COPASI API
4.16.103
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#include <CCopasiMethod.h>
Public Member Functions | |
CCopasiMethod (const CCopasiMethod &src, const CCopasiContainer *pParent=NULL) | |
const CCopasiMethod::SubType & | getSubType () const |
const CCopasiTask::Type & | getType () const |
virtual bool | isValidProblem (const CCopasiProblem *pProblem) |
virtual void | load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH) |
virtual void | print (std::ostream *ostream) const |
virtual void | printResult (std::ostream *ostream) const |
virtual bool | setCallBack (CProcessReport *pCallBack) |
virtual | ~CCopasiMethod () |
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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 () |
virtual bool | elevateChildren () |
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) |
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 Attributes | |
static const std::string | SubTypeName [] |
static const char * | XMLSubType [] |
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static const std::string | TypeName [] |
static const char * | XMLType [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
Protected Member Functions | |
CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL) | |
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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 | |
CProcessReport * | mpCallBack |
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std::string | mKey |
CCopasiObject * | mpValueReference |
size_t | mSize |
Value | mValue |
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objectMap | mObjects |
Private Member Functions | |
CCopasiMethod () | |
Private Attributes | |
CCopasiMethod::SubType | mSubType |
CCopasiTask::Type | mType |
Friends | |
std::ostream & | operator<< (std::ostream &os, const CCopasiMethod &o) |
Additional Inherited Members | |
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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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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 CRenameHandler * | smpRenameHandler = NULL |
Definition at line 34 of file CCopasiMethod.h.
Enumeration of the sub types of methods known to COPASI.
Definition at line 40 of file CCopasiMethod.h.
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A pointer to the report Default constructor
Definition at line 134 of file CCopasiMethod.cpp.
References mType, CCopasiObject::setObjectName(), and SubTypeName.
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Specific constructor
const | CCopasiTask::Type & type |
const | CCopasiMethod::SubType & subType |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 142 of file CCopasiMethod.cpp.
References mSubType, CCopasiObject::setObjectName(), and SubTypeName.
CCopasiMethod::CCopasiMethod | ( | const CCopasiMethod & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CCopasiMethodr & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 152 of file CCopasiMethod.cpp.
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const CCopasiMethod::SubType & CCopasiMethod::getSubType | ( | ) | const |
Retrieve the sub type of the method
Definition at line 173 of file CCopasiMethod.cpp.
References mSubType.
Referenced by CQTaskMethodWidget::addToHistory(), CCrossSectionTask::CCrossSectionTask(), CEFMTask::CEFMTask(), CFitTask::CFitTask(), CLNATask::CLNATask(), CMCATask::CMCATask(), CMoietiesTask::CMoietiesTask(), COptTask::COptTask(), COscillationTask::COscillationTask(), CSensTask::CSensTask(), CSteadyStateTask::CSteadyStateTask(), CTrajectoryTask::CTrajectoryTask(), CTSSATask::CTSSATask(), CEFMTask::getFluxModeDescription(), CEFMTask::getReactionEquation(), CNewtonMethod::initialize(), CTSSAMethod::isValidProblem(), CQTaskMethodWidget::loadMethod(), CQSimpleSelectionTree::populateTree(), CQTaskMethodWidget::removeFromHistory(), CQTaskMethodWidget::saveMethod(), CCopasiXML::saveTaskList(), CTSSAMethod::schur(), CFitTask::setMethodType(), CMoietiesTask::setMethodType(), COscillationTask::setMethodType(), COptTask::setMethodType(), CEFMTask::setMethodType(), CTrajectoryTask::setMethodType(), CLyapTask::setMethodType(), CTSSATask::setMethodType(), CCrossSectionTask::setMethodType(), CQTaskMethodWidget::setTask(), and CCopasiXMLParser::MethodElement::start().
const CCopasiTask::Type & CCopasiMethod::getType | ( | void | ) | const |
Retrieve the type of the method
Definition at line 169 of file CCopasiMethod.cpp.
References mType.
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Check if the method is suitable for this problem
Reimplemented in CTrajectoryMethodDsaLsodar, CScanMethod, CStochMethod, CLyapWolfMethod, CTrajAdaptiveSA, CLNAMethod, CStochDirectMethod, CHybridMethodLSODA, CHybridMethodODE45, CHybridMethod, CTauLeapMethod, CTrajectoryMethod, CSteadyStateMethod, CMCAMethod, CTSSAMethod, CLyapMethod, COptMethod, CNewtonMethod, CSensMethod, COscillationMethod, CEFMMethod, CFitMethod, and CCrossSectionMethod.
Definition at line 180 of file CCopasiMethod.cpp.
References CCopasiMessage::ERROR, CCopasiMessage::EXCEPTION, CModel::getEvents(), CCopasiProblem::getModel(), CCopasiTask::lna, CCopasiTask::lyap, MCCopasiMethod, mType, CCopasiVector< T >::size(), and CCopasiTask::tssAnalysis.
