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| CNewtonMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::Newton, const CTaskEnum::Task &taskType=CTaskEnum::Task::steadyState) |
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| CNewtonMethod (const CNewtonMethod &src, const CDataContainer *pParent) |
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virtual bool | elevateChildren () |
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virtual bool | initialize (const CSteadyStateProblem *pProblem) |
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bool | isSteadyState (const C_FLOAT64 &value) const |
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virtual bool | isValidProblem (const CCopasiProblem *pProblem) |
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virtual void | load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH) |
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virtual CSteadyStateMethod::ReturnCode | processInternal () |
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C_FLOAT64 | targetFunction () |
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| ~CNewtonMethod () |
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| CSteadyStateMethod (const CSteadyStateMethod &src, const CDataContainer *pParent) |
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void | doJacobian (CMatrix< C_FLOAT64 > &jacobian, CMatrix< C_FLOAT64 > &jacobianX) |
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bool | elevateChildren () |
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std::string | getMethodLog () const |
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C_FLOAT64 | getStabilityResolution () |
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CSteadyStateMethod::ReturnCode | process (CVectorCore< C_FLOAT64 > &State, CMatrix< C_FLOAT64 > &jacobianX, CProcessReportLevel handler) |
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| ~CSteadyStateMethod () |
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| CCopasiMethod (const CCopasiMethod &src, const CDataContainer *pParent) |
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virtual void | clearCallBack () |
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const CProcessReportLevel & | getCallBack () const |
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CMathContainer * | getMathContainer () const |
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const CTaskEnum::Method & | getSubType () const |
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const CTaskEnum::Task & | getType () const |
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CCopasiMethod & | operator= (const CCopasiMethod &rhs) |
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virtual void | print (std::ostream *ostream) const |
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virtual void | printResult (std::ostream *ostream) const |
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virtual bool | setCallBack (CProcessReportLevel callBack) |
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void | setMathContainer (CMathContainer *pContainer) |
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virtual | ~CCopasiMethod () |
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bool | addGroup (const std::string &name) |
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void | addParameter (CCopasiParameter *pParameter) |
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bool | addParameter (const CCopasiParameter ¶meter) |
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bool | addParameter (const std::string &name, const CCopasiParameter::Type type, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All) |
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template<class CType > |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All) |
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virtual bool | applyData (const CData &data, CUndoData::CChangeSet &changes) |
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CCopasiParameterGroup * | assertGroup (const std::string &name, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All) |
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template<class CType > |
CType * | assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All) |
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index_iterator | beginIndex () const |
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const_name_iterator | beginName () const |
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| CCopasiParameterGroup (const CCopasiParameterGroup &src, const CDataContainer *pParent=NULL) |
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| CCopasiParameterGroup (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="ParameterGroup") |
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void | clear () |
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virtual void | createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const |
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index_iterator | endIndex () const |
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const_name_iterator | endName () const |
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CCopasiParameterGroup & | getElementTemplates () |
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const CCopasiParameterGroup & | getElementTemplates () const |
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CCopasiParameterGroup * | getGroup (const size_t &index) |
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const CCopasiParameterGroup * | getGroup (const size_t &index) const |
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CCopasiParameterGroup * | getGroup (const std::string &name) |
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const CCopasiParameterGroup * | getGroup (const std::string &name) const |
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virtual size_t | getIndex (const CDataObject *pObject) const |
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size_t | getIndex (const std::string &name) const |
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std::string | getKey (const size_t &index) const |
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std::string | getKey (const std::string &name) const |
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virtual const std::string & | getName (const size_t &index) const |
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virtual const CObjectInterface * | getObject (const CCommonName &cn) const |
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CCopasiParameter * | getParameter (const size_t &index) |
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const CCopasiParameter * | getParameter (const size_t &index) const |
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CCopasiParameter * | getParameter (std::string name) |
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const CCopasiParameter * | getParameter (std::string name) const |
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CCopasiParameter::Type | getType (const size_t &index) const |
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CCopasiParameter::Type | getType (const std::string &name) const |
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std::string | getUniqueParameterName (const CCopasiParameter *pParameter) const |
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template<class CType > |
CType & | getValue (const size_t &index) |
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template<class CType > |
const CType & | getValue (const size_t &index) const |
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template<class CType > |
CType & | getValue (const std::string &name) |
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template<class CType > |
const CType & | getValue (const std::string &name) const |
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bool | haveTemplate () const |
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virtual CUndoObjectInterface * | insert (const CData &data) |
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CCopasiParameterGroup & | operator= (const CCopasiParameterGroup &rhs) |
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virtual bool | remove (CDataObject *pObject) |
