecificStatisticalValue(StatisticalMeasure type){
|
296
|
Float result = null;
|
297
|
for (StatisticalMeasurementValue value : statisticalValues){
|
298
|
if (type.equals(value.getType())){
|
299
|
result = value.getValue();
|
300
|
break;
|
301
|
}
|
302
|
}
|
303
|
return result;
|
304
|
}
|
305
|
|
306
|
|
307
|
/**
|
308
|
* Sets the statistical value for the minimum.
|
309
|
* If such value exists the old value is replaced by the new value.
|
310
|
* The new value is returned.
|
311
|
* @param type
|
312
|
* @param value
|
313
|
* @return the newValue
|
314
|
*/
|
315
|
@Transient
|
316
|
public StatisticalMeasurementValue setMinimum(Float value, Set<DefinedTerm> modifiers){
|
317
|
return setSpecificStatisticalValue(value, modifiers, StatisticalMeasure.MIN());
|
318
|
}
|
319
|
|
320
|
|
321
|
/**
|
322
|
* Sets the statistical value for the maximum.
|
323
|
* If such value exists the old value is replaced by the new value.
|
324
|
* The new value is returned.
|
325
|
* @param type
|
326
|
* @param value
|
327
|
* @return the newValue
|
328
|
*/
|
329
|
@Transient
|
330
|
public StatisticalMeasurementValue setMaximum(Float value, Set<DefinedTerm> modifiers){
|
331
|
return setSpecificStatisticalValue(value, modifiers, StatisticalMeasure.MAX());
|
332
|
}
|
333
|
|
334
|
|
335
|
/**
|
336
|
* Sets the statistical value for the average.
|
337
|
* If such value exists the old value is replaced by the new value.
|
338
|
* The new value is returned.
|
339
|
* @param type
|
340
|
* @param value
|
341
|
* @return the newValue
|
342
|
*/
|
343
|
@Transient
|
344
|
public StatisticalMeasurementValue setAverage(Float value, Set<DefinedTerm> modifiers){
|
345
|
return setSpecificStatisticalValue(value, modifiers, StatisticalMeasure.AVERAGE());
|
346
|
}
|
347
|
|
348
|
|
349
|
/**
|
350
|
* Sets the statistical value for the standard deviation.
|
351
|
* If such value exists the old value is replaced by the new value.
|
352
|
* The new value is returned.
|
353
|
* @param type
|
354
|
* @param value
|
355
|
* @return the newValue
|
356
|
*/
|
357
|
@Transient
|
358
|
public StatisticalMeasurementValue setStandardDeviation(Float value, Set<DefinedTerm> modifiers){
|
359
|
return setSpecificStatisticalValue(value, modifiers, StatisticalMeasure.STANDARD_DEVIATION());
|
360
|
}
|
361
|
|
362
|
/**
|
363
|
* Sets the statistical value for the sample size.
|
364
|
* If such value exists the old value is replaced by the new value.
|
365
|
* The new value is returned.
|
366
|
* @param type
|
367
|
* @param value
|
368
|
* @return the newValue
|
369
|
*/
|
370
|
@Transient
|
371
|
public StatisticalMeasurementValue setSampleSize(Float value, Set<DefinedTerm> modifiers){
|
372
|
return setSpecificStatisticalValue(value, modifiers, StatisticalMeasure.SAMPLE_SIZE());
|
373
|
}
|
374
|
|
375
|
|
376
|
/**
|
377
|
* Sets the statistical value for the typical lower boundary.
|
378
|
* If such value exists the old value is replaced by the new value.
|
379
|
* The new value is returned.
|
380
|
* @param type
|
381
|
* @param value
|
382
|
* @return the newValue
|
383
|
*/
|
384
|
@Transient
|
385
|
public StatisticalMeasurementValue setTypicalLowerBoundary(Float value, Set<DefinedTerm> modifiers){
|
386
|
return setSpecificStatisticalValue(value, modifiers, StatisticalMeasure.TYPICAL_LOWER_BOUNDARY());
|
387
|
}
|
388
|
|
389
|
|
390
|
/**
|
391
|
* Sets the statistical value for the typical upper boundary.
|
392
|
* If such value exists the old value is replaced by the new value.
|
393
|
* The new value is returned.
|
394
|
* @param type
|
395
|
* @param value
|
396
|
* @return the newValue
|
397
|
*/
|
398
|
@Transient
|
399
|
public StatisticalMeasurementValue setTypicalUpperBoundary(Float value, Set<DefinedTerm> modifiers){
|
400
|
return setSpecificStatisticalValue(value, modifiers, StatisticalMeasure.TYPICAL_UPPER_BOUNDARY());
|
401
|
}
|
402
|
|
403
|
/**
|
404
|
* Sets the statistical value of type <code>type</code>.
