COPASI API
4.16.103
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#include <CExperiment.h>
Public Types | |
enum | Type { ignore = 0, independent, dependent, time } |
enum | WeightMethod { MEAN = 0, MEAN_SQUARE, SD, VALUE_SCALING } |
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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 |
Public Member Functions | |
bool | calculateStatistics () |
bool | calculateWeights () |
CExperiment (const CCopasiContainer *pParent, const std::string &name="Experiment") | |
CExperiment (const CExperiment &src, const CCopasiContainer *pParent=NULL) | |
CExperiment (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL) | |
bool | compile (const std::vector< CCopasiContainer * > listOfContainer=CCopasiContainer::EmptyList) |
virtual bool | elevateChildren () |
size_t | extendedTimeSeriesSize () const |
void | fixBuild55 () |
const std::vector< std::string > & | getColumnNames () const |
size_t | getColumnValidValueCount (CCopasiObject *const &pObject) const |
C_FLOAT64 | getDefaultScale (const CCopasiObject *const &pObject) const |
const CMatrix< C_FLOAT64 > & | getDependentData () const |
const std::map< CCopasiObject *, size_t > & | getDependentObjects () const |
const C_FLOAT64 & | getErrorMean () const |
const C_FLOAT64 & | getErrorMeanSD () const |
C_FLOAT64 | getErrorMeanSD (CCopasiObject *const &pObject, const C_FLOAT64 &errorMean) const |
C_FLOAT64 | getErrorSum (CCopasiObject *const &pObject) const |
const CCopasiTask::Type & | getExperimentType () const |
const std::string & | getFileName () const |
const unsigned C_INT32 & | getFirstRow () const |
const CCopasiVector < CFittingPoint > & | getFittingPoints () const |
const unsigned C_INT32 & | getHeaderRow () const |
const CMatrix< C_FLOAT64 > & | getIndependentData () const |
const std::set< const CCopasiObject * > & | getIndependentObjects () const |
const unsigned C_INT32 & | getLastRow () const |
bool | getNormalizeWeightsPerExperiment () const |
const unsigned C_INT32 & | getNumColumns () const |
size_t | getNumDataRows () const |
const C_FLOAT64 & | getObjectiveValue () const |
C_FLOAT64 | getObjectiveValue (CCopasiObject *const &pObject) const |
CExperimentObjectMap & | getObjectMap () |
const C_FLOAT64 & | getRMS () const |
C_FLOAT64 | getRMS (CCopasiObject *const &pObject) const |
const std::string & | getSeparator () const |
const CVector< C_FLOAT64 > & | getTimeData () const |
const WeightMethod & | getWeightMethod () const |
size_t | guessColumnNumber () const |
void | initExtendedTimeSeries (size_t s) |
const bool & | isRowOriented () const |
CExperiment & | operator= (const CExperiment &rhs) |
virtual void | printResult (std::ostream *ostream) const |
bool | read (std::istream &in, size_t ¤tLine) |
bool | readColumnNames () |
bool | restoreModelIndependentData () |
bool | setExperimentType (const CCopasiTask::Type &type) |
bool | setFileName (const std::string &fileName) |
bool | setFirstRow (const unsigned C_INT32 &firstRow) |
bool | setHeaderRow (const unsigned C_INT32 &headerRow) |
bool | setIsRowOriented (const bool &isRowOriented) |
bool | setLastRow (const unsigned C_INT32 &lastRow) |
void | setNormalizeWeightsPerExperiment (bool flag) |
bool | setNumColumns (const unsigned C_INT32 &cols) |
bool | setSeparator (const std::string &seperator) |
bool | setWeightMethod (const WeightMethod &weightMethod) |
void | storeExtendedTimeSeriesData (C_FLOAT64 time) |
C_FLOAT64 | sumOfSquares (const size_t &index, C_FLOAT64 *&residuals) const |
C_FLOAT64 | sumOfSquaresStore (const size_t &index, C_FLOAT64 *&dependentValues) |
void | updateFittedPoints () |
void | updateFittedPointValues (const size_t &index, bool includeSimulation) |
void | updateFittedPointValuesFromExtendedTimeSeries (const size_t &index) |
bool | updateModelWithIndependentData (const size_t &index) |
virtual | ~CExperiment () |
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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 () |
Static Public Member Functions | |
static bool | compare (const CExperiment *lhs, const CExperiment *rhs) |
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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 const std::string | WeightMethodName [] |
static const char * | WeightMethodType [] |
static const char * | XMLType [] |
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static const std::string | TypeName [] |
static const char * | XMLType [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
Private Member Functions | |
void | initializeParameter () |
void | initializeScalingMatrix () |
Friends | |
bool | operator== (const CExperiment &lhs, const CExperiment &rhs) |
Additional Inherited Members | |
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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 61 of file CExperiment.h.
enum CExperiment::Type |
Enumeration of the types of columns known to COPASI.
Enumerator | |
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ignore | |
independent | |
dependent | |
time |
Definition at line 67 of file CExperiment.h.
Enumeration of methods to calculate the weight.
Enumerator | |
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MEAN | |
MEAN_SQUARE | |
SD | |
VALUE_SCALING |
Definition at line 89 of file CExperiment.h.
