COPASI API
4.16.103
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#include <CModelValue.h>
Public Types | |
enum | Status { FIXED = 0, ASSIGNMENT, REACTIONS, ODE, TIME } |
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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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typedef std::map< std::string, std::string > | UnsupportedAnnotation |
Public Member Functions | |
virtual void | calculate () |
CModelEntity (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const std::string &type="ModelEntity", const unsigned C_INT32 &flag=CCopasiObject::Container|CCopasiObject::ValueDbl) | |
CModelEntity (const CModelEntity &src, const CCopasiContainer *pParent=NULL) | |
virtual bool | compile () |
virtual std::set< const CCopasiObject * > | getDeletedObjects () const |
std::string | getExpression () const |
const CExpression * | getExpressionPtr () const |
CExpression * | getExpressionPtr () |
std::string | getInitialExpression () const |
const CExpression * | getInitialExpressionPtr () const |
CExpression * | getInitialExpressionPtr () |
const C_FLOAT64 & | getInitialValue () const |
CCopasiObject * | getInitialValueReference () const |
virtual const std::string & | getKey () const |
const C_FLOAT64 & | getRate () const |
CCopasiObject * | getRateReference () const |
const std::string & | getSBMLId () const |
const CModelEntity::Status & | getStatus () const |
const C_FLOAT64 & | getValue () const |
virtual const CCopasiObject * | getValueObject () const |
virtual void * | getValuePointer () const |
CCopasiObject * | getValueReference () const |
bool | isFixed () const |
const bool & | isUsed () const |
virtual bool | mustBeDeleted (const DataObjectSet &deletedObjects) const |
virtual void | refreshInitialValue () |
bool | setExpression (const std::string &expression) |
bool | setExpressionPtr (CExpression *pExpression) |
bool | setInitialExpression (const std::string &expression) |
bool | setInitialExpressionPtr (CExpression *pExpression) |
virtual void | setInitialValue (const C_FLOAT64 &initialValue) |
void | setInitialValuePtr (C_FLOAT64 *pInitialValue) |
virtual bool | setObjectParent (const CCopasiContainer *pParent) |
void | setRate (const C_FLOAT64 &rate) |
void | setSBMLId (const std::string &id) |
virtual void | setStatus (const CModelEntity::Status &status) |
void | setUsed (const bool &used) |
virtual void | setValue (const C_FLOAT64 &value) |
void | setValuePtr (C_FLOAT64 *pValue) |
~CModelEntity () | |
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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 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 |
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 void | print (std::ostream *ostream) const |
void | removeDirectDependency (const CCopasiObject *pObject) |
void | setDirectDependencies (const DataObjectSet &directDependencies) |
bool | setObjectName (const std::string &name) |
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 () |
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bool | addUnsupportedAnnotation (const std::string &name, const std::string &xml) |
CAnnotation () | |
CAnnotation (const CAnnotation &src) | |
const std::string & | getMiriamAnnotation () const |
const std::string & | getNotes () const |
UnsupportedAnnotation & | getUnsupportedAnnotations () |
const UnsupportedAnnotation & | getUnsupportedAnnotations () const |
bool | operator== (const CAnnotation &rhs) const |
bool | removeUnsupportedAnnotation (const std::string &name) |
bool | replaceUnsupportedAnnotation (const std::string &name, const std::string &xml) |
void | setMiriamAnnotation (const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId) |
void | setNotes (const std::string ¬es) |
virtual | ~CAnnotation () |
Static Public Attributes | |
static const std::string | StatusName [] |
static const char * | XMLStatus [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
Protected Attributes | |
CExpression * | mpExpression |
CExpression * | mpInitialExpression |
C_FLOAT64 * | mpIValue |
CCopasiObjectReference < C_FLOAT64 > * | mpIValueReference |
CModel * | mpModel |
CCopasiObjectReference < C_FLOAT64 > * | mpRateReference |
C_FLOAT64 * | mpValue |
CCopasiObjectReference < C_FLOAT64 > * | mpValueReference |
C_FLOAT64 | mRate |
std::string | mSBMLId |
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objectMap | mObjects |
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std::string | mKey |
Private Member Functions | |
void | initObjects () |
Private Attributes | |
Status | mStatus |
bool | mUsed |
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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static CAnnotation * | castObject (CCopasiObject *pObject) |
static const CAnnotation * | castObject (const CCopasiObject *pObject) |
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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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static CRenameHandler * | smpRenameHandler = NULL |
The base class for CCompartment, CMetab and CModelValue. CModelEntity is a base class for CCompartment, CMetab and CModelValue. These three classes have in common that (in the long run) they can each be model variables (subject to ODEs), constant, or subject to algebraic assignments. In addition, the CMetab objects can also be subject to reactions, and conservation rules.
Definition at line 39 of file CModelValue.h.
enum CModelEntity::Status |
The valid states for metabolites
Enumerator | |
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FIXED | |
ASSIGNMENT | |
REACTIONS | |
ODE | |
TIME |
Definition at line 53 of file CModelValue.h.
CModelEntity::CModelEntity | ( | const std::string & | name = "NoName" , |
const CCopasiContainer * | pParent = NULL , |
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const std::string & | type = "ModelEntity" , |
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const unsigned C_INT32 & | flag = CCopasiObject::Container | CCopasiObject::ValueDbl |
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Default constructor
const | std::string & name (default: "NoName") |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 62 of file CModelValue.cpp.
