API Documentation

Here the full API documentation

class cpsapi : public cpsapiContainer 

Public Types

typedef cpsapi self: The class

typedef cpsapiContainer base: The base class

Public Functions

cpsapi() = delete

cpsapi(const cpsapi &src) = delete

virtual ~cpsapi()

Public Static Functions

static void init()

static void release()

static cpsapiDataModel &addDataModel(const std::string &name = "")

static bool deleteDataModel(const std::string &name = "")

static cpsapiDataModel &dataModel(const std::string &name = "")

static cpsapiVector<cpsapiDataModel> getDataModels()

static const std::set<std::string> listModelNames()

static bool loadFromFile(const std::string &fileName, const std::string &modelName = "")

static bool loadFromString(const std::string &content, const std::string &referenceDir = "", const std::string &modelName = "")

static cpsapiModel &model(const std::string &name = "")

static void beginTransaction(const std::string &name = "")

static void endTransaction(const std::string &name = "")

static bool addCompartment(const std::string &name, const std::string &modelName = "")

static bool deleteCompartment(const std::string &name, const std::string &modelName = "")

static cpsapiCompartment compartment(const std::string &name = "", const std::string &modelName = "")

static cpsapiVector<cpsapiCompartment> getCompartments(const std::string &modelName = "")

static bool addSpecies(const std::string &name, const std::string &compartmentName = "", const std::string &modelName = "")

static bool deleteSpecies(const std::string &name, const std::string &compartmentName = "", const std::string &modelName = "")

static cpsapiSpecies species(const std::string &name, const std::string &compartmentName = "", const std::string &modelName = "")

static cpsapiVector<cpsapiSpecies> getSpecies(const std::string &modelName = "")

static bool addGlobalQuantity(const std::string &name, const std::string &modelName = "")

static bool deleteGlobalQuantity(const std::string &name, const std::string &modelName = "")

static cpsapiGlobalQuantity globalQuantity(const std::string &name = "", const std::string &modelName = "")

static cpsapiVector<cpsapiGlobalQuantity> getGlobalQuantities(const std::string &modelName = "")

static bool addReaction(const std::string &name, const std::string &modelName = "")

static bool deleteReaction(const std::string &name, const std::string &modelName = "")

static cpsapiReaction reaction(const std::string &name = "", const std::string &modelName = "")

static cpsapiVector<cpsapiReaction> getReactions(const std::string &modelName = "")

static bool addEvent(const std::string &name, const std::string &modelName = "")

static bool deleteEvent(const std::string &name, const std::string &modelName = "")

static cpsapiEvent event(const std::string &name = "", const std::string &modelName = "")

static cpsapiVector<cpsapiEvent> getEvents(const std::string &modelName = "")

Private Static Attributes

static std::map<std::string, CDataModel*> DataModels

static cpsapiDataModel DefaultDataModel

static CFunction *pDefaultFunction

static CUnitDefinition *pDefaultUnitDefinition

class cpsapiCompartment : public cpsapiModelEntity 

Public Types

enum Property

Enumeration of the exposed properties

Values:

enumerator DIMENSIONALITY

enumerator EXPRESSION

enumerator INITIAL_EXPRESSION

enumerator INITIAL_VALUE

enumerator SIMULATION_TYPE

enumerator ADD_NOISE

enumerator NOISE_EXPRESSION

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator CN

enumerator UNIT

typedef cpsapiCompartment self: The class

typedef cpsapiModelEntity base: The base class

typedef CCompartment wrapped: The wrapped COPASI class

Public Functions

cpsapiCompartment(wrapped *pWrapped = nullptr)

Specific constructor

Parameters: wrapped – * pWrapped

virtual ~cpsapiCompartment(): Destroy the cpsapi Compartment object.

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

cpsapiSpecies addSpecies(const std::string &name)

bool deleteSpecies(const std::string &name = "")

cpsapiSpecies species(const std::string &name = "")

cpsapiVector<cpsapiSpecies> getSpecies() const

bool setProperty(const Property &property, const cpsapiData &value, const CCore::Framework &framework = CCore::Framework::__SIZE)

cpsapiData getProperty(const Property &property, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Public Static Attributes

static const Properties SupportedProperties: Static set of supported properties

Protected Functions

virtual bool setProperty(const cpsapiProperty::Type &property, const cpsapiData &value, const CCore::Framework &framework) override

Set the property

Parameters

const – cpsapiProperty::Type & property
const – cpsapiData & value
const – CCore::Framework &framework

Returns

bool success

virtual cpsapiData getProperty(const cpsapiProperty::Type &property, const CCore::Framework &framework) const override

Retrieve the property

Parameters

const – cpsapiProperty::Type & property
const – CCore::Framework &framework

Returns

cpsapiData property

Private Functions

cpsapiSpecies __species(const std::string &name) const

void updateDefaultSpecies(const cpsapiSpecies &species)

class cpsapiContainer : public cpsapiObject 

Subclassed by cpsapi, cpsapiDataModel, cpsapiEvent, cpsapiEventAssignment, cpsapiModelEntity, cpsapiParameter, cpsapiReaction, cpsapiVector< Object >

Public Types

typedef cpsapiContainer self: The class

typedef cpsapiObject base: The base class

typedef CDataContainer wrapped: The wrapped COPASI class

Public Functions

virtual ~cpsapiContainer(): Destructor

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

Protected Functions

cpsapiContainer(wrapped *pWrapped = nullptr, const cpsapiObjectData::Type &type = cpsapiObjectData::Type::Container)

Specific constructor

Parameters

wrapped – * pWrapped (default: nullptr)
const – Type & type (default: Type::Container)

class cpsapiData : protected std::variant<C_FLOAT64, C_INT32, C_UINT32, size_t, bool, std::string, CRegisteredCommonName, std::shared_ptr<cpsapiObject>, std::vector<cpsapiData>>

Public Types

enum Type

Values:

enumerator Double

enumerator Int32

enumerator UnsignedInt32

enumerator SizeType

enumerator Bool

enumerator String

enumerator CommonName

enumerator Object

enumerator Vector

enumerator __SIZE

typedef std::vector<cpsapiData> Vector

Public Functions

cpsapiData()

cpsapiData(const C_FLOAT64 &value)

cpsapiData(const C_INT32 &value)

cpsapiData(const C_UINT32 &value)

cpsapiData(const size_t &value)

cpsapiData(const bool &value)

cpsapiData(const std::string &value)

cpsapiData(const char *value)

cpsapiData(const CCommonName &value)

cpsapiData(const Vector &value)

template<class Object> cpsapiData(const Object &value)

cpsapiData(const Type &type, void *pValue)

cpsapiData(const cpsapiData &src)

cpsapiData &operator=(const cpsapiData &rhs)

~cpsapiData()

C_FLOAT64 toDouble() const

C_INT32 toInt32() const

C_UINT32 toUnsignedInt32() const

size_t toSizeType() const

bool toBool() const

std::string toString() const

CCommonName toCommonName() const

const Vector &toData() const

template<class Object> Object toObject() const

Type getType() const

template<> inline cpsapiObject toObject() const

Private Types

typedef std::variant<C_FLOAT64, C_INT32, C_UINT32, size_t, bool, std::string, CRegisteredCommonName, std::shared_ptr<cpsapiObject>, std::vector<cpsapiData>> base

class cpsapiDataCollector : public COutputInterface

Public Functions

virtual ~cpsapiDataCollector(): Destructor

virtual bool compile(CObjectInterface::ContainerList listOfContainer) override

compile the object list from name vector

Parameters: CObjectInterface::ContainerList – listOfContainer
Returns: bool success

virtual void output(const Activity &activity) override

Perform an output event for the current activity

Parameters: const – Activity & activity

virtual void separate(const Activity &activity) override

Introduce an additional separator into the output

Parameters: const – Activity & activity

virtual void finish() override: Finish the output

void addDataReferenceBefore(const CCommonName &cn)

void addDataReferenceDuring(const CCommonName &cn)

void addDataRefenceAfter(const CCommonName &cn)

const std::vector<CRegisteredCommonName> &getDataReferencesBefore() const

const std::vector<CRegisteredCommonName> &getDataReferencesDuring() const

const std::vector<CRegisteredCommonName> &getDataReferencesAfter() const

void clearReferences()

const cpsapiData::Vector &getDataBefore() const

const cpsapiData::Vector &getDataDuring() const

const cpsapiData::Vector &getDataAfter() const

std::vector<cpsapiData::Type> getDataTypesBefore() const

std::vector<cpsapiData::Type> getDataTypesDuring() const

std::vector<cpsapiData::Type> getDataTypesAfter() const

void clearData()

