/* declares constant = false for any L1 compartment/parameter
* assigned by a rule
*/
void
Model::addConstantAttribute()
{
unsigned int n;
// parameters and compartments are declared to have constant=true
// by default. Since in L1 the constant attribute didnt exist
// parameters/compartments that are the subjcet of rules must have
// the value changed
for ( n = 0; n < getNumParameters(); n++)
{
if (getRule(getParameter(n)->getId()) != NULL)
{
getParameter(n)->setConstant(false);
}
}
for ( n = 0; n < getNumCompartments(); n++)
{
if (getRule(getCompartment(n)->getId()) != NULL)
{
getCompartment(n)->setConstant(false);
}
}
}
CMetab *
UndoSpeciesData::createObjectIn(CModel *pModel)
{
if (pModel == NULL)
return NULL;
createDependentObjects(pModel);
if (pModel->getCompartments().getIndex(mCompartment) == C_INVALID_INDEX)
return NULL;
CCompartment * pCompartment = &pModel->getCompartments()[getCompartment()];
if (pCompartment == NULL)
return NULL;
if (pCompartment->getMetabolites().getIndex(getName()) != C_INVALID_INDEX)
return NULL;
CMetab *pSpecies = pModel->createMetabolite(getName(), getCompartment(), getIConc(), getStatus());
if (pSpecies == NULL)
return NULL;
mKey = pSpecies->getKey();
return pSpecies;
}
/**
Adds a state to the state map, the creation queue and to a
Compartment with the given id
@param state
@param compartmentId
@return Returns the amount of state space allocated.
@warning Once you pass a state pointer into this method, you must
not use it again. It may be invalid.
*/
size_t
osc::StateHandler::addState(osc::State *state,
osc::compartment_id_t const &compartmentId,
osc::u16 priority)
{
DEBUG_STACK_FRAME;
state->retain();
osc::Compartment * compartment = getCompartment(compartmentId);
compartment->writeLock();
// Truncating as defined in RFC 3320 6.2.2
size_t max_size = compartment->totalStateMemoryAvailable();
if( (state->getStateSize() + 64) > max_size )
{
state->truncate(max_size - 64);
}
// Add to the global state map. If this state is a duplicate of
// a state that is already present, then addState will
// delete the state that was passed in and return a pointer
// to its doppelganger.
state = addState(state);
compartment->addState(state, priority);
compartment->unlock();
compartment->release();
state->release();
return 0;
}
/* in L1 spatialDimensions did not exist as an attribute
* but was considered to be '3'
* L3 does not require the attribute and will
* only record it is officially set
*/
void
Model::setSpatialDimensions(double dims)
{
for (unsigned int n = 0; n < getNumCompartments(); n++)
{
getCompartment(n)->setSpatialDimensions(dims);
}
}
/* converting to l1 any metaid attributes should be removed */
void
Model::removeMetaId()
{
unsigned int n, i;
unsetMetaId();
for (n = 0; n < getNumUnitDefinitions(); n++)
{
getUnitDefinition(n)->unsetMetaId();
for (i = 0; i < getUnitDefinition(n)->getNumUnits(); i++)
{
getUnitDefinition(n)->getUnit(i)->unsetMetaId();
}
}
for (n = 0; n < getNumCompartments(); n++)
{
getCompartment(n)->unsetMetaId();
}
for (n = 0; n < getNumSpecies(); n++)
{
getSpecies(n)->unsetMetaId();
}
for (n = 0; n < getNumParameters(); n++)
{
