COPASI API
4.16.103
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#include <CExperimentSet.h>
Public Member Functions | |
CCrossValidationSet (const CCopasiContainer *pParent, const std::string &name="Validation Set") | |
CCrossValidationSet (const CCrossValidationSet &src, const CCopasiContainer *pParent=NULL) | |
CCrossValidationSet (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL) | |
const unsigned C_INT32 & | getThreshold () const |
const C_FLOAT64 & | getWeight () const |
void | setThreshold (const unsigned C_INT32 &threshold) |
void | setWeight (const C_FLOAT64 &weight) |
virtual | ~CCrossValidationSet () |
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CExperiment * | addExperiment (const CExperiment &experiment) |
bool | calculateStatistics () |
CExperimentSet (const CCopasiContainer *pParent, const std::string &name="Experiment Set") | |
CExperimentSet (const CExperimentSet &src, const CCopasiContainer *pParent=NULL) | |
CExperimentSet (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL) | |
bool | compile (const std::vector< CCopasiContainer * > listOfContainer=CCopasiContainer::EmptyList) |
virtual bool | elevateChildren () |
void | fixBuild55 () |
size_t | getDataPointCount () const |
const CMatrix< C_FLOAT64 > & | getDependentData (const size_t &index) const |
const CVector< C_FLOAT64 > & | getDependentErrorMean () const |
const CVector< C_FLOAT64 > & | getDependentErrorMeanSD () const |
const CVector< C_FLOAT64 > & | getDependentObjectiveValues () const |
const CVector< CCopasiObject * > & | getDependentObjects () const |
const CVector< C_FLOAT64 > & | getDependentRMS () const |
CExperiment * | getExperiment (const size_t &index) |
const CExperiment * | getExperiment (const size_t &index) const |
CExperiment * | getExperiment (const std::string &name) |
const CExperiment * | getExperiment (const std::string &name) const |
size_t | getExperimentCount () const |
const CCopasiTask::Type & | getExperimentType (const size_t &index) const |
std::vector< std::string > | getFileNames () const |
const CMatrix< C_FLOAT64 > & | getIndependentData (const size_t &index) const |
const size_t & | getValidValueCount () const |
bool | hasDataForTaskType (const CCopasiTask::Type &type) const |
size_t | keyToIndex (const std::string &key) const |
void | removeExperiment (const size_t &index) |
void | sort () |
virtual | ~CExperimentSet () |
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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 () |
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) |
virtual void | print (std::ostream *ostream) const |
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 | |
void | initializeParameter () |
Private Attributes | |
unsigned C_INT32 * | mpThreshold |
C_FLOAT64 * | mpWeight |
Additional Inherited Members | |
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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 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 | 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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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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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 276 of file CExperimentSet.h.
CCrossValidationSet::CCrossValidationSet | ( | const CCopasiContainer * | pParent, |
const std::string & | name = "Validation Set" |
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Default constructor
const | std::string & name (default: Cross Validation Set) |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 479 of file CExperimentSet.cpp.
References initializeParameter().
CCrossValidationSet::CCrossValidationSet | ( | const CCrossValidationSet & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CCrossValidationSet & src |
const | CCopasiContainer * pParent (default: src data model) |
Definition at line 486 of file CExperimentSet.cpp.
References initializeParameter().
CCrossValidationSet::CCrossValidationSet | ( | const CCopasiParameterGroup & | group, |
const CCopasiContainer * | pParent = NULL |
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Specific constructor used for reading COPASI files
const | CCopasiParameterGroup & group |
const | CCopasiContainer * pParent (default: group data model) |
Definition at line 493 of file CExperimentSet.cpp.
References initializeParameter().
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const unsigned C_INT32 & CCrossValidationSet::getThreshold | ( | ) | const |
Retreive the threshold
Definition at line 518 of file CExperimentSet.cpp.
References mpThreshold.
Referenced by CFitProblem::calculateCrossValidation(), CQFittingWidget::saveTask(), and CQExperimentData::slotOK().
const C_FLOAT64 & CCrossValidationSet::getWeight | ( | ) | const |
Retreive the weight
Definition at line 512 of file CExperimentSet.cpp.
References mpWeight.
Referenced by CFitProblem::calculateCrossValidation(), CQFittingWidget::saveTask(), and CQExperimentData::slotOK().
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Allocates all group parameters and assures that they are properly initialized.
Definition at line 521 of file CExperimentSet.cpp.
References CCopasiParameterGroup::assertParameter(), C_FLOAT64, C_INT32, CExperimentSet::elevateChildren(), CCopasiParameter::getValue(), mpThreshold, mpWeight, CCopasiParameter::Value::pUDOUBLE, CCopasiParameter::Value::pUINT, CCopasiParameter::UDOUBLE, and CCopasiParameter::UINT.
Referenced by CCrossValidationSet().
Set the threshold
const | unsigned C_INT32 & threshold |
Definition at line 515 of file CExperimentSet.cpp.
References mpThreshold.
Referenced by CQExperimentData::slotOK().
Set the weight
const | C_FLOAT64 & weight |
Definition at line 502 of file CExperimentSet.cpp.
References mpWeight.
Referenced by CQFittingWidget::saveTask(), and CQExperimentData::slotOK().
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The threshold indicates the number of failed successive checks for which the objective function has not improved needed to terminate the parameter estimation.
Definition at line 352 of file CExperimentSet.h.
Referenced by getThreshold(), initializeParameter(), and setThreshold().
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The weight of each datapoint relative to a data point of the experiment set, i.e. 1 gives each point the same weight
Definition at line 345 of file CExperimentSet.h.
Referenced by getWeight(), initializeParameter(), and setWeight().