1 |
|
|
2 |
|
|
3 |
|
|
4 |
|
|
5 |
|
|
6 |
|
|
7 |
|
|
8 |
|
package jalview.schemabinding.version2; |
9 |
|
|
10 |
|
|
11 |
|
|
12 |
|
|
13 |
|
|
14 |
|
import org.exolab.castor.xml.Marshaller; |
15 |
|
import org.exolab.castor.xml.Unmarshaller; |
16 |
|
|
17 |
|
|
18 |
|
|
19 |
|
|
20 |
|
@version |
21 |
|
|
|
|
| 52.2% |
Uncovered Elements: 121 (253) |
Complexity: 113 |
Complexity Density: 0.81 |
|
22 |
|
public class Annotation implements java.io.Serializable |
23 |
|
{ |
24 |
|
|
25 |
|
|
26 |
|
|
27 |
|
|
28 |
|
|
29 |
|
|
30 |
|
|
31 |
|
|
32 |
|
private boolean _graph; |
33 |
|
|
34 |
|
|
35 |
|
|
36 |
|
|
37 |
|
private boolean _has_graph; |
38 |
|
|
39 |
|
|
40 |
|
|
41 |
|
|
42 |
|
private int _graphType; |
43 |
|
|
44 |
|
|
45 |
|
|
46 |
|
|
47 |
|
private boolean _has_graphType; |
48 |
|
|
49 |
|
|
50 |
|
|
51 |
|
|
52 |
|
private java.lang.String _sequenceRef; |
53 |
|
|
54 |
|
|
55 |
|
|
56 |
|
|
57 |
|
private java.lang.String _groupRef; |
58 |
|
|
59 |
|
|
60 |
|
|
61 |
|
|
62 |
|
private int _graphColour; |
63 |
|
|
64 |
|
|
65 |
|
|
66 |
|
|
67 |
|
private boolean _has_graphColour; |
68 |
|
|
69 |
|
|
70 |
|
|
71 |
|
|
72 |
|
private int _graphGroup; |
73 |
|
|
74 |
|
|
75 |
|
|
76 |
|
|
77 |
|
private boolean _has_graphGroup; |
78 |
|
|
79 |
|
|
80 |
|
|
81 |
|
|
82 |
|
private int _graphHeight; |
83 |
|
|
84 |
|
|
85 |
|
|
86 |
|
|
87 |
|
private boolean _has_graphHeight; |
88 |
|
|
89 |
|
|
90 |
|
|
91 |
|
|
92 |
|
private java.lang.String _id; |
93 |
|
|
94 |
|
|
95 |
|
|
96 |
|
|
97 |
|
private boolean _scoreOnly = false; |
98 |
|
|
99 |
|
|
100 |
|
|
101 |
|
|
102 |
|
private boolean _has_scoreOnly; |
103 |
|
|
104 |
|
|
105 |
|
|
106 |
|
|
107 |
|
private double _score; |
108 |
|
|
109 |
|
|
110 |
|
|
111 |
|
|
112 |
|
private boolean _has_score; |
113 |
|
|
114 |
|
|
115 |
|
|
116 |
|
|
117 |
|
private boolean _visible; |
118 |
|
|
119 |
|
|
120 |
|
|
121 |
|
|
122 |
|
private boolean _has_visible; |
123 |
|
|
124 |
|
|
125 |
|
|
126 |
|
|
127 |
|
private boolean _centreColLabels; |
128 |
|
|
129 |
|
|
130 |
|
|
131 |
|
|
132 |
|
private boolean _has_centreColLabels; |
133 |
|
|
134 |
|
|
135 |
|
|
136 |
|
|
137 |
|
private boolean _scaleColLabels; |
138 |
|
|
139 |
|
|
140 |
|
|
141 |
|
|
142 |
|
private boolean _has_scaleColLabels; |
143 |
|
|
144 |
|
|
145 |
|
|
146 |
|
|
147 |
|
private boolean _showAllColLabels; |
148 |
|
|
149 |
|
|
150 |
|
|
151 |
|
|
152 |
|
private boolean _has_showAllColLabels; |
153 |
|
|
154 |
|
|
155 |
|
|
156 |
|
|
157 |
|
private boolean _autoCalculated = false; |
158 |
|
|
159 |
|
|
160 |
|
|
161 |
|
|
162 |
|
private boolean _has_autoCalculated; |
163 |
|
|
164 |
|
|
165 |
|
|
166 |
|
|
167 |
|
|
168 |
|
private boolean _belowAlignment = true; |
169 |
|
|
170 |
|
|
171 |
|
|
172 |
|
|
173 |
|
private boolean _has_belowAlignment; |
174 |
|
|
175 |
|
|
176 |
|
|
177 |
|
|
178 |
|
|
179 |
|
|
180 |
|
private java.lang.String _calcId; |
181 |
|
|
182 |
|
|
183 |
|
|
184 |
|
|
185 |
|
private java.util.Vector _annotationElementList; |
186 |
|
|
187 |
|
|
188 |
|
|
189 |
|
|
190 |
|
private java.lang.String _label; |
191 |
|
|
192 |
|
|
193 |
|
|
194 |
|
|
195 |
|
private java.lang.String _description; |
196 |
|
|
197 |
|
|
198 |
|
|
199 |
|
|
200 |
|
private jalview.schemabinding.version2.ThresholdLine _thresholdLine; |
201 |
|
|
202 |
|
|
203 |
|
|
204 |
|
|
205 |
|
private java.util.Vector _propertyList; |
206 |
|
|
207 |
|
|
208 |
|
|
209 |
|
|
210 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (3) |
Complexity: 1 |
Complexity Density: 0.33 |
|
211 |
876 |
public Annotation()... |
212 |
|
{ |
213 |
876 |
super(); |
214 |
876 |
this._annotationElementList = new java.util.Vector(); |
215 |
876 |
this._propertyList = new java.util.Vector(); |
216 |
|
} |
217 |
|
|
218 |
|
|
219 |
|
|
220 |
|
|
221 |
|
|
222 |
|
|
223 |
|
|
224 |
|
|
225 |
|
@param |
226 |
|
@throws |
227 |
|
|
228 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
229 |
97584 |
public void addAnnotationElement(... |
230 |
|
final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) |
231 |
|
throws java.lang.IndexOutOfBoundsException |
232 |
|
{ |
233 |
97584 |
this._annotationElementList.addElement(vAnnotationElement); |
234 |
|
} |
235 |
|
|
236 |