getParameter(n)->unsetMetaId();
}
for (n = 0; n < getNumRules(); n++)
{
getRule(n)->unsetMetaId();
}
for (n = 0; n < getNumReactions(); n++)
{
getReaction(n)->unsetMetaId();
for (i = 0; i < getReaction(n)->getNumReactants(); i++)
{
getReaction(n)->getReactant(i)->unsetMetaId();
}
for (i = 0; i < getReaction(n)->getNumProducts(); i++)
{
getReaction(n)->getProduct(i)->unsetMetaId();
}
if (getReaction(n)->isSetKineticLaw())
{
getReaction(n)->getKineticLaw()->unsetMetaId();
}
}
}
/**
Debugging-only method
*/
void
osc::StateHandler::processChanges(osc::StateChanges & changes,
osc::compartment_id_t const &compartmentId)
{
DEBUG_STACK_FRAME;
osc::Compartment * compartment = getCompartment (compartmentId);
if (!compartment)
{
return;
}
compartment->writeLock();
processChanges(changes, *compartment);
compartment->unlock();
compartment->release();
}
void
Model::removeDuplicateTopLevelAnnotations()
{
unsigned int i, n;
this->removeDuplicateAnnotations();
if (getNumFunctionDefinitions() > 0)
{
getListOfFunctionDefinitions()->removeDuplicateAnnotations();
for (i = 0; i < getNumFunctionDefinitions(); i++)
{
getFunctionDefinition(i)->removeDuplicateAnnotations();
}
}
if (getNumUnitDefinitions() > 0)
{
getListOfUnitDefinitions()->removeDuplicateAnnotations();
for (i = 0; i < getNumUnitDefinitions(); i++)
{
getUnitDefinition(i)->removeDuplicateAnnotations();
getUnitDefinition(i)->getListOfUnits()->removeDuplicateAnnotations();
for (n = 0; n < getUnitDefinition(i)->getNumUnits(); n++)
{
getUnitDefinition(i)->getUnit(n)->removeDuplicateAnnotations();
}
}
}
if (getNumCompartmentTypes() > 0)
{
getListOfCompartmentTypes()->removeDuplicateAnnotations();
for (i = 0; i < getNumCompartmentTypes(); i++)
{
getCompartmentType(i)->removeDuplicateAnnotations();
}
}
if (getNumSpeciesTypes() > 0)
{
getListOfSpeciesTypes()->removeDuplicateAnnotations();
for (i = 0; i < getNumSpeciesTypes(); i++)
{
getSpeciesType(i)->removeDuplicateAnnotations();
}
}
if (getNumCompartments() > 0)
{
getListOfCompartments()->removeDuplicateAnnotations();
for (i = 0; i < getNumCompartments(); i++)
{
getCompartment(i)->removeDuplicateAnnotations();
}
}
if (getNumSpecies() > 0)
{
getListOfSpecies()->removeDuplicateAnnotations();
for (i = 0; i < getNumSpecies(); i++)
{
getSpecies(i)->removeDuplicateAnnotations();
}
}
if (getNumParameters() > 0)
{
getListOfParameters()->removeDuplicateAnnotations();
for (i = 0; i < getNumParameters(); i++)
{
getParameter(i)->removeDuplicateAnnotations();
}
}
if (getNumInitialAssignments() > 0)
{
getListOfInitialAssignments()->removeDuplicateAnnotations();
for (i = 0; i < getNumInitialAssignments(); i++)
{
getInitialAssignment(i)->removeDuplicateAnnotations();
}
}
if (getNumConstraints() > 0)
{
getListOfConstraints()->removeDuplicateAnnotations();
for (i = 0; i < getNumConstraints(); i++)
{
getConstraint(i)->removeDuplicateAnnotations();
}
}
if (getNumRules() > 0)
{
getListOfRules()->removeDuplicateAnnotations();
for (i = 0; i < getNumRules(); i++)
{
getRule(i)->removeDuplicateAnnotations();
}
}
if (getNumReactions() > 0)
{
getListOfReactions()->removeDuplicateAnnotations();
for (i = 0; i < getNumReactions(); i++)
{
