COPASI API
4.16.103
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#include <CSEDMLExporter.h>
Public Member Functions | |
void | createDataGenerators (CCopasiDataModel &dataModel, std::string &taskId, CCopasiTask *task=NULL) |
void | createModels (CCopasiDataModel &dataModel, std::string &modelRef) |
std::string | createScanTask (CCopasiDataModel &dataModel, const std::string &modelId) |
void | createSEDMLDocument (CCopasiDataModel &dataModel, std::string modelRef) |
std::string | createSteadyStateTask (CCopasiDataModel &dataModel, const std::string &modelId) |
void | createTasks (CCopasiDataModel &dataModel, std::string &modelRef) |
std::string | createTimeCourseTask (CCopasiDataModel &dataModel, const std::string &modelId) |
CSEDMLExporter () | |
bool | exportModelAndTasks (CCopasiDataModel &dataModel, const std::string &SEDMLFilename, const std::string &SBMLFilename, unsigned int sedmlLevel=1, unsigned int sedmlVersion=1, bool overwrite=false) |
const std::string | exportModelAndTasksToString (CCopasiDataModel &dataModel, std::string &sbmldocument, unsigned int sedmlLevel, unsigned int sedmlVersion) |
SedDocument * | getSEDMLDocument () |
~CSEDMLExporter () | |
Protected Attributes | |
SedDocument * | mpSEDMLDocument |
SedUniformTimeCourse * | mpTimecourse |
SedTask * | mpTimecourseTask |
unsigned int | mSEDMLLevel |
unsigned int | mSEDMLVersion |
Definition at line 37 of file CSEDMLExporter.h.
CSEDMLExporter::CSEDMLExporter | ( | ) |
Definition at line 649 of file CSEDMLExporter.cpp.
CSEDMLExporter::~CSEDMLExporter | ( | ) |
Definition at line 657 of file CSEDMLExporter.cpp.
void CSEDMLExporter::createDataGenerators | ( | CCopasiDataModel & | dataModel, |
std::string & | taskId, | ||
CCopasiTask * | task = NULL |
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Creates the data generators for SEDML.
Definition at line 431 of file CSEDMLExporter.cpp.
References createDataGenerator(), CCopasiMessage::ERROR, CReportDefinition::getBodyAddr(), CPlotItem::getChannels(), CCopasiObject::getCN(), CCopasiDataModel::getDataObject(), CReportDefinition::getHeaderAddr(), CPlotSpecification::getItems(), CCopasiDataModel::getModel(), SEDMLUtils::getNextId(), CCopasiContainer::getObject(), CCopasiObject::getObjectDisplayName(), CCopasiObject::getObjectName(), CCopasiDataModel::getPlotDefinitionList(), CCopasiTask::getReport(), CReport::getReportDefinition(), CReportDefinition::getSeparator(), CReportDefinition::getTableAddr(), CReport::getTarget(), SEDMLUtils::getXPathAndName(), CPlotSpecification::isLogX(), CPlotSpecification::isLogY(), CReportDefinition::isTable(), mpSEDMLDocument, SEDMLUtils::removeCharactersFromString(), SEDML_TIME_URN, CCopasiVector< T >::size(), and CCopasiMessage::WARNING.
Referenced by createTasks().
void CSEDMLExporter::createModels | ( | CCopasiDataModel & | dataModel, |
std::string & | modelRef | ||
) |
Creates the models for SEDML.
Definition at line 362 of file CSEDMLExporter.cpp.
References mpSEDMLDocument.
Referenced by createSEDMLDocument().
std::string CSEDMLExporter::createScanTask | ( | CCopasiDataModel & | dataModel, |
const std::string & | modelId | ||
) |
Creates a scan task for the given model id if the dataModel contains a number of scan items and returns its id.
Creates the simulations for SEDML.
Definition at line 181 of file CSEDMLExporter.cpp.
References createSteadyStateTask(), CScanProblem::getContinueFromCurrentState(), SEDMLUtils::getNextId(), CScanProblem::getNumberOfScanItems(), CCopasiContainer::getObject(), CCopasiParameterGroup::getParameter(), CCopasiTask::getProblem(), CScanProblem::getScanItem(), CScanProblem::getSubtask(), CCopasiDataModel::getTaskList(), CCopasiParameter::getValue(), SEDMLUtils::getXPathForObject(), max, min, mpSEDMLDocument, mpTimecourseTask, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pCN, CCopasiParameter::Value::pDOUBLE, pTask, CCopasiParameter::Value::pUINT, CScanProblem::SCAN_LINEAR, CScanProblem::SCAN_RANDOM, CScanProblem::SCAN_REPEAT, SEDML_TIME_URN, CCopasiTask::steadyState, CCopasiTask::timeCourse, and CCopasiMessage::WARNING.