References CKeyFactory::add(), CONSTRUCTOR_TRACE, CCopasiRootContainer::getKeyFactory(), CCopasiObject::getObjectType(), initObjects(), CAnnotation::mKey, mpIValue, and mpValue.
CModelEntity::CModelEntity | ( | const CModelEntity & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CModelValue & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 87 of file CModelValue.cpp.
References CKeyFactory::add(), CCopasiRootContainer::getKeyFactory(), CAnnotation::getMiriamAnnotation(), CCopasiObject::getObjectType(), initObjects(), CAnnotation::mKey, mpIValue, mpValue, mStatus, CAnnotation::setMiriamAnnotation(), and setStatus().
CModelEntity::~CModelEntity | ( | ) |
Destructor.
Definition at line 112 of file CModelValue.cpp.
References DESTRUCTOR_TRACE, CModel::getStateTemplate(), mpIValue, mpModel, mpValue, pdelete, and CStateTemplate::remove().
Calculate the value or the rate depending whether we have an ASIGNMENT or ODE
Reimplemented in CMetab.
Definition at line 197 of file CModelValue.cpp.
References ASSIGNMENT, CExpression::calcValue(), mpExpression, mpValue, mRate, mStatus, and ODE.
Referenced by setStatus().
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Compile the model value. This is only needed for status ASIGNMENT and ODE.
Reimplemented in CModel, and CMetab.
Definition at line 143 of file CModelValue.cpp.
References CCopasiContainer::add(), CCopasiObject::addDirectDependency(), ASSIGNMENT, CExpression::calcValue(), CExpression::compile(), CExpression::createInitialExpression(), CCopasiObject::getDirectDependencies(), CEvaluationTree::getInfix(), CCopasiObject::getObjectDataModel(), CEvaluationTree::isUsable(), mpExpression, mpInitialExpression, mpIValue, mpIValueReference, mpModel, mpRateReference, mpValueReference, mStatus, ODE, pdelete, CCopasiObject::setDirectDependencies(), and CCopasiObject::setObjectName().
Referenced by CModel::buildSimulatedSequence(), CModel::buildStateTemplate(), setExpression(), setExpressionPtr(), setInitialExpression(), and setInitialExpressionPtr().
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Retrieve the list of deleted numeric child objects;
Reimplemented in CMetab, and CCompartment.
Definition at line 587 of file CModelValue.cpp.
References mpIValueReference, mpRateReference, and mpValueReference.
Referenced by CModel::appendDependentModelObjects(), CModel::determineIsAutonomous(), CCompartment::getDeletedObjects(), CMetab::getDeletedObjects(), mustBeDeleted(), CModel::removeModelValue(), CQGlobalQuantityDM::removeRows(), and CQModelValue::slotBtnDelete().
std::string CModelEntity::getExpression | ( | ) | const |
Retrieve the expression for non FIXED model values.
Definition at line 236 of file CModelValue.cpp.
References CEvaluationTree::getInfix(), isFixed(), mpExpression, and CExpression::updateInfix().
Referenced by CModel::convert2NonReversible(), CMathObject::createExtensiveODERateExpression(), CSBMLExporter::createRule(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CQSpeciesDetail::load(), CQCompartment::load(), CQModelValue::load(), CQSpeciesDetail::save(), CQCompartment::save(), CQModelValue::save(), and CCopasiXML::saveModel().
const CExpression * CModelEntity::getExpressionPtr | ( | ) | const |
Retrieve the pointer to the expression for non FIXED model values.
Definition at line 250 of file CModelValue.cpp.
References mpExpression.
Referenced by CSBMLExporter::checkForPiecewiseFunctions(), CSBMLExporter::checkForUnsupportedFunctionCalls(), CSBMLExporter::checkForUnsupportedObjectReferences(), CMathObject::compileRate(), CMathObject::compileValue(), CModelAdd::copyExpression(), CSBMLExporter::createRule(), CQGlobalQuantityDM::data(), CQCompartmentDM::data(), CQSpecieDM::data(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CODEExporter::exportModelEntityExpression(), CODEExporter::exportModelValuesExpressions(), SBMLImporter::importRuleForModelEntity(), CModelMerging::mergeMetabolites(), SBMLImporter::removeUnusedFunctions(), CModelExpansion::replaceInModelEntity(), test000093::test_bug1503_1(), test000093::test_bug1503_2(), test000091::test_delay_in_kinetic_law(), test000091::test_delay_in_kinetic_law_local_parameter(), test000027::test_hasOnlySubstanceUnits(), test000034::test_hasOnlySubstanceUnits(), test000023::test_hasOnlySubstanceUnits(), test000025::test_hasOnlySubstanceUnits(), test000033::test_hasOnlySubstanceUnits(), test000087::test_import_reaction_flux_reference_2(), test000075::test_import_time_dependent_function_definition(), test000087::test_simulate_reaction_flux_reference_1(), and CMMLOutput::writeRHS_ModelEntity().
CExpression * CModelEntity::getExpressionPtr | ( | ) |
Retrieve the pointer to the expression for non FIXED model values.
Definition at line 245 of file CModelValue.cpp.
References mpExpression.
std::string CModelEntity::getInitialExpression | ( | ) | const |
Retrieve the expression for ODE or REACTION model values.
Definition at line 350 of file CModelValue.cpp.
References ASSIGNMENT, CEvaluationTree::getInfix(), mpInitialExpression, mStatus, and CExpression::updateInfix().
Referenced by CModelAdd::addCompartmentsExpressions(), CModelAdd::addMetabolitesExpressions(), CModelAdd::addModelValuesExpressions(), CModel::buildInitialRefreshSequence(), CModel::convert2NonReversible(), CSBMLExporter::createCompartment(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), CQGlobalQuantityDM::data(), CQSpecieDM::data(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), SliderDialog::fillSliderBox(), CQSimpleSelectionTree::filter(), CParticleReference::getDirectDependencies(), CQSpeciesDetail::load(), CQCompartment::load(), CQModelValue::load(), CModelMerging::mergeMetabolites(), CQSpeciesDetail::save(), CQCompartment::save(), CQModelValue::save(), CCopasiXML::saveModel(), test000041::test_hasOnlySubstanceUnits(), and test000040::test_hasOnlySubstanceUnits().
const CExpression * CModelEntity::getInitialExpressionPtr | ( | ) | const |
Retrieve the pointer to the expression for non FIXED model values.
Definition at line 294 of file CModelValue.cpp.
References mpInitialExpression.
Referenced by CSBMLExporter::checkForUnsupportedFunctionCalls(), CSBMLExporter::checkForUnsupportedObjectReferences(), CMathObject::compileInitialValue(), CModelAdd::copyInitialExpression(), CSBMLExporter::createInitialAssignment(), CQGlobalQuantityDM::data(), CQCompartmentDM::data(), CQSpecieDM::data(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), SBMLImporter::importInitialAssignments(), CModelMerging::mergeMetabolites(), SBMLImporter::removeUnusedFunctions(), CModelExpansion::replaceInModelEntity(), test000093::test_bug1503_1(), test000040::test_hasOnlySubstanceUnits(), test000041::test_hasOnlySubstanceUnits(), and test000075::test_import_time_dependent_function_definition().
CExpression * CModelEntity::getInitialExpressionPtr | ( | ) |
Retrieve the pointer to the expression for non FIXED model values.
Definition at line 289 of file CModelValue.cpp.
References mpInitialExpression.
const C_FLOAT64 & CModelEntity::getInitialValue | ( | ) | const |
Retrieve the initial value
Definition at line 138 of file CModelValue.cpp.
References mpIValue.
Referenced by CModelAdd::addCompartments(), CModelAdd::addModelValues(), CFunctionAnalyzer::constructCallParametersActualValues(), CMetab::convertToConcentration(), CMetab::convertToNumber(), CSBMLExporter::createCompartment(), CModelParameterSet::createFromModel(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), CCSPMethod::cspstep(), CQGlobalQuantityDM::data(), CQCompartmentDM::data(), CQSpecieDM::data(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CODEExporter::exportCompartments(), CODEExporter::exportExpression(), CODEExporter::exportMetabolites(), CODEExporter::exportModelValues(), CModel::initializeAtolVector(), CQSpeciesDetail::load(), CQCompartment::load(), CQModelValue::load(), CReactionInterface::loadMappingAndValues(), CQUpdatesWidget::loadObjectsTable(), CModelParameter::refreshFromModel(), CMetab::refreshInitialConcentration(), CMetab::refreshInitialValue(), CQSpeciesDetail::save(), CQCompartment::save(), CQModelValue::save(), CQSpecieDM::setData(), CQSpeciesDetail::slotCompartmentChanged(), CModel::suitableForStochasticSimulation(), test000091::test_delay_in_kinetic_law_local_parameter(), test000026::test_hasOnlySubstanceUnits(), test000087::test_simulate_reaction_flux_reference_1(), and ParameterTable::updateTable().
CCopasiObject * CModelEntity::getInitialValueReference | ( | ) | const |
Retrieve object referencing the initial value
Definition at line 367 of file CModelValue.cpp.
References mpIValueReference.
Referenced by DataModelGUI::buildChangedObjects(), CModel::buildInitialRefreshSequence(), CMetab::compileInitialValueDependencies(), CMathObject::createExtensiveValueExpression(), CModelParameterSet::createFromModel(), CSBMLExporter::createInitialAssignment(), CExpression::createInitialExpression(), CMathObject::createIntensiveValueExpression(), test000097::createModel(), SliderDialog::determineCorrectObjectForSlider(), findObjectByDisplayName(), CMetab::getChildObjectUnits(), getInitialCNForSBase(), CModelParameter::getUnit(), SBMLImporter::importInitialAssignments(), CMathContainer::initializeObjects(), CQSimpleSelectionTree::populateTree(), SBMLImporter::replace_time_with_initial_time(), test000058::test_bug1025_10(), test000058::test_bug1025_2(), test000058::test_bug1025_4(), test000058::test_bug1025_5(), test000058::test_bug1025_7(), test000058::test_bug1025_9(), test000059::test_unique_id_1(), test000059::test_unique_id_12(), test000059::test_unique_id_14(), test000059::test_unique_id_17(), test000059::test_unique_id_18(), test000059::test_unique_id_19(), test000059::test_unique_id_20(), test000059::test_unique_id_21(), test000059::test_unique_id_21_2(), test000059::test_unique_id_3(), test000059::test_unique_id_6(), and test000059::test_unique_id_8().
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Retrieve the key
Reimplemented from CAnnotation.
Reimplemented in CModel.
Definition at line 131 of file CModelValue.cpp.
References CAnnotation::getKey().
Referenced by CModelAdd::addCompartments(), CModelAdd::addCompartmentsExpressions(), CModelAdd::addMetabolites(), CModelAdd::addMetabolitesExpressions(), CModelAdd::addModelValues(), CModelAdd::addModelValuesExpressions(), CModelAdd::addReactions(), CFixLocalReactionParameters::changeModel(), CQCompartment::copy(), CLayoutInitializer::createCompartmentGlyph(), CMathObject::createExtensiveReactionRateExpression(), CCopasiSpringLayout::createLayout(), CLayoutInitializer::createMetabGlyph(), test000097::createModel(), CSBMLExporter::createSBMLDocument(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CModelExpansion::duplicateReaction(), CODEExporter::exportExpression(), CODEExporter::exportKineticFunction(), CODEExporter::exportMetabolitesConcentrations(), CODEExporter::exportModelEntityExpression(), CODEExporter::exportODEs(), CODEExporterBM::exportSingleCompartment(), CODEExporterXPPAUT::exportSingleCompartment(), CODEExporterC::exportSingleCompartment(), CODEExporterBM::exportSingleMetabolite(), CODEExporterXPPAUT::exportSingleMetabolite(), CODEExporterC::exportSingleMetabolite(), CODEExporterBM::exportSingleModelEntity(), CODEExporterXPPAUT::exportSingleModelEntity(), CODEExporterC::exportSingleModelEntity(), CODEExporterBM::exportSingleModVal(), CODEExporterXPPAUT::exportSingleModVal(), CODEExporterC::exportSingleModVal(), CODEExporterBM::exportSingleODE(), CODEExporterXPPAUT::exportSingleODE(), CODEExporterC::exportSingleODE(), CQSelectionWizardPage::fillTree(), getMetabGlyphForKey(), CMetabNameInterface::getMetaboliteKey(), CEFMTask::getSpeciesChanges(), SBMLImporter::importMIRIAM(), CCopasiSpringLayout::initFromLayout(), CQGlobalQuantityDM::insertRows(), CQCompartmentDM::insertRows(), CQSpecieDM::insertRows(), CODEExporterC::KineticFunction2ODEmember(), CModelMerging::mergeMetabolites(), CODEExporterC::preprocess(), CODEExporter::preprocess(), CCopasiSpringLayout::randomize(), CModelExpansion::replaceInReaction(), CCopasiXML::saveModel(), CQNewMainWindow::selectMetabolite(), CQGlobalQuantityDM::setData(), CQCompartmentDM::setData(), CQSpecieDM::setData(), CChemEq::setMultiplicity(), CModelMerging::simpleCall(), CModelExpansion::simpleCall(), CQEventWidget1::slotAddTarget(), CQSpeciesDetail::slotBtnNew(), CQCompartment::slotBtnNew(), CQModelValue::slotBtnNew(), CQEventWidget1::slotSelectObject(), CCopasiXMLParser::SourceParameterElement::start(), CCopasiXMLParser::ModifierElement::start(), CCopasiXMLParser::ProductElement::start(), CCopasiXMLParser::SubstrateElement::start(), CCopasiXMLParser::AssignmentElement::start(), CCopasiXMLParser::CompartmentGlyphElement::start(), CCopasiXMLParser::MetaboliteGlyphElement::start(), CCopasiXMLParser::TextGlyphElement::start(), test000091::test_delay_in_kinetic_law(), test000091::test_delay_in_kinetic_law_local_parameter(), test000087::test_simulate_reaction_flux_reference_1(), CSBMLExporter::updateMIRIAMAnnotation(), and CMMLOutput::writeRHS().
const C_FLOAT64 & CModelEntity::getRate | ( | ) | const |
Return rate of production of this entity
Definition at line 362 of file CModelValue.cpp.
References mRate.
Referenced by CQGlobalQuantityDM::data(), CQCompartmentDM::data(), CQSpecieDM::data(), CQCompartment::load(), CQModelValue::load(), operator<<(), CMetab::refreshConcentrationRate(), and CQSpeciesDetail::setFramework().
CCopasiObject * CModelEntity::getRateReference | ( | ) | const |
Retrieve object referencing the rate
Definition at line 373 of file CModelValue.cpp.
References mpRateReference.
Referenced by CMetab::compile(), CMathObject::createIntensiveRateExpression(), findObjectByDisplayName(), CMathContainer::initializeObjects(), and CQSimpleSelectionTree::populateTree().
const std::string & CModelEntity::getSBMLId | ( | ) | const |
Returns a reference to the SBML Id.
Definition at line 637 of file CModelValue.cpp.
References mSBMLId.
Referenced by SBMLImporter::applyStoichiometricExpressions(), CSBMLExporter::collectIds(), CSBMLExporter::createCompartment(), SBMLImporter::createCReactionFromReaction(), CSBMLExporter::createInitialAssignment(), CSBMLExporter::createKineticLaw(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), CSBMLExporter::createReaction(), CSBMLExporter::createRule(), CSBMLExporter::createRules(), CSBMLExporter::createSBMLDocument(), CSBMLExporter::createTimesTree(), SBMLImporter::replaceObjectNames(), CCopasiXML::saveModel(), test000055::test_bug1004(), test000057::test_bug1006(), test000103::test_bug1743_l2(), test000103::test_bug1743_l3(), and CEvaluationNodeObject::toAST().
const CModelEntity::Status & CModelEntity::getStatus | ( | ) | const |
Retrieve the status of the entity.
Definition at line 141 of file CModelValue.cpp.
References mStatus.
Referenced by CModelAdd::addCompartments(), CModelAdd::addMetabolites(), CModelAdd::addModelValues(), CModel::buildInitialRefreshSequence(), CMetab::calculate(), CLNAMethod::calculateCovarianceMatrixReduced(), CSBMLExporter::checkForODESpeciesInNonfixedCompartment(), CSBMLExporter::checkForPiecewiseFunctions(), CEventAssignment::compile(), CMetab::compile(), CMetab::compileInitialValueDependencies(), CFunctionAnalyzer::constructCallParametersActualValues(), CModel::convert2NonReversible(), CSBMLExporter::createCompartment(), CCopasiSpringLayout::createLayout(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), CSBMLExporter::createRule(), CQGlobalQuantityDM::data(), CQCompartmentDM::data(), CQSpecieDM::data(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CODEExporter::exportCompartments(), CODEExporter::exportExpression(), CODEExporter::exportMetabolites(), CODEExporter::exportMetabolitesConcentrations(), CODEExporter::exportModelEntityExpression(), CODEExporter::exportModelValues(), CODEExporter::exportModelValuesExpressions(), CODEExporter::exportODEs(), CODEExporterBM::exportSingleCompartment(), CODEExporterXPPAUT::exportSingleCompartment(), CODEExporterC::exportSingleCompartment(), CODEExporterBM::exportSingleMetabolite(), CODEExporterXPPAUT::exportSingleMetabolite(), CODEExporterC::exportSingleMetabolite(), CODEExporterBM::exportSingleModelEntity(), CODEExporterXPPAUT::exportSingleModelEntity(), CODEExporterC::exportSingleModelEntity(), CODEExporterBM::exportSingleModVal(), CODEExporterXPPAUT::exportSingleModVal(), CODEExporterC::exportSingleModVal(), CQSimpleSelectionTree::filter(), CParticleReference::getDirectDependencies(), SBMLImporter::importRuleForModelEntity(), CSteadyStateTask::initialize(), CMathContainer::initializeObjects(), CSBMLExporter::isEventAssignmentSBMLCompatible(), CODEExporter::isModelEntityExpressionODEExporterCompatible(), CParticleReference::isPrerequisiteForContext(), CQSpeciesDetail::load(), CQCompartment::load(), CQModelValue::load(), CQUpdatesWidget::loadObjectsTable(), CModelMerging::mergeMetabolites(), CMetab::mustBeDeleted(), operator<<(), CQSimpleSelectionTree::populateTree(), CODEExporterC::preprocess(), CODEExporter::preprocess(), CMetab::refreshRate(), CMetab::refreshTransitionTime(), SBMLImporter::removeUnusedFunctions(), CSBMLExporter::replaceSpeciesReferences(), CQSpeciesDetail::save(), CQCompartment::save(), CQModelValue::save(), CCopasiXML::saveModel(), CQSpeciesDetail::setFramework(), CMetab::setObjectParent(), CMetab::setStatus(), CHybridMethodODE45::setupBalances(), CHybridMethod::setupBalances(), CHybridMethodLSODA::setupBalances(), CHybridMethodODE45::setupMetab2React(), CTauLeapMethod::start(), CStochDirectMethod::start(), CTrajAdaptiveSA::start(), CTrajectoryMethodDsaLsodar::start(), test000093::test_bug1503_1(), test000093::test_bug1503_2(), test000091::test_delay_in_kinetic_law(), test000091::test_delay_in_kinetic_law_local_parameter(), test000040::test_hasOnlySubstanceUnits(), test000023::test_hasOnlySubstanceUnits(), test000033::test_hasOnlySubstanceUnits(), test000025::test_hasOnlySubstanceUnits(), test000041::test_hasOnlySubstanceUnits(), test000026::test_hasOnlySubstanceUnits(), test000034::test_hasOnlySubstanceUnits(), test000027::test_hasOnlySubstanceUnits(), test000087::test_import_reaction_flux_reference_2(), test000075::test_import_time_dependent_function_definition(), CSteadyStateTask::updateMatrices(), CModelParameter::updateModel(), and ParameterTable::updateTable().
const C_FLOAT64 & CModelEntity::getValue | ( | ) | const |
Retrieve the value
Definition at line 136 of file CModelValue.cpp.
References mpValue.
Referenced by CMetab::calculate(), CModel::calculateElasticityMatrix(), CQGlobalQuantityDM::data(), CQCompartmentDM::data(), CQSpecieDM::data(), CHybridMethod::fireReaction(), CHybridMethodLSODA::fireReaction(), CHybridMethodODE45::fireReaction(), CTSSAMethod::initializeAtol(), CSteadyStateMethod::isEquilibrium(), CQCompartment::load(), CQModelValue::load(), operator<<(), CMetab::refreshConcentration(), CMetab::refreshConcentrationRate(), CMetab::refreshNumber(), CSBMLExporter::replaceSpeciesReferences(), CMCAMethod::scaleMCA(), CQSpeciesDetail::setFramework(), CNewtonMethod::solveJacobianXeqB(), and CNewtonMethod::targetFunction().
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Retrieve the object representing the value;
Reimplemented from CCopasiContainer.
Reimplemented in CMetab.
Definition at line 484 of file CModelValue.cpp.
References mpValueReference.
Referenced by CEventAssignment::compile().
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Retrieve a pointer to the value;
Reimplemented from CCopasiObject.
Reimplemented in CMetab.
Definition at line 490 of file CModelValue.cpp.
References C_FLOAT64, and mpValue.
Referenced by CReaction::setScalingFactor().
CCopasiObject * CModelEntity::getValueReference | ( | ) | const |
Retrieve object referencing the value
Definition at line 370 of file CModelValue.cpp.
References mpValueReference.
Referenced by CMathModel::buildDependendRefreshList(), CMetab::compile(), CPlotSpecification::createDefaultPlot(), CMathObject::createExtensiveODERateExpression(), CMathObject::createExtensiveValueExpression(), CExpression::createInitialExpression(), CMathObject::createIntensiveRateExpression(), CMathObject::createIntensiveValueExpression(), CSBMLExporter::createRule(), CSBMLExporter::exportEventAssignments(), findObjectByDisplayName(), CModel::getCorrespondingTransientObject(), SBMLImporter::importEvent(), SBMLImporter::importRuleForModelEntity(), CMathContainer::initializeObjects(), CQSimpleSelectionTree::populateTree(), CReaction::setScalingFactor(), CMetab::setStatus(), CHybridMethodODE45::setupMetab2React(), CTauLeapMethod::start(), CStochDirectMethod::start(), CTrajAdaptiveSA::start(), and CTrajectoryMethodDsaLsodar::start().
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Initialize the contained CCopasiObjects
Definition at line 495 of file CModelValue.cpp.
References CStateTemplate::add(), CCopasiContainer::addObjectReference(), C_FLOAT64, CCopasiObject::getObjectAncestor(), CModel::getStateTemplate(), mpIValueReference, mpModel, mpRateReference, mpValueReference, mRate, mSBMLId, refreshInitialValue(), setInitialValue(), setInitialValuePtr(), CCopasiObject::setRefresh(), CCopasiObject::setUpdateMethod(), setValue(), setValuePtr(), CCopasiObject::ValueDbl, and CCopasiObject::ValueString.
Referenced by CModelEntity().
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Check whether the entity is FIXED or not.
Definition at line 124 of file CModelValue.h.
References FIXED, and mStatus.
Referenced by getExpression(), CMetab::refreshInitialConcentration(), CMetab::setConcentration(), setExpression(), and setExpressionPtr().
const bool & CModelEntity::isUsed | ( | ) | const |
Retrieve whether the model value is used during simulation
Definition at line 645 of file CModelValue.cpp.
References mUsed.
Referenced by CModel::buildUserOrder(), and CQUpdatesWidget::loadObjectsTable().
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Check whether an object must be deleted because its prerequisites can no longer be fulfilled due to the given deleted objects
const | DataObjectSet & deletedObjects |
Reimplemented from CCopasiObject.
Reimplemented in CMetab.
Definition at line 600 of file CModelValue.cpp.
References getDeletedObjects().
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Refresh the initial value
Reimplemented in CMetab.
Definition at line 214 of file CModelValue.cpp.
References CExpression::calcValue(), CEvaluationTree::getInfix(), mpInitialExpression, and mpIValue.
Referenced by initObjects().
bool CModelEntity::setExpression | ( | const std::string & | expression | ) |
Set the expression for non FIXED model values
const | std::string & expression |
Definition at line 221 of file CModelValue.cpp.
References compile(), isFixed(), mpExpression, mpModel, CModel::setCompileFlag(), and CExpression::setInfix().
Referenced by CModel::convert2NonReversible(), CModelAdd::copyExpression(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CQEventWidget1::loadFromEvent(), CQSpeciesDetail::save(), CQCompartment::save(), CQModelValue::save(), test000058::test_bug1025_10(), test000058::test_bug1025_5(), test000059::test_unique_id_17(), test000059::test_unique_id_18(), test000059::test_unique_id_19(), test000059::test_unique_id_20(), test000059::test_unique_id_21(), and test000059::test_unique_id_21_2().
bool CModelEntity::setExpressionPtr | ( | CExpression * | pExpression | ) |
Set the expression for non FIXED model values
CExpression* |
Definition at line 255 of file CModelValue.cpp.
References CCopasiContainer::add(), compile(), isFixed(), mpExpression, mpModel, pdelete, CModel::setCompileFlag(), CCopasiObject::setObjectName(), and CCopasiObject::setObjectParent().
Referenced by SBMLImporter::importRuleForModelEntity().
bool CModelEntity::setInitialExpression | ( | const std::string & | expression | ) |
Set the expression for ODE or REACTION model values
const | std::string & expression |
Definition at line 333 of file CModelValue.cpp.
References ASSIGNMENT, compile(), mpInitialExpression, mpModel, mStatus, CModel::setCompileFlag(), and CExpression::setInfix().
Referenced by CModel::convert2NonReversible(), CModelAdd::copyInitialExpression(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CCopasiXMLParser::ModelElement::end(), CQSpeciesDetail::save(), CQCompartment::save(), CQModelValue::save(), CQMoietiesTaskResult::slotCreateGlobalQuantity(), and CModelParameter::updateModel().
bool CModelEntity::setInitialExpressionPtr | ( | CExpression * | pExpression | ) |
Set the expression for non FIXED model values
CExpression* |
Definition at line 299 of file CModelValue.cpp.
References CCopasiContainer::add(), ASSIGNMENT, compile(), mpInitialExpression, mpModel, mStatus, pdelete, CModel::setCompileFlag(), CCopasiObject::setObjectName(), and CCopasiObject::setObjectParent().
Referenced by SBMLImporter::importInitialAssignments().
Set the initial value
const | C_FLOAT64 & initialValue |
Definition at line 383 of file CModelValue.cpp.
References mpIValue.
Referenced by CModel::createCompartment(), CModel::createModelValue(), CModel::determineIsAutonomous(), initObjects(), CCompartment::load(), CMetab::operator=(), CQSpeciesDetail::save(), CQCompartment::save(), CQModelValue::save(), CQGlobalQuantityDM::setData(), CQCompartmentDM::setData(), CQSpecieDM::setData(), CQSpeciesDetail::slotBtnNew(), and CModelParameter::updateModel().
Set the pointer to the initial value
C_FLOAT64 | * pInitialValue |
Definition at line 531 of file CModelValue.cpp.
References C_FLOAT64, mpIValue, mpIValueReference, and CCopasiObjectReference< CType >::setReference().
Referenced by CStateTemplate::add(), initObjects(), and CStateTemplate::remove().
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Set the object parent
const | CCopasiContainer * pParent |
Reimplemented from CCopasiObject.
Reimplemented in CMetab.
Definition at line 549 of file CModelValue.cpp.
References CStateTemplate::add(), C_FLOAT64, CCopasiObject::getObjectAncestor(), CModel::getStateTemplate(), mpIValue, mpModel, mpValue, pdelete, CStateTemplate::remove(), and CCopasiObject::setObjectParent().
Referenced by CCopasiDataModel::commonAfterLoad(), and CMetab::setObjectParent().
Set the rate (dmValue/dt)
const C_FLOAT64 & | rate |
Definition at line 388 of file CModelValue.cpp.
References mRate.
void CModelEntity::setSBMLId | ( | const std::string & | id | ) |
Sets the SBMLId.
Definition at line 632 of file CModelValue.cpp.
References mSBMLId.
Referenced by SBMLImporter::createCCompartmentFromCompartment(), SBMLImporter::createCMetabFromSpecies(), SBMLImporter::createCModelFromSBMLDocument(), SBMLImporter::createCModelValueFromParameter(), CSBMLExporter::createCompartment(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), CCopasiXMLParser::SBMLMapElement::start(), test000103::test_bug1743_l2(), and test000103::test_bug1743_l3().
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Set the status
const | CModelEntity::Status & status |
Reimplemented in CMetab.
Definition at line 395 of file CModelValue.cpp.
References CCopasiContainer::add(), ASSIGNMENT, calculate(), CCopasiObject::clearRefresh(), CExpression::createInitialExpression(), FIXED, CCopasiObject::getDirectDependencies(), CCopasiObject::getObjectDataModel(), mpExpression, mpInitialExpression, mpIValueReference, mpModel, mpRateReference, mpValue, mpValueReference, mRate, mStatus, mUsed, ODE, pdelete, REACTIONS, CModel::setCompileFlag(), CCopasiObject::setDirectDependencies(), CCopasiObject::setObjectName(), CCopasiObject::setRefresh(), setValuePtr(), and TIME.
Referenced by CModelAdd::addCompartments(), CModelAdd::addModelValues(), CCompartment::CCompartment(), CModel::CModel(), CModelEntity(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), SBMLImporter::importRuleForModelEntity(), CQCompartment::save(), CQModelValue::save(), CQGlobalQuantityDM::setData(), CQCompartmentDM::setData(), CMetab::setStatus(), test000058::test_bug1025_10(), test000058::test_bug1025_5(), test000059::test_unique_id_17(), test000059::test_unique_id_18(), test000059::test_unique_id_19(), test000059::test_unique_id_20(), test000059::test_unique_id_21(), and test000059::test_unique_id_21_2().
void CModelEntity::setUsed | ( | const bool & | used | ) |
Set whether the model entity is used during simulation
const | bool & used |
Definition at line 642 of file CModelValue.cpp.
References mUsed.
Referenced by CModel::buildStateTemplate(), and CModel::CModel().
Set the value
const | C_FLOAT64 & value |
Definition at line 378 of file CModelValue.cpp.
References mpValue.
Referenced by CHybridMethod::fireReaction(), CHybridMethodLSODA::fireReaction(), CHybridMethodODE45::fireReaction(), initObjects(), CQSpecieDM::setData(), and CStochMethod::updateSystemState().
Set the pointer to the value
C_FLOAT64 | * pValue |
Definition at line 540 of file CModelValue.cpp.
References C_FLOAT64, mpValue, mpValueReference, and CCopasiObjectReference< CType >::setReference().
Referenced by CStateTemplate::add(), initObjects(), CStateTemplate::remove(), and setStatus().
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The infix expression for objects of type ASSIGNMENT or ODE
Definition at line 336 of file CModelValue.h.
Referenced by calculate(), CMetab::calculate(), compile(), CMetab::compile(), getExpression(), getExpressionPtr(), setExpression(), setExpressionPtr(), setStatus(), and CMetab::setStatus().
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Optional initial expression
Definition at line 341 of file CModelValue.h.
Referenced by compile(), CMetab::compile(), CMetab::compileInitialValueDependencies(), getInitialExpression(), getInitialExpressionPtr(), CMetab::refreshInitialConcentration(), refreshInitialValue(), setInitialExpression(), setInitialExpressionPtr(), and setStatus().
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Pointer to the initial value of the model entity.
Definition at line 326 of file CModelValue.h.
