CAnnotation Class Reference

#include <CAnnotation.h>

Inheritance diagram for CAnnotation:

Public Types
typedef std::map< std::string, std::string >	UnsupportedAnnotation

Public Member Functions
bool	addUnsupportedAnnotation (const std::string &name, const std::string &xml)
bool	applyData (const CData &data, CUndoData::CChangeSet &changes)
	CAnnotation ()
	CAnnotation (const CAnnotation &src)
void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
virtual const std::string &	getKey () const
const std::string &	getMiriamAnnotation () const
const std::string &	getNotes () const
UnsupportedAnnotation &	getUnsupportedAnnotations ()
const UnsupportedAnnotation &	getUnsupportedAnnotations () const
void	initMiriamAnnotation (const std::string &newId)
bool	operator== (const CAnnotation &rhs) const
bool	removeUnsupportedAnnotation (const std::string &name)
bool	replaceUnsupportedAnnotation (const std::string &name, const std::string &xml)
void	setMiriamAnnotation (const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId)
void	setNotes (const std::string &notes)
CData	toData () const
virtual	~CAnnotation ()

Static Public Member Functions
static CMIRIAMInfo *	allocateMiriamInfo (CDataContainer *pParent)
static CAnnotation *	castObject (CDataObject *pObject)
static const CAnnotation *	castObject (const CDataObject *pObject)
static void	freeMiriamInfo (CDataContainer *pParent)

Protected Attributes
std::string	mKey

Static Private Member Functions
static bool	isValidXML (const std::string &xml)

Private Attributes
std::string	mMiriamAnnotation
std::string	mNotes
UnsupportedAnnotation	mUnsupportedAnnotations
std::string	mXMLId

Static Private Attributes
static std::map< CDataContainer *, CMIRIAMInfo * >	Container2Info

Member Typedef Documentation

UnsupportedAnnotation

typedef std::map< std::string, std::string > CAnnotation::UnsupportedAnnotation

Constructor & Destructor Documentation

CAnnotation() [1/2]

CAnnotation::CAnnotation

(

)

Default constructor

CAnnotation() [2/2]

CAnnotation::CAnnotation

(

const CAnnotation &

src

)

Copy constructor

Parameters

const

CAnnotation & src

~CAnnotation()

CAnnotation::~CAnnotation ( )

virtual

Destructor

References CRootContainer::getKeyFactory(), mKey, and CKeyFactory::remove().

Member Function Documentation

addUnsupportedAnnotation()

bool CAnnotation::addUnsupportedAnnotation	(	const std::string &	name,
		const std::string &	xml
	)

Add an unsupported annotation

Parameters

const	std::string & name
const	std::string & xml

Returns

bool success

References CCopasiMessage::ERROR, isValidXML(), MCAnnotation, and mUnsupportedAnnotations.

Referenced by SBMLImporter::importNotes().

allocateMiriamInfo()

CMIRIAMInfo * CAnnotation::allocateMiriamInfo ( CDataContainer *  pParent )

static

Allocat a MIRIAM Info object for the given CDataContainer * pParent. The ownership is with the parent

Parameters

CDataContainer

* pParent

Returns

CMIRIAMInfo * pMiriamInfo

References Container2Info.

Referenced by CDataContainer::getObject().

applyData()

bool CAnnotation::applyData	(	const CData &	data,
		CUndoData::CChangeSet &	changes
	)

Apply the provided data to the annotation

Parameters

const

CData & data

Returns

bool success

References CData::getProperty(), CData::isSetProperty(), mMiriamAnnotation, mNotes, and CDataValue::toString().

Referenced by CFunction::applyData(), CEvent::applyData(), CModelParameterSet::applyData(), CReaction::applyData(), CUnitDefinition::applyData(), and CModelEntity::applyData().

castObject() [1/2]

CAnnotation * CAnnotation::castObject ( CDataObject *  pObject )

static

Referenced by CDataContainer::getObject(), SBMLImporter::importMIRIAM(), CMIRIAMInfo::load(), and CSBMLExporter::updateMIRIAMAnnotation().

castObject() [2/2]

const CAnnotation * CAnnotation::castObject ( const CDataObject *  pObject )

static

createUndoData()

void CAnnotation::createUndoData	(	CUndoData &	undoData,
		const CUndoData::Type &	type,
		const CData &	oldData = CData(),
		const CCore::Framework &	framework = CCore::Framework::ParticleNumbers
	)		const

Create the undo data which represents the changes recording the differences between the provided oldData and the current data.

Parameters

CUndoData	& undoData
const	CUndoData::Type & type
const	CData & oldData (default: empty data)
const	CCore::Framework & framework (default: CCore::Framework::ParticleNumbers)

Returns

CUndoData undoData

References CUndoData::addProperty(), CUndoData::CHANGE, CData::getProperty(), CUndoData::INSERT, mMiriamAnnotation, mNotes, and CUndoData::REMOVE.

Referenced by CFunction::createUndoData(), CEvent::createUndoData(), CModelParameterSet::createUndoData(), CReaction::createUndoData(), CUnitDefinition::createUndoData(), and CModelEntity::createUndoData().

freeMiriamInfo()

void CAnnotation::freeMiriamInfo ( CDataContainer *  pParent )

static

Free if possible an existing MIRIAM Info object for the given CDataContainer * pParent.

Returns

CMIRIAMInfo * pMiriamInfo

References Container2Info.

Referenced by CMIRIAMInfo::~CMIRIAMInfo().

getKey()

const std::string & CAnnotation::getKey ( ) const

virtual

Retrieve the key

Returns

std::string key

Reimplemented in CModelEntity, CUnitDefinition, CReaction, CModelParameterSet, CModel, CEvent, and CFunction.

References mKey.

Referenced by CFunction::getKey(), CMIRIAMInfo::getKey(), CEvent::getKey(), CReaction::getKey(), CUnitDefinition::getKey(), CModelEntity::getKey(), SBMLImporter::importMIRIAM(), and CMIRIAMInfo::save().

getMiriamAnnotation()

const std::string & CAnnotation::getMiriamAnnotation

(

)

const

Retrieve the RDF/XML representation of the MIRIAM annotation

Returns

const std::string & miriamAnnotation

References mMiriamAnnotation.

Referenced by CEvent::CEvent(), CFunction::CFunction(), CModelEntity::CModelEntity(), CModelParameterSet::CModelParameterSet(), CReaction::CReaction(), CUnitDefinition::CUnitDefinition(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateEvent(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CModelExpansion::duplicateReaction(), SBMLImporter::importMIRIAM(), CMIRIAMInfo::load(), CCopasiXML::saveAnnotation(), and CSBMLExporter::updateMIRIAMAnnotation().

getNotes()

const std::string & CAnnotation::getNotes

(

)

const

Retrieve the XHTML notes

Returns

const std::string & notes

References mNotes.

Referenced by CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateEvent(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CModelExpansion::duplicateReaction(), CModel::initObjects(), CCopasiXML::saveAnnotation(), and CSBMLExporter::setSBMLNotes().

getUnsupportedAnnotations() [1/2]

CAnnotation::UnsupportedAnnotation & CAnnotation::getUnsupportedAnnotations

(

)

Retrieve the unsupported annotations in xml format.

Returns

std::map< std::string, std::string > & unsupportedAnnotations

References mUnsupportedAnnotations.

Referenced by CompartmentHandler::processEnd(), EventHandler::processEnd(), FunctionHandler::processEnd(), MetaboliteHandler::processEnd(), ModelHandler::processEnd(), ModelValueHandler::processEnd(), ReactionHandler::processEnd(), UnitDefinitionHandler::processEnd(), CCopasiXML::saveAnnotation(), and CSBMLExporter::setSBMLNotes().

getUnsupportedAnnotations() [2/2]

const CAnnotation::UnsupportedAnnotation & CAnnotation::getUnsupportedAnnotations

(

)

const

References mUnsupportedAnnotations.

initMiriamAnnotation()

void CAnnotation::initMiriamAnnotation

(

const std::string &

newId

)

References mMiriamAnnotation, and mXMLId.

Referenced by CEvent::CEvent(), CFunction::CFunction(), CModelEntity::CModelEntity(), CModelParameterSet::CModelParameterSet(), CReaction::CReaction(), and CUnitDefinition::CUnitDefinition().

isValidXML()

bool CAnnotation::isValidXML ( const std::string &  xml )

staticprivate

References BUFFER_SIZE, CCopasiMessage::getLastMessage(), CExpatTemplate< CType >::parse(), and CCopasiMessage::size().