Reaction * r = getReaction(i);
r->removeDuplicateAnnotations();
if (r->getNumReactants() > 0)
{
r->getListOfReactants()->removeDuplicateAnnotations();
for (n = 0; n < r->getNumReactants(); n++)
{
r->getReactant(n)->removeDuplicateAnnotations();
}
}
if (r->getNumProducts() > 0)
{
r->getListOfProducts()->removeDuplicateAnnotations();
for (n = 0; n < r->getNumProducts(); n++)
{
r->getProduct(n)->removeDuplicateAnnotations();
}
}
if (r->getNumModifiers() > 0)
{
r->getListOfModifiers()->removeDuplicateAnnotations();
for (n = 0; n < r->getNumModifiers(); n++)
{
r->getModifier(n)->removeDuplicateAnnotations();
}
}
if (r->isSetKineticLaw())
{
r->getKineticLaw()->removeDuplicateAnnotations();
if (r->getKineticLaw()->getNumParameters() > 0)
{
r->getKineticLaw()->getListOfParameters()
->removeDuplicateAnnotations();
for (n = 0; n < r->getKineticLaw()->getNumParameters(); n++)
{
r->getKineticLaw()->getParameter(n)->removeDuplicateAnnotations();
}
}
}
}
}
if (getNumEvents() > 0)
{
getListOfEvents()->removeDuplicateAnnotations();
for (i = 0; i < getNumEvents(); i++)
{
getEvent(i)->removeDuplicateAnnotations();
if (getEvent(i)->getNumEventAssignments() > 0)
{
getEvent(i)->getListOfEventAssignments()->removeDuplicateAnnotations();
for (n = 0; n < getEvent(i)->getNumEventAssignments(); n++)
{
getEvent(i)->getEventAssignment(n)->removeDuplicateAnnotations();
}
}
}
}
}
void
Model::removeSBOTermsNotInL2V2(bool strict)
{
unsigned int n, i;
if (strict == true)
{
for (n = 0; n < getNumUnitDefinitions(); n++)
{
getUnitDefinition(n)->unsetSBOTerm();
for (i = 0; i < getUnitDefinition(n)->getNumUnits(); i++)
{
getUnitDefinition(n)->getUnit(i)->unsetSBOTerm();
}
}
for (n = 0; n < getNumCompartments(); n++)
{
getCompartment(n)->unsetSBOTerm();
}
for (n = 0; n < getNumSpecies(); n++)
{
getSpecies(n)->unsetSBOTerm();
}
for (n = 0; n < getNumCompartmentTypes(); n++)
{
getCompartmentType(n)->unsetSBOTerm();
}
for (n = 0; n < getNumSpeciesTypes(); n++)
{
getSpeciesType(n)->unsetSBOTerm();
}
for (n = 0; n < getNumReactions(); n++)
{
for (i = 0; i < getReaction(n)->getNumReactants(); i++)
{
if (getReaction(n)->getReactant(i)->isSetStoichiometryMath())
{
getReaction(n)->getReactant(i)->getStoichiometryMath()->unsetSBOTerm();
}
}
for (i = 0; i < getReaction(n)->getNumProducts(); i++)
{
if (getReaction(n)->getProduct(i)->isSetStoichiometryMath())
{
getReaction(n)->getProduct(i)->getStoichiometryMath()->unsetSBOTerm();
}
}
}
for (n = 0; n < getNumEvents(); n++)
{
if (getEvent(n)->isSetTrigger())
{
getEvent(n)->getTrigger()->unsetSBOTerm();
}
if (getEvent(n)->isSetDelay())
{
getEvent(n)->getDelay()->unsetSBOTerm();
}
}
}
}
void
Model::removeSBOTerms(bool strict)
{
unsigned int n, i;
if (strict == true)
{
unsetSBOTerm();
for (n = 0; n < getNumUnitDefinitions(); n++)
{
getUnitDefinition(n)->unsetSBOTerm();
for (i = 0; i < getUnitDefinition(n)->getNumUnits(); i++)
{
getUnitDefinition(n)->getUnit(i)->unsetSBOTerm();
}
}
for (n = 0; n < getNumCompartments(); n++)
{
getCompartment(n)->unsetSBOTerm();
}
for (n = 0; n < getNumSpecies(); n++)
{
getSpecies(n)->unsetSBOTerm();
}
for (n = 0; n < getNumParameters(); n++)
{
getParameter(n)->unsetSBOTerm();
