COPASI API  4.16.103
Public Types | Static Public Member Functions | Static Public Attributes | Private Types | List of all members
CObjectLists Class Reference

#include <CObjectLists.h>

Collaboration diagram for CObjectLists:
Collaboration graph
[legend]

Public Types

enum  ListType {
  EMPTY_LIST = 0, SINGLE_OBJECT, METABS, METAB_INITIAL_CONCENTRATIONS,
  METAB_INITIAL_NUMBERS, METAB_CONCENTRATIONS, METAB_NUMBERS, NON_CONST_METAB_CONCENTRATIONS,
  NON_CONST_METAB_NUMBERS, CONST_METAB_CONCENTRATIONS, CONST_METAB_NUMBERS, ODE_METAB_CONCENTRATIONS,
  ODE_METAB_NUMBERS, REACTION_METAB_CONCENTRATIONS, REACTION_METAB_NUMBERS, ASS_METAB_CONCENTRATIONS,
  ASS_METAB_NUMBERS, METAB_CONC_RATES, METAB_PART_RATES, METAB_TRANSITION_TIME,
  REACTIONS, REACTION_CONC_FLUXES, REACTION_PART_FLUXES, GLOBAL_PARAMETERS,
  GLOBAL_PARAMETER_INITIAL_VALUES, GLOBAL_PARAMETER_VALUES, NON_CONST_GLOBAL_PARAMETER_VALUES, CONST_GLOBAL_PARAMETER_INITIAL_VALUES,
  ODE_GLOBAL_PARAMETER_VALUES, ASS_GLOBAL_PARAMETER_VALUES, GLOBAL_PARAMETER_RATES, COMPARTMENTS,
  COMPARTMENT_INITIAL_VOLUMES, COMPARTMENT_VOLUMES, NON_CONST_COMPARTMENT_VOLUMES, CONST_COMPARTMENT_VOLUMES,
  ODE_COMPARTMENT_VOLUMES, ASS_COMPARTMENT_VOLUMES, COMPARTMENT_RATES, ALL_INITIAL_VALUES,
  ALL_LOCAL_PARAMETER_VALUES, ALL_PARAMETER_VALUES, ALL_PARAMETER_AND_INITIAL_VALUES, ALL_VARIABLES,
  ALL_ODE_VARIABLES, REDUCED_JACOBIAN_EV_RE, REDUCED_JACOBIAN_EV_IM
}
 

Static Public Member Functions

static bool existsFixedMetab (const CModel *model)
 
static std::set< const
CModelEntity * > 		getEventTargets (const CModel *pModel)
 
static std::vector< const
CCopasiObject * > 		getListOfConstObjects (ListType t, const CModel *model)
 
static std::vector
< CCopasiObject * > 		getListOfObjects (ListType t, const CModel *model)
 

Static Public Attributes

static const std::string ListTypeName []
 

Private Types

typedef std::vector< const
CCopasiObject * > 		ObjectList
 

Detailed Description

Definition at line 34 of file CObjectLists.h.

Member Typedef Documentation

typedef std::vector< const CCopasiObject * > CObjectLists::ObjectList
private

Definition at line 118 of file CObjectLists.h.