Private Functions

bool generateValues(const CObjectInterface::ContainerList &listOfContainer, const std::vector<CRegisteredCommonName> &cns, std::vector<std::pair<cpsapiData::Type, void*>> &values)

Private Members

cpsapiData::Vector mDataBefore

cpsapiData::Vector mDataDuring

cpsapiData::Vector mDataAfter

std::vector<CRegisteredCommonName> mCNsBefore

std::vector<CRegisteredCommonName> mCNsDuring

std::vector<CRegisteredCommonName> mCNsAfter

std::vector<std::pair<cpsapiData::Type, void*>> mValuesBefore

std::vector<std::pair<cpsapiData::Type, void*>> mValuesDuring

std::vector<std::pair<cpsapiData::Type, void*>> mValuesAfter

Private Static Functions

static void collect(cpsapiData::Vector &data, const std::vector<std::pair<cpsapiData::Type, void*>> &values)

class cpsapiDataModel : public cpsapiContainer 

Public Types

enum Property

Enumeration of the exposed properties

Values:

typedef cpsapiDataModel self: Static set of supported properties The class

typedef cpsapiContainer base: The base class

typedef CDataModel wrapped: The wrapped COPASI class

Public Functions

cpsapiDataModel(wrapped *pDataModel = nullptr)

Specific constructor

Parameters: wrapped – * pDataModel (default: nullptr)

virtual ~cpsapiDataModel(): Destructor

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

bool loadFromFile(const std::string &fileName)

Load a model from a file (any supported format)

Parameters: const – std::string & fileName
Returns: bool success

bool loadFromString(const std::string &content, const std::string &referenceDir = "")

Load a model from a file (any supported format)

Parameters: const – std::string & fileName
Returns: bool success

cpsapiModel &model()

void beginTransaction()

void endTransaction()

cpsapiCompartment addCompartment(const std::string &name)

bool deleteCompartment(const std::string &name)

cpsapiCompartment compartment(const std::string &name = "")

cpsapiVector<cpsapiCompartment> getCompartments()

cpsapiSpecies addSpecies(const std::string &name, const std::string &compartmentName = "")

bool deleteSpecies(const std::string &name, const std::string &compartmentName = "")

cpsapiSpecies species(const std::string &name = "", const std::string &compartmentName = "")

cpsapiVector<cpsapiSpecies> getSpecies()

cpsapiReaction addReaction(const std::string &name)

bool deleteReaction(const std::string &name)

cpsapiReaction reaction(const std::string &name = "")

cpsapiVector<cpsapiReaction> getReactions()

cpsapiEvent addEvent(const std::string &name)

bool deleteEvent(const std::string &name)

cpsapiEvent event(const std::string &name = "")

cpsapiVector<cpsapiEvent> getEvents()

cpsapiGlobalQuantity addGlobalQuantity(const std::string &name)

bool deleteGlobalQuantity(const std::string &name)

cpsapiGlobalQuantity globalQuantity(const std::string &name = "")

cpsapiVector<cpsapiGlobalQuantity> getGlobalQuantities()

cpsapiVector<cpsapiTask> getTasks()

cpsapiTask task(const std::string &name = "")

cpsapiMethod method()

cpsapiProblem problem()

Private Functions

cpsapiTask __task(const std::string &name) const

class cpsapiEvent : public cpsapiContainer 

Public Types

enum Property

Enumeration of the exposed properties

Values:

enumerator DELAY_ASSIGNMENT

enumerator FIRE_AT_INITIALTIME

enumerator PERSISTENT_TRIGGER

enumerator TRIGGER_EXPRESSION

enumerator DELAY_EXPRESSION

enumerator PRIORITY_EXPRESSION

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator CN

enum Reference

Enumeration of the exposed references

Values:

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

typedef cpsapiEvent self: The class

typedef cpsapiContainer base: The base class

typedef CEvent wrapped: The wrapped COPASI class

Public Functions

cpsapiEvent(wrapped *pWrapped = nullptr, const cpsapiObjectData::Type &type = cpsapiObjectData::Type::Event)

Specific constructor

Parameters

wrapped – * pWrapped (default: nullptr)
const – Type & type (default: Type::cpsapiEvent)

virtual ~cpsapiEvent(): Destructor

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

cpsapiEventAssignment addEventAssignment(const std::string &name)

Add a an assignment to the event

Parameters: const – std::string & name
Returns: cpsapiEventAssignment

bool deleteEventAssignment(const std::string &name = "")

Delete the Assignment with the given name

Parameters: const – std::string & name = (default: current assignment)
Returns: bool success

cpsapiEventAssignment eventAssignment(const std::string &name = "")

Retrieve an assignment

Parameters: const – std::string & name = (default: current assignment)
Returns: cpsapiEventAssignment

cpsapiVector<cpsapiEventAssignment> getEventAssignments() const

Retrieve the vector af assignments

Returns: cpsapiVector< cpsapiEventAssignment >

bool setProperty(const Property &property, const cpsapiData &value, const CCore::Framework &framework = CCore::Framework::__SIZE)

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – cpsapiData & value
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

bool success

cpsapiData getProperty(const Property &property, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

cpsapiData property

CCommonName getDataCN(const Reference &reference, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Retrieve a property of the object to the provided value under the given framework. The default framework is unspecified

Parameters

const – Reference & reference
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

CCommonName

Public Static Attributes

static const Properties SupportedProperties: Static set of supported properties

static const Properties HiddenProperties: Static set of hidden properties

static const References SupportedReferences: Static set of supported references

static const References HiddenReferences: Static set of hidden references

Protected Functions

virtual bool setProperty(const cpsapiProperty::Type &property, const cpsapiData &value, const CCore::Framework &framework) override

Set the property

Parameters

const – cpsapiProperty::Type & property
const – cpsapiData & value
const – CCore::Framework &framework

Returns

bool success

virtual cpsapiData getProperty(const cpsapiProperty::Type &property, const CCore::Framework &framework) const override

Retrieve the property

Parameters

const – cpsapiProperty::Type & property
const – CCore::Framework &framework

Returns

cpsapiData property

virtual CCommonName getDataCN(const cpsapiReference::Type &reference, const CCore::Framework &framework) const override

Retrieve the data reference

Parameters

const – cpsapiReference::Type & reference
const – CCore::Framework &framework

Returns

CCommonName

Private Functions

cpsapiEventAssignment __eventAssignment(const std::string &name) const

Resolve and retrieve the event assignment by name

Parameters: const – std::string & name
Returns: cpsapiEventAssignment

void updateDefaultEventAssignment(const cpsapiEventAssignment &assignment)

Update the default event assignment

Parameters: assignment –

class cpsapiEventAssignment : public cpsapiContainer 

Public Types

enum Property

Enumeration of the exposed properties

Values:

enumerator EXPRESSION

enumerator OBJECT_REFERENCE_CN

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator CN

enum Reference

Enumeration of the exposed references

Values:

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

typedef cpsapiEventAssignment self: The class

typedef cpsapiContainer base: The base class

typedef CEventAssignment wrapped: The wrapped COPASI class

Public Functions

cpsapiEventAssignment(wrapped *pWrapped = nullptr, const cpsapiObjectData::Type &type = cpsapiObjectData::Type::EventAssignment)

Specific constructor

Parameters

wrapped – * pWrapped (default: nullptr)
const – Type & type (default: Type::cpsapiEventAssignment)

virtual ~cpsapiEventAssignment(): Destructor

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

bool setProperty(const Property &property, const cpsapiData &value, const CCore::Framework &framework = CCore::Framework::__SIZE)

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – cpsapiData & value
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

bool success

cpsapiData getProperty(const Property &property, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

cpsapiData property

CCommonName getDataCN(const Reference &reference, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Retrieve a property of the object to the provided value under the given framework. The default framework is unspecified

Parameters

const – Reference & reference
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

CCommonName

Public Static Attributes

static const Properties SupportedProperties: Static set of supported properties

static const Properties HiddenProperties: Static set of hidden properties

static const References SupportedReferences: Static set of supported references

static const References HiddenReferences: Static set of hidden references

Protected Functions

virtual bool setProperty(const cpsapiProperty::Type &property, const cpsapiData &value, const CCore::Framework &framework) override

