#include <CBitPatternMethod.h>

Inheritance diagram for CBitPatternMethod:

Collaboration diagram for CBitPatternMethod:

Public Member Functions
virtual bool	calculate ()

	CBitPatternMethod (const CBitPatternMethod &src, const CCopasiContainer *pParent=NULL)

virtual bool	initialize ()

	~CBitPatternMethod ()

Public Member Functions inherited from CEFMMethod
	CEFMMethod (const CEFMMethod &src, const CCopasiContainer *pParent=NULL)

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

virtual	~CEFMMethod ()

Public Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiMethod &src, const CCopasiContainer *pParent=NULL)

const CCopasiMethod::SubType &	getSubType () const

const CCopasiTask::Type &	getType () const

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

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

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

virtual bool	setCallBack (CProcessReport *pCallBack)

virtual	~CCopasiMethod ()

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

bool	addParameter (const CCopasiParameter &parameter)

bool	addParameter (const std::string &name, const CCopasiParameter::Type type)

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

void	addParameter (CCopasiParameter *pParameter)

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

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

index_iterator	beginIndex () const

name_iterator	beginName () const

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

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

void	clear ()

virtual bool	elevateChildren ()

index_iterator	endIndex () const

name_iterator	endName () const

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

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

CCopasiParameterGroup *	getGroup (const size_t &index)

const CCopasiParameterGroup *	getGroup (const size_t &index) const

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

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

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

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

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

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

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

CCopasiParameter *	getParameter (const size_t &index)

const CCopasiParameter *	getParameter (const size_t &index) const

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

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

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

const CCopasiParameter::Value &	getValue (const std::string &name) const

const CCopasiParameter::Value &	getValue (const size_t &index) const

CCopasiParameter::Value &	getValue (const std::string &name)

CCopasiParameter::Value &	getValue (const size_t &index)

CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)

bool	removeParameter (const std::string &name)

bool	removeParameter (const size_t &index)

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

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

size_t	size () const

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

bool	swap (index_iterator &from, index_iterator &to)

virtual	~CCopasiParameterGroup ()

Public Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL)

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

virtual CCopasiObjectName	getCN () const

virtual const std::string &	getKey () const

virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const

const CCopasiParameter::Type &	getType () const

const Value &	getValue () const

Value &	getValue ()

virtual void *	getValuePointer () const

CCopasiObject *	getValueReference () const

bool	isValidValue (const C_FLOAT64 &value) const

bool	isValidValue (const C_INT32 &value) const

bool	isValidValue (const unsigned C_INT32 &value) const

bool	isValidValue (const bool &value) const

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

bool	isValidValue (const CCopasiObjectName &value) const

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

CCopasiParameter &	operator= (const CCopasiParameter &rhs)

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

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

virtual	~CCopasiParameter ()

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

	CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)

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

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

virtual const objectMap &	getObjects () const

virtual std::string	getUnits () const

virtual const CCopasiObject *	getValueObject () const

virtual bool	remove (CCopasiObject *pObject)

virtual	~CCopasiContainer ()

Public Member Functions inherited from CCopasiObject
void	addDirectDependency (const CCopasiObject *pObject)

	CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL)

void	clearDirectDependencies ()

void	clearRefresh ()

bool	dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const

void	getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const

virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const

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

CCopasiDataModel *	getObjectDataModel ()

const CCopasiDataModel *	getObjectDataModel () const

const std::string &	getObjectName () const

CCopasiContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const

virtual Refresh *	getRefresh () const

UpdateMethod *	getUpdateMethod () const

bool	hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const

bool	hasUpdateMethod () const

bool	isArray () const

bool	isContainer () const

bool	isDataModel () const

bool	isMatrix () const

bool	isNameVector () const

bool	isNonUniqueName () const

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

bool	isReference () const

bool	isRoot () const

bool	isSeparator () const

bool	isStaticString () const

bool	isValueBool () const

bool	isValueDbl () const

bool	isValueInt () const

bool	isValueInt64 () const

bool	isValueString () const

bool	isVector () const

virtual bool	mustBeDeleted (const DataObjectSet &deletedObjects) const

void	removeDirectDependency (const CCopasiObject *pObject)

void	setDirectDependencies (const DataObjectSet &directDependencies)

bool	setObjectName (const std::string &name)

virtual bool	setObjectParent (const CCopasiContainer *pParent)

void	setObjectValue (const C_FLOAT64 &value)

void	setObjectValue (const C_INT32 &value)

void	setObjectValue (const bool &value)

template<class CType >
void	setRefresh (CType pType, void(CType::method)(void))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const C_FLOAT64 &))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const C_INT32 &))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const bool &))

virtual	~CCopasiObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

virtual	~CObjectInterface ()

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 CEFMMethod
static CEFMMethod *	createMethod (CCopasiMethod::SubType subType=CCopasiMethod::EFMAlgorithm)

Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())

static void	setRenameHandler (CRenameHandler *rh)

Protected Member Functions
	CBitPatternMethod (const CCopasiContainer *pParent=NULL)

	CBitPatternMethod (const CCopasiMethod::SubType subType, const CCopasiContainer *pParent=NULL)

Protected Member Functions inherited from CEFMMethod
	CEFMMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL)

Protected Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL)

Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()

Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObject *	addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

void	initObjects ()

Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()

	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)