Referenced by CCompartment::CCompartment(), CModel::CModel(), CModelEntity(), compile(), CModel::getInitialTime(), getInitialValue(), CModel::initObjects(), CModel::load(), operator<<(), CMetab::refreshInitialConcentration(), refreshInitialValue(), CMetab::refreshInitialValue(), CModel::setInitialTime(), setInitialValue(), setInitialValuePtr(), setObjectParent(), CModel::~CModel(), and ~CModelEntity().
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Definition at line 356 of file CModelValue.h.
Referenced by CMoiety::add(), compile(), CMetab::compileInitialValueDependencies(), CMetab::compileIsInitialConcentrationChangeAllowed(), CCompartment::getChildObjectUnits(), CMetab::getChildObjectUnits(), getDeletedObjects(), getInitialValueReference(), CCompartment::initObjects(), initObjects(), CMetab::initObjects(), CModel::initObjects(), setInitialValuePtr(), and setStatus().
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Definition at line 359 of file CModelValue.h.
Referenced by CMetab::calculate(), compile(), CMetab::compile(), CCompartment::getChildObjectUnits(), CMetab::getChildObjectUnits(), CMetab::getModel(), initObjects(), operator<<(), CMetab::operator=(), CMetab::refreshConcentration(), CMetab::refreshConcentrationRate(), CMetab::refreshInitialConcentration(), CMetab::refreshInitialValue(), CMetab::refreshNumber(), setExpression(), setExpressionPtr(), setInitialExpression(), setInitialExpressionPtr(), setObjectParent(), setStatus(), CMetab::setStatus(), and ~CModelEntity().
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Definition at line 358 of file CModelValue.h.
Referenced by compile(), CMetab::compile(), CCompartment::getChildObjectUnits(), CMetab::getChildObjectUnits(), getDeletedObjects(), getRateReference(), initObjects(), CMetab::initObjects(), CMetab::mustBeDeleted(), setStatus(), and CMetab::setStatus().
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Pointer to the value of the model entity.
Definition at line 321 of file CModelValue.h.
Referenced by calculate(), CMetab::calculate(), CModel::CModel(), CModelEntity(), CModel::getTime(), getValue(), getValuePointer(), CModel::initObjects(), operator<<(), CMetab::refreshConcentration(), CMetab::refreshNumber(), CMetab::refreshTransitionTime(), setObjectParent(), setStatus(), CModel::setTime(), setValue(), setValuePtr(), CModel::~CModel(), and ~CModelEntity().
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Definition at line 357 of file CModelValue.h.
Referenced by CMoiety::add(), compile(), CMetab::compile(), CModel::compile(), CCompartment::getChildObjectUnits(), CMetab::getChildObjectUnits(), getDeletedObjects(), getValueObject(), getValueReference(), CCompartment::initObjects(), initObjects(), CMetab::initObjects(), CModel::initObjects(), setStatus(), CMetab::setStatus(), and setValuePtr().
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Rate of change/time.
Definition at line 331 of file CModelValue.h.
Referenced by calculate(), CMetab::calculate(), CMetab::compile(), getRate(), initObjects(), CModel::initObjects(), operator<<(), CMetab::operator=(), CMetab::refreshConcentrationRate(), CMetab::refreshRate(), CMetab::refreshTransitionTime(), setRate(), and setStatus().
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The id of the corresponding parameter in an SBML file. This value is either set upon importing an SBML file, or when the object is first exported to an SBML file.
Definition at line 47 of file CModelValue.h.
Referenced by getSBMLId(), initObjects(), and setSBMLId().
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Status of the model entity.
Definition at line 347 of file CModelValue.h.
Referenced by calculate(), CModelEntity(), compile(), getInitialExpression(), getStatus(), isFixed(), setInitialExpression(), setInitialExpressionPtr(), and setStatus().
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Indicates whether the model value is used, i.e., must be calculated during the simulation
Definition at line 353 of file CModelValue.h.
Referenced by isUsed(), setStatus(), and setUsed().
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String representation of the states
Definition at line 67 of file CModelValue.h.
Referenced by CQCompartment::CQCompartment(), CQCompartmentDM::CQCompartmentDM(), CQGlobalQuantityDM::CQGlobalQuantityDM(), CQSpecieDM::CQSpecieDM(), CQSpeciesDetail::CQSpeciesDetail(), CQGlobalQuantityDM::data(), CQCompartmentDM::data(), CQSpecieDM::data(), CODEExporter::exportCompartments(), CODEExporter::exportMetabolites(), CODEExporter::exportMetabolitesConcentrations(), CODEExporter::exportModelEntityExpression(), CODEExporter::exportModelValues(), CQGlobalQuantityDM::flags(), CQCompartmentDM::flags(), CQSpecieDM::flags(), CQModelValue::init(), CQSpeciesDetail::load(), CQCompartment::load(), CQModelValue::load(), StateSubwidget::loadCompartments(), StateSubwidget::loadMetabolites(), StateSubwidget::loadModelValues(), CQUpdatesWidget::loadObjectsTable(), CQGlobalQuantityDM::setData(), CQCompartmentDM::setData(), CQSpecieDM::setData(), and CQParameterOverviewDM::typeData().
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XML representation of the states
Definition at line 72 of file CModelValue.h.
Referenced by CCopasiXML::saveModel(), CCopasiXML::saveModelParameter(), CCopasiXMLParser::ModelParameterElement::start(), CCopasiXMLParser::MetaboliteElement::start(), CCopasiXMLParser::CompartmentElement::start(), and CCopasiXMLParser::ModelValueElement::start().