Referenced by addUnsupportedAnnotation(), and replaceUnsupportedAnnotation().

operator==()

bool CAnnotation::operator==

(

const CAnnotation &

rhs

)

const

Comparison operator

Parameters

const

CAnnotation & rhs

Returns

bool equal

References CRDFUtilities::fixLocalFileAboutReference(), mMiriamAnnotation, mNotes, and mXMLId.

removeUnsupportedAnnotation()

bool CAnnotation::removeUnsupportedAnnotation

(

const std::string &

name

)

Remove an unsupported annotation

Parameters

const

std::string & name

Returns

bool success

References mUnsupportedAnnotations.

replaceUnsupportedAnnotation()

bool CAnnotation::replaceUnsupportedAnnotation	(	const std::string &	name,
		const std::string &	xml
	)

Replace an unsupported annotation

Parameters

const	std::string & name
const	std::string & xml

Returns

bool success

References CCopasiMessage::ERROR, isValidXML(), MCAnnotation, and mUnsupportedAnnotations.

setMiriamAnnotation()

void CAnnotation::setMiriamAnnotation	(	const std::string &	miriamAnnotation,
		const std::string &	newId,
		const std::string &	oldId
	)

Set the RDF/XML representation of the MIRIAM annotation

Parameters

const	std::string & miriamAnnotation
const	std::string & newId
const	std::string & oldId

References CRDFUtilities::fixLocalFileAboutReference(), mMiriamAnnotation, and mXMLId.

Referenced by CEvent::CEvent(), CFunction::CFunction(), CModelEntity::CModelEntity(), CModelParameterSet::CModelParameterSet(), CReaction::CReaction(), CUnitDefinition::CUnitDefinition(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateEvent(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CModelExpansion::duplicateReaction(), SBMLImporter::importMIRIAM(), CompartmentHandler::processEnd(), EventHandler::processEnd(), FunctionHandler::processEnd(), MetaboliteHandler::processEnd(), ModelHandler::processEnd(), ModelParameterSetHandler::processEnd(), ModelValueHandler::processEnd(), ReactionHandler::processEnd(), UnitDefinitionHandler::processEnd(), and CMIRIAMInfo::save().

setNotes()

void CAnnotation::setNotes

(

const std::string &

notes

)

Set the XHTML Notes

Parameters

const

std::string & notes

References mNotes.

Referenced by CModelVersion::CModelVersion(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateEvent(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CModelExpansion::duplicateReaction(), SBMLImporter::importNotes(), CModel::load(), CompartmentHandler::processEnd(), EventHandler::processEnd(), FunctionHandler::processEnd(), MetaboliteHandler::processEnd(), ModelHandler::processEnd(), ModelValueHandler::processEnd(), ReactionHandler::processEnd(), and UnitDefinitionHandler::processEnd().

toData()

CData CAnnotation::toData

(

)

const

Retrieve the data describing the annotation

Returns

CData data

References CData::addProperty(), mMiriamAnnotation, and mNotes.

Referenced by CFunction::toData(), CEvent::toData(), CModelParameterSet::toData(), CReaction::toData(), CUnitDefinition::toData(), and CModelEntity::toData().

Member Data Documentation

Container2Info

std::map< CDataContainer *, CMIRIAMInfo * > CAnnotation::Container2Info

staticprivate

Referenced by allocateMiriamInfo(), and freeMiriamInfo().

mKey

std::string CAnnotation::mKey

protected

Key of the model entity. It is stored here, but constructed in the derived classes.

Referenced by CEvent::CEvent(), CFunction::CFunction(), CModelEntity::CModelEntity(), CReaction::CReaction(), CUnitDefinition::CUnitDefinition(), getKey(), CModel::getKey(), CUnitDefinition::setup(), ~CAnnotation(), CCompartment::~CCompartment(), CEvent::~CEvent(), CFunction::~CFunction(), CMetab::~CMetab(), CModel::~CModel(), CReaction::~CReaction(), and CUnitDefinition::~CUnitDefinition().

mMiriamAnnotation

std::string CAnnotation::mMiriamAnnotation

private

MIRIAM compliant annotation in RDF/XML format

Referenced by applyData(), createUndoData(), getMiriamAnnotation(), initMiriamAnnotation(), operator==(), setMiriamAnnotation(), and toData().

mNotes

std::string CAnnotation::mNotes

private

Notes in XHTML format

Referenced by applyData(), createUndoData(), getNotes(), operator==(), setNotes(), and toData().

mUnsupportedAnnotations

UnsupportedAnnotation CAnnotation::mUnsupportedAnnotations

private

The annotations which are not supported by COPASI. Note, the name is enforced to be unique.

Referenced by addUnsupportedAnnotation(), getUnsupportedAnnotations(), removeUnsupportedAnnotation(), and replaceUnsupportedAnnotation().

mXMLId

std::string CAnnotation::mXMLId

private

The XMLId used in the about statement

Referenced by initMiriamAnnotation(), operator==(), and setMiriamAnnotation().

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

• CAnnotation.h
• CAnnotation.cpp