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COPASI / data /mca_test_wrapper /copasi_wrapper.cpp
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// Copyright (C) 2019 - 2020 by Pedro Mendes, Rector and Visitors of the
// University of Virginia, University of Heidelberg, and University
// of Connecticut School of Medicine.
// All rights reserved.
// Copyright (C) 2017 - 2018 by Pedro Mendes, Virginia Tech Intellectual
// Properties, Inc., University of Heidelberg, and University of
// of Connecticut School of Medicine.
// All rights reserved.
// Copyright (C) 2015 - 2016 by Pedro Mendes, Virginia Tech Intellectual
// Properties, Inc., University of Heidelberg, and The University
// of Manchester.
// All rights reserved.
#define COPASI_MAIN
#include <iostream>
#include <fstream>
#include <stdlib.h>
#include "copasi/copasi.h"
#include "copasi/CopasiDataModel/CDataModel.h"
#include "copasi/core/CRootContainer.h"
#include "copasi/model/CMetab.h"
#include "copasi/core/CRegisteredCommonName.h"
#include "copasi/core/CDataVector.h"
#include "copasi/model/CModel.h"
#include "copasi/utilities/CCopasiException.h"
#include "copasi/commandline/COptionParser.h"
#include "copasi/commandline/COptions.h"
#include "copasi/trajectory/CTrajectoryTask.h"
#include "copasi/trajectory/CTrajectoryMethod.h"
#include "copasi/trajectory/CTrajectoryProblem.h"
#include "copasi/steadystate/CSteadyStateTask.h"
#include "copasi/steadystate/CSteadyStateMethod.h"
#include "copasi/steadystate/CSteadyStateProblem.h"
#include "copasi/steadystate/CMCATask.h"
#include "copasi/steadystate/CMCAMethod.h"
#include "copasi/steadystate/CMCAProblem.h"
#include "copasi/report/CReportDefinitionVector.h"
#include "copasi/report/CReportDefinition.h"
int main(int argc, char *argv[])
{
// Parse the commandline options
// 1. argument is the SBML filename
// 2. argument is the filename where the results are to be written
try
{
// Create the root container.
CRootContainer::init(0, NULL, false);
}
catch (copasi::autoexcept &e)
{}
catch (copasi::option_error &e)
{}
if (argc < 3)
{
std::cout << "Usage: mca_test_wrapper SBMLFILENAME OUTPUTFILE_PREFIX" << std::endl;
exit(1);
}
char* pSBMLFilename = argv[1];
const char* pOutputFilename = argv[2];
std::string CWD = COptions::getPWD();
try
{
// Create the global data model.
CDataModel* pDataModel = CRootContainer::addDatamodel();
// Import the SBML File
pDataModel->importSBML(pSBMLFilename);
// create a report with the correct filename and all the species against
// time.
CReportDefinitionVector* pReports = pDataModel->getReportDefinitionList();
CReportDefinition* pSteadyStateReport = &(*pReports)["Steady-State"];
CReportDefinition* pReport = &(*pReports)["Metabolic Control Analysis"];
//**** create a task ****
CMCATask* pMCATask = new CMCATask(pDataModel);
//pMCATask->setMethodType(CCopasiMethod::Newton);
pMCATask->getProblem()->setModel(pDataModel->getModel());
pMCATask->setScheduled(true);
pMCATask->getReport().setReportDefinition(pSteadyStateReport);
pMCATask->getReport().setTarget(pOutputFilename + std::string(".res1"));
pMCATask->getReport().setAppend(false);
//**** specify problem ****
CMCAProblem* pProblem = dynamic_cast<CMCAProblem*>(pMCATask->getProblem());
//pProblem->setStepNumber((const unsigned C_INT32)stepNumber);
//pDataModel->getModel()->setInitialTime((const C_FLOAT64)startTime);
//**** method settings ****
CMCAMethod* pMethod = dynamic_cast<CMCAMethod*>(pMCATask->getMethod());
pMethod->getParameter("Maximum duration for forward integration")->setValue(1.0e5);
pMethod->getParameter("Use Back Integration")->setValue(false);
pMethod->getParameter("Maximum duration for backward integration")->setValue(1.0e3);
//pMethod->getParameter("Absolute Tolerance")->setValue(1.0e-12);
//***** run the task *********
CDataVectorN< CCopasiTask > & TaskList = * pDataModel->getTaskList();
TaskList.remove("Metabolic Control Analysis");
TaskList.add(pMCATask, true);
// save the file for control purposes
std::string saveFilename = pOutputFilename + std::string("1.cps");
pDataModel->saveModel(saveFilename, NULL, true);
pMCATask->getReport().setReportDefinition(pReport);
pMCATask->getReport().setTarget(pOutputFilename + std::string(".res"));
pMCATask->getReport().setAppend(false);
// save the file for control purposes
saveFilename = pOutputFilename + std::string(".cps");
pDataModel->saveModel(saveFilename, NULL, true);
// Run the task
// create another report that will write to the directory where the input file came from
// this can be used for debugging
// create a trajectory task
//pSSTask->getReport().setTarget(pOutputFilename);
pMCATask->initialize(CCopasiTask::OUTPUT_SE, pDataModel, NULL);
pMCATask->process(true);
pDataModel->finish();
pMCATask->restore();
//status output
//CSteadyStateMethod::ReturnCode rc = pSSTask->getResult();
std::string resultCode;
/*
switch (rc)
{
case CSteadyStateMethod::notFound: resultCode = "###0 No steady state found."; break;
case CSteadyStateMethod::found: resultCode = "###1 Steady state found."; break;
case CSteadyStateMethod::foundEquilibrium: resultCode = "###2 Equilibrium found."; break;
case CSteadyStateMethod::foundNegative: resultCode = "###3 Negative steady state found."; break;
}
std::cout << resultCode << std::endl;
*/
std::string resultFileName = pOutputFilename + std::string(".txt");
std::ofstream resultFile(resultFileName.c_str());
resultFile << resultCode << std::endl;
resultFile.close();
//write method log to separate file
//std::string methodlog = dynamic_cast<CSteadyStateMethod*>(pSSTask->getMethod())->getMethodLog();
//std::string logname = pOutputFilename + std::string(".log");
//std::ofstream ofs(logname.c_str());
//ofs << methodlog;
//ofs.close();
}
catch (CCopasiException Exception)
{
std::cerr << Exception.getMessage().getText() << std::endl;
}
std::string Text = "";
while (CCopasiMessage::size() > 0)
{
const CCopasiMessage& message = CCopasiMessage::getLastMessage();
if (message.getType() < CCopasiMessage::RAW_FILTERED)
{
if (Text != "") Text += "\n";
Text += message.getText();
}
}
if (Text != "") std::cerr << Text << std::endl;
//finish
CRootContainer::destroy();
return 0;
}