#include <SEDMLUtils.h>

Static Public Member Functions
static std::string	argbToRgba (const std::string &argb, bool includeHash=true)

static CModelValue *	createAmountMV (CModel pModel, const CMetab pMetab)

static std::string	findIdByNameAndType (const std::map< const CDataObject , SBase > &map, int typeCode, const std::string &name)

static int	getAlphaFromArgb (const std::string &argb)

static int	getAlphaFromRgba (const std::string &rgba)

static std::string	getNextId (const std::string &base, int count)

static const CDataObject *	getObjectForSbmlId (const CModel *pModel, const std::string &id, const std::string &SBMLType, bool initial=false)

static std::string	getSbmlId (const CDataObject &object)

static std::string	getSedMLStringForArchive (const std::string &fileName)

static std::string	getXPathAndName (std::string &sbmlId, const std::string &type, const CModel *pModel, const CDataModel &dataModel)

static std::string	getXPathForObject (const CDataObject &object)

static std::string	getXPathForObjectAndType (const CDataObject &object, const std::string &sbmlId)

static std::string	getXPathForSbmlIdAndType (const std::string &type, const std::string &sbmlId)

static int	lineTypeFromSed (int linetype)

static int	lineTypeToSed (int linetype)

static std::string &	removeCharactersFromString (std::string &str, const std::string &characters)

static const CDataObject *	resolveDatagenerator (CModel model, const SedDataGenerator dataReference)

static const CDataObject *	resolveVariable (CModel model, const SedVariable variable)

static const CDataObject *	resolveXPath (const CModel *model, const std::string &xpath, bool initial=false)

static std::string	rgbaToArgb (const std::string &rgba, bool includeHash=true)

static void	setLibCombineTempDir ()

static void	splitStrings (const std::string &xpath, char delim, std::vector< std::string > &stringsContainer)

static int	symbolFromSed (int symbol)

static int	symbolToSed (int symbol)

static std::string	translateTargetXpathInSBMLId (const std::string &xpath, std::string &SBMLType)

Static Public Attributes
static std::map< int, int >	COPASI_LINE_STYLE_MAP

static std::map< int, int >	COPASI_SYMBOL_MAP

static std::map< std::string, std::string >	PARAMETER_KISAO_MAP

Detailed Description

Utility methods for SED-ML Import / Export

Member Function Documentation

◆ argbToRgba()

std::string SEDMLUtils::argbToRgba	(	const std::string &	argb,
		bool	includeHash = `true`
	)

static

Referenced by CSEDMLExporter::exportStyleForItem().

◆ createAmountMV()

CModelValue * SEDMLUtils::createAmountMV	(	CModel *	pModel,
		const CMetab *	pMetab
	)

static

References CModelEntity::ASSIGNMENT, C_INVALID_INDEX, CModel::createModelValue(), CDataObject::getCN(), CMetab::getCompartment(), CMetab::getConcentrationReference(), CDataVectorN< CType >::getIndex(), CModel::getModelValues(), CDataObject::getObjectName(), CModelEntity::getValueReference(), CModelEntity::setExpression(), and CModelEntity::setStatus().

Referenced by resolveVariable().

◆ findIdByNameAndType()

std::string SEDMLUtils::findIdByNameAndType	(	const std::map< const CDataObject , SBase > &	map,
		int	typeCode,
		const std::string &	name
	)

static

tries to find a species id in the given map. Lookup will be performed by name

Returns: the species id if found or the empty string

References CDataObject::getObjectDisplayName(), and removeCharactersFromString().

Referenced by getXPathAndName().

◆ getAlphaFromArgb()

int SEDMLUtils::getAlphaFromArgb ( const std::string & argb )

static

◆ getAlphaFromRgba()

int SEDMLUtils::getAlphaFromRgba ( const std::string & rgba )

static

Referenced by SEDMLImporter::applyStyleToCopasiItem().

◆ getNextId()

std::string SEDMLUtils::getNextId	(	const std::string &	base,
		int	count
	)

static

Referenced by CSEDMLExporter::createScanTask(), CSEDMLExporter::createSteadyStateTask(), CSEDMLExporter::createTimeCourseTask(), CSEDMLExporter::exportNthScanItem(), CSEDMLExporter::exportStyleForItem(), SEDMLImporter::importOutputs(), and SEDMLImporter::importReport().

