SEDMLImporter Class Reference

#include <SEDMLImporter.h>

Public Member Functions
void	addCurveToCopasiPlot (LIBSEDML_CPP_NAMESPACE_QUALIFIER SedAbstractCurve *pCurve, CPlotSpecification *pPlot)
void	addSurfaceToCopasiPlot (LIBSEDML_CPP_NAMESPACE_QUALIFIER SedSurface *pSurface, CPlotSpecification *pPlot)
void	applyAlgorithm (CTrajectoryTask *tTask, const SedAlgorithm *alg)
void	applyStyleToCopasiItem (LIBSEDML_CPP_NAMESPACE_QUALIFIER SedStyle *pStyle, CPlotItem *plItem)
void	assignReportDefinitions (CDataVectorN< CCopasiTask > *pTaskList=NULL)
virtual void	clearCallBack ()
void	clearDocument ()
void	deleteCopasiModel ()
const std::string	getArchiveFileName ()
CDataModel *	getDataModel ()
const CProcessReport *	getProcessReport () const
SedDocument *	getSEDMLDocument ()
CModel *	importFirstSBMLModel ()
CModel *	importModel (const std::string &modelId)
void	importOutputs ()
void	importReport (LIBSEDML_CPP_NAMESPACE_QUALIFIER SedReport *report)
void	importTask (LIBSEDML_CPP_NAMESPACE_QUALIFIER SedAbstractTask *task, bool importModel=false, CDataVectorN< CCopasiTask > *pTaskList=NULL)
void	importTasks (CDataVectorN< CCopasiTask > *pTaskList=NULL)
void	initializeContent ()
CModel *	parseSEDML (const std::string &sedmlDocumentText, CDataModel *pDataModel, const SedmlImportOptions *pOptions=NULL)
CModel *	readSEDML (std::string filename, CDataModel *pDataModel, const SedmlImportOptions *pOptions=NULL)
std::string	resolveModelFile (const std::string &modelSource)
void	restoreFunctionDB ()
	SEDMLImporter ()
void	setCopasiModel (CModel *pModel)
void	setDataModel (CDataModel *pDataModel)
void	setImportHandler (CProcessReport *pProcessReport)
void	setSEDMLDocument (SedDocument *pDocument)
void	updateContent (CDataModel::CContent &data, CDataModel &dm)
void	updateCopasiTaskForSimulation (SedSimulation *sedmlsim, CDataVectorN< CCopasiTask > *pTaskList=NULL)
	~SEDMLImporter ()

Static Public Member Functions
static LIBSEDML_CPP_NAMESPACE_QUALIFIER SedVectorRange *	convertSimpleFunctionalRange (LIBSEDML_CPP_NAMESPACE_QUALIFIER SedFunctionalRange *frange, LIBSEDML_CPP_NAMESPACE_QUALIFIER SedRepeatedTask *repeat)

Static Protected Member Functions
static C_FLOAT64	round (const C_FLOAT64 &x)

Protected Attributes
std::string	mArchiveFileName
CDataModel::CContent	mContent
size_t	mhImportStep
std::set< unsigned int >	mIgnoredSEDMLMessages
std::string	mImportedModel
unsigned C_INT32	mImportStep
bool	mIncompleteModel
unsigned int	mLevel
unsigned int	mOriginalLevel
CModel *	mpCopasiModel
CDataModel *	mpDataModel
const SedmlImportOptions *	mpOptions
CProcessReport *	mpProcessReport
SedDocument *	mpSEDMLDocument
std::map< CReportDefinition *, std::pair< std::string, std::string > >	mReportMap
unsigned C_INT32	mTotalSteps
std::set< std::string >	mUsedSEDMLIds
bool	mUsedSEDMLIdsPopulated
unsigned int	mVersion

Private Member Functions
void	mergeNestedSubtasks ()

Constructor & Destructor Documentation

SEDMLImporter()

SEDMLImporter::SEDMLImporter

(

)

Constructor that initializes speciesMap and the FunctionDB object

References mIgnoredSEDMLMessages.

~SEDMLImporter()

SEDMLImporter::~SEDMLImporter

(

)

Destructor that does nothing.

References mReportMap.

