#include <CEFMMethod.h>

Inheritance diagram for CEFMMethod:

Collaboration diagram for CEFMMethod:

Public Member Functions
virtual bool	calculate ()

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

virtual bool	initialize ()

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 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
	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< 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
	CEFMMethod ()

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 25 of file CEFMMethod.h.

Constructor & Destructor Documentation

CEFMMethod::CEFMMethod ( )

private

Default constructor.

Definition at line 80 of file CEFMMethod.cpp.

References CONSTRUCTOR_TRACE.

                       :
     CCopasiMethod(CCopasiTask::fluxMode, CCopasiMethod::unset),
     mpFluxModes(NULL),
     mpReorderedReactions(NULL)
 {CONSTRUCTOR_TRACE;}

CEFMMethod::CEFMMethod	(	const CCopasiTask::Type &	taskType,
		const SubType &	subType,
		const CCopasiContainer *	pParent = `NULL`
	)

protected

Specific constructor

Parameters

const	CCopasiTask::Type & type
const	CCopasiMethod::SubType & subType
const	CCopasiContainer * pParent (default: NULL)

Definition at line 86 of file CEFMMethod.cpp.

References CONSTRUCTOR_TRACE.

                                                         :
     CCopasiMethod(taskType, subType, pParent),
     mpFluxModes(NULL),
     mpReorderedReactions(NULL)
 {CONSTRUCTOR_TRACE;}

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

Copy constructor

Parameters

const	CEFMMethod & src
const	CCopasiContainer * pParent (default: NULL)

Definition at line 94 of file CEFMMethod.cpp.

References CONSTRUCTOR_TRACE.

                                                         :
     CCopasiMethod(src, pParent),
     mpFluxModes(src.mpFluxModes),
     mpReorderedReactions(src.mpReorderedReactions)
 {CONSTRUCTOR_TRACE;}

CEFMMethod::~CEFMMethod ( )

virtual

Destructor

Definition at line 101 of file CEFMMethod.cpp.

102 {}

Member Function Documentation

bool CEFMMethod::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 in CBitPatternTreeMethod, CBitPatternMethod, CEFMAlgorithm, and CSSAMethod.

Definition at line 104 of file CEFMMethod.cpp.

 {
   return false;
 }

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

static

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

CEFMMethod class This class describes the interface to all optimization methods. The various method like RandomSearch or GA have to be derived from this class.

Created for COPASI by Stefan Hoops 2002

Definition at line 47 of file CEFMMethod.cpp.

References CCopasiMethod::EFMAlgorithm, CCopasiMethod::EFMBitPatternAlgorithm, and CCopasiMethod::EFMBitPatternTreeAlgorithm.

Referenced by CEFMTask::CEFMTask(), and CEFMTask::createMethod().

 {
   CEFMMethod * pMethod = NULL;
 
   switch (subType)
     {
       case EFMAlgorithm:
         pMethod = new CEFMAlgorithm();
         break;
 
       case EFMBitPatternTreeAlgorithm:
         pMethod = new CBitPatternTreeMethod();
         break;
 
       case EFMBitPatternAlgorithm:
         pMethod = new CBitPatternMethod();
         break;
 
 #ifdef COPASI_SSA
       case stoichiometricStabilityAnalysis:
         pMethod = new CSSAMethod();
         break;
 #endif
 
       default:
         pMethod = new CEFMAlgorithm();
         break;
     }
 
   return pMethod;
 }

bool CEFMMethod::initialize ( )

virtual

Initialize arrays and pointer.

Returns: bool success

Reimplemented in CBitPatternTreeMethod, CBitPatternMethod, CEFMAlgorithm, and CSSAMethod.

Definition at line 109 of file CEFMMethod.cpp.

References CCopasiMessage::ERROR, CEFMProblem::getFluxModes(), CCopasiObject::getObjectParent(), CCopasiTask::getProblem(), CEFMProblem::getReorderedReactions(), MCEFMAnalysis, mpFluxModes, mpReorderedReactions, and pTask.

Referenced by CEFMAlgorithm::initialize(), CBitPatternMethod::initialize(), and CBitPatternTreeMethod::initialize().

 {
   CEFMTask * pTask = dynamic_cast< CEFMTask * >(getObjectParent());
 
   if (pTask == NULL)
     {
       CCopasiMessage(CCopasiMessage::ERROR, MCEFMAnalysis + 1);
       return false;
     }
 
   CEFMProblem * pProblem = dynamic_cast< CEFMProblem *>(pTask->getProblem());
 
   if (pProblem == NULL)
     {
       CCopasiMessage(CCopasiMessage::ERROR, MCEFMAnalysis + 2);
       return false;
     }
 
   mpFluxModes = & pProblem->getFluxModes();
   mpReorderedReactions = & pProblem->getReorderedReactions();
 
   mpReorderedReactions->clear();
   mpFluxModes->clear();
 
   return true;
 }

bool CEFMMethod::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 136 of file CEFMMethod.cpp.

References CMatrix< CType >::array(), C_FLOAT64, CCopasiMessage::ERROR, CCopasiProblem::getModel(), CCopasiObject::getObjectName(), CModel::getReactions(), CModel::getRedStoi(), CCopasiMethod::isValidProblem(), MCEFMAnalysis, CMatrix< CType >::numCols(), and CMatrix< CType >::size().

 {
   if (!CCopasiMethod::isValidProblem(pProblem)) return false;
 
   if (pProblem == NULL)
     {
       return false;
     }
 
   const CModel * pModel = pProblem ->getModel();
 
   if (pModel == NULL)
     {
       return false;
     }
 
   // Check that the stoichiometry matrix contains only integers.
 
   const CMatrix< C_FLOAT64 > & RedStoi = pModel->getRedStoi();
   const C_FLOAT64 * pValue = RedStoi.array();
   const C_FLOAT64 * pValueEnd = pValue + RedStoi.size();
 
   for (; pValue != pValueEnd; ++pValue)
     {
       if (fabs(*pValue - floor(*pValue + 0.5)) > 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon())
         {
           break;
         }
     }
 
   if (pValue != pValueEnd)
     {
       const CReaction * pReaction = pModel->getReactions()[(pValue - RedStoi.array()) % RedStoi.numCols()];
 
       CCopasiMessage(CCopasiMessage::ERROR, MCEFMAnalysis + 3, pReaction->getObjectName().c_str());
 
       return false;
     }
 
   return true;
 }

Member Data Documentation

std::vector< CFluxMode >* CEFMMethod::mpFluxModes

protected

The resulting elementary flux modes

Definition at line 91 of file CEFMMethod.h.

Referenced by CBitPatternTreeMethod::addMode(), CBitPatternMethod::addMode(), CEFMAlgorithm::buildFluxModes(), initialize(), and CEFMAlgorithm::initialize().

std::vector< const CReaction * >* CEFMMethod::mpReorderedReactions

protected

Reactions in the order used in the analysis

Definition at line 96 of file CEFMMethod.h.

Referenced by CBitPatternTreeMethod::buildFluxModes(), CBitPatternMethod::buildFluxModes(), CBitPatternMethod::buildKernelMatrix(), CBitPatternTreeMethod::buildKernelMatrix(), initialize(), and CEFMAlgorithm::initialize().

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

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation