CChemEqInterface Class Reference

#include <CChemEqInterface.h>

Public Member Functions
void	addModifier (const std::string &name)
	CChemEqInterface ()
void	clearAll ()
void	clearModifiers ()
bool	createNonExistingMetabs (std::vector< std::string > &createdKeys)
std::pair< std::string, std::string >	displayNameToNamePair (CFunctionParameter::Role role, const std::string displayName) const
bool	fromDataValue (const std::string &dataValue)
std::string	getChemEqString (bool expanded) const
const CCompartment *	getCompartment () const
std::set< std::string >	getCompartments () const
std::string	getDefaultCompartment () const
const std::vector< std::string > &	getListOfCompartments (CFunctionParameter::Role role) const
const std::vector< std::string > &	getListOfDisplayNames (CFunctionParameter::Role role) const
const std::vector< C_FLOAT64 > &	getListOfMultiplicities (CFunctionParameter::Role role) const
const std::vector< std::string > &	getListOfSpecies (CFunctionParameter::Role role) const
size_t	getMolecularity (CFunctionParameter::Role role) const
bool	getReversibility () const
bool	init (const CChemEq &ce)
bool	isMulticompartment () const
std::set< std::pair< std::string, std::string > >	listOfNonExistingMetabNames () const
std::set< std::string >	listOfNonUniqueMetabNames () const
void	reverse ()
bool	setChemEqString (const std::string &ces)
void	setReversibility (bool rev)
std::string	toDataValue () const
bool	writeToChemEq (CChemEq *pChemEq=NULL) const
	~CChemEqInterface ()

Static Public Member Functions
static std::string	getChemEqString (const CReaction &rea, bool expanded)
static bool	isValidEq (const std::string &eq)
static bool	setChemEqFromString (CReaction &rea, const std::string &ces)

Private Member Functions
void	buildDisplayNames ()
void	completeCompartments ()

Static Private Member Functions
static std::string	writeElement (const std::string &name, C_FLOAT64 mult, bool expanded)

Private Attributes
std::vector< std::string >	mModifierCompartments
std::vector< std::string >	mModifierDisplayNames
std::vector< C_FLOAT64 >	mModifierMult
std::vector< std::string >	mModifierNames
const CChemEq *	mpChemEq
CModel *	mpModel
std::vector< std::string >	mProductCompartments
std::vector< std::string >	mProductDisplayNames
std::vector< C_FLOAT64 >	mProductMult
std::vector< std::string >	mProductNames
bool	mReversibility
std::vector< std::string >	mSubstrateCompartments
std::vector< std::string >	mSubstrateDisplayNames
std::vector< C_FLOAT64 >	mSubstrateMult
std::vector< std::string >	mSubstrateNames

Detailed Description

This class describes a chemical equation based on metabolite names It supports parsing and generating string representations. Note that this class handles only metab names without caring about whether these metabs exist in the model. There is however a method to create the missing metabs.

Constructor & Destructor Documentation

CChemEqInterface()

CChemEqInterface::CChemEqInterface

(

)

~CChemEqInterface()

CChemEqInterface::~CChemEqInterface

(

)

Member Function Documentation

addModifier()

void CChemEqInterface::addModifier

(

const std::string &

name

)

add a modifier to the chemical equation. It is only added if it is not already in there.

References CMetab::getCompartment(), CMetabNameInterface::getDisplayName(), CMetabNameInterface::getMetabolite(), CDataObject::getObjectName(), mModifierCompartments, mModifierDisplayNames, mModifierMult, mModifierNames, mpModel, quote(), and CMetabNameInterface::splitDisplayName().

Referenced by CReactionInterface::updateModifiersInChemEq().

buildDisplayNames()

void CChemEqInterface::buildDisplayNames ( )

private

References CMetabNameInterface::getDisplayName(), mModifierCompartments, mModifierDisplayNames, mModifierNames, mpModel, mProductCompartments, mProductDisplayNames, mProductNames, mSubstrateCompartments, mSubstrateDisplayNames, and mSubstrateNames.

