COPASI API
4.16.103
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#include <CCopasiProblem.h>
Public Member Functions | |
CCopasiProblem (const CCopasiProblem &src, const CCopasiContainer *pParent=NULL) | |
CModel * | getModel () const |
const CCopasiTask::Type & | getType () const |
virtual bool | initialize () |
virtual void | print (std::ostream *ostream) const |
virtual void | printResult (std::ostream *ostream) const |
virtual bool | restore (const bool &updateModel) |
virtual bool | setCallBack (CProcessReport *pCallBack) |
virtual bool | setModel (CModel *pModel) |
virtual | ~CCopasiProblem () |
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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 () |
Protected Member Functions | |
CCopasiProblem (const CCopasiTask::Type &type, 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 |
CModel * | mpModel |
CReport * | mpReport |
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std::string | mKey |
CCopasiObject * | mpValueReference |
size_t | mSize |
Value | mValue |
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objectMap | mObjects |
Private Member Functions | |
CCopasiProblem () | |
Private Attributes | |
CCopasiTask::Type | mType |
Friends | |
std::ostream & | operator<< (std::ostream &os, const CCopasiProblem &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 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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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 40 of file CCopasiProblem.h.
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Default constructor
CCopasiProblem class. This class is used to describe a task in COPASI. This class is intended to be used as the parent class for all tasks whithin COPASI.
Created for Copasi by Stefan Hoops 2003
Definition at line 34 of file CCopasiProblem.cpp.
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Specific constructor
const | CCopasiTask::Type & type |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 42 of file CCopasiProblem.cpp.
CCopasiProblem::CCopasiProblem | ( | const CCopasiProblem & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CCopasiProblemr & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 51 of file CCopasiProblem.cpp.
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CModel * CCopasiProblem::getModel | ( | ) | const |
Retrieve the model of the problem
Definition at line 70 of file CCopasiProblem.cpp.
References mpModel.
Referenced by CLyapWolfMethod::calculate(), COutputAssistant::createDefaultOutput(), CCrossSectionTask::createEvent(), CQTSSAResultSubWidget::displayResult(), CSensMethod::do_target_calculation(), CLyapWolfMethod::evalF(), CHybridMethodLSODA::evalF(), CCrossSectionTask::eventCallBack(), CCrossSectionTask::finish(), CEFMTask::getInternalSpecies(), CEFMTask::getNetReaction(), CEFMTask::getReactionEquation(), CQTSSAResultSubWidget::init(), CScanMethod::init(), CSSAMethod::initialize(), CLNATask::initialize(), CSensMethod::initialize(), CEFMAlgorithm::initialize(), CMCATask::initialize(), CBitPatternMethod::initialize(), CBitPatternTreeMethod::initialize(), CTrajectoryTask::initialize(), CTSSATask::initialize(), CNewtonMethod::initialize(), CSteadyStateTask::initialize(), CSteadyStateMethod::initialize(), CCrossSectionTask::initialize(), CCopasiTask::initialize(), CHybridMethodODE45::initMethod(), CHybridMethodLSODA::initMethod(), CHybridMethodLSODA::integrateDeterministicPart(), CTSSAMethod::integrationMethodStart(), CSteadyStateMethod::isEquilibrium(), CEFMMethod::isValidProblem(), CNewtonMethod::isValidProblem(), CLyapMethod::isValidProblem(), CTSSAMethod::isValidProblem(), CMCAMethod::isValidProblem(), CTauLeapMethod::isValidProblem(), CHybridMethod::isValidProblem(), CHybridMethodODE45::isValidProblem(), CCopasiMethod::isValidProblem(), CHybridMethodLSODA::isValidProblem(), CStochDirectMethod::isValidProblem(), CLNAMethod::isValidProblem(), CTrajAdaptiveSA::isValidProblem(), CStochMethod::isValidProblem(), CTrajectoryMethodDsaLsodar::isValidProblem(), operator<<(), CHybridMethodLSODA::partitionSystem(), CLNATask::printResult(), CMCATask::printResult(), CMoietiesMethod::process(), CSensTask::process(), CLNATask::process(), CScanTask::process(), CLyapTask::process(), CMCATask::process(), CTrajectoryTask::process(), CTSSATask::process(), CSteadyStateTask::process(), CCrossSectionTask::process(), CTrajectoryTask::processStart(), CTSSATask::processStart(), CCrossSectionTask::processStart(), CTrajectoryTask::processStep(), CTSSATask::processStep(), CCrossSectionTask::processStep(), CCrossSectionTask::removeEvent(), CMoietiesTask::restore(), CLyapTask::restore(), CTrajectoryTask::restore(), CTSSATask::restore(), CSteadyStateTask::restore(), CCrossSectionTask::restore(), CCopasiTask::restore(), CSteadyStateTask::setInitialState(), CQEFMSpeciesDM::setTask(), CQSteadyStateResult::slotUpdateModel(), CTauLeapMethod::start(), CHybridMethod::start(), CHybridMethodLSODA::start(), CStochDirectMethod::start(), CHybridMethodODE45::start(), CLyapWolfMethod::start(), CTrajAdaptiveSA::start(), CStochMethod::start(), CLsodaMethod::start(), CTauLeapMethod::step(), CHybridMethod::step(), CHybridMethodLSODA::step(), CStochDirectMethod::step(), CTrajAdaptiveSA::step(), CStochMethod::step(), CSensTask::updateMatrices(), CLNATask::updateMatrices(), CMCATask::updateMatrices(), CTSSATask::updateMatrices(), and CSteadyStateTask::updateMatrices().
