#include <CBitPatternMethod.h>

Inheritance diagram for CBitPatternMethod:

Public Member Functions
virtual bool	calculate ()

	CBitPatternMethod (const CBitPatternMethod &src, const CDataContainer *pParent)

	CBitPatternMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::EFMBitPatternAlgorithm, const CTaskEnum::Task &taskType=CTaskEnum::Task::fluxMode)

virtual bool	initialize ()

	~CBitPatternMethod ()

Public Member Functions inherited from CEFMMethod
	CEFMMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType=CTaskEnum::Task::fluxMode)

	CEFMMethod (const CEFMMethod &src, const CDataContainer *pParent)

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

virtual	~CEFMMethod ()

Public Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiMethod &src, const CDataContainer *pParent)

virtual void	clearCallBack ()

const CProcessReportLevel &	getCallBack () const

CMathContainer *	getMathContainer () const

const CTaskEnum::Method &	getSubType () const

const CTaskEnum::Task &	getType () const

virtual void	load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH)

CCopasiMethod &	operator= (const CCopasiMethod &rhs)

virtual void	print (std::ostream *ostream) const

virtual void	printResult (std::ostream *ostream) const

virtual bool	setCallBack (CProcessReportLevel callBack)

void	setMathContainer (CMathContainer *pContainer)

virtual	~CCopasiMethod ()

Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)

void	addParameter (CCopasiParameter *pParameter)

bool	addParameter (const CCopasiParameter &parameter)

bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

template<class CType >
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)

CCopasiParameterGroup *	assertGroup (const std::string &name, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

template<class CType >
CType *	assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

index_iterator	beginIndex () const

const_name_iterator	beginName () const

	CCopasiParameterGroup (const CCopasiParameterGroup &src, const CDataContainer *pParent=NULL)

	CCopasiParameterGroup (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="ParameterGroup")

void	clear ()

virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const

virtual bool	elevateChildren ()

index_iterator	endIndex () const

const_name_iterator	endName () const

CCopasiParameterGroup &	getElementTemplates ()

const CCopasiParameterGroup &	getElementTemplates () const

CCopasiParameterGroup *	getGroup (const size_t &index)

const CCopasiParameterGroup *	getGroup (const size_t &index) const

CCopasiParameterGroup *	getGroup (const std::string &name)

const CCopasiParameterGroup *	getGroup (const std::string &name) const

virtual size_t	getIndex (const CDataObject *pObject) const

size_t	getIndex (const std::string &name) const

std::string	getKey (const size_t &index) const

std::string	getKey (const std::string &name) const

virtual const std::string &	getName (const size_t &index) const

virtual const CObjectInterface *	getObject (const CCommonName &cn) const

CCopasiParameter *	getParameter (const size_t &index)

const CCopasiParameter *	getParameter (const size_t &index) const

CCopasiParameter *	getParameter (std::string name)

const CCopasiParameter *	getParameter (std::string name) const

CCopasiParameter::Type	getType (const size_t &index) const

CCopasiParameter::Type	getType (const std::string &name) const

std::string	getUniqueParameterName (const CCopasiParameter *pParameter) const

template<class CType >
CType &	getValue (const size_t &index)

template<class CType >
const CType &	getValue (const size_t &index) const

template<class CType >
CType &	getValue (const std::string &name)

template<class CType >
const CType &	getValue (const std::string &name) const

bool	haveTemplate () const

virtual CUndoObjectInterface *	insert (const CData &data)

CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)

virtual bool	remove (CDataObject *pObject)

bool	removeParameter (CCopasiParameter *pParameter)

bool	removeParameter (const size_t &index)

bool	removeParameter (const std::string &name)

virtual void	setUserInterfaceFlag (const UserInterfaceFlag &flag)

template<class CType >
bool	setValue (const size_t &index, const CType &value)

template<class CType >
bool	setValue (const std::string &name, const CType &value)

size_t	size (const UserInterfaceFlag &require=UserInterfaceFlag::None, const UserInterfaceFlag &exclude=UserInterfaceFlag::None) const

bool	swap (const size_t &iFrom, const size_t &iTo)

bool	swap (index_iterator &from, index_iterator &to)

virtual CData	toData () const

virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)

virtual	~CCopasiParameterGroup ()