|
|
237 |
|
|
238 |
|
|
239 |
|
@param |
240 |
|
@param |
241 |
|
@throws |
242 |
|
|
243 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
244 |
0 |
public void addAnnotationElement(... |
245 |
|
final int index, |
246 |
|
final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) |
247 |
|
throws java.lang.IndexOutOfBoundsException |
248 |
|
{ |
249 |
0 |
this._annotationElementList.add(index, vAnnotationElement); |
250 |
|
} |
251 |
|
|
252 |
|
|
253 |
|
|
254 |
|
|
255 |
|
@param |
256 |
|
@throws |
257 |
|
|
258 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
259 |
0 |
public void addProperty(... |
260 |
|
final jalview.schemabinding.version2.Property vProperty) |
261 |
|
throws java.lang.IndexOutOfBoundsException |
262 |
|
{ |
263 |
0 |
this._propertyList.addElement(vProperty); |
264 |
|
} |
265 |
|
|
266 |
|
|
267 |
|
|
268 |
|
|
269 |
|
@param |
270 |
|
@param |
271 |
|
@throws |
272 |
|
|
273 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
274 |
0 |
public void addProperty(final int index,... |
275 |
|
final jalview.schemabinding.version2.Property vProperty) |
276 |
|
throws java.lang.IndexOutOfBoundsException |
277 |
|
{ |
278 |
0 |
this._propertyList.add(index, vProperty); |
279 |
|
} |
280 |
|
|
281 |
|
|
282 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
283 |
0 |
public void deleteAutoCalculated()... |
284 |
|
{ |
285 |
0 |
this._has_autoCalculated = false; |
286 |
|
} |
287 |
|
|
288 |
|
|
289 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
290 |
0 |
public void deleteBelowAlignment()... |
291 |
|
{ |
292 |
0 |
this._has_belowAlignment = false; |
293 |
|
} |
294 |
|
|
295 |
|
|
296 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
297 |
0 |
public void deleteCentreColLabels()... |
298 |
|
{ |
299 |
0 |
this._has_centreColLabels = false; |
300 |
|
} |
301 |
|
|
302 |
|
|
303 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
304 |
0 |
public void deleteGraph()... |
305 |
|
{ |
306 |
0 |
this._has_graph = false; |
307 |
|
} |
308 |
|
|
309 |
|
|
310 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
311 |
0 |
public void deleteGraphColour()... |
312 |
|
{ |
313 |
0 |
this._has_graphColour = false; |
314 |
|
} |
315 |
|
|
316 |
|
|
317 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
318 |
0 |
public void deleteGraphGroup()... |
319 |
|
{ |
320 |
0 |
this._has_graphGroup = false; |
321 |
|
} |
322 |
|
|
323 |
|
|
324 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
325 |
0 |
public void deleteGraphHeight()... |
326 |
|
{ |
327 |
0 |
this._has_graphHeight = false; |
328 |
|
} |
329 |
|
|
330 |
|
|
331 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
332 |
0 |
public void deleteGraphType()... |
333 |
|
{ |
334 |
0 |
this._has_graphType = false; |
335 |
|
} |
336 |
|
|
337 |
|
|
338 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
339 |
0 |
public void deleteScaleColLabels()... |
340 |
|
{ |
341 |
0 |
this._has_scaleColLabels = false; |
342 |
|
} |
343 |
|
|
344 |
|
|
345 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
346 |
0 |
public void deleteScore()... |
347 |
|
{ |
348 |
0 |
this._has_score = false; |
349 |
|
} |
350 |
|
|
351 |
|
|
352 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
353 |
0 |
public void deleteScoreOnly()... |
354 |
|
{ |
355 |
0 |
this._has_scoreOnly = false; |
356 |
|
} |
357 |
|
|
358 |
|
|
359 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
360 |
0 |
public void deleteShowAllColLabels()... |
361 |
|
{ |
362 |
0 |
this._has_showAllColLabels = false; |
363 |
|
} |
364 |
|
|
365 |
|
|
366 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
367 |
0 |
public void deleteVisible()... |
368 |
|
{ |
369 |
0 |
this._has_visible = false; |
370 |
|
} |
371 |
|
|
372 |
|
|
373 |
|
|
374 |
|
|
375 |
|
@return |
376 |
|
|
377 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
378 |
0 |
public java.util.Enumeration enumerateAnnotationElement()... |
379 |
|
{ |
380 |
0 |
return this._annotationElementList.elements(); |
381 |
|
} |
382 |
|
|
383 |
|
|
384 |
|
|
385 |
|
|
386 |
|
@return |
387 |
|
|
388 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
389 |
0 |
public java.util.Enumeration enumerateProperty()... |
390 |
|
{ |
391 |
0 |
return this._propertyList.elements(); |