Referenced by createNonExistingMetabs(), init(), and setChemEqString().

clearAll()

void CChemEqInterface::clearAll

(

)

References mModifierCompartments, mModifierDisplayNames, mModifierMult, mModifierNames, mProductCompartments, mProductDisplayNames, mProductMult, mProductNames, mSubstrateCompartments, mSubstrateDisplayNames, mSubstrateMult, and mSubstrateNames.

Referenced by CReactionInterface::clearChemEquation(), and init().

clearModifiers()

void CChemEqInterface::clearModifiers

(

)

References mModifierCompartments, mModifierDisplayNames, mModifierMult, and mModifierNames.

Referenced by CReactionInterface::updateModifiersInChemEq().

completeCompartments()

void CChemEqInterface::completeCompartments ( )

private

References CMetab::getCompartment(), CModel::getCompartments(), CMetabNameInterface::getMetabolite(), CDataObject::getObjectName(), CMetabNameInterface::isUnique(), mModifierCompartments, mModifierNames, mpModel, mProductCompartments, mProductNames, mSubstrateCompartments, mSubstrateNames, and CDataVector< CType >::size().

Referenced by setChemEqString().

createNonExistingMetabs()

bool CChemEqInterface::createNonExistingMetabs

(

std::vector< std::string > &

createdKeys

)

creates all necessary metabolites (and volumes)

Parameters

createdKeys

this vector will be filled with keys of created elements

Returns

true, in case some elements were created, false otherwise

References buildDisplayNames(), C_INVALID_INDEX, CModel::createCompartment(), CModel::createMetabolite(), CModel::getCompartments(), CDataVectorN< CType >::getIndex(), CModelEntity::getKey(), CDataContainer::insert(), listOfNonExistingMetabNames(), mpModel, and CModelEntity::REACTIONS.

Referenced by CReactionInterface::createMetabolites().

displayNameToNamePair()

std::pair< std::string, std::string > CChemEqInterface::displayNameToNamePair	(	CFunctionParameter::Role	role,
		const std::string	displayName
	)		const

References getListOfCompartments(), getListOfDisplayNames(), getListOfSpecies(), and CMetabNameInterface::unQuote().

Referenced by CReactionInterface::createUndoData().

fromDataValue()

bool CChemEqInterface::fromDataValue

(

const std::string &

dataValue

)

References setChemEqString().

Referenced by CReaction::applyData().

getChemEqString() [1/2]

std::string CChemEqInterface::getChemEqString

(

bool

expanded

)

const

References mModifierDisplayNames, mModifierNames, mProductDisplayNames, mProductMult, mProductNames, mReversibility, mSubstrateDisplayNames, mSubstrateMult, mSubstrateNames, and writeElement().

Referenced by CReactionInterface::getChemEqString(), getChemEqString(), and CEFMTask::getReactionEquation().

getChemEqString() [2/2]

std::string CChemEqInterface::getChemEqString ( const CReaction &  rea, bool  expanded  )

static

References CReaction::getChemEq(), getChemEqString(), and init().

getCompartment()

const CCompartment * CChemEqInterface::getCompartment

(

)

const

convenience method. If the reaction is single compartment the compartment is returned, else NULL.

References CMetab::getCompartment(), CChemEq::getProducts(), CChemEq::getSubstrates(), isMulticompartment(), CDataVector< CType >::size(), and writeToChemEq().

Referenced by CReactionInterface::connectNonMetabolites().

getCompartments()

std::set< std::string > CChemEqInterface::getCompartments

(

)

const

References mModifierCompartments, mProductCompartments, and mSubstrateCompartments.

getDefaultCompartment()

std::string CChemEqInterface::getDefaultCompartment

(

)

const

References mModifierCompartments, mProductCompartments, and mSubstrateCompartments.

Referenced by CReactionInterface::getDefaultScalingCompartment().

getListOfCompartments()

const std::vector< std::string > & CChemEqInterface::getListOfCompartments

(

CFunctionParameter::Role

role

)

const

References fatalError, mModifierCompartments, CFunctionParameter::MODIFIER, mProductCompartments, mSubstrateCompartments, CFunctionParameter::PRODUCT, and CFunctionParameter::SUBSTRATE.

