COPASI API
4.16.103
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#include <CExperimentSet.h>
Public Member Functions | |
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 | |
CVector< size_t > | mDependentDataCount |
CVector< C_FLOAT64 > | mDependentErrorMean |
CVector< C_FLOAT64 > | mDependentErrorMeanSD |
CVector< C_FLOAT64 > | mDependentObjectiveValues |
CVector< CCopasiObject * > | mDependentObjects |
CVector< C_FLOAT64 > | mDependentRMS |
size_t | mNonExperiments |
std::vector< CExperiment * > * | mpExperiments |
size_t | mValidValueCount |
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 26 of file CExperimentSet.h.
CExperimentSet::CExperimentSet | ( | const CCopasiContainer * | pParent, |
const std::string & | name = "Experiment Set" |
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Default constructor
const | CCopasiContainer * pParent |
const | std::string & name (default: Experiment Set) |
Definition at line 30 of file CExperimentSet.cpp.
References initializeParameter().
CExperimentSet::CExperimentSet | ( | const CExperimentSet & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CExperimentSet & src |
const | CCopasiContainer * pParent (default: src data model) |
Definition at line 44 of file CExperimentSet.cpp.
References initializeParameter().
CExperimentSet::CExperimentSet | ( | 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 58 of file CExperimentSet.cpp.
References initializeParameter().
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CExperiment * CExperimentSet::addExperiment | ( | const CExperiment & | experiment | ) |
Add an experiment
Definition at line 327 of file CExperimentSet.cpp.
References CCopasiParameterGroup::addParameter(), CCopasiObject::getObjectName(), CCopasiParameterGroup::getParameter(), CCopasiObject::setObjectName(), sort(), and StringPrint().
Referenced by CQFittingWidget::saveTask(), CQExperimentData::slotExperimentAdd(), and CQExperimentData::slotOK().
bool CExperimentSet::calculateStatistics | ( | ) |
Calculate statistics across all experiments.
Definition at line 177 of file CExperimentSet.cpp.
References COutputInterface::AFTER, CVectorCore< CType >::array(), C_FLOAT64, CCopasiObject::getObjectAncestor(), max, mDependentDataCount, mDependentErrorMean, mDependentErrorMeanSD, mDependentObjectiveValues, mDependentObjects, mDependentRMS, mNonExperiments, mpExperiments, mValidValueCount, CCopasiTask::output(), CVector< CType >::resize(), CVectorCore< CType >::size(), and CCopasiTask::timeCourse.
Referenced by CFitProblem::calculateStatistics().
bool CExperimentSet::compile | ( | const std::vector< CCopasiContainer * > | listOfContainer = CCopasiContainer::EmptyList | ) |
Compile the experiment set. This function must be called before any evaluations can be performed.
const | std::vector< CCopasiContainer * > listOfContainer |
Definition at line 96 of file CExperimentSet.cpp.
References CVectorCore< CType >::array(), CCopasiMessage::ERROR, CLocaleString::fromUtf8(), MCFitting, mDependentDataCount, mDependentErrorMean, mDependentErrorMeanSD, mDependentObjectiveValues, mDependentObjects, mDependentRMS, mNonExperiments, mpExperiments, CVector< CType >::resize(), CVectorCore< CType >::size(), and sort().
Referenced by CFitProblem::initialize().
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This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.
Reimplemented from CCopasiParameterGroup.
Definition at line 77 of file CExperimentSet.cpp.
References mpExperiments, CCopasiParameter::mValue, CCopasiParameter::Value::pGROUP, CCopasiParameter::Value::pVOID, and sort().
Referenced by initializeParameter(), and CCrossValidationSet::initializeParameter().
void CExperimentSet::fixBuild55 | ( | ) |
Fix files written with Version 4.10.55, which wrote the square root of user defined weights for the parameter fitting task
Definition at line 466 of file CExperimentSet.cpp.
References mNonExperiments, and mpExperiments.
Referenced by CFitProblem::fixBuild55().
size_t CExperimentSet::getDataPointCount | ( | ) | const |
Retrieve the number of data points of all experiments combined.
Definition at line 449 of file CExperimentSet.cpp.
References mNonExperiments, and mpExperiments.
Referenced by CFitProblem::calculateCrossValidation(), CFitProblem::initialize(), and CFitProblem::setResidualsRequired().