Protected Attributes
bool	mContinueCombination

CMatrix< C_INT64 >	mExpandedStoiTranspose

size_t	mhProgressCounter

size_t	mhProgressCounter2

size_t	mMinimumSetSize

std::vector< CStepMatrixColumn * >	mNewColumns

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
CProcessReport *	mpCallBack

Protected Attributes inherited from CCopasiParameter
std::string	mKey

CCopasiObject *	mpValueReference

size_t	mSize

Value	mValue

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Private Member Functions
void	addMode (const CFluxMode &mode)

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

void	buildFluxModes ()

void	buildKernelMatrix (CMatrix< C_INT64 > &kernel)

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)

Friends
CEFMMethod *	CEFMMethod::createMethod (CCopasiMethod::SubType subType)

Additional Inherited Members
Public Types inherited from CCopasiMethod
enum	SubType { unset = 0, RandomSearch, RandomSearchMaster, SimulatedAnnealing, CoranaWalk, DifferentialEvolution, ScatterSearch, GeneticAlgorithm, EvolutionaryProgram, SteepestDescent, HybridGASA, GeneticAlgorithmSR, HookeJeeves, LevenbergMarquardt, NelderMead, SRES, Statistics, ParticleSwarm, Praxis, TruncatedNewton, Newton, deterministic, LSODAR, directMethod, stochastic, tauLeap, adaptiveSA, hybrid, hybridLSODA, hybridODE45, DsaLsodar, tssILDM, tssILDMModified, tssCSP, mcaMethodReder, scanMethod, lyapWolf, sensMethod, EFMAlgorithm, EFMBitPatternTreeAlgorithm, EFMBitPatternAlgorithm, Householder, crossSectionMethod, linearNoiseApproximation }

Public Types inherited from CCopasiParameterGroup
typedef parameterGroup::iterator	index_iterator

typedef CCopasiContainer::objectMap::iterator	name_iterator

typedef std::vector < CCopasiParameter * >	parameterGroup

Public Types inherited from CCopasiParameter
enum	Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID }

Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap

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

typedef std::vector< Refresh * >	DataUpdateSequence

Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet

typedef std::vector < CObjectInterface * >	UpdateSequence

Static Public Attributes inherited from CCopasiMethod
static const std::string	SubTypeName []

static const char *	XMLSubType []

Static Public Attributes inherited from CCopasiParameter
static const std::string	TypeName []

static const char *	XMLType []

Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Protected Types inherited from CCopasiObject
enum	Flag { Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8, Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80, ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800, Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000, Root = 0x10000, Gui = 0x20000 }

Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 34 of file CBitPatternMethod.h.

Constructor & Destructor Documentation

CBitPatternMethod::CBitPatternMethod ( const CCopasiContainer * pParent = NULL )

protected

Default constructor

Parameters

const CCopasiContainer * pParent (Default: NULL)

Definition at line 27 of file CBitPatternMethod.cpp.

References initObjects().

                                                                     :
   CEFMMethod(CCopasiTask::fluxMode, CCopasiMethod::EFMBitPatternAlgorithm, pParent),
   mpModel(NULL),
   mProgressCounter(0),
   mProgressCounterMax(0),
   mhProgressCounter(0),
   mProgressCounter2(0),
   mProgressCounter2Max(0),
   mhProgressCounter2(0),
   mReactionForward(),
   mReactionPivot(0),
   mExpandedStoiTranspose(0, 0),
   mpStepMatrix(NULL),
   mMinimumSetSize(0),
   mStep(0),
   mContinueCombination(true)
 {
   initObjects();
 }

CBitPatternMethod::CBitPatternMethod	(	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)

Definition at line 47 of file CBitPatternMethod.cpp.

References initObjects().

                                                                       :
   CEFMMethod(CCopasiTask::fluxMode, subType, pParent),
   mpModel(NULL),
   mProgressCounter(0),
   mProgressCounterMax(0),
   mhProgressCounter(0),
   mProgressCounter2(0),
   mProgressCounter2Max(0),
   mhProgressCounter2(0),
   mReactionForward(),
   mReactionPivot(0),
   mExpandedStoiTranspose(0, 0),
   mpStepMatrix(NULL),
   mMinimumSetSize(0),
   mStep(0),
   mContinueCombination(true)
 {
   initObjects();
 }

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

Copy Constructor

Parameters

const CBitPatternMethod & src

Definition at line 68 of file CBitPatternMethod.cpp.

References initObjects().

                                                                       :
   CEFMMethod(src, pParent),
   mpModel(src.mpModel),
   mProgressCounter(src.mProgressCounter),
   mProgressCounterMax(src.mProgressCounterMax),
   mhProgressCounter(src.mhProgressCounter),
   mProgressCounter2(src.mProgressCounter2),
   mProgressCounter2Max(src.mProgressCounter2Max),
   mhProgressCounter2(src.mhProgressCounter2),
   mReactionForward(src.mReactionForward),
   mReactionPivot(src.mReactionPivot),
   mExpandedStoiTranspose(src.mExpandedStoiTranspose),
   mpStepMatrix(src.mpStepMatrix),
   mMinimumSetSize(src.mMinimumSetSize),
   mStep(src.mStep),
   mContinueCombination(src.mContinueCombination)
 {
   initObjects();
 }

CBitPatternMethod::~CBitPatternMethod ( )

Destructor

Definition at line 89 of file CBitPatternMethod.cpp.