Member Function Documentation

addCurveToCopasiPlot()

void SEDMLImporter::addCurveToCopasiPlot	(	LIBSEDML_CPP_NAMESPACE_QUALIFIER SedAbstractCurve *	pCurve,
		CPlotSpecification *	pPlot
	)

adds the given SED-ML curve to the COPASI plot, if supported

prior to calling this function, please ensure to have the the document and model set already.

Parameters

pCurve	the SED-ML curve, that may include a style
pPlot	the COPASI plot specification to add the curve to

References CPlotItem::addChannel(), applyStyleToCopasiItem(), CPlotItem::bandedGraph, CPlotSpecification::createItem(), CPlotItem::curve2d, CDataObject::getCN(), CDataObject::getObjectDisplayName(), CPlotSpecification::hasItem(), mpCopasiModel, mpSEDMLDocument, SEDMLUtils::resolveDatagenerator(), CPlotSpecification::setLogX(), CPlotSpecification::setLogY(), CCopasiParameterGroup::setValue(), and CCopasiMessage::WARNING.

Referenced by importOutputs().

addSurfaceToCopasiPlot()

void SEDMLImporter::addSurfaceToCopasiPlot	(	LIBSEDML_CPP_NAMESPACE_QUALIFIER SedSurface *	pSurface,
		CPlotSpecification *	pPlot
	)

adds the given SED-ML surface to the COPASI plot, if supported

prior to calling this function, please ensure to have the the document and model set already.

Parameters

pSurface	the SED-ML surface, that may include a style
pPlot	the COPASI plot specification to add the curve to

References CPlotItem::addChannel(), applyStyleToCopasiItem(), CPlotSpecification::createItem(), CDataObject::getCN(), CDataObject::getObjectDisplayName(), CPlotSpecification::hasItem(), mpCopasiModel, mpSEDMLDocument, SEDMLUtils::resolveDatagenerator(), CPlotSpecification::setLogX(), CPlotSpecification::setLogY(), CCopasiParameterGroup::setValue(), CPlotItem::spectogram, and CCopasiMessage::WARNING.

Referenced by importOutputs().

applyAlgorithm()

void SEDMLImporter::applyAlgorithm	(	CTrajectoryTask *	tTask,
		const SedAlgorithm *	alg
	)

Updates the task / method settings from algorithm

Parameters

tTask,the	time course task to update
alg	the algorithm including algorithm parameters

References CCopasiParameter::BOOL, C_FLOAT64, C_INT32, CCopasiParameter::CN, CCopasiParameter::DOUBLE, CCopasiTask::getMethod(), getMethodType(), CCopasiParameterGroup::getParameter(), CCopasiParameter::getType(), CCopasiParameter::getValue(), CCopasiParameter::INT, SEDMLUtils::PARAMETER_KISAO_MAP, CCopasiTask::setMethodType(), CCopasiParameter::setValue(), CCopasiParameter::STRING, CCopasiParameter::UDOUBLE, and CCopasiParameter::UINT.

Referenced by updateCopasiTaskForSimulation().

applyStyleToCopasiItem()

void SEDMLImporter::applyStyleToCopasiItem	(	LIBSEDML_CPP_NAMESPACE_QUALIFIER SedStyle *	pStyle,
		CPlotItem *	plItem
	)

applies the given style to a plot item

prior to calling this function, please ensure to have the the document and model set already.

Parameters

pStyle	the SED-ML Style to apply
plItem	the copasi plot item

References CCopasiParameterGroup::assertParameter(), C_FLOAT64, C_INT32, SEDMLUtils::getAlphaFromRgba(), CCopasiParameter::INT, CPlotItem::Lines, CPlotItem::LinesAndSymbols, SEDMLUtils::lineTypeFromSed(), mpSEDMLDocument, SEDMLUtils::rgbaToArgb(), CCopasiParameterGroup::setValue(), SEDMLUtils::symbolFromSed(), and CPlotItem::Symbols.

Referenced by addCurveToCopasiPlot(), and addSurfaceToCopasiPlot().

assignReportDefinitions()

void SEDMLImporter::assignReportDefinitions

(

CDataVectorN< CCopasiTask > *

pTaskList = NULL

)

References CDataVectorN< CType >::add(), C_INVALID_INDEX, CDataVector< CType >::empty(), CDataVectorN< CType >::getIndex(), mContent, mReportMap, CDataModel::CContent::pReportDefinitionList, CDataModel::CContent::pTaskList, CReport::setAppend(), CReport::setConfirmOverwrite(), CReport::setReportDefinition(), and CReport::setTarget().