Public Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src, const CDataContainer *pParent)

	CCopasiParameter (const std::string &name, const Type &type, const void pValue=NULL, const CDataContainer pParent=NO_PARENT, const std::string &objectType="Parameter")

virtual CCommonName	getCN () const override

template<class CType >
const CType &	getDefault () const

virtual const std::string &	getKey () const override

virtual std::string	getObjectDisplayName () const override

const CCopasiParameter::Type &	getType () const

const UserInterfaceFlag &	getUserInterfaceFlag () const

template<class CType >
std::vector< std::pair< CType, CType > > &	getValidValues ()

template<class CType >
const std::vector< std::pair< CType, CType > > &	getValidValues () const

void *	getValidValuesPointer () const

template<class CType >
CType &	getValue ()

template<class CType >
const CType &	getValue () const

virtual void *	getValuePointer () const override

CDataObject *	getValueReference () const

bool	hasValidValues () const

bool	isBasic () const

bool	isDefault () const

bool	isEditable () const

bool	isUnsupported () const

bool	isValidValue (const bool &value) const

bool	isValidValue (const C_FLOAT64 &value) const

bool	isValidValue (const C_INT32 &value) const

bool	isValidValue (const CCommonName &value) const

template<class CType >
bool	isValidValue (const CType &) const

bool	isValidValue (const std::string &value) const

bool	isValidValue (const std::vector< CCopasiParameter * > &value) const

bool	isValidValue (const unsigned C_INT32 &value) const

CCopasiParameter &	operator= (const CCopasiParameter &rhs)

template<class CType >
bool	setDefault (const CType &defaultValue)

bool	setDefault (const std::vector< CCopasiParameter * > &defaultValue)

virtual bool	setObjectParent (const CDataContainer *pParent) override

template<class CType , class Enum >
bool	setValidValues (const CEnumAnnotation< CType, Enum > &validValues)

template<class CType >
bool	setValidValues (const std::vector< std::pair< CType, CType > > &validValues)

template<class CType >
bool	setValue (const CType &value)

bool	setValue (const std::vector< CCopasiParameter * > &value)

virtual	~CCopasiParameter ()

Public Member Functions inherited from CDataContainer
virtual bool	add (CDataObject *pObject, const bool &adopt=true)

virtual bool	appendDeletedDependentData (CUndoData &undoData) const

	CDataContainer (const CDataContainer &src, const CDataContainer *pParent)

	CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

virtual std::string	getChildObjectUnits (const CDataObject *pObject) const

void	getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const

virtual objectMap &	getObjects ()

virtual const objectMap &	getObjects () const

virtual const std::string	getUnits () const override

virtual const CDataObject *	getValueObject () const override

void	objectRenamed (CDataObject *pObject, const std::string &oldName)

virtual	~CDataContainer ()

Public Member Functions inherited from CDataObject
void	addIssue (const CIssue &issue)

void	addReference (const CDataContainer *pReference)

virtual void	calculateValue () override

	CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL)

virtual void	destruct () override

virtual const CDataObject *	getDataObject () const override

CDataContainer *	getObjectAncestor (const std::string &type) const

CDataModel *	getObjectDataModel () const

const CObjectInterface *	getObjectFromCN (const CCommonName &cn) const

const std::string &	getObjectName () const

CDataContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const override

virtual const CValidity &	getValidity () const override

bool	hasFlag (const Flag &flag) const

virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override

bool	prerequisitsContains (const DataObjectSet &objects) const

void	removeIssue (const CIssue &issue)

void	removeReference (const CDataContainer *pReference)

bool	setObjectName (const std::string &name)

void	validityChanged (const CValidity &changedValidity) override

void	validityRemoved (const CValidity &changedValidity)

virtual	~CDataObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

	CObjectInterface (const CObjectInterface &src)

virtual	~CObjectInterface ()