392 |
|
} |
393 |
|
|
394 |
|
|
395 |
|
|
396 |
|
|
397 |
|
@param |
398 |
|
@throws |
399 |
|
|
400 |
|
@return |
401 |
|
|
402 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
403 |
0 |
public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(... |
404 |
|
final int index) throws java.lang.IndexOutOfBoundsException |
405 |
|
{ |
406 |
|
|
407 |
0 |
if (index < 0 || index >= this._annotationElementList.size()) |
408 |
|
{ |
409 |
0 |
throw new IndexOutOfBoundsException( |
410 |
|
"getAnnotationElement: Index value '" + index |
411 |
|
+ "' not in range [0.." |
412 |
|
+ (this._annotationElementList.size() - 1) + "]"); |
413 |
|
} |
414 |
|
|
415 |
0 |
return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList |
416 |
|
.get(index); |
417 |
|
} |
418 |
|
|
419 |
|
|
420 |
|
|
421 |
|
|
422 |
|
|
423 |
|
|
424 |
|
|
425 |
|
|
426 |
|
|
427 |
|
@return |
428 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
429 |
1165 |
public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement()... |
430 |
|
{ |
431 |
1165 |
jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0]; |
432 |
1165 |
return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList |
433 |
|
.toArray(array); |
434 |
|
} |
435 |
|
|
436 |
|
|
437 |
|
|
438 |
|
|
439 |
|
@return |
440 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
441 |
0 |
public int getAnnotationElementCount()... |
442 |
|
{ |
443 |
0 |
return this._annotationElementList.size(); |
444 |
|
} |
445 |
|
|
446 |
|
|
447 |
|
|
448 |
|
|
449 |
|
|
450 |
|
@return |
451 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
452 |
162 |
public boolean getAutoCalculated()... |
453 |
|
{ |
454 |
162 |
return this._autoCalculated; |
455 |
|
} |
456 |
|
|
457 |
|
|
458 |
|
|
459 |
|
|
460 |
|
|
461 |
|
|
462 |
|
@return |
463 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
464 |
610 |
public boolean getBelowAlignment()... |
465 |
|
{ |
466 |
610 |
return this._belowAlignment; |
467 |
|
} |
468 |
|
|
469 |
|
|
470 |
|
|
471 |
|
|
472 |
|
|
473 |
|
|
474 |
|
|
475 |
|
|
476 |
|
@return |
477 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
478 |
1165 |
public java.lang.String getCalcId()... |
479 |
|
{ |
480 |
1165 |
return this._calcId; |
481 |
|
} |
482 |
|
|
483 |
|
|
484 |
|
|
485 |
|
|
486 |
|
@return |
487 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
488 |
1165 |
public boolean getCentreColLabels()... |
489 |
|
{ |
490 |
1165 |
return this._centreColLabels; |
491 |
|
} |
492 |
|
|
493 |
|
|
494 |
|
|
495 |
|
|
496 |
|
@return |
497 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
498 |
1165 |
public java.lang.String getDescription()... |
499 |
|
{ |
500 |
1165 |
return this._description; |
501 |
|
} |
502 |
|
|
503 |
|
|
504 |
|
|
505 |
|
|
506 |
|
@return |
507 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
508 |
1165 |
public boolean getGraph()... |
509 |
|
{ |
510 |
1165 |
return this._graph; |
511 |
|
} |
512 |
|
|
513 |
|
|
514 |
|
|
515 |
|
|
516 |
|
@return |
517 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
518 |
0 |
public int getGraphColour()... |
519 |
|
{ |
520 |
0 |
return this._graphColour; |
521 |
|
} |
522 |
|
|
523 |
|
|
524 |
|
|
525 |
|
|
526 |
|
@return |
527 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
528 |
672 |
public int getGraphGroup()... |
529 |
|
{ |
530 |
672 |
return this._graphGroup; |
531 |
|
} |
532 |
|
|
533 |
|
|
534 |
|
|
535 |
|
|
536 |
|
|
537 |
|
|
538 |
|
@return |
539 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
540 |
1165 |
public int getGraphHeight()... |
541 |
|
{ |
542 |
1165 |
return this._graphHeight; |
543 |
|
} |
544 |
|
|
545 |
|
|
546 |
|
|
547 |
|
|
548 |
|
@return |
549 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
550 |
672 |
public int getGraphType()... |
551 |
|
{ |
552 |
672 |
return this._graphType; |
553 |
|
} |
554 |
|
|
555 |
|
|
556 |
|
|
557 |
|
|
558 |
|
@return |
559 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
560 |
1273 |
public java.lang.String getGroupRef()... |
561 |
|
{ |
562 |
1273 |
return this._groupRef; |
563 |
|
} |
564 |
|
|
565 |
|
|
566 |
|
|
567 |
|
|
568 |
|
@return |
569 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
570 |
2348 |
public java.lang.String getId()... |
571 |
