COPASI API
4.16.103
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#include <CFitItem.h>
Public Member Functions | |
void | calculateConstraintViolation () |
CFitConstraint (const CCopasiContainer *pParent, const std::string &name="FitItem") | |
CFitConstraint (const CFitConstraint &src, const CCopasiContainer *pParent=NULL) | |
CFitConstraint (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL) | |
virtual C_INT32 | checkConstraint () const |
virtual C_FLOAT64 | getConstraintViolation () const |
void | resetConstraintViolation () |
virtual | ~CFitConstraint () |
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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 bool | compile (const std::vector< CCopasiContainer * > listOfContainer=CCopasiContainer::EmptyList) |
virtual bool | elevateChildren () |
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 () |
Protected Member Functions | |
CFitConstraint () | |
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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) | |
Private Attributes | |
C_INT32 | mCheckConstraint |
C_FLOAT64 | mConstraintViolation |
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 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) |
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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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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 |
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static CRandom * | mpRandom = NULL |
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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 243 of file CFitItem.h.
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Default constructor
CFitConstraint::CFitConstraint | ( | const CCopasiContainer * | pParent, |
const std::string & | name = "FitItem" |
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Specific constructor
const | CCopasiContainer * pParent |
const | std::string & name (default: FitItem) |
Definition at line 295 of file CFitItem.cpp.
CFitConstraint::CFitConstraint | ( | const CFitConstraint & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CFitItem & src |
const | CCopasiContainer * pParent (default: src data model) |
Definition at line 302 of file CFitItem.cpp.
CFitConstraint::CFitConstraint | ( | 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 309 of file CFitItem.cpp.
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void CFitConstraint::calculateConstraintViolation | ( | ) |
Calculate and save the constraint violation
Definition at line 324 of file CFitItem.cpp.
References mCheckConstraint, mConstraintViolation, COptItem::mpLowerBound, COptItem::mpObjectValue, and COptItem::mpUpperBound.
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This functions check whether the current value is within the limits of the constraint. The result depends on last performed calculateConstraintViolation, i.e., it may not be trusted.
Reimplemented from CFitItem.
Definition at line 345 of file CFitItem.cpp.
References mCheckConstraint.
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virtual |
Retrieve the magnitude of the constraint violation This is always a positive number or 0. It is the sum of all constraint violation for a single function evaluation.
Reimplemented from CFitItem.
Definition at line 348 of file CFitItem.cpp.
References mConstraintViolation.
void CFitConstraint::resetConstraintViolation | ( | ) |
Reset the constraint violation
Definition at line 318 of file CFitItem.cpp.
References mCheckConstraint, and mConstraintViolation.
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private |
The value that will be returned by checkConstraint
Definition at line 313 of file CFitItem.h.
Referenced by calculateConstraintViolation(), checkConstraint(), and resetConstraintViolation().
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private |
The value that will be returned by getConstraintViolation
Definition at line 318 of file CFitItem.h.
Referenced by calculateConstraintViolation(), getConstraintViolation(), and resetConstraintViolation().