Public Member Functions inherited from CUndoObjectInterface
	CUndoObjectInterface ()

	CUndoObjectInterface (const CUndoObjectInterface &src)

bool	generateUuid ()

const xg::Guid &	getUuid () const

bool	setUuid (const std::string &uuid)

bool	setUuid (const xg::Guid &uuid)

virtual	~CUndoObjectInterface ()

Static Public Member Functions
static bool	CalculateKernel (CMatrix< C_INT64 > &matrix, CMatrix< C_INT64 > &kernel, CVector< size_t > &rowPivot)

static void	GCD (C_INT64 &m, C_INT64 &n)

Static Public Member Functions inherited from CCopasiParameter
static void	allocateValidValues (const Type &type, void *&pValidValues)

static void	allocateValue (const Type &type, void *&pValue)

static void	assignValue (const Type &type, void &pValue, const void pNewValue)

static void	deleteValidValues (const Type &type, void *&pValidValues)

static void	deleteValue (const Type &type, void *&pValue)

static CCopasiParameter *	fromData (const CData &data, CUndoObjectInterface *pParent)

Static Public Member Functions inherited from CDataContainer
static CDataContainer *	fromData (const CData &data, CUndoObjectInterface *pParent)

Static Public Member Functions inherited from CDataObject
static CDataObject *	fromData (const CData &data, CUndoObjectInterface *pParent)

static void	sanitizeObjectName (std::string &name)

Static Public Member Functions inherited from CObjectInterface
static const CDataObject *	DataObject (const CObjectInterface *pInterface)

static CObjectInterface *	GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName)

Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType *	fromData (const CData &, CUndoObjectInterface *)

Protected Attributes
bool	mContinueCombination

CMatrix< C_INT64 >	mExpandedStoiTranspose

size_t	mhProgressCounter

size_t	mhProgressCounter2

size_t	mMinimumSetSize

std::vector< CStepMatrixColumn * >	mNewColumns

const CModel *	mpModel

unsigned C_INT32	mProgressCounter

unsigned C_INT32	mProgressCounter2

unsigned C_INT32	mProgressCounter2Max

unsigned C_INT32	mProgressCounterMax

CStepMatrix *	mpStepMatrix

std::vector< std::pair< size_t, bool > >	mReactionForward

CVector< size_t >	mReactionPivot

size_t	mStep

Protected Attributes inherited from CEFMMethod
std::vector< CFluxMode > *	mpFluxModes

std::vector< const CReaction * > *	mpReorderedReactions

Protected Attributes inherited from CCopasiMethod
CMathContainer *	mpContainer

CProcessReportLevel	mProcessReport

Protected Attributes inherited from CCopasiParameter
std::string	mKey

void *	mpDefault

void *	mpValidValues

void *	mpValue

CDataObject *	mpValueReference

UserInterfaceFlag	mUserInterfaceFlag

Protected Attributes inherited from CDataContainer
objectMap	mObjects

Protected Attributes inherited from CDataObject
ObjectSet	mPrerequisits

std::set< CDataContainer * >	mReferences

Protected Attributes inherited from CObjectInterface
CValidity	mValidity

Private Member Functions
void	addMode (const CFluxMode &mode)

void	buildFluxModeMatrix (CStepMatrix fluxModeMatrix, std::stack< CStepMatrixColumn > kernelStack)

void	buildFluxModes ()

void	buildKernelMatrix (CMatrix< C_INT64 > &kernel)

