40 "Initial Concentrations",
42 "Concentrations of Species",
44 "Non-Constant Concentrations of Species",
45 "Non-Constant Numbers of Species",
46 "Constant Concentrations of Species",
47 "Constant Numbers of Species",
48 "Concentrations of Species with ODE",
49 "Numbers of Species with ODE",
50 "Concentrations of Species determined by Reactions",
51 "Numbers of Species determined by Reactions",
52 "Concentrations of Species with Assignment",
53 "Numbers of Species with Assignment",
54 "Concentration Rates",
59 "Concentration Fluxes of Reactions",
60 "Particle Fluxes of Reactions",
63 "Global Quantity Initial Values",
64 "Global Quantity Values",
65 "Non-Constant Global Quantity Values",
66 "Constant Global Quantity Values",
67 "Values of Global Quantities with ODE",
68 "Values of Global Quantities with Assignment",
69 "Global Quantity Rates",
72 "Compartment Initial Volumes",
73 "Compartment Volumes",
74 "Non-Constant Compartment Volumes",
75 "Constant Compartment Volumes",
76 "Values of Compartment Volumes with ODE",
77 "Values of Compartment Volumes with Assignment",
78 "Compartment Volume Rates",
81 "Local Parameter Values",
83 "All Parameter Values",
84 "All Parameter and Initial Values",
86 "All Variables of the model",
87 "All independent Variables of the model",
89 "Real part of eigenvalues of the reduced jacobian",
90 "Imaginary part of eigenvalues of the reduced jacobian",
96 std::vector<CCopasiObject*>
100 std::vector< CCopasiObject * > target;
101 target.resize(src.size());
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();
107 for (; itSrc != endSrc; ++itSrc, ++itTarget)
108 *itTarget = const_cast< CCopasiObject * >(*itSrc);
116 std::vector<const CCopasiObject*>
133 std::set< const CModelEntity * > EventTargets =
getEventTargets(pModel);
144 for (; itMetab != endMetab; ++itMetab)
145 ret.push_back(*itMetab);
151 for (; itMetab != endMetab; ++itMetab)
153 ret.push_back((*itMetab)->getInitialConcentrationReference());
159 for (; itMetab != endMetab; ++itMetab)
161 ret.push_back((*itMetab)->getInitialValueReference());
167 for (; itMetab != endMetab; ++itMetab)
168 ret.push_back((*itMetab)->getConcentrationReference());
174 for (; itMetab != endMetab; ++itMetab)
175 ret.push_back((*itMetab)->getValueReference());
181 for (; itMetab != endMetab; ++itMetab)
183 EventTargets.count(*itMetab) > 0)
184 ret.push_back((*itMetab)->getConcentrationReference());
190 for (; itMetab != endMetab; ++itMetab)
192 EventTargets.count(*itMetab) > 0)
193 ret.push_back((*itMetab)->getValueReference());
199 for (; itMetab != endMetab; ++itMetab)
201 ret.push_back((*itMetab)->getConcentrationReference());
207 for (; itMetab != endMetab; ++itMetab)
209 ret.push_back((*itMetab)->getValueReference());
215 for (; itMetab != endMetab; ++itMetab)
217 ret.push_back((*itMetab)->getConcentrationReference());
223 for (; itMetab != endMetab; ++itMetab)
225 ret.push_back((*itMetab)->getValueReference());
231 for (; itMetab != endMetab; ++itMetab)
233 ret.push_back((*itMetab)->getConcentrationReference());
239 for (; itMetab != endMetab; ++itMetab)
241 ret.push_back((*itMetab)->getValueReference());
247 for (; itMetab != endMetab; ++itMetab)
249 ret.push_back((*itMetab)->getConcentrationReference());
255 for (; itMetab != endMetab; ++itMetab)
257 ret.push_back((*itMetab)->getValueReference());
263 for (; itMetab != endMetab; ++itMetab)
266 ret.push_back((*itMetab)->getConcentrationRateReference());
272 for (; itMetab != endMetab; ++itMetab)
275 ret.push_back((*itMetab)->getRateReference());
281 for (; itMetab != endMetab; ++itMetab)
284 ret.push_back(static_cast< const CCopasiObject * >((*itMetab)->getObject(
CCopasiObjectName(
"Reference=TransitionTime"))));
291 for (; itReaction != endReaction; ++itReaction)
292 ret.push_back(*itReaction);
298 for (; itReaction != endReaction; ++itReaction)
299 ret.push_back(static_cast< const CCopasiObject * >((*itReaction)->getObject(
CCopasiObjectName(
"Reference=Flux"))));
305 for (; itReaction != endReaction; ++itReaction)