Referenced by parseSEDML().

clearCallBack()

void SEDMLImporter::clearCallBack ( )

virtual

clears the currently set progress handler

References setImportHandler().

clearDocument()

void SEDMLImporter::clearDocument

(

)

frees the current SED-ML document

References mpSEDMLDocument, and pdelete.

convertSimpleFunctionalRange()

SedVectorRange * SEDMLImporter::convertSimpleFunctionalRange ( LIBSEDML_CPP_NAMESPACE_QUALIFIER SedFunctionalRange *  frange, LIBSEDML_CPP_NAMESPACE_QUALIFIER SedRepeatedTask *  repeat  )

static

Utility function trying to convert the given Functional Range into a Vector Range

Only functional ranges that are simple transformation of another vector range are currently supported.

Parameters

frange	the functional range to convert
repeat	the repeated task worked on

Returns

the newly created VectorRange or NULL

References pdelete, and CCopasiMessage::WARNING.

Referenced by importTask().

deleteCopasiModel()

void SEDMLImporter::deleteCopasiModel

(

)

This call deletes an existing COPASI model. The method can e.g. be called to clean up if an import fails.

References mpCopasiModel, and pdelete.

Referenced by CDataModel::importSEDML(), and CDataModel::importSEDMLFromString().

getArchiveFileName()

const std::string SEDMLImporter::getArchiveFileName

(

)

References mArchiveFileName.

getDataModel()

CDataModel * SEDMLImporter::getDataModel

(

)

Returns

the current datamodel

References mpDataModel.

getProcessReport()

const CProcessReport * SEDMLImporter::getProcessReport

(

)

const

Returns

the progress handler set

References mpProcessReport.

getSEDMLDocument()

SedDocument * SEDMLImporter::getSEDMLDocument

(

)

Returns

the current SED-ML document

References mpSEDMLDocument.

importFirstSBMLModel()

CModel * SEDMLImporter::importFirstSBMLModel

(

)

Imports the first viable SBML model

References CCopasiMessage::EXCEPTION, importModel(), MCSEDML, mpSEDMLDocument, and CCopasiMessage::WARNING.

Referenced by parseSEDML().

importModel()

CModel * SEDMLImporter::importModel

(

const std::string &

modelId

)

Imports the SBML model for the given model id

References applyAttributeChange(), SBMLImporter::deleteCopasiModel(), CCopasiMessage::EXCEPTION, CDirEntry::exist(), CModel::getActiveModelParameterSet(), mContent, CDataModel::CContent::mCopasi2SBMLMap, MCSEDML, mImportedModel, mpCopasiModel, mpDataModel, mpProcessReport, mpSEDMLDocument, CDataModel::CContent::pCurrentSBMLDocument, CDataModel::CContent::pListOfLayouts, SBMLImporter::readSBML(), resolveModelFile(), SBMLImporter::restoreFunctionDB(), SBMLImporter::setImportCOPASIMIRIAM(), SBMLImporter::setImportHandler(), CDataModel::setSBMLFileName(), CModelParameterSet::updateModel(), and CCopasiMessage::WARNING.

Referenced by importFirstSBMLModel(), and parseSEDML().

importOutputs()

void SEDMLImporter::importOutputs

(

)

References addCurveToCopasiPlot(), addSurfaceToCopasiPlot(), COutputDefinitionVector::createPlotSpec(), CDataModel::getCopasi2SBMLMap(), SEDMLUtils::getNextId(), CDataObject::getObjectDataModel(), CDataModel::getReportDefinitionList(), SedmlImportOptions::ignoreOutput(), importReport(), mContent, mpCopasiModel, mpDataModel, mpOptions, mpSEDMLDocument, CPlotItem::plot2d, CDataModel::CContent::pPlotDefinitionList, CPlotSpecification::setLogX(), CPlotSpecification::setLogY(), and CCopasiMessage::WARNING.

