COPASI API
4.16.103
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#include <CMetab.h>
Public Member Functions | |
virtual void | calculate () |
void | cleanup () |
CMetab (const std::string &name="NoName", const CCopasiContainer *pParent=NULL) | |
CMetab (const CMetab &src, const CCopasiContainer *pParent=NULL) | |
virtual bool | compile () |
bool | compileInitialValueDependencies () |
void | compileIsInitialConcentrationChangeAllowed () |
virtual std::string | getChildObjectUnits (const CCopasiObject *pObject) const |
const CCompartment * | getCompartment () const |
const C_FLOAT64 & | getConcentration () const |
C_FLOAT64 | getConcentrationRate () const |
CCopasiObject * | getConcentrationRateReference () const |
CConcentrationReference * | getConcentrationReference () const |
virtual DataObjectSet | getDeletedObjects () const |
const C_FLOAT64 & | getInitialConcentration () const |
CConcentrationReference * | getInitialConcentrationReference () const |
const CModel * | getModel () const |
const CMoiety * | getMoiety () const |
virtual std::string | getObjectDisplayName (bool regular=true, bool richtext=false) const |
const C_FLOAT64 & | getTransitionTime () const |
virtual const CCopasiObject * | getValueObject () const |
virtual void * | getValuePointer () const |
void | initCompartment (const CCompartment *pCompartment=NULL) |
bool | isDependent () const |
const bool & | isInitialConcentrationChangeAllowed () const |
C_INT32 | load (CReadConfig &configbuffer) |
virtual bool | mustBeDeleted (const DataObjectSet &deletedObjects) const |
CMetab & | operator= (const CMetabOld &rhs) |
void | refreshConcentration () |
void | refreshConcentrationRate () |
void | refreshInitialConcentration () |
virtual void | refreshInitialValue () |
void | refreshNumber () |
void | refreshRate () |
void | refreshTransitionTime () |
void | setConcentration (const C_FLOAT64 concentration) |
void | setDependentOn (const CMoiety *pMoiety) |
void | setInitialConcentration (const C_FLOAT64 &initialConcentration) |
virtual bool | setObjectParent (const CCopasiContainer *pParent) |
virtual void | setStatus (const CModelEntity::Status &status) |
void | setTransitionTime (const C_FLOAT64 &transitionTime) |
~CMetab () | |
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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) | |
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 |
CCopasiObject * | getValueReference () const |
bool | isFixed () const |
const bool & | isUsed () const |
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) |
void | setRate (const C_FLOAT64 &rate) |
void | setSBMLId (const std::string &id) |
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 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 |
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 Member Functions | |
static C_FLOAT64 | convertToConcentration (const C_FLOAT64 &number, const CCompartment &compartment, const CModel &model) |
static C_FLOAT64 | convertToNumber (const C_FLOAT64 &concentration, const CCompartment &compartment, const CModel &model) |
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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) |
Protected Attributes | |
CCopasiObjectReference < C_FLOAT64 > * | mpConcRateReference |
CConcentrationReference * | mpConcReference |
CConcentrationReference * | mpIConcReference |
CCopasiObjectReference < C_FLOAT64 > * | mpTTReference |
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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 | |
C_FLOAT64 | mConc |
C_FLOAT64 | mConcRate |
C_FLOAT64 | mIConc |
bool | mIsInitialConcentrationChangeAllowed |
const CCompartment * | mpCompartment |
const CMoiety * | mpMoiety |
std::vector< std::pair < C_FLOAT64, const C_FLOAT64 * > > | mRateVector |
C_FLOAT64 | mTT |
Friends | |
void | CMoiety::add (C_FLOAT64 value, CMetab *pMetabolite) |
std::ostream & | operator<< (std::ostream &os, const CMetab &d) |
Additional Inherited Members | |
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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 |
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static const std::string | StatusName [] |
static const char * | XMLStatus [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
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enum | Flag { Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8, Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80, ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800, Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000, Root = 0x10000, Gui = 0x20000 } |
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template<class CType > | |
CCopasiObject * | addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
template<class CType > | |
CCopasiObject * | addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
template<class CType > | |
CCopasiObject * | addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
void | initObjects () |
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CCopasiObject () | |
CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | |
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static CRenameHandler * | smpRenameHandler = NULL |
CMetab::CMetab | ( | const std::string & | name = "NoName" , |
const CCopasiContainer * | pParent = NULL |
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Default constructor
const | std::string & name (default: "NoName") |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 46 of file CMetab.cpp.