|
{ |
572 |
2348 |
return this._id; |
573 |
|
} |
574 |
|
|
575 |
|
|
576 |
|
|
577 |
|
|
578 |
|
@return |
579 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
580 |
2650 |
public java.lang.String getLabel()... |
581 |
|
{ |
582 |
2650 |
return this._label; |
583 |
|
} |
584 |
|
|
585 |
|
|
586 |
|
|
587 |
|
|
588 |
|
@param |
589 |
|
@throws |
590 |
|
|
591 |
|
@return |
592 |
|
|
593 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
594 |
0 |
public jalview.schemabinding.version2.Property getProperty(final int index)... |
595 |
|
throws java.lang.IndexOutOfBoundsException |
596 |
|
{ |
597 |
|
|
598 |
0 |
if (index < 0 || index >= this._propertyList.size()) |
599 |
|
{ |
600 |
0 |
throw new IndexOutOfBoundsException("getProperty: Index value '" |
601 |
|
+ index + "' not in range [0.." |
602 |
|
+ (this._propertyList.size() - 1) + "]"); |
603 |
|
} |
604 |
|
|
605 |
0 |
return (jalview.schemabinding.version2.Property) _propertyList |
606 |
|
.get(index); |
607 |
|
} |
608 |
|
|
609 |
|
|
610 |
|
|
611 |
|
|
612 |
|
|
613 |
|
|
614 |
|
|
615 |
|
|
616 |
|
@return |
617 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
618 |
610 |
public jalview.schemabinding.version2.Property[] getProperty()... |
619 |
|
{ |
620 |
610 |
jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0]; |
621 |
610 |
return (jalview.schemabinding.version2.Property[]) this._propertyList |
622 |
|
.toArray(array); |
623 |
|
} |
624 |
|
|
625 |
|
|
626 |
|
|
627 |
|
|
628 |
|
@return |
629 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
630 |
555 |
public int getPropertyCount()... |
631 |
|
{ |
632 |
555 |
return this._propertyList.size(); |
633 |
|
} |
634 |
|
|
635 |
|
|
636 |
|
|
637 |
|
|
638 |
|
@return |
639 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
640 |
1165 |
public boolean getScaleColLabels()... |
641 |
|
{ |
642 |
1165 |
return this._scaleColLabels; |
643 |
|
} |
644 |
|
|
645 |
|
|
646 |
|
|
647 |
|
|
648 |
|
@return |
649 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
650 |
417 |
public double getScore()... |
651 |
|
{ |
652 |
417 |
return this._score; |
653 |
|
} |
654 |
|
|
655 |
|
|
656 |
|
|
657 |
|
|
658 |
|
@return |
659 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
660 |
1165 |
public boolean getScoreOnly()... |
661 |
|
{ |
662 |
1165 |
return this._scoreOnly; |
663 |
|
} |
664 |
|
|
665 |
|
|
666 |
|
|
667 |
|
|
668 |
|
@return |
669 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
670 |
1165 |
public java.lang.String getSequenceRef()... |
671 |
|
{ |
672 |
1165 |
return this._sequenceRef; |
673 |
|
} |
674 |
|
|
675 |
|
|
676 |
|
|
677 |
|
|
678 |
|
@return |
679 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
680 |
610 |
public boolean getShowAllColLabels()... |
681 |
|
{ |
682 |
610 |
return this._showAllColLabels; |
683 |
|
} |
684 |
|
|
685 |
|
|
686 |
|
|
687 |
|
|
688 |
|
@return |
689 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
690 |
1064 |
public jalview.schemabinding.version2.ThresholdLine getThresholdLine()... |
691 |
|
{ |
692 |
1064 |
return this._thresholdLine; |
693 |
|
} |
694 |
|
|
695 |
|
|
696 |
|
|
697 |
|
|
698 |
|
@return |
699 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
700 |
1165 |
public boolean getVisible()... |
701 |
|
{ |
702 |
1165 |
return this._visible; |
703 |
|
} |
704 |
|
|
705 |
|
|
706 |
|
|
707 |
|
|
708 |
|
@return |
709 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
710 |
1720 |
public boolean hasAutoCalculated()... |
711 |
|
{ |
712 |
1720 |
return this._has_autoCalculated; |
713 |
|
} |
714 |
|
|
715 |
|
|
716 |
|
|
717 |
|
|
718 |
|
@return |
719 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
720 |
1165 |
public boolean hasBelowAlignment()... |
721 |
|
{ |
722 |
1165 |
return this._has_belowAlignment; |
723 |
|
} |
724 |
|
|
725 |
|
|
726 |
|
|
727 |
|
|
728 |
|
@return |
729 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
730 |
1165 |
public boolean hasCentreColLabels()... |
731 |
|
{ |
732 |
1165 |
return this._has_centreColLabels; |
733 |
|
} |
734 |
|
|
735 |
|
|
736 |
|
|
737 |
|
|
738 |
|
@return |
739 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
740 |
610 |
public boolean hasGraph()... |
741 |
|
{ |
742 |
610 |
return this._has_graph; |
