COPASI API  4.40.278
COptMethodSRES Class Reference

#include <COptMethodSRES.h>

Inheritance diagram for COptMethodSRES:
[legend]

Public Member Functions

 COptMethodSRES (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::SRES, const CTaskEnum::Task &taskType=CTaskEnum::Task::optimization)
 
 COptMethodSRES (const COptMethodSRES &src, const CDataContainer *pParent)
 
virtual unsigned C_INT32 getMaxLogVerbosity () const
 
virtual bool optimise ()
 
virtual ~COptMethodSRES ()
 
- Public Member Functions inherited from COptPopulationMethod
 COptPopulationMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType, const bool &parallel)
 
 COptPopulationMethod (const COptPopulationMethod &src, const CDataContainer *pParent)
 
C_INT32 getCurrentGeneration ()
 
C_INT32 getNumGenerations ()
 
const CVector< C_FLOAT64 > & getObjectiveValues ()
 
const std::vector< CVector< C_FLOAT64 > * > & getPopulation ()
 
C_INT32 getPopulationSize ()
 
void initObjects ()
 
virtual void print (std::ostream *ostream) const
 
virtual ~COptPopulationMethod ()
 
- Public Member Functions inherited from COptMethod
 COptMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType, const bool &parallel)
 
 COptMethod (const COptMethod &src, const CDataContainer *pParent)
 
virtual const CVector< C_FLOAT64 > * getBestParameters () const
 
virtual C_FLOAT64 getBestValue () const
 
virtual const CVector< C_FLOAT64 > * getCurrentParameters () const
 
virtual C_FLOAT64 getCurrentValue () const
 
const COptLog & getMethodLog () const
 
virtual bool isValidProblem (const CCopasiProblem *pProblem)
 
void setProblem (COptProblem *problem)
 
virtual ~COptMethod ()
 
- 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 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 ()
 

Private Member Functions

virtual bool cleanup ()
 
 COptMethodSRES ()
 
bool creation (size_t first)
 
bool evaluate (const CVector< C_FLOAT64 > &individual)
 
size_t fittest ()
 
virtual bool initialize ()
 
void initObjects ()
 
bool mutate ()
 
C_FLOAT64 phi (size_t indvNum)
 
bool replicate ()
 
void select ()
 
bool swap (size_t from, size_t to)
 

Private Attributes

C_FLOAT64 mBestValue
 
C_FLOAT64 mEvaluationValue
 
CVector< C_FLOAT64 > mMaxVariance
 
C_FLOAT64 mPf
 
CVector< C_FLOAT64 > mPhi
 
unsigned C_INT32 mStopAfterStalledGenerations
 
double mTau
 
double mTauPrime
 
std::vector< CVector< C_FLOAT64 > * > mVariance
 

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 COptMethod
virtual void signalMathContainerChanged ()
 
- Protected Member Functions inherited from CCopasiMethod
 CCopasiMethod (const CCopasiMethod &src)
 
 CCopasiMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType)
 
- 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)
 
- Static Protected Member Functions inherited from COptMethod
static std::pair< C_FLOAT64, bool > objectiveValue (COptProblem *pProblem, const CVectorCore< C_FLOAT64 > &parameters)
 
static void reflect (COptProblem *pProblem, const C_FLOAT64 &bestValue, C_FLOAT64 &objectiveValue)
 
- Protected Attributes inherited from COptPopulationMethod
unsigned C_INT32 mCurrentGeneration
 
unsigned C_INT32 mGenerations
 
size_t mhGenerations
 
std::vector< CVector< C_FLOAT64 > * > mIndividuals
 
unsigned C_INT32 mPopulationSize
 
CRandomContext mRandomContext
 
CVector< C_FLOAT64 > mValues
 
size_t mVariableSize
 
- Protected Attributes inherited from COptMethod
unsigned C_INT32 mLogVerbosity
 
CMathContext mMathContext
 
COptLog mMethodLog
 
bool mParallel
 
COptTask * mpParentTask
 
COptProblemContext mProblemContext
 
- 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
 

Detailed Description

Constructor & Destructor Documentation

◆ COptMethodSRES() [1/3]

COptMethodSRES::COptMethodSRES ( const CDataContainer *  pParent,
const CTaskEnum::Method &  methodType = CTaskEnum::Method::SRES,
const CTaskEnum::Task &  taskType = CTaskEnum::Task::optimization 
)

Specific constructor

Parameters
constCDataContainer * pParent
constCTaskEnum::Method & methodType (default: SRES)
constCTaskEnum::Task & taskType (default: optimization)

References CCopasiParameterGroup::assertParameter(), C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, CCopasiParameter::editable, initObjects(), CRandom::mt19937, and CCopasiParameter::UINT.

