CMIRIAMResource Class Reference

#include <CMIRIAMResource.h>

Inheritance diagram for CMIRIAMResource:

Public Member Functions
void	addDeprecatedURL (const std::string &URL)
	CMIRIAMResource (const CCopasiParameterGroup &group, const CDataContainer *pParent)
	CMIRIAMResource (const CMIRIAMResource &src, const CDataContainer *pParent)
	CMIRIAMResource (const std::string &name="MIRIAM Resource", const CDataContainer *pParent=NO_PARENT)
std::string	createIdentifiersOrgURL (const std::string id) const
std::string	extractId (const std::string &uri) const
std::string	getIdentifiersOrgURL (const bool &compact) const
const bool &	getMIRIAMCitation () const
const CCopasiParameterGroup &	getMIRIAMDeprecated () const
const std::string &	getMIRIAMDisplayName () const
const CMIRIAMResource &	getMIRIAMMIRIAMResource () const
const bool &	getMIRIAMNamespaceEmbeddedInPattern () const
const std::string &	getMIRIAMPattern () const
const std::string &	getMIRIAMURI () const
void	setMIRIAMCitation (const bool &isCitation)
void	setMIRIAMDisplayName (const std::string &displayName)
void	setMIRIAMNamespaceEmbeddedInPattern (const bool &isNamespaceEmbeddedInPattern)
void	setMIRIAMPattern (const std::string &pattern)
void	setMIRIAMURI (const std::string &URI)
virtual	~CMIRIAMResource ()
Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)
void	addParameter (CCopasiParameter *pParameter)
bool	addParameter (const CCopasiParameter &parameter)
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
template<class CType >
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)
CCopasiParameterGroup *	assertGroup (const std::string &name, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
template<class CType >
CType *	assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
index_iterator	beginIndex () const
const_name_iterator	beginName () const
	CCopasiParameterGroup (const CCopasiParameterGroup &src, const CDataContainer *pParent=NULL)
	CCopasiParameterGroup (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="ParameterGroup")
void	clear ()
virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
virtual bool	elevateChildren ()
index_iterator	endIndex () const
const_name_iterator	endName () const
CCopasiParameterGroup &	getElementTemplates ()
const CCopasiParameterGroup &	getElementTemplates () const
CCopasiParameterGroup *	getGroup (const size_t &index)
const CCopasiParameterGroup *	getGroup (const size_t &index) const
CCopasiParameterGroup *	getGroup (const std::string &name)
const CCopasiParameterGroup *	getGroup (const std::string &name) const
virtual size_t	getIndex (const CDataObject *pObject) const
size_t	getIndex (const std::string &name) const
std::string	getKey (const size_t &index) const
std::string	getKey (const std::string &name) const
virtual const std::string &	getName (const size_t &index) const
virtual const CObjectInterface *	getObject (const CCommonName &cn) const
CCopasiParameter *	getParameter (const size_t &index)
const CCopasiParameter *	getParameter (const size_t &index) const
CCopasiParameter *	getParameter (std::string name)
const CCopasiParameter *	getParameter (std::string name) const
CCopasiParameter::Type	getType (const size_t &index) const
CCopasiParameter::Type	getType (const std::string &name) const
std::string	getUniqueParameterName (const CCopasiParameter *pParameter) const
template<class CType >
CType &	getValue (const size_t &index)
template<class CType >
const CType &	getValue (const size_t &index) const
template<class CType >
CType &	getValue (const std::string &name)
template<class CType >
const CType &	getValue (const std::string &name) const
bool	haveTemplate () const
virtual CUndoObjectInterface *	insert (const CData &data)
CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)
virtual void	print (std::ostream *ostream) const
virtual bool	remove (CDataObject *pObject)
bool	removeParameter (CCopasiParameter *pParameter)
bool	removeParameter (const size_t &index)
bool	removeParameter (const std::string &name)
virtual void	setUserInterfaceFlag (const UserInterfaceFlag &flag)
template<class CType >
bool	setValue (const size_t &index, const CType &value)
template<class CType >
bool	setValue (const std::string &name, const CType &value)
size_t	size (const UserInterfaceFlag &require=UserInterfaceFlag::None, const UserInterfaceFlag &exclude=UserInterfaceFlag::None) const
bool	swap (const size_t &iFrom, const size_t &iTo)
bool	swap (index_iterator &from, index_iterator &to)
virtual CData	toData () const
virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)
