COPASI API
4.16.103
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#include <COptMethodEP2.h>
Public Member Functions | |
COptMethodEP2 (const COptMethodEP2 &src) | |
virtual void | copy (int o, int d) |
virtual void | exchange (int o, int d) |
virtual int | fittest (void) |
double | Get_BestFoundSoFar_candidate () |
int | Get_NumGeneration () |
int | Get_NumParameter () |
int | Get_PopulationSize () |
virtual bool | optimise () |
virtual void | select (int method) |
void | Set_BestFoundSoFar (int num) |
void | Set_CandidateValue (int i, double num) |
void | Set_individual (int i, int j, double num) |
void | Set_Maximum (double num) |
void | Set_Minimum (double num) |
void | Set_murvar (double num) |
void | Set_NumGeneration (int num) |
void | Set_NumParameter (int num) |
void | Set_PopulationSize (int num) |
virtual void | swap (int o, int d) |
virtual void | TrackDataFile (int i) |
virtual | ~COptMethodEP2 () |
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COptMethod (const COptMethod &src, const CCopasiContainer *pParent=NULL) | |
virtual bool | initialize () |
bool | isBounded (void) |
virtual bool | isValidProblem (const CCopasiProblem *pProblem) |
void | setProblem (COptProblem *problem) |
virtual | ~COptMethod () |
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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 () |
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bool | addGroup (const std::string &name) |
bool | addParameter (const CCopasiParameter ¶meter) |
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 () |
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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 () |
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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 () |
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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 () |
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CObjectInterface () | |
virtual | ~CObjectInterface () |
Private Member Functions | |
COptMethodEP2 () | |
Private Attributes | |
int | BestFoundSoFar |
double * | CandidateValue |
double * | CandidateValueRate |
int * | CrossPoint |
CVector< CVector< C_FLOAT64 > > | individual |
double | Maximum |
double | Minimum |
int | NumCrossPoint |
int | NumGeneration |
int | NumParameter |
int | PopulationSize |
int * | WinScore |
Friends | |
COptMethod * | COptMethod::createMethod (CCopasiMethod::SubType subType) |
Additional Inherited Members | |
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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 } |
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typedef parameterGroup::iterator | index_iterator |
typedef CCopasiContainer::objectMap::iterator | name_iterator |
typedef std::vector < CCopasiParameter * > | parameterGroup |
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enum | Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID } |
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typedef std::multimap < std::string, CCopasiObject * > | objectMap |
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typedef std::set< const CCopasiObject * > | DataObjectSet |
typedef std::vector< Refresh * > | DataUpdateSequence |
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typedef std::set< const CObjectInterface * > | ObjectSet |
typedef std::vector < CObjectInterface * > | UpdateSequence |
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static COptMethod * | createMethod (CCopasiMethod::SubType subType=CCopasiMethod::RandomSearch) |
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static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
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static const std::string | SubTypeName [] |
static const char * | XMLSubType [] |
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static const std::string | TypeName [] |
static const char * | XMLType [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
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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 } |
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virtual bool | cleanup () |
COptMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL) | |
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CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL) | |
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CCopasiParameterGroup () | |
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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 () |
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CCopasiObject () | |
CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | |
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const bool | mBounds |
const std::vector< COptItem * > * | mpOptContraints |
const std::vector< COptItem * > * | mpOptItem |
COptProblem * | mpOptProblem |
COptTask * | mpParentTask |
const std::vector < UpdateMethod * > * | mpSetCalculateVariable |
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CProcessReport * | mpCallBack |
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std::string | mKey |
CCopasiObject * | mpValueReference |
size_t | mSize |
Value | mValue |
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objectMap | mObjects |
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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 43 of file COptMethodEP2.h.
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Default Constructor
Definition at line 50 of file COptMethodEP2.cpp.
References CCopasiParameterGroup::addParameter(), C_INT32, CCopasiParameter::INT, CRandom::mt19937, and CCopasiParameter::UINT.
COptMethodEP2::COptMethodEP2 | ( | const COptMethodEP2 & | src | ) |
Copy Constructor
const | COptMethodEP2 & src |
Definition at line 46 of file COptMethodEP2.cpp.
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Definition at line 486 of file COptMethodEP2.cpp.
References CandidateValue, individual, and NumParameter.
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Definition at line 521 of file COptMethodEP2.cpp.
References CandidateValue, individual, and NumParameter.
Referenced by select().
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Definition at line 633 of file COptMethodEP2.cpp.
References CandidateValue, and PopulationSize.
Referenced by optimise().
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Definition at line 199 of file COptMethodEP2.h.
References BestFoundSoFar, and CandidateValue.
Referenced by optimise().
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GA Optimizer Function: Returns: nothing
Reimplemented from COptMethod.
Definition at line 76 of file COptMethodEP2.cpp.
References BestFoundSoFar, C_INT32, COptProblem::calculate(), CandidateValue, CandidateValueRate, CRandom::createGenerator(), CrossPoint, FALSE, fittest(), Get_BestFoundSoFar_candidate(), COptProblem::getCalculateVariableUpdateMethods(), CRandom::getRandomCC(), CCopasiParameter::getValue(), COptProblem::getVariableSize(), individual, linear(), max, Maximum, min, Minimum, COptMethod::mpOptProblem, NumGeneration, NumParameter, PopulationSize, CVector< CType >::resize(), select(), TrackDataFile(), TRUE, and WinScore.
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Definition at line 539 of file COptMethodEP2.cpp.
References CandidateValue, CandidateValueRate, exchange(), PopulationSize, swap(), and WinScore.
Referenced by optimise().
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Definition at line 172 of file COptMethodEP2.h.
References Maximum.
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Definition at line 168 of file COptMethodEP2.h.
References Minimum.
void COptMethodEP2::Set_murvar | ( | double | num | ) |
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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.
Definition at line 146 of file COptMethodEP2.h.
References NumParameter.
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Definition at line 499 of file COptMethodEP2.cpp.
References CandidateValue, individual, NumParameter, and WinScore.
Referenced by select().
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Definition at line 652 of file COptMethodEP2.cpp.
References BestFoundSoFar, CandidateValue, individual, and NumParameter.
Referenced by optimise().
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Definition at line 56 of file COptMethodEP2.h.
Referenced by Get_BestFoundSoFar_candidate(), optimise(), Set_BestFoundSoFar(), and TrackDataFile().
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Definition at line 61 of file COptMethodEP2.h.
Referenced by copy(), exchange(), fittest(), Get_BestFoundSoFar_candidate(), optimise(), select(), Set_CandidateValue(), swap(), and TrackDataFile().
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Definition at line 62 of file COptMethodEP2.h.
Referenced by optimise(), and select().
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Definition at line 64 of file COptMethodEP2.h.
Referenced by optimise().
Definition at line 60 of file COptMethodEP2.h.
Referenced by copy(), exchange(), optimise(), Set_individual(), swap(), and TrackDataFile().
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Definition at line 54 of file COptMethodEP2.h.
Referenced by optimise(), and Set_Maximum().
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Definition at line 54 of file COptMethodEP2.h.
Referenced by optimise(), and Set_Minimum().
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Definition at line 52 of file COptMethodEP2.h.
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Definition at line 50 of file COptMethodEP2.h.
Referenced by Get_NumGeneration(), optimise(), and Set_NumGeneration().
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Definition at line 57 of file COptMethodEP2.h.
Referenced by copy(), exchange(), Get_NumParameter(), optimise(), Set_NumParameter(), swap(), and TrackDataFile().
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Definition at line 51 of file COptMethodEP2.h.
Referenced by fittest(), Get_PopulationSize(), optimise(), select(), and Set_PopulationSize().
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Definition at line 65 of file COptMethodEP2.h.
Referenced by optimise(), select(), and swap().