90 {

91 }

Member Function Documentation

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

Definition at line 650 of file CBitPatternMethod.cpp.

References CEFMMethod::mpFluxModes.

Referenced by buildFluxModes().

 {
   std::vector< CFluxMode >::iterator itMode = mpFluxModes->begin();
   std::vector< CFluxMode >::iterator endMode = mpFluxModes->end();
 
   for (; itMode != endMode; ++itMode)
     {
       if (itMode->isReversed(mode))
         {
           return;
         }
     }
 
   mpFluxModes->push_back(mode);
   return;
 }

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

private

Definition at line 955 of file CBitPatternMethod.cpp.

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

 {
   CStepMatrixColumn * KernelCol;
   unsigned int col, row;
 
   while (!kernelStack.empty())
     {
       KernelCol = kernelStack.top();
 #ifdef COPASI_DEBUG_TRACE
       DebugFile << "Current Column: " << *KernelCol << std::endl;
 #endif // COPASI_DEBUG_TRACE
       CMatrix<C_INT64> RankKernel = performRankTest(KernelCol);
 #ifdef COPASI_DEBUG_TRACE
       DebugFile << "New Rank Kernel " << RankKernel << std::endl;
 #endif // COPASI_DEBUG_TRACE
 
       if (RankKernel.numCols() == 1)
         {
           fluxModeMatrix->add(KernelCol);
         }
       else if (RankKernel.numCols() > 1)
         {
           for (col = 0; col < RankKernel.numCols(); col++)
             {
               KernelCol = new CStepMatrixColumn(RankKernel.numRows());
 
               for (row = 0; row < RankKernel.numRows(); row++)
                 {
                   KernelCol->push_front(RankKernel(row, col));
                 }
 
               kernelStack.push(KernelCol);
             }
         }
 
       kernelStack.pop();
     }
 }

void CBitPatternMethod::buildFluxModes ( )

private

Postprocess the step matrix to construct the flux modes.

Definition at line 423 of file CBitPatternMethod.cpp.

References addMode(), CVectorCore< CType >::array(), CMatrix< 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().

 {
   CStepMatrix::const_iterator it = mpStepMatrix->begin();
   CStepMatrix::const_iterator end = mpStepMatrix->end();
 
   CVector< size_t > Indexes;
   size_t NumSpecies = mExpandedStoiTranspose.numCols();
 
   for (; it != end; ++it)
     {
       getUnsetBitIndexes(*it, Indexes);
 
       size_t NumReactions = Indexes.size();
 
       // Remove trivial modes, i.e., reversible reactions
       if (NumReactions == 2 &&
           (*mpReorderedReactions)[mReactionForward[Indexes[0]].first] ==
           (*mpReorderedReactions)[mReactionForward[Indexes[1]].first])
         {
           continue;
         }
 
       // Build the stoichiometry matrix reduced to the reactions participating in the current mode.
       CMatrix< C_INT64 > A(NumReactions, NumSpecies);
 
       size_t * pIndex = Indexes.array();
       size_t * pIndexEnd = pIndex + NumReactions;
       C_INT64 * pARow = A.array();
 
       for (; pIndex != pIndexEnd; ++pIndex, pARow += NumSpecies)
         {
           memcpy(pARow, &mExpandedStoiTranspose(*pIndex, 0), NumSpecies * sizeof(C_INT64));
         }
 
       // Calculate the kernel of the matrix
       CMatrix< C_INT64 > ExpandedStoiTranspose(A);
       CMatrix< C_INT64 > Kernel;
       CVector< size_t > Pivot;
       CalculateKernel(ExpandedStoiTranspose, Kernel, Pivot);
 
       size_t NumCols = Kernel.numCols();
 
       // Now we create the flux mode as we have the multiplier and reaction indexes.
       // We need to invert the sign of the multiplier for reactions which are not forward.
       // A flux mode is reversible if all reactions are reversible;
 
       C_INT64 * pColumn = Kernel.array();
       C_INT64 * pColumnEnd = pColumn + NumCols;
 
       for (; pColumn != pColumnEnd; ++pColumn)
         {
           std::map< size_t, C_FLOAT64 > Reactions;
           bool Reversible = true;
 
           pIndex = Indexes.array();
           C_INT64 * pFluxMultiplier = pColumn;
 
           for (; pIndex != pIndexEnd; ++pIndex, pFluxMultiplier += NumCols)
             {
               if (*pFluxMultiplier < 0)
                 {
                   break;
                 }
               else if (*pFluxMultiplier < 0)
                 {
                   continue;
                 }
 
               std::pair< size_t, bool > & ReactionForward = mReactionForward[*pIndex];
 
               Reactions[ReactionForward.first] =
                 (C_FLOAT64)((ReactionForward.second == true) ? *pFluxMultiplier : -*pFluxMultiplier);
 
               if (!(*mpReorderedReactions)[ReactionForward.first]->isReversible())
                 {
                   Reversible = false;
                 }
             }
 
           if (pIndex != pIndexEnd)
             {
               continue;
             }
 
           addMode(CFluxMode(Reactions, Reversible));
         }
     }
 }

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

private

Construct the kernel matrix

Parameters

CMatrix< C_FLOAT64> & kernel

Definition at line 343 of file CBitPatternMethod.cpp.