virtual	~CCopasiParameterGroup ()
Public Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src, const CDataContainer *pParent)
	CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="Parameter")
virtual CCommonName	getCN () const override
template<class CType >
const CType &	getDefault () const
virtual const std::string &	getKey () const override
virtual std::string	getObjectDisplayName () const override
const CCopasiParameter::Type &	getType () const
const UserInterfaceFlag &	getUserInterfaceFlag () const
template<class CType >
std::vector< std::pair< CType, CType > > &	getValidValues ()
template<class CType >
const std::vector< std::pair< CType, CType > > &	getValidValues () const
void *	getValidValuesPointer () const
template<class CType >
CType &	getValue ()
template<class CType >
const CType &	getValue () const
virtual void *	getValuePointer () const override
CDataObject *	getValueReference () const
bool	hasValidValues () const
bool	isBasic () const
bool	isDefault () const
bool	isEditable () const
bool	isUnsupported () const
bool	isValidValue (const bool &value) const
bool	isValidValue (const C_FLOAT64 &value) const
bool	isValidValue (const C_INT32 &value) const
bool	isValidValue (const CCommonName &value) const
template<class CType >
bool	isValidValue (const CType &) const
bool	isValidValue (const std::string &value) const
bool	isValidValue (const std::vector< CCopasiParameter * > &value) const
bool	isValidValue (const unsigned C_INT32 &value) const
CCopasiParameter &	operator= (const CCopasiParameter &rhs)
template<class CType >
bool	setDefault (const CType &defaultValue)
bool	setDefault (const std::vector< CCopasiParameter * > &defaultValue)
virtual bool	setObjectParent (const CDataContainer *pParent) override
template<class CType , class Enum >
bool	setValidValues (const CEnumAnnotation< CType, Enum > &validValues)
template<class CType >
bool	setValidValues (const std::vector< std::pair< CType, CType > > &validValues)
template<class CType >
bool	setValue (const CType &value)
bool	setValue (const std::vector< CCopasiParameter * > &value)
virtual	~CCopasiParameter ()
Public Member Functions inherited from CDataContainer
virtual bool	add (CDataObject *pObject, const bool &adopt=true)
virtual bool	appendDeletedDependentData (CUndoData &undoData) const
	CDataContainer (const CDataContainer &src, const CDataContainer *pParent)
	CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)
virtual std::string	getChildObjectUnits (const CDataObject *pObject) const
void	getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const
virtual objectMap &	getObjects ()
virtual const objectMap &	getObjects () const
virtual const std::string	getUnits () const override
virtual const CDataObject *	getValueObject () const override
void	objectRenamed (CDataObject *pObject, const std::string &oldName)
virtual	~CDataContainer ()
Public Member Functions inherited from CDataObject
void	addIssue (const CIssue &issue)
void	addReference (const CDataContainer *pReference)
virtual void	calculateValue () override
	CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL)
virtual void	destruct () override
virtual const CDataObject *	getDataObject () const override
CDataContainer *	getObjectAncestor (const std::string &type) const
CDataModel *	getObjectDataModel () const
const CObjectInterface *	getObjectFromCN (const CCommonName &cn) const
const std::string &	getObjectName () const
CDataContainer *	getObjectParent () const
const std::string &	getObjectType () const
virtual const CObjectInterface::ObjectSet &	getPrerequisites () const override
virtual const CValidity &	getValidity () const override
bool	hasFlag (const Flag &flag) const
virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override
bool	prerequisitsContains (const DataObjectSet &objects) const
void	removeIssue (const CIssue &issue)
void	removeReference (const CDataContainer *pReference)
bool	setObjectName (const std::string &name)
void	validityChanged (const CValidity &changedValidity) override
void	validityRemoved (const CValidity &changedValidity)
virtual	~CDataObject ()
Public Member Functions inherited from CObjectInterface
	CObjectInterface ()
	CObjectInterface (const CObjectInterface &src)
virtual	~CObjectInterface ()
Public Member Functions inherited from CUndoObjectInterface
	CUndoObjectInterface ()
	CUndoObjectInterface (const CUndoObjectInterface &src)
bool	generateUuid ()
const xg::Guid &	getUuid () const
bool	setUuid (const std::string &uuid)
bool	setUuid (const xg::Guid &uuid)
virtual	~CUndoObjectInterface ()