Referenced by displayNameToNamePair().

getListOfDisplayNames()

const std::vector< std::string > & CChemEqInterface::getListOfDisplayNames

(

CFunctionParameter::Role

role

)

const

References fatalError, mModifierDisplayNames, CFunctionParameter::MODIFIER, mProductDisplayNames, mSubstrateDisplayNames, CFunctionParameter::PRODUCT, and CFunctionParameter::SUBSTRATE.

Referenced by CReactionInterface::connectFromScratch(), displayNameToNamePair(), CReactionInterface::findAndSetFunction(), CReactionInterface::getExpandedMetabList(), CReactionInterface::getListOfMetabs(), CReactionInterface::isLocked(), and CReactionInterface::setMapping().

getListOfMultiplicities()

const std::vector< C_FLOAT64 > & CChemEqInterface::getListOfMultiplicities

(

CFunctionParameter::Role

role

)

const

References fatalError, mModifierMult, CFunctionParameter::MODIFIER, mProductMult, mSubstrateMult, CFunctionParameter::PRODUCT, and CFunctionParameter::SUBSTRATE.

Referenced by CReactionInterface::getExpandedMetabList().

getListOfSpecies()

const std::vector< std::string > & CChemEqInterface::getListOfSpecies

(

CFunctionParameter::Role

role

)

const

References fatalError, mModifierNames, CFunctionParameter::MODIFIER, mProductNames, mSubstrateNames, CFunctionParameter::PRODUCT, and CFunctionParameter::SUBSTRATE.

Referenced by displayNameToNamePair().

getMolecularity()

size_t CChemEqInterface::getMolecularity

(

CFunctionParameter::Role

role

)

const

References C_INVALID_INDEX, fatalError, mModifierMult, CFunctionParameter::MODIFIER, mProductMult, mSubstrateMult, CFunctionParameter::PRODUCT, and CFunctionParameter::SUBSTRATE.

Referenced by CReactionInterface::getFunction(), and CReactionInterface::getListOfPossibleFunctions().

getReversibility()

bool CChemEqInterface::getReversibility

(

)

const

References mReversibility.

Referenced by CReactionInterface::findAndSetFunction(), and CReactionInterface::isReversible().

init()

bool CChemEqInterface::init

(

const CChemEq &

ce

)

References buildDisplayNames(), clearAll(), CMetab::getCompartment(), CChemEq::getModifiers(), CDataObject::getObjectAncestor(), CDataObject::getObjectName(), CChemEq::getProducts(), CChemEq::getReversibility(), CChemEq::getSubstrates(), mModifierCompartments, mModifierMult, mModifierNames, mpChemEq, mpModel, mProductCompartments, mProductMult, mProductNames, mReversibility, mSubstrateCompartments, mSubstrateMult, mSubstrateNames, and CDataVector< CType >::size().

Referenced by CReaction::applyData(), CReaction::createUndoData(), getChemEqString(), CReactionInterface::init(), setChemEqFromString(), and CReaction::toData().

isMulticompartment()

bool CChemEqInterface::isMulticompartment

(

)

const

this method tries to find out if the chemical equation involves several compartments in a given model. It only takes into account the metabs that actually exist in the model. A non existing metabolite is assumed not to be in a different compartment

References mModifierCompartments, mProductCompartments, and mSubstrateCompartments.

Referenced by getCompartment(), and CReactionInterface::isMulticompartment().

isValidEq()

bool CChemEqInterface::isValidEq ( const std::string &  eq )

static

References CChemEqParserBase::yyparse().

listOfNonExistingMetabNames()

std::set< std::pair< std::string, std::string > > CChemEqInterface::listOfNonExistingMetabNames

(

)

const

References CMetabNameInterface::doesExist(), mModifierCompartments, mModifierNames, mpModel, mProductCompartments, mProductNames, mSubstrateCompartments, and mSubstrateNames.