References CKeyFactory::add(), CONSTRUCTOR_TRACE, CCopasiRootContainer::getKeyFactory(), CCopasiObject::getObjectParent(), initCompartment(), initObjects(), CAnnotation::mKey, CModelEntity::REACTIONS, setConcentration(), setInitialConcentration(), and setStatus().
CMetab::CMetab | ( | const CMetab & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CMetab & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 74 of file CMetab.cpp.
References CKeyFactory::add(), CONSTRUCTOR_TRACE, CCopasiRootContainer::getKeyFactory(), initCompartment(), initObjects(), CAnnotation::mKey, and mpCompartment.
CMetab::~CMetab | ( | ) |
Destructor.
Definition at line 111 of file CMetab.cpp.
References DESTRUCTOR_TRACE, CCopasiRootContainer::getKeyFactory(), CAnnotation::mKey, and CKeyFactory::remove().
Calculate the value or the rate depending whether we have an ASIGNMENT or ODE
Reimplemented from CModelEntity.
Definition at line 669 of file CMetab.cpp.
References CModelEntity::ASSIGNMENT, CExpression::calcValue(), CModelEntity::FIXED, CMoiety::getDependentNumber(), CModel::getQuantity2NumberFactor(), CModelEntity::getStatus(), CModelEntity::getValue(), isDependent(), mConc, mpCompartment, CModelEntity::mpExpression, CModelEntity::mpModel, mpMoiety, CModelEntity::mpValue, CModelEntity::mRate, CModelEntity::ODE, and CModelEntity::REACTIONS.
Referenced by compile(), and setStatus().
void CMetab::cleanup | ( | ) |
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Compile the model value.
Reimplemented from CModelEntity.
Definition at line 385 of file CMetab.cpp.
References CModelEntity::ASSIGNMENT, CCopasiVector< T >::begin(), calculate(), CCopasiObject::clearDirectDependencies(), CCopasiObject::clearRefresh(), CExpression::compile(), compileInitialValueDependencies(), CExpression::createInitialExpression(), CCopasiVector< T >::end(), CModelEntity::FIXED, CCopasiObject::getDirectDependencies(), CCopasiObject::getObjectAncestor(), CCopasiObject::getObjectDataModel(), CModelEntity::getRateReference(), CModel::getReactions(), CModelEntity::getStatus(), CModelEntity::getValueReference(), mConcRate, CAnnotation::mKey, mpCompartment, mpConcRateReference, mpConcReference, CModelEntity::mpExpression, CModelEntity::mpInitialExpression, CModelEntity::mpModel, CModelEntity::mpRateReference, mpTTReference, CModelEntity::mpValueReference, CModelEntity::mRate, mRateVector, mTT, CModelEntity::ODE, pdelete, CModelEntity::REACTIONS, refreshConcentration(), refreshConcentrationRate(), refreshNumber(), refreshRate(), refreshTransitionTime(), CCopasiObject::setDirectDependencies(), CCopasiObject::setObjectName(), and CCopasiObject::setRefresh().
bool CMetab::compileInitialValueDependencies | ( | ) |
Compile the initial particle number and initial concentration dependencies.
Definition at line 590 of file CMetab.cpp.
References CModelEntity::ASSIGNMENT, CExpression::calcValue(), CExpression::compile(), CCopasiObject::getDirectDependencies(), CEvaluationTree::getInfix(), CModelEntity::getInitialValueReference(), CCopasiObject::getObjectAncestor(), CModelEntity::getStatus(), CEvaluationTree::isUsable(), mIConc, mpCompartment, mpIConcReference, CModelEntity::mpInitialExpression, CModelEntity::mpIValueReference, and CCopasiObject::setDirectDependencies().