Referenced by parseSEDML().

importReport()

void SEDMLImporter::importReport

(

LIBSEDML_CPP_NAMESPACE_QUALIFIER SedReport *

report

)

imports the given report

prior to calling this function, please ensure to have the the document and model set already.

Parameters

report

the SED-ML report to import

References CReportDefinition::getBodyAddr(), CDataObject::getCN(), CReportDefinition::getHeaderAddr(), SEDMLUtils::getNextId(), SedmlImportOptions::getReportFile(), CReportDefinition::getSeparator(), isScan(), isTC(), mpCopasiModel, mpOptions, mpSEDMLDocument, mReportMap, SEDMLUtils::resolveDatagenerator(), CReportDefinition::setComment(), CReportDefinition::setIsTable(), and CReportDefinition::setSeparator().

Referenced by importOutputs().

importTask()

void SEDMLImporter::importTask	(	LIBSEDML_CPP_NAMESPACE_QUALIFIER SedAbstractTask *	task,
		bool	importModel = false,
		CDataVectorN< CCopasiTask > *	pTaskList = NULL
	)

Imports the specified SED-ML task

Parameters

task	the task to import
importModel	if true, the model referenced from the task will be imported
pTaskList	optional task list to import into

References CScanProblem::addScanItem(), C_FLOAT64, C_INVALID_INDEX, CScanProblem::clearScanItems(), convertSimpleFunctionalRange(), CTaskFactory::create(), CDataVectorN< CType >::getIndex(), CCopasiTask::getProblem(), mContent, mImportedModel, mpCopasiModel, mpSEDMLDocument, CDataModel::CContent::pTaskList, SEDMLUtils::resolveXPath(), CTaskEnum::scan, CScanProblem::SCAN_LINEAR, CScanProblem::SCAN_REPEAT, CScanProblem::setContinueFromCurrentState(), CCopasiTask::setMathContainer(), CScanProblem::setOutputInSubtask(), CCopasiTask::setScheduled(), CScanProblem::setSubtask(), CCopasiParameterGroup::setValue(), CTaskEnum::steadyState, CTaskEnum::timeCourse, updateCopasiTaskForSimulation(), and CCopasiMessage::WARNING.

Referenced by importTasks(), and parseSEDML().

importTasks()

void SEDMLImporter::importTasks

(

CDataVectorN< CCopasiTask > *

pTaskList = NULL

)

Import all tasks for the imported SBML model

References importTask(), mContent, mpSEDMLDocument, and CDataModel::CContent::pTaskList.

Referenced by parseSEDML().

initializeContent()

void SEDMLImporter::initializeContent

(

)

Initializes the content element from the currently set DataModel

References mContent, CDataModel::CContent::mCopasi2SBMLMap, CDataModel::CContent::mCopasi2SEDMLMap, NO_PARENT, CDataModel::CContent::pPlotDefinitionList, CDataModel::CContent::pReportDefinitionList, and CDataModel::CContent::pTaskList.

Referenced by parseSEDML().

mergeNestedSubtasks()

void SEDMLImporter::mergeNestedSubtasks ( )

private

merge nested subtasks if needed (as that is really the only way COPASI can handle them. So if we have

repeatedTask1: subtask simulationTask1 repeatedTask2: subtask repeatedTask1 repeatedTask3: subtask repeatedTask2 repeatedTask4: subtask repeatedTask3

we move all the ranges changes from 3 to 4, then from 2 to 4, then 1 to 4 that way we preserve the order of scan items.

References mpSEDMLDocument.

Referenced by parseSEDML().

parseSEDML()

CModel * SEDMLImporter::parseSEDML	(	const std::string &	sedmlDocumentText,
		CDataModel *	pDataModel,
		const SedmlImportOptions *	pOptions = NULL
	)

Function parses an SEDML document with libsedml and converts it to a COPASI CModel object which is returned. Deletion of the returned pointer is up to the caller.

References CProcessReport::addItem(), assignReportDefinitions(), C_INT32, C_INVALID_INDEX, CCopasiMessage::ERROR, CCopasiMessage::ERROR_FILTERED, CCopasiMessage::EXCEPTION, CProcessReport::finishItem(), CDataModel::getModel(), SedmlImportOptions::getModelId(), SedmlImportOptions::getTaskId(), importFirstSBMLModel(), importModel(), importOutputs(), importTask(), importTasks(), initializeContent(), MCSEDML, mergeNestedSubtasks(), mhImportStep, mIgnoredSEDMLMessages, mImportStep, mpCopasiModel, mpDataModel, mpOptions, mpProcessReport, mpSEDMLDocument, mReportMap, mTotalSteps, mUsedSEDMLIdsPopulated, pdelete, CCopasiMessage::RAW, CProcessReport::setName(), setSEDMLDocument(), SedmlImportOptions::skipModelImport(), CCopasiMessage::WARNING, and CCopasiMessage::WARNING_FILTERED.

Referenced by CDataModel::importSEDMLFromString(), and readSEDML().

readSEDML()

CModel * SEDMLImporter::readSEDML	(	std::string	filename,
		CDataModel *	pDataModel,
		const SedmlImportOptions *	pOptions = NULL
	)

Function reads an SEDML file with libsedml and converts it to a Copasi CModel

References CCopasiMessage::EXCEPTION, CLocaleString::fromUtf8(), MCSEDML, parseSEDML(), and CDataModel::setSEDMLFileName().

Referenced by CDataModel::importSEDML().

resolveModelFile()

std::string SEDMLImporter::resolveModelFile

(

const std::string &

modelSource

)

References CDirEntry::dirName(), CDirEntry::exist(), CDataModel::getReferenceDirectory(), CDataModel::getSEDMLFileName(), mpDataModel, and CDirEntry::Separator.

Referenced by importModel().

restoreFunctionDB()

void SEDMLImporter::restoreFunctionDB

(

)

not implemented

Referenced by CDataModel::importSEDML(), and CDataModel::importSEDMLFromString().

round()

C_FLOAT64 SEDMLImporter::round ( const C_FLOAT64 &  x )

staticprotected

SEDMLImporter.cpp $Rev: $: Revision of last commit

Author

: Author of last commit

Date

: Date of last commit $HeadURL: $

Id

setCopasiModel()

void SEDMLImporter::setCopasiModel

(

CModel *

pModel

)

Sets the copasi model to use (for time and object references)

Parameters

pModel

the model

References mpCopasiModel.

setDataModel()

void SEDMLImporter::setDataModel

(

CDataModel *

pDataModel

)

sets the data model to be used by the importer

References mpDataModel.

setImportHandler()

void SEDMLImporter::setImportHandler

(

CProcessReport *

pProcessReport

)

sets a progress handler to inform about updates

References mpProcessReport.

Referenced by clearCallBack(), CDataModel::importSEDML(), and CDataModel::importSEDMLFromString().

setSEDMLDocument()

void SEDMLImporter::setSEDMLDocument

(

SedDocument *

pDocument

)

sets the sed-ml document that will be used by the importer

(the document will not be automatically deleted) manually call clearDocument to delete the existing document

References mLevel, mOriginalLevel, mpSEDMLDocument, and mVersion.

Referenced by parseSEDML().

updateContent()

void SEDMLImporter::updateContent	(	CDataModel::CContent &	data,
		CDataModel &	dm
	)

updates the provided content element with imported tasks / output elements

This is an internal function to be called before commonAfterLoad.

Parameters

data	the content element to update
dm	the data model to add elements to

References CDataContainer::add(), mContent, CDataModel::CContent::mContentType, CDataModel::CContent::mCopasi2SBMLMap, CDataModel::CContent::mCopasi2SEDMLMap, mpCopasiModel, mpSEDMLDocument, CDataModel::CContent::pCurrentSBMLDocument, CDataModel::CContent::pCurrentSEDMLDocument, CDataModel::CContent::pListOfLayouts, CDataModel::CContent::pModel, CDataModel::CContent::pPlotDefinitionList, CDataModel::CContent::pReportDefinitionList, CDataModel::CContent::pTaskList, and CDataModel::SEDML.

Referenced by CDataModel::importSEDML(), and CDataModel::importSEDMLFromString().

updateCopasiTaskForSimulation()

void SEDMLImporter::updateCopasiTaskForSimulation	(	SedSimulation *	sedmlsim,
		CDataVectorN< CCopasiTask > *	pTaskList = NULL
	)

Updates COPASI tasks for a given SedML Simulation

Creates and returns a COPASI CTrajectoryTask from the SEDML simulation given as argument.