Set the property

Parameters

const – cpsapiProperty::Type & property
const – cpsapiData & value
const – CCore::Framework &framework

Returns

bool success

virtual cpsapiData getProperty(const cpsapiProperty::Type &property, const CCore::Framework &framework) const override

Retrieve the property

Parameters

const – cpsapiProperty::Type & property
const – CCore::Framework &framework

Returns

cpsapiData property

virtual CCommonName getDataCN(const cpsapiReference::Type &reference, const CCore::Framework &framework) const override

Retrieve the data reference

Parameters

const – cpsapiReference::Type & reference
const – CCore::Framework &framework

Returns

CCommonName

class cpsapiFactory

Public Types

enum PartType

Values:

enumerator vectorCompartment

enumerator vectorSpecies

enumerator vectorGlobalQuantity

enumerator vectorReaction

enumerator vectorReactionParameter

enumerator vectorEvent

enumerator vectorEventAssignment

enumerator vectorDataModel

enumerator vectorTask

enumerator value

enumerator model

enumerator compartment

enumerator species

enumerator globalQuantity

enumerator reaction

enumerator reactionParameter

enumerator event

enumerator eventAssignment

enumerator dataModel

enumerator parameter

enumerator group

enumerator method

enumerator problem

enumerator task

enumerator __SIZE

typedef void (*free_unique_t)(void*)

Public Functions

template<> inline std::shared_ptr<cpsapiObject> make_shared(CDataObject *pFrom)

template<> inline std::shared_ptr<cpsapiObject> make_shared(const cpsapiObject &from)

template<> inline std::unique_ptr<cpsapiObject, cpsapiFactory::free_unique_t> make_unique(CDataObject *pFrom)

template<> inline std::unique_ptr<cpsapiObject, cpsapiFactory::free_unique_t> make_unique(const cpsapiObject &from)

template<> inline void free_unique(void*)

Public Static Functions

template<class Type> static void free_unique(void*)

static void init()

static const PartInterface &info(const std::type_index &typeIndex)

static const PartInterface &info(CDataObject *pObject)

static const PartInterface &info(const cpsapiObject &object)

template<class CType> static inline std::shared_ptr<CType> make_shared(CDataObject *pFrom)

template<class CType> static inline std::shared_ptr<CType> make_shared(const cpsapiObject &from)

template<class CType> static std::unique_ptr<CType, free_unique_t> make_unique(CDataObject *pFrom)

template<class CType> static std::unique_ptr<CType, free_unique_t> make_unique(const cpsapiObject &from)

template<class Visitor> static void accept(Visitor &visitor, CDataObject *pObject)

static cpsapiObject *copy(const cpsapiObject &object)

static cpsapiObject *create(CDataObject *pFrom)

static CDataValue::Type getDataType(const CObjectInterface *pObject)

template<class Function> static void callDerived(CDataObject *pObject)

Private Types

typedef std::map<std::type_index, std::shared_ptr<PartInterface>> CopasiMap

Private Static Functions

template<class cpsapi, class copasi> static void insert(const PartType &partType)

static cpsapiObject *make(CDataObject *pObject, const PartInterface *pInfo = nullptr)

Private Static Attributes

static CopasiMap copasiMap

class cpsapiGlobalQuantity : public cpsapiModelEntity 

Public Types

enum Property

Enumeration of the exposed properties

Values:

enumerator EXPRESSION

enumerator INITIAL_EXPRESSION

enumerator INITIAL_VALUE

enumerator SIMULATION_TYPE

enumerator ADD_NOISE

enumerator NOISE_EXPRESSION

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator CN

enumerator UNIT

typedef cpsapiGlobalQuantity self: The class

typedef cpsapiModelEntity base: The base class

typedef CModelValue wrapped: The wrapped COPASI class

Public Functions

cpsapiGlobalQuantity(wrapped *pWrapped = nullptr)

Specific constructor

Parameters: wrapped – * pWrapped

virtual ~cpsapiGlobalQuantity()

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

bool setProperty(const Property &property, const cpsapiData &value, const CCore::Framework &framework = CCore::Framework::__SIZE)

cpsapiData getProperty(const Property &property, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Public Static Attributes

static const Properties SupportedProperties: Static set of supported properties

Protected Functions

virtual bool setProperty(const cpsapiProperty::Type &property, const cpsapiData &value, const CCore::Framework &framework) override

Set the property

Parameters

const – cpsapiProperty::Type & property
const – cpsapiData & value
const – CCore::Framework &framework

Returns

bool success

virtual cpsapiData getProperty(const cpsapiProperty::Type &property, const CCore::Framework &framework) const override

Retrieve the property

Parameters

const – cpsapiProperty::Type & property
const – CCore::Framework &framework

Returns

cpsapiData property

class cpsapiGroup : public cpsapiParameter 

Public Types

enum Property

Enumeration of the exposed properties

Values:

enumerator PARAMETER_VALUE

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator CN

enum Reference

Enumeration of the exposed references

Values:

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

typedef cpsapiGroup self: The class

typedef cpsapiParameter base: The base class

typedef CCopasiParameterGroup wrapped: The wrapped COPASI class

Public Functions

cpsapiGroup(wrapped *pGroup, const cpsapiObjectData::Type &type = cpsapiObjectData::Type::Group)

Specific constructor

Parameters: wrapped – * pGroup

virtual ~cpsapiGroup(): Destructor

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

cpsapiParameter addParameter(const std::string &name, const CDataValue &value, CCopasiParameter::Type type = CCopasiParameter::Type::__SIZE)

Add parameter

Parameters

const – std::string & name
const – CDataValue & value
CCopasiParameter::Type – type (default: CCopasiParameter::Type::__SIZE)

Returns

cpsapiParameter parameter

cpsapiGroup addGroup(const std::string &name)

Add a group

Parameters: const – std::string & name
Returns: cpsapiGroup group

bool deleteParameter(const std::string &name = "")

Delete a parameter

Parameters: const – std::string & name (default: name of current parameter)
Returns: bool success

cpsapiParameter parameter(const std::string &name = "")

Retrieve a parameter

Parameters: const – std::string & name (default: name of current parameter)
Returns: cpsapiParameter parameter

std::vector<cpsapiParameter> getParameters() const

Retrieve all parameters

Returns: std::vector< cpsapiParameter > parameters

bool setProperty(const Property &property, const cpsapiData &value, const CCore::Framework &framework = CCore::Framework::__SIZE)

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – cpsapiData & value
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

bool success

cpsapiData getProperty(const Property &property, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

cpsapiData property

CCommonName getDataCN(const Reference &reference, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Retrieve a property of the object to the provided value under the given framework. The default framework is unspecified

Parameters

const – Reference & reference
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

CCommonName

Public Static Attributes

static const Properties SupportedProperties: Static set of supported properties

static const Properties HiddenProperties: Static set of hidden properties

static const References SupportedReferences: Static set of supported references

static const References HiddenReferences: Static set of hidden references

Protected Functions

cpsapiParameter __parameter(const std::string &name) const

void updateDefaultParameter(const cpsapiParameter &parameter)

virtual bool setProperty(const cpsapiProperty::Type &property, const cpsapiData &value, const CCore::Framework &framework) override

Set the property

Parameters

const – cpsapiProperty::Type & property
const – cpsapiData & value
const – CCore::Framework &framework

Returns

bool success

virtual cpsapiData getProperty(const cpsapiProperty::Type &property, const CCore::Framework &framework) const override

Retrieve the property

Parameters

const – cpsapiProperty::Type & property
const – CCore::Framework &framework

Returns

cpsapiData property

virtual CCommonName getDataCN(const cpsapiReference::Type &reference, const CCore::Framework &framework) const override

Retrieve the data reference

Parameters

const – cpsapiReference::Type & reference
const – CCore::Framework &framework

Returns

CCommonName

class cpsapiKineticLawVariable : public cpsapiObject 

Public Types

enum Property

Enumeration of the exposed properties

Values:

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator CN

enumerator ROLE

enumerator VALUE

enumerator MAPPING

enum Reference

Enumeration of the exposed references

Values:

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator VALUE

typedef cpsapiKineticLawVariable self: The class

typedef cpsapiObject base: The base class

typedef KineticLawVariable wrapped: The wrapped COPASI class

Public Functions

cpsapiKineticLawVariable(wrapped *pWrapped = nullptr)

Specific constructor

Parameters: wrapped – * pWrapped

virtual ~cpsapiKineticLawVariable(): Destructor

virtual bool isValid() const override

Check whether the object is valid

Returns: bool valid

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

bool setProperty(const Property &property, const cpsapiData &value, const CCore::Framework &framework = CCore::Framework::__SIZE)

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – cpsapiData & value
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

bool success

cpsapiData getProperty(const Property &property, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

cpsapiData property

CCommonName getDataCN(const Reference &reference, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Retrieve a property of the object to the provided value under the given framework. The default framework is unspecified

Parameters

const – Reference & reference
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

CCommonName

Public Static Attributes

static const Properties SupportedProperties: Static set of supported properties

static const Properties HiddenProperties: Static set of hidden properties

static const References SupportedReferences: Static set of supported references

static const References HiddenReferences: Static set of hidden references

Protected Functions

virtual bool setProperty(const cpsapiProperty::Type &property, const cpsapiData &value, const CCore::Framework &framework) override

Set the property

Parameters

const – cpsapiProperty::Type & property
const – cpsapiData & value
const – CCore::Framework &framework

Returns

bool success

virtual cpsapiData getProperty(const cpsapiProperty::Type &property, const CCore::Framework &framework) const override

Retrieve the property

Parameters

const – cpsapiProperty::Type & property
const – CCore::Framework &framework

Returns

cspapiData

virtual CCommonName getDataCN(const cpsapiReference::Type &reference, const CCore::Framework &framework) const override

Retrieve the data reference

Parameters

const – cpsapiReference::Type & reference
const – CCore::Framework &framework

Returns

CCommonName

class cpsapiModel : public cpsapiModelEntity 

Public Types

enum Property

Enumeration of the exposed properties

Values:

enumerator INITIAL_VALUE

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator CN

enumerator UNIT

enumerator VOLUME_UNIT

enumerator AREA_UNIT

enumerator LENGTH_UNIT

enumerator TIME_UNIT

enumerator QUANTITY_UNIT

enumerator MODEL_TYPE

enumerator AVOGADRO_NUMBER

typedef cpsapiModel self: The class

typedef cpsapiModelEntity base: The base class

typedef CModel wrapped: The wrapped COPASI class

Public Functions

cpsapiModel(wrapped *pWrapped = nullptr)

Specific constructor

Parameters: wrapped – * pWrapped

virtual ~cpsapiModel()

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

void beginTransaction() const

void endTransaction() const

bool synchronize(std::set<const CDataObject*> &changedObjects, const CCore::Framework &framework)

bool compile()

cpsapiCompartment addCompartment(const std::string &name)

bool deleteCompartment(const std::string &name = "")

cpsapiCompartment compartment(const std::string &name = "")

cpsapiVector<cpsapiCompartment> getCompartments() const

cpsapiSpecies addSpecies(const std::string &name, const std::string &compartment = "")

bool deleteSpecies(const std::string &name = "", const std::string &compartment = "")

cpsapiSpecies species(const std::string &name = "", const std::string &compartment = "")

cpsapiVector<cpsapiSpecies> getSpecies() const

cpsapiGlobalQuantity addGlobalQuantity(const std::string &name)

bool deleteGlobalQuantity(const std::string &name = "")

cpsapiGlobalQuantity globalQuantity(const std::string &name = "")

cpsapiVector<cpsapiGlobalQuantity> getGlobalQuantities() const

cpsapiReaction addReaction(const std::string &name)

bool deleteReaction(const std::string &name = "")

cpsapiReaction reaction(const std::string &name = "")

cpsapiVector<cpsapiReaction> getReactions() const

cpsapiEvent addEvent(const std::string &name)

bool deleteEvent(const std::string &name = "")

cpsapiEvent event(const std::string &name = "")

cpsapiVector<cpsapiEvent> getEvents() const

cpsapiEventAssignment addEventAssignment(const std::string &name, const std::string &event = "")

bool deleteEventAssignment(const std::string &name = "", const std::string &event = "")

cpsapiEventAssignment eventAssignment(const std::string &name = "", const std::string &event = "")

cpsapiVector<cpsapiEventAssignment> getEventAssignments(const std::string &event = "") const

void deleteAllDependents(CDataContainer *pContainer)

bool setProperty(const Property &property, const cpsapiData &value, const CCore::Framework &framework = CCore::Framework::__SIZE)

cpsapiData getProperty(const Property &property, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Public Static Attributes

static const Properties SupportedProperties: Static set of supported properties

static const Properties HiddenProperties: Static set of hidden properties

Protected Functions

virtual bool setProperty(const cpsapiProperty::Type &property, const cpsapiData &value, const CCore::Framework &framework) override

Set the property

Parameters

const – cpsapiProperty::Type & property
const – cpsapiData & value
const – CCore::Framework &framework

Returns

bool success

virtual cpsapiData getProperty(const cpsapiProperty::Type &property, const CCore::Framework &framework) const override

Retrieve the property

Parameters

const – cpsapiProperty::Type & property
const – CCore::Framework &framework

Returns

cpsapiData property

Private Functions

cpsapiCompartment __compartment(const std::string &name) const

void updateDefaultCompartment(const cpsapiCompartment &compartment)

cpsapiSpecies __species(const std::string &name, const std::string &compartment) const

cpsapiGlobalQuantity __globalQuantity(const std::string &name) const

void updateDefaultGlobalQuantity(const cpsapiGlobalQuantity &globalQuantity)

cpsapiReaction __reaction(const std::string &name) const

void updateDefaultReaction(const cpsapiReaction &reaction)

cpsapiEvent __EVENT(const std::string &name) const

Retrieve the event with the given name Upper case name due __event being a Visual C keyword

Parameters: const – std::string & name
Returns: cpsapiEvent

void updateDefaultEvent(const cpsapiEvent &event)

void deleteDependents(const CDataObject::DataObjectSet &set)

class cpsapiModelEntity : public cpsapiContainer 

Subclassed by cpsapiCompartment, cpsapiGlobalQuantity, cpsapiModel, cpsapiSpecies

Public Types

enum Property

Values:

enumerator EXPRESSION

enumerator INITIAL_EXPRESSION

enumerator INITIAL_VALUE

enumerator SIMULATION_TYPE

enumerator ADD_NOISE

enumerator NOISE_EXPRESSION

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator CN

typedef cpsapiModelEntity self: The class

typedef cpsapiContainer base: The base class

Public Functions

cpsapiModelEntity() = delete

virtual ~cpsapiModelEntity()

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

bool setProperty(const Property &property, const cpsapiData &value, const CCore::Framework &framework = CCore::Framework::__SIZE)

cpsapiData getProperty(const Property &property, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Public Static Attributes

static const Properties SupportedProperties

Protected Functions

cpsapiModelEntity(CModelEntity *pModelEntity, const cpsapiObjectData::Type &type)

Specific constructor

Parameters

CModelEntity – * pContainer
const – Type & type

virtual bool setProperty(const cpsapiProperty::Type &property, const cpsapiData &value, const CCore::Framework &framework) override

Set the property

Parameters

const – cpsapiProperty::Type & property
const – cpsapiData & value
const – CCore::Framework &framework

Returns

bool success

virtual cpsapiData getProperty(const cpsapiProperty::Type &property, const CCore::Framework &framework) const override

Retrieve the property

Parameters

const – cpsapiProperty::Type & property
const – CCore::Framework &framework

Returns

cpsapiData property

class cpsapiObject

#include <cpsapiObject.h>

The cpsapiObject class is the base class for all COPASI CDataObjects exposed in the cpsapi.

Subclassed by cpsapiContainer, cpsapiKineticLawVariable, cpsapiValue

Public Types

enum Property

Enumeration of the exposed properties

Values:

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator CN

enum Reference

Enumeration of the exposed references

Values:

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

typedef std::set<cpsapiProperty::Type> Properties

typedef std::set<cpsapiReference::Type> References

typedef cpsapiObjectData Data

typedef cpsapiObject self: The base class

Public Functions

cpsapiObject(const cpsapiObject &src)

Copy constructor

Parameters: const – cpsapiObject & src

virtual ~cpsapiObject(): Destructor

cpsapiObject &operator=(const cpsapiObject &rhs)

Assignment operator =

Parameters: const – cpsapiObject & rhs
Returns: cpsapiObject &

cpsapiObject &operator=(CDataObject *pObject)

Assignment operator =

Parameters: CDataObject – * pObject
Returns: cpsapiObject &

CDataObject *operator->() const

Dereferencing operator ->

Returns: CDataObject*

CDataObject *operator*() const

Dereferencing operator *

Returns: CDataObject*

bool operator==(const cpsapiObject &rhs) const

Comparison operator for equality

Parameters: const – cpsapiObject & rhs
Returns: bool equal

bool operator!=(const cpsapiObject &rhs) const

Comparison operator for inequality

Parameters: const – cpsapiObject & rhs
Returns: bool notEqual

cpsapiObjectData::Type getType() const

Retrieve the type of the object

Returns: cpsapiObjectData::Type type

operator bool() const: Conversion to bool indicating whether the underlying COPASI CDataObject is accessible. The underlying CDataObject might have been deleted, e.g., a species if the parent compartment has been deleted

virtual bool isValid() const

Check whether the object is valid

Returns: bool valid

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

bool setProperty(const Property &property, const cpsapiData &value, const CCore::Framework &framework = CCore::Framework::__SIZE)

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – cpsapiData & value
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

bool success

bool setProperty(const std::string &property, const cpsapiData &value, const std::string &framework = "")

Set a property of the object to the provided value under the given framework. The property must be the string in cpsapiProperty::Names The value must match the underlying value of the property. The framework must be string in CCore::FrameworkNames

Parameters

const – std::string & property
const – cpsapiData & value
const – std::string & framework (default: “”)

Returns

bool success

cpsapiData getProperty(const Property &property, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Retrieve a property of the object to the provided value under the given framework. The default framework is unspecified

Parameters

const – Property & property
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

cpsapiData property

cpsapiData getProperty(const std::string &property, const std::string &framework = "") const

Retrieve a property of the object to the provided value under the given framework. The property must be the string in cpsapiProperty::Names The framework must be string in CCore::FrameworkNames

Parameters

const – std::string & property
const – std::string & framework (default: “”)

Returns

cpsapiData property

CCommonName getDataCN(const Reference &reference, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Retrieve a data reference of the object under the given framework. The default framework is unspecified

Parameters

const – Reference & reference
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

CCommonName

CCommonName getDataCN(const std::string &reference, const std::string &framework = "") const

Retrieve a property of the object the given framework. The property must be the string in cpsapiReferences::Names The framework must be string in CCore::FrameworkNames

Parameters

const – std::string & reference
const – std::string & framework (default: “”)

Returns

CCommonName

template<class Visitor> CPSAPI_NAMESPACE_END CPSAPI_NAMESPACE_BEGIN void accept (Visitor &visitor)

template<> inline cpsapiObject::Properties supportedProperties()

template<> inline cpsapiObject::References supportedReferences()

Public Static Functions

template<class CType> static Properties supportedProperties()

Retrieve the effective list of supported properties

Template Parameters: class – CType cpsapiObject or a derived class
Returns: Properties SupportedProperties

template<class CType> static bool isSupportedProperty(const cpsapiProperty::Type &property)

Check whether the property is supported

Template Parameters: class – CType cpsapiObject or a derived class
Parameters: const – cpsapiProperty::Type & property
Returns: bool supported

template<class CType> static References supportedReferences()

Retrieve the effective list of supported references

Template Parameters: class – CType cpsapiObject or a derived class
Returns: References SupportedReferences

template<class CType> static bool isSupportedReference(const cpsapiReference::Type &reference)

Check whether the reference is supported

Template Parameters: class – CType cpsapiObject or a derived class
Parameters: const – cpsapiReference::Type & reference
Returns: bool supported

Public Static Attributes

static const CCommonName Invalid

static const Properties SupportedProperties: Static set of supported properties

static const Properties HiddenProperties: Static set of hidden properties

static const References SupportedReferences: Static set of supported references

static const References HiddenReferences: Static set of hidden references

Protected Functions

cpsapiObject(CDataObject *pObject = nullptr, const cpsapiObjectData::Type &type = cpsapiObjectData::Type::Object)

Specific constructor

Parameters

CDataObject – * pObject (default: nullptr)
const – Type & type (default: Type::Object)

CDataObject *getObject() const

Retrieve the pointer to the underlying COPASI CDataObject.

Returns: CDataObject * pObject

virtual bool setProperty(const cpsapiProperty::Type &property, const cpsapiData &value, const CCore::Framework &framework)

Set the property

Parameters

const – cpsapiProperty::Type & property
const – cpsapiData & value
const – CCore::Framework &framework

Returns

bool success

virtual cpsapiData getProperty(const cpsapiProperty::Type &property, const CCore::Framework &framework) const

Retrieve the property

Parameters

const – cpsapiProperty::Type & property
const – CCore::Framework &framework

Returns

cpsapiData property

virtual CCommonName getDataCN(const cpsapiReference::Type &reference, const CCore::Framework &framework) const

Retrieve the data reference

Parameters

const – cpsapiReference::Type & reference
const – CCore::Framework &framework

Returns

CCommonName

Protected Attributes

Data::Pointer mpData

Protected Static Functions

template<class CType> static bool isImplementedProperty(const cpsapiProperty::Type &property)

Check whether the given property is supported by the class

Template Parameters: class – CType cpsapiObject or a derived class
Parameters: const – cpsapiProperty::Type & property
Returns: bool supported

template<class CType> static bool isHiddenProperty(const cpsapiProperty::Type &property)

Check whether the given property is hidden by the class

Template Parameters: class – CType cpsapiObject or a derived class
Parameters: const – cpsapiProperty::Type & property
Returns: bool supported

template<class CType> static bool isImplementedReference(const cpsapiReference::Type &reference)

Check whether the given reference is supported by the class

Template Parameters: class – CType cpsapiObject or a derived class
Parameters: const – cpsapiReference::Type & reference
Returns: bool supported

template<class CType> static bool isHiddenReference(const cpsapiReference::Type &reference)

Check whether the given reference is hidden by the class

Template Parameters: class – CType cpsapiObject or a derived class
Parameters: const – cpsapiReference::Type & reference
Returns: bool hidden

Friends

friend class cpsapiData

class cpsapiObjectData

#include <cpsapiObjectData.h>

The cpsapiObject class is the base class for all COPASI CDataObjects exposed in the cpsapi.

Subclassed by cpsapiCompartment::Data, cpsapiEvent::Data, cpsapiModel::Data, cpsapiReaction::Data

Public Types

enum Type

Values:

enumerator Object

enumerator Value

enumerator Container

enumerator Vector

enumerator ModelEntity

enumerator Model

enumerator Compartment

enumerator Species

enumerator GlobalQuantity

enumerator Reaction

enumerator ReactionParameter

enumerator Event

enumerator EventAssignment

enumerator DataModel

enumerator Parameter

enumerator Group

enumerator Method

enumerator Problem

enumerator Task

enumerator __SIZE

typedef std::shared_ptr<cpsapiObjectData> Pointer

typedef std::map<const CDataObject*, Pointer> Map

Public Functions

cpsapiObjectData(const cpsapiObjectData&) = default

cpsapiObjectData(CDataObject *pObject, const Type &type)

inline virtual ~cpsapiObjectData()

template<> inline void assertDataType(Pointer &data)

Public Static Functions

static void release()

static void erase(const CDataObject *pObject)

static void deleted(const CDataObject *pObject)

template<class CType> static void assertDataType(Pointer &baseData)

Assert that mpData points of the proper class

Tparam

Public Static Attributes

static const CEnumAnnotation<std::string, Type> TypeName

static Map Manager

Protected Attributes

CDataObject *mpObject = nullptr

Type mType = Type::Object 

Private Functions

cpsapiObjectData() = default

cpsapiObjectData(cpsapiObjectData&&) = default

Friends

friend class cpsapiObject

class cpsapiParameter : public cpsapiContainer 

Subclassed by cpsapiGroup

Public Types

enum Property

Enumeration of the exposed properties

Values:

enumerator PARAMETER_VALUE

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator CN

enum Reference

Enumeration of the exposed references

Values:

enumerator PARAMETER_VALUE

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

typedef cpsapiParameter self: The class

typedef cpsapiContainer base: The base class

typedef CCopasiParameter wrapped: The wrapped COPASI class

Public Functions

cpsapiParameter(wrapped *pWrapped = nullptr, const cpsapiObjectData::Type &type = cpsapiObjectData::Type::Parameter)

