#include <CLNAMethod.h>

Inheritance diagram for CLNAMethod:

Collaboration diagram for CLNAMethod:

Public Types
enum	EVStatus { allNeg = 0, nonNegEigenvaluesExist }

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

Public Member Functions
void	calculateCovarianceMatrixFull ()

int	calculateCovarianceMatrixReduced ()

int	CalculateLNA ()

	CLNAMethod (const CCopasiContainer *pParent=NULL)

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

virtual bool	elevateChildren ()

const CMatrix< C_FLOAT64 > &	getBMatrixReduced () const

const CArrayAnnotation *	getBMatrixReducedAnn () const

const CMatrix< C_FLOAT64 > &	getCovarianceMatrix () const

const CArrayAnnotation *	getCovarianceMatrixAnn () const

const CMatrix< C_FLOAT64 > &	getCovarianceMatrixReduced () const

const CArrayAnnotation *	getCovarianceMatrixReducedAnn () const

const CLNAMethod::EVStatus &	getEigenValueStatus () const

const CModel *	getModel () const

const CArrayAnnotation *	getScaledBMatrixReducedAnn () const

const CArrayAnnotation *	getScaledCovarianceMatrixAnn () const

const CArrayAnnotation *	getScaledCovarianceMatrixReducedAnn () const

const CSteadyStateMethod::ReturnCode &	getSteadyStateStatus () const

const CArrayAnnotation *	getUnscaledBMatrixReducedAnn () const

const CArrayAnnotation *	getUnscaledCovarianceMatrixAnn () const

const CArrayAnnotation *	getUnscaledCovarianceMatrixReducedAnn () const

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

C_INT32	load (CReadConfig &configBuffer)

virtual bool	process ()

virtual void	resizeAllMatrices ()

void	setEigenValueStatus (CLNAMethod::EVStatus status)

void	setModel (CModel *model)

void	setSteadyStateResolution (C_FLOAT64 factor)

void	setSteadyStateStatus (CSteadyStateMethod::ReturnCode SSStatus)

virtual	~CLNAMethod ()

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 ()

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 CLNAMethod *	createMethod (CCopasiMethod::SubType subType=CCopasiMethod::linearNoiseApproximation)

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)

Private Member Functions
void	initializeParameter ()

void	initObjects ()

Additional Inherited Members
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 }

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 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

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

Detailed Description

Definition at line 28 of file CLNAMethod.h.

Member Enumeration Documentation

enum CLNAMethod::EVStatus

Enumerator
allNeg
nonNegEigenvaluesExist

Definition at line 31 of file CLNAMethod.h.

   {
     allNeg = 0,
     nonNegEigenvaluesExist
   };

Constructor & Destructor Documentation

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

Default constructor

Parameters

const CCopasiContainer * pParent (Default: NULL)

Default constructor

Definition at line 29 of file CLNAMethod.cpp.

References initializeParameter(), and initObjects().

Referenced by createMethod().

                                                      :
   CCopasiMethod(CCopasiTask::lna, CCopasiMethod::linearNoiseApproximation, pParent),
   mpModel(NULL),
   mSteadyStateResolution(1.0e-9),
   mSSStatus(CSteadyStateMethod::notFound)
 {
   initializeParameter();
   initObjects();
 }

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

Copy constructor

Parameters

const	CLNAMethod & src
const	CCopasiContainer * pParent (Default: NULL)

Definition at line 39 of file CLNAMethod.cpp.

References initializeParameter(), and initObjects().

                                                         :
   CCopasiMethod(src, pParent),
   mpModel(NULL),
   mSteadyStateResolution(src.mSteadyStateResolution),
   mSSStatus(CSteadyStateMethod::notFound)
 {
   initializeParameter();
   initObjects();
 }

CLNAMethod::~CLNAMethod ( )

virtual

Deconstructor

Definition at line 82 of file CLNAMethod.cpp.

References DESTRUCTOR_TRACE.

 {
   DESTRUCTOR_TRACE;
 }

Member Function Documentation

void CLNAMethod::calculateCovarianceMatrixFull ( )

Re-calculate covariances for the full system

Definition at line 518 of file CLNAMethod.cpp.

References CMatrix< CType >::array(), C_FLOAT64, C_INT, dgemm_(), CModel::getL0(), CModel::getNumDependentReactionMetabs(), CModel::getNumIndependentReactionMetabs(), mCovarianceMatrix, mCovarianceMatrixReduced, mL, mpModel, and CMatrix< CType >::resize().

Referenced by CalculateLNA().

 {
   // the covariance matrix of the full system is calculated from
   // the covariance matrix of the reduced system by:
   // mL*mCovarianceMatrixReduced*mL^T, with mL the link matrix
 
   C_INT i, j;
 
   C_INT numIndependentMetabs = (C_INT)mpModel->getNumIndependentReactionMetabs();
   C_INT numReactionMetabs = (C_INT)mpModel->getNumIndependentReactionMetabs() + mpModel->getNumDependentReactionMetabs();
   C_INT numDependentMetabs = numReactionMetabs - numIndependentMetabs;
 
   CMatrix<C_FLOAT64> mL0;
   mL0 = mpModel->getL0();
   mL.resize((size_t)numReactionMetabs, (size_t)numIndependentMetabs);
   mL = 0.0;
 
   for (i = 0; i < numIndependentMetabs; i++) mL[(size_t)i][(size_t)i] = 1.0;
 
   for (i = 0; i < numDependentMetabs; i++)
     for (j = 0; j < numIndependentMetabs; j++)
       mL[(size_t)i + (size_t)numIndependentMetabs][(size_t)j] = mL0[(size_t)i][(size_t)j];
 
