1 |
|
|
2 |
|
|
3 |
|
|
4 |
|
|
5 |
|
|
6 |
|
|
7 |
|
|
8 |
|
package jalview.xml.binding.uniprot; |
9 |
|
|
10 |
|
import java.util.ArrayList; |
11 |
|
import java.util.List; |
12 |
|
import javax.xml.bind.annotation.XmlAccessType; |
13 |
|
import javax.xml.bind.annotation.XmlAccessorType; |
14 |
|
import javax.xml.bind.annotation.XmlAttribute; |
15 |
|
import javax.xml.bind.annotation.XmlElement; |
16 |
|
import javax.xml.bind.annotation.XmlRootElement; |
17 |
|
import javax.xml.bind.annotation.XmlSchemaType; |
18 |
|
import javax.xml.bind.annotation.XmlType; |
19 |
|
import javax.xml.datatype.XMLGregorianCalendar; |
20 |
|
|
21 |
|
|
22 |
|
|
23 |
|
|
24 |
|
|
25 |
|
|
26 |
|
|
27 |
|
|
28 |
|
|
29 |
|
|
30 |
|
|
31 |
|
|
32 |
|
|
33 |
|
|
34 |
|
|
35 |
|
|
36 |
|
|
37 |
|
|
38 |
|
|
39 |
|
|
40 |
|
|
41 |
|
|
42 |
|
|
43 |
|
|
44 |
|
|
45 |
|
|
46 |
|
|
47 |
|
|
48 |
|
|
49 |
|
|
50 |
|
|
51 |
|
|
52 |
|
|
53 |
|
|
54 |
|
|
55 |
|
|
56 |
|
|
57 |
|
|
58 |
|
|
59 |
|
|
60 |
|
|
61 |
|
|
62 |
|
|
63 |
|
|
64 |
|
|
65 |
|
|
66 |
|
|
67 |
|
|
68 |
|
@XmlAccessorType(XmlAccessType.FIELD) |
69 |
|
@XmlType( |
70 |
|
name = "", |
71 |
|
propOrder = |
72 |
|
{ "accession", "name", "protein", "gene", "organism", "organismHost", |
73 |
|
"geneLocation", "reference", "comment", "dbReference", |
74 |
|
"proteinExistence", "keyword", "feature", "evidence", "sequence" }) |
75 |
|
@XmlRootElement(name = "entry") |
|
|
| 22.4% |
Uncovered Elements: 76 (98) |
Complexity: 38 |
Complexity Density: 0.78 |
|
76 |
|
public class Entry |
77 |
|
{ |
78 |
|
|
79 |
|
@XmlElement(required = true) |
80 |
|
protected List<String> accession; |
81 |
|
|
82 |
|
@XmlElement(required = true) |
83 |
|
protected List<String> name; |
84 |
|
|
85 |
|
@XmlElement(required = true) |
86 |
|
protected ProteinType protein; |
87 |
|
|
88 |
|
protected List<GeneType> gene; |
89 |
|
|
90 |
|
@XmlElement(required = true) |
91 |
|
protected OrganismType organism; |
92 |
|
|
93 |
|
protected List<OrganismType> organismHost; |
94 |
|
|
95 |
|
protected List<GeneLocationType> geneLocation; |
96 |
|
|
97 |
|
@XmlElement(required = true) |
98 |
|
protected List<ReferenceType> reference; |
99 |
|
|
100 |
|
@XmlElement(nillable = true) |
101 |
|
protected List<CommentType> comment; |
102 |
|
|
103 |
|
protected List<DbReferenceType> dbReference; |
104 |
|
|
105 |
|
@XmlElement(required = true) |
106 |
|
protected ProteinExistenceType proteinExistence; |
107 |
|
|
108 |
|
protected List<KeywordType> keyword; |
109 |
|
|
110 |
|
protected List<FeatureType> feature; |
111 |
|
|
112 |
|
protected List<EvidenceType> evidence; |
113 |
|
|
114 |
|
@XmlElement(required = true) |
115 |
|
protected SequenceType sequence; |
116 |
|
|
117 |
|
@XmlAttribute(name = "dataset", required = true) |
118 |
|
protected String dataset; |
119 |
|
|
120 |
|
@XmlAttribute(name = "created", required = true) |
121 |
|
@XmlSchemaType(name = "date") |
122 |
|
protected XMLGregorianCalendar created; |
123 |
|
|
124 |
|
@XmlAttribute(name = "modified", required = true) |
125 |
|
@XmlSchemaType(name = "date") |
126 |
|
protected XMLGregorianCalendar modified; |
127 |
|
|
128 |
|
@XmlAttribute(name = "version", required = true) |
129 |
|
protected int version; |
130 |
|
|
131 |
|
|
132 |
|
|
133 |
|
|
134 |
|
|
135 |
|
|
136 |
|
|
137 |
|
|
138 |
|
|
139 |
|
|
140 |
|
|
141 |
|
|
142 |
|
|
143 |
|
|
144 |
|
|
145 |
|
|
146 |
|
|
147 |
|
|
148 |
|
|
149 |
|
@link |
150 |
|
|
151 |
|
|
152 |
|
|
|
|
| 60% |
Uncovered Elements: 2 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
153 |
5 |
public List<String> getAccession()... |
154 |
|
{ |
155 |
5 |
if (accession == null) |
156 |
|
{ |
157 |
0 |
accession = new ArrayList<String>(); |
158 |
|
} |
159 |
5 |
return this.accession; |
160 |
|
} |
161 |
|
|
162 |
|
|
163 |
|
|
164 |
|
|
165 |
|
|
166 |
|
|
167 |
|
|
168 |
|
|
169 |
|
|
170 |
|
|
171 |
|
|
172 |
|
|
173 |
|
|
174 |
|
|
175 |
|
|
176 |
|
|
177 |
|
|
178 |
|
|
179 |
|
|
180 |
|
@link |
181 |
|
|
182 |
|
|
183 |
|
|
|
|
| 60% |
Uncovered Elements: 2 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
184 |
6 |
public List<String> getName()... |
185 |
|
{ |
186 |
6 |
if (name == null) |
187 |
|
{ |
188 |
0 |
name = new ArrayList<String>(); |
189 |
|
} |
190 |
6 |
return this.name; |
191 |
|
} |
192 |
|
|
193 |
|
|
194 |
|
|
195 |
|
|
196 |
|
@return@link |
197 |
|
|
198 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
199 |
10 |
public ProteinType getProtein()... |
200 |
|
{ |
201 |
10 |
return protein; |
202 |
|
} |
203 |
|
|
204 |
|
|
205 |
|
|
206 |
|
|
207 |
|
@param |
208 |
|
@link |
209 |
|
|
210 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
211 |
0 |
public void setProtein(ProteinType value)... |
212 |
|
{ |
213 |
0 |
this.protein = value; |
214 |
|
} |
215 |
|
|
216 |
|
|
217 |
|
|
218 |
|
|
219 |
|
|
220 |
|
|
221 |
|
|
222 |
|
|
223 |
|
|
224 |
|
|
225 |
|
|
226 |
|
|
227 |
|
|
228 |
|
|
229 |
|
|
230 |
|
|
231 |
|
|
232 |
|
|
233 |
|
|
234 |
|
@link |
235 |
|
|
236 |
|
|
237 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
238 |
0 |
public List<GeneType> getGene()... |
239 |
|
{ |
240 |
0 |
if (gene == null) |
241 |
|
{ |
242 |
0 |
gene = new ArrayList<GeneType>(); |
243 |
|
} |
244 |
0 |
return this.gene; |
245 |
|
} |
246 |
|
|
247 |
|
|
248 |
|
|
249 |
|
|
250 |
|
@return@link |
251 |
|
|
252 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
253 |
0 |
public OrganismType getOrganism()... |
254 |
|
{ |
255 |
0 |
return organism; |
256 |
|
} |
257 |
|
|
258 |
|
|
259 |
|
|
260 |
|
|
261 |
|
@param |
262 |
|
@link |
263 |
|
|
264 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
265 |
0 |
public void setOrganism(OrganismType value)... |
266 |
|
{ |
267 |
0 |
this.organism = value; |
268 |
|
} |
269 |
|
|
270 |
|
|
271 |
|
|
272 |
|
|
273 |
|
|
274 |
|
|
275 |
|
|
276 |
|
|
277 |
|
|
278 |
|
|
279 |
|
|
280 |
|
|
281 |
|
|
282 |
|
|
283 |
|
|
284 |
|
|
285 |
|
|
286 |
|
|
287 |
|
|
288 |
|
|
289 |
|
@link |
290 |
|
|
291 |
|
|
292 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
293 |
0 |
public List<OrganismType> getOrganismHost()... |
294 |
|
{ |
295 |
0 |
if (organismHost == null) |
296 |
|
{ |
297 |
0 |
organismHost = new ArrayList<OrganismType>(); |
298 |
|
} |
299 |
0 |
return this.organismHost; |
300 |
|
} |
301 |
|
|
302 |
|
|
303 |
|
|
304 |
|
|
305 |
|
|
306 |
|
|
307 |
|
|
308 |
|
|
309 |
|
|
310 |
|
|
311 |
|
|
312 |
|
|
313 |
|
|
314 |
|
|
315 |
|
|
316 |
|
|
317 |
|
|
318 |
|
|
319 |
|