References applyAlgorithm(), C_INVALID_INDEX, CTaskFactory::create(), CCopasiMessage::EXCEPTION, CDataVectorN< CType >::getIndex(), CModelEntity::getInitialValueReference(), CModel::getMathContainer(), CTrajectoryProblem::getOutputStartTime(), CCopasiTask::getProblem(), mContent, mpCopasiModel, CDataModel::CContent::pTaskList, CTrajectoryProblem::setDuration(), CModel::setInitialTime(), CCopasiTask::setMathContainer(), CTrajectoryProblem::setOutputStartTime(), CCopasiTask::setScheduled(), CTrajectoryProblem::setStepNumber(), CTaskEnum::steadyState, CTaskEnum::timeCourse, and CModel::updateInitialValues().

Referenced by importTask().

Member Data Documentation

mArchiveFileName

std::string SEDMLImporter::mArchiveFileName

protected

Referenced by getArchiveFileName().

mContent

CDataModel::CContent SEDMLImporter::mContent

protected

Referenced by assignReportDefinitions(), importModel(), importOutputs(), importTask(), importTasks(), initializeContent(), updateContent(), and updateCopasiTaskForSimulation().

mhImportStep

size_t SEDMLImporter::mhImportStep

protected

Referenced by parseSEDML().

mIgnoredSEDMLMessages

std::set<unsigned int> SEDMLImporter::mIgnoredSEDMLMessages

protected

Referenced by parseSEDML(), and SEDMLImporter().

mImportedModel

std::string SEDMLImporter::mImportedModel

protected

Referenced by importModel(), and importTask().

mImportStep

unsigned C_INT32 SEDMLImporter::mImportStep

protected

Referenced by parseSEDML().

mIncompleteModel

bool SEDMLImporter::mIncompleteModel

protected

mLevel

unsigned int SEDMLImporter::mLevel

protected

Referenced by setSEDMLDocument().

mOriginalLevel

unsigned int SEDMLImporter::mOriginalLevel

protected

Referenced by setSEDMLDocument().

mpCopasiModel

CModel* SEDMLImporter::mpCopasiModel

protected

Referenced by addCurveToCopasiPlot(), addSurfaceToCopasiPlot(), deleteCopasiModel(), importModel(), importOutputs(), importReport(), importTask(), parseSEDML(), setCopasiModel(), updateContent(), and updateCopasiTaskForSimulation().

mpDataModel

CDataModel* SEDMLImporter::mpDataModel

protected

Referenced by getDataModel(), importModel(), importOutputs(), parseSEDML(), resolveModelFile(), and setDataModel().

mpOptions

const SedmlImportOptions* SEDMLImporter::mpOptions

protected

Referenced by importOutputs(), importReport(), and parseSEDML().

mpProcessReport

CProcessReport* SEDMLImporter::mpProcessReport

protected

Referenced by getProcessReport(), importModel(), parseSEDML(), and setImportHandler().

mpSEDMLDocument

SedDocument* SEDMLImporter::mpSEDMLDocument

protected

Referenced by addCurveToCopasiPlot(), addSurfaceToCopasiPlot(), applyStyleToCopasiItem(), clearDocument(), getSEDMLDocument(), importFirstSBMLModel(), importModel(), importOutputs(), importReport(), importTask(), importTasks(), mergeNestedSubtasks(), parseSEDML(), setSEDMLDocument(), and updateContent().

mReportMap

std::map<CReportDefinition*, std::pair< std::string, std::string > > SEDMLImporter::mReportMap

protected

Referenced by assignReportDefinitions(), importReport(), parseSEDML(), and ~SEDMLImporter().

mTotalSteps

unsigned C_INT32 SEDMLImporter::mTotalSteps

protected

Referenced by parseSEDML().

mUsedSEDMLIds

std::set<std::string> SEDMLImporter::mUsedSEDMLIds

protected

mUsedSEDMLIdsPopulated

bool SEDMLImporter::mUsedSEDMLIdsPopulated

protected

Referenced by parseSEDML().

mVersion

unsigned int SEDMLImporter::mVersion

protected

Referenced by setSEDMLDocument().

---

The documentation for this class was generated from the following files:

• SEDMLImporter.h
• SEDMLImporter.cpp