Referenced by compile().
void CMetab::compileIsInitialConcentrationChangeAllowed | ( | ) |
Determine whether changing the initial concentration is allowed
Definition at line 644 of file CMetab.cpp.
References CCopasiObject::hasCircularDependencies(), mIsInitialConcentrationChangeAllowed, mpIConcReference, and CModelEntity::mpIValueReference.
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Converts the number to concentration
const | C_FLOAT64 & number |
const | CCompartment & compartment |
const | CModel & model |
Definition at line 41 of file CMetab.cpp.
References CModelEntity::getInitialValue(), and CModel::getNumber2QuantityFactor().
Referenced by CQSpecieDM::setData(), and CQSpeciesDetail::slotInitialValueLostFocus().
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Converts the concentration to number
const | C_FLOAT64 & concentration |
const | CCompartment & compartment |
const | CModel & model |
Definition at line 35 of file CMetab.cpp.
References CModelEntity::getInitialValue(), and CModel::getQuantity2NumberFactor().
Referenced by operator=(), CQSpecieDM::setData(), and CQSpeciesDetail::slotInitialValueLostFocus().
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Retrieve the units of the child object.
Reimplemented from CCopasiContainer.
Definition at line 118 of file CMetab.cpp.
References CCompartment::getChildObjectUnits(), CModel::getFrequencyUnitsDisplayString(), CModelEntity::getInitialValueReference(), CModel::getQuantityUnitsDisplayString(), CModel::getTimeUnitsDisplayString(), mpCompartment, mpConcRateReference, mpConcReference, mpIConcReference, CModelEntity::mpIValueReference, CModelEntity::mpModel, CModelEntity::mpRateReference, mpTTReference, and CModelEntity::mpValueReference.
Referenced by CModelParameter::getUnit().
const CCompartment * CMetab::getCompartment | ( | ) | const |
Definition at line 222 of file CMetab.cpp.
References mpCompartment.
Referenced by CModelAdd::addMetabolites(), CModel::calculateElasticityMatrix(), CTimeSeries::compile(), CChemEqInterface::completeCompartments(), CQSpeciesDetail::copy(), CMathObject::createExtensiveODERateExpression(), CMathObject::createExtensiveValueExpression(), CSBMLExporter::createInitialAssignment(), CMathObject::createIntensiveRateExpression(), CMathObject::createIntensiveValueExpression(), CCopasiSpringLayout::createLayout(), CModelExpansion::createLinearArray(), CSBMLExporter::createMetabolite(), CModelExpansion::createRectangularArray(), CSBMLExporter::createRule(), CCSPMethod::cspstep(), CQSpecieDM::data(), CModelExpansion::duplicateMetab(), CSBMLExporter::exportEventAssignments(), CODEExporter::exportMetabolites(), CODEExporter::exportModelEntityExpression(), CChemEqInterface::getCompartment(), CMetabNameInterface::getDisplayName(), SBMLImporter::importEvent(), SBMLImporter::importInitialAssignments(), CCopasiSpringLayout::initFromLayout(), CTSSAMethod::initializeAtol(), CModel::initializeAtolVector(), CQSpeciesDetail::load(), CQSimpleSelectionTree::populateTree(), CCopasiSpringLayout::randomize(), CModelExpansion::replaceInMetab(), CSBMLExporter::replaceSpeciesReferences(), CQSpeciesDetail::save(), CCopasiXML::saveModel(), CQSpecieDM::setData(), CReaction::setScalingFactor(), CNewtonMethod::solveJacobianXeqB(), CNewtonMethod::targetFunction(), and CMMLOutput::writeRHS().
const C_FLOAT64 & CMetab::getConcentration | ( | ) | const |
Definition at line 218 of file CMetab.cpp.
References mConc.
Referenced by CModel::calculateElasticityMatrix(), CQSpecieDM::data(), operator<<(), and CQSpeciesDetail::setFramework().
C_FLOAT64 CMetab::getConcentrationRate | ( | ) | const |
Return rate of production of this metaboLite
Definition at line 870 of file CMetab.cpp.
References mConcRate, and refreshConcentrationRate().