743 |
|
} |
744 |
|
|
745 |
|
|
746 |
|
|
747 |
|
|
748 |
|
@return |
749 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
750 |
610 |
public boolean hasGraphColour()... |
751 |
|
{ |
752 |
610 |
return this._has_graphColour; |
753 |
|
} |
754 |
|
|
755 |
|
|
756 |
|
|
757 |
|
|
758 |
|
@return |
759 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
760 |
610 |
public boolean hasGraphGroup()... |
761 |
|
{ |
762 |
610 |
return this._has_graphGroup; |
763 |
|
} |
764 |
|
|
765 |
|
|
766 |
|
|
767 |
|
|
768 |
|
@return |
769 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
770 |
1165 |
public boolean hasGraphHeight()... |
771 |
|
{ |
772 |
1165 |
return this._has_graphHeight; |
773 |
|
} |
774 |
|
|
775 |
|
|
776 |
|
|
777 |
|
|
778 |
|
@return |
779 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
780 |
610 |
public boolean hasGraphType()... |
781 |
|
{ |
782 |
610 |
return this._has_graphType; |
783 |
|
} |
784 |
|
|
785 |
|
|
786 |
|
|
787 |
|
|
788 |
|
@return |
789 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
790 |
1165 |
public boolean hasScaleColLabels()... |
791 |
|
{ |
792 |
1165 |
return this._has_scaleColLabels; |
793 |
|
} |
794 |
|
|
795 |
|
|
796 |
|
|
797 |
|
|
798 |
|
@return |
799 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
800 |
1165 |
public boolean hasScore()... |
801 |
|
{ |
802 |
1165 |
return this._has_score; |
803 |
|
} |
804 |
|
|
805 |
|
|
806 |
|
|
807 |
|
|
808 |
|
@return |
809 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
810 |
610 |
public boolean hasScoreOnly()... |
811 |
|
{ |
812 |
610 |
return this._has_scoreOnly; |
813 |
|
} |
814 |
|
|
815 |
|
|
816 |
|
|
817 |
|
|
818 |
|
@return |
819 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
820 |
610 |
public boolean hasShowAllColLabels()... |
821 |
|
{ |
822 |
610 |
return this._has_showAllColLabels; |
823 |
|
} |
824 |
|
|
825 |
|
|
826 |
|
|
827 |
|
|
828 |
|
@return |
829 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
830 |
1165 |
public boolean hasVisible()... |
831 |
|
{ |
832 |
1165 |
return this._has_visible; |
833 |
|
} |
834 |
|
|
835 |
|
|
836 |
|
|
837 |
|
|
838 |
|
|
839 |
|
@return |
840 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
841 |
482 |
public boolean isAutoCalculated()... |
842 |
|
{ |
843 |
482 |
return this._autoCalculated; |
844 |
|
} |
845 |
|
|
846 |
|
|
847 |
|
|
848 |
|
|
849 |
|
|
850 |
|
|
851 |
|
@return |
852 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
853 |
315 |
public boolean isBelowAlignment()... |
854 |
|
{ |
855 |
315 |
return this._belowAlignment; |
856 |
|
} |
857 |
|
|
858 |
|
|
859 |
|
|
860 |
|
|
861 |
|
@return |
862 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
863 |
0 |
public boolean isCentreColLabels()... |
864 |
|
{ |
865 |
0 |
return this._centreColLabels; |
866 |
|
} |
867 |
|
|
868 |
|
|
869 |
|
|
870 |
|
|
871 |
|
@return |
872 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
873 |
0 |
public boolean isGraph()... |
874 |
|
{ |
875 |
0 |
return this._graph; |
876 |
|
} |
877 |
|
|
878 |
|
|
879 |
|
|
880 |
|
|
881 |
|
@return |
882 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
883 |
0 |
public boolean isScaleColLabels()... |
884 |
|
{ |
885 |
0 |
return this._scaleColLabels; |
886 |
|
} |
887 |
|
|
888 |
|
|
889 |
|
|
890 |
|
|
891 |
|
@return |
892 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
893 |
0 |
public boolean isScoreOnly()... |
894 |
|
{ |
895 |
0 |
return this._scoreOnly; |
896 |
|
} |
897 |
|
|
898 |
|
|
899 |
|
|
900 |
|
|
901 |
|
@return |
902 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
903 |
0 |
public boolean isShowAllColLabels()... |
904 |
|
{ |
905 |
0 |
return this._showAllColLabels; |
906 |
|
} |
907 |
|
|
908 |
|
|
909 |
|
|
910 |
|
|
911 |
|
@return |
912 |
|
|
|
|
| 0% |
Uncovered Elements: 4 (4) |
Complexity: 2 |
Complexity Density: 0.5 |
|
913 |
0 |
public boolean isValid()... |
914 |
|
{ |
915 |
0 |
try |
916 |
|
{ |
917 |
0 |
validate(); |
918 |
|
} catch (org.exolab.castor.xml.ValidationException vex) |
919 |
|
{ |
920 |
0 |
return false; |
921 |
|
} |
922 |
0 |
return true; |
923 |
|
} |
924 |
|
|
925 |
|
|
926 |
|
|
927 |
|
|
928 |
|
@return |
929 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