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bool | removeParameter (CCopasiParameter *pParameter) |
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bool | removeParameter (const size_t &index) |
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bool | removeParameter (const std::string &name) |
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virtual void | setUserInterfaceFlag (const UserInterfaceFlag &flag) |
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template<class CType > |
bool | setValue (const size_t &index, const CType &value) |
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template<class CType > |
bool | setValue (const std::string &name, const CType &value) |
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size_t | size (const UserInterfaceFlag &require=UserInterfaceFlag::None, const UserInterfaceFlag &exclude=UserInterfaceFlag::None) const |
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bool | swap (const size_t &iFrom, const size_t &iTo) |
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bool | swap (index_iterator &from, index_iterator &to) |
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virtual CData | toData () const |
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virtual void | updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject) |
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virtual | ~CCopasiParameterGroup () |
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| CCopasiParameter (const CCopasiParameter &src, const CDataContainer *pParent) |
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| CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="Parameter") |
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virtual CCommonName | getCN () const override |
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template<class CType > |
const CType & | getDefault () const |
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virtual const std::string & | getKey () const override |
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virtual std::string | getObjectDisplayName () const override |
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const CCopasiParameter::Type & | getType () const |
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const UserInterfaceFlag & | getUserInterfaceFlag () const |
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template<class CType > |
std::vector< std::pair< CType, CType > > & | getValidValues () |
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template<class CType > |
const std::vector< std::pair< CType, CType > > & | getValidValues () const |
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void * | getValidValuesPointer () const |
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template<class CType > |
CType & | getValue () |
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template<class CType > |
const CType & | getValue () const |
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virtual void * | getValuePointer () const override |
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CDataObject * | getValueReference () const |
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bool | hasValidValues () const |
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bool | isBasic () const |
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bool | isDefault () const |
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bool | isEditable () const |
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bool | isUnsupported () const |
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bool | isValidValue (const bool &value) const |
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bool | isValidValue (const C_FLOAT64 &value) const |
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bool | isValidValue (const C_INT32 &value) const |
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bool | isValidValue (const CCommonName &value) const |
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template<class CType > |
bool | isValidValue (const CType &) const |
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bool | isValidValue (const std::string &value) const |
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bool | isValidValue (const std::vector< CCopasiParameter * > &value) const |
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bool | isValidValue (const unsigned C_INT32 &value) const |
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CCopasiParameter & | operator= (const CCopasiParameter &rhs) |
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template<class CType > |
bool | setDefault (const CType &defaultValue) |
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bool | setDefault (const std::vector< CCopasiParameter * > &defaultValue) |
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virtual bool | setObjectParent (const CDataContainer *pParent) override |
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template<class CType , class Enum > |
bool | setValidValues (const CEnumAnnotation< CType, Enum > &validValues) |
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template<class CType > |
bool | setValidValues (const std::vector< std::pair< CType, CType > > &validValues) |
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template<class CType > |
bool | setValue (const CType &value) |
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bool | setValue (const std::vector< CCopasiParameter * > &value) |
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virtual | ~CCopasiParameter () |
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virtual bool | add (CDataObject *pObject, const bool &adopt=true) |
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virtual bool | appendDeletedDependentData (CUndoData &undoData) const |
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| CDataContainer (const CDataContainer &src, const CDataContainer *pParent) |
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| CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None) |
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virtual std::string | getChildObjectUnits (const CDataObject *pObject) const |
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void | getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const |
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virtual objectMap & | getObjects () |
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virtual const objectMap & | getObjects () const |
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virtual const std::string | getUnits () const override |
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virtual const CDataObject * | getValueObject () const override |
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void | objectRenamed (CDataObject *pObject, const std::string &oldName) |
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virtual | ~CDataContainer () |
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void | addIssue (const CIssue &issue) |
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void | addReference (const CDataContainer *pReference) |
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virtual void | calculateValue () override |
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| CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL) |
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virtual void | destruct () override |
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virtual const CDataObject * | getDataObject () const override |
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CDataContainer * | getObjectAncestor (const std::string &type) const |
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CDataModel * | getObjectDataModel () const |
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const CObjectInterface * | getObjectFromCN (const CCommonName &cn) const |
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const std::string & | getObjectName () const |
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CDataContainer * | getObjectParent () const |
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const std::string & | getObjectType () const |