◆ getObjectForSbmlId()

const CDataObject * SEDMLUtils::getObjectForSbmlId	(	const CModel *	pModel,
		const std::string &	id,
		const std::string &	SBMLType,
		bool	initial = `false`
	)

static

References CModel::getCompartments(), CModel::getMetabolites(), CModel::getModelValues(), CDataContainer::getObject(), CModel::getReactions(), and CDataVector< CType >::size().

Referenced by resolveXPath().

◆ getSbmlId()

std::string SEDMLUtils::getSbmlId ( const CDataObject & object )

static

Returns: the sbml id of the object (or its parent, in case of a reference) or the empty string if not set

References CModelEntity::getSBMLId().

Referenced by getXPathForObject().

◆ getSedMLStringForArchive()

std::string SEDMLUtils::getSedMLStringForArchive ( const std::string & fileName )

static

References CCopasiMessage::ERROR, and setLibCombineTempDir().

Referenced by SedmlInfo::forArchive().

◆ getXPathAndName()

std::string SEDMLUtils::getXPathAndName	(	std::string &	sbmlId,
		const std::string &	type,
		const CModel *	pModel,
		const CDataModel &	dataModel
	)

static

This function uses the Copasi2SBML map of the datamodel, to resolve the element with the display name provided in the 'sbmlId' parameter. Once the object has been resolved the xpath string will be created for it, and the object sbmlId returned.

Parameters

sbmlId	input parameter with the displayName of the object sought, will be the output 'sbmlId' if the element cannot be resolved, sbmlId will be set to the empty string
type	the object type of the element
pModel	the model to search through
dataModel	the datamodel to use

Returns: the xpath expression, if resolving worked, an empty string otherwise

References findIdByNameAndType(), removeCharactersFromString(), SEDML_TIME_URN, and splitStrings().

Referenced by getXPathForObject().

◆ getXPathForObject()

std::string SEDMLUtils::getXPathForObject ( const CDataObject & object )

static

Parameters

object the object to generate an xpath expression for

Returns: the xpath for the object or the empty string if it could not be generated

References CDataModel::getModel(), CDataObject::getObjectDataModel(), CDataObject::getObjectDisplayName(), getSbmlId(), getXPathAndName(), and getXPathForSbmlIdAndType().

Referenced by CSEDMLExporter::exportNthScanItem().

◆ getXPathForObjectAndType()

std::string SEDMLUtils::getXPathForObjectAndType	(	const CDataObject &	object,
		const std::string &	sbmlId
	)

static

References CDataObject::getObjectAncestor(), CDataObject::getObjectName(), CDataObject::getObjectType(), and CReaction::getSBMLId().

Referenced by VariableInfo::VariableInfo().

◆ getXPathForSbmlIdAndType()

std::string SEDMLUtils::getXPathForSbmlIdAndType	(	const std::string &	type,
		const std::string &	sbmlId
	)

static

Wraps the given sbml id into an xpath expression according to type

Parameters

type	one of 'Concentration', 'InitialConcentration', 'Volume', 'Value', 'Flux'
sbmlid	the sbmlid of the object

Returns: the sbml xpath expression

Referenced by getXPathForObject().

◆ lineTypeFromSed()

int SEDMLUtils::lineTypeFromSed ( int linetype )

static

References COPASI_LINE_STYLE_MAP.

Referenced by SEDMLImporter::applyStyleToCopasiItem().

◆ lineTypeToSed()

int SEDMLUtils::lineTypeToSed ( int linetype )

static

References COPASI_LINE_STYLE_MAP.

Referenced by CSEDMLExporter::exportStyleForItem().

◆ removeCharactersFromString()

std::string & SEDMLUtils::removeCharactersFromString	(	std::string &	str,
		const std::string &	characters
	)

static

Referenced by CSEDMLExporter::exportNthPlot(), CSEDMLExporter::exportReport(), findIdByNameAndType(), getXPathAndName(), and translateTargetXpathInSBMLId().