References CMatrix< CType >::array(), CCopasiVector< T >::begin(), C_FLOAT64, C_INT64, CalculateKernel(), CCopasiVector< T >::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 the kernel matrix
   // of the reduced stoichiometry matrix to get the kernel matrix for the:
   //   Nullspace Approach to Determine the Elementary Modes of Chemical Reaction Systems (Wagner 2004)
 
   CCopasiVector< CReaction >::const_iterator itReaction = mpModel->getReactions().begin();
   CCopasiVector< CReaction >::const_iterator endReaction = mpModel->getReactions().end();
 
   size_t ReactionCounter = 0;
 
   for (; itReaction != endReaction; ++itReaction, ++ReactionCounter)
     {
       if ((*itReaction)->isReversible())
         {
           // mpReorderedReactons->push_back(*itReaction);
           mReactionForward.push_back(std::make_pair(ReactionCounter, false));
         }
 
       mpReorderedReactions->push_back(*itReaction);
       mReactionForward.push_back(std::make_pair(ReactionCounter, true));
     }
 
   const CMatrix< C_FLOAT64 > & Stoi = mpModel->getRedStoi();
 
   size_t NumReactions = Stoi.numCols();
 
   size_t NumExpandedReactions = mReactionForward.size();
 
   size_t NumSpecies = Stoi.numRows();
 
   size_t Dim = std::min(NumExpandedReactions, NumSpecies);
 
   if (Dim == 0)
     {
       return;
     }
 
   mExpandedStoiTranspose.resize(NumExpandedReactions, NumSpecies);
 
   const C_FLOAT64 *pStoi = Stoi.array();
   const C_FLOAT64 *pStoiEnd = pStoi + Stoi.size();
   const C_FLOAT64 *pStoiRowEnd;
 
   C_INT64 *pExpandedStoiTranspose;
   C_INT64 *pExpandedStoiTransposeColumn = mExpandedStoiTranspose.array();
 
   std::vector< const CReaction * >::const_iterator itReactionPivot;
   std::vector< const CReaction * >::const_iterator endReactionPivot;
   std::vector< std::pair< size_t, bool > >::const_iterator itReactionExpansion;
 
   for (; pStoi != pStoiEnd; ++pExpandedStoiTransposeColumn)
     {
       pStoiRowEnd = pStoi + NumReactions;
       pExpandedStoiTranspose = pExpandedStoiTransposeColumn;
       itReactionExpansion = mReactionForward.begin();
 
       for (; pStoi < pStoiRowEnd; ++pStoi, pExpandedStoiTranspose += NumSpecies, ++itReactionExpansion)
         {
           // TODO We should check the we have integer stoichiometry.
           if (itReactionExpansion->second == false)
             {
               *pExpandedStoiTranspose = (C_INT64) - floor(*pStoi + 0.5);
 
               // Advance the iterators
               ++itReactionExpansion;
               pExpandedStoiTranspose += NumSpecies;
             }
 
           *pExpandedStoiTranspose = (C_INT64) floor(*pStoi + 0.5);
         }
     }
 
   // Calculate the kernel of the matrix
   CMatrix< C_INT64 > ExpandedStoiTranspose(mExpandedStoiTranspose);
   CalculateKernel(ExpandedStoiTranspose, kernelInt, mReactionPivot);
 
   return;
 }

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.

Definition at line 165 of file CBitPatternMethod.cpp.

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

 {
   bool Continue = true;
 
   if (!initialize())
     {
       if (mpCallBack)
         mpCallBack->finishItem(mhProgressCounter);
 
       return false;
     }
 
   while (mpStepMatrix->getNumUnconvertedRows() > 0 &&
          Continue)
     {
       mStep = mpStepMatrix->getFirstUnconvertedRow();
 
       std::vector< CStepMatrixColumn * > PositiveColumns;
       std::vector< CStepMatrixColumn * > NegativeColumns;
       std::vector< CStepMatrixColumn * > NullColumns;
 
       if (mpStepMatrix->splitColumns(PositiveColumns,
                                      NegativeColumns,
                                      NullColumns))
         {
           // Process each step.
           // Iterate over all combinations and add/remove columns to the step matrix
           mProgressCounter2 = 0;
           mProgressCounter2Max = (unsigned C_INT32)(PositiveColumns.size() * NegativeColumns.size());
 
           if (mpCallBack)
             mhProgressCounter2 =
               mpCallBack->addItem("Combinations",
                                   mProgressCounter2,
                                   & mProgressCounter2Max);
 
           for (unsigned int i = 0; i < NegativeColumns.size(); i++)
             for (unsigned int j = 0; j < PositiveColumns.size(); j++)
               combine(PositiveColumns[j], NegativeColumns[i], NullColumns);
 
           if (mpCallBack)
             mpCallBack->finishItem(mhProgressCounter2);
 
           Continue &= mContinueCombination;
 
           if (Continue)
             {
               // We can now destroy all negative columns, which removes them from
               // the step matrix.
               mpStepMatrix->removeInvalidColumns(NegativeColumns);
 
               // Remove columns of the step matrix which are no longer extreme rays.
               findRemoveInvalidColumns(NullColumns);
 
               // We compact the step matrix which has empty columns due to the removal of columns above.
               mpStepMatrix->compact();
 
               // Now we can convert the processed row.
               mpStepMatrix->convertRow();
             }
         }
 
       mProgressCounter = mProgressCounterMax - (unsigned C_INT32) mpStepMatrix->getNumUnconvertedRows();
 
       if (mpCallBack)
         Continue &= mpCallBack->progressItem(mhProgressCounter);
     }
 
   if (Continue)
     {
       buildFluxModes();
     }
 
   if (mpCallBack)
     Continue &= mpCallBack->finishItem(mhProgressCounter);
 
   return true;
 }

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

Definition at line 668 of file CBitPatternMethod.cpp.

