#include <CMetabNameInterface.h>

Static Public Member Functions
static std::string	createUniqueDisplayName (const CMetab &metab, const bool &quoted)

static std::string	createUniqueDisplayName (const std::string &metabolite, const std::string &compartment, const bool &quoted)

static bool	doesExist (const CModel *model, const std::string &metabolite, const std::string &compartment)

static std::string	getDisplayName (const CModel *model, const CMetab &metab, const bool &quoted)

static std::string	getDisplayName (const CModel *model, const std::string &key, const bool &quoted)

static std::string	getDisplayName (const CModel *model, const std::string &metabolite, const std::string &compartment, const bool &quoted)

static CMetab *	getMetabolite (const CModel *model, const std::string &metabolite, const std::string &compartment)

static std::string	getMetaboliteKey (const CModel *model, const std::string &metabolite, const std::string &compartment)

static std::string	getSpeciesCN (const CModel *pModel, const std::string &species, const std::string &compartment)

static bool	isUnique (const CModel *model, const std::string &name)

static std::pair< std::string, std::string >	splitDisplayName (const std::string &name)

static std::string	unQuote (const std::string &displayName)

Detailed Description

This class handles the display names of metabolites. It converts "Species" to "Species {Compartment}" if the metabolite name is not unique. If it is unique (that means it occurs in only one compartment) then the "{Compartment}" is not added.

Member Function Documentation

◆ createUniqueDisplayName() [1/2]

std::string CMetabNameInterface::createUniqueDisplayName	(	const CMetab &	metab,
		const bool &	quoted
	)

static

Returns the unique display name in the form metabolite{compartment}

Parameters

metab the metabolite

Returns: the unique display name in the form metabolite{compartment}

References createUniqueDisplayName(), CMetab::getCompartment(), and CDataObject::getObjectName().

◆ createUniqueDisplayName() [2/2]

std::string CMetabNameInterface::createUniqueDisplayName	(	const std::string &	metabolite,
		const std::string &	compartment,
		const bool &	quoted
	)

static

Returns the unique display name in the form metabolite{compartment}

Parameters

metabolite	the metabolite name
compartment	the compartment name

Returns: the unique display name in the form metabolite{compartment}

References isNumber(), and quote().

Referenced by createUniqueDisplayName(), CDataModel::findObjectByDisplayName(), getDisplayName(), and CChemEqInterface::toDataValue().

◆ doesExist()

bool CMetabNameInterface::doesExist	(	const CModel *	model,
		const std::string &	metabolite,
		const std::string &	compartment
	)

static

This returns whether a metabolite with the given name does exist. If a compartment is also given (as an appendix to the name) then it only returns true if the metabolite exists in the specified compartment.

References CDataObjectMap::equal_range(), CMetab::getCompartment(), CModel::getMetabolites(), CDataObject::getObjectName(), and CDataContainer::getObjects().

Referenced by getDisplayName(), and CChemEqInterface::listOfNonExistingMetabNames().

◆ getDisplayName() [1/3]

std::string CMetabNameInterface::getDisplayName	(	const CModel *	model,
		const CMetab &	metab,
		const bool &	quoted
	)

static

This returns a name to use for display in the GUI. If the name of the metabolite is unique it is used unaltered. If it is not then the compartment is added to the name to make it unique.

References CMetab::getCompartment(), getDisplayName(), and CDataObject::getObjectName().

◆ getDisplayName() [2/3]

std::string CMetabNameInterface::getDisplayName	(	const CModel *	model,
		const std::string &	key,
		const bool &	quoted
	)

static

This returns a name to use for display in the GUI. If the name of the metabolite is unique it is used unaltered. If it is not then the compartment is added to the name to make it unique.

References CKeyFactory::get(), and CRootContainer::getKeyFactory().

Referenced by CChemEqInterface::addModifier(), CChemEqInterface::buildDisplayNames(), CTimeSeries::compile(), CODEExporter::exportMetabolites(), CODEExporter::exportMetabolitesConcentrations(), CMoiety::getDescription(), getDisplayName(), CEFMTask::getInternalSpecies(), CModelParameterSpecies::getName(), CEFMTask::getNetReaction(), CMetab::getObjectDisplayName(), CReactionInterface::loadMappingAndValues(), and CEFMProblem::printResult().

◆ getDisplayName() [3/3]

std::string CMetabNameInterface::getDisplayName	(	const CModel *	model,
		const std::string &	metabolite,
		const std::string &	compartment,
		const bool &	quoted
	)

static

This returns a name to use for display in the GUI. If the name of the metabolite is unique it is used unaltered. If it is not then the compartment is added to the name to make it unique.

References createUniqueDisplayName(), doesExist(), CModel::getCompartments(), CDataObject::getObjectName(), isNumber(), isUnique(), quote(), and CDataVector< CType >::size().

◆ getMetabolite()

CMetab * CMetabNameInterface::getMetabolite	(	const CModel *	model,
		const std::string &	metabolite,
		const std::string &	compartment
	)

static

This tries to find the metabolite with the given name. If the name is not unique and is given without a compartment then the first occurrence of a metabolite with this name is returned.

References C_INVALID_INDEX, CModel::findMetabByName(), CModel::getCompartments(), CDataVectorN< CType >::getIndex(), and CCompartment::getMetabolites().

Referenced by CChemEqInterface::addModifier(), CChemEqInterface::completeCompartments(), getMetaboliteKey(), and CReactionInterface::writeBackToReaction().