Referenced by CQSpecieDM::data(), operator<<(), and CQSpeciesDetail::setFramework().
CCopasiObject * CMetab::getConcentrationRateReference | ( | ) | const |
Retrieve object referencing the concentration
Definition at line 867 of file CMetab.cpp.
References mpConcRateReference.
Referenced by findObjectByDisplayName(), CMathContainer::initializeMathObjects(), and CQSimpleSelectionTree::populateTree().
CConcentrationReference * CMetab::getConcentrationReference | ( | ) | const |
Retrieve object referencing the concentration
Definition at line 864 of file CMetab.cpp.
References mpConcReference.
Referenced by CModel::buildDependencyGraphs(), CModel::buildSimulatedSequence(), CMathObject::compileValue(), CMathObject::createExtensiveValueExpression(), CExpression::createInitialExpression(), findObjectByDisplayName(), CModel::getCorrespondingTransientObject(), CParticleReference::getDirectDependencies(), CMathContainer::initializeMathObjects(), CParticleReference::isPrerequisiteForContext(), and CQSimpleSelectionTree::populateTree().
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Retrieve the list of deleted numeric child objects;
Reimplemented from CModelEntity.
Definition at line 806 of file CMetab.cpp.
References CModelEntity::getDeletedObjects(), mpConcRateReference, mpConcReference, mpIConcReference, and mpTTReference.
Referenced by CModel::appendDependentModelObjects(), CQSpeciesDetail::loadReactionTable(), mustBeDeleted(), CModel::removeMetabolite(), CQSpecieDM::removeRows(), CQSpeciesDetail::slotBtnDelete(), and CQSpeciesDetail::slotSwitchToReaction().
const C_FLOAT64 & CMetab::getInitialConcentration | ( | ) | const |
Definition at line 220 of file CMetab.cpp.
References mIConc.
Referenced by CModelAdd::addMetabolites(), DataModelGUI::buildChangedObjects(), CSBMLExporter::createMetabolite(), CQSpecieDM::data(), CModelExpansion::duplicateMetab(), CODEExporter::exportExpression(), CODEExporter::exportMetabolites(), CQSpeciesDetail::load(), CQSpeciesDetail::save(), and test000087::test_simulate_reaction_flux_reference_1().
CConcentrationReference * CMetab::getInitialConcentrationReference | ( | ) | const |
Retrieve object referencing the initial concentration
Definition at line 861 of file CMetab.cpp.
References mpIConcReference.
Referenced by DataModelGUI::buildChangedObjects(), CModel::buildDependencyGraphs(), CModel::buildInitialRefreshSequence(), CMathObject::compileInitialValue(), CMathObject::createExtensiveValueExpression(), CExpression::createInitialExpression(), SliderDialog::determineCorrectObjectForSlider(), findObjectByDisplayName(), CModel::getCorrespondingTransientObject(), CParticleReference::getDirectDependencies(), getInitialCNForSBase(), CModelParameter::getUnit(), CMathContainer::initializeMathObjects(), CParticleReference::isPrerequisiteForContext(), CQSimpleSelectionTree::populateTree(), test000058::test_bug1025_3(), test000058::test_bug1025_8(), test000059::test_unique_id_11(), test000059::test_unique_id_2(), and test000059::test_unique_id_5().
const CModel * CMetab::getModel | ( | ) | const |
Definition at line 224 of file CMetab.cpp.
References CModelEntity::mpModel.
Referenced by CQSpeciesDetail::load(), CQSpeciesDetail::loadReactionTable(), CQSpeciesDetail::save(), CQSpeciesDetail::setFramework(), CQSpeciesDetail::slotBtnDelete(), CQSpeciesDetail::slotCompartmentChanged(), CQSpeciesDetail::slotInitialValueLostFocus(), and CQSpeciesDetail::slotSwitchToReaction().
const CMoiety * CMetab::getMoiety | ( | ) | const |
Retrieve a pointer to the moiety the species depends on
Definition at line 992 of file CMetab.cpp.
References mpMoiety.
Referenced by CMathObject::compileValue().
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Reimplemented from CCopasiObject.