   CMatrix< C_FLOAT64 > D;
   D.resize((size_t)numIndependentMetabs, (size_t)numReactionMetabs);
   D = 0.0;
 
   // take care of different memory layouts in C and FORTRAN (e.g. BLAS routines)
   char transa = 'T';
   char transb = 'T';
   C_FLOAT64 alpha = 1.0;
   C_FLOAT64 beta = 0.0;
 
   dgemm_(&transa,
          &transb,
          &numReactionMetabs,
          &numIndependentMetabs,
          &numIndependentMetabs,
          &alpha,
          mL.array(),
          &numIndependentMetabs,
          mCovarianceMatrixReduced.array(),
          &numIndependentMetabs,
          &beta,
          D.array(),
          &numReactionMetabs);
 
   // take care of different memory layouts in C and FORTRAN (e.g. BLAS routines)
   transa = 'N';
   transb = 'N';
   alpha = 1.0;
   beta = 0.0;
   mCovarianceMatrix.resize((size_t)numReactionMetabs, (size_t)numReactionMetabs);
   mCovarianceMatrix = 0.0;
 
   dgemm_(&transa,
          &transb,
          &numReactionMetabs,
          &numReactionMetabs,
          &numIndependentMetabs,
          &alpha,
          D.array(),
          &numReactionMetabs,
          mL.array(),
          &numIndependentMetabs,
          &beta,
          mCovarianceMatrix.array(),
          &numReactionMetabs);
 }

int CLNAMethod::calculateCovarianceMatrixReduced ( )

Definition at line 127 of file CLNAMethod.cpp.

References CVectorCore< CType >::array(), CMatrix< CType >::array(), CCopasiVector< T >::begin(), C_FLOAT64, C_INT, C_LOGICAL, CModel::calculateJacobianX(), dgees_(), dgemm_(), dtrsyl_(), CCopasiVector< T >::end(), CCopasiVector< T >::getIndex(), CModel::getMetabolitesX(), CModel::getNumIndependentReactionMetabs(), CModel::getParticleFlux(), CModel::getReactions(), CModelEntity::getStatus(), CMetab::isDependent(), LNA_OK, max, mBMatrixReduced, mCovarianceMatrixReduced, mJacobianReduced, mpModel, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), CModelEntity::REACTIONS, CMatrix< CType >::resize(), CVector< CType >::resize(), CMatrix< CType >::size(), and CCopasiVector< T >::size().

Referenced by CalculateLNA().

 {
   // code snippet: transform something into particle space:
   // *(metabs[i]->getCompartment())->getValue()*mpModel->getQuantity2NumberFactor();
 
   assert(mpModel);
 
   CCopasiVector< CMetab > & metabs = mpModel->getMetabolitesX();
   CCopasiVector< CReaction > & reacs = mpModel->getReactions();
   const CVector< C_FLOAT64 > & ParticleFlux = mpModel->getParticleFlux();
 
   size_t numReacs = reacs.size();
 
   // We need the number of independent metabolites determined by
   // reactions.
   size_t numMetabs = mpModel->getNumIndependentReactionMetabs();
 
   size_t i, j, k;
   const CMetab * pMetabolite;
   C_FLOAT64 balance_i, balance_j, BContrib;
 
   // calculate covariances
   // first, set BMatrix (reduced) to zero
   mBMatrixReduced.resize(numMetabs, numMetabs);
   mBMatrixReduced = 0.0;
 
   // second, set CovarianceMatrixReduced to zero
   mCovarianceMatrixReduced.resize(numMetabs, numMetabs);
   mCovarianceMatrixReduced = 0.0;
 
   // then, calculate the contribution for each reaction
   // and add these contributions to the respective mBMatrix elements
   // only consider independent metabolites determined by reactions,
   // e.g. those that contribute to the reduced stoichiometry matrix.
   // Note: This could also be computed using mRedStoi in CModel.
   //       However, then it would probably be less efficient for very
   //       big systems since mRedStoi should be sparse there.
   for (k = 0; k < numReacs; k++)
     {
       const CCopasiVector <CChemEqElement> & Balances =
         reacs[k]->getChemEq().getBalances();
 
       CCopasiVector<CChemEqElement>::const_iterator itRow;
       CCopasiVector<CChemEqElement>::const_iterator itColumn;
       CCopasiVector<CChemEqElement>::const_iterator itEnd = Balances.end();
 
       for (itRow = Balances.begin(); itRow != itEnd; ++itRow)
         {
           pMetabolite = (*itRow)->getMetabolite();
           i = metabs.getIndex(pMetabolite);
 
           if (i < numMetabs)
             {
               balance_i = (*itRow)->getMultiplicity();
 
               // This check is no longer needed since we check the index for validity, i.e. we are assured to have an independent metabolite
               if ((pMetabolite->getStatus() != CModelEntity::REACTIONS) || (pMetabolite->isDependent())) balance_i = 0.0;
 
               for (itColumn = Balances.begin(); itColumn != itEnd; ++itColumn)
                 {
                   pMetabolite = (*itColumn)->getMetabolite();
                   j = metabs.getIndex(pMetabolite);
 
                   if (j < numMetabs)
                     {
                       balance_j = (*itColumn)->getMultiplicity();
 
                       // This check is no longer needed since we check the index for validity, i.e. we are assured to have an independent metabolite
                       if ((pMetabolite->getStatus() != CModelEntity::REACTIONS) || (pMetabolite->isDependent())) balance_j = 0.0;
 
                       BContrib = ParticleFlux[k] * balance_i * balance_j;
                       mBMatrixReduced[i][j] += BContrib;
                     }
                 }
             }
         }
     }
 
   // finally, solve the Lyapunov equation A*C + C*A^T + B = 0 for C
   // using the Bartels & Stewart algorithm (1972)
 
   // 1. (Schur) transform the Jacobian matrix A (reduced) and its transpose At
 
   // get the Jacobian (reduced)
   C_FLOAT64 derivationFactor = 1e-6;
   C_FLOAT64 resolution = 1e-12;
   mpModel->calculateJacobianX(mJacobianReduced, derivationFactor, resolution);
 
   // copy the Jacobian (reduced) into A
   CMatrix< C_FLOAT64 > A;
   A.resize(mJacobianReduced.numRows(), mJacobianReduced.numCols());
   C_FLOAT64 * pA = A.array();
   C_FLOAT64 * pAEnd = pA + A.size();
   const C_FLOAT64 * pMatrix = mJacobianReduced.array();
 
   for (; pA != pAEnd; ++pA, ++pMatrix)
     {
       *pA = *pMatrix;
 
       if (!finite(*pA) && !isnan(*pA))
         {
           if (*pA > 0)
             *pA = std::numeric_limits< C_FLOAT64 >::max();
           else
             *pA = - std::numeric_limits< C_FLOAT64 >::max();
         }
     }
 
   char jobvs = 'V'; // Schur vectors are computed
   char sort = 'N'; // Eigenvalues are not ordered
   C_INT n = (C_INT)A.numRows();
   C_INT lda = n > 1 ? n : 1;
   C_INT sdim; // output
   CVector< C_FLOAT64 > wr_A;
   wr_A.resize((size_t)n);
   CVector< C_FLOAT64 > wi_A;
   wi_A.resize((size_t)n);
   CMatrix< C_FLOAT64> vs_A; // output (unitary matrix)
   C_INT ldvs_A = n;
   vs_A.resize((size_t)ldvs_A, (size_t)ldvs_A);
   CVector< C_FLOAT64 > work = 1;
   C_INT lwork;
   C_LOGICAL * pbwork = NULL;
   C_INT info;
 
   // LWORK workspace query
   lwork = -1;
   dgees_(&jobvs,
          &sort,
          NULL,
          &n,
          A.array(),
          &lda,
          &sdim,
          wr_A.array(),
          wi_A.array(),
          vs_A.array(),
          &ldvs_A,
          work.array(),
          &lwork,
          pbwork,
          &info);
 
   if (info != 0)
     {
       // TODO(juergen): add appropriate exception message(s)!
       //      CCopasiMessage(CCopasiMessage::EXCEPTION, MCLNA + 1, -mInfo);
     }
 
   lwork = (C_INT) work[0];
   work.resize((size_t)lwork);
 
   dgees_(&jobvs,
          &sort,
          NULL,
          &n,
          A.array(), // input: matrix / output: real Schur form
          &lda,
          &sdim,
          wr_A.array(),
          wi_A.array(),
          vs_A.array(),
          &ldvs_A,
          work.array(),
          &lwork,
          pbwork,
          &info);
 
   if (info != 0)
     {
       // TODO(juergen): add appropriate exception message(s)!
       //      CCopasiMessage(CCopasiMessage::EXCEPTION, MCLNA + 1, -mInfo);
     }
 
   // now, (Schur) transform the transposed Jacobian (reduced)
 
   // copy the transposed Jacobian (reduced) into At
   CMatrix< C_FLOAT64 > At;
   At.resize(mJacobianReduced.numCols(), mJacobianReduced.numRows());
 
   for (i = 0; i < mJacobianReduced.numRows(); i++)
     {
       for (j = 0; j < mJacobianReduced.numCols(); j++)
         {
           At[j][i] = mJacobianReduced[i][j];
 
           if (!finite(At[j][i]) && !isnan(At[j][i]))
             {
               if (At[j][i] > 0)
                 At[j][i] = std::numeric_limits< C_FLOAT64 >::max();
               else
                 At[j][i] = - std::numeric_limits< C_FLOAT64 >::max();
             }
         }
     }
 
   jobvs = 'V'; // Schur vectors are computed
   sort = 'N'; // Eigenvalues are not ordered
   n = (C_INT)At.numRows();
   lda = n > 1 ? n : 1;
   //  C_INT sdim; // output
   CVector< C_FLOAT64 > wr_At;
   wr_At.resize((size_t)n);
   CVector< C_FLOAT64 > wi_At;
   wi_At.resize((size_t)n);
   CMatrix< C_FLOAT64 > vs_At; // output (unitary matrix)
   C_INT ldvs_At = n;
   vs_At.resize((size_t)ldvs_At, (size_t)ldvs_At);
   work = 1;
   //  C_INT lwork;
   pbwork = NULL;
   //  C_INT info;
 
   // LWORK workspace query
   lwork = -1;
   dgees_(&jobvs,
          &sort,
          NULL,
          &n,
          At.array(),
          &lda,
          &sdim,
          wr_At.array(),
          wi_At.array(),
          vs_At.array(),
          &ldvs_At,
          work.array(),
          &lwork,
          pbwork,
          &info);
 
   if (info != 0)
     {
       // TODO(juergen): add appropriate exception message(s)!
       //      CCopasiMessage(CCopasiMessage::EXCEPTION, MCLNA + 1, -mInfo);
     }
 
   lwork = (C_INT) work[0];
   work.resize((size_t)lwork);
 
   dgees_(&jobvs,
          &sort,
          NULL,
          &n,
          At.array(), // input: matrix / output: real Schur form
          &lda,
          &sdim,
          wr_At.array(),
          wi_At.array(),
          vs_At.array(),
          &ldvs_At,
          work.array(),
          &lwork,
          pbwork,
          &info);
 
   if (info != 0)
     {
       // TODO(juergen): add appropriate exception message(s)!
       //      CCopasiMessage(CCopasiMessage::EXCEPTION, MCLNA + 1, -mInfo);
     }
 
   // 2. transform the mBMatrixReduced B to new coordinates
   //    BMatrixReduced_transformed = (unitary At)^T * mBMatrixReduced * (unitary A);
 
   char transa = 'T'; // (unitary A) will be transposed
   char transb = 'N'; // mBMatrixReduced will not be transposed
   C_FLOAT64 alpha = 1.0;
   C_FLOAT64 beta = 0.0;
   CMatrix< C_FLOAT64 > D;
   C_INT ldd = n;
   D.resize((size_t)n, (size_t)n);
 
   dgemm_(&transa,
          &transb,
          &n,
          &n,
          &n,
          &alpha,
          vs_At.array(),
          &n,
          mBMatrixReduced.array(),
          &n,
          &beta,
          D.array(), // output: multiplied matrix
          &ldd);
 
   transa = 'N';
   CMatrix< C_FLOAT64 > BMatrixReduced_transformed;
   C_INT BMatrixReduced_transformed_d = n;
   BMatrixReduced_transformed.resize((size_t)n, (size_t)n);
 
   dgemm_(&transa,
          &transb,
          &n,
          &n,
          &n,
          &alpha,
          D.array(),
          &n,
          vs_A.array(), // (unitary At)
          &n,
          &beta,
          BMatrixReduced_transformed.array(),
          &BMatrixReduced_transformed_d);
 
   // 3. Solve the simplified Lyapunov (Sylvester) Equation
 
   char trana = 'N'; // no transpose of A
   char tranb = 'N'; // no transpose of B
   C_INT isgn = 1; // sign in the equation is "+"
   C_FLOAT64 scale; // output
 
   //  DTRSYL solves the real Sylvester matrix equation:
   //
   //     op(A)*X + X*op(B) = scale*C or
   //     op(A)*X - X*op(B) = scale*C,
   //
   //  where op(A) = A or A**T, and  A and B are both upper quasi-
   //  triangular. A is M-by-M and B is N-by-N; the right hand side C and
   //  the solution X are M-by-N; and scale is an output scale factor, set
   //  <= 1 to avoid overflow in X.
   dtrsyl_(&trana,
           &tranb,
           &isgn,
           &n,
           &n,
           At.array(), // Schur transform of the Jacobian (reduced)
           &n,
           A.array(), // Schur transform of the transposed Jacobian (reduced)
           &n,
           BMatrixReduced_transformed.array(), // output / input (the coordinate-transformed mBMatrix (reduced))
           &n,
           &scale,
           &info);
 
   if (info != 0)
     {
       // TODO(juergen): add appropriate exception message(s)!
       //      CCopasiMessage(CCopasiMessage::EXCEPTION, MCLNA + 1, -mInfo);
     }
 
   // 4. Calculate the original matrix C: -(unitary At)*BMatrixReduced_transformed*(unitary A)^T;
 
   transa = 'N';
   transb = 'N';
   alpha = -1.0;
   beta = 0.0;
   ldd = n;
   D.resize((size_t)n, (size_t)n);
 
   dgemm_(&transa,
          &transb,
          &n,
          &n,
          &n,
          &alpha,
          vs_At.array(),
          &n,
          BMatrixReduced_transformed.array(), // BMatrixReduced_transformed.array() holds the output of dtrsyl() now
          &n,
          &beta,
          D.array(),
          &ldd);
 
   transa = 'N';
   transb = 'T';
   alpha = 1.0;
   beta = 0.0;
   mCovarianceMatrixReduced.resize((size_t)n, (size_t)n);
 
   dgemm_(&transa,
          &transb,
          &n,
          &n,
          &n,
          &alpha,
          D.array(),
          &n,
          vs_A.array(),
          &n,
          &beta,
          mCovarianceMatrixReduced.array(),
          &n);
 
   return LNA_OK;
 }

int CLNAMethod::CalculateLNA ( )

the LNA entry point

Parameters

status	refers to the steady-state solution
res	refers to the resolution

Definition at line 601 of file CLNAMethod.cpp.

References allNeg, calculateCovarianceMatrixFull(), calculateCovarianceMatrixReduced(), CSteadyStateMethod::found, CSteadyStateMethod::foundEquilibrium, LNA_NOT_OK, LNA_OK, mBMatrixReduced, mCovarianceMatrix, mCovarianceMatrixReduced, mEVStatus, mpModel, and mSSStatus.

Referenced by process().

