COPASI API  4.40.278
Classes | Public Member Functions | Protected Attributes | Private Member Functions | List of all members
CEFMAlgorithm Class Reference

#include <CEFMAlgorithm.h>

Inheritance diagram for CEFMAlgorithm:
[legend]

Classes

class  CSpeciesOrderNode
 

Public Member Functions

virtual bool calculate ()
 
void calculateFluxModes ()
 
 CEFMAlgorithm (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::EFMAlgorithm, const CTaskEnum::Task &taskType=CTaskEnum::Task::fluxMode)
 
 CEFMAlgorithm (const CEFMAlgorithm &src, const CDataContainer *pParent)
 
virtual bool initialize ()
 
 ~CEFMAlgorithm ()
 
- Public Member Functions inherited from CEFMMethod
 CEFMMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType=CTaskEnum::Task::fluxMode)
 
 CEFMMethod (const CEFMMethod &src, const CDataContainer *pParent)
 
virtual bool isValidProblem (const CCopasiProblem *pProblem)
 
virtual ~CEFMMethod ()
 
- Public Member Functions inherited from CCopasiMethod
 CCopasiMethod (const CCopasiMethod &src, const CDataContainer *pParent)
 
virtual void clearCallBack ()
 
const CProcessReportLevel & getCallBack () const
 
CMathContainer * getMathContainer () const
 
const CTaskEnum::Method & getSubType () const
 
const CTaskEnum::Task & getType () const
 
virtual void load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH)
 
CCopasiMethod & operator= (const CCopasiMethod &rhs)
 
virtual void print (std::ostream *ostream) const
 
virtual void printResult (std::ostream *ostream) const
 
virtual bool setCallBack (CProcessReportLevel callBack)
 
void setMathContainer (CMathContainer *pContainer)
 
virtual ~CCopasiMethod ()
 
- Public Member Functions inherited from CCopasiParameterGroup
bool addGroup (const std::string &name)
 
void addParameter (CCopasiParameter *pParameter)
 
bool addParameter (const CCopasiParameter &parameter)
 
bool addParameter (const std::string &name, const CCopasiParameter::Type type, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
 
template<class CType >
bool addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
 
virtual bool applyData (const CData &data, CUndoData::CChangeSet &changes)
 
CCopasiParameterGroup * assertGroup (const std::string &name, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
 
template<class CType >
CType * assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
 
index_iterator beginIndex () const
 
const_name_iterator beginName () const
 
 CCopasiParameterGroup (const CCopasiParameterGroup &src, const CDataContainer *pParent=NULL)
 
 CCopasiParameterGroup (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="ParameterGroup")
 
void clear ()
 
virtual void createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
 
virtual bool elevateChildren ()
 
index_iterator endIndex () const
 
const_name_iterator endName () const
 
CCopasiParameterGroup & getElementTemplates ()
 
const CCopasiParameterGroup & getElementTemplates () const
 
CCopasiParameterGroup * getGroup (const size_t &index)
 
const CCopasiParameterGroup * getGroup (const size_t &index) const
 
CCopasiParameterGroup * getGroup (const std::string &name)
 
const CCopasiParameterGroup * getGroup (const std::string &name) const
 
virtual size_t getIndex (const CDataObject *pObject) const
 
size_t getIndex (const std::string &name) const
 
std::string getKey (const size_t &index) const
 
std::string getKey (const std::string &name) const
 
virtual const std::string & getName (const size_t &index) const
 
virtual const CObjectInterface * getObject (const CCommonName &cn) const
 
CCopasiParameter * getParameter (const size_t &index)
 
const CCopasiParameter * getParameter (const size_t &index) const
 
CCopasiParameter * getParameter (std::string name)
 
const CCopasiParameter * getParameter (std::string name) const
 
CCopasiParameter::Type getType (const size_t &index) const
 
CCopasiParameter::Type getType (const std::string &name) const
 
std::string getUniqueParameterName (const CCopasiParameter *pParameter) const
 
template<class CType >
CType & getValue (const size_t &index)
 
template<class CType >
const CType & getValue (const size_t &index) const
 
template<class CType >
CType & getValue (const std::string &name)
 
template<class CType >
const CType & getValue (const std::string &name) const
 
bool haveTemplate () const
 
virtual CUndoObjectInterface * insert (const CData &data)
 
CCopasiParameterGroup & operator= (const CCopasiParameterGroup &rhs)
 
virtual bool remove (CDataObject *pObject)
 
bool removeParameter (CCopasiParameter *pParameter)
 
bool removeParameter (const size_t &index)
 
bool removeParameter (const std::string &name)
 
virtual void setUserInterfaceFlag (const UserInterfaceFlag &flag)
 
template<class CType >
bool setValue (const size_t &index, const CType &value)
 
template<class CType >
bool setValue (const std::string &name, const CType &value)
 
size_t size (const UserInterfaceFlag &require=UserInterfaceFlag::None, const UserInterfaceFlag &exclude=UserInterfaceFlag::None) const
 
bool swap (const size_t &iFrom, const size_t &iTo)
 
bool swap (index_iterator &from, index_iterator &to)
 
virtual CData toData () const
 
virtual void updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)
 
virtual ~CCopasiParameterGroup ()
 
- Public Member Functions inherited from CCopasiParameter
 CCopasiParameter (const CCopasiParameter &src, const CDataContainer *pParent)
 
 CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="Parameter")
 
virtual CCommonName getCN () const override
 
template<class CType >
const CType & getDefault () const
 
virtual const std::string & getKey () const override
 
virtual std::string getObjectDisplayName () const override
 
const CCopasiParameter::Type & getType () const
 
const UserInterfaceFlag & getUserInterfaceFlag () const
 
template<class CType >
std::vector< std::pair< CType, CType > > & getValidValues ()
 
template<class CType >
const std::vector< std::pair< CType, CType > > & getValidValues () const
 
void * getValidValuesPointer () const
 
template<class CType >
CType & getValue ()
 
template<class CType >
const CType & getValue () const
 
virtual void * getValuePointer () const override
 
CDataObject * getValueReference () const
 
bool hasValidValues () const
 
bool isBasic () const
 
bool isDefault () const
 
bool isEditable () const
 
bool isUnsupported () const
 
bool isValidValue (const bool &value) const
 
bool isValidValue (const C_FLOAT64 &value) const
 
bool isValidValue (const C_INT32 &value) const
 
bool isValidValue (const CCommonName &value) const
 
template<class CType >
bool isValidValue (const CType &) const
 
bool isValidValue (const std::string &value) const
 
bool isValidValue (const std::vector< CCopasiParameter * > &value) const
 
bool isValidValue (const unsigned C_INT32 &value) const
 
CCopasiParameter & operator= (const CCopasiParameter &rhs)
 
template<class CType >
bool setDefault (const CType &defaultValue)
 
bool setDefault (const std::vector< CCopasiParameter * > &defaultValue)
 
virtual bool setObjectParent (const CDataContainer *pParent) override
 
template<class CType , class Enum >
bool setValidValues (const CEnumAnnotation< CType, Enum > &validValues)
 
template<class CType >
bool setValidValues (const std::vector< std::pair< CType, CType > > &validValues)
 
template<class CType >
bool setValue (const CType &value)
 
bool setValue (const std::vector< CCopasiParameter * > &value)
 
virtual ~CCopasiParameter ()
 
- Public Member Functions inherited from CDataContainer
virtual bool add (CDataObject *pObject, const bool &adopt=true)
 
virtual bool appendDeletedDependentData (CUndoData &undoData) const
 
 CDataContainer (const CDataContainer &src, const CDataContainer *pParent)
 
 CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)
 
virtual std::string getChildObjectUnits (const CDataObject *pObject) const
 
void getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const
 
virtual objectMap & getObjects ()
 
virtual const objectMap & getObjects () const
 
virtual const std::string getUnits () const override
 
virtual const CDataObject * getValueObject () const override
 
void objectRenamed (CDataObject *pObject, const std::string &oldName)
 
virtual ~CDataContainer ()
 
- Public Member Functions inherited from CDataObject
void addIssue (const CIssue &issue)
 
void addReference (const CDataContainer *pReference)
 
virtual void calculateValue () override
 
 CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL)
 
virtual void destruct () override
 
virtual const CDataObject * getDataObject () const override
 
CDataContainer * getObjectAncestor (const std::string &type) const
 
CDataModel * getObjectDataModel () const
 
const CObjectInterface * getObjectFromCN (const CCommonName &cn) const
 
const std::string & getObjectName () const
 
CDataContainer * getObjectParent () const
 
const std::string & getObjectType () const
 
virtual const CObjectInterface::ObjectSet & getPrerequisites () const override
 
virtual const CValidity & getValidity () const override
 
bool hasFlag (const Flag &flag) const
 
virtual bool isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override
 
bool prerequisitsContains (const DataObjectSet &objects) const
 
void removeIssue (const CIssue &issue)
 
void removeReference (const CDataContainer *pReference)
 
bool setObjectName (const std::string &name)
 
void validityChanged (const CValidity &changedValidity) override
 
void validityRemoved (const CValidity &changedValidity)
 
virtual ~CDataObject ()
 
- Public Member Functions inherited from CObjectInterface
 CObjectInterface ()
 
 CObjectInterface (const CObjectInterface &src)
 
virtual ~CObjectInterface ()
 
- Public Member Functions inherited from CUndoObjectInterface
 CUndoObjectInterface ()
 
 CUndoObjectInterface (const CUndoObjectInterface &src)
 
bool generateUuid ()
 
const xg::Guid & getUuid () const
 
bool setUuid (const std::string &uuid)
 
bool setUuid (const xg::Guid &uuid)
 
virtual ~CUndoObjectInterface ()
 

Protected Attributes

size_t mhSteps
 
std::vector< size_t > mIndexSet
 
unsigned C_INT32 mMaxStep
 
CTableauMatrix * mpCurrentTableau
 
const 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
CMathContainer * mpContainer
 
CProcessReportLevel mProcessReport
 
- Protected Attributes inherited from CCopasiParameter
std::string mKey
 
void * mpDefault
 
void * mpValidValues
 
void * mpValue
 
CDataObject * mpValueReference
 
UserInterfaceFlag mUserInterfaceFlag
 
- Protected Attributes inherited from CDataContainer
objectMap mObjects
 
- Protected Attributes inherited from CDataObject
ObjectSet mPrerequisits
 
std::set< CDataContainer * > mReferences
 
- Protected Attributes inherited from CObjectInterface
CValidity mValidity
 

Private Member Functions

void buildFluxModes ()
 
double calculateCombinations (size_t index)
 
void calculateNextTableau ()
 
 CEFMAlgorithm ()
 
bool findMinimalCombinationIndex ()
 
void initObjects ()
 

Additional Inherited Members

- Public Types inherited from CCopasiParameterGroup
typedef CDataObjectMap::const_type_iterator< CCopasiParameter > const_name_iterator
 
typedef std::vector< CCopasiParameter * > elements
 
typedef elements::iterator index_iterator
 
typedef CDataObjectMap::type_iterator< CCopasiParameter > name_iterator
 
- Public Types inherited from CCopasiParameter
enum class  eUserInterfaceFlag { editable , basic , unsupported , __SIZE }
 
enum class  Type {
  DOUBLE = 0 , UDOUBLE , INT , UINT ,
  BOOL , GROUP , STRING , CN ,
  KEY , FILE , EXPRESSION , INVALID ,
  __SIZE
}
 
typedef CFlags< eUserInterfaceFlag > UserInterfaceFlag
 
- Public Types inherited from CDataContainer
typedef CDataObjectMap objectMap
 
- Public Types inherited from CDataObject
typedef std::set< const CDataObject * > DataObjectSet
 
enum  Flag {
  Container , Vector , Matrix , NameVector ,
  Reference , ValueBool , ValueInt , ValueInt64 ,
  ValueDbl , NonUniqueName , StaticString , ValueString ,
  Separator , DisplayName , ModelEntity , Array ,
  DataModel , Root , Gui , __SIZE
}
 
- Public Types inherited from CObjectInterface
typedef std::vector< const CDataContainer * > ContainerList
 
typedef std::set< const CObjectInterface * > ObjectSet
 
- Static Public Member Functions inherited from CCopasiParameter
static void allocateValidValues (const Type &type, void *&pValidValues)
 
static void allocateValue (const Type &type, void *&pValue)
 
static void assignValue (const Type &type, void *&pValue, const void *pNewValue)
 
static void deleteValidValues (const Type &type, void *&pValidValues)
 
static void deleteValue (const Type &type, void *&pValue)
 
static CCopasiParameter * fromData (const CData &data, CUndoObjectInterface *pParent)
 
- Static Public Member Functions inherited from CDataContainer
static CDataContainer * fromData (const CData &data, CUndoObjectInterface *pParent)
 
- Static Public Member Functions inherited from CDataObject
static CDataObject * fromData (const CData &data, CUndoObjectInterface *pParent)
 
static void sanitizeObjectName (std::string &name)
 
- Static Public Member Functions inherited from CObjectInterface
static const CDataObject * DataObject (const CObjectInterface *pInterface)
 
static CObjectInterface * GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName)
 
- Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType * fromData (const CData &, CUndoObjectInterface *)
 
- Static Public Attributes inherited from CCopasiParameter
static const CEnumAnnotation< std::string, Type > TypeName
 
static const CEnumAnnotation< std::string, Type > XMLType
 
- Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList EmptyList
 
- Protected Member Functions inherited from CCopasiMethod
 CCopasiMethod (const CCopasiMethod &src)
 
 CCopasiMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType)
 
virtual void signalMathContainerChanged ()
 
- Protected Member Functions inherited from CCopasiParameterGroup
 CCopasiParameterGroup ()
 
- Protected Member Functions inherited from CCopasiParameter
 CCopasiParameter (const CCopasiParameter &src)
 
- Protected Member Functions inherited from CDataContainer
template<class CType >
CDataMatrixReference< CType > * addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
 
template<class CType >
CDataObjectReference< CType > * addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
 
template<class CType >
CDataVectorReference< CType > * addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
 
 CDataContainer (const CDataContainer &src)
 
void initObjects ()
 
- Protected Member Functions inherited from CDataObject
 CDataObject ()
 
 CDataObject (const std::string &name, const CDataContainer *pParent=static_cast< CDataContainer * >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)
 

Constructor & Destructor Documentation

◆ CEFMAlgorithm() [1/3]

CEFMAlgorithm::CEFMAlgorithm ( )
private

Default constructor.

◆ CEFMAlgorithm() [2/3]

CEFMAlgorithm::CEFMAlgorithm ( const CDataContainer *  pParent,
const CTaskEnum::Method &  methodType = CTaskEnum::Method::EFMAlgorithm,
const CTaskEnum::Task &  taskType = CTaskEnum::Task::fluxMode 
)

Specific constructor

Parameters
constCDataContainer * pParent
constCTaskEnum::Method & methodType (default: EFMAlgorithm)
constCTaskEnum::Task & taskType (default: fluxMode)

References initObjects().

◆ CEFMAlgorithm() [3/3]

CEFMAlgorithm::CEFMAlgorithm ( const CEFMAlgorithm &  src,
const CDataContainer *  pParent 
)

Copy Constructor

Parameters
constCEFMAlgorithm & src

References initObjects().

◆ ~CEFMAlgorithm()

CEFMAlgorithm::~CEFMAlgorithm ( )

Destructor

References DESTRUCTOR_TRACE, mpCurrentTableau, mpNextTableau, and pdelete.

Member Function Documentation

◆ buildFluxModes()

void CEFMAlgorithm::buildFluxModes ( )
private

Construct the flux modes

References CTableauMatrix::begin(), CTableauMatrix::end(), mpCurrentTableau, and CEFMMethod::mpFluxModes.

Referenced by calculateFluxModes().

◆ calculate()

bool CEFMAlgorithm::calculate ( void  )
virtual

Execute the optimization algorithm calling simulation routine when needed. It is noted that this procedure can give feedback of its progress by the callback function set with SetCallback. @ return success;

Reimplemented from CEFMMethod.

Reimplemented in CSSAMethod.

References calculateFluxModes(), CProcessReportLevel::finishItem(), initialize(), mhSteps, and CCopasiMethod::mProcessReport.

◆ calculateCombinations()

double CEFMAlgorithm::calculateCombinations ( size_t  index)
private

Calculate number of combinations for an index

References CTableauMatrix::begin(), CTableauMatrix::end(), and mpCurrentTableau.

Referenced by findMinimalCombinationIndex().

◆ calculateFluxModes()

void CEFMAlgorithm::calculateFluxModes ( )

Do the actual calculation

References buildFluxModes(), calculateNextTableau(), COutputInterface::DURING, findMinimalCombinationIndex(), CProcessReportLevel::finishItem(), CDataObject::getObjectParent(), mhSteps, mIndexSet, mMaxStep, mpCurrentTableau, CCopasiMethod::mProcessReport, mReversible, mStep, mStepProcess, mStoi, pdelete, and CProcessReportLevel::progressItem().

Referenced by CSSAMethod::buildExtremeCurrents(), and calculate().

◆ calculateNextTableau()

void CEFMAlgorithm::calculateNextTableau ( )
private

Initialize arrays and pointer called by calculate.

References CProcessReportLevel::addItem(), CTableauMatrix::addLine(), CTableauMatrix::begin(), C_FLOAT64, C_INT32, CTableauMatrix::end(), CProcessReportLevel::finishItem(), mpCurrentTableau, mpNextTableau, CCopasiMethod::mProcessReport, mStep, pdelete, CProcessReportLevel::proceed(), CProcessReportLevel::progressItem(), CTableauMatrix::removeLine(), and CTableauMatrix::size().

Referenced by calculateFluxModes().

◆ findMinimalCombinationIndex()

bool CEFMAlgorithm::findMinimalCombinationIndex ( )
private

Find index containing smallest number of combinations

References C_INT32, calculateCombinations(), mIndexSet, and mStep.

Referenced by calculateFluxModes().

◆ initialize()

bool CEFMAlgorithm::initialize ( )
virtual

Initialize arrays and pointer.

Returns
bool success

Reimplemented from CEFMMethod.

Reimplemented in CSSAMethod.

References CProcessReportLevel::addItem(), C_INT32, CMathContainer::getModel(), CDataObject::getObjectParent(), CModel::getReactions(), CModel::getStoi(), CEFMMethod::initialize(), mhSteps, mMaxStep, CCopasiMethod::mpContainer, CEFMMethod::mpFluxModes, mpModel, CEFMMethod::mpReorderedReactions, CCopasiMethod::mProcessReport, mReversible, mStep, mStepProcess, mStoi, CTransposeView< Matrix >::numCols(), and CTransposeView< Matrix >::numRows().

Referenced by calculate().

◆ initObjects()

void CEFMAlgorithm::initObjects ( )
private

References CDataContainer::addObjectReference(), mStep, and CDataObject::ValueInt.

Referenced by CEFMAlgorithm().

Member Data Documentation

◆ mhSteps

size_t CEFMAlgorithm::mhSteps
protected

Handle to the process report item "Current Step"

Referenced by calculate(), CSSAMethod::calculate(), calculateFluxModes(), initialize(), and CSSAMethod::initialize().

◆ mIndexSet

std::vector<size_t> CEFMAlgorithm::mIndexSet
protected

Vector set containing all step indexes for iteration when calculating flux modes.

Referenced by calculateFluxModes(), and findMinimalCombinationIndex().

◆ mMaxStep

unsigned C_INT32 CEFMAlgorithm::mMaxStep
protected

The max step used for process report.

Referenced by calculateFluxModes(), initialize(), and CSSAMethod::initialize().

◆ mpCurrentTableau

CTableauMatrix* CEFMAlgorithm::mpCurrentTableau
protected

A pointer to the current tableau matrix

Referenced by buildFluxModes(), calculateCombinations(), calculateFluxModes(), calculateNextTableau(), and ~CEFMAlgorithm().

◆ mpModel

const CModel* CEFMAlgorithm::mpModel
protected

A pointer to the model

Referenced by CSSAMethod::buildKineticMatrix(), CSSAMethod::buildStoichiometry(), CSSAMethod::calculate(), initialize(), and CSSAMethod::initialize().

◆ mpNextTableau

CTableauMatrix* CEFMAlgorithm::mpNextTableau
protected

A pointer to the next tableaun matrix

Referenced by calculateNextTableau(), and ~CEFMAlgorithm().

◆ mReversible

size_t CEFMAlgorithm::mReversible
protected

The number of reversible reactions.

Referenced by calculateFluxModes(), initialize(), and CSSAMethod::initialize().

◆ mStep

unsigned C_INT32 CEFMAlgorithm::mStep
protected

The current step used for process report.

Referenced by calculateFluxModes(), calculateNextTableau(), findMinimalCombinationIndex(), initialize(), CSSAMethod::initialize(), and initObjects().

◆ mStepProcess

unsigned C_INT32 CEFMAlgorithm::mStepProcess
protected

The current step used for process report.

Referenced by calculateFluxModes(), and initialize().

◆ mStoi

std::vector< std::vector< C_FLOAT64 > > CEFMAlgorithm::mStoi
protected

Matrix containing the reordered stoichiometry matrix.

Referenced by CSSAMethod::buildStoichiometry(), calculateFluxModes(), initialize(), CSSAMethod::initialize(), and CSSAMethod::testForMixingStability().

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