References abs64, CVectorCore< CType >::array(), CMatrix< 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().

 {
   // Gaussian elimination
   size_t NumRows = matrix.numRows();
   size_t NumCols = matrix.numCols();
 
   assert(NumRows > 0);
   assert(NumCols > 0);
 
   // Initialize row pivots
   rowPivot.resize(NumRows);
   size_t * pPivot = rowPivot.array();
 
   for (size_t i = 0; i < NumRows; i++, pPivot++)
     {
       *pPivot = i;
     }
 
   CVector< size_t > RowPivot(rowPivot);
 
   CVector< C_INT64 > Identity(NumRows);
   Identity = 1;
 
   C_INT64 * pColumn = matrix.array();
   C_INT64 * pColumnEnd = pColumn + NumCols;
 
   C_INT64 * pActiveRow;
   C_INT64 * pActiveRowStart = pColumn;
   C_INT64 * pActiveRowEnd = pColumnEnd;
 
   C_INT64 * pRow;
   C_INT64 * pRowEnd = pColumn + matrix.size();
 
   C_INT64 * pCurrent;
   C_INT64 * pIdentity;
 
   CVector< C_INT64 > SwapTmp(NumCols);
 
   size_t CurrentRowIndex = 0;
   size_t CurrentColumnIndex = 0;
   size_t NonZeroIndex = 0;
 
   CVector< bool > IgnoredColumns(NumCols);
   IgnoredColumns = false;
   bool * pIgnoredColumn = IgnoredColumns.array();
   size_t IgnoredColumnCount = 0;
 
   // For each column
   for (; pColumn < pColumnEnd; ++pColumn, ++CurrentColumnIndex, ++pIgnoredColumn)
     {
       assert(CurrentColumnIndex == CurrentRowIndex + IgnoredColumnCount);
 
       // Find non zero entry in current column.
       pRow = pActiveRowStart + CurrentColumnIndex;
       NonZeroIndex = CurrentRowIndex;
 
       for (; pRow < pRowEnd; pRow += NumCols, ++NonZeroIndex)
         {
           if (*pRow != 0)
             break;
         }
 
       if (NonZeroIndex >= NumRows)
         {
           *pIgnoredColumn = true;
           IgnoredColumnCount++;
 
           continue;
         }
 
       if (NonZeroIndex != CurrentRowIndex)
         {
           // Swap rows
           memcpy(SwapTmp.array(), matrix[CurrentRowIndex], NumCols * sizeof(C_INT64));
           memcpy(matrix[CurrentRowIndex], matrix[NonZeroIndex], NumCols * sizeof(C_INT64));
           memcpy(matrix[NonZeroIndex], SwapTmp.array(), NumCols * sizeof(C_INT64));
 
           // Record pivot
           size_t tmp = RowPivot[CurrentRowIndex];
           RowPivot[CurrentRowIndex] = RowPivot[NonZeroIndex];
           RowPivot[NonZeroIndex] = tmp;
 
           C_INT64 TMP = Identity[CurrentRowIndex];
           Identity[CurrentRowIndex]  = Identity[NonZeroIndex];
           Identity[NonZeroIndex] = TMP;
         }
 
       if (*(pActiveRowStart + CurrentColumnIndex) < 0)
         {
           for (pRow = pActiveRowStart; pRow < pActiveRowEnd; ++pRow)
             {
               *pRow *= -1;
             }
 
           Identity[CurrentRowIndex] *= -1;
         }
 
       // For each row
       pRow = pActiveRowStart + NumCols;
       pIdentity = Identity.array() + CurrentRowIndex + 1;
 
       C_INT64 ActiveRowValue = *(pActiveRowStart + CurrentColumnIndex);
       *(pActiveRowStart + CurrentColumnIndex) = Identity[CurrentRowIndex];
 
       for (; pRow < pRowEnd; pRow += NumCols, ++pIdentity)
         {
           C_INT64 RowValue = *(pRow + CurrentColumnIndex);
 
           if (RowValue == 0)
             continue;
 
           *(pRow + CurrentColumnIndex) = 0;
 
           // compute GCD(*pActiveRowStart, *pRow)
           C_INT64 GCD1 = abs64(ActiveRowValue);
           C_INT64 GCD2 = abs64(RowValue);
 
           GCD(GCD1, GCD2);
 
           C_INT64 alpha = ActiveRowValue / GCD1;
           C_INT64 beta = RowValue / GCD1;
 
           // update rest of row
           pActiveRow = pActiveRowStart;
           pCurrent = pRow;
           *pIdentity *= alpha;
 