Specific constructor

Parameters

wrapped – * pWrapped (default: nullptr)
const – Type & type (default: Type::cpsapiParameter)

virtual ~cpsapiParameter(): Destructor

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

bool setProperty(const Property &property, const cpsapiData &value, const CCore::Framework &framework = CCore::Framework::__SIZE)

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – cpsapiData & value
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

bool success

cpsapiData getProperty(const Property &property, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

cpsapiData property

CCommonName getDataCN(const Reference &reference, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Retrieve a property of the object to the provided value under the given framework. The default framework is unspecified

Parameters

const – Reference & reference
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

CCommonName

Public Static Attributes

static const Properties SupportedProperties: Static set of supported properties

static const Properties HiddenProperties: Static set of hidden properties

static const References SupportedReferences: Static set of supported references

static const References HiddenReferences: Static set of hidden references

Protected Functions

virtual bool setProperty(const cpsapiProperty::Type &property, const cpsapiData &value, const CCore::Framework &framework) override

Set the property

Parameters

const – cpsapiProperty::Type & property
const – cpsapiData & value
const – CCore::Framework &framework

Returns

bool success

virtual cpsapiData getProperty(const cpsapiProperty::Type &property, const CCore::Framework &framework) const override

Retrieve the property

Parameters

const – cpsapiProperty::Type & property
const – CCore::Framework &framework

Returns

cpsapiData property

virtual CCommonName getDataCN(const cpsapiReference::Type &reference, const CCore::Framework &framework) const override

Retrieve the data reference

Parameters

const – cpsapiReference::Type & reference
const – CCore::Framework &framework

Returns

CCommonName

class cpsapiProperty

Public Types

enum Type

Values:

enumerator EXPRESSION

enumerator VALUE

enumerator INTENSIVE_VALUE

enumerator RATE

enumerator INTENSIVE_RATE

enumerator INITIAL_EXPRESSION

enumerator INITIAL_VALUE

enumerator INITIAL_INTENSIVE_VALUE

enumerator INITIAL_RATE

enumerator INITIAL_INTENSIVE_RATE

enumerator SIMULATION_TYPE

enumerator SPATIAL_DIMENSION

enumerator ADD_NOISE

enumerator NOISE_EXPRESSION

enumerator CHEMICAL_EQUATION

enumerator KINETIC_LAW

enumerator KINETIC_LAW_EXPRESSION

enumerator KINETIC_LAW_UNIT_TYPE

enumerator KINETIC_LAW_VARIABLE_MAPPING

enumerator LOCAL_REACTION_PARAMETERS

enumerator SCALING_COMPARTMENT

enumerator FLUX

enumerator PARTICLE_FLUX

enumerator INITIAL_FLUX

enumerator INITIAL_PARTICLE_FLUX

enumerator OBJECT_UUID

enumerator NAME

enumerator OBJECT_PARENT_CN

enumerator OBJECT_TYPE

enumerator OBJECT_FLAG

enumerator OBJECT_HASH

enumerator OBJECT_INDEX

enumerator OBJECT_REFERENCES

enumerator OBJECT_REFERENCE

enumerator OBJECT_REFERENCE_CN

enumerator OBJECT_REFERENCE_INDEX

enumerator OBJECT_POINTER

enumerator OBJECT_UNIQUE_NAME

enumerator CN

enumerator EVALUATION_TREE_TYPE

enumerator TASK_TYPE

enumerator TASK_SCHEDULED

enumerator TASK_UPDATE_MODEL

enumerator TASK_REPORT

enumerator TASK_REPORT_TARGET

enumerator TASK_REPORT_APPEND

enumerator TASK_REPORT_CONFIRM_OVERWRITE

enumerator PROBLEM

enumerator METHOD

enumerator METHOD_TYPE

enumerator PLOT_TYPE

enumerator PLOT_ITEM_TYPE

enumerator PARAMETER

enumerator PARAMETER_TYPE

enumerator PARAMETER_ROLE

enumerator PARAMETER_USED

enumerator PARAMETER_VALUE

enumerator PARAMETER_MAPPING

enumerator UNIT

enumerator VOLUME_UNIT

enumerator AREA_UNIT

enumerator LENGTH_UNIT

enumerator TIME_UNIT

enumerator QUANTITY_UNIT

enumerator MODEL_TYPE

enumerator AVOGADRO_NUMBER

enumerator DIMENSIONALITY

enumerator ARRAY_ELEMENT_INDEX

enumerator REPORT_SEPARATOR

enumerator REPORT_IS_TABLE

enumerator REPORT_SHOW_TITLE

enumerator REPORT_PRECISION

enumerator NOTES

enumerator MIRIAM_RDF_XML

enumerator MIRIAM_PREDICATE

enumerator MIRIAM_RESOURCE

enumerator MIRIAM_DESCRIPTION

enumerator MIRIAM_ID

enumerator DATE

enumerator GIVEN_NAME

enumerator FAMILY_NAME

enumerator EMAIL

enumerator ORGANIZATION

enumerator FRAMEWORK

enumerator DELAY_ASSIGNMENT

enumerator FIRE_AT_INITIALTIME

enumerator PERSISTENT_TRIGGER

enumerator TRIGGER_EXPRESSION

enumerator DELAY_EXPRESSION

enumerator PRIORITY_EXPRESSION

enumerator ASSIGNMENTS

enumerator VECTOR_CONTENT

enumerator UNIT_SYMBOL

enumerator UNIT_EXPRESSION

enumerator NOISE

enumerator PROPENSITY

enumerator __SIZE

Public Static Attributes

static const CEnumAnnotation<std::string, Type> Name

class cpsapiReaction : public cpsapiContainer 

Public Types

enum Property

Enumeration of the exposed properties

Values:

enumerator CHEMICAL_EQUATION

enumerator KINETIC_LAW

enumerator KINETIC_LAW_EXPRESSION

enumerator KINETIC_LAW_UNIT_TYPE

enumerator SCALING_COMPARTMENT

enumerator ADD_NOISE

enumerator NOISE_EXPRESSION

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator CN

enum Reference

Enumeration of the exposed references

Values:

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator FLUX

enumerator PARTICLE_FLUX

enumerator INITIAL_FLUX

enumerator INITIAL_PARTICLE_FLUX

enumerator NOISE

enumerator PROPENSITY

typedef cpsapiReaction self: The class

typedef cpsapiContainer base: The base class

typedef CReaction wrapped: The wrapped COPASI class

typedef std::map<std::string, cpsapiKineticLawVariable> VariableManager

typedef CDataVector<cpsapiKineticLawVariable::KineticLawVariable> VariableVector

Public Functions

cpsapiReaction(wrapped *pWrapped = nullptr)

Specific constructor

Parameters: wrapped – * pWrapped

virtual ~cpsapiReaction(): Destructor

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

cpsapiKineticLawVariable variable(const std::string &name = "")

Retrieve the kinetic law variable with the givent name

Parameters: const – std::string & name
Returns: cpsapiKineticLawVariable variable

cpsapiVector<cpsapiKineticLawVariable> variables()

Retrieve a vector of the kinetic law variables

Returns: cpsapiVector< cpsapiKineticLawVariable > variables

bool setProperty(const Property &property, const cpsapiData &value, const CCore::Framework &framework = CCore::Framework::__SIZE)

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – cpsapiData & value
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

bool success

cpsapiData getProperty(const Property &property, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

cpsapiData property

CCommonName getDataCN(const Reference &reference, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Retrieve a property of the object to the provided value under the given framework. The default framework is unspecified

Parameters

const – Reference & reference
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

CCommonName

Public Static Attributes

static const Properties SupportedProperties: Static set of supported properties

static const Properties HiddenProperties: Static set of hidden properties

static const References SupportedReferences: Static set of supported references

static const References HiddenReferences: Static set of hidden references

Protected Functions

virtual bool setProperty(const cpsapiProperty::Type &property, const cpsapiData &value, const CCore::Framework &framework) override

Set the property

Parameters

const – cpsapiProperty::Type & property
const – cpsapiData & value
const – CCore::Framework &framework

Returns

bool success

virtual cpsapiData getProperty(const cpsapiProperty::Type &property, const CCore::Framework &framework) const override

Retrieve the property

Parameters

const – cpsapiProperty::Type & property
const – CCore::Framework &framework

Returns

cpsapiData property

virtual CCommonName getDataCN(const cpsapiReference::Type &reference, const CCore::Framework &framework) const override