Member Enumeration Documentation

enum CObjectLists::ListType
Enumerator
EMPTY_LIST 
SINGLE_OBJECT 
METABS 
METAB_INITIAL_CONCENTRATIONS 
METAB_INITIAL_NUMBERS 
METAB_CONCENTRATIONS 
METAB_NUMBERS 
NON_CONST_METAB_CONCENTRATIONS 
NON_CONST_METAB_NUMBERS 
CONST_METAB_CONCENTRATIONS 
CONST_METAB_NUMBERS 
ODE_METAB_CONCENTRATIONS 
ODE_METAB_NUMBERS 
REACTION_METAB_CONCENTRATIONS 
REACTION_METAB_NUMBERS 
ASS_METAB_CONCENTRATIONS 
ASS_METAB_NUMBERS 
METAB_CONC_RATES 
METAB_PART_RATES 
METAB_TRANSITION_TIME 
REACTIONS 
REACTION_CONC_FLUXES 
REACTION_PART_FLUXES 
GLOBAL_PARAMETERS 
GLOBAL_PARAMETER_INITIAL_VALUES 
GLOBAL_PARAMETER_VALUES 
NON_CONST_GLOBAL_PARAMETER_VALUES 
CONST_GLOBAL_PARAMETER_INITIAL_VALUES 
ODE_GLOBAL_PARAMETER_VALUES 
ASS_GLOBAL_PARAMETER_VALUES 
GLOBAL_PARAMETER_RATES 
COMPARTMENTS 
COMPARTMENT_INITIAL_VOLUMES 
COMPARTMENT_VOLUMES 
NON_CONST_COMPARTMENT_VOLUMES 
CONST_COMPARTMENT_VOLUMES 
ODE_COMPARTMENT_VOLUMES 
ASS_COMPARTMENT_VOLUMES 
COMPARTMENT_RATES 
ALL_INITIAL_VALUES 
ALL_LOCAL_PARAMETER_VALUES 
ALL_PARAMETER_VALUES 
ALL_PARAMETER_AND_INITIAL_VALUES 
ALL_VARIABLES 
ALL_ODE_VARIABLES 
REDUCED_JACOBIAN_EV_RE 
REDUCED_JACOBIAN_EV_IM 

Definition at line 38 of file CObjectLists.h.

39  {
40  EMPTY_LIST = 0,
41  SINGLE_OBJECT,
42 
43  METABS,
44  METAB_INITIAL_CONCENTRATIONS,
45  METAB_INITIAL_NUMBERS,
46  METAB_CONCENTRATIONS,
47  METAB_NUMBERS,
48  NON_CONST_METAB_CONCENTRATIONS,
49  NON_CONST_METAB_NUMBERS,
50  CONST_METAB_CONCENTRATIONS,
51  CONST_METAB_NUMBERS,
52  ODE_METAB_CONCENTRATIONS,
53  ODE_METAB_NUMBERS,
54  REACTION_METAB_CONCENTRATIONS,
55  REACTION_METAB_NUMBERS,
56  ASS_METAB_CONCENTRATIONS,
57  ASS_METAB_NUMBERS,
58  METAB_CONC_RATES,
59  METAB_PART_RATES,
60  METAB_TRANSITION_TIME,
61 
62  REACTIONS,
63  REACTION_CONC_FLUXES,
64  REACTION_PART_FLUXES,
65 
66  GLOBAL_PARAMETERS,
67  GLOBAL_PARAMETER_INITIAL_VALUES,
68  GLOBAL_PARAMETER_VALUES,
69  NON_CONST_GLOBAL_PARAMETER_VALUES,
70  CONST_GLOBAL_PARAMETER_INITIAL_VALUES,
71  ODE_GLOBAL_PARAMETER_VALUES,
72  ASS_GLOBAL_PARAMETER_VALUES,
73  GLOBAL_PARAMETER_RATES,
74 
75  COMPARTMENTS,
76  COMPARTMENT_INITIAL_VOLUMES,
77  COMPARTMENT_VOLUMES,
78  NON_CONST_COMPARTMENT_VOLUMES,
79  CONST_COMPARTMENT_VOLUMES,
80  ODE_COMPARTMENT_VOLUMES,
81  ASS_COMPARTMENT_VOLUMES,
82  COMPARTMENT_RATES,
83 
84  ALL_INITIAL_VALUES,
85  ALL_LOCAL_PARAMETER_VALUES,
86 
87  ALL_PARAMETER_VALUES,
88  ALL_PARAMETER_AND_INITIAL_VALUES,
89 
90  ALL_VARIABLES, //
91  ALL_ODE_VARIABLES,
92 
93  REDUCED_JACOBIAN_EV_RE,
94  REDUCED_JACOBIAN_EV_IM
95 
96  };

Member Function Documentation

bool CObjectLists::existsFixedMetab ( const CModel *  model)
static

Definition at line 557 of file CObjectLists.cpp.

References CModelEntity::FIXED, CModel::getMetabolites(), and CCopasiVector< T >::size().

