CSteadyStateTask.cpp File Reference

#include "copasi.h"
#include "CSteadyStateTask.h"
#include "CSteadyStateProblem.h"
#include "CSteadyStateMethod.h"
#include "model/CModel.h"
#include "model/CState.h"
#include "model/CMetabNameInterface.h"
#include "report/CKeyFactory.h"
#include "report/CReport.h"
#include <sstream>

Include dependency graph for CSteadyStateTask.cpp:

Go to the source code of this file.

Macros
#define	XXXX_Reporting

Functions
std::ostream &	operator<< (std::ostream &os, const CSteadyStateTask &A)

Macro Definition Documentation

#define XXXX_Reporting

CSteadyStateTask class.

This class implements a steady state task which is comprised of a of a problem and a method. Additionally calls to the reporting methods are done when initialized.

Created for COPASI by Stefan Hoops 2002

Definition at line 38 of file CSteadyStateTask.cpp.

Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const CSteadyStateTask &	A
	)

Definition at line 439 of file CSteadyStateTask.cpp.

References CSteadyStateMethod::found, CSteadyStateMethod::foundEquilibrium, CSteadyStateMethod::foundNegative, CMetab::getConcentration(), CMetab::getConcentrationRate(), CModel::getConcentrationRateUnitsDisplayString(), CModel::getConcentrationUnitsDisplayString(), CMetabNameInterface::getDisplayName(), CReaction::getFlux(), CModel::getFrequencyUnitsDisplayString(), CEigen::getI(), CModel::getMetabolites(), CCopasiProblem::getModel(), CCopasiObject::getObjectName(), CReaction::getParticleFlux(), CModel::getQuantityRateUnitsDisplayString(), CEigen::getR(), CModelEntity::getRate(), CModel::getReactions(), CSteadyStateTask::getResult(), CSteadyStateTask::getState(), CModel::getTimeUnitsDisplayString(), CMetab::getTransitionTime(), CModelEntity::getValue(), CSteadyStateTask::mEigenValues, CSteadyStateTask::mEigenValuesX, CSteadyStateTask::mpJacobianAnn, CSteadyStateTask::mpJacobianXAnn, CCopasiTask::mpProblem, CSteadyStateMethod::notFound, CModel::setState(), CVectorCore< CType >::size(), CCopasiVector< T >::size(), CModel::updateNonSimulatedValues(), and CModel::updateSimulatedValues().

{
  switch (A.getResult())
    {
      case CSteadyStateMethod::found:
        os << "A steady state with given resolution was found." << std::endl;
        break;

      case CSteadyStateMethod::notFound:
        os << "No steady state with given resolution was found!" << std::endl;
        os << "(below are the last unsuccessful trial values)" << std::endl;
        break;

      case CSteadyStateMethod::foundEquilibrium:
        os << "An equilibrium steady state (zero fluxes) was found." << std::endl;
        break;

      case CSteadyStateMethod::foundNegative:
        os << "An invalid steady state (negative concentrations) was found." << std::endl;
    }

  os << std::endl;

  // Update all necessary values.
  CState * pState = const_cast<CState *>(A.getState());

  if (!pState) return os;

  CModel * pModel = A.mpProblem->getModel();

  if (!pModel) return os;

  pModel->setState(*pState);
  pModel->updateSimulatedValues(true);
  pModel->updateNonSimulatedValues();

  // Metabolite Info: Name, Concentration, Concentration Rate, Particle Number, Particle Rate, Transition Time
  const CCopasiVector<CMetab> & Metabolites = pModel->getMetabolites();
  const CMetab * pMetab;

  size_t i, imax = Metabolites.size();

  os << "Species" << "\t";
  os << "Concentration";

  std::string Units = pModel->getConcentrationUnitsDisplayString();

  if (Units != "")
    os << " (" << Units << ")";

  os << "\t";

  os << "Concentration Rate";
  Units = pModel->getConcentrationRateUnitsDisplayString();

  if (Units != "")
    os << " (" << Units << ")";

  os << "\t";

  os << "Particle Number" << "\t";

  os << "Particle Number Rate";
  Units = pModel->getFrequencyUnitsDisplayString();

  if (Units != "")
    os << " (" << Units << ")";

  os << "\t";

  os << "Transition Time";
  Units = pModel->getTimeUnitsDisplayString();

  if (Units != "")
    os << " (" << Units << ")";

  os << std::endl;

  for (i = 0; i < imax; ++i)
    {
      pMetab = Metabolites[i];
      os << CMetabNameInterface::getDisplayName(pModel, *pMetab, false) << "\t";
      os << pMetab->getConcentration() << "\t";
      os << pMetab->getConcentrationRate() << "\t";
      os << pMetab->getValue() << "\t";
      os << pMetab->getRate() << "\t";
      os << pMetab->getTransitionTime() << std::endl;
    }

  os << std::endl;

  // Reaction Info: Name, Flux, Particle Flux
  const CCopasiVector<CReaction>& Reactions = pModel->getReactions();
  const CReaction * pReaction;

  imax = Reactions.size();

  os << "Reaction" << "\t";

  os << "Flux";
  Units = pModel->getQuantityRateUnitsDisplayString();

  if (Units != "")
    os << " (" << Units << ")";

  os << "\t";

  os << "Particle Flux";
  Units = pModel->getFrequencyUnitsDisplayString();;

  if (Units != "")
    os << " (" << Units << ")";

  os << std::endl;

  for (i = 0; i < imax; ++i)
    {
      pReaction = Reactions[i];
      os << pReaction->getObjectName() << "\t";
      os << pReaction->getFlux() << "\t";
      os << pReaction->getParticleFlux() << std::endl;
    }

  os << std::endl;

  if (static_cast<CSteadyStateProblem *>(A.mpProblem)->isJacobianRequested())
    {
      os << *A.mpJacobianAnn << std::endl;

      if (static_cast<CSteadyStateProblem *>(A.mpProblem)->isStabilityAnalysisRequested())
        {
          os << "Eigenvalues\treal\timaginary" << std::endl;
          imax = A.mEigenValues.getR().size();

          for (i = 0; i < imax; i++)
            os << "\t" << A.mEigenValues.getR()[i] << "\t" << A.mEigenValues.getI()[i] << std::endl;

          os << std::endl;
        }

      os << *A.mpJacobianXAnn << std::endl;

      if (static_cast<CSteadyStateProblem *>(A.mpProblem)->isStabilityAnalysisRequested())
        {
          os << "Eigenvalues\treal\timaginary" << std::endl;
          imax = A.mEigenValuesX.getR().size();

          for (i = 0; i < imax; i++)
            os << "\t" << A.mEigenValuesX.getR()[i] << "\t" << A.mEigenValuesX.getI()[i] << std::endl;

          os << std::endl;
        }
    }

  if (static_cast<CSteadyStateProblem *>(A.mpProblem)->isStabilityAnalysisRequested())
    {
      os << "Stability Analysis of the Reduced System" << std::endl;
      os << A.mEigenValuesX << std::endl;
    }

  return os;
}