#include <CSSAMethod.h>

Inheritance diagram for CSSAMethod:

Collaboration diagram for CSSAMethod:

Public Member Functions
bool	calculate ()

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

	CSSAMethod (const CCopasiContainer *pParent=NULL)

bool	initialize ()

TriLogic	isMixingStable (int indexEC)

bool	isReactionReversed (int index) const

bool	process (CProcessReport *handler)

Public Member Functions inherited from CEFMAlgorithm
void	calculateFluxModes ()

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

	~CEFMAlgorithm ()

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 ()

Protected Member Functions
bool	buildExtremeCurrents ()

bool	buildJacobian ()

bool	buildKineticMatrix ()

bool	buildStoichiometry ()

bool	decomposeJacobian ()

template<class CType >
CMatrix< CType >	diag (CVector< CType > vector)

bool	testForMixingStability ()

Protected Member Functions inherited from CEFMAlgorithm
	CEFMAlgorithm (const CCopasiContainer *pParent=NULL)

	CEFMAlgorithm (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
std::vector< CVector< C_FLOAT64 > >	mExtremeCurrents

std::vector< bool >	mIsBackwardReaction

std::vector< TriLogic >	mIsMixingStable

C_INT32	mNumReactions

CCopasiVectorNS< CReaction >	mReactions

CMatrix< C_FLOAT64 >	mStoichiometry

std::vector< std::vector < C_FLOAT64 > >	mStoiRows

std::vector< CMatrix< C_FLOAT64 > >	mTransformedSubJacobians

CMatrix< C_FLOAT64 >	mTransposedKineticMatrix

Protected Attributes inherited from CEFMAlgorithm
size_t	mhSteps

std::vector< size_t >	mIndexSet

unsigned C_INT32	mMaxStep

CTableauMatrix *	mpCurrentTableau

CModel *	mpModel

CTableauMatrix *	mpNextTableau

size_t	mReversible

unsigned C_INT32	mStep

unsigned C_INT32	mStepProcess

std::vector< std::vector < C_FLOAT64 > >	mStoi

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

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 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)

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 28 of file CSSAMethod.h.

Constructor & Destructor Documentation

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

CSSAMethod class. Methods to conduct Stoichiometric Stability Analysis.- Copy constructor.

Parameters

const CSSAMethod & src

Definition at line 35 of file CSSAMethod.cpp.

                                                         :
   CEFMAlgorithm(src, pParent)
 {}

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

Definition at line 40 of file CSSAMethod.cpp.

                                                        :
   CEFMAlgorithm(CCopasiMethod::stoichiometricStabilityAnalysis, pParent)
 {}

Member Function Documentation

bool CSSAMethod::buildExtremeCurrents ( )

protected

Definition at line 418 of file CSSAMethod.cpp.

References CVectorCore< CType >::array(), C_FLOAT64, C_INT32, CEFMAlgorithm::calculateFluxModes(), mExtremeCurrents, mNumReactions, CVector< CType >::resize(), and CVectorCore< CType >::size().

Referenced by calculate().

 {
   mExtremeCurrents.clear();
 
   calculateFluxModes();
 
   std::vector< CFluxMode > fluxmodes = getFluxModes();
 
   CVector< C_FLOAT64 > extremecurrent;
   extremecurrent.resize(mNumReactions);
 
   std::vector< CFluxMode >::iterator iter;
 
   for (iter = fluxmodes.begin(); iter != fluxmodes.end(); ++iter)
     {
       memset(extremecurrent.array(), 0, extremecurrent.size()*sizeof(C_FLOAT64));
       unsigned C_INT32 i;
 
       for (i = 0; i < iter->size(); ++i)
         {
           extremecurrent[iter->getReactionIndex(i)] = iter->getMultiplier(i);
         }
     }
 
   return true;
 }

bool CSSAMethod::buildJacobian ( )

protected

bool CSSAMethod::buildKineticMatrix ( )

protected

Definition at line 379 of file CSSAMethod.cpp.