	CBitPatternMethod ()

void	combine (const CStepMatrixColumn pPositive, const CStepMatrixColumn pNegative, const std::vector< CStepMatrixColumn * > NullColumns)

void	findRemoveInvalidColumns (const std::vector< CStepMatrixColumn * > &nullColumns)

void	getAllUnsetBitIndexes (const CStepMatrixColumn *pColumn, CVector< size_t > &indexes) const

void	getUnsetBitIndexes (const CStepMatrixColumn *pColumn, CVector< size_t > &indexes) const

void	initObjects ()

CMatrix< C_INT64 >	performRankTest (CStepMatrixColumn *pIntersectColumn)

Additional Inherited Members
Public Types inherited from CCopasiParameterGroup
typedef CDataObjectMap::const_type_iterator< CCopasiParameter >	const_name_iterator

typedef std::vector< CCopasiParameter * >	elements

typedef elements::iterator	index_iterator

typedef CDataObjectMap::type_iterator< CCopasiParameter >	name_iterator

Public Types inherited from CCopasiParameter
enum class	eUserInterfaceFlag { editable , basic , unsupported , __SIZE }

enum class	Type { DOUBLE = 0 , UDOUBLE , INT , UINT , BOOL , GROUP , STRING , CN , KEY , FILE , EXPRESSION , INVALID , __SIZE }

typedef CFlags< eUserInterfaceFlag >	UserInterfaceFlag

Public Types inherited from CDataContainer
typedef CDataObjectMap	objectMap

Public Types inherited from CDataObject
typedef std::set< const CDataObject * >	DataObjectSet

enum	Flag { Container , Vector , Matrix , NameVector , Reference , ValueBool , ValueInt , ValueInt64 , ValueDbl , NonUniqueName , StaticString , ValueString , Separator , DisplayName , ModelEntity , Array , DataModel , Root , Gui , __SIZE }

Public Types inherited from CObjectInterface
typedef std::vector< const CDataContainer * >	ContainerList

typedef std::set< const CObjectInterface * >	ObjectSet

Static Public Attributes inherited from CCopasiParameter
static const CEnumAnnotation< std::string, Type >	TypeName

static const CEnumAnnotation< std::string, Type >	XMLType

Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList

Protected Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiMethod &src)

	CCopasiMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType)

virtual void	signalMathContainerChanged ()

Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()

Protected Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src)

Protected Member Functions inherited from CDataContainer
template<class CType >
CDataMatrixReference< CType > *	addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

template<class CType >
CDataObjectReference< CType > *	addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

template<class CType >
CDataVectorReference< CType > *	addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

	CDataContainer (const CDataContainer &src)

void	initObjects ()

Protected Member Functions inherited from CDataObject
	CDataObject ()

	CDataObject (const std::string &name, const CDataContainer pParent=static_cast< CDataContainer >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

Constructor & Destructor Documentation

◆ CBitPatternMethod() [1/3]

CBitPatternMethod::CBitPatternMethod ( )

private

Default constructor.

◆ CBitPatternMethod() [2/3]

CBitPatternMethod::CBitPatternMethod	(	const CDataContainer *	pParent,
		const CTaskEnum::Method &	methodType = `CTaskEnum::Method::EFMBitPatternAlgorithm`,
		const CTaskEnum::Task &	taskType = `CTaskEnum::Task::fluxMode`
	)

Specific constructor

Parameters

const	CDataContainer * pParent
const	CTaskEnum::Method & methodType (default: EFMBitPatternAlgorithm)
const	CTaskEnum::Task & taskType (default: fluxMode)

References initObjects().

◆ CBitPatternMethod() [3/3]

CBitPatternMethod::CBitPatternMethod	(	const CBitPatternMethod &	src,
		const CDataContainer *	pParent
	)

Copy Constructor

Parameters

const CBitPatternMethod & src

References initObjects().

◆ ~CBitPatternMethod()

CBitPatternMethod::~CBitPatternMethod ( )

Destructor

Member Function Documentation

◆ addMode()

void CBitPatternMethod::addMode ( const CFluxMode & mode )

private

Add the flux mode to the list only if the reversed does not exist

Parameters

const CFluxMode & mode

References CEFMMethod::mpFluxModes.