           GCD1 = abs64(*pIdentity);
 
           for (; pActiveRow < pActiveRowEnd; ++pActiveRow, ++pCurrent)
             {
               // Assert that we do not have a numerical overflow.
               assert(fabs(((C_FLOAT64) alpha) * ((C_FLOAT64) * pCurrent) - ((C_FLOAT64) beta) * ((C_FLOAT64) * pActiveRow)) < std::numeric_limits< C_INT64 >::max());
 
               *pCurrent = alpha * *pCurrent - beta * *pActiveRow;
 
               // We check that the row values do not have any common divisor.
               if (GCD1 > 1 &&
                   (GCD2 = abs64(*pCurrent)) > 0)
                 {
                   GCD(GCD1, GCD2);
                 }
             }
 
           if (GCD1 > 1)
             {
               *pIdentity /= GCD1;
 
               pActiveRow = pActiveRowStart;
               pCurrent = pRow;
 
               for (; pActiveRow < pActiveRowEnd; ++pActiveRow, ++pCurrent)
                 {
                   *pCurrent /= GCD1;
                 }
             }
         }
 
       pActiveRowStart += NumCols;
       pActiveRowEnd += NumCols;
       CurrentRowIndex++;
 
       // DebugFile << matrix << std::endl;
       // DebugFile << Identity << std::endl;
     }
 
   assert(CurrentColumnIndex == CurrentRowIndex + IgnoredColumnCount);
   assert(CurrentColumnIndex == NumCols);
 
   // std::cout << matrix << std::endl;
   // std::cout << IgnoredColumns << std::endl;
   // std::cout << Identity << std::endl;
   // std::cout << RowPivot << std::endl << std::endl;
 
   size_t KernelRows = NumRows;
   size_t KernelCols = NumRows + IgnoredColumnCount - NumCols;
 
   assert(KernelCols > 0);
 
   kernel.resize(KernelRows, KernelCols);
 
   CMatrix< C_INT64 > Kernel(KernelRows, KernelCols);
   Kernel = 0;
 
   C_INT64 * pKernelInt = Kernel.array();
   C_INT64 * pKernelIntEnd = pKernelInt + Kernel.size();
 
   pActiveRowStart = matrix[CurrentRowIndex];
   pActiveRowEnd = matrix[NumRows];
 
   // Null space matrix identity part
   pIdentity = Identity.array() + CurrentRowIndex;
   C_INT64 * pKernelColumn = Kernel.array();
 
   for (; pActiveRowStart < pActiveRowEnd; pActiveRowStart += NumCols, ++pKernelColumn, ++pIdentity)
     {
       pKernelInt = pKernelColumn;
       pIgnoredColumn = IgnoredColumns.array();
 
       pRow = pActiveRowStart;
       pRowEnd = pRow + NumCols;
 
       if (*pIdentity < 0)
         {
           *pIdentity *= -1;
 
           for (; pRow < pRowEnd; ++pRow, ++pIgnoredColumn)
             {
               if (*pIgnoredColumn)
                 {
                   continue;
                 }
 
               *pKernelInt = - *pRow;
               pKernelInt += KernelCols;
             }
         }
       else
         {
           for (; pRow < pRowEnd; ++pRow, ++pIgnoredColumn)
             {
               if (*pIgnoredColumn)
                 {
                   continue;
                 }
 
               *pKernelInt = *pRow;
               pKernelInt += KernelCols;
             }
         }
     }
 
   pIdentity = Identity.array() + CurrentRowIndex;
   pKernelInt = Kernel[CurrentRowIndex];
 
   for (; pKernelInt < pKernelIntEnd; pKernelInt += KernelCols + 1, ++pIdentity)
     {
       *pKernelInt = *pIdentity;
     }
 
   // Undo the reordering introduced by Gaussian elimination to the kernel matrix.
   pPivot = RowPivot.array();
   pRow = Kernel.array();
   pRowEnd = pRow + Kernel.size();
 
   for (; pRow < pRowEnd; ++pPivot, pRow += KernelCols)
     {
       memcpy(kernel[*pPivot], pRow, KernelCols * sizeof(C_INT64));
     }
 
   return true;
 }

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

Definition at line 245 of file CBitPatternMethod.cpp.

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

Referenced by calculate().

 {
   if (mContinueCombination && mpCallBack)
     {
       mContinueCombination = mpCallBack->proceed();
     }
 
   if (!mContinueCombination)
     {
       return;
     }
 
   CZeroSet Intersection = CZeroSet::intersection(pPositive->getZeroSet(),
                           pNegative->getZeroSet());
 
   // Adjacency test
   if (Intersection.getNumberOfSetBits() < mMinimumSetSize)
     {
       return;
     }
 
   //INSERT RANK TEST HERE
 
   CStepMatrixColumn * RankTestColumn = new CStepMatrixColumn(Intersection, pPositive, pNegative);
   CMatrix<C_INT64> rtKernel = performRankTest(RankTestColumn);
 
   if (rtKernel.numCols() > 1)
     {
       return;
     }
 
   // Assert columns are not null
   if (pPositive != NULL && pNegative != NULL)
     {
       // We need to check whether the existing matrix contains already a leaf which is a superset
       if (Intersection.isExtremeRay(NullColumns))
         {
           // We are sure that the previous Null Tree did not contain any
           // super sets, however the new columns may.
 
