COPASI API
4.16.103
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#include <CFitTask.h>
Public Member Functions | |
CFitTask (const CCopasiTask::Type &type=CCopasiTask::parameterFitting, const CCopasiContainer *pParent=NULL) | |
CFitTask (const CFitTask &src, const CCopasiContainer *pParent=NULL) | |
void | cleanup () |
virtual CCopasiMethod * | createMethod (const int &type) const |
void | fixBuild55 () |
virtual bool | initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream) |
virtual bool | process (const bool &useInitialValues) |
virtual bool | setCallBack (CProcessReport *pCallBack) |
virtual bool | setMethodType (const int &type) |
~CFitTask () | |
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void | cleanup () |
COptTask (const CCopasiTask::Type &type=CCopasiTask::optimization, const CCopasiContainer *pParent=NULL) | |
COptTask (const COptTask &src, const CCopasiContainer *pParent=NULL) | |
~COptTask () | |
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CCopasiTask (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const std::string &type="Task") | |
CCopasiTask (const Type &taskType, const CCopasiContainer *pParent=NULL, const std::string &type="Task") | |
CCopasiTask (const CCopasiTask &src, const CCopasiContainer *pParent=NULL) | |
void | cleanup () |
CProcessReport * | getCallBack () const |
const CDescription & | getDescription () const |
virtual const std::string & | getKey () const |
CCopasiMethod * | getMethod () |
const CCopasiMethod * | getMethod () const |
COutputHandler * | getOutputHandler () const |
const OutputFlag & | getOutputMode () const |
CCopasiProblem * | getProblem () |
const CCopasiProblem * | getProblem () const |
CReport & | getReport () |
const CResult & | getResult () const |
CCopasiParameterGroup * | getSliders () |
Type | getType () const |
const bool & | isScheduled () const |
const bool & | isUpdateModel () const |
virtual void | output (const COutputInterface::Activity &activity) |
virtual bool | restore () |
virtual void | separate (const COutputInterface::Activity &activity) |
void | setScheduled (const bool &scheduled) |
void | setType (const Type &type) |
void | setUpdateModel (const bool &updateModel) |
virtual bool | updateMatrices () |
virtual | ~CCopasiTask () |
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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 CObjectInterface * | getObject (const CCopasiObjectName &cn) 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 CCopasiObjectName | getCN () const |
virtual const DataObjectSet & | getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const |
CCopasiContainer * | getObjectAncestor (const std::string &type) const |
CCopasiDataModel * | getObjectDataModel () |
const CCopasiDataModel * | getObjectDataModel () const |
virtual std::string | getObjectDisplayName (bool regular=true, bool richtext=false) 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 |
virtual void * | getValuePointer () 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 |
virtual void | print (std::ostream *ostream) 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 () |
Additional Inherited Members | |
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enum | eOutputFlagBase { INITIALIZE = 0x01, STREAM = 0x02, FINISH = 0x04, REPORT = 0x10, PLOT = 0x20, TIME_SERIES = 0x40 } |
enum | OutputFlag { NO_OUTPUT = 0, OUTPUT_BEFORE = INITIALIZE, OUTPUT_AFTER = FINISH, OUTPUT = REPORT | PLOT | STREAM, OUTPUT_SE = REPORT | PLOT | INITIALIZE | STREAM | FINISH, OUTPUT_UI = REPORT | PLOT | TIME_SERIES | INITIALIZE | STREAM | FINISH, ONLY_TIME_SERIES = TIME_SERIES | INITIALIZE | STREAM | FINISH } |
enum | Type { steadyState = 0, timeCourse, scan, fluxMode, optimization, parameterFitting, mca, lyap, tssAnalysis, sens, moieties, crosssection, lna, unset } |
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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 | isValidMethod (const unsigned int &method, const unsigned int *validMethods) |
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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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std::string | Error |
std::string | Warning |
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static const unsigned int | ValidMethods [] |
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static const std::string | TypeName [] |
static const unsigned int | ValidMethods [] |
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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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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CDescription | mDescription |
OutputFlag | mDoOutput |
std::string | mKey |
unsigned C_INT32 | mOutputCounter |
CProcessReport * | mpCallBack |
CState * | mpInitialState |
CCopasiMethod * | mpMethod |
COutputHandler * | mpOutputHandler |
CCopasiProblem * | mpProblem |
CCopasiParameterGroup * | mpSliders |
CReport | mReport |
CResult | mResult |
bool | mScheduled |
Type | mType |
bool | mUpdateModel |
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objectMap | mObjects |
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static CRenameHandler * | smpRenameHandler = NULL |
CFitTask class.
This class implements a parameter estimation task which is comprised of a of a problem and a method.
Definition at line 28 of file CFitTask.h.
CFitTask::CFitTask | ( | const CCopasiTask::Type & | type = CCopasiTask::parameterFitting , |
const CCopasiContainer * | pParent = NULL |
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default constructor
const | CCopasiTask::Type & type (default: parameterFitting) |
const | CCopasiContainer * pParent (default: NULL) |
CFitTask class.
This class implements a parameter estimation task which is comprised of a of a problem and a method.
Definition at line 30 of file CFitTask.cpp.
References CCopasiContainer::add(), CFitMethod::createMethod(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, and pdelete.
CFitTask::CFitTask | ( | const CFitTask & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CFitTask & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 43 of file CFitTask.cpp.
References CCopasiContainer::add(), CFitMethod::createMethod(), CCopasiMethod::getSubType(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, and pdelete.
CFitTask::~CFitTask | ( | ) |
void CFitTask::cleanup | ( | ) |
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virtual |
Create a method of the specified type to solve the task. It is the duty of the caller to release the CCopasiMethod.
const | CCopasiMethod::SubType & type |
Reimplemented from COptTask.
Definition at line 122 of file CFitTask.cpp.
References CFitMethod::createMethod().
Referenced by setMethodType().
void CFitTask::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 129 of file CFitTask.cpp.
References CFitProblem::fixBuild55(), and CCopasiTask::mpProblem.
Referenced by CCopasiXML::fixBuild55().
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Initialize the task. If an ostream is given this ostream is used instead of the target specified in the report. This allows nested tasks to share the same output device.
const | OutputFlag & of |
COutputHandler | * pOutputHandler |
std::ostream | * pOstream (default: NULL) |
Reimplemented from COptTask.
Definition at line 72 of file CFitTask.cpp.
References COptTask::initialize().
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virtual |
Process the task with or without initializing to the initial state.
const | bool & useInitialValues |
Reimplemented from COptTask.
Definition at line 79 of file CFitTask.cpp.
References COutputInterface::AFTER, COutputInterface::BEFORE, CFitProblem::calculateStatistics(), CCopasiMethod::isValidProblem(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, COptMethod::optimise(), CCopasiTask::output(), COptProblem::randomizeStartValues(), COptProblem::rememberStartValues(), and CFitProblem::updateInitialState().
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virtual |
Set the call back of the task
CProcessReport | * pCallBack |
Reimplemented from COptTask.
Definition at line 61 of file CFitTask.cpp.
References CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiProblem::setCallBack(), CCopasiMethod::setCallBack(), and CCopasiTask::setCallBack().
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Set the method type applied to solve the task
const | CCopasiMethod::SubType & type |
Reimplemented from COptTask.
Definition at line 107 of file CFitTask.cpp.
References CCopasiContainer::add(), createMethod(), CCopasiMethod::getSubType(), CCopasiTask::mpMethod, and pdelete.