CModel Member List

This is the complete list of members for CModel, including all inherited members.

add(CCopasiObject *pObject, const bool &adopt=true)	CCopasiContainer	[virtual]
addDirectDependency(const CCopasiObject *pObject)	CCopasiObject
addMatrixReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)	CCopasiContainer	[inline, protected]
addObjectReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)	CCopasiContainer	[inline, protected]
addVectorReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)	CCopasiContainer	[inline, protected]
appendDependentCompartments(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const	CModel
appendDependentEvents(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const	CModel
appendDependentMetabolites(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const	CModel
appendDependentModelObjects(const std::set< const CCopasiObject * > &candidates, std::set< const CCopasiObject * > &dependentReactions, std::set< const CCopasiObject * > &dependentMetabolites, std::set< const CCopasiObject * > &dependentCompartments, std::set< const CCopasiObject * > &dependentModelValues, std::set< const CCopasiObject * > &dependentEvents) const	CModel
appendDependentModelValues(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const	CModel
appendDependentReactions(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const	CModel
applyInitialValues()	CModel
AreaUnit enum name	CModel
AreaUnitNames	CModel	[static]
Array enum value	CCopasiObject	[protected]
ASSIGNMENT enum value	CModelEntity
buildInitialRefreshSequence(std::set< const CCopasiObject * > &changedObjects)	CModel
buildLinkZero()	CModel
buildMoieties()	CModel
buildRedStoi()	CModel
buildStoi()	CModel
buildUpdateSequence(const std::set< const CCopasiObject * > &objects, const std::set< const CCopasiObject * > &uptoDateObjects, const std::set< const CCopasiObject * > &context=std::set< const CCopasiObject * >())	CCopasiObject	[static]
calculate()	CModelEntity	[virtual]
calculateDerivatives(C_FLOAT64 *derivatives)	CModel
calculateDerivativesX(C_FLOAT64 *derivativesX)	CModel
calculateDivergence() const	CModel
calculateElasticityMatrix(const C_FLOAT64 &factor, const C_FLOAT64 &resolution)	CModel
calculateJacobian(CMatrix< C_FLOAT64 > &jacobian, const C_FLOAT64 &derivationFactor, const C_FLOAT64 &resolution)	CModel
calculateJacobianX(CMatrix< C_FLOAT64 > &jacobianX, const C_FLOAT64 &derivationFactor, const C_FLOAT64 &resolution)	CModel
calculateRootDerivatives(CVector< C_FLOAT64 > &rootDerivatives)	CModel
CAnnotation()	CAnnotation
CAnnotation(const CAnnotation &src)	CAnnotation
CCopasiContainer(const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)	CCopasiContainer
CCopasiContainer(const CCopasiContainer &src, const CCopasiContainer *pParent=NULL)	CCopasiContainer
CCopasiObject()	CCopasiObject	[protected]
CCopasiObject(const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)	CCopasiObject	[protected]
CCopasiObject(const CCopasiObject &src, const CCopasiContainer *pParent=NULL)	CCopasiObject
cleanup()	CModel
clearDirectDependencies()	CCopasiObject
clearRefresh()	CCopasiObject
cm enum value	CModel
cm2 enum value	CModel
CModel(CCopasiContainer *pParent)	CModel
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
CModelEntity(const CModelEntity &src, const CCopasiContainer *pParent=NULL)	CModelEntity
compileDefaultMetabInitialValueDependencies()	CModel
compileIfNecessary(CProcessReport *pProcessReport)	CModel
Container enum value	CCopasiObject	[protected]
convert2NonReversible()	CModel
createCompartment(const std::string &name, const C_FLOAT64 &volume=1.0)	CModel
createEvent(const std::string &name)	CModel
createMetabolite(const std::string &name, const std::string &compartment, const C_FLOAT64 &iconc=1.0, const CModelEntity::Status &status=CModelEntity::REACTIONS)	CModel
createModelValue(const std::string &name, const C_FLOAT64 &value=0.0)	CModel
createReaction(const std::string &name)	CModel
d enum value	CModel
DataModel enum value	CCopasiObject	[protected]
dependsOn(std::set< const CCopasiObject * > candidates, const std::set< const CCopasiObject * > &context=std::set< const CCopasiObject * >()) const	CCopasiObject
deterministic enum value	CModel
dimensionlessArea enum value	CModel
