COPASI API
4.16.103
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#include <CFitItem.h>
Public Member Functions | |
bool | addCrossValidation (const std::string &key) |
bool | addExperiment (const std::string &key) |
CFitItem (const CCopasiContainer *pParent, const std::string &name="FitItem") | |
CFitItem (const CFitItem &src, const CCopasiContainer *pParent=NULL) | |
CFitItem (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL) | |
virtual C_INT32 | checkConstraint () const |
virtual bool | compile (const std::vector< CCopasiContainer * > listOfContainer=CCopasiContainer::EmptyList) |
virtual bool | elevateChildren () |
virtual C_FLOAT64 | getConstraintViolation () const |
const std::string & | getCrossValidation (const size_t &index) const |
size_t | getCrossValidationCount () const |
std::string | getCrossValidations () const |
const std::string & | getExperiment (const size_t &index) const |
size_t | getExperimentCount () const |
std::string | getExperiments () const |
const C_FLOAT64 & | getLocalValue () const |
virtual const C_FLOAT64 * | getObjectValue () const |
virtual UpdateMethod * | getUpdateMethod () const |
virtual bool | isValid () const |
bool | removeCrossValidation (const size_t &index) |
bool | removeExperiment (const size_t &index) |
void | setLocalValue (const C_FLOAT64 &value) |
bool | updateBounds (std::vector< COptItem * >::iterator it) |
virtual | ~CFitItem () |
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C_INT32 | checkConstraint (const C_FLOAT64 &value) const |
bool | checkLowerBound (const C_FLOAT64 &value) const |
bool | checkUpperBound (const C_FLOAT64 &value) const |
COptItem (const CCopasiContainer *pParent, const std::string &name="OptimizationItem") | |
COptItem (const COptItem &src, const CCopasiContainer *pParent=NULL) | |
COptItem (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL) | |
const C_FLOAT64 & | getLastStartValue () const |
const std::string | getLowerBound () const |
const C_FLOAT64 * | getLowerBoundValue () const |
const CCopasiObject * | getObject () const |
const CCopasiObjectName | getObjectCN () const |
std::string | getObjectDisplayName () const |
C_FLOAT64 | getRandomValue (CRandom *pRandom=NULL) |
const C_FLOAT64 & | getStartValue () const |
const std::string | getUpperBound () const |
const C_FLOAT64 * | getUpperBoundValue () const |
void | rememberStartValue () |
bool | setLowerBound (const CCopasiObjectName &lowerBound) |
bool | setObjectCN (const CCopasiObjectName &objectCN) |
bool | setStartValue (const C_FLOAT64 &value) |
bool | setUpperBound (const CCopasiObjectName &upperBound) |
virtual | ~COptItem () |
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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 | isValid (CCopasiParameterGroup &group) |
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static bool | isValid (CCopasiParameterGroup &group) |
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static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
Protected Member Functions | |
CFitItem () | |
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COptItem () | |
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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) | |
Protected Attributes | |
C_FLOAT64 | mLocalValue |
CCopasiParameterGroup * | mpGrpAffectedCrossValidations |
CCopasiParameterGroup * | mpGrpAffectedExperiments |
UpdateMethod * | mpLocalMethod |
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C_FLOAT64 | mLastStartValue |
C_FLOAT64 | mLowerBound |
const C_FLOAT64 * | mpLowerBound |
const CCopasiObject * | mpLowerObject |
UpdateMethod * | mpMethod |
const CCopasiObject * | mpObject |
const C_FLOAT64 * | mpObjectValue |
std::string * | mpParmLowerBound |
std::string * | mpParmObjectCN |
C_FLOAT64 * | mpParmStartValue |
std::string * | mpParmUpperBound |
const C_FLOAT64 * | mpUpperBound |
const CCopasiObject * | mpUpperObject |
C_FLOAT64 | mUpperBound |
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std::string | mKey |
CCopasiObject * | mpValueReference |
size_t | mSize |
Value | mValue |
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objectMap | mObjects |
Private Member Functions | |
void | initializeParameter () |
Friends | |
class | CFitProblem |
std::ostream & | operator<< (std::ostream &os, const CFitItem &o) |
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 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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static CRandom * | mpRandom = NULL |
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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 22 of file CFitItem.h.
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Default constructor
CFitItem::CFitItem | ( | const CCopasiContainer * | pParent, |
const std::string & | name = "FitItem" |
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Specific constructor
const | CCopasiContainer * pParent (default: NULL) |
const | std::string & name (default: FitItem) |
Definition at line 27 of file CFitItem.cpp.
References initializeParameter().
CFitItem::CFitItem | ( | const CFitItem & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CFitItem & src |
const | CCopasiContainer * pParent (default: src data model) |
Definition at line 36 of file CFitItem.cpp.
References initializeParameter().
CFitItem::CFitItem | ( | 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 45 of file CFitItem.cpp.
References initializeParameter().
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bool CFitItem::addCrossValidation | ( | const std::string & | key | ) |
Add an experiment to the list of affected cross validations.
const | std::string & key |
Definition at line 234 of file CFitItem.cpp.
References CCopasiParameterGroup::addParameter(), CCopasiParameterGroup::getValue(), CCopasiParameter::KEY, mpGrpAffectedCrossValidations, CCopasiParameter::Value::pKEY, and CCopasiParameterGroup::size().
Referenced by CQFittingItemWidget::save().
bool CFitItem::addExperiment | ( | const std::string & | key | ) |
Add an experiment to the list of affected experiments.
const | std::string & key |
Definition at line 184 of file CFitItem.cpp.
References CCopasiParameterGroup::addParameter(), CCopasiParameterGroup::getValue(), CCopasiParameter::KEY, mpGrpAffectedExperiments, CCopasiParameter::Value::pKEY, and CCopasiParameterGroup::size().
Referenced by CQFittingItemWidget::save(), and CQFittingItemWidget::slotDuplicatePerExperiment().
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This functions check whether the current value is within the limits of the optimization item.
Reimplemented from COptItem.
Reimplemented in CFitConstraint.
Definition at line 111 of file CFitItem.cpp.
References mLocalValue, COptItem::mpLowerBound, and COptItem::mpUpperBound.
Referenced by getConstraintViolation().
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Compile the optimization item. This function must be called before any of the check functions are called.
const | std::vector< CCopasiContainer * > listOfContainer |
Reimplemented from COptItem.
Definition at line 102 of file CFitItem.cpp.
References COptItem::compile(), mLocalValue, and COptItem::mpParmStartValue.
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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 66 of file CFitItem.cpp.
References CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), mpGrpAffectedCrossValidations, mpGrpAffectedExperiments, CCopasiParameter::Value::pDOUBLE, CCopasiParameterGroup::removeParameter(), and COptItem::setStartValue().
Referenced by initializeParameter().
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Retrieve the magnitude of the constraint violation This is always a positive number
Reimplemented from COptItem.
Reimplemented in CFitConstraint.
Definition at line 120 of file CFitItem.cpp.
References checkConstraint(), mLocalValue, COptItem::mpLowerBound, and COptItem::mpUpperBound.
const std::string & CFitItem::getCrossValidation | ( | const size_t & | index | ) | const |
Retreive the key of the indexed experiment.
const | size_t & index |
Definition at line 244 of file CFitItem.cpp.
References CCopasiParameterGroup::getValue(), mpGrpAffectedCrossValidations, CCopasiParameter::Value::pKEY, and CCopasiParameterGroup::size().
Referenced by CFitProblem::initialize(), CQFittingItemWidget::load(), operator<<(), and CQFittingItemWidget::save().
size_t CFitItem::getCrossValidationCount | ( | ) | const |
Retrieve the number of cross validations
Definition at line 257 of file CFitItem.cpp.
References mpGrpAffectedCrossValidations, and CCopasiParameterGroup::size().
Referenced by CFitProblem::initialize(), CQFittingItemWidget::load(), and CQFittingItemWidget::save().
std::string CFitItem::getCrossValidations | ( | ) | const |
Retrieve a string listing all cross validations the item applies to
Definition at line 260 of file CFitItem.cpp.
References CKeyFactory::get(), CCopasiRootContainer::getKeyFactory(), CCopasiObject::getObjectName(), CCopasiParameterGroup::getValue(), mpGrpAffectedCrossValidations, CCopasiParameter::Value::pKEY, and CCopasiParameterGroup::size().
const std::string & CFitItem::getExperiment | ( | const size_t & | index | ) | const |
Retreive the key of the indexed experiment.
const | size_t & index |
Definition at line 194 of file CFitItem.cpp.
References CCopasiParameterGroup::getValue(), mpGrpAffectedExperiments, CCopasiParameter::Value::pKEY, and CCopasiParameterGroup::size().
Referenced by CFitProblem::initialize(), CQFittingItemWidget::load(), operator<<(), CFitProblem::printResult(), and CQFittingItemWidget::save().
size_t CFitItem::getExperimentCount | ( | ) | const |
Retrieve the number of experiments
Definition at line 207 of file CFitItem.cpp.
References mpGrpAffectedExperiments, and CCopasiParameterGroup::size().
Referenced by CFitProblem::initialize(), CQFittingItemWidget::load(), CFitProblem::printResult(), and CQFittingItemWidget::save().
std::string CFitItem::getExperiments | ( | ) | const |
Retrieve a string listing all experiments the item applies to
Definition at line 210 of file CFitItem.cpp.
References CKeyFactory::get(), CCopasiRootContainer::getKeyFactory(), CCopasiObject::getObjectName(), CCopasiParameterGroup::getValue(), mpGrpAffectedExperiments, CCopasiParameter::Value::pKEY, and CCopasiParameterGroup::size().
Referenced by CFitProblem::initialize().
const C_FLOAT64 & CFitItem::getLocalValue | ( | ) | const |
Retreive the local value.
Definition at line 175 of file CFitItem.cpp.
References mLocalValue.
Referenced by CFitProblem::calculate(), and updateBounds().
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Retrieve the value of the optimization object.
Reimplemented from COptItem.
Definition at line 178 of file CFitItem.cpp.
References mLocalValue.
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Retrieve the update method
Reimplemented from COptItem.
Definition at line 181 of file CFitItem.cpp.
References mpLocalMethod.
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Allocates all group parameters and assures that they are properly initialized.
Definition at line 57 of file CFitItem.cpp.
References CCopasiParameterGroup::assertGroup(), elevateChildren(), mpGrpAffectedCrossValidations, and mpGrpAffectedExperiments.
Referenced by CFitItem().
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Check the validity of the optimization item.
Reimplemented from COptItem.
Definition at line 92 of file CFitItem.cpp.
References COptItem::isValid().
Referenced by isValid().
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Check whether the group describes a valid optimization item.
CCopasiParameterGroup | & group |
Definition at line 95 of file CFitItem.cpp.
References isValid().
bool CFitItem::removeCrossValidation | ( | const size_t & | index | ) |
Remove the indexed experiment from the affected cross validations
const | size_t & index |
Definition at line 254 of file CFitItem.cpp.
References mpGrpAffectedCrossValidations, and CCopasiParameterGroup::removeParameter().
Referenced by CQFittingItemWidget::save(), and CQFittingItemWidget::slotCrossValidationChanged().
bool CFitItem::removeExperiment | ( | const size_t & | index | ) |
Remove the indexed experiment from the affected experiments
const | size_t & index |
Definition at line 204 of file CFitItem.cpp.
References mpGrpAffectedExperiments, and CCopasiParameterGroup::removeParameter().
Referenced by CQFittingItemWidget::save(), CQFittingItemWidget::slotDuplicatePerExperiment(), and CQFittingItemWidget::slotExperimentChanged().
Set the local value.
const | C_FLOAT64 & value |
Definition at line 169 of file CFitItem.cpp.
References mLocalValue.
bool CFitItem::updateBounds | ( | std::vector< COptItem * >::iterator | it | ) |
Update bounds
std::vector<COptItem | * >::iterator it |
Definition at line 279 of file CFitItem.cpp.
References getLocalValue(), COptItem::getLowerBound(), COptItem::getUpperBound(), COptItem::mpLowerBound, COptItem::mpLowerObject, COptItem::mpUpperBound, and COptItem::mpUpperObject.
Referenced by CFitProblem::initialize().
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Definition at line 24 of file CFitItem.h.
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Output stream operator
ostream | & os |
const | CFitItem & A |
Definition at line 136 of file CFitItem.cpp.
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The value for local items, which affect the experiments in the list.
Definition at line 235 of file CFitItem.h.
Referenced by checkConstraint(), compile(), getConstraintViolation(), getLocalValue(), getObjectValue(), and setLocalValue().
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A pointer to the value of the CCopasiParameterGroup holding the list of Affected Validation Experiments
Definition at line 230 of file CFitItem.h.
Referenced by addCrossValidation(), elevateChildren(), getCrossValidation(), getCrossValidationCount(), getCrossValidations(), initializeParameter(), operator<<(), and removeCrossValidation().
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A pointer to the value of the CCopasiParameterGroup holding the list of AffectedExperiments
Definition at line 224 of file CFitItem.h.
Referenced by addExperiment(), elevateChildren(), getExperiment(), getExperimentCount(), getExperiments(), initializeParameter(), operator<<(), and removeExperiment().
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A pointer to the local update method
Definition at line 240 of file CFitItem.h.
Referenced by getUpdateMethod(), and ~CFitItem().