|
405
|
* If such value exists the old value is replaced by the new value.
|
406
|
* The new value is returned.
|
407
|
* @param type
|
408
|
* @param value
|
409
|
* @return the newValue
|
410
|
*/
|
411
|
public StatisticalMeasurementValue setSpecificStatisticalValue(Float value, Set<DefinedTerm> modifiers, StatisticalMeasure type){
|
412
|
StatisticalMeasurementValue result = null;
|
413
|
if (value != null){
|
414
|
StatisticalMeasurementValue newValue = StatisticalMeasurementValue.NewInstance();
|
415
|
newValue.setValue(value);
|
416
|
if (modifiers != null){
|
417
|
newValue.getModifiers().addAll(modifiers);
|
418
|
}
|
419
|
newValue.setType(type);
|
420
|
result = newValue;
|
421
|
}
|
422
|
for (StatisticalMeasurementValue existingValue : statisticalValues){
|
423
|
if (type.equals(existingValue.getType())){
|
424
|
result = existingValue;
|
425
|
statisticalValues.remove(existingValue);
|
426
|
break;
|
427
|
}
|
428
|
}
|
429
|
if (result != null){
|
430
|
statisticalValues.add(result);
|
431
|
}
|
432
|
return result;
|
433
|
}
|
434
|
|
435
|
public Boolean getUnknownData() {
|
436
|
return unknownData;
|
437
|
}
|
438
|
|
439
|
public void setUnknownData(Boolean unknownData) {
|
440
|
this.unknownData = unknownData;
|
441
|
}
|
442
|
|
443
|
//
|
444
|
// public BigDecimal getMinimum() {
|
445
|
// return minimum;
|
446
|
// }
|
447
|
//
|
448
|
// public void setMinimum(BigDecimal minimum) {
|
449
|
// this.minimum = minimum;
|
450
|
// }
|
451
|
//
|
452
|
// public BigDecimal getMaximum() {
|
453
|
// return maximum;
|
454
|
// }
|
455
|
//
|
456
|
// public void setMaximum(BigDecimal maximum) {
|
457
|
// this.maximum = maximum;
|
458
|
// }
|
459
|
//
|
460
|
// public BigDecimal getVariance() {
|
461
|
// return variance;
|
462
|
// }
|
463
|
//
|
464
|
// public void setVariance(BigDecimal variance) {
|
465
|
// this.variance = variance;
|
466
|
// }
|
467
|
//
|
468
|
// public BigDecimal getSingleValue() {
|
469
|
// return singleValue;
|
470
|
// }
|
471
|
//
|
472
|
// public void setSingleValue(BigDecimal singleValue) {
|
473
|
// this.singleValue = singleValue;
|
474
|
// }
|
475
|
|
476
|
//
|
477
|
// public void setAverage(BigDecimal average) {
|
478
|
// this.average = average;
|
479
|
// }
|
480
|
//
|
481
|
// public void setStandardDeviation(BigDecimal standardDeviation) {
|
482
|
// this.standardDeviation = standardDeviation;
|
483
|
// }
|
484
|
//
|
485
|
// public void setSampleSize(Integer sampleSize) {
|
486
|
// this.sampleSize = sampleSize;
|
487
|
// }
|
488
|
|
489
|
|
490
|
//*********************************** CLONE *****************************************/
|
491
|
|
492
|
/**
|
493
|
* Clones <i>this</i> quantitative data. This is a shortcut that enables to create
|
494
|
* a new instance that differs only slightly from <i>this</i> quantitative data by
|
495
|
* modifying only some of the attributes.
|
496
|
*
|
497
|
* @see eu.etaxonomy.cdm.model.description.DescriptionElementBase#clone()
|
498
|
* @see java.lang.Object#clone()
|
499
|
*/
|
500
|
@Override
|
501
|
public Object clone() {
|
502
|
|
503
|
try {
|
504
|
QuantitativeData result = (QuantitativeData)super.clone();
|
505
|
|
506
|
//states
|
507
|
result.statisticalValues = new HashSet<StatisticalMeasurementValue>();
|
508
|
for (StatisticalMeasurementValue data : getStatisticalValues()){
|
509
|
//TODO do we need to clone here?
|
510
|
StatisticalMeasurementValue newData = (StatisticalMeasurementValue)data.clone();
|
511
|
result.statisticalValues.add(newData);
|
512
|
}
|
513
|
|
514
|
return result;
|
515
|
//no changes to: unit
|
516
|
} catch (CloneNotSupportedException e) {
|
517
|
logger.warn("Object does not implement cloneable");
|
518
|
e.printStackTrace();
|
519
|
return null;
|
520
|
}
|
521
|
}
|
522
|
|
523
|
}
|