◆ resolveDatagenerator()

const CDataObject * SEDMLUtils::resolveDatagenerator	(	CModel *	model,
		const SedDataGenerator *	dataReference
	)

static

References CDataContainer::getObject(), resolveVariable(), and SEDML_TIME_URN.

Referenced by SEDMLImporter::addCurveToCopasiPlot(), SEDMLImporter::addSurfaceToCopasiPlot(), and SEDMLImporter::importReport().

◆ resolveVariable()

const CDataObject * SEDMLUtils::resolveVariable	(	CModel *	model,
		const SedVariable *	variable
	)

static

References createAmountMV(), CMetab::getConcentrationRateReference(), CMetab::getConcentrationReference(), CDataObject::getObjectParent(), CDataObject::getObjectType(), CModelEntity::getRateReference(), CModelEntity::getValueReference(), resolveXPath(), SEDML_KISAO_AMOUNT, SEDML_KISAO_CONCENTRATION, SEDML_KISAO_CONCENTRATION_RATE, SEDML_KISAO_PARTICLE_RATE, SEDML_KISAO_PARTICLENUMBER, SEDML_KISAO_RATE, SEDML_KISAO_RATEOFCHANGE, and CCopasiMessage::WARNING.

Referenced by resolveDatagenerator().

◆ resolveXPath()

const CDataObject * SEDMLUtils::resolveXPath	(	const CModel *	model,
		const std::string &	xpath,
		bool	initial = `false`
	)

static

References CDataObject::getObject(), getObjectForSbmlId(), CDataObject::getObjectParent(), and translateTargetXpathInSBMLId().

Referenced by applyAttributeChange(), SEDMLImporter::importTask(), and resolveVariable().

◆ rgbaToArgb()

std::string SEDMLUtils::rgbaToArgb	(	const std::string &	rgba,
		bool	includeHash = `true`
	)

static

Referenced by SEDMLImporter::applyStyleToCopasiItem().

◆ setLibCombineTempDir()

void SEDMLUtils::setLibCombineTempDir ( )

static

updates the libcombine temp directory to the COPASI temp path

References COptions::getValue().

Referenced by getSedMLStringForArchive().

◆ splitStrings()

void SEDMLUtils::splitStrings	(	const std::string &	xpath,
		char	delim,
		std::vector< std::string > &	stringsContainer
	)

static

This is a hack at the moment better solution for processing XPath string may be developed in the future

Referenced by getXPathAndName(), and translateTargetXpathInSBMLId().

◆ symbolFromSed()

int SEDMLUtils::symbolFromSed ( int symbol )

static

References COPASI_SYMBOL_MAP.

Referenced by SEDMLImporter::applyStyleToCopasiItem().

◆ symbolToSed()

int SEDMLUtils::symbolToSed ( int symbol )

static

References COPASI_SYMBOL_MAP.

Referenced by CSEDMLExporter::exportStyleForItem().

◆ translateTargetXpathInSBMLId()

std::string SEDMLUtils::translateTargetXpathInSBMLId	(	const std::string &	xpath,
		std::string &	SBMLType
	)

static

References removeCharactersFromString(), and splitStrings().

Referenced by resolveXPath().

Member Data Documentation

◆ COPASI_LINE_STYLE_MAP

std::map< int, int > SEDMLUtils::COPASI_LINE_STYLE_MAP

static

Initial value:

=
{
  {(int) CPlotItem::LineStyle::Dashed, SEDML_LINETYPE_DASH},
  {(int) CPlotItem::LineStyle::DotDash, SEDML_LINETYPE_DASHDOT},
  {(int) CPlotItem::LineStyle::DotDotDash, SEDML_LINETYPE_DASHDOTDOT},
  {(int) CPlotItem::LineStyle::Dotted, SEDML_LINETYPE_DOT},
  {(int) CPlotItem::LineStyle::None, SEDML_LINETYPE_NONE},
  {(int) CPlotItem::LineStyle::Solid, SEDML_LINETYPE_SOLID},
}

Referenced by lineTypeFromSed(), and lineTypeToSed().