Retrieve the data reference

Parameters

const – cpsapiReference::Type & reference
const – CCore::Framework &framework

Returns

CCommonName

Private Functions

cpsapiKineticLawVariable::KineticLawVariable *assertVariable(const std::string &name)

Assert that the variable manager contains a variable with the given

Parameters: const – std::string & name
Returns: cpsapiKineticLawVariable::KineticLawVariable*

class cpsapiSpecies : public cpsapiModelEntity 

Public Types

enum Property

Enumeration of the exposed properties

Values:

enumerator EXPRESSION

enumerator INITIAL_EXPRESSION

enumerator INITIAL_VALUE

enumerator SIMULATION_TYPE

enumerator ADD_NOISE

enumerator NOISE_EXPRESSION

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator CN

enumerator UNIT

typedef cpsapiSpecies self: The class

typedef cpsapiModelEntity base: The base class

typedef CMetab wrapped: The wrapped COPASI class

Public Functions

cpsapiSpecies(wrapped *pWrapped = nullptr)

Specific constructor

Parameters

wrapped – * pWrapped Specific constructor
wrapped – * pWrapped

virtual ~cpsapiSpecies()

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

bool setProperty(const Property &property, const cpsapiData &value, const CCore::Framework &framework = CCore::Framework::__SIZE)

cpsapiData getProperty(const Property &property, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Public Static Attributes

static const Properties SupportedProperties: Static set of supported properties

Protected Functions

virtual bool setProperty(const cpsapiProperty::Type &property, const cpsapiData &value, const CCore::Framework &framework) override

Set the property

Parameters

const – cpsapiProperty::Type & property
const – cpsapiData & value
const – CCore::Framework &framework

Returns

bool success

virtual cpsapiData getProperty(const cpsapiProperty::Type &property, const CCore::Framework &framework) const override

Retrieve the property

Parameters

const – cpsapiProperty::Type & property
const – CCore::Framework &framework

Returns

cpsapiData property

class cpsapiTransaction

Private Types

typedef std::map<CModel*, sChangeInfo> Map

typedef std::map<CModel*, bool> MapStructureChange

Private Static Functions

static bool beginTransaction(CModel *pModel)

static bool endTransaction(CModel *pModel)

static bool synchronize(const CDataObject *pObject, const CCore::Framework &framework)

static bool beginStructureChange(CModel *pModel)

static bool endStructureChange(CModel *pModel)

Private Static Attributes

static Map Transactions

static MapStructureChange StructureChange

Friends

friend class cpsapiObject

friend class cpsapiModelEntity

friend class cpsapiCompartment

friend class cpsapiSpecies

friend class cpsapiGlobalQuantity

friend class cpsapiReaction

friend class cpsapiKineticLawVariable

friend class cpsapiModel

friend class cpsapiEvent

friend class cpsapiEventAssignment

class cpsapiValue : public cpsapiObject 

Public Types

enum Property

Enumeration of the exposed properties

Values:

enumerator VALUE

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

enumerator CN

enum Reference

Enumeration of the exposed references

Values:

enumerator VALUE

enumerator NAME

enumerator OBJECT_UNIQUE_NAME

typedef cpsapiValue self: The class

typedef cpsapiObject base: The base class

typedef CDataObject wrapped: The wrapped COPASI class

Public Functions

cpsapiValue(wrapped *pWrapped = nullptr)

Specific constructor

Parameters: wrapped – * pWrapped (default: nullptr)

virtual ~cpsapiValue(): Destructor

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

bool setProperty(const Property &property, const cpsapiData &value, const CCore::Framework &framework = CCore::Framework::__SIZE)

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – cpsapiData & value
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

bool success

cpsapiData getProperty(const Property &property, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Set a property of the object to the provided value under the given framework. The value must match the underlying value of the property. The default framework is unspecified

Parameters

const – Property & property
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

cpsapiData property

CCommonName getDataCN(const Reference &reference, const CCore::Framework &framework = CCore::Framework::__SIZE) const

Retrieve a property of the object to the provided value under the given framework. The default framework is unspecified

Parameters

const – Reference & reference
const – CCore::Framework & framework (default: CCore::Framework::__SIZE)

Returns

CCommonName

operator cpsapiData() const

Convert the contained value into cpsapiData

Returns: cpsapiData

bool valid() const

Check whether it contains valid value

Returns: bool valid
Returns

Public Static Attributes

static const Properties SupportedProperties: Static set of supported properties

static const Properties HiddenProperties: Static set of hidden properties

static const References SupportedReferences: Static set of supported references

static const References HiddenReferences: Static set of hidden references

Protected Functions

virtual bool setProperty(const cpsapiProperty::Type &property, const cpsapiData &value, const CCore::Framework &framework) override

Set the property

Parameters

const – cpsapiProperty::Type & property
const – cpsapiData & value
const – CCore::Framework &framework

Returns

bool success

virtual cpsapiData getProperty(const cpsapiProperty::Type &property, const CCore::Framework &framework) const override

Retrieve the property

Parameters

const – cpsapiProperty::Type & property
const – CCore::Framework &framework

Returns

cpsapiData property

virtual CCommonName getDataCN(const cpsapiReference::Type &reference, const CCore::Framework &framework) const override

Retrieve the data reference

Parameters

const – cpsapiReference::Type & reference
const – CCore::Framework &framework

Returns

CCommonName

template<class Object> class cpsapiVector : public cpsapiContainer 

Public Types

enum Property

Enumeration of the exposed properties

Values:

typedef cpsapiVector<Object> self: The class

typedef cpsapiContainer base: The base class

typedef CDataVector<typename Object::wrapped> wrapped: The wrapped COPASI class

typedef std::map<typename Object::wrapped*, Object> ObjectMap: We need to keep the cpsapiObjects around since the iterator returns references or pointers.

Public Functions

cpsapiVector(wrapped *pWrapped = nullptr, const cpsapiObjectData::Type &type = cpsapiObjectData::Type::Vector)

Specific constructor

Parameters

wrapped – * pWrapped (default: nullptr)
const – Type & type (default: Type::cpsapiVector)

virtual ~cpsapiVector(): Destructor

template<typename Visitor> void accept(Visitor &visitor)

Accept the given visitor

Template Parameters: Visitor –
Parameters: Visitor – & visitor

size_t size() const

iterator begin()

iterator end()

Object &operator[](const size_t &index)

Object &operator[](const std::string &name)

size_t index(const std::string &name) const

template<> inline size_t index(const std::string &name) const

Public Static Attributes

static const Properties SupportedProperties = {}: Static set of supported properties

struct cpsapiVisitor

Public Static Functions

template<typename Visitor, typename Visited> static inline void acceptIfVisitable(Visitor &visitor, Visited *pVisited)

template<class Visitor> static void accept(Visitor &visitor, CDataObject *pObject)

Private Static Functions

template<typename visitor, typename visited, typename Z = decltype(std::declval<visitor>().visit(std::declval<visited*>()))> static inline void doVisit(visitor &v, visited *pV, int)

template<typename visitor, typename visited> static inline void doVisit(visitor, visited*, ...)

class cpsapiGroup::Data : public Data 

Public Functions

inline Data(const base::Data &data)

inline virtual ~Data()

Public Members

cpsapiParameter mDefaultParameter

class cpsapiDataModel::Data : public Data 

Public Functions

inline Data(const base::Data &data)

inline virtual ~Data()

Public Members

cpsapiModel mModel

cpsapiTask mDefaultTask

CReportDefinition *mpDefaultReportDefinition

CPlotSpecification *mpDefaultPlotSpecification

class cpsapiVector::Data : public Data 

Public Functions

inline Data(const base::Data &data)

inline virtual ~Data()

Public Members

ObjectMap mMap

class cpsapiReaction::Data : public cpsapiObjectData 

Public Functions

inline Data(const base::Data &data)

inline virtual ~Data()

Public Members

VariableManager mVariableManager

VariableVector *mpVector

cpsapiKineticLawVariable mDefaultVariable

class cpsapiCompartment::Data : public cpsapiObjectData 

Public Functions

inline Data(const base::Data &data)

inline virtual ~Data()

Public Members

cpsapiSpecies mDefaultSpecies

class cpsapiEvent::Data : public cpsapiObjectData 

Public Functions

inline Data(const base::Data &data)

inline virtual ~Data()

Public Members

cpsapiEventAssignment mDefaultEventAssignment

class cpsapiModel::Data : public cpsapiObjectData 

Public Functions

inline Data(const base::Data &data)

inline virtual ~Data()