Referenced by CMoietiesTask::initialize(), CLNATask::initialize(), CEFMTask::initialize(), CScanTask::initialize(), CLyapTask::initialize(), CMCATask::initialize(), CTrajectoryTask::initialize(), CTSSATask::initialize(), CSteadyStateTask::initialize(), CCrossSectionTask::initialize(), CCrossSectionMethod::isValidProblem(), CEFMMethod::isValidProblem(), COscillationMethod::isValidProblem(), CSensMethod::isValidProblem(), COptMethod::isValidProblem(), CLyapMethod::isValidProblem(), CTSSAMethod::isValidProblem(), CMCAMethod::isValidProblem(), CSteadyStateMethod::isValidProblem(), CTrajectoryMethod::isValidProblem(), CLNAMethod::isValidProblem(), CScanMethod::isValidProblem(), CFitTask::process(), CSensTask::process(), COscillationTask::process(), COptTask::process(), CLNATask::updateMatrices(), CMCATask::updateMatrices(), and CTSSATask::updateMatrices().
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Load a list of parameters
CReadConfig & | configBuffer |
CReadConfig::Mode | mode Default(CReadConfig::SEARCH) |
Reimplemented in CNewtonMethod.
Definition at line 220 of file CCopasiMethod.cpp.
References fatalError.
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This is the output method for any object. The default implementation provided with CCopasiObject uses the ostream operator<< of the object to print the object.To overide this default behaviour one needs to reimplement the virtual print function.
std::ostream | * ostream |
Reimplemented from CCopasiParameterGroup.
Definition at line 224 of file CCopasiMethod.cpp.
Referenced by operator<<(), CILDMModifiedMethod::printResult(), and CCSPMethod::printResult().
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This is the output method for any result of a method. The default implementation provided with CCopasiMethod. Does only print "Not implmented." To overide this default behaviour one needs to reimplement the virtual printResult function.
std::ostream | * ostream |
Reimplemented in CCSPMethod, CILDMMethod, and CILDMModifiedMethod.
Definition at line 245 of file CCopasiMethod.cpp.
Referenced by CTSSAProblem::printResult().
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Set the call back of the problem
CProcessReport | * pCallBack |
Definition at line 163 of file CCopasiMethod.cpp.
References mpCallBack.
Referenced by CMoietiesTask::setCallBack(), CFitTask::setCallBack(), COscillationTask::setCallBack(), CEFMTask::setCallBack(), and COptTask::setCallBack().
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Output stream operator
ostream | & os |
const | CCopasiMethod & A |
Definition at line 227 of file CCopasiMethod.cpp.
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a pointer to the callback
Definition at line 118 of file CCopasiMethod.h.
Referenced by CSSAMethod::calculate(), CEFMAlgorithm::calculate(), CBitPatternMethod::calculate(), CBitPatternTreeMethod::calculate(), CEFMAlgorithm::calculateFluxModes(), CEFMAlgorithm::calculateNextTableau(), CBitPatternTreeMethod::combine(), CBitPatternMethod::combine(), CSensMethod::do_target_calculation(), CNewtonMethod::doIntegration(), CSSAMethod::initialize(), COptMethodEP::initialize(), COptMethodDE::initialize(), COptMethodSRES::initialize(), COptMethodPS::initialize(), COptMethodGA::initialize(), COptMethodGASR::initialize(), COptMethodHookeJeeves::initialize(), COptMethodCoranaWalk::initialize(), COptMethodSA::initialize(), COptMethodLevenbergMarquardt::initialize(), COptMethodNelderMead::initialize(), CEFMAlgorithm::initialize(), COptMethodSS::initialize(), CBitPatternMethod::initialize(), CBitPatternTreeMethod::initialize(), COptMethodDE::optimise(), COptMethodSRES::optimise(), COptMethodSS::optimise(), COptMethodGA::optimise(), COptMethodPS::optimise(), COptMethodHookeJeeves::optimise(), COptMethodGASR::optimise(), COptMethodSA::optimise(), COptMethodNelderMead::optimise(), COptMethodCoranaWalk::optimise(), COptMethodLevenbergMarquardt::optimise(), COptMethodEP::optimise(), CMoietiesMethod::process(), CSensMethod::process(), CSteadyStateMethod::process(), CNewtonMethod::processInternal(), CNewtonMethod::processNewton(), and setCallBack().
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The type of the method
Definition at line 112 of file CCopasiMethod.h.
Referenced by CCopasiMethod(), and getSubType().
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The type of the method
Definition at line 107 of file CCopasiMethod.h.
Referenced by CCopasiMethod(), getType(), and isValidProblem().
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String literals for the GUI to display sub type names of methods known to COPASI.
CCopasiMethod class. This class is used to describe a task in COPASI. This class is intended to be used as the parent class for all methods whithin COPASI.
Created for Copasi by Stefan Hoops 2003
Definition at line 95 of file CCopasiMethod.h.
Referenced by CCopasiMethod(), CQTaskMethodWidget::changeMethod(), CQTaskMethodWidget::loadMethod(), and CQTaskMethodWidget::setValidMethods().
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XML sub type names of methods known to COPASI.
Definition at line 100 of file CCopasiMethod.h.
Referenced by CCopasiXML::saveTaskList(), and CCopasiXMLParser::MethodElement::start().