COPASI API
4.40.278
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#include <COptMethodDE.h>
Public Member Functions | |
COptMethodDE (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::DifferentialEvolution, const CTaskEnum::Task &taskType=CTaskEnum::Task::optimization) | |
COptMethodDE (const COptMethodDE &src, const CDataContainer *pParent) | |
virtual unsigned C_INT32 | getMaxLogVerbosity () const |
virtual bool | optimise () |
virtual | ~COptMethodDE () |
Public Member Functions inherited from COptPopulationMethod | |
COptPopulationMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType, const bool ¶llel) | |
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 ¶llel) | |
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 ¶meter) |
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 | |
void | boost () |
virtual bool | cleanup () |
COptMethodDE () | |
bool | creation (size_t first, size_t last=std::numeric_limits< size_t >::max()) |
bool | evaluate (const CVector< C_FLOAT64 > &individual) |
size_t | fittest () |
virtual bool | initialize () |
void | initObjects () |
bool | replicate () |
Private Attributes | |
size_t | mBestIndex |
C_FLOAT64 | mBestValue |
C_FLOAT64 | mEvaluationValue |
C_FLOAT64 | mMutationVarians |
CPermutation * | mpPermutation |
unsigned C_INT32 | mStopAfterStalledGenerations |
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 > ¶meters) |
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 |
COptMethodDE::COptMethodDE | ( | const CDataContainer * | pParent, |
const CTaskEnum::Method & | methodType = CTaskEnum::Method::DifferentialEvolution , |
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const CTaskEnum::Task & | taskType = CTaskEnum::Task::optimization |
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Specific constructor
const | CDataContainer * pParent |
const | CTaskEnum::Method & methodType (default: DifferentialEvolution) |
const | CTaskEnum::Task & taskType (default: optimization) |
References CCopasiParameterGroup::assertParameter(), C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, CCopasiParameter::editable, initObjects(), CRandom::mt19937, and CCopasiParameter::UINT.
COptMethodDE::COptMethodDE | ( | const COptMethodDE & | src, |
const CDataContainer * | pParent | ||
) |
Copy Constructor
const | COptMethodDE & src |
const | CDataContainer * pParent (default: NULL) |
References initObjects().
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Destructor
References cleanup().
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Default Constructor
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Cleanup arrays and pointers.
Reimplemented from COptPopulationMethod.
References COptPopulationMethod::cleanup(), mpPermutation, and pdelete.
Referenced by initialize(), optimise(), and ~COptMethodDE().
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Initialise the population
size_t | first |
size_t | last (default: population size) |
References C_FLOAT64, COptItem::checkConstraint(), evaluate(), COptItem::getLowerBoundValue(), COptItem::getUpperBoundValue(), CContext< Data >::master(), max, mBestIndex, mEvaluationValue, min, COptPopulationMethod::mIndividuals, COptPopulationMethod::mPopulationSize, COptMethod::mProblemContext, COptPopulationMethod::mRandomContext, COptPopulationMethod::mValues, and COptPopulationMethod::mVariableSize.
Referenced by optimise().
Evaluate the fitness of one individual
const | CVector< C_FLOAT64 > & individual |
References CContext< Data >::master(), mEvaluationValue, and COptMethod::mProblemContext.
Referenced by creation(), optimise(), and replicate().
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Find the best individual at this generation
References C_FLOAT64, C_INVALID_INDEX, max, COptPopulationMethod::mPopulationSize, and COptPopulationMethod::mValues.
Referenced by optimise().
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Returns the maximum verbosity at which the method can log.
Reimplemented from COptMethod.
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Initialize arrays and pointer.
Reimplemented from COptPopulationMethod.
References cleanup(), COptLog::enterLogEntry(), CProcessReportLevel::finishItem(), CCopasiParameterGroup::getParameter(), COptPopulationMethod::initialize(), CContext< Data >::master(), mBestValue, COptPopulationMethod::mhGenerations, COptPopulationMethod::mIndividuals, COptMethod::mLogVerbosity, COptMethod::mMethodLog, mMutationVarians, COptPopulationMethod::mPopulationSize, mpPermutation, CCopasiMethod::mProcessReport, COptPopulationMethod::mRandomContext, mStopAfterStalledGenerations, COptPopulationMethod::mValues, COptPopulationMethod::mVariableSize, CVector< CType >::resize(), and CCopasiParameterGroup::setValue().
Referenced by optimise().
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Initialize contained objects.
Referenced by COptMethodDE().
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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 COptMethod.
References C_FLOAT64, C_INVALID_INDEX, COptItem::checkConstraint(), cleanup(), creation(), COutputInterface::DURING, COptLog::enterLogEntry(), evaluate(), CProcessReportLevel::finishItem(), fittest(), COptItem::getLowerBoundValue(), COptItem::getStartValue(), COptItem::getUpperBoundValue(), initialize(), CContext< Data >::master(), mBestIndex, mBestValue, COptPopulationMethod::mCurrentGeneration, mEvaluationValue, COptPopulationMethod::mGenerations, COptPopulationMethod::mhGenerations, COptPopulationMethod::mIndividuals, COptMethod::mLogVerbosity, COptMethod::mMethodLog, COutputInterface::MONITORING, COptPopulationMethod::mPopulationSize, COptMethod::mpParentTask, COptMethod::mProblemContext, CCopasiMethod::mProcessReport, mStopAfterStalledGenerations, COptPopulationMethod::mValues, COptPopulationMethod::mVariableSize, CCopasiTask::output(), CProcessReportLevel::progressItem(), and replicate().
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Replicate the individuals with crossover
References C_FLOAT64, C_INVALID_INDEX, COptItem::checkConstraint(), evaluate(), COptItem::getLowerBoundValue(), COptItem::getUpperBoundValue(), CContext< Data >::master(), mBestIndex, mEvaluationValue, COptPopulationMethod::mIndividuals, mMutationVarians, COptPopulationMethod::mPopulationSize, mpPermutation, COptMethod::mProblemContext, COptPopulationMethod::mRandomContext, COptPopulationMethod::mValues, COptPopulationMethod::mVariableSize, CPermutation::next(), CPermutation::pick(), and CPermutation::shuffle().
Referenced by optimise().
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Referenced by creation(), optimise(), and replicate().
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Referenced by initialize(), and optimise().
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The value of the last evaluation.
Referenced by creation(), evaluate(), optimise(), and replicate().
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variance for mutations
Referenced by initialize(), and replicate().
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A permutation of integers used to for replication;
Referenced by cleanup(), initialize(), and replicate().
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if no improvement was made after # stalled generations stop
Referenced by initialize(), and optimise().