COPASI API  4.16.103
Public Member Functions | Static Public Member Functions | Static Public Attributes | Protected Member Functions | Protected Attributes | Private Member Functions | List of all members
CFitMethod Class Reference

#include <CFitMethod.h>

Inheritance diagram for CFitMethod:
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Collaboration diagram for CFitMethod:
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Public Member Functions

 CFitMethod (const CFitMethod &src, const CCopasiContainer *pParent=NULL)
 
virtual bool initialize ()
 
virtual bool isValidProblem (const CCopasiProblem *pProblem)
 
virtual ~CFitMethod ()
 
- Public Member Functions inherited from COptMethod
 COptMethod (const COptMethod &src, const CCopasiContainer *pParent=NULL)
 
bool isBounded (void)
 
virtual bool optimise ()
 
void setProblem (COptProblem *problem)
 
virtual ~COptMethod ()
 
- Public Member Functions inherited from CCopasiMethod
 CCopasiMethod (const CCopasiMethod &src, const CCopasiContainer *pParent=NULL)
 
const CCopasiMethod::SubTypegetSubType () const
 
const CCopasiTask::TypegetType () 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 ()
 
- Public Member Functions inherited from CCopasiParameterGroup
bool addGroup (const std::string &name)
 
bool addParameter (const CCopasiParameter &parameter)
 
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)
 
CCopasiParameterGroupassertGroup (const std::string &name)
 
template<class CType >
CCopasiParameterassertParameter (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
 
CCopasiParameterGroupgetGroup (const std::string &name)
 
const CCopasiParameterGroupgetGroup (const std::string &name) const
 
CCopasiParameterGroupgetGroup (const size_t &index)
 
const CCopasiParameterGroupgetGroup (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 CObjectInterfacegetObject (const CCopasiObjectName &cn) const
 
CCopasiParametergetParameter (const std::string &name)
 
const CCopasiParametergetParameter (const std::string &name) const
 
CCopasiParametergetParameter (const size_t &index)
 
const CCopasiParametergetParameter (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::ValuegetValue (const std::string &name) const
 
const CCopasiParameter::ValuegetValue (const size_t &index) const
 
CCopasiParameter::ValuegetValue (const std::string &name)
 
CCopasiParameter::ValuegetValue (const size_t &index)
 
CCopasiParameterGroupoperator= (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 ()
 
- Public Member Functions inherited from CCopasiParameter
 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::TypegetType () const
 
const ValuegetValue () const
 
ValuegetValue ()
 
virtual voidgetValuePointer () const
 
CCopasiObjectgetValueReference () 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
 
CCopasiParameteroperator= (const CCopasiParameter &rhs)
 
template<class CType >
bool setValue (const CType &value)
 
bool setValue (const std::vector< CCopasiParameter * > &value)
 
virtual ~CCopasiParameter ()
 
- Public Member Functions inherited from CCopasiContainer
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 objectMapgetObjects () const
 
virtual std::string getUnits () const
 
virtual const CCopasiObjectgetValueObject () const
 
virtual bool remove (CCopasiObject *pObject)
 
virtual ~CCopasiContainer ()
 
- Public Member Functions inherited from CCopasiObject
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 DataObjectSetgetDirectDependencies (const DataObjectSet &context=DataObjectSet()) const
 
CCopasiContainergetObjectAncestor (const std::string &type) const
 
CCopasiDataModelgetObjectDataModel ()
 
const CCopasiDataModelgetObjectDataModel () const
 
const std::string & getObjectName () const
 
CCopasiContainergetObjectParent () const
 
const std::string & getObjectType () const
 
virtual const
CObjectInterface::ObjectSet
getPrerequisites () const
 
virtual RefreshgetRefresh () const
 
UpdateMethodgetUpdateMethod () 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 ()
 
- Public Member Functions inherited from CObjectInterface
 CObjectInterface ()
 
virtual ~CObjectInterface ()
 

Static Public Member Functions

static COptMethodcreateMethod (CCopasiMethod::SubType subType=CCopasiMethod::EvolutionaryProgram)
 