           // We check whether the new columns do not already contain a superset
           if (Intersection.isExtremeRay(mNewColumns))
             {
               CStepMatrixColumn * pColumn = mpStepMatrix->addColumn(Intersection, pPositive, pNegative);
 
               // Remove all new column which are no longer extreme rays
               std::vector< CStepMatrixColumn * >::iterator it = mNewColumns.begin();
               std::vector< CStepMatrixColumn * >::iterator end = mNewColumns.end();
 
               for (; it != end; ++it)
                 {
                   if ((*it) != NULL &&
                       (*it)->getZeroSet() >= Intersection)
                     {
                       // We need to remove the column from the step matrix, which can be done by deleting it.
                       mpStepMatrix->removeColumn(*it);
                       *it = NULL;
                     }
                 }
 
               mNewColumns.push_back(pColumn);
             }
         }
 
       mProgressCounter2++;
 
       if (mpCallBack)
         mContinueCombination = mpCallBack->progressItem(mhProgressCounter2);
     }
 }

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

private

Remove the invalid columns from the step matrix

Parameters

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

Definition at line 318 of file CBitPatternMethod.cpp.

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

Referenced by calculate().

 {
   if (mNewColumns.empty())
     {
       return;
     }
 
   // Determine the columns which became invalid.
   std::vector< CStepMatrixColumn * > InvalidColumns;
 
   std::vector< CStepMatrixColumn * >::const_iterator NullIt = nullColumns.begin();
   std::vector< CStepMatrixColumn * >::const_iterator NullEnd = nullColumns.end();
 
   for (; NullIt != NullEnd; ++NullIt)
     {
       if (!((*NullIt)->getZeroSet()).isExtremeRay(mNewColumns))
         {
           InvalidColumns.push_back(*NullIt);
         }
     }
 
   mpStepMatrix->removeInvalidColumns(InvalidColumns);
   mNewColumns.clear();
 }

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

Definition at line 57 of file CBitPatternMethod.h.

Referenced by CalculateKernel().

   {
     assert(m > 0 && n > 0);
 
     while (m != n)
       {
         if (m > n)
           {
             m %= n;
 
             if (m == 0)
               {
                 m = n;
               }
           }
         else
           {
             n %= m;
 
             if (n == 0)
               {
                 n = m;
               }
           }
       }
   }

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

private

Definition at line 619 of file CBitPatternMethod.cpp.

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

Referenced by performRankTest().

 {
   mpStepMatrix->getAllUnsetBitIndexes(pColumn, indexes);
 
   // Apply the QR pivot
   size_t * pIndex = indexes.array();
   size_t * pIndexEnd = pIndex + indexes.size();
 
   for (; pIndex != pIndexEnd; ++pIndex)
     *pIndex = mReactionPivot[*pIndex];
 
   //DebugFile << "@CBPM: " << indexes << std::endl;
 }

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

private

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

Definition at line 634 of file CBitPatternMethod.cpp.

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

Referenced by buildFluxModes().

 {
   mpStepMatrix->getUnsetBitIndexes(pColumn, indexes);
 
   // Apply the QR pivot
   size_t * pIndex = indexes.array();
   size_t * pIndexEnd = pIndex + indexes.size();
 
   for (; pIndex != pIndexEnd; ++pIndex)
     {
       *pIndex = mReactionPivot[*pIndex];
     }
 }

bool CBitPatternMethod::initialize ( )

virtual

Initialize arrays and pointer.

Returns: bool success

Reimplemented from CEFMMethod.

Definition at line 98 of file CBitPatternMethod.cpp.

References CProcessReport::addItem(), buildKernelMatrix(), C_INT32, CCopasiProblem::getModel(), CStepMatrix::getNumUnconvertedRows(), CCopasiObject::getObjectParent(), CCopasiTask::getProblem(), CEFMMethod::initialize(), mContinueCombination, mhProgressCounter, mMinimumSetSize, CCopasiMethod::mpCallBack, mpModel, mProgressCounter, mProgressCounterMax, mpStepMatrix, mReactionForward, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), pdelete, pTask, and CStepMatrixColumn::push_front().

Referenced by calculate().

 {
   if (!CEFMMethod::initialize())
     {
       return false;
     }
 
   pdelete(mpStepMatrix);
   mReactionForward.clear();
 
   mContinueCombination = true;
 
   CEFMTask * pTask = dynamic_cast< CEFMTask *>(getObjectParent());
 
   if (pTask == NULL) return false;
 
   mpModel = pTask->getProblem()->getModel();
 
   if (mpModel == NULL) return false;
 
   // We first build the kernel matrix
   CMatrix< C_INT64 > KernelMatrix;
   buildKernelMatrix(KernelMatrix);
 
   mMinimumSetSize = KernelMatrix.numCols() - 2;
 
   std::stack< CStepMatrixColumn * > KernelStack;
   CStepMatrixColumn * KernelCol;
 
   for (unsigned int col = 0; col < KernelMatrix.numCols(); col++)
     {
       KernelCol = new CStepMatrixColumn(KernelMatrix.numRows());
 
       for (unsigned int row = 0; row < KernelMatrix.numRows(); row++)
         {
           KernelCol->push_front(KernelMatrix(row, col));
         }
 
       KernelStack.push(KernelCol);
     }
 
   // Now we create the initial step matrix
   mpStepMatrix = new CStepMatrix(KernelMatrix);
   /*mpStepMatrix = new CStepMatrix(KernelMatrix.numRows());
   buildFluxModeMatrix(mpStepMatrix, KernelStack);
 
   DebugFile << *mpStepMatrix << std::endl;*/
 
   /*
   mpStepMatrix = FluxModeMatrix;
   mpStepMatrix.convertMatrix();
   */
 
   //mpStepMatrix = new CStepMatrix(KernelMatrix);
 
   mProgressCounter = 0;
   mProgressCounterMax = (unsigned C_INT32) mpStepMatrix->getNumUnconvertedRows();
 
   if (mpCallBack)
     mhProgressCounter =
       mpCallBack->addItem("Current Step",
                           mProgressCounter,
                           & mProgressCounterMax);
 
   return true;
 }

void CBitPatternMethod::initObjects ( )

private

Initialize the needed CCopasiObjects.