930 |
0 |
public boolean isVisible()... |
931 |
|
{ |
932 |
0 |
return this._visible; |
933 |
|
} |
934 |
|
|
935 |
|
|
936 |
|
|
937 |
|
|
938 |
|
@param |
939 |
|
@throws |
940 |
|
|
941 |
|
|
942 |
|
@throws |
943 |
|
|
944 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
945 |
0 |
public void marshal(final java.io.Writer out)... |
946 |
|
throws org.exolab.castor.xml.MarshalException, |
947 |
|
org.exolab.castor.xml.ValidationException |
948 |
|
{ |
949 |
0 |
Marshaller.marshal(this, out); |
950 |
|
} |
951 |
|
|
952 |
|
|
953 |
|
|
954 |
|
|
955 |
|
@param |
956 |
|
@throws |
957 |
|
|
958 |
|
@throws |
959 |
|
|
960 |
|
@throws |
961 |
|
|
962 |
|
|
963 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
964 |
0 |
public void marshal(final org.xml.sax.ContentHandler handler)... |
965 |
|
throws java.io.IOException, |
966 |
|
org.exolab.castor.xml.MarshalException, |
967 |
|
org.exolab.castor.xml.ValidationException |
968 |
|
{ |
969 |
0 |
Marshaller.marshal(this, handler); |
970 |
|
} |
971 |
|
|
972 |
|
|
973 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
974 |
0 |
public void removeAllAnnotationElement()... |
975 |
|
{ |
976 |
0 |
this._annotationElementList.clear(); |
977 |
|
} |
978 |
|
|
979 |
|
|
980 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
981 |
0 |
public void removeAllProperty()... |
982 |
|
{ |
983 |
0 |
this._propertyList.clear(); |
984 |
|
} |
985 |
|
|
986 |
|
|
987 |
|
|
988 |
|
|
989 |
|
@param |
990 |
|
@return |
991 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
992 |
0 |
public boolean removeAnnotationElement(... |
993 |
|
final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) |
994 |
|
{ |
995 |
0 |
boolean removed = _annotationElementList.remove(vAnnotationElement); |
996 |
0 |
return removed; |
997 |
|
} |
998 |
|
|
999 |
|
|
1000 |
|
|
1001 |
|
|
1002 |
|
@param |
1003 |
|
@return |
1004 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1005 |
0 |
public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt(... |
1006 |
|
final int index) |
1007 |
|
{ |
1008 |
0 |
java.lang.Object obj = this._annotationElementList.remove(index); |
1009 |
0 |
return (jalview.schemabinding.version2.AnnotationElement) obj; |
1010 |
|
} |
1011 |
|
|
1012 |
|
|
1013 |
|
|
1014 |
|
|
1015 |
|
@param |
1016 |
|
@return |
1017 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1018 |
0 |
public boolean removeProperty(... |
1019 |
|
final jalview.schemabinding.version2.Property vProperty) |
1020 |
|
{ |
1021 |
0 |
boolean removed = _propertyList.remove(vProperty); |
1022 |
0 |
return removed; |
1023 |
|
} |
1024 |
|
|
1025 |
|
|
1026 |
|
|
1027 |
|
|
1028 |
|
@param |
1029 |
|
@return |
1030 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1031 |
0 |
public jalview.schemabinding.version2.Property removePropertyAt(... |
1032 |
|
final int index) |
1033 |
|
{ |
1034 |
0 |
java.lang.Object obj = this._propertyList.remove(index); |
1035 |
0 |
return (jalview.schemabinding.version2.Property) obj; |
1036 |
|
} |
1037 |
|
|
1038 |
|
|
1039 |
|
|
1040 |
|
|
1041 |
|
@param |
1042 |
|
@param |
1043 |
|
@throws |
1044 |
|
|
1045 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
1046 |
0 |
public void setAnnotationElement(... |
1047 |
|
final int index, |
1048 |
|
final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) |
1049 |
|
throws java.lang.IndexOutOfBoundsException |
1050 |
|
{ |
1051 |
|
|
1052 |
0 |
if (index < 0 || index >= this._annotationElementList.size()) |
1053 |
|
{ |
1054 |
0 |
throw new IndexOutOfBoundsException( |
1055 |
|
"setAnnotationElement: Index value '" + index |
1056 |
|
+ "' not in range [0.." |
1057 |
|
+ (this._annotationElementList.size() - 1) + "]"); |
1058 |
|
} |
1059 |
|
|
1060 |
0 |
this._annotationElementList.set(index, vAnnotationElement); |
1061 |
|
} |
1062 |
|
|
1063 |
|
|
1064 |
|
|
1065 |
|
|
1066 |
|
@param |
1067 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1068 |
0 |
public void setAnnotationElement(... |
1069 |
|
final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) |
1070 |
|
{ |
1071 |
|
|
1072 |
0 |
_annotationElementList.clear(); |
1073 |
|
|
1074 |
0 |
for (int i = 0; i < vAnnotationElementArray.length; i++) |
1075 |
|
{ |
1076 |
0 |
this._annotationElementList.add(vAnnotationElementArray[i]); |