558 {
559  bool fixedMetab = false;
560  const CCopasiVector< CMetab > & metabs = pModel->getMetabolites();
561  size_t i, imax = metabs.size();
562 
563  for (i = 0; i < imax; ++i)
564  if (metabs[i]->getStatus() == CModelEntity::FIXED)
565  {fixedMetab = true; break;}
566 
567  return fixedMetab;
568 }
CCopasiVector::size
virtual size_t size() const
Definition: CCopasiVector.h:386
std::set< const CModelEntity * > CObjectLists::getEventTargets ( const CModel *  pModel)
static

Create a set of all entities which are event targets

Returns
std::set< const CModelEntity * > eventTargets

Definition at line 571 of file CObjectLists.cpp.

References CCopasiVector< T >::begin(), CCopasiVector< T >::end(), CKeyFactory::get(), CModel::getEvents(), and CCopasiRootContainer::getKeyFactory().

Referenced by getListOfConstObjects(), CMathContainer::initializeObjects(), and CModel::isStateVariable().

572 {
573  std::set< const CModelEntity * > EventTargets;
574 
575  CKeyFactory * pKeyFactory = CCopasiRootContainer::getKeyFactory();
576 
577  CCopasiVectorN< CEvent >::const_iterator itEvent = pModel->getEvents().begin();
578  CCopasiVectorN< CEvent >::const_iterator endEvent = pModel->getEvents().end();
579 
580  for (; itEvent != endEvent; ++itEvent)
581  {
582  CCopasiVectorN< CEventAssignment >::const_iterator itAssignment =
583  (*itEvent)->getAssignments().begin();
584  CCopasiVectorN< CEventAssignment >::const_iterator endAssignment =
585  (*itEvent)->getAssignments().end();
586 
587  for (; itAssignment != endAssignment; ++itAssignment)
588  {
589  const CModelEntity * pModelEntity =
590  dynamic_cast< const CModelEntity * >(pKeyFactory->get((*itAssignment)->getObjectName()));
591 
592  if (pModelEntity != NULL)
593  {
594  EventTargets.insert(pModelEntity);
595  }
596  }
597  }
598 
599  return EventTargets;
600 }
CModel::getEvents
CCopasiVectorN< CEvent > & getEvents()
Definition: CModel.cpp:1110
CKeyFactory::get
CCopasiObject * get(const std::string &key)
Definition: CKeyFactory.cpp:235
CCopasiVector::begin
iterator begin()
Definition: CCopasiVector.h:185
CCopasiVector::end
iterator end()
Definition: CCopasiVector.h:191
CCopasiRootContainer::getKeyFactory
static CKeyFactory * getKeyFactory()
Definition: CCopasiRootContainer.cpp:163
std::vector< const CCopasiObject * > CObjectLists::getListOfConstObjects ( ListType  t,
const CModel *  model 
)
static

Definition at line 117 of file CObjectLists.cpp.

References CArrayAnnotation::addElementReference(), ALL_INITIAL_VALUES, ALL_LOCAL_PARAMETER_VALUES, ALL_PARAMETER_AND_INITIAL_VALUES, ALL_PARAMETER_VALUES, ALL_VARIABLES, ASS_COMPARTMENT_VOLUMES, ASS_GLOBAL_PARAMETER_VALUES, ASS_METAB_CONCENTRATIONS, ASS_METAB_NUMBERS, CModelEntity::ASSIGNMENT, CCopasiVector< T >::begin(), COMPARTMENT_INITIAL_VOLUMES, COMPARTMENT_RATES, COMPARTMENT_VOLUMES, COMPARTMENTS, CONST_COMPARTMENT_VOLUMES, CONST_GLOBAL_PARAMETER_INITIAL_VALUES, CONST_METAB_CONCENTRATIONS, CONST_METAB_NUMBERS, CArrayAnnotation::dimensionality(), EMPTY_LIST, CCopasiVector< T >::end(), CModelEntity::FIXED, CKeyFactory::get(), CModel::getCompartments(), getEventTargets(), CCopasiRootContainer::getKeyFactory(), CModel::getMetabolites(), CModel::getModelValues(), CCopasiContainer::getObject(), CCopasiObject::getObjectParent(), CModel::getReactions(), CCopasiParameter::getValueReference(), GLOBAL_PARAMETER_INITIAL_VALUES, GLOBAL_PARAMETER_RATES, GLOBAL_PARAMETER_VALUES, GLOBAL_PARAMETERS, METAB_CONC_RATES, METAB_CONCENTRATIONS, METAB_INITIAL_CONCENTRATIONS, METAB_INITIAL_NUMBERS, METAB_NUMBERS, METAB_PART_RATES, METAB_TRANSITION_TIME, METABS, NON_CONST_COMPARTMENT_VOLUMES, NON_CONST_GLOBAL_PARAMETER_VALUES, NON_CONST_METAB_CONCENTRATIONS, NON_CONST_METAB_NUMBERS, CModelEntity::ODE, ODE_COMPARTMENT_VOLUMES, ODE_GLOBAL_PARAMETER_VALUES, ODE_METAB_CONCENTRATIONS, ODE_METAB_NUMBERS, CFunctionParameter::PARAMETER, REACTION_CONC_FLUXES, REACTION_METAB_CONCENTRATIONS, REACTION_METAB_NUMBERS, REACTION_PART_FLUXES, CModelEntity::REACTIONS, REACTIONS, REDUCED_JACOBIAN_EV_IM, REDUCED_JACOBIAN_EV_RE, SINGLE_OBJECT, CFunctionParameters::size(), and CArrayAnnotation::size().