◆ COptMethodSRES() [2/3]

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

Copy Constructor

Parameters
constCOptMethodSRES & src
constCDataContainer * pParent (default: NULL)

References initObjects().

◆ ~COptMethodSRES()

COptMethodSRES::~COptMethodSRES ( )
virtual

Destructor

References cleanup().

◆ COptMethodSRES() [3/3]

COptMethodSRES::COptMethodSRES ( )
private

Default Constructor

Member Function Documentation

◆ cleanup()

bool COptMethodSRES::cleanup ( )
privatevirtual

Cleanup arrays and pointers.

Returns
bool success

Reimplemented from COptPopulationMethod.

References COptPopulationMethod::cleanup(), mVariance, and pdelete.

Referenced by initialize(), optimise(), and ~COptMethodSRES().

◆ creation()

◆ evaluate()

bool COptMethodSRES::evaluate ( const CVector< C_FLOAT64 > &  individual)
private

Evaluate the fitness of one individual

Parameters
constCVector< C_FLOAT64 > & individual
Returns
bool continue

References CContext< Data >::master(), mEvaluationValue, and COptMethod::mProblemContext.

Referenced by creation(), and mutate().

◆ fittest()

size_t COptMethodSRES::fittest ( )
private

Find the best individual at this generation

Returns
size_t fittest

References C_FLOAT64, C_INVALID_INDEX, max, mPhi, COptPopulationMethod::mPopulationSize, and COptPopulationMethod::mValues.

Referenced by optimise().

◆ getMaxLogVerbosity()

unsigned C_INT32 COptMethodSRES::getMaxLogVerbosity ( ) const
virtual

Returns the maximum verbosity at which the method can log.

Reimplemented from COptMethod.

◆ initialize()

◆ initObjects()

void COptMethodSRES::initObjects ( )
private

Initialize contained objects.

Referenced by COptMethodSRES().

◆ mutate()

◆ optimise()

◆ phi()

C_FLOAT64 COptMethodSRES::phi ( size_t  indvNum)
private

For Stochastic Ranking, evaluate the distance of parameters to boundaries

Returns
C_FLOAT64 phiVal

References C_FLOAT64, CContext< Data >::master(), COptPopulationMethod::mIndividuals, and COptMethod::mProblemContext.

Referenced by creation(), and mutate().

◆ replicate()

bool COptMethodSRES::replicate ( )
private

◆ select()

void COptMethodSRES::select ( )
private

◆ swap()

bool COptMethodSRES::swap ( size_t  from,
size_t  to 
)
private

Swap individuals from and to

Parameters
size_tfrom
size_tto
Returns
bool success

References C_FLOAT64, COptPopulationMethod::mIndividuals, mPhi, COptPopulationMethod::mValues, and mVariance.

Referenced by select().

Member Data Documentation

◆ mBestValue

C_FLOAT64 COptMethodSRES::mBestValue
private

Referenced by initialize(), and optimise().

◆ mEvaluationValue

C_FLOAT64 COptMethodSRES::mEvaluationValue
private

The value of the last evaluation.

Referenced by creation(), evaluate(), and mutate().

◆ mMaxVariance

CVector< C_FLOAT64 > COptMethodSRES::mMaxVariance
private

A vector of maximal variances

Referenced by creation(), initialize(), and mutate().

◆ mPf

C_FLOAT64 COptMethodSRES::mPf
private

Probability value used for SR ****

Referenced by initialize(), and select().

◆ mPhi

CVector< C_FLOAT64 > COptMethodSRES::mPhi
private

For Stochastic Ranking. Used for array of Phi values for the individuals

Referenced by creation(), fittest(), initialize(), mutate(), select(), and swap().

◆ mStopAfterStalledGenerations

unsigned C_INT32 COptMethodSRES::mStopAfterStalledGenerations
private

if no improvement was made after # stalled generations stop

Referenced by initialize(), and optimise().

◆ mTau

double COptMethodSRES::mTau
private

Referenced by initialize(), and mutate().

◆ mTauPrime

double COptMethodSRES::mTauPrime
private

Referenced by initialize(), and mutate().

◆ mVariance

std::vector< CVector < C_FLOAT64 > * > COptMethodSRES::mVariance
private

for array of variances w/ variance values for the parameters

Referenced by cleanup(), creation(), initialize(), mutate(), replicate(), and swap().


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