SEDMLImporter.cpp File Reference

#include <iostream>
#include <vector>
#include <string>
#include <sstream>
#include <map>
#include <limits>
#include <cmath>
#include <algorithm>
#include <sedml/SedTypes.h>
#include <sbml/math/FormulaFormatter.h>
#include "copasi.h"
#include "report/CKeyFactory.h"
#include "model/CModel.h"
#include "model/CCompartment.h"
#include "model/CMetab.h"
#include "model/CReaction.h"
#include "model/CModelValue.h"
#include "model/CEvent.h"
#include "function/CNodeK.h"
#include "function/CFunctionDB.h"
#include "function/CEvaluationTree.h"
#include "function/CExpression.h"
#include "function/CFunctionParameters.h"
#include "report/CCopasiObjectReference.h"
#include "utilities/CCopasiTree.h"
#include "utilities/CNodeIterator.h"
#include "CopasiDataModel/CCopasiDataModel.h"
#include "report/CCopasiRootContainer.h"
#include "MIRIAM/CRDFGraphConverter.h"
#include "compareExpressions/CEvaluationNodeNormalizer.h"
#include "commandline/CLocaleString.h"
#include "commandline/COptions.h"
#include "utilities/CProcessReport.h"
#include "copasi/commandline/CConfigurationFile.h"
#include "utilities/CCopasiMessage.h"
#include "trajectory/CTrajectoryTask.h"
#include "trajectory/CTrajectoryProblem.h"
#include "sbml/SBMLImporter.h"
#include "utilities/CDirEntry.h"
#include "utilities/CCopasiException.h"
#include "utilities/CCopasiTask.h"
#include "plot/COutputDefinitionVector.h"
#include "plot/CPlotSpecification.h"
#include "report/CReportDefinitionVector.h"
#include <steadystate/CSteadyStateTask.h>
#include <scan/CScanTask.h>
#include "SEDMLImporter.h"
#include "SEDMLUtils.h"

Include dependency graph for SEDMLImporter.cpp:

Go to the source code of this file.

Functions
bool	applyAttributeChange (CModel *pCopasiModel, CModelParameterSet &set, const std::string &target, const std::string &newValue)
bool	applyValueToModelParameter (CModelParameter *modelParameter, CCopasiObject *obj, double newValue)
bool	applyValueToParameterSet (CModelParameterSet &set, CCopasiObject *obj, double newValue)
bool	isScan (const SedTask *task)
bool	isScan (const SedRepeatedTask *task)
bool	isTC (const SedTask *task)

Function Documentation

bool applyAttributeChange	(	CModel *	pCopasiModel,
		CModelParameterSet &	set,
		const std::string &	target,
		const std::string &	newValue
	)

Definition at line 787 of file SEDMLImporter.cpp.

References applyValueToParameterSet(), CCopasiObject::getObjectParent(), and SEDMLUtils::resolveXPath().

Referenced by SEDMLImporter::importFirstSBMLModel().

{
  CCopasiObject *obj = const_cast<CCopasiObject*>(SEDMLUtils::resolveXPath(pCopasiModel, target, true));

  if (obj == NULL)
    return false;

  // convert the string to double
  std::stringstream str;
  str << newValue;
  double result;
  str >> result;

  // set the value
  applyValueToParameterSet(set, obj->getObjectParent(), result);
  return true;
}

bool applyValueToModelParameter	(	CModelParameter *	modelParameter,
		CCopasiObject *	obj,
		double	newValue
	)

Definition at line 746 of file SEDMLImporter.cpp.

References CModelParameter::Concentration, CModelParameter::getChild(), CModelParameter::getCN(), CCopasiObject::getCN(), CModelParameter::getNumChildren(), and CModelParameter::setValue().

Referenced by applyValueToParameterSet().

{
  if (modelParameter == NULL || obj == NULL) return false;

  size_t numChilren = modelParameter->getNumChildren();

  const CCopasiObjectName& cn = modelParameter->getCN();
  const CCopasiObjectName& targetCN = obj->getCN();

  if (cn == targetCN)
    {
      modelParameter->setValue(newValue, CModelParameter::Concentration);
      return true;
    }

  for (unsigned int i = 0; i < numChilren; ++i)
    {
      CModelParameter* current = const_cast<CModelParameter* >(modelParameter->getChild(i));

      if (applyValueToModelParameter(current, obj, newValue))
        return true;
    }

  return false;
}

bool applyValueToParameterSet	(	CModelParameterSet &	set,
		CCopasiObject *	obj,
		double	newValue
	)

Definition at line 772 of file SEDMLImporter.cpp.

References applyValueToModelParameter(), CModelParameterGroup::begin(), and CModelParameterGroup::end().

Referenced by applyAttributeChange().

{
  CModelParameterGroup::iterator it = set.begin();

  while (it != set.end())
    {
      if (applyValueToModelParameter(*it, obj, newValue))
        return true;

      ++it;
    }

  return false;
}

bool isScan

(

const SedTask *

task

)

Definition at line 184 of file SEDMLImporter.cpp.

Referenced by isScan(), and SEDMLImporter::readListOfPlotsFromSedMLOutput().

{

  if (task == NULL || task->getSedDocument() == NULL) return false;

  const SedDocument* doc = task->getSedDocument();

  if (task->isSetSimulationReference())
    {
      const SedSimulation* sim = doc->getSimulation(task->getSimulationReference());

      if (sim != NULL && (
            sim->getTypeCode() == SEDML_SIMULATION_STEADYSTATE ||
            sim->getTypeCode() == SEDML_SIMULATION_ONESTEP ||
            sim->getTypeCode() == SEDML_SIMULATION_UNIFORMTIMECOURSE))
        return true;
    }

  return false;
}

bool isScan

(

const SedRepeatedTask *

task

)

Definition at line 205 of file SEDMLImporter.cpp.

References isScan().

{
  if (task == NULL || task->getSedDocument() == NULL) return false;

  const SedDocument* doc = task->getSedDocument();

  if (task->isSetSimulationReference())
    {
      const SedSimulation* sim = doc->getSimulation(task->getSimulationReference());

      if (sim != NULL && (
            sim->getTypeCode() == SEDML_SIMULATION_STEADYSTATE ||
            sim->getTypeCode() == SEDML_SIMULATION_ONESTEP ||
            sim->getTypeCode() == SEDML_SIMULATION_UNIFORMTIMECOURSE))
        return true;
    }

  for (size_t i = 0; i < task->getNumSubTasks(); ++i)
    {
      const SedSubTask* subTask = task->getSubTask(i);
      const SedTask* t = doc->getTask(subTask->getTask());

      if (isScan(t)) return true;
    }

  return false;
}

bool isTC

(

const SedTask *

task

)

Definition at line 166 of file SEDMLImporter.cpp.

Referenced by SEDMLImporter::readListOfPlotsFromSedMLOutput().

{
  if (task == NULL || task->getSedDocument() == NULL) return false;

  const SedDocument* doc = task->getSedDocument();

  if (task->isSetSimulationReference())
    {
      const SedSimulation* sim = doc->getSimulation(task->getSimulationReference());

      if (sim != NULL && (
            sim->getTypeCode() == SEDML_SIMULATION_UNIFORMTIMECOURSE))
        return true;
    }

  return false;
}