}
for (n = 0; n < getNumRules(); n++)
{
getRule(n)->unsetSBOTerm();
}
for (n = 0; n < getNumReactions(); n++)
{
getReaction(n)->unsetSBOTerm();
for (i = 0; i < getReaction(n)->getNumReactants(); i++)
{
getReaction(n)->getReactant(i)->unsetSBOTerm();
if (getReaction(n)->getReactant(i)->isSetStoichiometryMath())
{
getReaction(n)->getReactant(i)->getStoichiometryMath()->unsetSBOTerm();
}
}
for (i = 0; i < getReaction(n)->getNumProducts(); i++)
{
getReaction(n)->getProduct(i)->unsetSBOTerm();
if (getReaction(n)->getProduct(i)->isSetStoichiometryMath())
{
getReaction(n)->getProduct(i)->getStoichiometryMath()->unsetSBOTerm();
}
}
for (i = 0; i < getReaction(n)->getNumModifiers(); i++)
{
getReaction(n)->getModifier(i)->unsetSBOTerm();
}
if (getReaction(n)->isSetKineticLaw())
{
getReaction(n)->getKineticLaw()->unsetSBOTerm();
}
}
for (n = 0; n < getNumFunctionDefinitions(); n++)
{
getFunctionDefinition(n)->unsetSBOTerm();
}
for (n = 0; n < getNumEvents(); n++)
{
getEvent(n)->unsetSBOTerm();
for (i = 0; i < getEvent(n)->getNumEventAssignments(); i++)
{
getEvent(n)->getEventAssignment(i)->unsetSBOTerm();
}
if (getEvent(n)->isSetTrigger())
{
getEvent(n)->getTrigger()->unsetSBOTerm();
}
if (getEvent(n)->isSetDelay())
{
getEvent(n)->getDelay()->unsetSBOTerm();
}
}
}
}
/* in L1 and L2 there were built in values for key units
* such as 'volume', 'length', 'area', 'substance' and 'time'
* In L3 these have been removed - thus if a model uses one of these
* it needs a unitDefinition to define it
*/
void
Model::addDefinitionsForDefaultUnits()
{
/* create a list of unit values */
IdList unitsUsed;
unsigned int n;
bool implicitVolume = false;
bool implicitArea = false;
bool implicitLength = false;
bool implicitSubstance = false;
for (n = 0; n < getNumCompartments(); n++)
{
if (getCompartment(n)->isSetUnits())
{
unitsUsed.append(getCompartment(n)->getUnits());
}
else
{
if (getCompartment(n)->getSpatialDimensions() == 3)
{
implicitVolume = true;
getCompartment(n)->setUnits("volume");
}
else if (getCompartment(n)->getSpatialDimensions() == 2)
{
implicitArea = true;
getCompartment(n)->setUnits("area");
}
else if (getCompartment(n)->getSpatialDimensions() == 1)
{
implicitLength = true;
getCompartment(n)->setUnits("length");
}
}
}
for (n = 0; n < getNumSpecies(); n++)
{
if (getSpecies(n)->isSetSubstanceUnits())
{
unitsUsed.append(getSpecies(n)->getSubstanceUnits());
}
else
{
implicitSubstance = true;
getSpecies(n)->setSubstanceUnits("substance");
}
if (getSpecies(n)->isSetSpatialSizeUnits())
unitsUsed.append(getSpecies(n)->getSpatialSizeUnits());
}
for (n = 0; n < getNumParameters(); n++)
{
if (getParameter(n)->isSetUnits())
unitsUsed.append(getParameter(n)->getUnits());
}
if (getUnitDefinition("volume") == NULL)
{
if (unitsUsed.contains("volume") || implicitVolume)
{
UnitDefinition * ud = createUnitDefinition();
ud->setId("volume");
Unit * u = ud->createUnit();
u->setKind(UnitKind_forName("litre"));
u->setScale(0);
u->setExponent(1.0);
u->setMultiplier(1.0);
setVolumeUnits("volume");
}
else
{
setVolumeUnits("litre");
}
}
else
{
setVolumeUnits("volume");
}
if (getUnitDefinition("substance") == NULL)
{