|
320 |
|
|
321 |
|
@link |
322 |
|
|
323 |
|
|
324 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
325 |
0 |
public List<GeneLocationType> getGeneLocation()... |
326 |
|
{ |
327 |
0 |
if (geneLocation == null) |
328 |
|
{ |
329 |
0 |
geneLocation = new ArrayList<GeneLocationType>(); |
330 |
|
} |
331 |
0 |
return this.geneLocation; |
332 |
|
} |
333 |
|
|
334 |
|
|
335 |
|
|
336 |
|
|
337 |
|
|
338 |
|
|
339 |
|
|
340 |
|
|
341 |
|
|
342 |
|
|
343 |
|
|
344 |
|
|
345 |
|
|
346 |
|
|
347 |
|
|
348 |
|
|
349 |
|
|
350 |
|
|
351 |
|
|
352 |
|
|
353 |
|
@link |
354 |
|
|
355 |
|
|
356 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
357 |
0 |
public List<ReferenceType> getReference()... |
358 |
|
{ |
359 |
0 |
if (reference == null) |
360 |
|
{ |
361 |
0 |
reference = new ArrayList<ReferenceType>(); |
362 |
|
} |
363 |
0 |
return this.reference; |
364 |
|
} |
365 |
|
|
366 |
|
|
367 |
|
|
368 |
|
|
369 |
|
|
370 |
|
|
371 |
|
|
372 |
|
|
373 |
|
|
374 |
|
|
375 |
|
|
376 |
|
|
377 |
|
|
378 |
|
|
379 |
|
|
380 |
|
|
381 |
|
|
382 |
|
|
383 |
|
|
384 |
|
@link |
385 |
|
|
386 |
|
|
387 |
|
|
388 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
389 |
0 |
public List<CommentType> getComment()... |
390 |
|
{ |
391 |
0 |
if (comment == null) |
392 |
|
{ |
393 |
0 |
comment = new ArrayList<CommentType>(); |
394 |
|
} |
395 |
0 |
return this.comment; |
396 |
|
} |
397 |
|
|
398 |
|
|
399 |
|
|
400 |
|
|
401 |
|
|
402 |
|
|
403 |
|
|
404 |
|
|
405 |
|
|
406 |
|
|
407 |
|
|
408 |
|
|
409 |
|
|
410 |
|
|
411 |
|
|
412 |
|
|
413 |
|
|
414 |
|
|
415 |
|
|
416 |
|
|
417 |
|
@link |
418 |
|
|
419 |
|
|
420 |
|
|
|
|
| 60% |
Uncovered Elements: 2 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
421 |
3 |
public List<DbReferenceType> getDbReference()... |
422 |
|
{ |
423 |
3 |
if (dbReference == null) |
424 |
|
{ |
425 |
0 |
dbReference = new ArrayList<DbReferenceType>(); |
426 |
|
} |
427 |
3 |
return this.dbReference; |
428 |
|
} |
429 |
|
|
430 |
|
|
431 |
|
|
432 |
|
|
433 |
|
@return@link |
434 |
|
|
435 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
436 |
0 |
public ProteinExistenceType getProteinExistence()... |
437 |
|
{ |
438 |
0 |
return proteinExistence; |
439 |
|
} |
440 |
|
|
441 |
|
|
442 |
|
|
443 |
|
|
444 |
|
@param |
445 |
|
@link |
446 |
|
|
447 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
448 |
0 |
public void setProteinExistence(ProteinExistenceType value)... |
449 |
|
{ |
450 |
0 |
this.proteinExistence = value; |
451 |
|
} |
452 |
|
|
453 |
|
|
454 |
|
|
455 |
|
|
456 |
|
|
457 |
|
|
458 |
|
|
459 |
|
|
460 |
|
|
461 |
|
|
462 |
|
|
463 |
|
|
464 |
|
|
465 |
|
|
466 |
|
|
467 |
|
|
468 |
|
|
469 |
|
|
470 |
|
|
471 |
|
@link |
472 |
|
|
473 |
|
|
474 |
|
|
475 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
476 |
0 |
public List<KeywordType> getKeyword()... |
477 |
|
{ |
478 |
0 |
if (keyword == null) |
479 |
|
{ |
480 |
0 |
keyword = new ArrayList<KeywordType>(); |
481 |
|
} |
482 |
0 |
return this.keyword; |
483 |
|
} |
484 |
|
|
485 |
|
|
486 |
|
|
487 |
|
|
488 |
|
|
489 |
|
|
490 |
|
|
491 |
|
|
492 |
|
|
493 |
|
|
494 |
|
|
495 |
|
|
496 |
|
|
497 |
|
|
498 |
|
|
499 |
|
|
500 |
|
|
501 |
|
|
502 |
|
|
503 |
|
@link |
504 |
|
|
505 |