 {
   assert(mpModel);
 
   if (((mSSStatus == CSteadyStateMethod::found) || (mSSStatus == CSteadyStateMethod::foundEquilibrium)) && (mEVStatus == CLNAMethod::allNeg))
     {
       if (calculateCovarianceMatrixReduced() == LNA_OK)
         {
           calculateCovarianceMatrixFull();
           return LNA_OK;
         }
     }
 
   // something went wrong
   mBMatrixReduced = std::numeric_limits< C_FLOAT64 >::quiet_NaN();
   mCovarianceMatrixReduced = std::numeric_limits< C_FLOAT64 >::quiet_NaN();
   mCovarianceMatrix = std::numeric_limits< C_FLOAT64 >::quiet_NaN();
   return LNA_NOT_OK;
 }

CLNAMethod * CLNAMethod::createMethod ( CCopasiMethod::SubType subType = CCopasiMethod::linearNoiseApproximation )

static

Create a LNA method. Note: the returned object has to be released after use with delete

Definition at line 21 of file CLNAMethod.cpp.

References CLNAMethod().

Referenced by CLNATask::createMethod().

 {
   return new CLNAMethod();
 }

bool CLNAMethod::elevateChildren ( )

virtual

This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.

Returns: bool success

Reimplemented from CCopasiParameterGroup.

Definition at line 101 of file CLNAMethod.cpp.

References initializeParameter().

 {
   initializeParameter();
   return true;
 }

const CMatrix<C_FLOAT64>& CLNAMethod::getBMatrixReduced ( ) const

inline

Definition at line 101 of file CLNAMethod.h.

References mBMatrixReduced.

102 {return mBMatrixReduced;}

CLNAMethod::mBMatrixReduced

CMatrix< C_FLOAT64 > mBMatrixReduced

Definition: CLNAMethod.h:44

const CArrayAnnotation* CLNAMethod::getBMatrixReducedAnn ( ) const

inline

Definition at line 104 of file CLNAMethod.h.

References mBMatrixReducedAnn.

105 {return mBMatrixReducedAnn;}

CLNAMethod::mBMatrixReducedAnn

CArrayAnnotation * mBMatrixReducedAnn

Definition: CLNAMethod.h:45

const CMatrix<C_FLOAT64>& CLNAMethod::getCovarianceMatrix ( ) const

inline

Definition at line 107 of file CLNAMethod.h.

References mCovarianceMatrix.

108 {return mCovarianceMatrix;}

CLNAMethod::mCovarianceMatrix

CMatrix< C_FLOAT64 > mCovarianceMatrix

Definition: CLNAMethod.h:50

const CArrayAnnotation* CLNAMethod::getCovarianceMatrixAnn ( ) const

inline

Definition at line 110 of file CLNAMethod.h.

References mCovarianceMatrixAnn.

Referenced by CLNATask::printResult().

111 {return mCovarianceMatrixAnn;}

CLNAMethod::mCovarianceMatrixAnn

CArrayAnnotation * mCovarianceMatrixAnn

Definition: CLNAMethod.h:51

const CMatrix<C_FLOAT64>& CLNAMethod::getCovarianceMatrixReduced ( ) const

inline

Definition at line 113 of file CLNAMethod.h.

References mCovarianceMatrixReduced.

114 {return mCovarianceMatrixReduced;}

CLNAMethod::mCovarianceMatrixReduced

CMatrix< C_FLOAT64 > mCovarianceMatrixReduced

Definition: CLNAMethod.h:47

const CArrayAnnotation* CLNAMethod::getCovarianceMatrixReducedAnn ( ) const

inline

Definition at line 116 of file CLNAMethod.h.

References mCovarianceMatrixReducedAnn.

117 {return mCovarianceMatrixReducedAnn;}

CLNAMethod::mCovarianceMatrixReducedAnn

CArrayAnnotation * mCovarianceMatrixReducedAnn

Definition: CLNAMethod.h:48

const CLNAMethod::EVStatus& CLNAMethod::getEigenValueStatus ( ) const

inline

Definition at line 188 of file CLNAMethod.h.

References mEVStatus.

Referenced by CLNAResultSubwidget::loadAll().

189 {return mEVStatus;}

CLNAMethod::mEVStatus

CLNAMethod::EVStatus mEVStatus

Definition: CLNAMethod.h:63

const CModel * CLNAMethod::getModel ( ) const

Get the Model

Definition at line 657 of file CLNAMethod.cpp.

References mpModel.

Referenced by CLNAResultSubwidget::loadAll().

 {
   return this->mpModel;
 }

const CArrayAnnotation* CLNAMethod::getScaledBMatrixReducedAnn ( ) const

inline

Definition at line 121 of file CLNAMethod.h.

References mBMatrixReducedAnn.

Referenced by CLNAResultSubwidget::loadBMatrixReduced().

122 {return mBMatrixReducedAnn;}

CLNAMethod::mBMatrixReducedAnn

CArrayAnnotation * mBMatrixReducedAnn

Definition: CLNAMethod.h:45

const CArrayAnnotation* CLNAMethod::getScaledCovarianceMatrixAnn ( ) const

inline

Definition at line 127 of file CLNAMethod.h.

References mCovarianceMatrixAnn.

Referenced by CLNAResultSubwidget::loadCovarianceMatrix().