Referenced by createNonExistingMetabs(), and CReactionInterface::createUndoData().

listOfNonUniqueMetabNames()

std::set< std::string > CChemEqInterface::listOfNonUniqueMetabNames

(

)

const

References CMetabNameInterface::isUnique(), mModifierNames, mpModel, mProductNames, and mSubstrateNames.

reverse()

void CChemEqInterface::reverse

(

)

References mProductCompartments, mProductMult, mProductNames, mSubstrateCompartments, mSubstrateMult, and mSubstrateNames.

Referenced by CReactionInterface::reverse().

setChemEqFromString()

bool CChemEqInterface::setChemEqFromString ( CReaction &  rea, const std::string &  ces  )

static

References CReaction::getChemEq(), init(), setChemEqString(), and writeToChemEq().

Referenced by CReaction::load().

setChemEqString()

bool CChemEqInterface::setChemEqString

(

const std::string &

ces

)

References buildDisplayNames(), completeCompartments(), CChemEqParserBase::getModifierCompartments(), CChemEqParserBase::getModifierMulitplicities(), CChemEqParserBase::getModifierNames(), CChemEqParserBase::getProductCompartments(), CChemEqParserBase::getProductMulitplicities(), CChemEqParserBase::getProductNames(), CChemEqParserBase::getSubstrateCompartments(), CChemEqParserBase::getSubstrateMulitplicities(), CChemEqParserBase::getSubstrateNames(), CChemEqParserBase::isReversible(), mModifierCompartments, mModifierMult, mModifierNames, mProductCompartments, mProductMult, mProductNames, mReversibility, mSubstrateCompartments, mSubstrateMult, mSubstrateNames, and CChemEqParserBase::yyparse().

Referenced by fromDataValue(), setChemEqFromString(), and CReactionInterface::setChemEqString().

setReversibility()

void CChemEqInterface::setReversibility

(

bool

rev

)

References mReversibility.

Referenced by CReactionInterface::reverse(), and CReactionInterface::setReversibility().

toDataValue()

std::string CChemEqInterface::toDataValue

(

)

const

References CMetabNameInterface::createUniqueDisplayName(), mModifierCompartments, mModifierNames, mProductCompartments, mProductMult, mProductNames, mReversibility, mSubstrateCompartments, mSubstrateMult, and mSubstrateNames.

Referenced by CReactionInterface::createUndoData(), CReaction::createUndoData(), and CReaction::toData().

writeElement()

std::string CChemEqInterface::writeElement ( const std::string &  name, C_FLOAT64  mult, bool  expanded  )

staticprivate

References C_INT32, and isNumber().

Referenced by getChemEqString().

writeToChemEq()

bool CChemEqInterface::writeToChemEq

(

CChemEq *

pChemEq = NULL

)

const

References CChemEq::addMetabolite(), CChemEq::cleanup(), CMetabNameInterface::getMetaboliteKey(), CDataObject::getObjectAncestor(), mModifierCompartments, mModifierMult, mModifierNames, CChemEq::MODIFIER, mpChemEq, mpModel, mProductCompartments, mProductMult, mProductNames, mReversibility, mSubstrateCompartments, mSubstrateMult, mSubstrateNames, CChemEq::PRODUCT, CChemEq::setReversibility(), and CChemEq::SUBSTRATE.

Referenced by CReaction::applyData(), getCompartment(), setChemEqFromString(), and CReactionInterface::writeBackToReaction().