◆ COPASI_SYMBOL_MAP

std::map< int, int > SEDMLUtils::COPASI_SYMBOL_MAP

static

Initial value:

=
{
  {(int) CPlotItem::SymbolType::Circle, SEDML_MARKERTYPE_CIRCLE},
  {(int) CPlotItem::SymbolType::Diamond, SEDML_MARKERTYPE_DIAMOND},
  {(int) CPlotItem::SymbolType::hDash, SEDML_MARKERTYPE_HDASH},
  {(int) CPlotItem::SymbolType::None, SEDML_MARKERTYPE_NONE},
  {(int) CPlotItem::SymbolType::Plus, SEDML_MARKERTYPE_PLUS},
  {(int) CPlotItem::SymbolType::LargeCross, SEDML_MARKERTYPE_PLUS},
  {(int) CPlotItem::SymbolType::SmallCross, SEDML_MARKERTYPE_PLUS},
  {(int) CPlotItem::SymbolType::Square, SEDML_MARKERTYPE_SQUARE},
  {(int) CPlotItem::SymbolType::Star, SEDML_MARKERTYPE_STAR},
  {(int) CPlotItem::SymbolType::TriangleDown, SEDML_MARKERTYPE_TRIANGLEDOWN},
  {(int) CPlotItem::SymbolType::TriangleLeft, SEDML_MARKERTYPE_TRIANGLELEFT},
  {(int) CPlotItem::SymbolType::TriangleRight, SEDML_MARKERTYPE_TRIANGLERIGHT},
  {(int) CPlotItem::SymbolType::TriangleUp, SEDML_MARKERTYPE_TRIANGLEUP},
  {(int) CPlotItem::SymbolType::vDash, SEDML_MARKERTYPE_VDASH},
  {(int) CPlotItem::SymbolType::xCross, SEDML_MARKERTYPE_XCROSS}
}

Referenced by symbolFromSed(), and symbolToSed().

◆ PARAMETER_KISAO_MAP

std::map< std::string, std::string > SEDMLUtils::PARAMETER_KISAO_MAP

static

Initial value:

=
{
  {"KISAO:0000209", "Relative Tolerance"},
  {"KISAO:0000211", "Absolute Tolerance"},
  {"KISAO:0000216", "Integrate Reduced Model"},
  {"KISAO:0000415", "Max Internal Steps"},
  {"KISAO:0000467", "Max Internal Step Size"},
  {
    "KISAO:0000488",
    "Random Seed",
  },
  {"KISAO:0000228", "Epsilon"},
  {"KISAO:0000203", "Lower Limit"},
  {"KISAO:0000205", "Partitioning Interval"},
  {"KISAO:0000559", "Initial Step Size"},
  {"KISAO:0000483", "Runge Kutta Stepsize"},
  {"KISAO:0000483", "Internal Steps Size"},
  {"KISAO:0000565", "Tolerance for Root Finder"},
  {"KISAO:0000567", "Force Physical Correctness"},
}

Referenced by SEDMLImporter::applyAlgorithm(), and CSEDMLExporter::exportAlgorithm().

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

Static Public Member Functions

Static Public Attributes

Detailed Description

Member Function Documentation

◆ argbToRgba()

◆ createAmountMV()

◆ findIdByNameAndType()

◆ getAlphaFromArgb()

◆ getAlphaFromRgba()

◆ getNextId()

◆ getObjectForSbmlId()

◆ getSbmlId()

◆ getSedMLStringForArchive()

◆ getXPathAndName()

◆ getXPathForObject()

◆ getXPathForObjectAndType()

◆ getXPathForSbmlIdAndType()

◆ lineTypeFromSed()

◆ lineTypeToSed()

◆ removeCharactersFromString()

◆ resolveDatagenerator()

◆ resolveVariable()

◆ resolveXPath()

◆ rgbaToArgb()

◆ setLibCombineTempDir()

◆ splitStrings()

◆ symbolFromSed()

◆ symbolToSed()

◆ translateTargetXpathInSBMLId()

Member Data Documentation

◆ COPASI_LINE_STYLE_MAP

◆ COPASI_SYMBOL_MAP

◆ PARAMETER_KISAO_MAP