Definition at line 974 of file CMetab.cpp.
References CMetabNameInterface::getDisplayName(), CCopasiObject::getObjectAncestor(), and CCopasiObject::getObjectDisplayName().
Referenced by CSBMLExporter::createMetabolite(), CQSelectionWizardPage::fillTree(), findObjectByDisplayName(), and CQSideCompoundWizardPage::alphaSorter::operator()().
const C_FLOAT64 & CMetab::getTransitionTime | ( | ) | const |
Retrieves the transition time
Definition at line 229 of file CMetab.cpp.
References mTT.
Referenced by CQSpeciesDetail::load(), and operator<<().
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Retrieve the object representing the value;
Reimplemented from CModelEntity.
Definition at line 889 of file CMetab.cpp.
References mpConcReference.
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Retrieve a pointer to the value;
Reimplemented from CModelEntity.
Definition at line 895 of file CMetab.cpp.
References C_FLOAT64, and mConc.
void CMetab::initCompartment | ( | const CCompartment * | pCompartment = NULL | ) |
Definition at line 209 of file CMetab.cpp.
References CCopasiObject::getObjectAncestor(), and mpCompartment.
Referenced by CMetab(), and setObjectParent().
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Initialize the contained CCopasiObjects
Definition at line 777 of file CMetab.cpp.
References CCopasiContainer::addObjectReference(), C_FLOAT64, CCopasiObjectReference< CType >::getValuePointer(), mConc, mConcRate, mIConc, mpConcRateReference, mpConcReference, mpIConcReference, CModelEntity::mpIValueReference, CModelEntity::mpRateReference, mpTTReference, CModelEntity::mpValueReference, mTT, pdelete, refreshInitialConcentration(), refreshInitialValue(), CCopasiObject::setObjectName(), CCopasiObject::setRefresh(), and CCopasiObject::ValueDbl.
Referenced by CMetab().
bool CMetab::isDependent | ( | ) | const |
Retrieve whether the metabolite dependent
Definition at line 989 of file CMetab.cpp.
References mpMoiety.
Referenced by calculate(), CLNAMethod::calculateCovarianceMatrixReduced(), CODEExporter::exportExpression(), CODEExporter::exportMetabolites(), CODEExporter::exportODEs(), CODEExporterBM::exportSingleMetabolite(), CODEExporterXPPAUT::exportSingleMetabolite(), CODEExporterC::exportSingleMetabolite(), CODEExporter::isModelEntityExpressionODEExporterCompatible(), CParticleReference::isPrerequisiteForContext(), CODEExporterC::preprocess(), and CODEExporter::preprocess().
const bool & CMetab::isInitialConcentrationChangeAllowed | ( | ) | const |
Check whether changing the initial concentration is allowed
Definition at line 664 of file CMetab.cpp.
References mIsInitialConcentrationChangeAllowed.
Referenced by DataModelGUI::buildChangedObjects(), CModel::buildInitialRefreshSequence(), SliderDialog::determineCorrectObjectForSlider(), CQSpecieDM::flags(), and CQSpeciesDetail::setFramework().
C_INT32 CMetab::load | ( | CReadConfig & | configbuffer | ) |
Loads an object with data coming from a CReadConfig object. (CReadConfig object reads an input stream)
pconfigbuffer | reference to a CReadConfig object. |
Definition at line 922 of file CMetab.cpp.
References C_INT32, CCopasiObject::getObjectName(), CReadConfig::getVariable(), METAB_MOIETY, mIConc, CModelEntity::REACTIONS, CReadConfig::SEARCH, setConcentration(), setInitialConcentration(), CCopasiObject::setObjectName(), setStatus(), and CCopasiMessage::WARNING.
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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 CModelEntity.
Definition at line 819 of file CMetab.cpp.
References getDeletedObjects(), CModelEntity::getStatus(), mpConcRateReference, CModelEntity::mpRateReference, mpTTReference, and CModelEntity::REACTIONS.
Assignment operator.
Definition at line 93 of file CMetab.cpp.