if (unitsUsed.contains("substance") || implicitSubstance)
{
UnitDefinition * ud = createUnitDefinition();
ud->setId("substance");
Unit * u = ud->createUnit();
u->setKind(UnitKind_forName("mole"));
u->setScale(0);
u->setExponent(1.0);
u->setMultiplier(1.0);
setSubstanceUnits("substance");
setExtentUnits("substance");
}
else
{
setSubstanceUnits("mole");
setExtentUnits("mole");
}
}
else
{
setSubstanceUnits("substance");
setExtentUnits("substance");
}
if (getUnitDefinition("area") == NULL)
{
UnitDefinition * ud = createUnitDefinition();
ud->setId("area");
Unit * u = ud->createUnit();
u->setKind(UnitKind_forName("metre"));
u->setScale(0);
u->setExponent(2.0);
u->setMultiplier(1.0);
setAreaUnits("area");
}
else
{
setAreaUnits("area");
}
if (getUnitDefinition("length") == NULL)
{
if (unitsUsed.contains("length") || implicitLength)
{
UnitDefinition * ud = createUnitDefinition();
ud->setId("length");
Unit * u = ud->createUnit();
u->setKind(UnitKind_forName("metre"));
u->setScale(0);
u->setExponent(1.0);
u->setMultiplier(1.0);
setLengthUnits("length");
}
else
{
setLengthUnits("metre");
}
}
else
{
setLengthUnits("length");
}
if (getUnitDefinition("time") == NULL)
{
setTimeUnits("second");
}
else
{
setTimeUnits("time");
}
}
void
Model::assignRequiredValues()
{
// when converting to L3 some attributes which have default values in L1/L2
// but are required in L3 are not present or set
unsigned int i, n;
if (getNumUnitDefinitions() > 0)
{
for (i = 0; i < getNumUnitDefinitions(); i++)
{
for (n = 0; n < getUnitDefinition(i)->getNumUnits(); n++)
{
Unit *u = getUnitDefinition(i)->getUnit(n);
if (!u->isSetExponent())
u->setExponent(1.0);
if (!u->isSetScale())
u->setScale(0);
if (!u->isSetMultiplier())
u->setMultiplier(1.0);
}
}
}
if (getNumCompartments() > 0)
{
for (i = 0; i < getNumCompartments(); i++)
{
Compartment *c = getCompartment(i);
c->setConstant(c->getConstant());
}
}
if (getNumSpecies() > 0)
{
for (i = 0; i < getNumSpecies(); i++)
{
Species * s = getSpecies(i);
s->setBoundaryCondition(s->getBoundaryCondition());
s->setHasOnlySubstanceUnits(s->getHasOnlySubstanceUnits());
s->setConstant(s->getConstant());
}
}
if (getNumParameters() > 0)
{
for (i = 0; i < getNumParameters(); i++)
{
Parameter * p = getParameter(i);
p->setConstant(p->getConstant());
}
}
if (getNumReactions() > 0)
{
for (i = 0; i < getNumReactions(); i++)
{
Reaction * r = getReaction(i);
r->setFast(r->getFast());
r->setReversible(r->getReversible());
if (r->getNumReactants() > 0)
{
for (n = 0; n < r->getNumReactants(); n++)
{
SpeciesReference *sr = r->getReactant(n);
if (sr->isSetStoichiometryMath())
{
sr->setConstant(false);
}
else
{
sr->setConstant(true);
}
}
}
if (r->getNumProducts() > 0)
{
for (n = 0; n < r->getNumProducts(); n++)
{
SpeciesReference *sr = r->getProduct(n);
if (sr->isSetStoichiometryMath())
{
sr->setConstant(false);
}
else
{
sr->setConstant(true);
}
}
}
}
}
if (getNumEvents() > 0)
{
for (i = 0; i < getNumEvents(); i++)
{
Event * e = getEvent(i);
e->setUseValuesFromTriggerTime(e->getUseValuesFromTriggerTime());
if (e->isSetTrigger())
{
Trigger *t = e->getTrigger();
t->setPersistent(true);
t->setInitialValue(true);
}
}
}
}