dimensionlessLength enum value	CModel
dimensionlessQuantity enum value	CModel
dimensionlessTime enum value	CModel
dimensionlessVolume enum value	CModel
dm enum value	CModel
dm2 enum value	CModel
EmptyList	CCopasiContainer	[static]
evaluateRoots(CVectorCore< C_FLOAT64 > &rootValues, const bool &ignoreDiscrete)	CModel
findMetabByName(const std::string &Target) const	CModel
findMoiety(const std::string &Target) const	CModel
FIXED enum value	CModelEntity
fl enum value	CModel
Flag enum name	CCopasiObject	[protected]
fm enum value	CModel
fm2 enum value	CModel
fMol enum value	CModel
forceCompile(CProcessReport *pProcessReport)	CModel
fs enum value	CModel
getAllDependencies(std::set< const CCopasiObject * > &dependencies, const std::set< const CCopasiObject * > &context) const	CCopasiObject
getAreaUnitEnum() const	CModel
getAreaUnitName() const	CModel
getAvogadro() const	CModel
getChildObjectUnits(const CCopasiObject *pObject) const	CModel	[virtual]
getCN() const	CCopasiObject	[virtual]
getCompartments()	CModel
getCompartments() const	CModel
getConcentrationRateUnitsDisplayString() const	CModel
getConcentrationUnitsDisplayString() const	CModel
getDeletedObjects() const	CModelEntity	[virtual]
getDirectDependencies(const std::set< const CCopasiObject * > &context=std::set< const CCopasiObject * >()) const	CCopasiObject	[virtual]
getEvents()	CModel
getEvents() const	CModel
getExpression() const	CModelEntity
getExpressionPtr() const	CModelEntity
getExpressionPtr()	CModelEntity
getFrequencyUnitsDisplayString() const	CModel
getInitialExpression() const	CModelEntity
getInitialExpressionPtr() const	CModelEntity
getInitialExpressionPtr()	CModelEntity
getInitialState() const	CModel
getInitialTime() const	CModel
getInitialValue() const	CModelEntity
getInitialValueReference() const	CModelEntity
getKey() const	CModel	[virtual]
getL() const	CModel
getL0() const	CModel
getLengthUnitEnum() const	CModel
getLengthUnitName() const	CModel
getListOfConstantRefreshes() const	CModel
getListOfInitialRefreshes() const	CModel
getListOfNonSimulatedRefreshes() const	CModel
getListOfSimulatedRefreshes() const	CModel
getMetabolitePermutation() const	CModel
getMetabolites() const	CModel
getMetabolites()	CModel
getMetabolitesX() const	CModel
getMetabolitesX()	CModel
getMiriamAnnotation() const	CAnnotation
getModelType() const	CModel
getModelValues() const	CModel
getModelValues()	CModel
getMoieties() const	CModel
getNotes() const	CAnnotation
getNumAssignmentMetabs() const	CModel
getNumber2QuantityFactor() const	CModel
getNumDependentReactionMetabs() const	CModel
getNumIndependentReactionMetabs() const	CModel
getNumMetabs() const	CModel
getNumModelValues() const	CModel
getNumODEMetabs() const	CModel
getNumRoots() const	CModel
getNumVariableMetabs() const	CModel
getObject(const CCopasiObjectName &cn) const	CCopasiContainer	[virtual]
getObjectAncestor(const std::string &type) const	CCopasiObject
getObjectDataModel()	CCopasiObject
getObjectDataModel() const	CCopasiObject
getObjectDisplayName(bool regular=true, bool richtext=false) const	CCopasiObject	[virtual]
getObjectName() const	CCopasiObject
getObjectParent() const	CCopasiObject
getObjects() const	CCopasiContainer	[virtual]
getObjectType() const	CCopasiObject
getParticleFlux() const	CModel
getProcessQueueExecutionTime() const	CModel
getQuantity2NumberFactor() const	CModel
getQuantityRateUnitsDisplayString() const	CModel
getQuantityUnitEnum() const	CModel
getQuantityUnitName() const	CModel
getQuantityUnitOldXMLName() const	CModel
getRate() const	CModelEntity
getRateReference() const	CModelEntity
getReactions()	CModel
getReactions() const	CModel
getRedStoi() const	CModel
getRefresh() const	CCopasiObject
getRootFinders() const	CModel
getSBMLId() const	CModelEntity
getState() const	CModel
getStateTemplate() const	CModel
getStateTemplate()	CModel
getStatus() const	CModelEntity
getStoi() const	CModel
getStoiReordered() const	CModel
getTime() const	CModel
getTimeUnitEnum() const	CModel
getTimeUnitName() const	CModel
getTimeUnitsDisplayString() const	CModel
getTotSteps() const	CModel
getUnits() const	CCopasiContainer	[virtual]
getUpdateMethod() const	CCopasiObject
getUptoDateObjects() const	CModel
getValue() const	CModelEntity
getValueObject() const	CModelEntity	[virtual]