References C_FLOAT64, convertToNumber(), CCopasiObject::getObjectName(), mConcRate, CMetabOld::mIConc, mpCompartment, CModelEntity::mpModel, CModelEntity::mRate, CMetabOld::mStatus, mTT, CModelEntity::setInitialValue(), CCopasiObject::setObjectName(), and setStatus().
void CMetab::refreshConcentration | ( | ) |
Definition at line 281 of file CMetab.cpp.
References CModel::getNumber2QuantityFactor(), CModelEntity::getValue(), mConc, mpCompartment, CModelEntity::mpModel, and CModelEntity::mpValue.
Referenced by CConcentrationReference::CConcentrationReference(), compile(), CHybridMethod::fireReaction(), CHybridMethodLSODA::fireReaction(), CHybridMethodODE45::fireReaction(), setStatus(), and CStochMethod::updateSystemState().
void CMetab::refreshConcentrationRate | ( | ) |
Calculate the concentration rate.
Definition at line 876 of file CMetab.cpp.
References CModel::getNumber2QuantityFactor(), CModelEntity::getRate(), CModelEntity::getValue(), mConc, mConcRate, mpCompartment, CModelEntity::mpModel, and CModelEntity::mRate.
Referenced by compile(), getConcentrationRate(), and setStatus().
void CMetab::refreshInitialConcentration | ( | ) |
Definition at line 269 of file CMetab.cpp.
References CExpression::calcValue(), CEvaluationTree::getInfix(), CModelEntity::getInitialValue(), CModel::getNumber2QuantityFactor(), CModelEntity::isFixed(), mConc, mIConc, mpCompartment, CModelEntity::mpInitialExpression, CModelEntity::mpIValue, and CModelEntity::mpModel.
Referenced by initObjects().
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Refresh the initial value
Reimplemented from CModelEntity.
Definition at line 264 of file CMetab.cpp.
References CModelEntity::getInitialValue(), CModel::getQuantity2NumberFactor(), mIConc, mpCompartment, CModelEntity::mpIValue, and CModelEntity::mpModel.
Referenced by CModel::createMetabolite(), and initObjects().
void CMetab::refreshNumber | ( | ) |
Definition at line 286 of file CMetab.cpp.
References CModel::getQuantity2NumberFactor(), CModelEntity::getValue(), mConc, mpCompartment, CModelEntity::mpModel, and CModelEntity::mpValue.
Referenced by compile(), setStatus(), and CSensMethod::setValue().
void CMetab::refreshRate | ( | ) |
Calculate the particle rate.
Definition at line 696 of file CMetab.cpp.
References CModelEntity::ASSIGNMENT, CModelEntity::FIXED, CModelEntity::getStatus(), CModelEntity::mRate, mRateVector, CModelEntity::ODE, and CModelEntity::REACTIONS.
Referenced by compile(), and setStatus().
void CMetab::refreshTransitionTime | ( | ) |
Calculate the transition time.
Definition at line 728 of file CMetab.cpp.
References CModelEntity::ASSIGNMENT, C_FLOAT64, CModelEntity::FIXED, CModelEntity::getStatus(), min, CModelEntity::mpValue, CModelEntity::mRate, mRateVector, mTT, CModelEntity::ODE, and CModelEntity::REACTIONS.
Referenced by compile().
Definition at line 250 of file CMetab.cpp.
References CModelEntity::isFixed(), and mConc.
Referenced by CMetab(), load(), and CSensMethod::setValue().
Set whether the metabolite is dependent, i.e., calculated by a moiety
const | CMoiety * pMoiety |
Definition at line 986 of file CMetab.cpp.
References mpMoiety.
Referenced by CMoiety::add().
Definition at line 257 of file CMetab.cpp.
References mIConc.
Referenced by CMetab(), CModel::createMetabolite(), load(), CQSpeciesDetail::save(), CQSpecieDM::setData(), and CQSpeciesDetail::slotBtnNew().
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Sets the parent of the metabolite;
const | CCopasiContainer * pParent |
Reimplemented from CModelEntity.
Definition at line 231 of file CMetab.cpp.