Referenced by CMathContainer::allocate(), getListOfObjects(), and CMathContainer::initializeObjects().

118 {
119  ObjectList ret;
120 
121  CCopasiVector< CMetab >::const_iterator itMetab = pModel->getMetabolites().begin();
122  CCopasiVector< CMetab >::const_iterator endMetab = pModel->getMetabolites().end();
123 
124  CCopasiVector< CModelValue >::const_iterator itValue = pModel->getModelValues().begin();
125  CCopasiVector< CModelValue >::const_iterator endValue = pModel->getModelValues().end();
126 
127  CCopasiVector< CCompartment >::const_iterator itComp = pModel->getCompartments().begin();
128  CCopasiVector< CCompartment >::const_iterator endComp = pModel->getCompartments().end();
129 
130  CCopasiVector< CReaction >::const_iterator itReaction = pModel->getReactions().begin();
131  CCopasiVector< CReaction >::const_iterator endReaction = pModel->getReactions().end();
132 
133  std::set< const CModelEntity * > EventTargets = getEventTargets(pModel);
134 
135  switch (t)
136  {
137  case EMPTY_LIST:
138  case SINGLE_OBJECT:
139  break;
140 
141  // Metabolites
142  case METABS:
143 
144  for (; itMetab != endMetab; ++itMetab)
145  ret.push_back(*itMetab);
146 
147  break;
148 
149  case METAB_INITIAL_CONCENTRATIONS:
150 
151  for (; itMetab != endMetab; ++itMetab)
152  if ((*itMetab)->getStatus() != CModelEntity::ASSIGNMENT)
153  ret.push_back((*itMetab)->getInitialConcentrationReference());
154 
155  break;
156 
157  case METAB_INITIAL_NUMBERS:
158 
159  for (; itMetab != endMetab; ++itMetab)
160  if ((*itMetab)->getStatus() != CModelEntity::ASSIGNMENT)
161  ret.push_back((*itMetab)->getInitialValueReference());
162 
163  break;
164 
165  case METAB_CONCENTRATIONS:
166 
167  for (; itMetab != endMetab; ++itMetab)
168  ret.push_back((*itMetab)->getConcentrationReference());
169 
170  break;
171 
172  case METAB_NUMBERS:
173 
174  for (; itMetab != endMetab; ++itMetab)
175  ret.push_back((*itMetab)->getValueReference());
176 
177  break;
178 
179  case NON_CONST_METAB_CONCENTRATIONS:
180 
181  for (; itMetab != endMetab; ++itMetab)
182  if ((*itMetab)->getStatus() != CModelEntity::FIXED ||
183  EventTargets.count(*itMetab) > 0)
184  ret.push_back((*itMetab)->getConcentrationReference());
185 
186  break;
187 
188  case NON_CONST_METAB_NUMBERS:
189 
190  for (; itMetab != endMetab; ++itMetab)
191  if ((*itMetab)->getStatus() != CModelEntity::FIXED ||
192  EventTargets.count(*itMetab) > 0)
193  ret.push_back((*itMetab)->getValueReference());
194 
195  break;
196 
197  case CONST_METAB_CONCENTRATIONS:
198 
199  for (; itMetab != endMetab; ++itMetab)
200  if ((*itMetab)->getStatus() == CModelEntity::FIXED)
201  ret.push_back((*itMetab)->getConcentrationReference());
202 
203  break;
204 
205  case CONST_METAB_NUMBERS:
206 
207  for (; itMetab != endMetab; ++itMetab)
208  if ((*itMetab)->getStatus() == CModelEntity::FIXED)
209  ret.push_back((*itMetab)->getValueReference());
210 
211  break;
212 
213  case ODE_METAB_CONCENTRATIONS:
214 
215  for (; itMetab != endMetab; ++itMetab)
216  if ((*itMetab)->getStatus() == CModelEntity::ODE)
217  ret.push_back((*itMetab)->getConcentrationReference());
218 
219  break;
220 
221  case ODE_METAB_NUMBERS:
222 
223  for (; itMetab != endMetab; ++itMetab)
224  if ((*itMetab)->getStatus() == CModelEntity::ODE)
225  ret.push_back((*itMetab)->getValueReference());
226 
227  break;
228 
229  case REACTION_METAB_CONCENTRATIONS:
230 
231  for (; itMetab != endMetab; ++itMetab)
232  if ((*itMetab)->getStatus() == CModelEntity::REACTIONS)
233  ret.push_back((*itMetab)->getConcentrationReference());