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virtual const CObjectInterface::ObjectSet & | getPrerequisites () const override |
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virtual const CValidity & | getValidity () const override |
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bool | hasFlag (const Flag &flag) const |
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virtual bool | isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override |
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bool | prerequisitsContains (const DataObjectSet &objects) const |
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void | removeIssue (const CIssue &issue) |
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void | removeReference (const CDataContainer *pReference) |
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bool | setObjectName (const std::string &name) |
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void | validityChanged (const CValidity &changedValidity) override |
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void | validityRemoved (const CValidity &changedValidity) |
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virtual | ~CDataObject () |
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| CObjectInterface () |
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| CObjectInterface (const CObjectInterface &src) |
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virtual | ~CObjectInterface () |
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| CUndoObjectInterface () |
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| CUndoObjectInterface (const CUndoObjectInterface &src) |
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bool | generateUuid () |
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const xg::Guid & | getUuid () const |
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bool | setUuid (const std::string &uuid) |
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bool | setUuid (const xg::Guid &uuid) |
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virtual | ~CUndoObjectInterface () |
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static void | allocateValidValues (const Type &type, void *&pValidValues) |
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static void | allocateValue (const Type &type, void *&pValue) |
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static void | assignValue (const Type &type, void *&pValue, const void *pNewValue) |
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static void | deleteValidValues (const Type &type, void *&pValidValues) |
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static void | deleteValue (const Type &type, void *&pValue) |
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static CCopasiParameter * | fromData (const CData &data, CUndoObjectInterface *pParent) |
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static CDataContainer * | fromData (const CData &data, CUndoObjectInterface *pParent) |
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static CDataObject * | fromData (const CData &data, CUndoObjectInterface *pParent) |
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static void | sanitizeObjectName (std::string &name) |
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static const CDataObject * | DataObject (const CObjectInterface *pInterface) |
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static CObjectInterface * | GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName) |
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template<class CType > |
static CType * | fromData (const CData &, CUndoObjectInterface *) |
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bool | allPositive () |
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void | calculateJacobian (const C_FLOAT64 &oldMaxRate, const bool &reduced) |
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| CSteadyStateMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType=CTaskEnum::Task::steadyState) |
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| CSteadyStateMethod (CTaskEnum::Method subType, const CDataContainer *pParent=NO_PARENT) |
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void | initializeParameter () |
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bool | isEquilibrium (const C_FLOAT64 &resolution) const |
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virtual CSteadyStateMethod::ReturnCode | returnProcess (bool steadyStateFound) |
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| CCopasiMethod (const CCopasiMethod &src) |
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| CCopasiMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType) |
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virtual void | signalMathContainerChanged () |
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| CCopasiParameterGroup () |
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| CCopasiParameter (const CCopasiParameter &src) |
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template<class CType > |
CDataMatrixReference< CType > * | addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None) |
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template<class CType > |
CDataObjectReference< CType > * | addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None) |
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template<class CType > |
CDataVectorReference< CType > * | addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None) |
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| CDataContainer (const CDataContainer &src) |
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void | initObjects () |
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| CDataObject () |
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| CDataObject (const std::string &name, const CDataContainer *pParent=static_cast< CDataContainer * >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None) |
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CVector< C_FLOAT64 > | mAtol |
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CVector< C_FLOAT64 * > | mCompartmentVolumes |
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CVectorCore< C_FLOAT64 > | mContainerState |
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CVectorCore< C_FLOAT64 > | mContainerStateReduced |
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std::ostringstream | mMethodLog |
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C_FLOAT64 * | mpContainerStateTime |
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C_FLOAT64 * | mpDerivationFactor |
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C_FLOAT64 * | mpDerivationResolution |
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CMatrix< C_FLOAT64 > * | mpJacobian |
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CSteadyStateTask * | mpParentTask |
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const CSteadyStateProblem * | mpProblem |
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C_FLOAT64 * | mpSSResolution |
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CVector< C_FLOAT64 > | mStartState |
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CVectorCore< C_FLOAT64 > | mSteadyState |
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CMathContainer * | mpContainer |
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CProcessReportLevel | mProcessReport |
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std::string | mKey |
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void * | mpDefault |
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void * | mpValidValues |
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void * | mpValue |
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CDataObject * | mpValueReference |
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UserInterfaceFlag | mUserInterfaceFlag |
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objectMap | mObjects |
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ObjectSet | mPrerequisits |
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std::set< CDataContainer * > | mReferences |
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CValidity | mValidity |
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