Private Member Functions
std::string	extractNamespaceFromPattern () const
void	initializeParameter ()

Private Attributes
bool *	mpCitation
CCopasiParameterGroup *	mpDeprecated
std::string *	mpDisplayName
bool *	mpNamespaceEmbeddedInPattern
std::string *	mpPattern
std::string *	mpURI

Additional Inherited Members
Public Types inherited from CCopasiParameterGroup
typedef CDataObjectMap::const_type_iterator< CCopasiParameter >	const_name_iterator
typedef std::vector< CCopasiParameter * >	elements
typedef elements::iterator	index_iterator
typedef CDataObjectMap::type_iterator< CCopasiParameter >	name_iterator
Public Types inherited from CCopasiParameter
enum class	eUserInterfaceFlag { editable , basic , unsupported , __SIZE }
enum class	Type {   DOUBLE = 0 , UDOUBLE , INT , UINT ,   BOOL , GROUP , STRING , CN ,   KEY , FILE , EXPRESSION , INVALID ,   __SIZE }
typedef CFlags< eUserInterfaceFlag >	UserInterfaceFlag
Public Types inherited from CDataContainer
typedef CDataObjectMap	objectMap
Public Types inherited from CDataObject
typedef std::set< const CDataObject * >	DataObjectSet
enum	Flag {   Container , Vector , Matrix , NameVector ,   Reference , ValueBool , ValueInt , ValueInt64 ,   ValueDbl , NonUniqueName , StaticString , ValueString ,   Separator , DisplayName , ModelEntity , Array ,   DataModel , Root , Gui , __SIZE }
Public Types inherited from CObjectInterface
typedef std::vector< const CDataContainer * >	ContainerList
typedef std::set< const CObjectInterface * >	ObjectSet
Static Public Member Functions inherited from CCopasiParameter
static void	allocateValidValues (const Type &type, void *&pValidValues)
static void	allocateValue (const Type &type, void *&pValue)
static void	assignValue (const Type &type, void *&pValue, const void *pNewValue)
static void	deleteValidValues (const Type &type, void *&pValidValues)
static void	deleteValue (const Type &type, void *&pValue)
static CCopasiParameter *	fromData (const CData &data, CUndoObjectInterface *pParent)
Static Public Member Functions inherited from CDataContainer
static CDataContainer *	fromData (const CData &data, CUndoObjectInterface *pParent)
Static Public Member Functions inherited from CDataObject
static CDataObject *	fromData (const CData &data, CUndoObjectInterface *pParent)
static void	sanitizeObjectName (std::string &name)
Static Public Member Functions inherited from CObjectInterface
static const CDataObject *	DataObject (const CObjectInterface *pInterface)
static CObjectInterface *	GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName)
Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType *	fromData (const CData &, CUndoObjectInterface *)
Static Public Attributes inherited from CCopasiParameter
static const CEnumAnnotation< std::string, Type >	TypeName
static const CEnumAnnotation< std::string, Type >	XMLType
Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList
Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()
Protected Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src)
Protected Member Functions inherited from CDataContainer
template<class CType >
CDataMatrixReference< CType > *	addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
template<class CType >
CDataObjectReference< CType > *	addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
template<class CType >
CDataVectorReference< CType > *	addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
	CDataContainer (const CDataContainer &src)
void	initObjects ()
Protected Member Functions inherited from CDataObject
	CDataObject ()
	CDataObject (const std::string &name, const CDataContainer *pParent=static_cast< CDataContainer * >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)
Protected Attributes inherited from CCopasiParameter
std::string	mKey
void *	mpDefault
void *	mpValidValues
void *	mpValue
CDataObject *	mpValueReference
UserInterfaceFlag	mUserInterfaceFlag
Protected Attributes inherited from CDataContainer
objectMap	mObjects
Protected Attributes inherited from CDataObject
ObjectSet	mPrerequisits
std::set< CDataContainer * >	mReferences
Protected Attributes inherited from CObjectInterface
CValidity	mValidity

Constructor & Destructor Documentation

CMIRIAMResource() [1/3]

CMIRIAMResource::CMIRIAMResource	(	const std::string &	name = "MIRIAM Resource",
		const CDataContainer *	pParent = NO_PARENT
	)

Default constructor

Parameters

const	std::string & name (default: MIRIAM Resource)
const	CDataContainer * pParent (default: NULL)

References initializeParameter().