CExperiment::CExperiment | ( | const CCopasiContainer * | pParent, |
const std::string & | name = "Experiment" |
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Default constructor
const | CCopasiContainer * pParent |
const | std::string & name (default: Experiment) |
Definition at line 76 of file CExperiment.cpp.
References CVectorCore< CType >::array(), initializeParameter(), mExtendedTimeSeries, and mStorageIt.
CExperiment::CExperiment | ( | const CExperiment & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CExperiment & src |
const | CCopasiContainer * pParent (default: src data model) |
Definition at line 126 of file CExperiment.cpp.
References CVectorCore< CType >::array(), initializeParameter(), mExtendedTimeSeries, and mStorageIt.
CExperiment::CExperiment | ( | 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 177 of file CExperiment.cpp.
References CVectorCore< CType >::array(), initializeParameter(), mExtendedTimeSeries, and mStorageIt.
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bool CExperiment::calculateStatistics | ( | ) |
Calculate statistics by comparing the stored calculated values with the measurements.
Definition at line 601 of file CExperiment.cpp.
References CMatrix< CType >::array(), C_FLOAT64, CCopasiDataModel::getModel(), CCopasiObject::getObjectDataModel(), CModel::getTime(), max, mColumnObjectiveValue, mColumnRMS, mColumnValidValueCount, mDataDependent, mMean, mMeanSD, mObjectiveValue, mpDataDependentCalculated, mpTaskType, mRMS, mRowObjectiveValue, mRowRMS, mScale, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), CVector< CType >::resize(), and CCopasiTask::timeCourse.
bool CExperiment::calculateWeights | ( | ) |
Calculate/set the weights used in the sum of squares.
Definition at line 1051 of file CExperiment.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, max, mColumnValidValueCount, mDataDependent, mDefaultColumnScale, MEAN, MEAN_SQUARE, mMeans, mMissingData, mNumDataRows, mpNormalizeWeightsPerExperiment, mpWeightMethod, SD, CVectorCore< CType >::size(), and VALUE_SCALING.
Referenced by read(), CQExperimentData::slotCheckNormalizeWeightsPerExperiment(), and CQExperimentData::slotWeightMethod().
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static |
Comparison used to evaluate the order of the experiment based on the filename and starting line number.
const | CExperiment * lhs; |
const | CExperiment * rhs; |
Definition at line 1386 of file CExperiment.cpp.
References mpFileName, and mpFirstRow.
Referenced by CExperimentSet::sort().
bool CExperiment::compile | ( | const std::vector< CCopasiContainer * > | listOfContainer = CCopasiContainer::EmptyList | ) |
Compile the experiment. This function must be called before any evaluations can be performed.
const | std::vector< CCopasiContainer * > listOfContainer |
Definition at line 735 of file CExperiment.cpp.
References CCopasiObject::buildUpdateSequence(), C_FLOAT64, C_INVALID_INDEX, CExperimentObjectMap::compile(), dependent, CCopasiMessage::ERROR, CCopasiObjectName::escape(), CExperimentObjectMap::getLastColumn(), CExperimentObjectMap::getLastNotIgnoredColumn(), CExperimentObjectMap::getMappedObjects(), CCopasiObject::getObjectDataModel(), CCopasiParameter::getObjectDisplayName(), CCopasiObject::getObjectName(), CExperimentObjectMap::getRole(), CExperimentObjectMap::getScale(), CModel::getUptoDateObjects(), CCopasiContainer::getValueObject(), CCopasiParameter::getValuePointer(), ignore, independent, initializeScalingMatrix(), CCopasiObject::isValueDbl(), MCFitting, mColumnObjectiveValue, mColumnRMS, mColumnScale, mColumnValidValueCount, mDataDependent, mDataIndependent, mDependentObjects, mDependentValues, mIndependentObjects, mIndependentUpdateMethods, mIndependentValues, mMean, mMeanSD, mObjectiveValue, mpNumColumns, mpObjectMap, mpTaskType, mRefreshMethods, mRMS, mRowObjectiveValue, mRowRMS, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), CCopasiDataModel::ObjectFromName(), CVector< CType >::resize(), time, and CCopasiTask::timeCourse.
Referenced by CQExperimentData::slotCheckNormalizeWeightsPerExperiment(), CQExperimentData::slotExperimentChanged(), CQExperimentData::slotWeightMethod(), and CQExperimentData::updateScales().
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virtual |
This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.
Reimplemented from CCopasiParameterGroup.
Definition at line 300 of file CExperiment.cpp.
References CCopasiParameterGroup::clear(), CCopasiParameterGroup::getGroup(), CExperimentObjectMap::getObjectCN(), CCopasiParameterGroup::getValue(), mpObjectMap, mpWeightMethod, CCopasiParameter::Value::pUINT, CCopasiParameterGroup::removeParameter(), SD, CExperimentObjectMap::setNumCols(), CExperimentObjectMap::setObjectCN(), CExperimentObjectMap::setRole(), CCopasiParameterGroup::size(), StringPrint(), and updateFittedPoints().
Referenced by initializeParameter(), and operator=().
size_t CExperiment::extendedTimeSeriesSize | ( | ) | const |
Definition at line 596 of file CExperiment.cpp.