Referenced by buildFluxModes().

◆ buildFluxModeMatrix()

void CBitPatternMethod::buildFluxModeMatrix	(	CStepMatrix *	fluxModeMatrix,
		std::stack< CStepMatrixColumn * >	kernelStack
	)

private

References CStepMatrix::add(), CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), performRankTest(), and CStepMatrixColumn::push_front().

◆ buildFluxModes()

void CBitPatternMethod::buildFluxModes ( )

private

Postprocess the step matrix to construct the flux modes.

References addMode(), CMatrix< CType >::array(), CVectorCore< CType >::array(), CStepMatrix::begin(), C_FLOAT64, C_INT64, CalculateKernel(), CStepMatrix::end(), getUnsetBitIndexes(), mExpandedStoiTranspose, CEFMMethod::mpReorderedReactions, mpStepMatrix, mReactionForward, CMatrix< CType >::numCols(), and CVectorCore< CType >::size().

Referenced by calculate().

◆ buildKernelMatrix()

void CBitPatternMethod::buildKernelMatrix ( CMatrix< C_INT64 > & kernel )

private

Construct the kernel matrix

Parameters

CMatrix< C_FLOAT64> & kernel

References CMatrix< CType >::array(), CDataVector< CType >::begin(), C_FLOAT64, C_INT64, CalculateKernel(), CDataVector< CType >::end(), CModel::getReactions(), CModel::getRedStoi(), mExpandedStoiTranspose, min, mpModel, CEFMMethod::mpReorderedReactions, mReactionForward, mReactionPivot, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), CMatrix< CType >::resize(), and CMatrix< CType >::size().

Referenced by initialize().

◆ calculate()

bool CBitPatternMethod::calculate ( void )

virtual

Execute the optimization algorithm calling simulation routine when needed. It is noted that this procedure can give feedback of its progress by the callback function set with SetCallback. @ return success;

Reimplemented from CEFMMethod.

References CProcessReportLevel::addItem(), buildFluxModes(), C_INT32, combine(), CStepMatrix::compact(), CStepMatrix::convertRow(), findRemoveInvalidColumns(), CProcessReportLevel::finishItem(), CStepMatrix::getFirstUnconvertedRow(), CStepMatrix::getNumUnconvertedRows(), initialize(), mContinueCombination, mhProgressCounter, mhProgressCounter2, CCopasiMethod::mProcessReport, mProgressCounter, mProgressCounter2, mProgressCounter2Max, mProgressCounterMax, mpStepMatrix, mStep, CProcessReportLevel::progressItem(), CStepMatrix::removeInvalidColumns(), and CStepMatrix::splitColumns().

◆ CalculateKernel()

bool CBitPatternMethod::CalculateKernel	(	CMatrix< C_INT64 > &	matrix,
		CMatrix< C_INT64 > &	kernel,
		CVector< size_t > &	rowPivot
	)

static

A static method that calculates the kernel of a full column rank matrix. Note, the input matrix is used as work area and will be modified during the calculation.

Parameters

const	CMatrix< C_INT64 > & matrix
CMatrix<	C_INT64 > & kernel
CVector<	size_t > & rowPivot

Returns: bool success

References abs64, CMatrix< CType >::array(), CVectorCore< CType >::array(), C_FLOAT64, C_INT64, GCD(), max, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), CMatrix< CType >::resize(), CVector< CType >::resize(), and CMatrix< CType >::size().

Referenced by buildFluxModes(), buildKernelMatrix(), and performRankTest().

◆ combine()

void CBitPatternMethod::combine	(	const CStepMatrixColumn *	pPositive,
		const CStepMatrixColumn *	pNegative,
		const std::vector< CStepMatrixColumn * >	NullColumns
	)

private

Create all possible linear combinations of the bit pattern nodes pPositive and pNegative and all their child nodes.