Member Data Documentation

mModifierCompartments

std::vector< std::string > CChemEqInterface::mModifierCompartments

private

Referenced by addModifier(), buildDisplayNames(), clearAll(), clearModifiers(), completeCompartments(), getCompartments(), getDefaultCompartment(), getListOfCompartments(), init(), isMulticompartment(), listOfNonExistingMetabNames(), setChemEqString(), toDataValue(), and writeToChemEq().

mModifierDisplayNames

std::vector< std::string > CChemEqInterface::mModifierDisplayNames

private

Referenced by addModifier(), buildDisplayNames(), clearAll(), clearModifiers(), getChemEqString(), and getListOfDisplayNames().

mModifierMult

std::vector< C_FLOAT64 > CChemEqInterface::mModifierMult

private

Referenced by addModifier(), clearAll(), clearModifiers(), getListOfMultiplicities(), getMolecularity(), init(), setChemEqString(), and writeToChemEq().

mModifierNames

std::vector< std::string > CChemEqInterface::mModifierNames

private

Referenced by addModifier(), buildDisplayNames(), clearAll(), clearModifiers(), completeCompartments(), getChemEqString(), getListOfSpecies(), init(), listOfNonExistingMetabNames(), listOfNonUniqueMetabNames(), setChemEqString(), toDataValue(), and writeToChemEq().

mpChemEq

const CChemEq* CChemEqInterface::mpChemEq

private

Referenced by init(), and writeToChemEq().

mpModel

CModel* CChemEqInterface::mpModel

mutableprivate

Referenced by addModifier(), buildDisplayNames(), completeCompartments(), createNonExistingMetabs(), init(), listOfNonExistingMetabNames(), listOfNonUniqueMetabNames(), and writeToChemEq().

mProductCompartments

std::vector< std::string > CChemEqInterface::mProductCompartments

private

Referenced by buildDisplayNames(), clearAll(), completeCompartments(), getCompartments(), getDefaultCompartment(), getListOfCompartments(), init(), isMulticompartment(), listOfNonExistingMetabNames(), reverse(), setChemEqString(), toDataValue(), and writeToChemEq().

mProductDisplayNames

std::vector< std::string > CChemEqInterface::mProductDisplayNames

private

Referenced by buildDisplayNames(), clearAll(), getChemEqString(), and getListOfDisplayNames().

mProductMult

std::vector< C_FLOAT64 > CChemEqInterface::mProductMult

private

Referenced by clearAll(), getChemEqString(), getListOfMultiplicities(), getMolecularity(), init(), reverse(), setChemEqString(), toDataValue(), and writeToChemEq().

mProductNames

std::vector< std::string > CChemEqInterface::mProductNames

private

Referenced by buildDisplayNames(), clearAll(), completeCompartments(), getChemEqString(), getListOfSpecies(), init(), listOfNonExistingMetabNames(), listOfNonUniqueMetabNames(), reverse(), setChemEqString(), toDataValue(), and writeToChemEq().

mReversibility

bool CChemEqInterface::mReversibility

private

Referenced by getChemEqString(), getReversibility(), init(), setChemEqString(), setReversibility(), toDataValue(), and writeToChemEq().

mSubstrateCompartments

std::vector< std::string > CChemEqInterface::mSubstrateCompartments

private

Referenced by buildDisplayNames(), clearAll(), completeCompartments(), getCompartments(), getDefaultCompartment(), getListOfCompartments(), init(), isMulticompartment(), listOfNonExistingMetabNames(), reverse(), setChemEqString(), toDataValue(), and writeToChemEq().

mSubstrateDisplayNames

std::vector< std::string > CChemEqInterface::mSubstrateDisplayNames

private

Referenced by buildDisplayNames(), clearAll(), getChemEqString(), and getListOfDisplayNames().

mSubstrateMult

std::vector< C_FLOAT64 > CChemEqInterface::mSubstrateMult

private

Referenced by clearAll(), getChemEqString(), getListOfMultiplicities(), getMolecularity(), init(), reverse(), setChemEqString(), toDataValue(), and writeToChemEq().

mSubstrateNames

std::vector< std::string > CChemEqInterface::mSubstrateNames

private

Referenced by buildDisplayNames(), clearAll(), completeCompartments(), getChemEqString(), getListOfSpecies(), init(), listOfNonExistingMetabNames(), listOfNonUniqueMetabNames(), reverse(), setChemEqString(), toDataValue(), and writeToChemEq().

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

• CChemEqInterface.h
• CChemEqInterface.cpp