CBitPatternTreeMethod Class Reference

#include <CBitPatternTreeMethod.h>

Inheritance diagram for CBitPatternTreeMethod:

List of all members.

Public Member Functions
	CBitPatternTreeMethod (const CBitPatternTreeMethod &src, const CCopasiContainer *pParent=NULL)
	~CBitPatternTreeMethod ()
virtual bool	calculate ()
virtual bool	initialize ()
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)
Protected Member Functions
	CBitPatternTreeMethod (const CCopasiContainer *pParent=NULL)
	CBitPatternTreeMethod (const CCopasiMethod::SubType subType, const CCopasiContainer *pParent=NULL)
Protected Attributes
CModel *	mpModel
unsigned C_INT32	mProgressCounter
unsigned C_INT32	mProgressCounterMax
unsigned C_INT32	mhProgressCounter
unsigned C_INT32	mProgressCounter2
unsigned C_INT32	mProgressCounter2Max
unsigned C_INT32	mhProgressCounter2
std::vector< std::pair< size_t, bool > >	mReactionForward
CVector< size_t >	mReactionPivot
CMatrix< C_INT64 >	mExpandedStoiTranspose
CStepMatrix *	mpStepMatrix
CBitPatternTree *	mpNullTree
std::vector< CStepMatrixColumn * >	mNewColumns
size_t	mMinimumSetSize
size_t	mStep
bool	mContinueCombination
Friends
CEFMMethod *	CEFMMethod::createMethod (CCopasiMethod::SubType subType)

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Constructor & Destructor Documentation

CBitPatternTreeMethod::CBitPatternTreeMethod

(

const CCopasiContainer *

pParent = NULL

)

[protected]

Default constructor

Parameters:

const

CCopasiContainer * pParent (Default: NULL)

CBitPatternTreeMethod::CBitPatternTreeMethod	(	const CCopasiMethod::SubType	subType,
		const CCopasiContainer *	pParent = NULL
	)		[protected]

Constructor to be called by derived methods

Parameters:

const	CCopasiMethod::SubType subType
const	CCopasiContainer * pParent (Default: NULL)

CBitPatternTreeMethod::CBitPatternTreeMethod	(	const CBitPatternTreeMethod &	src,
		const CCopasiContainer *	pParent = NULL
	)

Copy Constructor

Parameters:

const

CBitPatternTreeMethod & src

CBitPatternTreeMethod::~CBitPatternTreeMethod

(

)

Destructor

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Member Function Documentation

bool CBitPatternTreeMethod::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.

bool CBitPatternTreeMethod::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

static void CBitPatternTreeMethod::GCD	(	C_INT64 &	m,
		C_INT64 &	n
	)		[inline, static]

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

bool CBitPatternTreeMethod::initialize

(

)

[virtual]

Initialize arrays and pointer.

Returns:

bool success

Reimplemented from CEFMMethod.

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Friends And Related Function Documentation

CEFMMethod* CEFMMethod::createMethod

(

CCopasiMethod::SubType

subType

)

[friend]

---

Member Data Documentation

bool CBitPatternTreeMethod::mContinueCombination [protected]

Boolean value indicating whether combination should continue.

CMatrix< C_INT64 > CBitPatternTreeMethod::mExpandedStoiTranspose [protected]

The transpose of the expanded stoichiometry matrix.

unsigned C_INT32 CBitPatternTreeMethod::mhProgressCounter [protected]

Handle to the process report item "Current Step"

unsigned C_INT32 CBitPatternTreeMethod::mhProgressCounter2 [protected]

Handle to the process report item "Combination"

size_t CBitPatternTreeMethod::mMinimumSetSize [protected]

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

std::vector< CStepMatrixColumn * > CBitPatternTreeMethod::mNewColumns [protected]

A list of invalid columns currently in the step matrix

CModel* CBitPatternTreeMethod::mpModel [protected]

A pointer to the model which is analyzed.

CBitPatternTree* CBitPatternTreeMethod::mpNullTree [protected]

The bit pattern tree for the current step

unsigned C_INT32 CBitPatternTreeMethod::mProgressCounter [protected]

The current step used for process report.

unsigned C_INT32 CBitPatternTreeMethod::mProgressCounter2 [protected]

The current combination used for process report.

unsigned C_INT32 CBitPatternTreeMethod::mProgressCounter2Max [protected]

The max combination used for process report.

unsigned C_INT32 CBitPatternTreeMethod::mProgressCounterMax [protected]

The max step used for process report.

CStepMatrix* CBitPatternTreeMethod::mpStepMatrix [protected]

A pointer to the step matrix for creating the flux modes

std::vector< std::pair< size_t, bool > > CBitPatternTreeMethod::mReactionForward [protected]

A vector to recording the expansion of the stoichiometry matrix.

CVector< size_t > CBitPatternTreeMethod::mReactionPivot [protected]

A vector recording the pivots for the QR factorization

size_t CBitPatternTreeMethod::mStep [protected]

The currently process step

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

• copasi/elementaryFluxModes/CBitPatternTreeMethod.h
• copasi/elementaryFluxModes/CBitPatternTreeMethod.cpp