References CMatrix< CType >::array(), CCopasiVector< T >::begin(), C_FLOAT64, C_INT64, CCopasiVector< T >::end(), CModel::getMetabolitesX(), CModel::getNumIndependentReactionMetabs(), mIsBackwardReaction, mNumReactions, CEFMAlgorithm::mpModel, mTransposedKineticMatrix, CMatrix< CType >::resize(), and CCopasiVector< T >::size().

Referenced by calculate().

 {
   if (!mpModel) return false;
 
   C_FLOAT64 num_metabolites = mpModel->getNumIndependentReactionMetabs();
 
   C_FLOAT64 num_reactions = mNumReactions;
 
   mTransposedKineticMatrix.resize((C_INT64)num_reactions, (C_INT64)num_metabolites);
   memset(mTransposedKineticMatrix.array(), 0, (int)(num_metabolites * num_reactions * sizeof(C_FLOAT64)));
 
   CCopasiVector< CMetab > & metabOrder = mpModel->getMetabolitesX();
 
   for (int ireac = 0; ireac < mIsBackwardReaction.size(); ++ireac)
     {
       CCopasiVector< CChemEqElement > substrates;
 
       if (mIsBackwardReaction[ireac])
         substrates = mReorderedReactions[ireac]->getChemEq().getProducts();
       else
         substrates = mReorderedReactions[ireac]->getChemEq().getSubstrates();
 
       for (int jsubst = 0; jsubst < substrates.size(); ++jsubst)
         {
           CCopasiVector< CMetab >::iterator found = find(metabOrder.begin(),
               metabOrder.end(),
               substrates[jsubst]->getMetabolite());
 
           if ((*found)->isDependent()) continue;
 
           int kmetab = std::distance(metabOrder.begin(), found);
           mTransposedKineticMatrix[ireac][kmetab] = substrates[jsubst]->getMultiplicity();
         }
     }
 
   return true;
 }

bool CSSAMethod::buildStoichiometry ( )

protected

Definition at line 358 of file CSSAMethod.cpp.

References CMatrix< CType >::array(), C_FLOAT64, CEFMAlgorithm::mpModel, CEFMAlgorithm::mStoi, mStoichiometry, and CMatrix< CType >::resize().

Referenced by calculate().

 {
   if (!mpModel) return false;
 
   //rebuild the stoichiometric matrix with reversible reactions divided into two.
 
   // build the _transposed_ of stoichiometry, with expanded reversible reactions
   int numRows = mStoi[0].size();
   int numCols = mStoi.size();
 
   mStoichiometry.resize(numRows, numCols);
   memset(mStoichiometry.array(), 0, numRows * numCols * sizeof(C_FLOAT64));
 
   for (int i = 0; i < numRows; ++i)
     for (int j = 0; j < numCols; ++j)
       mStoichiometry(i, j) = mStoi[j][i];
 
   return true;
 }

bool CSSAMethod::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 CEFMAlgorithm.

Definition at line 152 of file CSSAMethod.cpp.

References buildExtremeCurrents(), buildKineticMatrix(), buildStoichiometry(), CProcessReport::finishItem(), initialize(), CEFMAlgorithm::mhSteps, CCopasiMethod::mpCallBack, CEFMAlgorithm::mpModel, and testForMixingStability().

 {
   if (!initialize())
     {
       if (mpCallBack)
         mpCallBack->finishItem(mhSteps);
 
       return false;
     }
 
   if (!mpModel)
     {
       if (mpCallBack)
         mpCallBack->finishItem(mhSteps);
 
       return false;
     }
 
   //initialize matrices for calculation;
   //  if (mpModel->compileIfNecessary(NULL))
   //    {
   buildStoichiometry();
   buildKineticMatrix();
   buildExtremeCurrents();
   //}
   //  else
   //    return false;
 
   if (!testForMixingStability())
     {
       if (mpCallBack)
         mpCallBack->finishItem(mhSteps);
 
       return false;
     }
 
   if (mpCallBack)
     mpCallBack->finishItem(mhSteps);
 
   return true;
 }

bool CSSAMethod::decomposeJacobian ( )

protected

Definition at line 313 of file CSSAMethod.cpp.

References CMatrix< CType >::array(), C_FLOAT64, C_INT, dgemm_(), diag(), mExtremeCurrents, mStoichiometry, mTransformedSubJacobians, mTransposedKineticMatrix, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), and CMatrix< CType >::resize().

Referenced by testForMixingStability().

 {
   mTransformedSubJacobians.clear();
 
   // parameters for the double matrix multiplication with dgemm_
   char cN = 'N';                         // don't transpose matrices
   C_INT m = mStoichiometry.numRows();    // the leading dimension of the Stoi.M. and of the resulting M.
   C_INT n = mStoichiometry.numCols();    // the dimensions of matrix diagE, also used as 'k'.
 
   C_FLOAT64 alpha = 1.;
   C_FLOAT64 beta = 0.;
 
   CMatrix< C_FLOAT64 > product;
   product.resize(m, m);
 
   std::vector< CVector<C_FLOAT64> >::iterator iter;
 
   for (iter = mExtremeCurrents.begin(); iter != mExtremeCurrents.end(); ++iter)
     {
       CMatrix<C_FLOAT64> diagE = diag(*iter);
 
       // compute N*Ei*kappa^T:
       // As the representation of the matrices in their arrays is in
       // transposed (mathematical) order, we compute kappa*Ei*N^T,
       // which corresponds to
       // (mTransposedKineticMatrix*diagE)*mStoichiometry
       C_FLOAT64 dummy[m * n];
       dgemm_(&cN, &cN,
              &m, &n, &n, &alpha,
              mTransposedKineticMatrix.array(), &m ,
              diagE.array(), &n,
              &beta, dummy, &m);
       dgemm_(&cN, &cN,
              &m, &m, &n, &alpha,
              dummy, &m,
              mStoichiometry.array(), &n,
              &beta, product.array(), &m);
 
       mTransformedSubJacobians.push_back(product);
     }
 
   return true;
 }

template<class CType >

CMatrix<CType> CSSAMethod::diag ( CVector< CType > vector )

inlineprotected

Definition at line 103 of file CSSAMethod.h.

References CMatrix< CType >::array(), CMatrix< CType >::resize(), CVectorCore< CType >::size(), and CMatrix< CType >::size().

Referenced by decomposeJacobian().

     {
       CMatrix<CType> matrix;
 
       matrix.resize(vector.size(), vector.size());
       memset(matrix.array(), 0, matrix.size()*sizeof(CType));
 
       for (unsigned int i = 0; i < vector.size(); ++i)
         matrix(i, i) = vector[i];
 
       return matrix;
     }

bool CSSAMethod::initialize ( )

virtual

Initialize arrays and pointer.

Returns: bool success

Reimplemented from CEFMAlgorithm.

Definition at line 46 of file CSSAMethod.cpp.

References CProcessReport::addItem(), C_INT32, CCopasiVector< T >::cleanup(), CCopasiProblem::getModel(), CCopasiObject::getObjectParent(), CCopasiTask::getProblem(), CModel::getReactions(), CModel::getRedStoi(), CEFMAlgorithm::mhSteps, mIsBackwardReaction, CEFMAlgorithm::mMaxStep, mNumReactions, CCopasiMethod::mpCallBack, CEFMAlgorithm::mpModel, mReactions, CEFMAlgorithm::mReversible, CEFMAlgorithm::mStep, CEFMAlgorithm::mStoi, pTask, and CCopasiParameter::UINT.

Referenced by calculate().