CMIRIAMResource() [2/3]

CMIRIAMResource::CMIRIAMResource	(	const CMIRIAMResource &	src,
		const CDataContainer *	pParent
	)

Copy constructor

Parameters

const	CMIRIAMResource & src
const	CDataContainer * pParent (default: NULL)

References initializeParameter().

CMIRIAMResource() [3/3]

CMIRIAMResource::CMIRIAMResource	(	const CCopasiParameterGroup &	group,
		const CDataContainer *	pParent
	)

Specific constructor

Parameters

const	CCopasiParameterGroup & group
const	CDataContainer * pParent (default: NULL)

References initializeParameter().

~CMIRIAMResource()

CMIRIAMResource::~CMIRIAMResource ( )

virtual

Destructor

Member Function Documentation

addDeprecatedURL()

void CMIRIAMResource::addDeprecatedURL

(

const std::string &

URL

)

Add a deprecated URL to the MIRIAM Resource

Parameters

const

std::string & URL

References CCopasiParameterGroup::addParameter(), mpDeprecated, and CCopasiParameter::STRING.

Referenced by CMIRIAMResources::updateMIRIAMResourcesFromFile().

createIdentifiersOrgURL()

std::string CMIRIAMResource::createIdentifiersOrgURL

(

const std::string

id

)

const

Create the URL for the provided Id

Parameters

const

std::string id

Returns

std::string IdentifiersOrgURL

References getIdentifiersOrgURL(), and mpNamespaceEmbeddedInPattern.

Referenced by CMIRIAMResourceObject::getIdentifiersOrgURL().

extractId()

std::string CMIRIAMResource::extractId

(

const std::string &

uri

)

const

Extract the ID from the given URI

Parameters

const

std::string & uri

Returns

std::string ID

References CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::endIndex(), extractNamespaceFromPattern(), getIdentifiersOrgURL(), getMIRIAMDeprecated(), getMIRIAMURI(), and mpNamespaceEmbeddedInPattern.

Referenced by CMIRIAMResourceObject::extractId().

extractNamespaceFromPattern()

std::string CMIRIAMResource::extractNamespaceFromPattern ( ) const

private

Extract the embedded namespace from the pattern

Returns

std::string namespace

References mpNamespaceEmbeddedInPattern, and mpPattern.

Referenced by extractId(), and getIdentifiersOrgURL().

getIdentifiersOrgURL()

std::string CMIRIAMResource::getIdentifiersOrgURL

(

const bool &

compact

)

const

Retrieve the identifiers.org URL of the MIRIAM Resource.

Parameters

const

bool & compact

Returns

std::string URL

References extractNamespaceFromPattern(), mpNamespaceEmbeddedInPattern, and mpURI.

Referenced by createIdentifiersOrgURL(), CMIRIAMResources::createURIMap(), and extractId().

getMIRIAMCitation()

const bool & CMIRIAMResource::getMIRIAMCitation

(

)

const

Retrieve whether the resource can be used as reference.

Returns

const bool & isCitation

References mpCitation.

getMIRIAMDeprecated()

const CCopasiParameterGroup & CMIRIAMResource::getMIRIAMDeprecated

(

)

const

Retrieve the deprecated URL of the MIRIAM Resource

Returns

const CCopasiParameterGroup & deprecatedURLs

References mpDeprecated.

Referenced by CMIRIAMResources::createURIMap(), and extractId().

getMIRIAMDisplayName()

const std::string & CMIRIAMResource::getMIRIAMDisplayName

(

)

const

Retrieve the Display Name of the MIRIAM Resource.

Returns

const std::string & DisplayName

References mpDisplayName.

Referenced by CMIRIAMResources::createDisplayNameMap().

getMIRIAMMIRIAMResource()

const CMIRIAMResource & CMIRIAMResource::getMIRIAMMIRIAMResource

(

)

const

Retrieve the list of MIRIAM Resource.

Returns

const CMIRIAMResource & MIRIAMResource

getMIRIAMNamespaceEmbeddedInPattern()

const bool & CMIRIAMResource::getMIRIAMNamespaceEmbeddedInPattern

(

)

const

Retrieve whether the resource can be used as reference.

Returns

const bool & isCitation

References mpNamespaceEmbeddedInPattern.

getMIRIAMPattern()

const std::string & CMIRIAMResource::getMIRIAMPattern

(

)

const

Retrieve the Pattern of the MIRIAM Resource.