1077 |
|
} |
1078 |
|
} |
1079 |
|
|
1080 |
|
|
1081 |
|
|
1082 |
|
|
1083 |
|
|
1084 |
|
@param |
1085 |
|
|
1086 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1087 |
322 |
public void setAutoCalculated(final boolean autoCalculated)... |
1088 |
|
{ |
1089 |
322 |
this._autoCalculated = autoCalculated; |
1090 |
322 |
this._has_autoCalculated = true; |
1091 |
|
} |
1092 |
|
|
1093 |
|
|
1094 |
|
|
1095 |
|
|
1096 |
|
|
1097 |
|
|
1098 |
|
@param |
1099 |
|
|
1100 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1101 |
636 |
public void setBelowAlignment(final boolean belowAlignment)... |
1102 |
|
{ |
1103 |
636 |
this._belowAlignment = belowAlignment; |
1104 |
636 |
this._has_belowAlignment = true; |
1105 |
|
} |
1106 |
|
|
1107 |
|
|
1108 |
|
|
1109 |
|
|
1110 |
|
|
1111 |
|
|
1112 |
|
|
1113 |
|
|
1114 |
|
@param |
1115 |
|
|
1116 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1117 |
588 |
public void setCalcId(final java.lang.String calcId)... |
1118 |
|
{ |
1119 |
588 |
this._calcId = calcId; |
1120 |
|
} |
1121 |
|
|
1122 |
|
|
1123 |
|
|
1124 |
|
|
1125 |
|
@param |
1126 |
|
|
1127 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1128 |
876 |
public void setCentreColLabels(final boolean centreColLabels)... |
1129 |
|
{ |
1130 |
876 |
this._centreColLabels = centreColLabels; |
1131 |
876 |
this._has_centreColLabels = true; |
1132 |
|
} |
1133 |
|
|
1134 |
|
|
1135 |
|
|
1136 |
|
|
1137 |
|
@param |
1138 |
|
|
1139 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1140 |
876 |
public void setDescription(final java.lang.String description)... |
1141 |
|
{ |
1142 |
876 |
this._description = description; |
1143 |
|
} |
1144 |
|
|
1145 |
|
|
1146 |
|
|
1147 |
|
|
1148 |
|
@param |
1149 |
|
|
1150 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1151 |
876 |
public void setGraph(final boolean graph)... |
1152 |
|
{ |
1153 |
876 |
this._graph = graph; |
1154 |
876 |
this._has_graph = true; |
1155 |
|
} |
1156 |
|
|
1157 |
|
|
1158 |
|
|
1159 |
|
|
1160 |
|
@param |
1161 |
|
|
1162 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1163 |
0 |
public void setGraphColour(final int graphColour)... |
1164 |
|
{ |
1165 |
0 |
this._graphColour = graphColour; |
1166 |
0 |
this._has_graphColour = true; |
1167 |
|
} |
1168 |
|
|
1169 |
|
|
1170 |
|
|
1171 |
|
|
1172 |
|
@param |
1173 |
|
|
1174 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1175 |
526 |
public void setGraphGroup(final int graphGroup)... |
1176 |
|
{ |
1177 |
526 |
this._graphGroup = graphGroup; |
1178 |
526 |
this._has_graphGroup = true; |
1179 |
|
} |
1180 |
|
|
1181 |
|
|
1182 |
|
|
1183 |
|
|
1184 |
|
|
1185 |
|
|
1186 |
|
@param |
1187 |
|
|
1188 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1189 |
876 |
public void setGraphHeight(final int graphHeight)... |
1190 |
|
{ |
1191 |
876 |
this._graphHeight = graphHeight; |
1192 |
876 |
this._has_graphHeight = true; |
1193 |
|
} |
1194 |
|
|
1195 |
|
|
1196 |
|
|
1197 |
|
|
1198 |
|
@param |
1199 |
|
|
1200 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1201 |
526 |
public void setGraphType(final int graphType)... |
1202 |
|
{ |
1203 |
526 |
this._graphType = graphType; |
1204 |
526 |
this._has_graphType = true; |
1205 |
|
} |
1206 |
|
|
1207 |
|
|
1208 |
|
|
1209 |
|
|
1210 |
|
@param |
1211 |
|
|
1212 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1213 |
42 |
public void setGroupRef(final java.lang.String groupRef)... |
1214 |
|
{ |
1215 |
42 |
this._groupRef = groupRef; |
1216 |
|
} |
1217 |
|
|
1218 |
|
|
1219 |
|
|
1220 |
|
|
1221 |
|
@param |
1222 |
|
|
1223 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1224 |
1117 |
public void setId(final java.lang.String id)... |
1225 |
|
{ |
1226 |
1117 |
this._id = id; |
1227 |
|
} |
1228 |
|
|
1229 |
|
|
1230 |
|
|
1231 |
|
|
1232 |
|
@param |
1233 |
|
|
1234 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1235 |
876 |
public void setLabel(final java.lang.String label)... |
1236 |
|
{ |
1237 |
876 |
this._label = label; |
1238 |
|
} |
1239 |
|
|
1240 |
|
|
1241 |
|
|
1242 |
|
|
1243 |
|
@param |
1244 |
|
@param |
1245 |
|
@throws |
1246 |
|
|
1247 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 3 |
Complexity Density: 1 |
|
1248 |
0 |