Definition at line 93 of file CBitPatternMethod.cpp.

References CCopasiContainer::addObjectReference(), mProgressCounter, and CCopasiObject::ValueInt.

Referenced by CBitPatternMethod().

 {
   addObjectReference("Current Step", mProgressCounter, CCopasiObject::ValueInt);
 }

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

private

Performs rank test on given intersection.

Definition at line 923 of file CBitPatternMethod.cpp.

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

Referenced by buildFluxModeMatrix(), and combine().

 {
   CVector<size_t> Indexes;
 
   getAllUnsetBitIndexes(pIntersectColumn, Indexes);
 
   size_t NumReactions = Indexes.size();
   size_t NumSpecies = mExpandedStoiTranspose.numCols();
 
   // Build the stoichiometry matrix reduced to the reactions participating in the current mode.
   CMatrix< C_INT64 > A(NumReactions, NumSpecies);
 
   size_t * pIndex = Indexes.array();
   size_t * pIndexEnd = pIndex + NumReactions;
   C_INT64 * pARow = A.array();
 
   for (; pIndex != pIndexEnd; ++pIndex, pARow += NumSpecies)
     {
       memcpy(pARow, &mExpandedStoiTranspose(*pIndex, 0), NumSpecies * sizeof(C_INT64));
     }
 
   // Calculate the kernel of the matrix
   CMatrix< C_INT64 > ExpandedStoiTranspose(A);
   CMatrix< C_INT64 > Kernel;
   CVector< size_t > Pivot;
 
   //DebugFile << ExpandedStoiTranspose << std::endl;
   CalculateKernel(ExpandedStoiTranspose, Kernel, Pivot);
 
   return Kernel;
 }

Friends And Related Function Documentation

CEFMMethod* CEFMMethod::createMethod ( CCopasiMethod::SubType subType )

friend

Member Data Documentation

bool CBitPatternMethod::mContinueCombination

protected

Boolean value indicating whether combination should continue.

Definition at line 257 of file CBitPatternMethod.h.

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

CMatrix< C_INT64 > CBitPatternMethod::mExpandedStoiTranspose

protected

The transpose of the expanded stoichiometry matrix.

Definition at line 232 of file CBitPatternMethod.h.

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

size_t CBitPatternMethod::mhProgressCounter

protected

Handle to the process report item "Current Step"

Definition at line 202 of file CBitPatternMethod.h.

Referenced by calculate(), and initialize().

size_t CBitPatternMethod::mhProgressCounter2

protected

Handle to the process report item "Combination"

Definition at line 217 of file CBitPatternMethod.h.

Referenced by calculate(), and combine().

size_t CBitPatternMethod::mMinimumSetSize

protected

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

Definition at line 247 of file CBitPatternMethod.h.

Referenced by combine(), and initialize().

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

protected

A list of invalid columns currently in the step matrix

Definition at line 242 of file CBitPatternMethod.h.

Referenced by combine(), and findRemoveInvalidColumns().

CModel* CBitPatternMethod::mpModel

protected

A pointer to the model which is analyzed.

Definition at line 187 of file CBitPatternMethod.h.

Referenced by buildKernelMatrix(), and initialize().

unsigned C_INT32 CBitPatternMethod::mProgressCounter

protected

The current step used for process report.

Definition at line 192 of file CBitPatternMethod.h.

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

unsigned C_INT32 CBitPatternMethod::mProgressCounter2

protected

The current combination used for process report.

Definition at line 207 of file CBitPatternMethod.h.

Referenced by calculate(), and combine().

unsigned C_INT32 CBitPatternMethod::mProgressCounter2Max

protected

The max combination used for process report.

Definition at line 212 of file CBitPatternMethod.h.

Referenced by calculate().

unsigned C_INT32 CBitPatternMethod::mProgressCounterMax

protected

The max step used for process report.

Definition at line 197 of file CBitPatternMethod.h.

Referenced by calculate(), and initialize().

CStepMatrix* CBitPatternMethod::mpStepMatrix

protected

A pointer to the step matrix for creating the flux modes

Definition at line 237 of file CBitPatternMethod.h.

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

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

protected

A vector to recording the expansion of the stoichiometry matrix.

Definition at line 222 of file CBitPatternMethod.h.

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

CVector< size_t > CBitPatternMethod::mReactionPivot

protected

A vector recording the pivots for the QR factorization

Definition at line 227 of file CBitPatternMethod.h.

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

size_t CBitPatternMethod::mStep

protected

The currently process step

Definition at line 252 of file CBitPatternMethod.h.

Referenced by calculate().

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