COPASI API
4.16.103
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#include <CRandomSearch.h>
Public Member Functions | |
CRandomSearch (const CRandomSearch &src) | |
virtual bool | optimise () |
virtual | ~CRandomSearch () |
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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 | |
CRandomSearch () | |
bool | evaluate (const CVector< C_FLOAT64 > &individual) |
size_t | fittest () |
virtual bool | initialize () |
void | initObjects () |
Private Attributes | |
C_FLOAT64 | mBestValue |
unsigned C_INT32 | mCurrentIteration |
CVector< C_FLOAT64 > | mIndividual |
unsigned C_INT32 | mIterations |
CRandom * | mpRandom |
C_FLOAT64 | mValue |
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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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 36 of file CRandomSearch.h.
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Default Constructor
Definition at line 48 of file CRandomSearch.cpp.
References CCopasiParameterGroup::addParameter(), C_INT32, initObjects(), CRandom::mt19937, and CCopasiParameter::UINT.
CRandomSearch::CRandomSearch | ( | const CRandomSearch & | src | ) |
Copy Constructor
const | CRandomSearch & src |
Definition at line 58 of file CRandomSearch.cpp.
References initObjects().
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Evaluate the fitness of one individual
const | CVector< C_FLOAT64 > & individual |
Definition at line 208 of file CRandomSearch.cpp.
References COptProblem::calculate(), COptProblem::checkFunctionalConstraints(), COptProblem::getCalculateValue(), COptMethod::mpOptProblem, and mValue.
Referenced by optimise().
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Find the best individual at this generation
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Initialize arrays and pointer.
Optimizer Function Returns: true if properly initialized should return a boolean
Reimplemented from COptMethod.
Definition at line 80 of file CRandomSearch.cpp.
References COptMethod::cleanup(), CRandom::createGenerator(), CCopasiParameter::getValue(), COptMethod::initialize(), mBestValue, mIndividual, mIterations, COptMethod::mpOptItem, mpRandom, mVariableSize, CCopasiParameter::Value::pUINT, and CVector< CType >::resize().
Referenced by optimise().
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Initialize contained objects.
Definition at line 70 of file CRandomSearch.cpp.
References CCopasiContainer::addObjectReference(), mCurrentIteration, and CCopasiObject::ValueInt.
Referenced by CRandomSearch().
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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.
Optimizer Function Returns: nothing should return a boolean
Reimplemented from COptMethod.
Definition at line 104 of file CRandomSearch.cpp.
References C_FLOAT64, C_INT32, COptItem::checkConstraint(), COptItem::checkLowerBound(), COptItem::checkUpperBound(), COutputInterface::DURING, evaluate(), COptItem::getLowerBoundValue(), COptItem::getRandomValue(), COptItem::getStartValue(), COptItem::getUpperBoundValue(), initialize(), mBestValue, mCurrentIteration, min, mIndividual, mIterations, COptMethod::mpOptProblem, COptMethod::mpParentTask, mpRandom, mValue, mVariableSize, CCopasiTask::output(), and COptProblem::setSolution().
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The best value found so far.
Definition at line 104 of file CRandomSearch.h.
Referenced by initialize(), and optimise().
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The current iteration
Definition at line 79 of file CRandomSearch.h.
Referenced by initObjects(), and optimise().
a vector of the number of individuals.
Definition at line 84 of file CRandomSearch.h.
Referenced by initialize(), and optimise().
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number of iterations
Definition at line 74 of file CRandomSearch.h.
Referenced by initialize(), and optimise().
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a pointer to the randomnumber generator.
Definition at line 94 of file CRandomSearch.h.
Referenced by initialize(), and optimise().
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array of values of objective function f/ individuals
Definition at line 89 of file CRandomSearch.h.
Referenced by evaluate(), and optimise().
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*** Perhaps this is actually not needed ****number of parameters
Definition at line 99 of file CRandomSearch.h.
Referenced by initialize(), and optimise().