public void setProperty(final int index,... |
1249 |
|
final jalview.schemabinding.version2.Property vProperty) |
1250 |
|
throws java.lang.IndexOutOfBoundsException |
1251 |
|
{ |
1252 |
|
|
1253 |
0 |
if (index < 0 || index >= this._propertyList.size()) |
1254 |
|
{ |
1255 |
0 |
throw new IndexOutOfBoundsException("setProperty: Index value '" |
1256 |
|
+ index + "' not in range [0.." |
1257 |
|
+ (this._propertyList.size() - 1) + "]"); |
1258 |
|
} |
1259 |
|
|
1260 |
0 |
this._propertyList.set(index, vProperty); |
1261 |
|
} |
1262 |
|
|
1263 |
|
|
1264 |
|
|
1265 |
|
|
1266 |
|
@param |
1267 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 2 |
Complexity Density: 0.67 |
|
1268 |
0 |
public void setProperty(... |
1269 |
|
final jalview.schemabinding.version2.Property[] vPropertyArray) |
1270 |
|
{ |
1271 |
|
|
1272 |
0 |
_propertyList.clear(); |
1273 |
|
|
1274 |
0 |
for (int i = 0; i < vPropertyArray.length; i++) |
1275 |
|
{ |
1276 |
0 |
this._propertyList.add(vPropertyArray[i]); |
1277 |
|
} |
1278 |
|
} |
1279 |
|
|
1280 |
|
|
1281 |
|
|
1282 |
|
|
1283 |
|
@param |
1284 |
|
|
1285 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1286 |
876 |
public void setScaleColLabels(final boolean scaleColLabels)... |
1287 |
|
{ |
1288 |
876 |
this._scaleColLabels = scaleColLabels; |
1289 |
876 |
this._has_scaleColLabels = true; |
1290 |
|
} |
1291 |
|
|
1292 |
|
|
1293 |
|
|
1294 |
|
|
1295 |
|
@param |
1296 |
|
|
1297 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1298 |
278 |
public void setScore(final double score)... |
1299 |
|
{ |
1300 |
278 |
this._score = score; |
1301 |
278 |
this._has_score = true; |
1302 |
|
} |
1303 |
|
|
1304 |
|
|
1305 |
|
|
1306 |
|
|
1307 |
|
@param |
1308 |
|
|
1309 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1310 |
876 |
public void setScoreOnly(final boolean scoreOnly)... |
1311 |
|
{ |
1312 |
876 |
this._scoreOnly = scoreOnly; |
1313 |
876 |
this._has_scoreOnly = true; |
1314 |
|
} |
1315 |
|
|
1316 |
|
|
1317 |
|
|
1318 |
|
|
1319 |
|
@param |
1320 |
|
|
1321 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1322 |
422 |
public void setSequenceRef(final java.lang.String sequenceRef)... |
1323 |
|
{ |
1324 |
422 |
this._sequenceRef = sequenceRef; |
1325 |
|
} |
1326 |
|
|
1327 |
|
|
1328 |
|
|
1329 |
|
|
1330 |
|
@param |
1331 |
|
|
1332 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1333 |
876 |
public void setShowAllColLabels(final boolean showAllColLabels)... |
1334 |
|
{ |
1335 |
876 |
this._showAllColLabels = showAllColLabels; |
1336 |
876 |
this._has_showAllColLabels = true; |
1337 |
|
} |
1338 |
|
|
1339 |
|
|
1340 |
|
|
1341 |
|
|
1342 |
|
@param |
1343 |
|
|
1344 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1345 |
60 |
public void setThresholdLine(... |
1346 |
|
final jalview.schemabinding.version2.ThresholdLine thresholdLine) |
1347 |
|
{ |
1348 |
60 |
this._thresholdLine = thresholdLine; |
1349 |
|
} |
1350 |
|
|
1351 |
|
|
1352 |
|
|
1353 |
|
|
1354 |
|
@param |
1355 |
|
|
1356 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1357 |
876 |
public void setVisible(final boolean visible)... |
1358 |
|
{ |
1359 |
876 |
this._visible = visible; |
1360 |
876 |
this._has_visible = true; |
1361 |
|
} |
1362 |
|
|
1363 |
|
|
1364 |
|
|
1365 |
|
|
1366 |
|
@param |
1367 |
|
@throws |
1368 |
|
|
1369 |
|
|
1370 |
|
@throws |
1371 |
|
|
1372 |
|
@return |
1373 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
1374 |
0 |
public static jalview.schemabinding.version2.Annotation unmarshal(... |
1375 |
|
final java.io.Reader reader) |
1376 |
|
throws org.exolab.castor.xml.MarshalException, |
1377 |
|
org.exolab.castor.xml.ValidationException |
1378 |
|
{ |
1379 |
0 |
return (jalview.schemabinding.version2.Annotation) Unmarshaller |
1380 |
|
.unmarshal(jalview.schemabinding.version2.Annotation.class, |
1381 |
|
reader); |
1382 |
|
} |
1383 |
|
|
1384 |
|
|
1385 |
|
|
1386 |
|
|
1387 |
|
@throws |
1388 |
|
|
1389 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
1390 |
0 |
public void validate() throws org.exolab.castor.xml.ValidationException... |
1391 |
|
{ |
1392 |
0 |
org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); |
1393 |
0 |
validator.validate(this); |
1394 |
|
} |
1395 |
|
|
1396 |
|
} |