128 {return mCovarianceMatrixAnn;}

CLNAMethod::mCovarianceMatrixAnn

CArrayAnnotation * mCovarianceMatrixAnn

Definition: CLNAMethod.h:51

const CArrayAnnotation* CLNAMethod::getScaledCovarianceMatrixReducedAnn ( ) const

inline

Definition at line 130 of file CLNAMethod.h.

References mCovarianceMatrixReducedAnn.

Referenced by CLNAResultSubwidget::loadCovarianceMatrixReduced().

131 {return mCovarianceMatrixReducedAnn;}

CLNAMethod::mCovarianceMatrixReducedAnn

CArrayAnnotation * mCovarianceMatrixReducedAnn

Definition: CLNAMethod.h:48

const CSteadyStateMethod::ReturnCode& CLNAMethod::getSteadyStateStatus ( ) const

inline

Definition at line 185 of file CLNAMethod.h.

References mSSStatus.

Referenced by CLNAResultSubwidget::loadAll(), and CLNATask::printResult().

186 {return mSSStatus;}

CLNAMethod::mSSStatus

CSteadyStateMethod::ReturnCode mSSStatus

Definition: CLNAMethod.h:61

const CArrayAnnotation* CLNAMethod::getUnscaledBMatrixReducedAnn ( ) const

inline

Definition at line 124 of file CLNAMethod.h.

References mBMatrixReducedAnn.

Referenced by CLNAResultSubwidget::loadBMatrixReduced().

125 {return mBMatrixReducedAnn;}

CLNAMethod::mBMatrixReducedAnn

CArrayAnnotation * mBMatrixReducedAnn

Definition: CLNAMethod.h:45

const CArrayAnnotation* CLNAMethod::getUnscaledCovarianceMatrixAnn ( ) const

inline

Definition at line 133 of file CLNAMethod.h.

References mCovarianceMatrixAnn.

Referenced by CLNAResultSubwidget::loadCovarianceMatrix().

134 {return mCovarianceMatrixAnn;}

CLNAMethod::mCovarianceMatrixAnn

CArrayAnnotation * mCovarianceMatrixAnn

Definition: CLNAMethod.h:51

const CArrayAnnotation* CLNAMethod::getUnscaledCovarianceMatrixReducedAnn ( ) const

inline

Definition at line 136 of file CLNAMethod.h.

References mCovarianceMatrixReducedAnn.

Referenced by CLNAResultSubwidget::loadCovarianceMatrixReduced().

137 {return mCovarianceMatrixReducedAnn;}

CLNAMethod::mCovarianceMatrixReducedAnn

CArrayAnnotation * mCovarianceMatrixReducedAnn

Definition: CLNAMethod.h:48

void CLNAMethod::initializeParameter ( )

private

Intialize the method parameter

Definition at line 87 of file CLNAMethod.cpp.

Referenced by CLNAMethod(), and elevateChildren().

 {
   /*  CCopasiParameter *pParm;
 
       assertParameter("Placeholder Factor", CCopasiParameter::UDOUBLE, 1.0e-009);
 
       if ((pParm = getParameter("LNA.PlaceholderFactor")) != NULL)
       {
       setValue("Placeholder Factor", *pParm->getValue().pUDOUBLE);
       removeParameter("LNA.PlaceholderFactor");
       }
   */
 }

void CLNAMethod::initObjects ( )

private

Definition at line 50 of file CLNAMethod.cpp.

References mBMatrixReduced, mBMatrixReducedAnn, mCovarianceMatrix, mCovarianceMatrixAnn, mCovarianceMatrixReduced, mCovarianceMatrixReducedAnn, CArrayAnnotation::setDescription(), CArrayAnnotation::setDimensionDescription(), CArrayAnnotation::setMode(), and CArrayAnnotation::VECTOR.

Referenced by CLNAMethod().

 {
   CArrayAnnotation * tmp;
 
   tmp = new CArrayAnnotation("B matrix (reduced)", this,
                              new CCopasiMatrixInterface<CMatrix<C_FLOAT64> >(&mBMatrixReduced), true);
   tmp->setMode(CArrayAnnotation::VECTOR);
   tmp->setDescription("B matrix (reduced)");
   tmp->setDimensionDescription(0, "Species (reduced system)");
   tmp->setDimensionDescription(1, "Species (reduced system)");
   mBMatrixReducedAnn = tmp;
 
   tmp = new CArrayAnnotation("Covariance matrix (reduced)", this,
                              new CCopasiMatrixInterface<CMatrix<C_FLOAT64> >(&mCovarianceMatrixReduced), true);
   tmp->setMode(CArrayAnnotation::VECTOR);
   tmp->setDescription("Covariance matrix (reduced)");
   tmp->setDimensionDescription(0, "Species (reduced system)");
   tmp->setDimensionDescription(1, "Species (reduced system)");
   mCovarianceMatrixReducedAnn = tmp;
 
   tmp = new CArrayAnnotation("Covariance matrix", this,
                              new CCopasiMatrixInterface<CMatrix<C_FLOAT64> >(&mCovarianceMatrix), true);
   tmp->setMode(CArrayAnnotation::VECTOR);
   tmp->setDescription("Covariance matrix");
   tmp->setDimensionDescription(0, "Species (full system)");
   tmp->setDimensionDescription(1, "Species (full system)");
   mCovarianceMatrixAnn = tmp;
 }

bool CLNAMethod::isValidProblem ( const CCopasiProblem * pProblem )

virtual

Check if the method is suitable for this problem

Returns: bool suitability of the method

Reimplemented from CCopasiMethod.