Public Members

cpsapiCompartment mDefaultCompartment

cpsapiReaction mDefaultReaction

cpsapiGlobalQuantity mDefaultGlobalQuantity

cpsapiEvent mDefaultEvent

class cpsapiVector::iterator : public iterator 

Public Functions

inline iterator()

inline iterator(const typename wrapped::iterator &src, ObjectMap &map)

inline iterator(ObjectMap &map)

inline ~iterator()

inline Object &operator*() const

inline Object *operator->() const

inline operator Object*() const

inline iterator &operator++()

inline iterator operator++(int)

inline iterator &operator--()

inline iterator operator--(int)

inline iterator &operator+=(const typename wrapped::iterator::difference_type &n)

inline iterator operator+(const typename wrapped::iterator::difference_type &n) const

inline iterator &operator-=(const typename wrapped::iterator::difference_type &n)

inline iterator operator-(const typename wrapped::iterator::difference_type &n) const

Protected Attributes

ObjectMap *mpMap

class cpsapiKineticLawVariable::KineticLawVariable : public CDataObject

#include <cpsapiKineticLawVariable.h>

A fake CDataObject representing the the variables of the kinetic law

Public Functions

KineticLawVariable(const KineticLawVariable &src, CDataContainer *pParent = nullptr)

Copy constructor

Parameters

const – KineticLawVariable & src,
CDataContainer – * pParent (default: nullptr)

virtual ~KineticLawVariable(): Destructor

void updateMappedObject()

Public Members

cpsapiObject *mpMappedObject

Public Static Functions

static KineticLawVariable *fromData(const CData &data, CUndoObjectInterface *pParent)

Required for objects to be insterted into CDataVector

Parameters

const – CData & data
CUndoObjectInterface – * pParent

Returns

KineticLawVariable * pData

Private Functions

KineticLawVariable(): Default constructor (not implemented)

KineticLawVariable(CReaction *pReaction, const std::string &name = "")

Construct a new Fake Data object

Parameters

CReaction – * pReaction
const – std::string & name

Friends

friend class cpsapiReaction

template<class cpsapi, class copasi> struct cpsapiFactory::Part : public cpsapiFactory::PartInterface 

Public Functions

inline Part(const PartType &partType = PartType::__SIZE)

inline virtual ~Part()

virtual cpsapiObject *create(CDataObject *pDataObject) const override

virtual cpsapiObject *copy(const cpsapiObject &src) const override

virtual const std::type_info &cpsapiType() const override

virtual const std::type_info &copasiType() const override

virtual void accept(CDataObject *pDataObject, const cpsapiVisitor::VisitorInterface &visitor) const override

template<> inline virtual cpsapiObject *create(CDataObject*) const

template<> inline virtual cpsapiObject *copy(const cpsapiObject&) const

template<> inline virtual void accept(CDataObject*, const cpsapiVisitor::VisitorInterface&) const

struct cpsapiFactory::PartInterface

Subclassed by cpsapiFactory::Part< cpsapi, copasi >

Public Functions

inline PartInterface(const PartType &partType)

inline virtual ~PartInterface()

virtual cpsapiObject *create(CDataObject*) const = 0

virtual cpsapiObject *copy(const cpsapiObject&) const = 0

virtual const std::type_info &cpsapiType() const = 0

virtual const std::type_info &copasiType() const = 0

virtual void accept(CDataObject*, const cpsapiVisitor::VisitorInterface&) const = 0

Public Members

const PartType type

struct cpsapiTransaction::sChangeInfo

Public Members

std::set<const CDataObject*> changed

CCore::Framework framework = CCore::Framework::__SIZE

template<class cpsapi, class Visitor> struct cpsapiVisitor::VisitorImplementation : public cpsapiVisitor::VisitorInterface 

Public Functions

inline VisitorImplementation(Visitor &visitor)

inline virtual ~VisitorImplementation()

inline virtual void visit(cpsapiObject *pObject) const override

Public Members

Visitor &mVisitor

struct cpsapiVisitor::VisitorInterface

Subclassed by cpsapiVisitor::VisitorImplementation< cpsapi, Visitor >

Public Functions

inline virtual ~VisitorInterface()

virtual void visit(cpsapiObject *pObject) const = 0

file cpsapiContainer.h: #include “cpsapi/core/cpsapiObject.h”

#include <>

file cpsapiData.h: #include <>

#include <>

#include <>

#include <>

#include <>

#include <>

file cpsapiDataCollector.h: #include <>

#include “cpsapi/core/cpsapiObject.h”

file cpsapiDataModel.h: #include “cpsapi/core/cpsapiContainer.h”

#include “cpsapi/model/cpsapiModel.h”

#include “”

#include <>

file cpsapiFactory.h: #include <>

#include <>

#include <>

#include <>

#include <>

#include <>

#include <>

#include <>

file cpsapiGroup.h: #include “cpsapi/core/cpsapiParameter.h”

#include <>

file cpsapiObject.h

#include <>

#include “cpsapi/core/cpsapiProperty.h”

#include “cpsapi/core/cpsapiObjectData.h”

#include “cpsapi/core/cpsapiVisitor.h”

#include “cpsapi/core/cpsapiFactory.h”

#include “cpsapi/core/cpsapiData.h”

Defines

DATA

WRAPPED

Functions

CPSAPI_NAMESPACE_END std::ostream & operator<< (std::ostream &os, const CPSAPI_NAMESPACE_QUALIFIER cpsapiObject &object)

file cpsapiObjectData.h: #include <>

#include <>

#include <>

#include <>

#include “”

file cpsapiParameter.h: #include “cpsapi/core/cpsapiContainer.h”

#include <>

file cpsapiProperty.h

#include <>

#include “”

Typedefs

typedef cpsapiProperty cpsapiReference

file cpsapiRoot.h: #include <>

#include “cpsapi/core/cpsapiContainer.h”

#include “cpsapi/model/cpsapiModel.h”

#include “cpsapi/model/cpsapiCompartment.h”

#include “cpsapi/model/cpsapiSpecies.h”

#include “cpsapi/model/cpsapiGlobalQuantity.h”

#include “cpsapi/model/cpsapiReaction.h”

#include “cpsapi/model/cpsapiEvent.h”

#include “cpsapi/model/cpsapiEventAssignment.h”

file cpsapiValue.h: #include “cpsapi/core/cpsapiObject.h”

#include <>

#include <>

file cpsapiVector.h: #include “cpsapi/core/cpsapiContainer.h”

#include <>

file cpsapiVisitor.h: #include <>

#include <>

#include <>

#include “”

file cpsapiCompartment.h: #include “cpsapi/core/cpsapiVector.h”

#include “cpsapi/model/cpsapiModelEntity.h”

#include “cpsapi/model/cpsapiSpecies.h”

#include <>

#include <>

file cpsapiEvent.h: #include “cpsapi/core/cpsapiVector.h”

#include “cpsapi/model/cpsapiEventAssignment.h”

file cpsapiEventAssignment.h: #include “cpsapi/core/cpsapiContainer.h”

file cpsapiGlobalQuantity.h: #include “cpsapi/model/cpsapiModelEntity.h”

file cpsapiKineticLawVariable.h: #include “cpsapi/core/cpsapiContainer.h”

#include “cpsapi/core/cpsapiVector.h”

#include <>

file cpsapiModel.h: #include “cpsapi/model/cpsapiModelEntity.h”

#include “cpsapi/model/cpsapiCompartment.h”

#include “cpsapi/model/cpsapiSpecies.h”

#include “cpsapi/model/cpsapiGlobalQuantity.h”

#include “cpsapi/model/cpsapiReaction.h”

#include “cpsapi/model/cpsapiEvent.h”

#include <>

file cpsapiModelEntity.h: #include “cpsapi/core/cpsapiContainer.h”

#include <>

file cpsapiReaction.h: #include “cpsapi/model/cpsapiKineticLawVariable.h”

#include “cpsapi/core/cpsapiContainer.h”

#include “cpsapi/core/cpsapiVector.h”

file cpsapiSpecies.h: #include “cpsapi/model/cpsapiModelEntity.h”

file cpsapiTransaction.h: #include <>

#include <>

#include “”

#include <>

dir /home/docs/checkouts/readthedocs.org/user_builds/copasi-api/checkouts/latest/cpsapi/core

dir /home/docs/checkouts/readthedocs.org/user_builds/copasi-api/checkouts/latest/cpsapi

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