234 
235  break;
236 
237  case REACTION_METAB_NUMBERS:
238 
239  for (; itMetab != endMetab; ++itMetab)
240  if ((*itMetab)->getStatus() == CModelEntity::REACTIONS)
241  ret.push_back((*itMetab)->getValueReference());
242 
243  break;
244 
245  case ASS_METAB_CONCENTRATIONS:
246 
247  for (; itMetab != endMetab; ++itMetab)
248  if ((*itMetab)->getStatus() == CModelEntity::ASSIGNMENT)
249  ret.push_back((*itMetab)->getConcentrationReference());
250 
251  break;
252 
253  case ASS_METAB_NUMBERS:
254 
255  for (; itMetab != endMetab; ++itMetab)
256  if ((*itMetab)->getStatus() == CModelEntity::ASSIGNMENT)
257  ret.push_back((*itMetab)->getValueReference());
258 
259  break;
260 
261  case METAB_CONC_RATES:
262 
263  for (; itMetab != endMetab; ++itMetab)
264  if ((*itMetab)->getStatus() == CModelEntity::ODE ||
265  (*itMetab)->getStatus() == CModelEntity::REACTIONS)
266  ret.push_back((*itMetab)->getConcentrationRateReference());
267 
268  break; //not possible at the moment
269 
270  case METAB_PART_RATES:
271 
272  for (; itMetab != endMetab; ++itMetab)
273  if ((*itMetab)->getStatus() == CModelEntity::ODE ||
274  (*itMetab)->getStatus() == CModelEntity::REACTIONS)
275  ret.push_back((*itMetab)->getRateReference());
276 
277  break;
278 
279  case METAB_TRANSITION_TIME:
280 
281  for (; itMetab != endMetab; ++itMetab)
282  if ((*itMetab)->getStatus() == CModelEntity::ODE ||
283  (*itMetab)->getStatus() == CModelEntity::REACTIONS)
284  ret.push_back(static_cast< const CCopasiObject * >((*itMetab)->getObject(CCopasiObjectName("Reference=TransitionTime"))));
285 
286  break;
287 
288  // reactions
289  case REACTIONS:
290 
291  for (; itReaction != endReaction; ++itReaction)
292  ret.push_back(*itReaction);
293 
294  break;
295 
296  case REACTION_CONC_FLUXES:
297 
298  for (; itReaction != endReaction; ++itReaction)
299  ret.push_back(static_cast< const CCopasiObject * >((*itReaction)->getObject(CCopasiObjectName("Reference=Flux"))));
300 
301  break;
302 
303  case REACTION_PART_FLUXES:
304 
305  for (; itReaction != endReaction; ++itReaction)
306  ret.push_back(static_cast< const CCopasiObject * >((*itReaction)->getObject(CCopasiObjectName("Reference=ParticleFlux"))));
307 
308  break;
309 
310  // global quantities
311  case GLOBAL_PARAMETERS:
312 
313  for (; itValue != endValue; ++itValue)
314  ret.push_back(*itValue);
315 
316  break;
317 
318  case GLOBAL_PARAMETER_INITIAL_VALUES:
319 
320  for (; itValue != endValue; ++itValue)
321  if ((*itValue)->getStatus() != CModelEntity::ASSIGNMENT)
322  ret.push_back((*itValue)->getInitialValueReference());
323 
324  break;
325 
326  case GLOBAL_PARAMETER_VALUES:
327 
328  for (; itValue != endValue; ++itValue)
329  ret.push_back((*itValue)->getValueReference());
330 
331  break;
332 
333  case NON_CONST_GLOBAL_PARAMETER_VALUES:
334 
335  for (; itValue != endValue; ++itValue)
336  if ((*itValue)->getStatus() != CModelEntity::FIXED ||
337  EventTargets.count(*itValue) > 0)
338  ret.push_back((*itValue)->getValueReference());
339 
340  break;
341 
342  case CONST_GLOBAL_PARAMETER_INITIAL_VALUES:
343 
344  for (; itValue != endValue; ++itValue)
345  if ((*itValue)->getStatus() == CModelEntity::FIXED)
346  ret.push_back((*itValue)->getInitialValueReference());
347 
348  break;
349 
350  case ODE_GLOBAL_PARAMETER_VALUES:
351 
352  for (; itValue != endValue; ++itValue)
353  if ((*itValue)->getStatus() == CModelEntity::ODE)
354  ret.push_back((*itValue)->getValueReference());
355 
356  break;
357 
358  case ASS_GLOBAL_PARAMETER_VALUES:
359 
360  for (; itValue != endValue; ++itValue)
361  if ((*itValue)->getStatus() == CModelEntity::ASSIGNMENT)
362  ret.push_back((*itValue)->getValueReference());
363 
364  break;
365 
366  case GLOBAL_PARAMETER_RATES:
367 
368  for (; itValue != endValue; ++itValue)
369  if ((*itValue)->getStatus() == CModelEntity::ODE)
370  ret.push_back((*itValue)->getRateReference());
371 
372  break;
373 
374  // compartments
375  case COMPARTMENTS:
376 
377  for (; itComp != endComp; ++itComp)
378  ret.push_back(*itComp);
379 
380  break;
381 
382  case COMPARTMENT_INITIAL_VOLUMES:
383 
384  for (; itComp != endComp; ++itComp)
385  if ((*itComp)->getStatus() != CModelEntity::ASSIGNMENT)
386  ret.push_back((*itComp)->getInitialValueReference());
387 
388  break;
389 
390  case COMPARTMENT_VOLUMES:
391 
392  for (; itComp != endComp; ++itComp)
393  ret.push_back((*itComp)->getValueReference());
394 
395  break;
396 
397  case NON_CONST_COMPARTMENT_VOLUMES:
398 
399  for (; itComp != endComp; ++itComp)
400  if ((*itComp)->getStatus() != CModelEntity::FIXED ||
401  EventTargets.count(*itComp) > 0)
402  ret.push_back((*itComp)->getValueReference());
403 
404  break;
405 
406  case CONST_COMPARTMENT_VOLUMES:
407 
408  for (; itComp != endComp; ++itComp)
409  if ((*itComp)->getStatus() == CModelEntity::FIXED)
410  ret.push_back((*itComp)->getValueReference());
411 
412  break;
413 
414  case ODE_COMPARTMENT_VOLUMES:
415 
416  for (; itComp != endComp; ++itComp)
417  if ((*itComp)->getStatus() == CModelEntity::ODE)
418  ret.push_back((*itComp)->getValueReference());
419 
420  break;
421 
422  case ASS_COMPARTMENT_VOLUMES:
423 
424  for (; itComp != endComp; ++itComp)
425  if ((*itComp)->getStatus() == CModelEntity::ASSIGNMENT)
426  ret.push_back((*itComp)->getValueReference());
427 
428  break;
429 
430  case COMPARTMENT_RATES:
431 
432  for (; itComp != endComp; ++itComp)
433  if ((*itComp)->getStatus() == CModelEntity::ODE)
434  ret.push_back((*itComp)->getRateReference());
435 
436  break;
437 
438  case ALL_INITIAL_VALUES:
439  {
440  ret = getListOfConstObjects(METAB_INITIAL_CONCENTRATIONS, pModel);
441 
442  ObjectList tmp = getListOfConstObjects(GLOBAL_PARAMETER_INITIAL_VALUES, pModel);
443  ret.insert(ret.end(), tmp.begin(), tmp.end());
444 
445  tmp = getListOfConstObjects(COMPARTMENT_INITIAL_VOLUMES, pModel);
446  ret.insert(ret.end(), tmp.begin(), tmp.end());
447  }
448  break;
449 
450  case ALL_LOCAL_PARAMETER_VALUES:
451  {
452  for (; itReaction != endReaction; ++itReaction)
453  {
454  const CFunctionParameters & params = (*itReaction)->getFunctionParameters();
455  size_t j, jmax = params.size();
456 
457  for (j = 0; j < jmax; ++j)
458  if (params[j]->getUsage() == CFunctionParameter::PARAMETER)
459  if ((*itReaction)->isLocalParameter(j))
460  {
461  CCopasiParameter * par =
462  dynamic_cast<CCopasiParameter*>
463  (CCopasiRootContainer::getKeyFactory()->get((*itReaction)->getParameterMappings()[j][0]));
464 
465  if (par)
466  ret.push_back(par->getValueReference());
467  }
468  }
469  }
470  break;
471 
472  case ALL_PARAMETER_VALUES:
473  {
474  ret = getListOfConstObjects(CONST_GLOBAL_PARAMETER_INITIAL_VALUES, pModel);
475 
476  ObjectList tmp = getListOfConstObjects(ALL_LOCAL_PARAMETER_VALUES, pModel);
477  ret.insert(ret.end(), tmp.begin(), tmp.end());
478  }
479  break;
480 
481  case ALL_PARAMETER_AND_INITIAL_VALUES:
482  {
483  ret = getListOfConstObjects(ALL_PARAMETER_VALUES, pModel);
484 
485  ObjectList tmp = getListOfConstObjects(ALL_INITIAL_VALUES, pModel);
486  ret.insert(ret.end(), tmp.begin(), tmp.end());
487  }
488  break;
489 
490  case ALL_VARIABLES:
491  {
492  ret = getListOfConstObjects(NON_CONST_METAB_CONCENTRATIONS, pModel);
493 
494  ObjectList tmp = getListOfConstObjects(NON_CONST_GLOBAL_PARAMETER_VALUES, pModel);
495  ret.insert(ret.end(), tmp.begin(), tmp.end());
496 
497  tmp = getListOfConstObjects(NON_CONST_COMPARTMENT_VOLUMES, pModel);
498  ret.insert(ret.end(), tmp.begin(), tmp.end());
499  }
500  break;
501 
502  case REDUCED_JACOBIAN_EV_RE:
503  {
504  CCopasiContainer * pParent = dynamic_cast<CCopasiContainer*>(pModel->getObjectParent());
505 
506  if (!pParent)
507  break;
508 
509  const CArrayAnnotation * pEV = dynamic_cast<const CArrayAnnotation*>(pParent->getObject(CCopasiObjectName("Vector=TaskList[Steady-State],Array=Eigenvalues of reduced system Jacobian")));
510 
511  if (pEV->dimensionality() != 2) //2d matrix
512  break;
513 
514  if (pEV->size()[1] != 2) //must be two columns for Re and Im part
515  break;
516 
517  size_t imax = pEV->size()[0];
518  size_t i;
519 
520  for (i = 0; i < imax; ++i)
521  ret.push_back(static_cast< const CCopasiObject * >(pEV->addElementReference(i, 0)));
522  }
523  break;
524 
525  case REDUCED_JACOBIAN_EV_IM:
526  {
527  CCopasiContainer * pParent = dynamic_cast<CCopasiContainer*>(pModel->getObjectParent());
528 
529  if (!pParent)
530  break;
531 
532  const CArrayAnnotation * pEV = dynamic_cast<const CArrayAnnotation*>(pParent->getObject(CCopasiObjectName("Vector=TaskList[Steady-State],Array=Eigenvalues of reduced system Jacobian")));
533 
534  if (pEV->dimensionality() != 2) //2d matrix
535  break;
536 
537  if (pEV->size()[1] != 2) //must be two columns for Re and Im part
538  break;
539 
540  size_t imax = pEV->size()[0];
541  size_t i;
542 
543  for (i = 0; i < imax; ++i)
544  ret.push_back(static_cast< const CCopasiObject * >(pEV->addElementReference(i, 1)));
545 
546  }
547  break;
548 
549  default:
550  break;
551  }
552 
553  return ret;
554 }
ObjectList::insert
void insert(ObjectBrowserItem *pItem)
Definition: ObjectBrowserItem.cpp:233
CObjectLists::getListOfConstObjects
static std::vector< const CCopasiObject * > getListOfConstObjects(ListType t, const CModel *model)
Definition: CObjectLists.cpp:117
CKeyFactory::get
CCopasiObject * get(const std::string &key)
Definition: CKeyFactory.cpp:235
CCopasiVector::begin
iterator begin()
Definition: CCopasiVector.h:185
CCopasiParameter::getValueReference
CCopasiObject * getValueReference() const
Definition: CCopasiParameter.cpp:251
CCopasiVector::end
iterator end()
Definition: CCopasiVector.h:191
CCopasiVector::const_iterator
std::vector< CType * >::const_iterator const_iterator
Definition: CCopasiVector.h:57
CCopasiRootContainer::getKeyFactory
static CKeyFactory * getKeyFactory()
Definition: CCopasiRootContainer.cpp:163
CArrayAnnotation::addElementReference
const CObjectInterface * addElementReference(CCopasiAbstractArray::index_type index) const
Definition: CAnnotatedMatrix.cpp:251
CCopasiContainer::getObject
virtual const CObjectInterface * getObject(const CCopasiObjectName &cn) const
Definition: CCopasiContainer.cpp:74
CArrayAnnotation::size
CCopasiAbstractArray::index_type size() const
Definition: CAnnotatedMatrix.h:148
CArrayAnnotation::dimensionality
size_t dimensionality() const
Definition: CAnnotatedMatrix.cpp:79
CObjectLists::getEventTargets
static std::set< const CModelEntity * > getEventTargets(const CModel *pModel)
Definition: CObjectLists.cpp:571
std::vector< CCopasiObject * > CObjectLists::getListOfObjects ( ListType  t,
const CModel *  model 
)
static