- Static Public Member Functions inherited from COptMethod
static COptMethodcreateMethod (CCopasiMethod::SubType subType=CCopasiMethod::RandomSearch)
 
- Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * > buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())
 
static void setRenameHandler (CRenameHandler *rh)
 

Static Public Attributes

static const std::string TypeName []
 
- Static Public Attributes inherited from CCopasiMethod
static const std::string SubTypeName []
 
static const char * XMLSubType []
 
- Static Public Attributes inherited from CCopasiParameter
static const std::string TypeName []
 
static const char * XMLType []
 
- Static Public Attributes inherited from CCopasiContainer
static const std::vector
< CCopasiContainer * > 
EmptyList
 

Protected Member Functions

 CFitMethod (CCopasiMethod::SubType subType, const CCopasiContainer *pParent=NULL)
 
- Protected Member Functions inherited from COptMethod
virtual bool cleanup ()
 
 COptMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL)
 
- Protected Member Functions inherited from CCopasiMethod
 CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL)
 
- Protected Member Functions inherited from CCopasiParameterGroup
 CCopasiParameterGroup ()
 
- Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObjectaddMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
 
template<class CType >
CCopasiObjectaddObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
 
template<class CType >
CCopasiObjectaddVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
 
void initObjects ()
 
- Protected Member Functions inherited from CCopasiObject
 CCopasiObject ()
 
 CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)
 

Protected Attributes

CFitProblemmpFitProblem
 
CFitTaskmpFitTask
 
- Protected Attributes inherited from COptMethod
const bool mBounds
 
const std::vector< COptItem * > * mpOptContraints
 
const std::vector< COptItem * > * mpOptItem
 
COptProblemmpOptProblem
 
COptTaskmpParentTask
 
const std::vector
< UpdateMethod * > * 
mpSetCalculateVariable
 
- Protected Attributes inherited from CCopasiMethod
CProcessReportmpCallBack
 
- Protected Attributes inherited from CCopasiParameter
std::string mKey
 
CCopasiObjectmpValueReference
 
size_t mSize
 
Value mValue
 
- Protected Attributes inherited from CCopasiContainer
objectMap mObjects
 

Private Member Functions

 CFitMethod ()
 

Additional Inherited Members

- Public Types inherited from CCopasiMethod
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
}
 
- Public Types inherited from CCopasiParameterGroup
typedef parameterGroup::iterator index_iterator
 
typedef
CCopasiContainer::objectMap::iterator 
name_iterator
 
typedef std::vector
< CCopasiParameter * > 
parameterGroup
 
- Public Types inherited from CCopasiParameter
enum  Type {
  DOUBLE = 0, UDOUBLE, INT, UINT,
  BOOL, GROUP, STRING, CN,
  KEY, FILE, EXPRESSION, INVALID
}
 
- Public Types inherited from CCopasiContainer
typedef std::multimap
< std::string, CCopasiObject * > 
objectMap
 
- Public Types inherited from CCopasiObject
typedef std::set< const
CCopasiObject * > 
DataObjectSet
 
typedef std::vector< Refresh * > DataUpdateSequence
 
- Public Types inherited from CObjectInterface
typedef std::set< const
CObjectInterface * > 
ObjectSet
 
typedef std::vector
< CObjectInterface * > 
UpdateSequence
 
- Protected Types inherited from CCopasiObject
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
}
 
- Static Protected Attributes inherited from CCopasiObject
static CRenameHandlersmpRenameHandler = NULL
 

Detailed Description

The CFitMehod class contains optimization methods which can utilize special properties of the objective function for fitting.

Definition at line 27 of file CFitMethod.h.

Constructor & Destructor Documentation

CFitMethod::CFitMethod ( )
private

Default constructor.

Definition at line 49 of file CFitMethod.cpp.

References CONSTRUCTOR_TRACE.

CFitMethod::CFitMethod ( CCopasiMethod::SubType  subType,
const CCopasiContainer pParent = NULL 
)
protected
Parameters
CCopasiMethod::SubTypesubType
constCCopasiContainer * pParent (default: NULL)

Definition at line 55 of file CFitMethod.cpp.

