COPASI API
4.16.103
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#include <COptMethodHookeJeeves.h>
Public Member Functions | |
COptMethodHookeJeeves (const COptMethodHookeJeeves &src, const CCopasiContainer *pParent=NULL) | |
virtual bool | optimise () |
virtual | ~COptMethodHookeJeeves () |
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COptMethod (const COptMethod &src, const CCopasiContainer *pParent=NULL) | |
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 | |
C_FLOAT64 | bestNearby () |
virtual bool | cleanup () |
COptMethodHookeJeeves (const CCopasiContainer *pParent=NULL) | |
bool | evaluate () |
virtual bool | initialize () |
void | initObjects () |
Private Attributes | |
CVector< C_FLOAT64 > | mBefore |
C_FLOAT64 | mBestValue |
bool | mContinue |
CVector< C_FLOAT64 > | mDelta |
C_FLOAT64 | mEvaluationValue |
size_t | mhIteration |
CVector< C_FLOAT64 > | mIndividual |
unsigned C_INT32 | mIteration |
unsigned C_INT32 | mIterationLimit |
CVector< C_FLOAT64 > | mNew |
C_FLOAT64 | mRho |
C_FLOAT64 | mTolerance |
size_t | mVariableSize |
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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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 30 of file COptMethodHookeJeeves.h.
COptMethodHookeJeeves::COptMethodHookeJeeves | ( | const COptMethodHookeJeeves & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy Constructor
const | COptMethodHookeJeeves & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 51 of file COptMethodHookeJeeves.cpp.
References initObjects().
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Default Constructor
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 41 of file COptMethodHookeJeeves.cpp.
References CCopasiParameterGroup::addParameter(), C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, initObjects(), and CCopasiParameter::UINT.
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Finds the best value in the neighborhood of mNew and updates mNew
Definition at line 293 of file COptMethodHookeJeeves.cpp.
References C_FLOAT64, COptItem::checkConstraint(), evaluate(), COptItem::getLowerBoundValue(), COptItem::getUpperBoundValue(), mBestValue, mDelta, mEvaluationValue, mIndividual, mNew, COptMethod::mpSetCalculateVariable, and mVariableSize.
Referenced by optimise().
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Cleanup arrays and pointers.
Reimplemented from COptMethod.
Definition at line 263 of file COptMethodHookeJeeves.cpp.
Referenced by initialize(), optimise(), and ~COptMethodHookeJeeves().
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Evaluate the fitness of one individual
Definition at line 268 of file COptMethodHookeJeeves.cpp.
References COptProblem::calculate(), COptProblem::checkFunctionalConstraints(), COptProblem::checkParametricConstraints(), COptProblem::getCalculateValue(), max, mContinue, mEvaluationValue, and COptMethod::mpOptProblem.
Referenced by bestNearby(), and optimise().
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Initialize arrays and pointer.
Reimplemented from COptMethod.
Definition at line 233 of file COptMethodHookeJeeves.cpp.
References CProcessReport::addItem(), cleanup(), CCopasiParameter::getValue(), COptMethod::initialize(), mBefore, mBestValue, mDelta, mhIteration, mIndividual, mIteration, mIterationLimit, mNew, CCopasiMethod::mpCallBack, COptMethod::mpOptItem, mRho, mTolerance, mVariableSize, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pUINT, and CVector< CType >::resize().
Referenced by optimise().
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Initialize contained objects.
Definition at line 228 of file COptMethodHookeJeeves.cpp.
References CCopasiContainer::addObjectReference(), mIteration, and CCopasiObject::ValueInt.
Referenced by COptMethodHookeJeeves().
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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.
Definition at line 61 of file COptMethodHookeJeeves.cpp.
References bestNearby(), C_FLOAT64, COptItem::checkConstraint(), cleanup(), COutputInterface::DURING, evaluate(), CProcessReport::finishItem(), COptItem::getLowerBoundValue(), COptItem::getStartValue(), COptItem::getUpperBoundValue(), initialize(), mBefore, mBestValue, mContinue, mDelta, mEvaluationValue, mhIteration, mIndividual, mIteration, mIterationLimit, mNew, CCopasiMethod::mpCallBack, COptMethod::mpOptProblem, COptMethod::mpParentTask, mRho, mTolerance, mVariableSize, CCopasiTask::output(), CProcessReport::progressItem(), and COptProblem::setSolution().
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The last individual
Definition at line 134 of file COptMethodHookeJeeves.h.
Referenced by initialize(), and optimise().
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The best value found so far
Definition at line 154 of file COptMethodHookeJeeves.h.
Referenced by bestNearby(), initialize(), and optimise().
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Flag indicating whether the computation shall continue
Definition at line 159 of file COptMethodHookeJeeves.h.
Referenced by evaluate(), and optimise().
The step taken
Definition at line 144 of file COptMethodHookeJeeves.h.
Referenced by bestNearby(), initialize(), and optimise().
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The value of the last evaluation.
Definition at line 149 of file COptMethodHookeJeeves.h.
Referenced by bestNearby(), evaluate(), and optimise().
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Handle to the process report item "Current Iteration"
Definition at line 119 of file COptMethodHookeJeeves.h.
Referenced by initialize(), and optimise().
The current individual
Definition at line 129 of file COptMethodHookeJeeves.h.
Referenced by bestNearby(), initialize(), and optimise().
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The number of iterations
Definition at line 114 of file COptMethodHookeJeeves.h.
Referenced by initialize(), initObjects(), and optimise().
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The maximum number of iterations
Definition at line 99 of file COptMethodHookeJeeves.h.
Referenced by initialize(), and optimise().
The new individual
Definition at line 139 of file COptMethodHookeJeeves.h.
Referenced by bestNearby(), initialize(), and optimise().
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The length of steps taken
Definition at line 109 of file COptMethodHookeJeeves.h.
Referenced by initialize(), and optimise().
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The tolerance
Definition at line 104 of file COptMethodHookeJeeves.h.
Referenced by initialize(), and optimise().
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number of parameters
Definition at line 124 of file COptMethodHookeJeeves.h.
Referenced by bestNearby(), initialize(), and optimise().