Returns

std::string & Pattern

References mpPattern.

getMIRIAMURI()

const std::string & CMIRIAMResource::getMIRIAMURI

(

)

const

Retrieve the URI of the MIRIAM Resource.

Returns

const std::string & URI

References mpURI.

Referenced by CMIRIAMResources::createURIMap(), and extractId().

initializeParameter()

void CMIRIAMResource::initializeParameter ( )

private

Allocates all group parameters and assures that they are properly initialized.

References CCopasiParameterGroup::assertGroup(), CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, mpCitation, mpDeprecated, mpDisplayName, mpNamespaceEmbeddedInPattern, mpPattern, mpURI, and CCopasiParameter::STRING.

Referenced by CMIRIAMResource().

setMIRIAMCitation()

void CMIRIAMResource::setMIRIAMCitation

(

const bool &

isCitation

)

Set whether the resource can be used as reference.

Parameters

const

bool & isCitation

References mpCitation.

Referenced by CMIRIAMResources::updateMIRIAMResourcesFromFile().

setMIRIAMDisplayName()

void CMIRIAMResource::setMIRIAMDisplayName

(

const std::string &

displayName

)

Set the Display Name of the MIRIAM Resource.

Parameters

const

std::string & DisplayName

References mpDisplayName.

Referenced by CRootContainer::initializeChildren(), and CMIRIAMResources::updateMIRIAMResourcesFromFile().

setMIRIAMNamespaceEmbeddedInPattern()

void CMIRIAMResource::setMIRIAMNamespaceEmbeddedInPattern

(

const bool &

isNamespaceEmbeddedInPattern

)

Set whether the namespace is embedded in the pattern.

Parameters

const

bool & isNamespaceEmbeddedInPattern

References mpNamespaceEmbeddedInPattern.

Referenced by CMIRIAMResources::updateMIRIAMResourcesFromFile().

setMIRIAMPattern()

void CMIRIAMResource::setMIRIAMPattern

(

const std::string &

pattern

)

Set the Pattern of the MIRIAM Resource.

Parameters

const

std::string & Pattern

References mpPattern.

Referenced by CMIRIAMResources::updateMIRIAMResourcesFromFile().

setMIRIAMURI()

void CMIRIAMResource::setMIRIAMURI

(

const std::string &

URI

)

Set the URI of the MIRIAM Resource. (this is expected to be of the legacy format (urn:miriam:...))

Parameters

const

std::string & URI

References mpURI.

Referenced by CRootContainer::initializeChildren(), and CMIRIAMResources::updateMIRIAMResourcesFromFile().

Member Data Documentation

mpCitation

bool* CMIRIAMResource::mpCitation

private

A pointer to a bool indication the the resource an be used as reference

Referenced by getMIRIAMCitation(), initializeParameter(), and setMIRIAMCitation().

mpDeprecated

CCopasiParameterGroup* CMIRIAMResource::mpDeprecated

private

A parameter group holding all deprecated URIs

Referenced by addDeprecatedURL(), getMIRIAMDeprecated(), and initializeParameter().

mpDisplayName

std::string* CMIRIAMResource::mpDisplayName

private

The name used in the GUI

Referenced by getMIRIAMDisplayName(), initializeParameter(), and setMIRIAMDisplayName().

mpNamespaceEmbeddedInPattern

bool* CMIRIAMResource::mpNamespaceEmbeddedInPattern

private

A pointer to a bool indication the the resource an be used as reference

Referenced by createIdentifiersOrgURL(), extractId(), extractNamespaceFromPattern(), getIdentifiersOrgURL(), getMIRIAMNamespaceEmbeddedInPattern(), initializeParameter(), and setMIRIAMNamespaceEmbeddedInPattern().

mpPattern

std::string* CMIRIAMResource::mpPattern

private

A pointer to the pattern

Referenced by extractNamespaceFromPattern(), getMIRIAMPattern(), initializeParameter(), and setMIRIAMPattern().

mpURI

std::string* CMIRIAMResource::mpURI

private

A pointer to the URI

Referenced by getIdentifiersOrgURL(), getMIRIAMURI(), initializeParameter(), and setMIRIAMURI().

---

The documentation for this class was generated from the following files:

• CMIRIAMResource.h
• CMIRIAMResource.cpp