Definition at line 97 of file CObjectLists.cpp.

References getListOfConstObjects().

Referenced by CSensItem::getVariablesPointerList().

98 {
99  std::vector< const CCopasiObject * > src = getListOfConstObjects(t, model);
100  std::vector< CCopasiObject * > target;
101  target.resize(src.size());
102 
103  std::vector< const CCopasiObject * >::iterator itSrc = src.begin();
104  std::vector< const CCopasiObject * >::iterator endSrc = src.end();
105  std::vector< CCopasiObject * >::iterator itTarget = target.begin();
106 
107  for (; itSrc != endSrc; ++itSrc, ++itTarget)
108  *itTarget = const_cast< CCopasiObject * >(*itSrc);
109 
110  return target;
111 
112  //I know this is unnecessary copying. But I want to avoid reinterpret_cast
113 }
CObjectLists::getListOfConstObjects
static std::vector< const CCopasiObject * > getListOfConstObjects(ListType t, const CModel *model)
Definition: CObjectLists.cpp:117

Member Data Documentation

const std::string CObjectLists::ListTypeName
static

Definition at line 98 of file CObjectLists.h.

Referenced by SensWidgetComboBox::fillFromList(), and CSensItem::getListTypeDisplayName().

The documentation for this class was generated from the following files:
Generated on Thu Jul 2 2015 14:51:54 for COPASI API by   doxygen 1.8.6