1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
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
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
|
% toolbox\Validate_MATLAB_SBML_Structures
%
% This folder contains tests that checks that the structure supplied as argument
% is of the appropriate form to represent the intended element of an SBML model.
%
%======================================================================================
% [valid, message] = isSBML_AlgebraicRule(SBMLAlgebraicRule, level, version(optional))
%======================================================================================
% Takes
% 1. SBMLAlgebraicRule, an SBML AlgebraicRule structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML AlgebraicRule structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%========================================================================================
% [valid, message] = isSBML_AssignmentRule(SBMLAssignmentRule, level, version(optional))
%========================================================================================
% Takes
% 1. SBMLAssignmentRule, an SBML AssignmentRule structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML AssignmentRule structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%==================================================================================
% [valid, message] = isSBML_Compartment(SBMLCompartment, level, version(optional))
%==================================================================================
% Takes
% 1. SBMLCompartment, an SBML Compartment structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Compartment structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%==========================================================================================
% [valid, message] = isSBML_CompartmentType(SBMLCompartmentType, level, version(optional))
%==========================================================================================
% Takes
% 1. SBMLCompartmentType, an SBML CompartmentType structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML CompartmentType structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%======================================================================================================
% [valid, message] = isSBML_CompartmentVolumeRule(SBMLCompartmentVolumeRule, level, version(optional))
%======================================================================================================
% Takes
% 1. SBMLCompartmentVolumeRule, an SBML CompartmentVolumeRule structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML CompartmentVolumeRule structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%================================================================================
% [valid, message] = isSBML_Constraint(SBMLConstraint, level, version(optional))
%================================================================================
% Takes
% 1. SBMLConstraint, an SBML Constraint structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Constraint structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%======================================================================
% [valid, message] = isSBML_Delay(SBMLDelay, level, version(optional))
%======================================================================
% Takes
% 1. SBMLDelay, an SBML Delay structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Delay structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%======================================================================
% [valid, message] = isSBML_Event(SBMLEvent, level, version(optional))
%======================================================================
% Takes
% 1. SBMLEvent, an SBML Event structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Event structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%==========================================================================================
% [valid, message] = isSBML_EventAssignment(SBMLEventAssignment, level, version(optional))
%==========================================================================================
% Takes
% 1. SBMLEventAssignment, an SBML EventAssignment structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML EventAssignment structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%================================================================================================
% [valid, message] = isSBML_FunctionDefinition(SBMLFunctionDefinition, level, version(optional))
%================================================================================================
% Takes
% 1. SBMLFunctionDefinition, an SBML FunctionDefinition structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML FunctionDefinition structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%==============================================================================================
% [valid, message] = isSBML_InitialAssignment(SBMLInitialAssignment, level, version(optional))
%==============================================================================================
% Takes
% 1. SBMLInitialAssignment, an SBML InitialAssignment structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML InitialAssignment structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%================================================================================
% [valid, message] = isSBML_KineticLaw(SBMLKineticLaw, level, version(optional))
%================================================================================
% Takes
% 1. SBMLKineticLaw, an SBML KineticLaw structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML KineticLaw structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%========================================================================================
% [valid, message] = isSBML_LocalParameter(SBMLLocalParameter, level, version(optional))
%========================================================================================
% Takes
% 1. SBMLLocalParameter, an SBML LocalParameter structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML LocalParameter structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%============================================
% [valid, message] = isValidSBML_Model(SBMLModel)
%============================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Model structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%============================================================================================================
% [valid, message] = isSBML_ModifierSpeciesReference(SBMLModifierSpeciesReference, level, version(optional))
%============================================================================================================
% Takes
% 1. SBMLModifierSpeciesReference, an SBML ModifierSpeciesReference structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML ModifierSpeciesReference structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%==============================================================================
% [valid, message] = isSBML_Parameter(SBMLParameter, level, version(optional))
%==============================================================================
% Takes
% 1. SBMLParameter, an SBML Parameter structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Parameter structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%======================================================================================