Parameters

const	CBitPatternTreeNode * pPositive
const	CBitPatternTreeNode * pNegative

References CStepMatrix::addColumn(), CZeroSet::getNumberOfSetBits(), CStepMatrixColumn::getZeroSet(), CZeroSet::intersection(), CZeroSet::isExtremeRay(), mContinueCombination, mhProgressCounter2, mMinimumSetSize, mNewColumns, CCopasiMethod::mProcessReport, mProgressCounter2, mpStepMatrix, CMatrix< CType >::numCols(), performRankTest(), CProcessReportLevel::proceed(), CProcessReportLevel::progressItem(), and CStepMatrix::removeColumn().

Referenced by calculate().

◆ findRemoveInvalidColumns()

void CBitPatternMethod::findRemoveInvalidColumns ( const std::vector< CStepMatrixColumn * > & nullColumns )

private

Remove the invalid columns from the step matrix

Parameters

const std::vector< CStepMatrix::iterator > & nullColumns

References mNewColumns, mpStepMatrix, and CStepMatrix::removeInvalidColumns().

Referenced by calculate().

◆ GCD()

static void CBitPatternMethod::GCD	(	C_INT64 &	m,
		C_INT64 &	n
	)

inlinestatic

Calculate the greatest common divisor (GCD) of 2 positive integers. On return m and n contain the GCD

Parameters

C_INT64	& m
C_INT64	& n

Referenced by CalculateKernel().

◆ getAllUnsetBitIndexes()

void CBitPatternMethod::getAllUnsetBitIndexes	(	const CStepMatrixColumn *	pColumn,
		CVector< size_t > &	indexes
	)		const

private

References CVectorCore< CType >::array(), CStepMatrix::getAllUnsetBitIndexes(), mpStepMatrix, mReactionPivot, and CVectorCore< CType >::size().

Referenced by performRankTest().

◆ getUnsetBitIndexes()

void CBitPatternMethod::getUnsetBitIndexes	(	const CStepMatrixColumn *	pColumn,
		CVector< size_t > &	indexes
	)		const

private

Get the index of the unset bits of the flux mode.

References CVectorCore< CType >::array(), CStepMatrix::getUnsetBitIndexes(), mpStepMatrix, mReactionPivot, and CVectorCore< CType >::size().

Referenced by buildFluxModes().

◆ initialize()

bool CBitPatternMethod::initialize ( )

virtual

Initialize arrays and pointer.

Returns: bool success

Reimplemented from CEFMMethod.

References CProcessReportLevel::addItem(), buildKernelMatrix(), C_INT32, CMathContainer::getModel(), CStepMatrix::getNumUnconvertedRows(), CDataObject::getObjectParent(), CEFMMethod::initialize(), mContinueCombination, mhProgressCounter, mMinimumSetSize, CCopasiMethod::mpContainer, mpModel, CCopasiMethod::mProcessReport, mProgressCounter, mProgressCounterMax, mpStepMatrix, mReactionForward, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), pdelete, and CStepMatrixColumn::push_front().

Referenced by calculate().

◆ initObjects()

void CBitPatternMethod::initObjects ( )

private

Initialize the needed CDataObjects.

References CDataContainer::addObjectReference(), mProgressCounter, and CDataObject::ValueInt.

Referenced by CBitPatternMethod().

◆ performRankTest()

CMatrix< C_INT64 > CBitPatternMethod::performRankTest ( CStepMatrixColumn * pIntersectColumn )

private

Performs rank test on given intersection.

References CMatrix< CType >::array(), CVectorCore< CType >::array(), C_INT64, CalculateKernel(), getAllUnsetBitIndexes(), mExpandedStoiTranspose, CMatrix< CType >::numCols(), and CVectorCore< CType >::size().

Referenced by buildFluxModeMatrix(), and combine().

Member Data Documentation

◆ mContinueCombination

bool CBitPatternMethod::mContinueCombination

protected

Boolean value indicating whether combination should continue.

Referenced by calculate(), combine(), and initialize().