Retrieve the dependent data of the indexed experiment.
const | size_t & index, |
Definition at line 386 of file CExperimentSet.cpp.
References CExperiment::getDependentData(), and getExperiment().
Retrieve all dependent data error mean values.
Definition at line 318 of file CExperimentSet.cpp.
References mDependentErrorMean.
Referenced by CQFittingResult::enterProtected().
Retrieve all dependent data error mean std. deviations.
Definition at line 321 of file CExperimentSet.cpp.
References mDependentErrorMeanSD.
Referenced by CQFittingResult::enterProtected().
Retrieve all dependent data objective values.
Definition at line 312 of file CExperimentSet.cpp.
References mDependentObjectiveValues.
Referenced by CQFittingResult::enterProtected().
const CVector< CCopasiObject * > & CExperimentSet::getDependentObjects | ( | ) | const |
Retrieve the list of dependent data objects
Definition at line 309 of file CExperimentSet.cpp.
References mDependentObjects.
Referenced by CQFittingResult::enterProtected().
Retrieve all dependent data objective values.
Definition at line 315 of file CExperimentSet.cpp.
References mDependentRMS.
Referenced by CQFittingResult::enterProtected().
CExperiment * CExperimentSet::getExperiment | ( | const size_t & | index | ) |
Retrieve the indexed experiment
const | size_t & index, |
Definition at line 352 of file CExperimentSet.cpp.
References mNonExperiments, and mpExperiments.
Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), COutputAssistant::createDefaultOutput(), CFitProblem::elevateChildren(), CQFittingResult::enterProtected(), getDependentData(), getExperimentType(), getIndependentData(), CFitProblem::initialize(), CQExperimentData::isLikePreviousExperiment(), keyToIndex(), CQExperimentSelection::load(), CQExperimentData::load(), CQExperimentData::loadExperiment(), CQFittingWidget::loadTask(), CFitProblem::printResult(), CQExperimentData::saveExperiment(), CQFittingWidget::saveTask(), CQExperimentData::slotCheckNormalizeWeightsPerExperiment(), CQExperimentData::slotCheckTo(), CQExperimentData::slotExperimentDelete(), CQExperimentData::slotFileDelete(), CQExperimentData::slotOK(), CQExperimentData::slotWeightMethod(), and CExperimentFileInfo::sync().
const CExperiment * CExperimentSet::getExperiment | ( | const size_t & | index | ) | const |
Retrieve the indexed experiment
const | size_t & index, |
Definition at line 355 of file CExperimentSet.cpp.
References mNonExperiments, and mpExperiments.
CExperiment * CExperimentSet::getExperiment | ( | const std::string & | name | ) |
Retrieve the indexed experiment
const | std::string & name, |
Definition at line 358 of file CExperimentSet.cpp.
References CCopasiParameterGroup::getGroup().
const CExperiment * CExperimentSet::getExperiment | ( | const std::string & | name | ) | const |
Retrieve the indexed experiment
const | std::string & name, |
Definition at line 361 of file CExperimentSet.cpp.
References CCopasiParameterGroup::getGroup().
size_t CExperimentSet::getExperimentCount | ( | ) | const |
Retrieve the number of the experiments in the set
Definition at line 324 of file CExperimentSet.cpp.
References mNonExperiments, and CCopasiParameterGroup::size().
Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), COutputAssistant::createDefaultOutput(), CQFittingResult::enterProtected(), CFitProblem::initialize(), CQFittingResultTab1::load(), CQExperimentSelection::load(), CQExperimentData::load(), CQFittingWidget::loadTask(), CFitProblem::printResult(), CQFittingWidget::saveTask(), CQFittingItemWidget::setCrossValidationSet(), CFitProblem::setSolution(), CQExperimentData::slotFileDelete(), CQExperimentData::slotOK(), and CExperimentFileInfo::sync().
const CCopasiTask::Type & CExperimentSet::getExperimentType | ( | const size_t & | index | ) | const |
Retrieve the indexed experiment type
const | size_t & index, |
Definition at line 380 of file CExperimentSet.cpp.
References getExperiment(), and CExperiment::getExperimentType().
std::vector< std::string > CExperimentSet::getFileNames | ( | ) | const |
Retrieve the list of file names
Definition at line 431 of file CExperimentSet.cpp.
References mNonExperiments, and mpExperiments.
Referenced by CQExperimentData::load().
Retrieve the independent data of the indexed experiment.
const | size_t & index, |
Definition at line 383 of file CExperimentSet.cpp.
References getExperiment(), and CExperiment::getIndependentData().
const size_t & CExperimentSet::getValidValueCount | ( | ) | const |
Retrieve the count of valid data points of all experiments combined.
Definition at line 461 of file CExperimentSet.cpp.
References mValidValueCount.
Referenced by CFitProblem::calculateStatistics().
bool CExperimentSet::hasDataForTaskType | ( | const CCopasiTask::Type & | type | ) | const |
Check whether the set contains data for the the given task type
const | CCopasiTask::Type & type |
Definition at line 364 of file CExperimentSet.cpp.
References mNonExperiments, and mpExperiments.
Referenced by CFitProblem::initialize().
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Allocates all group parameters and assures that they are properly initialized.
Definition at line 74 of file CExperimentSet.cpp.
References elevateChildren().
Referenced by CExperimentSet().
size_t CExperimentSet::keyToIndex | ( | const std::string & | key | ) | const |
Convert an experiment key to an index
const | std::string & key |
Definition at line 389 of file CExperimentSet.cpp.
References C_INVALID_INDEX, CKeyFactory::get(), getExperiment(), CCopasiRootContainer::getKeyFactory(), and CCopasiParameterGroup::size().
Referenced by CFitProblem::initialize(), CQExperimentData::isLikePreviousExperiment(), CQExperimentData::loadExperiment(), CQExperimentData::saveExperiment(), CQExperimentData::slotCheckNormalizeWeightsPerExperiment(), CQExperimentData::slotCheckTo(), CQExperimentData::slotExperimentDelete(), and CQExperimentData::slotWeightMethod().
void CExperimentSet::removeExperiment | ( | const size_t & | index | ) |
Remove an experiment from the set
const | size_t & index |
Definition at line 349 of file CExperimentSet.cpp.
References mNonExperiments, and CCopasiParameterGroup::removeParameter().
Referenced by CQFittingWidget::saveTask(), CQExperimentData::slotExperimentDelete(), CQExperimentData::slotFileDelete(), and CQExperimentData::slotOK().
void CExperimentSet::sort | ( | ) |
Sort the experiments in the set
Definition at line 403 of file CExperimentSet.cpp.
References CCopasiParameterGroup::beginIndex(), CExperiment::compare(), CCopasiParameterGroup::endIndex(), mNonExperiments, mpExperiments, and CCopasiParameterGroup::swap().
Referenced by addExperiment(), compile(), elevateChildren(), and CExperimentFileInfo::sync().
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A list of the number of data points for each dependent object;
Definition at line 268 of file CExperimentSet.h.
Referenced by calculateStatistics(), and compile().
A list of all dependent data error mean values;
Definition at line 258 of file CExperimentSet.h.
Referenced by calculateStatistics(), compile(), and getDependentErrorMean().
A list of all dependent data error mean std. deviations;
Definition at line 263 of file CExperimentSet.h.
Referenced by calculateStatistics(), compile(), and getDependentErrorMeanSD().
A list of all dependent data objective values;
Definition at line 248 of file CExperimentSet.h.
Referenced by calculateStatistics(), compile(), and getDependentObjectiveValues().
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A set of all dependent data objects;
Definition at line 243 of file CExperimentSet.h.
Referenced by calculateStatistics(), compile(), and getDependentObjects().
A list of all dependent data objective values;
Definition at line 253 of file CExperimentSet.h.
Referenced by calculateStatistics(), compile(), and getDependentRMS().
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The number of parameters which are not of type CExperiment
Definition at line 238 of file CExperimentSet.h.
Referenced by calculateStatistics(), compile(), fixBuild55(), getDataPointCount(), getExperiment(), getExperimentCount(), getFileNames(), hasDataForTaskType(), removeExperiment(), and sort().
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This is realized a CCopasiParameter type GROUP
Definition at line 233 of file CExperimentSet.h.
Referenced by calculateStatistics(), compile(), elevateChildren(), fixBuild55(), getDataPointCount(), getExperiment(), getFileNames(), hasDataForTaskType(), and sort().
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The total count of valid data values.
Definition at line 273 of file CExperimentSet.h.
Referenced by calculateStatistics(), and getValidValueCount().