// virtual
bool COPASIHandler::processEnd(const XML_Char * pszName)
{
bool finished = false;
switch (mCurrentElement.first)
{
case COPASI:
{
// We need to handle the unmapped parameters of type key.
std::vector< std::string >::iterator it = mpData->UnmappedKeyParameters.begin();
std::vector< std::string >::iterator end = mpData->UnmappedKeyParameters.end();
for (; it != end; ++it)
{
CCopasiParameter * pParameter =
dynamic_cast< CCopasiParameter * >(CCopasiRootContainer::getKeyFactory()->get(*it));
if (pParameter != NULL &&
pParameter->getType() == CCopasiParameter::KEY)
{
CCopasiObject * pObject =
mpData->mKeyMap.get(pParameter->getValue< std::string >());
if (pObject != NULL)
pParameter->setValue(pObject->getKey());
else
pParameter->setValue(std::string(""));
}
}
// We need to remove the no longer needed expression "Objective Function" from the function list.
if (mpData->pFunctionList != NULL &&
mpData->pFunctionList->getIndex("Objective Function") != C_INVALID_INDEX)
{
mpData->pFunctionList->remove("Objective Function");
}
}
finished = true;
break;
case ParameterGroup:
finished = true;
break;
case ListOfFunctions:
case Model:
case ListOfTasks:
case ListOfReports:
case ListOfPlots:
case ListOfLayouts:
case SBMLReference:
case ListOfUnitDefinitions:
break;
case GUI:
if (mpData->pGUI == NULL)
{
CCopasiMessage::getLastMessage();
}
break;
default:
CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 2,
mpParser->getCurrentLineNumber(), mpParser->getCurrentColumnNumber(), pszName);
break;
}
return finished;
}
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();
}
// virtual
bool CModelParameter::updateModel()
{
bool success = true;
if (mpObject != NULL)
{
switch (mType)
{
case Model:
{
CModel * pModel = static_cast< CModel * >(mpObject);
if (!pModel->isAutonomous())
{
pModel->setInitialValue(mValue);
}
else
{
pModel->setInitialValue(0.0);
}
}
break;
case Compartment:
case Species:
case ModelValue:
{
CModelEntity * pEntity = static_cast< CModelEntity * >(mpObject);
if (pEntity->getStatus() != CModelEntity::ASSIGNMENT)
{
pEntity->setInitialValue(mValue);
if (mIsInitialExpressionValid)
{
pEntity->setInitialExpression(getInitialExpression());
}
}
}
break;
case ReactionParameter:
{
CCopasiParameter * pParameter = static_cast< CCopasiParameter * >(mpObject);
CReaction * pReaction = static_cast< CReaction * >(mpObject->getObjectAncestor("Reaction"));
if (mIsInitialExpressionValid &&
getInitialExpression() != "")
{
CModel * pModel = mpParent->getModel();
assert(pModel != NULL);
std::vector< CCopasiContainer * > ListOfContainer;
ListOfContainer.push_back(pModel);
CCopasiObjectName CN = static_cast< CEvaluationNodeObject * >(mpInitialExpression->getRoot())->getObjectCN();
CCopasiObject * pObject = pModel->getObjectDataModel()->ObjectFromName(ListOfContainer, CN);
assert(pObject != NULL);
// We assign the object value
pParameter->setValue(* (C_FLOAT64 *) pObject->getValuePointer());
// We map the parameter to the global quantity
pReaction->setParameterMapping(pParameter->getObjectName(), pObject->getObjectParent()->getKey());
}
else
{
pParameter->setValue(mValue);
// We need to remove the existing mapping to a global quantity1.
pReaction->setParameterMapping(pParameter->getObjectName(), pParameter->getKey());
}
}
break;
default:
success = false;
break;
}
}
return success;
}
void CQPreferenceDialog::slotBtnOk()
{
// We need to commit the changes
unsigned C_INT32 newMaxFiles = 0;
CConfigurationFile * configFile = CCopasiRootContainer::getConfiguration();
QList< QTreeWidgetItem *> Items = mpTreeWidget->findItems("Max Last Visited Files", 0, 0);
CCopasiParameter * pParameter = configFile->getRecentFiles().getParameter("MaxFiles");
if (Items.size() > 0 &&
pParameter != NULL)
{
newMaxFiles = Items[0]->text(COL_VALUE).toUInt();
unsigned C_INT32 maxFiles = *pParameter->getValue().pUINT;
if (newMaxFiles > 0 && newMaxFiles <= 20)
pParameter->setValue(newMaxFiles);
else
{
CQMessageBox::critical(this, "Incorrect Setting",
"Max Last Visited Files should be a number between 1 and 20.",
QMessageBox::Ok, QMessageBox::Ok);
Items[0]->setText(COL_VALUE, QString::number(maxFiles));
return;
}
}
Items = mpTreeWidget->findItems("Max Last Visited SBML Files", 0, 0);
pParameter = configFile->getRecentSBMLFiles().getParameter("MaxFiles");
if (Items.size() > 0 &&
pParameter != NULL)
{
newMaxFiles = Items[0]->text(COL_VALUE).toUInt();
unsigned C_INT32 maxFiles = *pParameter->getValue().pUINT;
if (newMaxFiles > 0 && newMaxFiles <= 20)
pParameter->setValue(newMaxFiles);
else
{
CQMessageBox::critical(this, "Incorrect Setting", "Max Last Visited SBML Files should be a number between 1 and 20.",
QMessageBox::Ok, QMessageBox::Ok);
Items[0]->setText(COL_VALUE, QString::number(maxFiles));
return;
}
}
Items = mpTreeWidget->findItems("Application for opening URLs", 0, 0);
pParameter = configFile->getParameter("Application for opening URLs");
if (Items.size() > 0 &&
pParameter != NULL)
{
if (Items[0]->text(COL_VALUE) != FROM_UTF8(*pParameter->getValue().pSTRING))
pParameter->setValue(std::string(TO_UTF8(Items[0]->text(COL_VALUE))));
}
Items = mpTreeWidget->findItems("Validate Units", 0, 0);
pParameter = configFile->getParameter("Validate Units");
if (Items.size() > 0 &&
pParameter != NULL)
{
pParameter->setValue(Items[0]->text(COL_VALUE).toUpper() == "YES");
}
Items = mpTreeWidget->findItems("Use OpenGL", 0, 0);
pParameter = configFile->getParameter("Use OpenGL");
if (Items.size() > 0 &&
pParameter != NULL)
{
pParameter->setValue(Items[0]->text(COL_VALUE).toUpper() == "YES");
}
Items = mpTreeWidget->findItems("Use Advanced Editing", 0, 0);
pParameter = configFile->getParameter("Use Advanced Editing");
if (Items.size() > 0 &&
pParameter != NULL)
{
pParameter->setValue(Items[0]->text(COL_VALUE).toUpper() == "YES");
}
done(1);
}