References mExtendedTimeSeriesSize.
Referenced by updateFittedPointValuesFromExtendedTimeSeries().
void CExperiment::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 1711 of file CExperiment.cpp.
References CExperimentObjectMap::fixBuild55(), and mpObjectMap.
const std::vector< std::string > & CExperiment::getColumnNames | ( | ) | const |
Retrieve the column names
Definition at line 1214 of file CExperiment.cpp.
References mColumnName.
Referenced by CQExperimentData::loadTable().
size_t CExperiment::getColumnValidValueCount | ( | CCopasiObject *const & | pObject | ) | const |
Retrieve the data point count for the object.
CCopasiObject | * const & pObject |
Definition at line 1665 of file CExperiment.cpp.
References mColumnValidValueCount, and mDependentObjects.
C_FLOAT64 CExperiment::getDefaultScale | ( | const CCopasiObject *const & | pObject | ) | const |
Retrieve the default scaling factor for the object.
CCopasiObject | *const& pObject |
Definition at line 1573 of file CExperiment.cpp.
References mDefaultColumnScale, and mDependentObjects.
Referenced by CExperimentObjectMap::CDataColumn::getDefaultScale().
Retrieve the dependent data of the experiment.
Definition at line 1276 of file CExperiment.cpp.
References mDataDependent.
Referenced by CExperimentSet::getDependentData(), and initExtendedTimeSeries().
const std::map< CCopasiObject *, size_t > & CExperiment::getDependentObjects | ( | ) | const |
Retrieve the list of dependent data objects
Definition at line 1156 of file CExperiment.cpp.
References mDependentObjects.
const C_FLOAT64 & CExperiment::getErrorMean | ( | ) | const |
Retrieve the mean of the error
const | C_FLOAT64 & errorMean |
Definition at line 1556 of file CExperiment.cpp.
References mMean.
Referenced by CQFittingResult::enterProtected().
const C_FLOAT64 & CExperiment::getErrorMeanSD | ( | ) | const |
Retrieve the std. deviation of the error
const | C_FLOAT64 & errorMeanSD |
Definition at line 1559 of file CExperiment.cpp.
References mMeanSD.
Referenced by CQFittingResult::enterProtected().
C_FLOAT64 CExperiment::getErrorMeanSD | ( | CCopasiObject *const & | pObject, |
const C_FLOAT64 & | errorMean | ||
) | const |
Retrieve the error mean std. deviations for the object. More specifically this is the sum of the squared deviations of the residuals from the provided errorMean. The sum is over all data points for the object.
CCopasiObject | *const& pObject |
C_FLOAT64 | errorMean |
Definition at line 1627 of file CExperiment.cpp.
References CMatrix< CType >::array(), C_FLOAT64, max, mDataDependent, mDependentObjects, mpDataDependentCalculated, mScale, CMatrix< CType >::numCols(), and CMatrix< CType >::numRows().
C_FLOAT64 CExperiment::getErrorSum | ( | CCopasiObject *const & | pObject | ) | const |
Retrieve the sum of errors (scaled residuals) for the object.
CCopasiObject | *const& pObject |
Definition at line 1595 of file CExperiment.cpp.
References CMatrix< CType >::array(), C_FLOAT64, mColumnScale, mDataDependent, mDependentObjects, mpDataDependentCalculated, CMatrix< CType >::numCols(), and CMatrix< CType >::numRows().
const CCopasiTask::Type & CExperiment::getExperimentType | ( | ) | const |
Retrieve the experiment type
Definition at line 1237 of file CExperiment.cpp.
References mpTaskType.
Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), COutputAssistant::createDefaultOutput(), CExperimentSet::getExperimentType(), CQExperimentData::isLikePreviousExperiment(), and CQExperimentData::loadExperiment().
const std::string & CExperiment::getFileName | ( | ) | const |
Retrieve the file name
Definition at line 1279 of file CExperiment.cpp.
References CDirEntry::fileName(), CCopasiObject::getObjectDataModel(), CDirEntry::isRelativePath(), CDirEntry::makePathAbsolute(), and mpFileName.
Referenced by guessColumnNumber(), printResult(), readColumnNames(), CQExperimentData::slotCheckNormalizeWeightsPerExperiment(), CQExperimentData::slotExperimentChanged(), CQExperimentData::slotFileDelete(), CQExperimentData::slotWeightMethod(), CExperimentFileInfo::sync(), and CQExperimentData::updateScales().
const unsigned C_INT32 & CExperiment::getFirstRow | ( | ) | const |
Retrieve the first row
Definition at line 1303 of file CExperiment.cpp.
References mpFirstRow.
Referenced by CQExperimentData::loadExperiment(), and CQExperimentData::slotCheckFrom().
const CCopasiVector< CFittingPoint > & CExperiment::getFittingPoints | ( | ) | const |
Retrieve the list of fitting points
Definition at line 1300 of file CExperiment.cpp.
References mFittingPoints.
Referenced by COutputAssistant::createDefaultOutput().
const unsigned C_INT32 & CExperiment::getHeaderRow | ( | ) | const |
Retrieve the header row
Definition at line 1327 of file CExperiment.cpp.
References mpHeaderRow.
Referenced by CQExperimentData::isLikePreviousExperiment(), and CQExperimentData::loadExperiment().
Retrieve the independent data of the experiment.
Definition at line 1273 of file CExperiment.cpp.
References mDataIndependent.
Referenced by CExperimentSet::getIndependentData().
const std::set< const CCopasiObject * > & CExperiment::getIndependentObjects | ( | ) | const |
Retrieve the list of independent objects
Definition at line 1676 of file CExperiment.cpp.
References mIndependentObjects.
Referenced by CFitProblem::initialize().
const unsigned C_INT32 & CExperiment::getLastRow | ( | ) | const |
Retrieve the last row
Definition at line 1315 of file CExperiment.cpp.
References mpLastRow.
Referenced by CQExperimentData::loadExperiment(), CQExperimentData::slotCheckFrom(), and CQExperimentDataValidator::validate().
bool CExperiment::getNormalizeWeightsPerExperiment | ( | ) | const |
Definition at line 1262 of file CExperiment.cpp.
References mpNormalizeWeightsPerExperiment.
Referenced by CQExperimentData::isLikePreviousExperiment(), and CQExperimentData::loadExperiment().
const unsigned C_INT32 & CExperiment::getNumColumns | ( | ) | const |
Retrieve the number of columns
Definition at line 1338 of file CExperiment.cpp.
References mpNumColumns.
size_t CExperiment::getNumDataRows | ( | ) | const |
Retrieve the number of data rows
Definition at line 1347 of file CExperiment.cpp.
References mNumDataRows.
Referenced by CFitProblem::calculate(), and CFitProblem::calculateCrossValidation().
const C_FLOAT64 & CExperiment::getObjectiveValue | ( | ) | const |
Retrieve the value of the objective function
const | C_FLOAT64 & errorMean |
Definition at line 1550 of file CExperiment.cpp.
References mObjectiveValue.
Referenced by CQFittingResult::enterProtected().
C_FLOAT64 CExperiment::getObjectiveValue | ( | CCopasiObject *const & | pObject | ) | const |
Retrieve the objective value for the object.
CCopasiObject | *const& pObject |
Definition at line 1562 of file CExperiment.cpp.
References mColumnObjectiveValue, and mDependentObjects.
CExperimentObjectMap & CExperiment::getObjectMap | ( | ) |
Retrieve the object map
Definition at line 1297 of file CExperiment.cpp.
References mpObjectMap.
Referenced by CQExperimentData::isLikePreviousExperiment(), CQExperimentData::loadTable(), CQExperimentData::saveTable(), CQExperimentData::slotExprimentType(), and CQExperimentData::updateScales().
const C_FLOAT64 & CExperiment::getRMS | ( | ) | const |
Retrieve the RMS
const | C_FLOAT64 & RMS |
Definition at line 1553 of file CExperiment.cpp.
References mRMS.
Referenced by CQFittingResult::enterProtected().
C_FLOAT64 CExperiment::getRMS | ( | CCopasiObject *const & | pObject | ) | const |
Retrieve the RMS for the object.
CCopasiObject | *const& pObject |
Definition at line 1584 of file CExperiment.cpp.
References mColumnRMS, and mDependentObjects.
const std::string & CExperiment::getSeparator | ( | ) | const |
Retrieve the separator
Definition at line 1350 of file CExperiment.cpp.
References mpSeparator.
Referenced by CQExperimentData::isLikePreviousExperiment(), and CQExperimentData::loadExperiment().
Retrieve the time data of the experiment.
Definition at line 1270 of file CExperiment.cpp.
References mDataTime.
Referenced by CFitProblem::calculate(), and CFitProblem::calculateCrossValidation().
const CExperiment::WeightMethod & CExperiment::getWeightMethod | ( | ) | const |
Retrieve the method used for calculating the default weights.
Definition at line 1359 of file CExperiment.cpp.
References mpWeightMethod.
Referenced by CQExperimentData::isLikePreviousExperiment(), CQExperimentData::loadExperiment(), CQExperimentData::slotCheckTo(), and CQExperimentData::slotWeightMethod().
size_t CExperiment::guessColumnNumber | ( | ) | const |
Try to guess the number of columns
Definition at line 1190 of file CExperiment.cpp.
References CLocaleString::fromUtf8(), getFileName(), CTableRow::guessColumnNumber(), mpFirstRow, mpLastRow, mpSeparator, and skipLine().
Referenced by CQExperimentData::slotExperimentAdd(), and CQExperimentData::slotSeparator().
void CExperiment::initExtendedTimeSeries | ( | size_t | s | ) |
Initialize the storage of an extended time series for plotting. This clears the storage, resizes it to the given size and sets the iterator to the start of the storage. The size given is the number of time points, not the number of data
Definition at line 569 of file CExperiment.cpp.
References CVectorCore< CType >::array(), getDependentData(), mExtendedTimeSeries, mExtendedTimeSeriesSize, mStorageIt, and CVector< CType >::resize().
Referenced by CFitProblem::calculate(), and CFitProblem::calculateCrossValidation().
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Allocates all group parameters and assures that they are properly initialized.
Definition at line 256 of file CExperiment.cpp.
References CKeyFactory::add(), CCopasiParameterGroup::assertGroup(), CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_INT32, elevateChildren(), CCopasiParameter::FILE, CCopasiRootContainer::getKeyFactory(), CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), InvalidIndex, CCopasiParameter::KEY, MEAN_SQUARE, CCopasiParameter::mKey, mpFileName, mpFirstRow, mpHeaderRow, mpLastRow, mpNormalizeWeightsPerExperiment, mpNumColumns, mpRowOriented, mpSeparator, mpTaskType, mpWeightMethod, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pFILE, CCopasiParameter::Value::pSTRING, CCopasiParameter::Value::pUINT, CKeyFactory::remove(), CCopasiParameterGroup::removeParameter(), CCopasiParameter::setValue(), CCopasiParameter::STRING, CCopasiParameter::UINT, and CCopasiTask::unset.
Referenced by CExperiment().
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Initialize the scaling matrix
Definition at line 1681 of file CExperiment.cpp.
References CVectorCore< CType >::array(), CMatrix< CType >::array(), C_FLOAT64, max, mColumnScale, mDataDependent, mpWeightMethod, mScale, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), CMatrix< CType >::resize(), CVectorCore< CType >::size(), CMatrix< CType >::size(), and VALUE_SCALING.
Referenced by compile().
const bool & CExperiment::isRowOriented | ( | ) | const |
Check whter the data is row oriented.
Definition at line 1377 of file CExperiment.cpp.
References mpRowOriented.
Referenced by setIsRowOriented().
CExperiment & CExperiment::operator= | ( | const CExperiment & | rhs | ) |
Assignment operator
const | CExperiment & rhs |
Definition at line 229 of file CExperiment.cpp.
References CCopasiParameterGroup::clear(), elevateChildren(), CCopasiParameter::getValue(), mpFileName, mpFirstRow, mpHeaderRow, mpLastRow, mpNormalizeWeightsPerExperiment, mpNumColumns, mpRowOriented, mpSeparator, mpTaskType, mpWeightMethod, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pFILE, CCopasiParameter::Value::pKEY, CCopasiParameter::Value::pSTRING, CCopasiParameter::Value::pUINT, and CCopasiParameterGroup::setValue().
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This is the output method for the statistics for the experiment. This method is called from CFitProblem::printResult.
std::ostream | * ostream |
Definition at line 1409 of file CExperiment.cpp.
References C_FLOAT64, dependent, getFileName(), CExperimentObjectMap::getLastNotIgnoredColumn(), CExperimentObjectMap::getMappedObjects(), CCopasiParameter::getObjectDisplayName(), CCopasiObject::getObjectName(), CExperimentObjectMap::getRole(), mColumnObjectiveValue, mColumnRMS, mColumnScale, mDataDependent, mDataTime, mMean, mNumDataRows, mObjectiveValue, mpDataDependentCalculated, mpObjectMap, mpTaskType, mRMS, mRowObjectiveValue, mRowRMS, mScale, CMatrix< CType >::numCols(), CVectorCore< CType >::size(), and CCopasiTask::timeCourse.
Referenced by CFitProblem::printResult().
bool CExperiment::read | ( | std::istream & | in, |
size_t & | currentLine | ||
) |
Reads the experiment data form a the given stream
std::istream | & in |
size_t | & currentLine |
Definition at line 874 of file CExperiment.cpp.
References CVectorCore< CType >::applyPivot(), CMatrix< CType >::applyPivot(), CVectorCore< CType >::array(), C_INVALID_INDEX, calculateWeights(), dependent, CCopasiMessage::ERROR, CTableRow::getCells(), CCopasiParameterGroup::getName(), CCopasiObject::getObjectName(), CExperimentObjectMap::getRole(), ignore, independent, MCFitting, mColumnName, mColumnScale, mColumnValidValueCount, mDataDependent, mDataIndependent, mDataTime, mDefaultColumnScale, mMeans, mNumDataRows, mpDataDependentCalculated, mpFileName, mpFirstRow, mpHeaderRow, mpLastRow, mpNumColumns, mpObjectMap, mpSeparator, mpTaskType, CMatrix< CType >::resize(), CVector< CType >::resize(), CVectorCore< CType >::size(), CCopasiParameterGroup::size(), skipLine(), sortWithPivot(), time, and CCopasiTask::timeCourse.
Referenced by CQExperimentData::slotCheckNormalizeWeightsPerExperiment(), CQExperimentData::slotExperimentChanged(), CQExperimentData::slotWeightMethod(), and CQExperimentData::updateScales().
bool CExperiment::readColumnNames | ( | ) |
Reads the header row for the experiment data
Definition at line 1159 of file CExperiment.cpp.
References CLocaleString::fromUtf8(), CTableRow::getCells(), getFileName(), CCopasiParameterGroup::getName(), InvalidIndex, mColumnName, mpHeaderRow, mpNumColumns, mpSeparator, and skipLine().
Referenced by CQExperimentData::loadTable(), and CQExperimentData::slotSeparator().
bool CExperiment::restoreModelIndependentData | ( | ) |
Restore the model with the independent data from before the experiment
Definition at line 1227 of file CExperiment.cpp.
References mIndependentUpdateMethods, mIndependentValues, and CVectorCore< CType >::size().
Referenced by CFitProblem::calculate(), and CFitProblem::calculateCrossValidation().
bool CExperiment::setExperimentType | ( | const CCopasiTask::Type & | type | ) |
set the experiment type
const | CCopasiTask::Type & experimentType |
Definition at line 1240 of file CExperiment.cpp.
References mpTaskType, CCopasiTask::steadyState, and CCopasiTask::timeCourse.
Referenced by CQExperimentData::saveExperiment(), and CQExperimentData::slotExprimentType().
bool CExperiment::setFileName | ( | const std::string & | fileName | ) |
Set the file name
const | std::string & fileName |
Definition at line 1291 of file CExperiment.cpp.
References mpFileName.
Referenced by CQExperimentData::slotExperimentAdd().
bool CExperiment::setFirstRow | ( | const unsigned C_INT32 & | firstRow | ) |
Set the first row containing data
const | unsigned C_INT32 & firstRow |
Definition at line 1306 of file CExperiment.cpp.
References mpFirstRow, mpHeaderRow, and mpLastRow.
Referenced by CQExperimentData::saveExperiment(), CQExperimentData::slotExperimentAdd(), and CQExperimentDataValidator::validate().
bool CExperiment::setHeaderRow | ( | const unsigned C_INT32 & | headerRow | ) |
Set the header row containing data
const | unsigned C_INT32 & headerRow |
Definition at line 1330 of file CExperiment.cpp.
References mpFirstRow, mpHeaderRow, and mpLastRow.
Referenced by CQExperimentData::saveExperiment(), CQExperimentData::slotExperimentAdd(), and CQExperimentDataValidator::validate().
bool CExperiment::setIsRowOriented | ( | const bool & | isRowOriented | ) |
Set whether the data is row oriented. This only impacts reading the data from a stream
const | bool & isRowOriented |
Definition at line 1380 of file CExperiment.cpp.
References isRowOriented(), and mpRowOriented.
bool CExperiment::setLastRow | ( | const unsigned C_INT32 & | lastRow | ) |
Set the last row containing data
const | unsigned C_INT32 & lastRow |
Definition at line 1318 of file CExperiment.cpp.
References mpFirstRow, mpHeaderRow, and mpLastRow.
Referenced by CQExperimentData::saveExperiment(), CQExperimentData::slotExperimentAdd(), and CQExperimentDataValidator::validate().
void CExperiment::setNormalizeWeightsPerExperiment | ( | bool | flag | ) |
Definition at line 1257 of file CExperiment.cpp.
References mpNormalizeWeightsPerExperiment.
Referenced by CQExperimentData::saveExperiment(), CQExperimentData::slotCheckNormalizeWeightsPerExperiment(), and CQExperimentData::slotExperimentAdd().
bool CExperiment::setNumColumns | ( | const unsigned C_INT32 & | cols | ) |
Set the number of columns in a stream
const | unsigned C_INT32 & cols |
Definition at line 1341 of file CExperiment.cpp.
References mpNumColumns.
Referenced by CQExperimentData::slotExperimentAdd(), and CQExperimentData::slotSeparator().
bool CExperiment::setSeparator | ( | const std::string & | seperator | ) |
Set the seperator used when reading a stream
const | std::string & separator |
Definition at line 1353 of file CExperiment.cpp.
References mpSeparator.
Referenced by CQExperimentData::saveExperiment(), and CQExperimentData::slotSeparator().
bool CExperiment::setWeightMethod | ( | const WeightMethod & | weightMethod | ) |
Set the weight calculation method and resets manual adjusted weights
const | WeightMethod & weightMethod |
Definition at line 1362 of file CExperiment.cpp.
References mpObjectMap, mpWeightMethod, and CExperimentObjectMap::setScale().
Referenced by CQExperimentData::saveExperiment(), and CQExperimentData::slotWeightMethod().
Add one dataset to the extended time series. The time and the simulated dependent values are stored and the iterator is increased
Definition at line 576 of file CExperiment.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, mDataDependent, mDependentValues, mRefreshMethods, mStorageIt, CMatrix< CType >::numCols(), and time.
Referenced by CFitProblem::calculate(), and CFitProblem::calculateCrossValidation().
Calculate the sum of squares for the indexed row of the experiment. If residuals is not NULL residuals will contain the differences between the calculated and the experiment values.
const | size_t & index |
C_FLOAT64 | *& residuals (may be NULL) |
Definition at line 426 of file CExperiment.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, max, mDataDependent, mDependentValues, mMissingData, mRefreshMethods, mScale, and CMatrix< CType >::numCols().
Referenced by CFitProblem::calculate(), and CFitProblem::calculateCrossValidation().
Calculate the sum of squares for the indexed row of the experiment. On return dependentValues contains the calculated values. If residuals is not NULL residuals will contain the differences between the calculated and the experiment values.
const | size_t & index |
C_FLOAT64 | *& dependentValues (must not be NULL) |
Definition at line 511 of file CExperiment.cpp.
References CVectorCore< CType >::array(), C_FLOAT64, max, mDataDependent, mDependentValues, mMissingData, mpDataDependentCalculated, mRefreshMethods, mScale, and CMatrix< CType >::numCols().
Referenced by CFitProblem::calculate(), and CFitProblem::calculateCrossValidation().
void CExperiment::updateFittedPoints | ( | ) |
This method needs to be called whenever the Object Map is changed
Definition at line 336 of file CExperiment.cpp.
References CCopasiVector< T >::add(), CCopasiVector< T >::clear(), dependent, CExperimentObjectMap::getObjectCN(), CExperimentObjectMap::getRole(), mFittingPoints, mpObjectMap, and CCopasiParameterGroup::size().
Referenced by elevateChildren(), and CQExperimentData::saveTable().
void CExperiment::updateFittedPointValues | ( | const size_t & | index, |
bool | includeSimulation | ||
) |
This method is used for output to fill the fitted points with the values of the index data record. If index exceedds the number of data records all values are set to NaN. If includeSimulation = false the entries for the simulation results are set to NaN. (This means the simulated time series is not plotted and can be output using a different mechanism)
Definition at line 351 of file CExperiment.cpp.
References CCopasiVector< T >::begin(), C_FLOAT64, CCopasiVector< T >::end(), mDataDependent, mDataTime, mFittingPoints, mNumDataRows, mpDataDependentCalculated, mpTaskType, mScale, CMatrix< CType >::numCols(), and CCopasiTask::timeCourse.
void CExperiment::updateFittedPointValuesFromExtendedTimeSeries | ( | const size_t & | index | ) |
Fill the fitted points with values from the extended time series
Definition at line 399 of file CExperiment.cpp.
References CCopasiVector< T >::begin(), CCopasiVector< T >::end(), extendedTimeSeriesSize(), mDataDependent, mExtendedTimeSeries, mFittingPoints, and CMatrix< CType >::numCols().
bool CExperiment::updateModelWithIndependentData | ( | const size_t & | index | ) |
Update the model with the independent data of the experiment
const | size_t & index |
Definition at line 1217 of file CExperiment.cpp.
References mDataIndependent, mIndependentUpdateMethods, and CVectorCore< CType >::size().
Referenced by CFitProblem::calculate(), and CFitProblem::calculateCrossValidation().
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Comparison operator
const | CExperiment & lhs |
const | CExperiment & rhs |
Definition at line 1394 of file CExperiment.cpp.
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The column names if available after reading a file
Definition at line 610 of file CExperiment.h.
Referenced by getColumnNames(), read(), and readColumnNames().
Definition at line 673 of file CExperiment.h.
Referenced by calculateStatistics(), compile(), getObjectiveValue(), and printResult().
Definition at line 674 of file CExperiment.h.
Referenced by calculateStatistics(), compile(), getRMS(), and printResult().
Definition at line 644 of file CExperiment.h.
Referenced by compile(), getErrorSum(), initializeScalingMatrix(), printResult(), and read().
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Definition at line 675 of file CExperiment.h.
Referenced by calculateStatistics(), calculateWeights(), compile(), getColumnValidValueCount(), and read().
The relevant dependent experimental data after reading a file
Definition at line 630 of file CExperiment.h.
Referenced by calculateStatistics(), calculateWeights(), compile(), getDependentData(), getErrorMeanSD(), getErrorSum(), initializeScalingMatrix(), printResult(), read(), storeExtendedTimeSeriesData(), sumOfSquares(), sumOfSquaresStore(), updateFittedPointValues(), and updateFittedPointValuesFromExtendedTimeSeries().
The relevant independent experimental data after reading a file
Definition at line 625 of file CExperiment.h.
Referenced by compile(), getIndependentData(), read(), and updateModelWithIndependentData().
The vector of time points
Definition at line 620 of file CExperiment.h.
Referenced by getTimeData(), printResult(), read(), and updateFittedPointValues().
Definition at line 646 of file CExperiment.h.
Referenced by calculateWeights(), getDefaultScale(), and read().
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A map of all dependent data objects to dependent data columns;
Definition at line 680 of file CExperiment.h.
Referenced by compile(), getColumnValidValueCount(), getDefaultScale(), getDependentObjects(), getErrorMeanSD(), getErrorSum(), getObjectiveValue(), and getRMS().
Definition at line 648 of file CExperiment.h.
Referenced by compile(), storeExtendedTimeSeriesData(), sumOfSquares(), and sumOfSquaresStore().
Definition at line 685 of file CExperiment.h.
Referenced by CExperiment(), initExtendedTimeSeries(), and updateFittedPointValuesFromExtendedTimeSeries().
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Definition at line 691 of file CExperiment.h.
Referenced by extendedTimeSeriesSize(), and initExtendedTimeSeries().
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Definition at line 682 of file CExperiment.h.
Referenced by getFittingPoints(), updateFittedPoints(), updateFittedPointValues(), and updateFittedPointValuesFromExtendedTimeSeries().
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Definition at line 654 of file CExperiment.h.
Referenced by compile(), and getIndependentObjects().
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Definition at line 650 of file CExperiment.h.
Referenced by compile(), restoreModelIndependentData(), and updateModelWithIndependentData().
Definition at line 656 of file CExperiment.h.
Referenced by compile(), and restoreModelIndependentData().
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Definition at line 665 of file CExperiment.h.
Referenced by calculateStatistics(), compile(), getErrorMean(), and printResult().
Definition at line 642 of file CExperiment.h.
Referenced by calculateWeights(), and read().
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Definition at line 666 of file CExperiment.h.
Referenced by calculateStatistics(), compile(), and getErrorMeanSD().
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Indicates whether we have missing data
Definition at line 640 of file CExperiment.h.
Referenced by calculateWeights(), sumOfSquares(), and sumOfSquaresStore().
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Definition at line 658 of file CExperiment.h.
Referenced by calculateWeights(), getNumDataRows(), printResult(), read(), and updateFittedPointValues().
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Definition at line 667 of file CExperiment.h.
Referenced by calculateStatistics(), compile(), getObjectiveValue(), and printResult().
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The relevant dependent experimental data after reading a file
Definition at line 663 of file CExperiment.h.
Referenced by calculateStatistics(), getErrorMeanSD(), getErrorSum(), printResult(), read(), sumOfSquaresStore(), and updateFittedPointValues().
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This is realized as a CCopasiParameter type STRING
Definition at line 560 of file CExperiment.h.
Referenced by compare(), getFileName(), initializeParameter(), operator=(), read(), and setFileName().
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This is realized as a CCopasiParameter type UINT
Definition at line 565 of file CExperiment.h.
Referenced by compare(), getFirstRow(), guessColumnNumber(), initializeParameter(), operator=(), read(), setFirstRow(), setHeaderRow(), and setLastRow().
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This is realized as a CCopasiParameter type UINT
Definition at line 600 of file CExperiment.h.
Referenced by getHeaderRow(), initializeParameter(), operator=(), read(), readColumnNames(), setFirstRow(), setHeaderRow(), and setLastRow().
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This is realized as a CCopasiParameter type UINT
Definition at line 570 of file CExperiment.h.
Referenced by getLastRow(), guessColumnNumber(), initializeParameter(), operator=(), read(), setFirstRow(), setHeaderRow(), and setLastRow().
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Indicates whether the weights of this experiment should be normalized to 1
Definition at line 580 of file CExperiment.h.
Referenced by calculateWeights(), getNormalizeWeightsPerExperiment(), initializeParameter(), operator=(), and setNormalizeWeightsPerExperiment().
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This is realized as a CCopasiParameter type UINT
Definition at line 605 of file CExperiment.h.
Referenced by compile(), getNumColumns(), initializeParameter(), operator=(), read(), readColumnNames(), and setNumColumns().
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This is realized as a CCopasiParameter type GROUP
Definition at line 615 of file CExperiment.h.
Referenced by compile(), elevateChildren(), fixBuild55(), getObjectMap(), printResult(), read(), setWeightMethod(), and updateFittedPoints().
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This is realized as a CCopasiParameter type BOOL
Definition at line 595 of file CExperiment.h.
Referenced by initializeParameter(), isRowOriented(), operator=(), and setIsRowOriented().
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This is realized as a CCopasiParameter type STRING
Definition at line 585 of file CExperiment.h.
Referenced by getSeparator(), guessColumnNumber(), initializeParameter(), operator=(), read(), readColumnNames(), and setSeparator().
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This is realized as a CCopasiParameter type UINT
Definition at line 575 of file CExperiment.h.
Referenced by calculateStatistics(), compile(), getExperimentType(), initializeParameter(), operator=(), printResult(), read(), setExperimentType(), and updateFittedPointValues().
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This is realized as a CCopasiParameter type UINT
Definition at line 590 of file CExperiment.h.
Referenced by calculateWeights(), elevateChildren(), getWeightMethod(), initializeParameter(), initializeScalingMatrix(), operator=(), and setWeightMethod().
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Definition at line 652 of file CExperiment.h.
Referenced by compile(), storeExtendedTimeSeriesData(), sumOfSquares(), and sumOfSquaresStore().
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Definition at line 668 of file CExperiment.h.
Referenced by calculateStatistics(), compile(), getRMS(), and printResult().
Definition at line 670 of file CExperiment.h.
Referenced by calculateStatistics(), compile(), and printResult().
Definition at line 671 of file CExperiment.h.
Referenced by calculateStatistics(), compile(), and printResult().
The individual scale for each residual
Definition at line 635 of file CExperiment.h.
Referenced by calculateStatistics(), getErrorMeanSD(), initializeScalingMatrix(), printResult(), sumOfSquares(), sumOfSquaresStore(), and updateFittedPointValues().
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Definition at line 688 of file CExperiment.h.
Referenced by CExperiment(), initExtendedTimeSeries(), and storeExtendedTimeSeriesData().
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String literals for the GUI to display type names of columns known to COPASI.
Definition at line 79 of file CExperiment.h.
Referenced by CQExperimentData::init(), CQExperimentData::loadTable(), CQExperimentData::saveTable(), and CQExperimentData::slotTypeChanged().
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String literals for the GUI to display weight method known to COPASI.
Definition at line 101 of file CExperiment.h.
Referenced by CQExperimentData::init().
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XML type names of weight methods known to COPASI.
Definition at line 106 of file CExperiment.h.
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XML type names of tasks known to COPASI.
Definition at line 84 of file CExperiment.h.