 {
   CEFMTask * pTask = dynamic_cast< CEFMTask *>(getObjectParent());
 
   if (pTask == NULL) return false;
 
   mpModel = pTask->getProblem()->getModel();
 
   if (mpModel == NULL) return false;
 
   mFluxModes.clear();
   mReactions.cleanup();
 
   /* ModelStoi is the transpose of the models stoichiometry matrix */
   const CTransposeView< CMatrix< C_FLOAT64 > > ModelStoi(mpModel->getRedStoi());
 
   unsigned C_INT32 row, numRows = ModelStoi.numRows();
   unsigned C_INT32 col, numCols = ModelStoi.numCols();
 
   /* Get the reactions from the model */
   /* Note: We have as many reactions as we have rows in ModelStoi */
   CCopasiVectorNS < CReaction > & Reaction = mpModel->getReactions();
 
   /* Reversible reaction counter */
   mReversible = 0;
 
   for (row = 0; row < numRows; row++)
     {
       if (Reaction[row]->isReversible())
         mReversible++;
     }
 
   unsigned C_INT32 numOrigRows = numRows;
   numRows += mReversible;
   mNumReactions = numRows;
 
   mReversible = 0;
   /* Size the stoichiometry matrix passed to the algorithm */
   mStoi.resize(numRows);
   std::vector< std::vector< C_FLOAT64 > >::iterator it = mStoi.begin();
   std::vector< std::vector< C_FLOAT64 > >::iterator end = mStoi.end();
 
   for (; it != end; ++it)
     it->resize(numCols);
 
   /* Vector to keep track of the rearrangements necessary to put the */
   /* reversible reactions to the top of stoichiometry matrix */
   mReorderedReactions.resize(numRows);
   mIsBackwardReaction.resize(numRows);
 
   unsigned C_INT32 Insert;
   unsigned C_INT32 InsertReversible = 0;
   unsigned C_INT32 InsertIrreversible = numRows - 1;
 
   /* Build the transpose of the stoichiometry matrix, */
 
   /* sort reversible reactions to the top, count them */
 
   /* and keep track of the rearrangement */
 
   //for (row = 0; row < numOrigRows; row++)
   for (row = 0; row < numOrigRows; row++)
     {
       if (Reaction[row]->isReversible())
         {
           Insert = InsertReversible++;
           mIsBackwardReaction[Insert] = true;
 
           mReversible++;
         }
       else
         {
           Insert = InsertIrreversible--;
           mIsBackwardReaction[Insert] = false;
         }
 
       mReorderedReactions[Insert] = Reaction[row];
 
       for (col = 0; col < numCols; col++)
         {
           mStoi[Insert][col] = ModelStoi(row, col);
 
           if (Reaction[row]->isReversible())
             mStoi[InsertReversible - 1][col] = - ModelStoi(row, col);
         }
     }
 
   mStep = 0;
   mMaxStep = numCols;
 
   if (mpCallBack)
     mhSteps =
       mpCallBack->addItem("Current Step",
                           CCopasiParameter::UINT,
                           & mStep,
                           & mMaxStep);
 
   return true;
 }

TriLogic CSSAMethod::isMixingStable ( int indexEC )

Definition at line 195 of file CSSAMethod.cpp.

References mIsMixingStable.

196 {return mIsMixingStable[indexEC];}

CSSAMethod::mIsMixingStable

std::vector< TriLogic > mIsMixingStable

Definition: CSSAMethod.h:79

bool CSSAMethod::isReactionReversed ( int index ) const

Definition at line 199 of file CSSAMethod.cpp.

References mIsBackwardReaction.

Referenced by CEFMTask::getFluxModeDescription(), and CEFMTask::getReactionEquation().

200 {return mIsBackwardReaction[index];}

CSSAMethod::mIsBackwardReaction

std::vector< bool > mIsBackwardReaction

Definition: CSSAMethod.h:62

bool CSSAMethod::process ( CProcessReport * handler )

Definition at line 146 of file CSSAMethod.cpp.