const CCopasiTask::Type & CCopasiProblem::getType | ( | void | ) | const |
Retrieve the type of the problem
Definition at line 62 of file CCopasiProblem.cpp.
References mType.
Referenced by COutputAssistant::getDefaultPlotIndex(), COutputAssistant::getDefaultReportIndex(), and COptProblem::setSubtaskType().
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Sets the initial value (in case this applies to the specific problem) Do all neccessary initialization so that calls to caluclate will be successful. This is called once from CCopasiTask::process()
Reimplemented in COptProblem, CEFMProblem, CFitProblem, CSteadyStateProblem, and COscillationProblem.
Definition at line 80 of file CCopasiProblem.cpp.
Referenced by CEFMProblem::initialize().
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calculate function for optimization
std::ostream | * ostream |
Reimplemented from CCopasiParameterGroup.
Reimplemented in COptProblem, CSensProblem, CCrossSectionProblem, CLNAProblem, CMCAProblem, CFitProblem, and COscillationProblem.
Definition at line 84 of file CCopasiProblem.cpp.
Referenced by operator<<(), and CTSSAProblem::printResult().
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This is the output method for any rsult of a problem. The default implementation provided with CCopasiProblem. Does only print "Not implmented." To overide this default behaviour one needs to reimplement the virtual printResult function.
std::ostream | * ostream |
Reimplemented in COptProblem, CTSSAProblem, CSensProblem, CLyapProblem, CFitProblem, CEFMProblem, CLNAProblem, CMCAProblem, COscillationProblem, and CMoietiesProblem.
Definition at line 87 of file CCopasiProblem.cpp.
Referenced by operator<<(), and CQTSSAResultSubWidget::saveDataToFile().
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Do the calculatting based on CalculateVariables and fill CalculateResults with the results.
Reimplemented in COptProblem, and CFitProblem.
Definition at line 82 of file CCopasiProblem.cpp.
Referenced by CCopasiTask::restore().
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Set the call back of the problem
CProcessReport | * pCallBack |
Reimplemented in COptProblem, CEFMProblem, CFitProblem, and COscillationProblem.
Definition at line 72 of file CCopasiProblem.cpp.
References mpCallBack.
Referenced by CMoietiesTask::setCallBack(), COscillationProblem::setCallBack(), CFitTask::setCallBack(), COscillationTask::setCallBack(), CEFMProblem::setCallBack(), CEFMTask::setCallBack(), COptTask::setCallBack(), and COptProblem::setCallBack().
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Set the model of the problem
CModel | * pModel |
Reimplemented in COptProblem, CLNAProblem, CMCAProblem, CFitProblem, and COscillationProblem.
Definition at line 64 of file CCopasiProblem.cpp.
References mpModel.
Referenced by CCopasiDataModel::addTask(), CSensMethod::initialize(), CNewtonMethod::initialize(), CScanTask::initSubtask(), CCopasiXMLParser::TaskElement::start(), and test000087::test_simulate_reaction_flux_reference_1().
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Output stream operator
ostream | & os |
const | CCopasiProblem & A |
Definition at line 90 of file CCopasiProblem.cpp.
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a pointer to the callback
Definition at line 58 of file CCopasiProblem.h.
Referenced by CFitProblem::calculate(), COptProblem::calculate(), CFitProblem::calculateCrossValidation(), COscillationProblem::initialize(), COptProblem::initialize(), COptProblem::setCallBack(), setCallBack(), and COptProblem::setSolution().
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The model of the problem
Definition at line 53 of file CCopasiProblem.h.
Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), getModel(), COscillationProblem::initialize(), CSteadyStateProblem::initialize(), CFitProblem::initialize(), COptProblem::initialize(), CSteadyStateProblem::load(), CTrajectoryProblem::load(), CMoietiesProblem::printResult(), CEFMProblem::printResult(), COptProblem::restoreModel(), COscillationProblem::setModel(), CLNAProblem::setModel(), CMCAProblem::setModel(), COptProblem::setModel(), setModel(), and CFitProblem::updateInitialState().
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A pointer to the report
Definition at line 63 of file CCopasiProblem.h.
Referenced by COptProblem::initialize().
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