Referenced by createTasks().
void CSEDMLExporter::createSEDMLDocument | ( | CCopasiDataModel & | dataModel, |
std::string | modelRef | ||
) |
Creates an SEDMLDocument and SBMLDocument from the given CCopasiDataModelObject. It checks if an SEDMLDocument and SBMLDocument already exists from an import and if this is the case, the old document is copied. If none exists a new one is created. Copying the old one makes sure that if something goes wrong during export, the original model is still consistent.
Definition at line 155 of file CSEDMLExporter.cpp.
References createModels(), createTasks(), fatalError, CCopasiDataModel::getModel(), CCopasiDataModel::getPlotDefinitionList(), mpSEDMLDocument, mSEDMLLevel, and mSEDMLVersion.
Referenced by exportModelAndTasksToString().
std::string CSEDMLExporter::createSteadyStateTask | ( | CCopasiDataModel & | dataModel, |
const std::string & | modelId | ||
) |
Creates the steady state task for the given model id and returns its id.
Creates the simulations for SEDML.
Definition at line 338 of file CSEDMLExporter.cpp.
References SEDMLUtils::getNextId(), CCopasiTask::getProblem(), CCopasiDataModel::getTaskList(), mpSEDMLDocument, and pTask.
Referenced by createScanTask().
void CSEDMLExporter::createTasks | ( | CCopasiDataModel & | dataModel, |
std::string & | modelRef | ||
) |
Creates the Tasks for SEDML.
Creates the Tasks for SEDML. This will always create a task running a time course simulation. If the parameter scan has been specified, it will be exported as well.
Definition at line 374 of file CSEDMLExporter.cpp.
References createDataGenerators(), createScanTask(), createTimeCourseTask(), and CCopasiDataModel::getTaskList().
Referenced by createSEDMLDocument().
std::string CSEDMLExporter::createTimeCourseTask | ( | CCopasiDataModel & | dataModel, |
const std::string & | modelId | ||
) |
Creates the timecourse task for the given model id and returns its id.
Creates the simulations for SEDML.
Definition at line 306 of file CSEDMLExporter.cpp.
References CCopasiTask::getMethod(), SEDMLUtils::getNextId(), CCopasiObject::getObjectName(), CTrajectoryProblem::getOutputStartTime(), CCopasiTask::getProblem(), CTrajectoryProblem::getStepNumber(), CTrajectoryProblem::getStepSize(), CCopasiDataModel::getTaskList(), mpSEDMLDocument, mpTimecourse, mpTimecourseTask, and pTask.
Referenced by createTasks().
bool CSEDMLExporter::exportModelAndTasks | ( | CCopasiDataModel & | dataModel, |
const std::string & | filename, | ||
const std::string & | sbmlDocument, | ||
unsigned int | sedmlLevel = 1 , |
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unsigned int | sedmlVersion = 1 , |
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bool | overwrite = false |
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Export the model and Task to SEDML. The SEDML document is written to the file given by SEDMLFilename and reference SBML model is written to SBMLFilename . If the export fails, false is returned.
Definition at line 92 of file CSEDMLExporter.cpp.
References createUniqueModelFileName(), CDirEntry::dirName(), CCopasiMessage::ERROR, exportModelAndTasksToString(), CLocaleString::fromUtf8(), MCDirEntry, and CDirEntry::Separator.
const std::string CSEDMLExporter::exportModelAndTasksToString | ( | CCopasiDataModel & | dataModel, |
std::string & | sbmlModelSource, | ||
unsigned int | sedmlLevel, | ||
unsigned int | sedmlVersion | ||
) |
Export the model and Task to SEDML. The SEDML document is returned as a string and SBML model is copied to sbmldocument parameter. In case of an error, an empty string is returned.
Definition at line 46 of file CSEDMLExporter.cpp.
References createSEDMLDocument(), mpSEDMLDocument, mSEDMLLevel, mSEDMLVersion, pdelete, and CVersion::VERSION.
Referenced by exportModelAndTasks().
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Definition at line 41 of file CSEDMLExporter.h.
Referenced by createDataGenerators(), createModels(), createScanTask(), createSEDMLDocument(), createSteadyStateTask(), createTimeCourseTask(), exportModelAndTasksToString(), and getSEDMLDocument().
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Definition at line 44 of file CSEDMLExporter.h.
Referenced by createTimeCourseTask().
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Definition at line 45 of file CSEDMLExporter.h.
Referenced by createScanTask(), and createTimeCourseTask().
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Definition at line 42 of file CSEDMLExporter.h.
Referenced by createSEDMLDocument(), and exportModelAndTasksToString().
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Definition at line 43 of file CSEDMLExporter.h.
Referenced by createSEDMLDocument(), and exportModelAndTasksToString().