306 ret.push_back(static_cast< const CCopasiObject * >((*itReaction)->getObject(
CCopasiObjectName(
"Reference=ParticleFlux"))));
313 for (; itValue != endValue; ++itValue)
314 ret.push_back(*itValue);
320 for (; itValue != endValue; ++itValue)
322 ret.push_back((*itValue)->getInitialValueReference());
328 for (; itValue != endValue; ++itValue)
329 ret.push_back((*itValue)->getValueReference());
335 for (; itValue != endValue; ++itValue)
337 EventTargets.count(*itValue) > 0)
338 ret.push_back((*itValue)->getValueReference());
344 for (; itValue != endValue; ++itValue)
346 ret.push_back((*itValue)->getInitialValueReference());
352 for (; itValue != endValue; ++itValue)
354 ret.push_back((*itValue)->getValueReference());
360 for (; itValue != endValue; ++itValue)
362 ret.push_back((*itValue)->getValueReference());
368 for (; itValue != endValue; ++itValue)
370 ret.push_back((*itValue)->getRateReference());
377 for (; itComp != endComp; ++itComp)
378 ret.push_back(*itComp);
384 for (; itComp != endComp; ++itComp)
386 ret.push_back((*itComp)->getInitialValueReference());
392 for (; itComp != endComp; ++itComp)
393 ret.push_back((*itComp)->getValueReference());
399 for (; itComp != endComp; ++itComp)
401 EventTargets.count(*itComp) > 0)
402 ret.push_back((*itComp)->getValueReference());
408 for (; itComp != endComp; ++itComp)
410 ret.push_back((*itComp)->getValueReference());
416 for (; itComp != endComp; ++itComp)
418 ret.push_back((*itComp)->getValueReference());
424 for (; itComp != endComp; ++itComp)
426 ret.push_back((*itComp)->getValueReference());
432 for (; itComp != endComp; ++itComp)
434 ret.push_back((*itComp)->getRateReference());
443 ret.insert(ret.end(), tmp.begin(), tmp.end());
446 ret.insert(ret.end(), tmp.begin(), tmp.end());
452 for (; itReaction != endReaction; ++itReaction)
455 size_t j, jmax = params.
size();
457 for (j = 0; j < jmax; ++j)
459 if ((*itReaction)->isLocalParameter(j))
477 ret.insert(ret.end(), tmp.begin(), tmp.end());
486 ret.insert(ret.end(), tmp.begin(), tmp.end());
495 ret.insert(ret.end(), tmp.begin(), tmp.end());
498 ret.insert(ret.end(), tmp.begin(), tmp.end());
514 if (pEV->
size()[1] != 2)
517 size_t imax = pEV->
size()[0];
520 for (i = 0; i < imax; ++i)
537 if (pEV->
size()[1] != 2)
540 size_t imax = pEV->
size()[0];
543 for (i = 0; i < imax; ++i)
559 bool fixedMetab =
false;
561 size_t i, imax = metabs.
size();
563 for (i = 0; i < imax; ++i)
565 {fixedMetab =
true;
break;}
573 std::set< const CModelEntity * > EventTargets;
580 for (; itEvent != endEvent; ++itEvent)
583 (*itEvent)->getAssignments().
begin();
585 (*itEvent)->getAssignments().
end();
587 for (; itAssignment != endAssignment; ++itAssignment)
590 dynamic_cast< const CModelEntity *
>(pKeyFactory->
get((*itAssignment)->getObjectName()));
592 if (pModelEntity != NULL)
594 EventTargets.insert(pModelEntity);
CCopasiVectorN< CEvent > & getEvents()
static std::vector< const CCopasiObject * > getListOfConstObjects(ListType t, const CModel *model)
const CCopasiVector< CMetab > & getMetabolites() const
const CCopasiVectorN< CModelValue > & getModelValues() const
virtual size_t size() const
CCopasiObject * get(const std::string &key)
static bool existsFixedMetab(const CModel *model)
CCopasiObject * getValueReference() const
std::vector< const CCopasiObject * > ObjectList
std::vector< CType * >::const_iterator const_iterator
static const std::string ListTypeName[]
CCopasiVectorNS< CCompartment > & getCompartments()
static CKeyFactory * getKeyFactory()
Header file of class CArrayAnnotation.
static std::vector< CCopasiObject * > getListOfObjects(ListType t, const CModel *model)
CCopasiVectorNS< CReaction > & getReactions()
const CObjectInterface * addElementReference(CCopasiAbstractArray::index_type index) const
virtual const CObjectInterface * getObject(const CCopasiObjectName &cn) const
CCopasiAbstractArray::index_type size() const
size_t dimensionality() const
static std::set< const CModelEntity * > getEventTargets(const CModel *pModel)
CCopasiContainer * getObjectParent() const