 {
   return false;
 }

bool CSSAMethod::testForMixingStability ( )

protected

Definition at line 203 of file CSSAMethod.cpp.

References C_FLOAT64, C_INT32, decomposeJacobian(), dsyev_(), mExtremeCurrents, mIsMixingStable, CEFMAlgorithm::mStoi, mTransformedSubJacobians, CVectorCore< CType >::size(), TriFalse, TriTrue, and TriUnspecified.

Referenced by calculate().

 {
   decomposeJacobian();
 
   C_INT32 numECs = mExtremeCurrents.size();
 
   C_INT32 ijmax = mTransformedSubJacobians[0].numRows();
 
   mIsMixingStable.clear();
 
   C_FLOAT64 outarray[ijmax * ijmax];
   memset(outarray, 0, ijmax * ijmax * sizeof(C_FLOAT64));
 
   for (int ecIndex = 0; ecIndex < numECs; ++ecIndex)
     {
       C_FLOAT64 *inarray = mTransformedSubJacobians[ecIndex].array();
 
       // add matrix and its extremeCurrent - upper triangle only
       for (int i = 0; i < ijmax; ++i)
         for (int j = i; j < ijmax; ++j)
           outarray[i + j * ijmax] = inarray[i + j * ijmax] + inarray[j + i * ijmax];
 
       // get the eigenvalues AND eigenvectors:
       // input to dsyev_()
       char jobz = 'V';
       char uplo = 'U';
       C_INT32 n = ijmax;
       C_FLOAT64 *A = outarray;
       C_INT32 lda = ijmax;
       C_INT32 lwork = 64 * ijmax;
       // dsyev_() output
       C_FLOAT64 eigenvalues[ijmax];
       C_FLOAT64 work[lwork];
       C_INT32 info;
 
       dsyev_(&jobz, &uplo, &n, A, &lda, eigenvalues, work, &lwork, &info);
 
       if (info)
         return false;  // maybe raise an exception here, to discriminate from the sane case
 
       CVector<C_FLOAT64> EC = mExtremeCurrents[ecIndex];
 
       // set the state to 'stable' (1 - stable; 0 - unknown; -1 - not mixing stable)
       TriLogic state = TriTrue;
 
       int partMetabs[ijmax];
       memset(&partMetabs, 0, ijmax * sizeof(int));
 
       for (int j = 0; j < EC.size(); ++j)
         {
           if (EC[j])
             {
               // if one reaction's kinetic function is not Mass Action Law,
               //  this method is not valid and we can say nothing definite
               //  about the stability of this EC.
               std::string type = mReorderedReactions[j]->getFunction()->getObjectName();
 
               if (type.find("Mass action") == std::string::npos &&
                   type.find("Constant flux") == std::string::npos)
                 {
                   state = TriUnspecified;
                   break;
                 }
 
               for (int i = 0; i < ijmax; ++i)
                 {
                   if (mStoi[j][i])
                     {
                       partMetabs[i] = 1;
                       break;
                     }
                 }
             }
         }
 
       if (state == TriTrue)
         {
           // eigenvalues are sorted in rising order, and if the last ev is
           //   not positive, we have still to look after zero evs.
           if (eigenvalues[ijmax - 1] > 0)
             state = TriFalse;
           else
             {
               int zeroes = 0;
 
               for (int i = 0; i < ijmax && state == 1; ++i)
                 {
                   // only count zero eigenvals if the eigenvector contains a reaction
                   //  that is participating in this extreme current.
                   if (eigenvalues[i] == 0)
                     {
                       for (int j = 0; j < ijmax; ++ j)
                         if (partMetabs[j] && outarray[i * ijmax + j])
                           if (++zeroes)
                             break;
 
                       if (zeroes == 2)
                         state = TriFalse;
                     }
                 }
             }
         }
 
       mIsMixingStable.push_back(state);
     }
 
   return true;
 }