bool CMathObject::createExtensiveODERateExpression(const CMetab * pSpecies,
CMathContainer & container)
{
bool success = true;
std::ostringstream Infix;
Infix.imbue(std::locale::classic());
Infix.precision(16);
/*
mRate = mpModel->getQuantity2NumberFactor() *
mpCompartment->getValue() * mpExpression->calcValue();
*/
if (!pSpecies->getExpression().empty())
{
Infix << container.getModel().getQuantity2NumberFactor();
Infix << "*";
Infix << pointerToString(container.getMathObject(pSpecies->getCompartment()->getValueReference())->getValuePointer());
Infix << "*(";
Infix << pSpecies->getExpression();
Infix << ")";
}
CExpression E("ExtensiveODERateExpression", &container);
success &= E.setInfix(Infix.str());
pdelete(mpExpression);
mpExpression = new CMathExpression(E, container, !mIsInitialValue);
compileExpression();
return success;
}
bool CMathObject::compileParticleFlux(CMathContainer & container)
{
bool success = true;
// The default value is NaN
*mpValue = InvalidValue;
// Reset the prerequisites
mPrerequisites.clear();
const CReaction * pReaction = static_cast< const CReaction * >(mpDataObject->getObjectParent());
// We need to check whether this reaction is a single compartment reaction and scale
// it if true.
// mParticleFlux = *mUnitScalingFactor * mFlux;
// mUnitScalingFactor = & pModel->getQuantity2NumberFactor();
std::ostringstream Infix;
Infix.imbue(std::locale::classic());
Infix.precision(16);
Infix << container.getModel().getQuantity2NumberFactor();
Infix << "*";
Infix << pointerToString(container.getMathObject(pReaction->getFluxReference())->getValuePointer());
CExpression E("ParticleFluxExpression", &container);
success &= E.setInfix(Infix.str());
pdelete(mpExpression);
mpExpression = new CMathExpression(E, container, !mIsInitialValue);
compileExpression();
return success;
}
// virtual
CValidatedUnit CEvaluationNodeDelay::setUnit(const CMathContainer & container,
const std::map < CEvaluationNode * , CValidatedUnit > & currentUnits,
std::map < CEvaluationNode * , CValidatedUnit > & targetUnits) const
{
CValidatedUnit Delay(CEvaluationNode::setUnit(container, currentUnits, targetUnits));
targetUnits[mpDelayValueNode] = Delay;
targetUnits[mpDelayLagNode] = CValidatedUnit(container.getModel().getTimeUnit(), false);
return Delay;
}
// virtual
CValidatedUnit CEvaluationNodeDelay::getUnit(const CMathContainer & container,
const std::vector< CValidatedUnit > & units) const
{
// The units of the delay functions are the units of the delay value which is the first child
CValidatedUnit Delay = units[0];
CValidatedUnit Lag = CValidatedUnit::merge(CValidatedUnit(container.getModel().getTimeUnit(), false), units[1]);
Delay.setConflict(Delay.conflict() || Lag.conflict());
return Delay;
}
bool TaskWidget::commonAfterRunTask()
{
if (!mpTask) return false;
if (CRootContainer::getConfiguration()->displayPopulations())
{
if (dynamic_cast<COptTask*>(mpTask) != NULL || dynamic_cast<CFitTask*>(mpTask) != NULL)
{
CopasiUI3Window* pWindow = CopasiUI3Window::getMainWindow();
CQOptPopulation* pPopWidget = pWindow->getPopulationDisplay();
COptPopulationMethod* pMethod = dynamic_cast<COptPopulationMethod*>(mpTask->getMethod());
pPopWidget->setMethod(NULL);
if (pMethod != NULL)
{
mpDataModel->removeInterface(pPopWidget);
}
}
}
if (mProgressBar != NULL)
{
mProgressBar->finish();
mProgressBar->deleteLater();
mProgressBar = NULL;
}
mpTask->setCallBack(NULL);
CCopasiMessage::clearDeque();
assert(mpDataModel != NULL);
mpDataModel->finish();
CMathContainer * pContainer = mpTask->getMathContainer();
protectedNotify(ListViews::ObjectType::STATE, ListViews::CHANGE, pContainer->getModel().getKey());
unsetCursor();
CopasiUI3Window::getMainWindow()->suspendAutoSave(false);
return loadTask();
}
bool CMathObject::createExtensiveValueExpression(const CMetab * pSpecies,
CMathContainer & container)
{
bool success = true;
// mConc * mpCompartment->getValue() * mpModel->getQuantity2NumberFactor();
CObjectInterface * pDensity = NULL;
CObjectInterface * pCompartment = NULL;
if (mIsInitialValue)
{
pDensity = pSpecies->getInitialConcentrationReference();
pCompartment = pSpecies->getCompartment()->getInitialValueReference();
}
else
{
pDensity = pSpecies->getConcentrationReference();
pCompartment = pSpecies->getCompartment()->getValueReference();
}
std::ostringstream Infix;
Infix.imbue(std::locale::classic());
Infix.precision(16);
Infix << container.getModel().getQuantity2NumberFactor();
Infix << "*";
Infix << pointerToString(container.getMathObject(pDensity)->getValuePointer());
Infix << "*";
Infix << pointerToString(container.getMathObject(pCompartment)->getValuePointer());
CExpression E("ExtensiveValueExpression", &container);
success &= E.setInfix(Infix.str());
pdelete(mpExpression);
mpExpression = new CMathExpression(E, container, !mIsInitialValue);
compileExpression();
return success;
}
bool CMathObject::createIntensiveValueExpression(const CMetab * pSpecies,
CMathContainer & container)
{
bool success = true;
// mConc = *mpValue / mpCompartment->getValue() * mpModel->getNumber2QuantityFactor();
CObjectInterface * pNumber = NULL;
CObjectInterface * pCompartment = NULL;
if (mIsInitialValue)
{
pNumber = pSpecies->getInitialValueReference();
pCompartment = pSpecies->getCompartment()->getInitialValueReference();
}
else
{
pNumber = pSpecies->getValueReference();
pCompartment = pSpecies->getCompartment()->getValueReference();
}
std::ostringstream Infix;
Infix.imbue(std::locale::classic());
Infix.precision(16);
Infix << container.getModel().getNumber2QuantityFactor();
Infix << "*<";
Infix << pNumber->getCN();
Infix << ">/<";
Infix << pCompartment->getCN();
Infix << ">";
CExpression E("IntensiveValueExpression", &container);
success &= E.setInfix(Infix.str());
mpExpression = new CMathExpression(E, container, !mIsInitialValue);
compileExpression();
return success;
}
bool CMathObject::createIntensiveRateExpression(const CMetab * pSpecies,
CMathContainer & container)
{
bool success = true;
/*
mConcRate =
(mRate * mpModel->getNumber2QuantityFactor() - mConc * mpCompartment->getRate())
/ mpCompartment->getValue();
*/
std::ostringstream Infix;
Infix.imbue(std::locale::classic());
Infix.precision(16);
Infix << "(";
Infix << pointerToString(container.getMathObject(pSpecies->getRateReference())->getValuePointer());
Infix << "*";
Infix << container.getModel().getNumber2QuantityFactor();
Infix << "-";
Infix << pointerToString(container.getMathObject(pSpecies->getCompartment()->getValueReference())->getValuePointer());
Infix << "*";
Infix << pointerToString(container.getMathObject(pSpecies->getCompartment()->getRateReference())->getValuePointer());
Infix << ")/";
Infix << pointerToString(container.getMathObject(pSpecies->getCompartment()->getValueReference())->getValuePointer());
CExpression E("IntensiveRateExpression", &container);
success &= E.setInfix(Infix.str());
pdelete(mpExpression);
mpExpression = new CMathExpression(E, container, !mIsInitialValue);
compileExpression();
return success;
}
bool CMathObject::compilePropensity(CMathContainer & container)
{
bool success = true;
// The default value is NaN
*mpValue = InvalidValue;
// Reset the prerequisites
mPrerequisites.clear();
const CReaction * pReaction = static_cast< const CReaction * >(mpDataObject->getObjectParent());
std::ostringstream Infix;
Infix.imbue(std::locale::classic());
Infix.precision(16);
// Propensity for reversible reactions must be NaN
if (pReaction->isReversible())
{
Infix << "NAN";
}
else
{
// Propensity is the same as the flux, but it must now be negative.
Infix << "max(0," << pointerToString(container.getMathObject(pReaction->getParticleFluxReference())->getValuePointer());
// Apply correction for deterministic models
if (container.getModel().getModelType() == CModel::deterministic)
{
std::ostringstream Divisor;
Divisor.imbue(std::locale::classic());
Divisor.precision(16);
const CCopasiVector<CChemEqElement> & Substrates = pReaction->getChemEq().getSubstrates();
CCopasiVector< CChemEqElement >::const_iterator itSubstrate = Substrates.begin();
CCopasiVector< CChemEqElement >::const_iterator endSubstrate = Substrates.end();
bool first = true;
for (; itSubstrate != endSubstrate; ++itSubstrate)
{
const std::string NumberPointer = pointerToString(container.getMathObject(itSubstrate->getMetabolite()->getValueReference())->getValuePointer());
C_FLOAT64 Multiplicity = itSubstrate->getMultiplicity();
Multiplicity -= 1.0; // Nothing to correct if the multiplicity is 1.
if (Multiplicity > 2.0 - 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon())
{
if (!first)
{
Divisor << "*";
}
first = false;
Divisor << NumberPointer << "^" << Multiplicity;
}
else if (Multiplicity > 1.0 - 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon())
{
if (!first)
{
Divisor << "*";
}
first = false;
Divisor << NumberPointer;
}
while (Multiplicity > 1.0 - 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon())
{
Infix << "*(" << NumberPointer << "-" << Multiplicity << ")";
Multiplicity -= 1.0;
}
}
if (Divisor.str() != "")
{
Infix << "/(" << Divisor.str() << ")";
}
}
Infix << ")";
}
CExpression E("PropensityExpression", &container);
success &= E.setInfix(Infix.str());
pdelete(mpExpression);
mpExpression = new CMathExpression(E, container, !mIsInitialValue);
compileExpression();
return success;
}
bool CMathObject::createExtensiveReactionRateExpression(const CMetab * pSpecies,
CMathContainer & container)
{
bool success = true;
std::ostringstream Infix;
Infix.imbue(std::locale::classic());
Infix.precision(16);
std::string Key = pSpecies->getKey();
bool First = true;
CCopasiVectorN< CReaction >::const_iterator it = container.getModel().getReactions().begin();
CCopasiVectorN< CReaction >::const_iterator end = container.getModel().getReactions().end();
for (; it != end; ++it)
{
const CCopasiVector< CChemEqElement > &Balances =
it->getChemEq().getBalances();
CCopasiVector< CChemEqElement >::const_iterator itChem = Balances.begin();
CCopasiVector< CChemEqElement >::const_iterator endChem = Balances.end();
for (; itChem != endChem; ++itChem)
if (itChem->getMetaboliteKey() == Key)
break;
if (itChem != endChem)
{
const C_FLOAT64 & Multiplicity = itChem->getMultiplicity();
if (First || Multiplicity < 0.0)
{
if (Multiplicity == std::numeric_limits< C_FLOAT64 >::infinity())
{
Infix << "infinity";
}
else if (Multiplicity == -std::numeric_limits< C_FLOAT64 >::infinity())
{
Infix << "-infinity";
}
else
{
Infix << Multiplicity;
}
}
else
{
if (Multiplicity == std::numeric_limits< C_FLOAT64 >::infinity())
{
Infix << "+infinity";
}
else
{
Infix << "+" << Multiplicity;
}
}
First = false;
Infix << "*";
Infix << pointerToString(container.getMathObject(it->getParticleFluxReference())->getValuePointer());
}
}
CExpression E("ExtensiveReactionExpression", &container);
success &= E.setInfix(Infix.str());
pdelete(mpExpression);
mpExpression = new CMathExpression(E, container, !mIsInitialValue);
compileExpression();
return success;
}
bool CMathObject::compileTransitionTime(CMathContainer & container)
{
bool success = true;
// The default value is NaN
*mpValue = InvalidValue;
// Reset the prerequisites
mPrerequisites.clear();
const CMetab * pSpecies = static_cast< const CMetab *>(mpDataObject->getObjectParent());
std::ostringstream Infix;
Infix.imbue(std::locale::classic());
Infix.precision(16);
switch (pSpecies->getStatus())
{
case CModelEntity::ODE:
// mTT = *mpValue / fabs(mRate);
Infix << "abs(";
Infix << pointerToString(container.getMathObject(pSpecies->getValueReference())->getValuePointer());
Infix << "/";
Infix << pointerToString(container.getMathObject(pSpecies->getRateReference())->getValuePointer());
Infix << ")";
break;
case CModelEntity::REACTIONS:
{
std::ostringstream PositiveFlux;
PositiveFlux.imbue(std::locale::classic());
PositiveFlux.precision(16);
std::ostringstream NegativeFlux;
NegativeFlux.imbue(std::locale::classic());
NegativeFlux.precision(16);
std::string Key = pSpecies->getKey();
bool First = true;
CCopasiVectorN< CReaction >::const_iterator it = container.getModel().getReactions().begin();
CCopasiVectorN< CReaction >::const_iterator end = container.getModel().getReactions().end();
for (; it != end; ++it)
{
const CCopasiVector< CChemEqElement > &Balances =
it->getChemEq().getBalances();
CCopasiVector< CChemEqElement >::const_iterator itChem = Balances.begin();
CCopasiVector< CChemEqElement >::const_iterator endChem = Balances.end();
for (; itChem != endChem; ++itChem)
if (itChem->getMetaboliteKey() == Key)
break;
if (itChem != endChem)
{
const C_FLOAT64 & Multiplicity = itChem->getMultiplicity();
if (!First)
{
PositiveFlux << "+";
NegativeFlux << "+";
}
PositiveFlux << "max(";
NegativeFlux << "min(";
if (Multiplicity == std::numeric_limits< C_FLOAT64 >::infinity())
{
PositiveFlux << "infinity";
NegativeFlux << "infinity";
}
else if (Multiplicity == -std::numeric_limits< C_FLOAT64 >::infinity())
{
PositiveFlux << "-infinity";
NegativeFlux << "-infinity";
}
else
{
PositiveFlux << Multiplicity;
NegativeFlux << Multiplicity;
}
PositiveFlux << "*";
NegativeFlux << "*";
PositiveFlux << pointerToString(container.getMathObject(it->getParticleFluxReference())->getValuePointer());
NegativeFlux << pointerToString(container.getMathObject(it->getParticleFluxReference())->getValuePointer());
PositiveFlux << ",0)";
NegativeFlux << ",0)";
First = false;
}
}
if (!First)
{
Infix << "abs(";
Infix << pointerToString(container.getMathObject(pSpecies->getValueReference())->getValuePointer());
Infix << ")/if(";
Infix << pointerToString(container.getMathObject(pSpecies->getRateReference())->getValuePointer());
Infix << "<0,-(" << NegativeFlux.str() << ")," << PositiveFlux.str() << ")";
}
}
break;
default:
break;
}
CExpression E("TransitionTimeExpression", &container);
success &= E.setInfix(Infix.str());
pdelete(mpExpression);
mpExpression = new CMathExpression(E, container, false);
compileExpression();
return success;
}