|
|
506 |
|
|
507 |
|
|
|
|
| 60% |
Uncovered Elements: 2 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
508 |
5 |
public List<FeatureType> getFeature()... |
509 |
|
{ |
510 |
5 |
if (feature == null) |
511 |
|
{ |
512 |
0 |
feature = new ArrayList<FeatureType>(); |
513 |
|
} |
514 |
5 |
return this.feature; |
515 |
|
} |
516 |
|
|
517 |
|
|
518 |
|
|
519 |
|
|
520 |
|
|
521 |
|
|
522 |
|
|
523 |
|
|
524 |
|
|
525 |
|
|
526 |
|
|
527 |
|
|
528 |
|
|
529 |
|
|
530 |
|
|
531 |
|
|
532 |
|
|
533 |
|
|
534 |
|
|
535 |
|
|
536 |
|
@link |
537 |
|
|
538 |
|
|
539 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
540 |
0 |
public List<EvidenceType> getEvidence()... |
541 |
|
{ |
542 |
0 |
if (evidence == null) |
543 |
|
{ |
544 |
0 |
evidence = new ArrayList<EvidenceType>(); |
545 |
|
} |
546 |
0 |
return this.evidence; |
547 |
|
} |
548 |
|
|
549 |
|
|
550 |
|
|
551 |
|
|
552 |
|
@return@link |
553 |
|
|
554 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
555 |
3 |
public SequenceType getSequence()... |
556 |
|
{ |
557 |
3 |
return sequence; |
558 |
|
} |
559 |
|
|
560 |
|
|
561 |
|
|
562 |
|
|
563 |
|
@param |
564 |
|
@link |
565 |
|
|
566 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
567 |
0 |
public void setSequence(SequenceType value)... |
568 |
|
{ |
569 |
0 |
this.sequence = value; |
570 |
|
} |
571 |
|
|
572 |
|
|
573 |
|
|
574 |
|
|
575 |
|
@return@link |
576 |
|
|
577 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
578 |
0 |
public String getDataset()... |
579 |
|
{ |
580 |
0 |
return dataset; |
581 |
|
} |
582 |
|
|
583 |
|
|
584 |
|
|
585 |
|
|
586 |
|
@param |
587 |
|
@link |
588 |
|
|
589 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
590 |
0 |
public void setDataset(String value)... |
591 |
|
{ |
592 |
0 |
this.dataset = value; |
593 |
|
} |
594 |
|
|
595 |
|
|
596 |
|
|
597 |
|
|
598 |
|
@return@link |
599 |
|
|
600 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
601 |
0 |
public XMLGregorianCalendar getCreated()... |
602 |
|
{ |
603 |
0 |
return created; |
604 |
|
} |
605 |
|
|
606 |
|
|
607 |
|
|
608 |
|
|
609 |
|
@param |
610 |
|
@link |
611 |
|
|
612 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
613 |
0 |
public void setCreated(XMLGregorianCalendar value)... |
614 |
|
{ |
615 |
0 |
this.created = value; |
616 |
|
} |
617 |
|
|
618 |
|
|
619 |
|
|
620 |
|
|
621 |
|
@return@link |
622 |
|
|
623 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
624 |
0 |
public XMLGregorianCalendar getModified()... |
625 |
|
{ |
626 |
0 |
return modified; |
627 |
|
} |
628 |
|
|
629 |
|
|
630 |
|
|
631 |
|
|
632 |
|
@param |
633 |
|
@link |
634 |
|
|
635 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
636 |
0 |
public void setModified(XMLGregorianCalendar value)... |
637 |
|
{ |
638 |
0 |
this.modified = value; |
639 |
|
} |
640 |
|
|
641 |
|
|
642 |
|
|
643 |
|
|
644 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
645 |
2 |
public int getVersion()... |
646 |
|
{ |
647 |
2 |
return version; |
648 |
|
} |
649 |
|
|
650 |
|
|
651 |
|
|
652 |
|
|
653 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
654 |
0 |
public void setVersion(int value)... |
655 |
|
{ |
656 |
0 |
this.version = value; |
657 |
|
} |
658 |
|
|
659 |
|
} |