◆ mExpandedStoiTranspose

CMatrix< C_INT64 > CBitPatternMethod::mExpandedStoiTranspose

protected

The transpose of the expanded stoichiometry matrix.

Referenced by buildFluxModes(), buildKernelMatrix(), and performRankTest().

◆ mhProgressCounter

size_t CBitPatternMethod::mhProgressCounter

protected

Handle to the process report item "Current Step"

Referenced by calculate(), and initialize().

◆ mhProgressCounter2

size_t CBitPatternMethod::mhProgressCounter2

protected

Handle to the process report item "Combination"

Referenced by calculate(), and combine().

◆ mMinimumSetSize

size_t CBitPatternMethod::mMinimumSetSize

protected

The minimum set size use to determine whether a linear combination is allowed.

Referenced by combine(), and initialize().

◆ mNewColumns

std::vector< CStepMatrixColumn * > CBitPatternMethod::mNewColumns

protected

A list of invalid columns currently in the step matrix

Referenced by combine(), and findRemoveInvalidColumns().

◆ mpModel

const CModel* CBitPatternMethod::mpModel

protected

A pointer to the model which is analyzed.

Referenced by buildKernelMatrix(), and initialize().

◆ mProgressCounter

unsigned C_INT32 CBitPatternMethod::mProgressCounter

protected

The current step used for process report.

Referenced by calculate(), initialize(), and initObjects().

◆ mProgressCounter2

unsigned C_INT32 CBitPatternMethod::mProgressCounter2

protected

The current combination used for process report.

Referenced by calculate(), and combine().

◆ mProgressCounter2Max

unsigned C_INT32 CBitPatternMethod::mProgressCounter2Max

protected

The max combination used for process report.

Referenced by calculate().

◆ mProgressCounterMax

unsigned C_INT32 CBitPatternMethod::mProgressCounterMax

protected

The max step used for process report.

Referenced by calculate(), and initialize().

◆ mpStepMatrix

CStepMatrix* CBitPatternMethod::mpStepMatrix

protected

A pointer to the step matrix for creating the flux modes

Referenced by buildFluxModes(), calculate(), combine(), findRemoveInvalidColumns(), getAllUnsetBitIndexes(), getUnsetBitIndexes(), and initialize().

◆ mReactionForward

std::vector< std::pair< size_t, bool > > CBitPatternMethod::mReactionForward

protected

A vector to recording the expansion of the stoichiometry matrix.

Referenced by buildFluxModes(), buildKernelMatrix(), and initialize().

◆ mReactionPivot

CVector< size_t > CBitPatternMethod::mReactionPivot

protected

A vector recording the pivots for the QR factorization

Referenced by buildKernelMatrix(), getAllUnsetBitIndexes(), and getUnsetBitIndexes().

◆ mStep

size_t CBitPatternMethod::mStep

protected

The currently process step

Referenced by calculate().

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

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ CBitPatternMethod() [1/3]

◆ CBitPatternMethod() [2/3]

◆ CBitPatternMethod() [3/3]

◆ ~CBitPatternMethod()

Member Function Documentation

◆ addMode()

◆ buildFluxModeMatrix()

◆ buildFluxModes()

◆ buildKernelMatrix()

◆ calculate()

◆ CalculateKernel()

◆ combine()

◆ findRemoveInvalidColumns()

◆ GCD()

◆ getAllUnsetBitIndexes()

◆ getUnsetBitIndexes()

◆ initialize()

◆ initObjects()

◆ performRankTest()

Member Data Documentation

◆ mContinueCombination

◆ mExpandedStoiTranspose

◆ mhProgressCounter

◆ mhProgressCounter2

◆ mMinimumSetSize

◆ mNewColumns

◆ mpModel

◆ mProgressCounter

◆ mProgressCounter2

◆ mProgressCounter2Max

◆ mProgressCounterMax

◆ mpStepMatrix

◆ mReactionForward

◆ mReactionPivot

◆ mStep