References CONSTRUCTOR_TRACE.

56  :
57  COptMethod(CCopasiTask::parameterFitting, subType, pParent),
58  mpFitProblem(NULL),
59  mpFitTask(NULL)
CFitProblem * mpFitProblem
Definition: CFitMethod.h:82
CFitTask * mpFitTask
Definition: CFitMethod.h:84
#define CONSTRUCTOR_TRACE
Definition: copasi.h:202
CFitMethod::CFitMethod ( const CFitMethod src,
const CCopasiContainer pParent = NULL 
)

Copy constructor

Parameters
constCFitMethod & src
constCCopasiContainer * pParent (default: NULL)

Definition at line 62 of file CFitMethod.cpp.

References CONSTRUCTOR_TRACE.

63  :
64  COptMethod(src, pParent),
66  mpFitTask(src.mpFitTask)
CFitProblem * mpFitProblem
Definition: CFitMethod.h:82
CFitTask * mpFitTask
Definition: CFitMethod.h:84
#define CONSTRUCTOR_TRACE
Definition: copasi.h:202
CFitMethod::~CFitMethod ( )
virtual

Destructor

Definition at line 69 of file CFitMethod.cpp.

70 {}

Member Function Documentation

COptMethod * CFitMethod::createMethod ( CCopasiMethod::SubType  subType = CCopasiMethod::EvolutionaryProgram)
static

Create a fitting method. Note: the returned object has to be released after use with delete

Definition at line 26 of file CFitMethod.cpp.

References COptMethod::createMethod().

Referenced by CFitTask::CFitTask(), CQFittingWidget::createMethod(), and CFitTask::createMethod().

27 {
28  COptMethod * pMethod = NULL;
29 
30  /*
31  switch (subType)
32  {
33  case GeneticAlgorithmSR:
34  pMethod = new COptMethodGASR();
35  break;
36 
37  default:
38  */
39  pMethod = COptMethod::createMethod(subType);
40  /*
41  break;
42  }
43  */
44 
45  return pMethod;
46 }
static COptMethod * createMethod(CCopasiMethod::SubType subType=CCopasiMethod::RandomSearch)
Definition: COptMethod.cpp:50
bool CFitMethod::initialize ( )
virtual

Initialize arrays and pointer.

Returns
bool success

Reimplemented from COptMethod.

Definition at line 72 of file CFitMethod.cpp.

References CCopasiObject::getObjectParent(), COptMethod::initialize(), and mpFitTask.

73 {
74  if (!COptMethod::initialize()) return false;
75 
76  mpFitTask = dynamic_cast<CFitTask *>(getObjectParent());
77  if (!mpFitTask) return false;
78 
79  return true;
80 }
virtual bool initialize()
Definition: COptMethod.cpp:189
CFitTask * mpFitTask
Definition: CFitMethod.h:84
CCopasiContainer * getObjectParent() const
bool CFitMethod::isValidProblem ( const CCopasiProblem pProblem)
virtual

Check if the method is suitable for this problem

Returns
bool suitability of the method

Reimplemented from COptMethod.

Definition at line 82 of file CFitMethod.cpp.

References CCopasiMessage::EXCEPTION, and COptMethod::isValidProblem().

83 {
84  if (!COptMethod::isValidProblem(pProblem)) return false;
85 
86  const CFitProblem * pTP = dynamic_cast<const CFitProblem *>(pProblem);
87  if (!pTP)
88  {
89  CCopasiMessage(CCopasiMessage::EXCEPTION, "Problem is not a parameter estimation problem.");
90  return false;
91  }
92 
93  return true;
94 }
virtual bool isValidProblem(const CCopasiProblem *pProblem)
Definition: COptMethod.cpp:219

Member Data Documentation

CFitProblem* CFitMethod::mpFitProblem
protected

Definition at line 82 of file CFitMethod.h.

CFitTask* CFitMethod::mpFitTask
protected

Definition at line 84 of file CFitMethod.h.

Referenced by initialize().

const std::string CFitMethod::TypeName
static
Initial value:
=
{
""
}

Definition at line 30 of file CFitMethod.h.


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