Definition at line 663 of file CLNAMethod.cpp.

References CCopasiVector< T >::begin(), CCopasiVector< T >::end(), CCopasiMessage::ERROR, CModelEntity::FIXED, CModel::getCompartments(), CCopasiProblem::getModel(), CModel::getNumAssignmentMetabs(), CModel::getNumODEMetabs(), CModel::getReactions(), CCopasiMethod::isValidProblem(), and CCopasiVector< T >::size().

 {
   if (!CCopasiMethod::isValidProblem(pProblem)) return false;
 
   const CLNAProblem * pP = dynamic_cast<const CLNAProblem *>(pProblem);
 
   if (!pP)
     {
       //not a CLNAProblem
       CCopasiMessage(CCopasiMessage::ERROR, "Problem is not a LNA problem.");
       return false;
     }
 
   CModel * pModel = pP->getModel();
 
   if (pModel == NULL)
     return false;
 
   // Check if the model contains species that have assignments or
   // explicit ODEs.
   if (pModel->getNumAssignmentMetabs() > 0)
     {
       CCopasiMessage(CCopasiMessage::ERROR, "LNA is not applicable for a system with species assignments.");
       return false;
     }
 
   if (pModel->getNumODEMetabs() > 0)
     {
       CCopasiMessage(CCopasiMessage::ERROR, "LNA is not applicable for a system with explicit ODEs for species.");
       return false;
     }
 
   //if (pModel->getCompartments().size() > 1)
   //  {
   //    CCopasiMessage(CCopasiMessage::ERROR, "LNA is not applicable for a system with more than one compartment.");
   //    return false;
   //}
 
   // Check if the model has a compartment with an assignment or ODE
   CCopasiVector< CCompartment >::const_iterator it = pModel->getCompartments().begin();
   CCopasiVector< CCompartment >::const_iterator end = pModel->getCompartments().end();
 
   for (; it != end; ++it)
     if ((*it)->getStatus() != CModelEntity::FIXED)
       {
         CCopasiMessage(CCopasiMessage::ERROR, "LNA is not applicable for a system with changing volumes, e.g. compartment assignments or ODEs.");
         return false;
       }
 
   CCopasiVector< CReaction > & reacs = pModel->getReactions();
   size_t numReacs = reacs.size();
   size_t i;
 
   for (i = 0; i < numReacs; i++) // for every reaction
     {
       // TEST isReversible() == 0
       if (reacs[i]->isReversible() != 0)
         {
           CCopasiMessage(CCopasiMessage::ERROR, "At least one reaction is reversible. That means it is not possible to calculate the LNA. \nYou can use \"Tools|Convert to irreversible\" which will split the reversible reactions \n into two irreversible reactions. However you should check the kinetics afterwards.");
           return false;
         }
     }
 
   return true;
 }

C_INT32 CLNAMethod::load ( CReadConfig & configBuffer )

Read some parameters from configuration file

Read some parameters from configuration file.

Definition at line 624 of file CLNAMethod.cpp.

References C_INT32.

 {
   C_INT32 Fail = 0;
   /*
     if ((Fail = configBuffer.getVariable("SSMCAUnscaled", "C_INT16",
                                           (void *) & mSSReder,
                                           CReadConfig::LOOP)))
     return Fail;
   */
   return Fail;
 }

bool CLNAMethod::process ( )

virtual

Definition at line 636 of file CLNAMethod.cpp.

References CalculateLNA(), and LNA_OK.

Referenced by CLNATask::process().

 {
   return (CalculateLNA() == LNA_OK);
   // maybe, introduce additional checks here later
 }

void CLNAMethod::resizeAllMatrices ( )

virtual

Resizes all result matrices and updates the corresponding array annotations. This needs to be called before output initialization (in case the output references parts of the matrix) from the task initialization, but it also needs to be called before selecting elements of the matrices in the object selection dialog. The model needs to be set before calling this.

Definition at line 107 of file CLNAMethod.cpp.

References CModel::getMetabolitesX(), CModel::getNumDependentReactionMetabs(), CModel::getNumIndependentReactionMetabs(), mBMatrixReduced, mBMatrixReducedAnn, mCovarianceMatrix, mCovarianceMatrixAnn, mCovarianceMatrixReduced, mCovarianceMatrixReducedAnn, mpModel, CMatrix< CType >::resize(), CArrayAnnotation::resize(), and CArrayAnnotation::setCopasiVector().

Referenced by CLNATask::updateMatrices().

 {
   if (!mpModel) return;
 
   mBMatrixReduced.resize(mpModel->getNumIndependentReactionMetabs(), mpModel->getNumIndependentReactionMetabs());
   mBMatrixReducedAnn->resize();
   mBMatrixReducedAnn->setCopasiVector(0, &mpModel->getMetabolitesX());
   mBMatrixReducedAnn->setCopasiVector(1, &mpModel->getMetabolitesX());
 
   mCovarianceMatrixReduced.resize(mpModel->getNumIndependentReactionMetabs(), mpModel->getNumIndependentReactionMetabs());
   mCovarianceMatrixReducedAnn->resize();
   mCovarianceMatrixReducedAnn->setCopasiVector(0, &mpModel->getMetabolitesX());
   mCovarianceMatrixReducedAnn->setCopasiVector(1, &mpModel->getMetabolitesX());
 
   mCovarianceMatrix.resize(mpModel->getNumIndependentReactionMetabs() + mpModel->getNumDependentReactionMetabs(), mpModel->getNumIndependentReactionMetabs() + mpModel->getNumDependentReactionMetabs());
   mCovarianceMatrixAnn->resize();
   mCovarianceMatrixAnn->setCopasiVector(0, &mpModel->getMetabolitesX());
   mCovarianceMatrixAnn->setCopasiVector(1, &mpModel->getMetabolitesX());
 }

void CLNAMethod::setEigenValueStatus ( CLNAMethod::EVStatus status )

Definition at line 647 of file CLNAMethod.cpp.