References CModelEntity::FIXED, CModelEntity::getStatus(), initCompartment(), CModelEntity::REACTIONS, CModelEntity::setObjectParent(), and setStatus().
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Set the status
const | CModelEntity::Status & status |
Reimplemented from CModelEntity.
Definition at line 291 of file CMetab.cpp.
References CModelEntity::ASSIGNMENT, calculate(), CCopasiObject::clearRefresh(), CModelEntity::FIXED, CCopasiObject::getDirectDependencies(), CModelEntity::getStatus(), CModelEntity::getValueReference(), mpCompartment, mpConcRateReference, mpConcReference, CModelEntity::mpExpression, CModelEntity::mpModel, CModelEntity::mpRateReference, CModelEntity::mpValueReference, CModelEntity::ODE, CModelEntity::REACTIONS, refreshConcentration(), refreshConcentrationRate(), refreshNumber(), refreshRate(), CCopasiObject::setDirectDependencies(), CCopasiObject::setRefresh(), and CModelEntity::setStatus().
Referenced by CModelAdd::addMetabolites(), CMetab(), SBMLImporter::createCMetabFromSpecies(), CModel::createMetabolite(), load(), operator=(), CQSpeciesDetail::save(), CQSpecieDM::setData(), and setObjectParent().
Set transition time
const C_FLOAT64 & | transitionTime |
Definition at line 226 of file CMetab.cpp.
References mTT.
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ostream operator
Definition at line 900 of file CMetab.cpp.
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Concentration of the metabolite as double.
Definition at line 211 of file CMetab.h.
Referenced by calculate(), getConcentration(), getValuePointer(), initObjects(), operator<<(), refreshConcentration(), refreshConcentrationRate(), refreshInitialConcentration(), refreshNumber(), and setConcentration().
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The rate of concentration change
Definition at line 221 of file CMetab.h.
Referenced by compile(), getConcentrationRate(), initObjects(), operator=(), and refreshConcentrationRate().
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Initial concentration of the metabolite as double
Definition at line 216 of file CMetab.h.
Referenced by compileInitialValueDependencies(), getInitialConcentration(), initObjects(), load(), operator<<(), refreshInitialConcentration(), refreshInitialValue(), and setInitialConcentration().
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Definition at line 241 of file CMetab.h.
Referenced by compileIsInitialConcentrationChangeAllowed(), and isInitialConcentrationChangeAllowed().
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pointer to the compartment the metabolite is located in. The metab needs to know about volumes.
Definition at line 232 of file CMetab.h.
Referenced by calculate(), CMetab(), compile(), compileInitialValueDependencies(), getChildObjectUnits(), getCompartment(), initCompartment(), operator<<(), operator=(), refreshConcentration(), refreshConcentrationRate(), refreshInitialConcentration(), refreshInitialValue(), refreshNumber(), and setStatus().
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Definition at line 246 of file CMetab.h.
Referenced by compile(), getChildObjectUnits(), getConcentrationRateReference(), getDeletedObjects(), initObjects(), mustBeDeleted(), and setStatus().
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Definition at line 245 of file CMetab.h.
Referenced by compile(), getChildObjectUnits(), getConcentrationReference(), getDeletedObjects(), getValueObject(), initObjects(), and setStatus().
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Definition at line 244 of file CMetab.h.
Referenced by compileInitialValueDependencies(), compileIsInitialConcentrationChangeAllowed(), getChildObjectUnits(), getDeletedObjects(), getInitialConcentrationReference(), and initObjects().
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If dependent the moiety the metabolite is calculated from
Definition at line 237 of file CMetab.h.
Referenced by calculate(), getMoiety(), isDependent(), and setDependentOn().
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Definition at line 247 of file CMetab.h.
Referenced by compile(), getChildObjectUnits(), getDeletedObjects(), initObjects(), and mustBeDeleted().
Definition at line 239 of file CMetab.h.
Referenced by compile(), refreshRate(), and refreshTransitionTime().
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Transition time of the metabolite
Definition at line 226 of file CMetab.h.
Referenced by compile(), getTransitionTime(), initObjects(), operator<<(), operator=(), refreshTransitionTime(), and setTransitionTime().