% [valid, message] = isSBML_ParameterRule(SBMLParameterRule, level, version(optional))
%======================================================================================
% Takes
% 1. SBMLParameterRule, an SBML ParameterRule structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML ParameterRule structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%============================================================================
% [valid, message] = isSBML_Priority(SBMLPriority, level, version(optional))
%============================================================================
% Takes
% 1. SBMLPriority, an SBML Priority structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Priority structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%============================================================================
% [valid, message] = isSBML_RateRule(SBMLRateRule, level, version(optional))
%============================================================================
% Takes
% 1. SBMLRateRule, an SBML RateRule structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML RateRule structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%============================================================================
% [valid, message] = isSBML_Reaction(SBMLReaction, level, version(optional))
%============================================================================
% Takes
% 1. SBMLReaction, an SBML Reaction structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Reaction structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%====================================================================
% [valid, message] = isSBML_Rule(SBMLRule, level, version(optional))
%====================================================================
% Takes
% 1. SBMLRule, an SBML Rule structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Rule structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%==========================================================================
% [valid, message] = isSBML_Species(SBMLSpecies, level, version(optional))
%==========================================================================
% Takes
% 1. SBMLSpecies, an SBML Species structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Species structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%============================================================================================================
% [valid, message] = isSBML_SpeciesConcentrationRule(SBMLSpeciesConcentrationRule, level, version(optional))
%============================================================================================================
% Takes
% 1. SBMLSpeciesConcentrationRule, an SBML SpeciesConcentrationRule structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML SpeciesConcentrationRule structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%============================================================================================
% [valid, message] = isSBML_SpeciesReference(SBMLSpeciesReference, level, version(optional))
%============================================================================================
% Takes
% 1. SBMLSpeciesReference, an SBML SpeciesReference structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML SpeciesReference structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%==================================================================================
% [valid, message] = isSBML_SpeciesType(SBMLSpeciesType, level, version(optional))
%==================================================================================
% Takes
% 1. SBMLSpeciesType, an SBML SpeciesType structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML SpeciesType structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%==============================================================================================
% [valid, message] = isSBML_StoichiometryMath(SBMLStoichiometryMath, level, version(optional))
%==============================================================================================
% Takes
% 1. SBMLStoichiometryMath, an SBML StoichiometryMath structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML StoichiometryMath structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%==========================================================================
% [valid, message] = isSBML_Trigger(SBMLTrigger, level, version(optional))
%==========================================================================
% Takes
% 1. SBMLTrigger, an SBML Trigger structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Trigger structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%====================================================================
% [valid, message] = isSBML_Unit(SBMLUnit, level, version(optional))
%====================================================================
% Takes
% 1. SBMLUnit, an SBML Unit structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Unit structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%========================================================================================
% [valid, message] = isSBML_UnitDefinition(SBMLUnitDefinition, level, version(optional))
%========================================================================================
% Takes
% 1. SBMLUnitDefinition, an SBML UnitDefinition structure
% 2. level, an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML UnitDefinition structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%============================================================================
% [valid, message] = isValid(SBMLStruct, level(optional), version(optional))
%============================================================================
% Takes
% 1. SBMLStruct, an SBML structure
% 2. level (optional), an integer representing an SBML level
% 3. version (optional), an integer representing an SBML version
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%============================================
% [valid, message] = isValidSBML_Model(SBMLModel)
%============================================
% Takes
% 1. SBMLModel, an SBML Model structure
% Returns
% 1. valid =
% - 1, if the structure represents
% a MATLAB_SBML Model structure of the appropriate
% level and version
% - 0, otherwise
% 2. a message explaining any failure
%
%<!---------------------------------------------------------------------------
% This file is part of SBMLToolbox. Please visit http://sbml.org for more
% information about SBML, and the latest version of SBMLToolbox.
%
% Copyright (C) 2009-2012 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
%
% Copyright (C) 2006-2008 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. University of Hertfordshire, Hatfield, UK
%
% Copyright (C) 2003-2005 jointly by the following organizations:
% 1. California Institute of Technology, Pasadena, CA, USA
% 2. Japan Science and Technology Agency, Japan
% 3. University of Hertfordshire, Hatfield, UK
%
% SBMLToolbox is free software; you can redistribute it and/or modify it
% under the terms of the GNU Lesser General Public License as published by
% the Free Software Foundation. A copy of the license agreement is provided
% in the file named "LICENSE.txt" included with this software distribution.
%----------------------------------------------------------------------- -->
|