References mEVStatus.

Referenced by CLNATask::process().

 {
   mEVStatus = status;
 }

void CLNAMethod::setModel ( CModel * model )

Set the Model

Definition at line 591 of file CLNAMethod.cpp.

References mpModel.

Referenced by CLNATask::printResult(), and CLNATask::updateMatrices().

 {
   mpModel = model;
 }

void CLNAMethod::setSteadyStateResolution ( C_FLOAT64 factor )

Definition at line 652 of file CLNAMethod.cpp.

References mSteadyStateResolution.

 {
   this->mSteadyStateResolution = resolution;
 }

void CLNAMethod::setSteadyStateStatus ( CSteadyStateMethod::ReturnCode SSStatus )

Definition at line 642 of file CLNAMethod.cpp.

References mSSStatus.

Referenced by CLNATask::process().

 {
   mSSStatus = SSStatus;
 }

Member Data Documentation

CMatrix<C_FLOAT64> CLNAMethod::mBMatrixReduced

private

LNA Matrices

Definition at line 44 of file CLNAMethod.h.

Referenced by calculateCovarianceMatrixReduced(), CalculateLNA(), getBMatrixReduced(), initObjects(), and resizeAllMatrices().

CArrayAnnotation* CLNAMethod::mBMatrixReducedAnn

private

Definition at line 45 of file CLNAMethod.h.

Referenced by getBMatrixReducedAnn(), getScaledBMatrixReducedAnn(), getUnscaledBMatrixReducedAnn(), initObjects(), and resizeAllMatrices().

CMatrix<C_FLOAT64> CLNAMethod::mCovarianceMatrix

private

Definition at line 50 of file CLNAMethod.h.

Referenced by calculateCovarianceMatrixFull(), CalculateLNA(), getCovarianceMatrix(), initObjects(), and resizeAllMatrices().

CArrayAnnotation* CLNAMethod::mCovarianceMatrixAnn

private

Definition at line 51 of file CLNAMethod.h.

Referenced by getCovarianceMatrixAnn(), getScaledCovarianceMatrixAnn(), getUnscaledCovarianceMatrixAnn(), initObjects(), and resizeAllMatrices().

CMatrix<C_FLOAT64> CLNAMethod::mCovarianceMatrixReduced

private

Definition at line 47 of file CLNAMethod.h.

Referenced by calculateCovarianceMatrixFull(), calculateCovarianceMatrixReduced(), CalculateLNA(), getCovarianceMatrixReduced(), initObjects(), and resizeAllMatrices().

CArrayAnnotation* CLNAMethod::mCovarianceMatrixReducedAnn

private

Definition at line 48 of file CLNAMethod.h.

Referenced by getCovarianceMatrixReducedAnn(), getScaledCovarianceMatrixReducedAnn(), getUnscaledCovarianceMatrixReducedAnn(), initObjects(), and resizeAllMatrices().

CLNAMethod::EVStatus CLNAMethod::mEVStatus

private

Definition at line 63 of file CLNAMethod.h.

Referenced by CalculateLNA(), getEigenValueStatus(), and setEigenValueStatus().

CMatrix<C_FLOAT64> CLNAMethod::mJacobianReduced

private

Definition at line 54 of file CLNAMethod.h.

Referenced by calculateCovarianceMatrixReduced().

CMatrix<C_FLOAT64> CLNAMethod::mL

private

Definition at line 57 of file CLNAMethod.h.

Referenced by calculateCovarianceMatrixFull().

CModel* CLNAMethod::mpModel

private

Definition at line 39 of file CLNAMethod.h.

Referenced by calculateCovarianceMatrixFull(), calculateCovarianceMatrixReduced(), CalculateLNA(), getModel(), resizeAllMatrices(), and setModel().

CSteadyStateMethod::ReturnCode CLNAMethod::mSSStatus

private

Definition at line 61 of file CLNAMethod.h.

Referenced by CalculateLNA(), getSteadyStateStatus(), and setSteadyStateStatus().

C_FLOAT64 CLNAMethod::mSteadyStateResolution

private

Definition at line 59 of file CLNAMethod.h.

Referenced by setSteadyStateResolution().

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

Private Attributes
CMatrix< C_FLOAT64 >	mBMatrixReduced

CArrayAnnotation *	mBMatrixReducedAnn

CMatrix< C_FLOAT64 >	mCovarianceMatrix

CArrayAnnotation *	mCovarianceMatrixAnn

CMatrix< C_FLOAT64 >	mCovarianceMatrixReduced

CArrayAnnotation *	mCovarianceMatrixReducedAnn

CLNAMethod::EVStatus	mEVStatus

CMatrix< C_FLOAT64 >	mJacobianReduced

CMatrix< C_FLOAT64 >	mL

CModel *	mpModel

CSteadyStateMethod::ReturnCode	mSSStatus

C_FLOAT64	mSteadyStateResolution

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation