int main(int argc, char** argv)
{
// initialize the backend library
CCopasiRootContainer::init(argc, argv);
assert(CCopasiRootContainer::getRoot() != NULL);
// create a new datamodel
CCopasiDataModel* pDataModel = CCopasiRootContainer::addDatamodel();
assert(CCopasiRootContainer::getDatamodelList()->size() == 1);
// the only argument to the main routine should be the name of an SBML file
if (argc == 2)
{
std::string filename = argv[1];
try
{
// load the model without progress report
pDataModel->importSBML(filename, NULL);
}
catch (...)
{
std::cerr << "Error while importing the model from file named \"" << filename << "\"." << std::endl;
CCopasiRootContainer::destroy();
return 1;
}
CModel* pModel = pDataModel->getModel();
assert(pModel != NULL);
// create a report with the correct filename and all the species against
// time.
CReportDefinitionVector* pReports = pDataModel->getReportDefinitionList();
// create a new report definition object
CReportDefinition* pReport = pReports->createReportDefinition("Report", "Output for timecourse");
// set the task type for the report definition to timecourse
pReport->setTaskType(CTaskEnum::timeCourse);
// we don't want a table
pReport->setIsTable(false);
// the entries in the output should be seperated by a ", "
pReport->setSeparator(", ");
// we need a handle to the header and the body
// the header will display the ids of the metabolites and "time" for
// the first column
// the body will contain the actual timecourse data
std::vector<CRegisteredObjectName>* pHeader = pReport->getHeaderAddr();
std::vector<CRegisteredObjectName>* pBody = pReport->getBodyAddr();
pBody->push_back(CCopasiObjectName(pDataModel->getModel()->getCN() + ",Reference=Time"));
pBody->push_back(CRegisteredObjectName(pReport->getSeparator().getCN()));
pHeader->push_back(CCopasiStaticString("time").getCN());
pHeader->push_back(pReport->getSeparator().getCN());
size_t i, iMax = pModel->getMetabolites().size();
for (i = 0; i < iMax; ++i)
{
CMetab* pMetab = &pModel->getMetabolites()[i];
assert(pMetab != NULL);
// we don't want output for FIXED metabolites right now
if (pMetab->getStatus() != CModelEntity::FIXED)
{
// we want the concentration oin the output
// alternatively, we could use "Reference=Amount" to get the
// particle number
pBody->push_back(pMetab->getObject(CCopasiObjectName("Reference=Concentration"))->getCN());
// after each entry, we need a seperator
pBody->push_back(pReport->getSeparator().getCN());
// add the corresponding id to the header
pHeader->push_back(CCopasiStaticString(pMetab->getSBMLId()).getCN());
// and a seperator
pHeader->push_back(pReport->getSeparator().getCN());
}
}
if (iMax > 0)
{
// delete the last separator
// since we don't need one after the last element on each line
if ((*pBody->rbegin()) == pReport->getSeparator().getCN())
{
pBody->erase(--pBody->end());
}
if ((*pHeader->rbegin()) == pReport->getSeparator().getCN())
{
pHeader->erase(--pHeader->end());
}
}
// get the task list
CCopasiVectorN< CCopasiTask > & TaskList = * pDataModel->getTaskList();
// get the trajectory task object
CTrajectoryTask* pTrajectoryTask = dynamic_cast<CTrajectoryTask*>(&TaskList["Time-Course"]);
// if there isn't one
if (pTrajectoryTask == NULL)
{
// remove any existing trajectory task just to be sure since in
// theory only the cast might have failed above
TaskList.remove("Time-Course");
// create a new one
pTrajectoryTask = new CTrajectoryTask(& TaskList);
// add the new time course task to the task list
TaskList.add(pTrajectoryTask, true);
}
// run a deterministic time course
pTrajectoryTask->setMethodType(CTaskEnum::deterministic);
// Activate the task so that it will be run when the model is saved
// and passed to CopasiSE
pTrajectoryTask->setScheduled(true);
// set the report for the task
pTrajectoryTask->getReport().setReportDefinition(pReport);
// set the output filename
pTrajectoryTask->getReport().setTarget("example3.txt");
// don't append output if the file exists, but overwrite the file
pTrajectoryTask->getReport().setAppend(false);
// get the problem for the task to set some parameters
CTrajectoryProblem* pProblem = dynamic_cast<CTrajectoryProblem*>(pTrajectoryTask->getProblem());
// simulate 100 steps
pProblem->setStepNumber(100);
// start at time 0
pDataModel->getModel()->setInitialTime(0.0);
// simulate a duration of 10 time units
pProblem->setDuration(10);
// tell the problem to actually generate time series data
pProblem->setTimeSeriesRequested(true);
// set some parameters for the LSODA method through the method
CTrajectoryMethod* pMethod = dynamic_cast<CTrajectoryMethod*>(pTrajectoryTask->getMethod());
CCopasiParameter* pParameter = pMethod->getParameter("Absolute Tolerance");
assert(pParameter != NULL);
pParameter->setValue(1.0e-12);
try
{
// initialize the trajectory task
// we want complete output (HEADER, BODY and FOOTER)
//
// The output has to be set to OUTPUT_UI, otherwise the time series will not be
// kept in memory and some of the assert further down will fail
// If it is OK that the output is only written to file, the output type can
// be set to OUTPUT_SE
pTrajectoryTask->initialize(CCopasiTask::OUTPUT_UI, pDataModel, NULL);
// now we run the actual trajectory
pTrajectoryTask->process(true);
}
catch (...)
{
std::cerr << "Error. Running the time course simulation failed." << std::endl;
// check if there are additional error messages
if (CCopasiMessage::size() > 0)
{
// print the messages in chronological order
std::cerr << CCopasiMessage::getAllMessageText(true);
}
CCopasiRootContainer::destroy();
return 1;
}
// restore the state of the trajectory
pTrajectoryTask->restore();
// look at the timeseries
const CTimeSeries* pTimeSeries = &pTrajectoryTask->getTimeSeries();
// we simulated 100 steps, including the initial state, this should be
// 101 step in the timeseries
assert(pTimeSeries->getRecordedSteps() == 101);
std::cout << "The time series consists of " << pTimeSeries->getRecordedSteps() << "." << std::endl;
std::cout << "Each step contains " << pTimeSeries->getNumVariables() << " variables." << std::endl;
std::cout << "The final state is: " << std::endl;
iMax = pTimeSeries->getNumVariables();
size_t lastIndex = pTimeSeries->getRecordedSteps() - 1;
for (i = 0; i < iMax; ++i)
{
// here we get the particle number (at least for the species)
// the unit of the other variables may not be particle numbers
// the concentration data can be acquired with getConcentrationData
std::cout << pTimeSeries->getTitle(i) << ": " << pTimeSeries->getData(lastIndex, i) << std::endl;
}
}
else
{
std::cerr << "Usage: example3 SBMLFILE" << std::endl;
CCopasiRootContainer::destroy();
return 1;
}
// clean up the library
CCopasiRootContainer::destroy();
}