getValuePointer() const	CModelEntity	[virtual]
getValueReference() const	CModelEntity
getVolumeRateUnitsDisplayString() const	CModel
getVolumeUnitEnum() const	CModel
getVolumeUnitName() const	CModel
getVolumeUnitsDisplayString() const	CModel
Gui enum value	CCopasiObject	[protected]
h enum value	CModel
hasCircularDependencies(std::set< const CCopasiObject * > &candidates, std::set< const CCopasiObject * > &verified, const std::set< const CCopasiObject * > &context) const	CCopasiObject
hasReversibleReaction() const	CModel
hasUpdateMethod() const	CCopasiObject
initializeAtolVector(const C_FLOAT64 &baseTolerance, const bool &reducedModel) const	CModel
initializeMetabolites()	CModel
isArray() const	CCopasiObject
isAutonomous() const	CModel
isContainer() const	CCopasiObject
isDataModel() const	CCopasiObject
isFixed() const	CModelEntity	[inline]
isMatrix() const	CCopasiObject
isNameVector() const	CCopasiObject
isNonUniqueName() const	CCopasiObject
isReference() const	CCopasiObject
isRoot() const	CCopasiObject
isSeparator() const	CCopasiObject
isStaticString() const	CCopasiObject
isUsed() const	CModelEntity
isValueBool() const	CCopasiObject
isValueDbl() const	CCopasiObject
isValueInt() const	CCopasiObject
isValueString() const	CCopasiObject
isVector() const	CCopasiObject
l enum value	CModel
LengthUnit enum name	CModel
LengthUnitNames	CModel	[static]
load(CReadConfig &configBuffer)	CModel
m enum value	CModel
m2 enum value	CModel
m3 enum value	CModel
Matrix enum value	CCopasiObject	[protected]
microl enum value	CModel
microm enum value	CModel
microm2 enum value	CModel
microMol enum value	CModel
micros enum value	CModel
min enum value	CModel
mKey	CModelEntity	[protected]
ml enum value	CModel
mm enum value	CModel
mm2 enum value	CModel
mMol enum value	CModel
mObjects	CCopasiContainer	[protected]
ModelEntity enum value	CCopasiObject	[protected]
ModelType enum name	CModel
ModelTypeNames	CModel	[static]
Mol enum value	CModel
mpExpression	CModelEntity	[protected]
mpInitialExpression	CModelEntity	[protected]
mpIValue	CModelEntity	[protected]
mpIValueReference	CModelEntity	[protected]
mpModel	CModelEntity	[protected]
mpRateReference	CModelEntity	[protected]
mpValue	CModelEntity	[protected]
mpValueReference	CModelEntity	[protected]
mRate	CModelEntity	[protected]
ms enum value	CModel
mSBMLId	CModelEntity	[protected]
NameVector enum value	CCopasiObject	[protected]
nl enum value	CModel
nm enum value	CModel
nm2 enum value	CModel
nMol enum value	CModel
NonUniqueName enum value	CCopasiObject	[protected]
ns enum value	CModel
number enum value	CModel
objectMap typedef	CCopasiContainer
ODE enum value	CModelEntity
OldMinute enum value	CModel
OldXML enum value	CModel
operator<<(std::ostream &os, const CCopasiObject &o)	CCopasiObject	[friend]
pl enum value	CModel
pm enum value	CModel
pm2 enum value	CModel
pMol enum value	CModel
print(std::ostream *ostream) const	CCopasiObject	[virtual]
printParameterOverview()	CModel
processQueue(const C_FLOAT64 &time, const bool &equality, CProcessQueue::resolveSimultaneousAssignments pResolveSimultaneousAssignments)	CModel
processRoots(const C_FLOAT64 &time, const bool &equality, const CVector< C_INT > &roots)	CModel
ps enum value	CModel
QuantityUnit enum name	CModel
QuantityUnitNames	CModel	[static]
QuantityUnitOldXMLNames	CModel	[static]
REACTIONS enum value	CModelEntity
Reference enum value	CCopasiObject	[protected]
refreshInitialValue()	CModelEntity	[virtual]
remove(CCopasiObject *pObject)	CCopasiContainer	[virtual]
removeCompartment(const unsigned C_INT32 index, const bool &recursive=true)	CModel
removeCompartment(const std::string &key, const bool &recursive=true)	CModel
removeCompartment(const CCompartment *pCompartment, const bool &recursive=true)	CModel
removeDependentModelObjects(const std::set< const CCopasiObject * > &deletedObjects)	CModel
removeDirectDependency(const CCopasiObject *pObject)	CCopasiObject
removeEvent(const unsigned C_INT32 index, const bool &recursive=true)	CModel
removeEvent(const std::string &key, const bool &recursive=true)	CModel
removeEvent(const CEvent *pEvent, const bool &recursive=true)	CModel
removeLocalReactionParameter(const std::string &key, const bool &recursive=true)	CModel
removeMetabolite(const std::string &key, const bool &recursive=true)	CModel
removeMetabolite(const unsigned C_INT32 index, const bool &recursive=true)	CModel
removeMetabolite(const CMetab *pMetabolite, const bool &recursive=true)	CModel
removeModelValue(const CModelValue *pModelValue, const bool &recursive=true)	CModel
removeModelValue(const std::string &key, const bool &recursive=true)	CModel
removeModelValue(const unsigned C_INT32 index, const bool &recursive=true)	CModel
removeReaction(const CReaction *pReaction, const bool &recursive=true)	CModel
removeReaction(const std::string &key, const bool &recursive=true)	CModel
removeReaction(const unsigned C_INT32 index, const bool &recursive=true)	CModel
Root enum value	CCopasiObject	[protected]
s enum value	CModel
Separator enum value	CCopasiObject	[protected]
setAreaUnit(const std::string &name)	CModel
setAreaUnit(const CModel::AreaUnit &unit)	CModel
setAvogadro(const C_FLOAT64 &avogadro)	CModel
setCompileFlag(bool flag=true)	CModel
setDirectDependencies(const std::set< const CCopasiObject * > &directDependencies)	CCopasiObject
setExpression(const std::string &expression)	CModelEntity
setExpressionPtr(CExpression *pExpression)	CModelEntity
setInitialExpression(const std::string &expression)	CModelEntity
setInitialExpressionPtr(CExpression *pExpression)	CModelEntity
setInitialState(const CState &state)	CModel
setInitialTime(const C_FLOAT64 &time)	CModel
setInitialValue(const C_FLOAT64 &initialValue)	CModelEntity	[virtual]
setInitialValuePtr(C_FLOAT64 *pInitialValue)	CModelEntity
setLengthUnit(const std::string &name)	CModel
setLengthUnit(const CModel::LengthUnit &unit)	CModel
setMiriamAnnotation(const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId)	CAnnotation
setModelType(const ModelType &modelType)	CModel
setNotes(const std::string &notes)	CAnnotation
setObjectName(const std::string &name)	CCopasiObject
setObjectParent(const CCopasiContainer *pParent)	CModelEntity	[virtual]
setObjectValue(const C_FLOAT64 &value)	CCopasiObject
setObjectValue(const C_INT32 &value)	CCopasiObject
setObjectValue(const bool &value)	CCopasiObject
setQuantityUnit(const std::string &name)	CModel
setQuantityUnit(const CModel::QuantityUnit &unit)	CModel
setRate(const C_FLOAT64 &rate)	CModelEntity
setRefresh(CType *pType, void(CType::*method)(void))	CCopasiObject	[inline]
setRenameHandler(CRenameHandler *rh)	CCopasiObject	[inline, static]
setSBMLId(const std::string &id)	CModelEntity
setState(const CState &state)	CModel
setStatus(const CModelEntity::Status &status)	CModelEntity	[virtual]
setTime(const C_FLOAT64 &time)	CModel
setTimeUnit(const std::string &name)	CModel
setTimeUnit(const CModel::TimeUnit &unit)	CModel
setTitle(const std::string &title)	CModel
setUpdateMethod(CType *pType, void(CType::*method)(const C_FLOAT64 &))	CCopasiObject	[inline]
setUpdateMethod(CType *pType, void(CType::*method)(const C_INT32 &))	CCopasiObject	[inline]
setUpdateMethod(CType *pType, void(CType::*method)(const bool &))	CCopasiObject	[inline]
setUsed(const bool &used)	CModelEntity
setValue(const C_FLOAT64 &value)	CModelEntity	[virtual]
setValuePtr(C_FLOAT64 *pValue)	CModelEntity
setVolumeUnit(const std::string &name)	CModel
setVolumeUnit(const CModel::VolumeUnit &unit)	CModel
smpRenameHandler	CCopasiObject	[protected, static]
StaticString enum value	CCopasiObject	[protected]
Status enum name	CModelEntity
StatusName	CModelEntity	[static]
stochastic enum value	CModel
suitableForStochasticSimulation() const	CModel
synchronizeEventOrder(const CEvent *pEvent, const unsigned C_INT32 newOrder)	CModel
TIME enum value	CModelEntity
TimeUnit enum name	CModel
TimeUnitNames	CModel	[static]
updateInitialValues()	CModel
updateNonSimulatedValues(void)	CModel
updateSimulatedValues(const bool &updateMoieties)	CModel
ValueBool enum value	CCopasiObject	[protected]
ValueDbl enum value	CCopasiObject	[protected]
ValueInt enum value	CCopasiObject	[protected]
ValueString enum value	CCopasiObject	[protected]
Vector enum value	CCopasiObject	[protected]
VolumeUnit enum name	CModel
VolumeUnitNames	CModel	[static]
XMLStatus	CModelEntity	[static]
~CAnnotation()	CAnnotation
~CCopasiContainer()	CCopasiContainer	[virtual]
~CCopasiObject()	CCopasiObject	[virtual]
~CModel()	CModel
~CModelEntity()	CModelEntity