CMIRIAMInfo Class Reference

#include <CModelMIRIAMInfo.h>

Inheritance diagram for CMIRIAMInfo:

Public Member Functions
bool	addDefaultCreatedDT ()
CCreator *	addDefaultCreator (bool force=false)
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)
	CMIRIAMInfo ()
CBiologicalDescription *	createBiologicalDescription ()
CCreator *	createCreator (const std::string &objectName)
CModification *	createModification (const std::string &objectName)
CReference *	createReference (const std::string &objectName)
virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
bool	empty () const
CDataVector< CBiologicalDescription > &	getBiologicalDescriptions ()
const CDataVector< CBiologicalDescription > &	getBiologicalDescriptions () const
const std::string	getCreatedDT () const
CDataVector< CCreator > &	getCreators ()
const CDataVector< CCreator > &	getCreators () const
virtual const std::string &	getKey () const
CDataVector< CModification > &	getModifications ()
const CDataVector< CModification > &	getModifications () const
CRDFGraph *	getRDFGraph ()
CDataVector< CReference > &	getReferences ()
const CDataVector< CReference > &	getReferences () const
void	load (CDataContainer *pObject)
void	loadBiologicalDescriptions ()
void	loadCreators ()
void	loadModifications ()
void	loadReferences ()
bool	removeBiologicalDescription (CBiologicalDescription *pBiologicalDescription)
bool	removeCreator (CCreator *pCreator)
bool	removeModification (CModification *pModified)
bool	removeReference (CReference *pReference)
bool	save ()
void	setCreatedDT (const std::string &dt)
virtual CData	toData () const
	~CMIRIAMInfo ()
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 size_t	getIndex (const CDataObject *pObject) const
virtual const CObjectInterface *	getObject (const CCommonName &cn) const override
virtual objectMap &	getObjects ()
virtual const objectMap &	getObjects () const
virtual const std::string	getUnits () const override
virtual const CDataObject *	getValueObject () const override
virtual CUndoObjectInterface *	insert (const CData &data) override
void	objectRenamed (CDataObject *pObject, const std::string &oldName)
virtual bool	remove (CDataObject *pObject)
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 CCommonName	getCN () const override
virtual const CDataObject *	getDataObject () const override
CDataContainer *	getObjectAncestor (const std::string &type) const
CDataModel *	getObjectDataModel () const
virtual std::string	getObjectDisplayName () const override
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
virtual void *	getValuePointer () 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
virtual void	print (std::ostream *ostream) const override
void	removeIssue (const CIssue &issue)
void	removeReference (const CDataContainer *pReference)
bool	setObjectName (const std::string &name)
virtual bool	setObjectParent (const CDataContainer *pParent)
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 void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)
virtual	~CUndoObjectInterface ()

Private Attributes
CDataVector< CBiologicalDescription >	mBiologicalDescriptions
CRDFTriplet	mCreated
CRDFObject	mCreatedObj
CDataVector< CCreator >	mCreators
CDataVector< CModification >	mModifications
CAnnotation *	mpAnnotation
CDataContainer *	mpObject
CRDFGraph *	mpRDFGraph
CDataVector< CReference >	mReferences
CRDFTriplet	mTriplet

Additional Inherited Members
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 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 CDataContainer
static const CObjectInterface::ContainerList	EmptyList
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 CDataContainer
objectMap	mObjects
Protected Attributes inherited from CDataObject
ObjectSet	mPrerequisits
std::set< CDataContainer * >	mReferences
Protected Attributes inherited from CObjectInterface
CValidity	mValidity

Constructor & Destructor Documentation

CMIRIAMInfo()

CMIRIAMInfo::CMIRIAMInfo

(

)

~CMIRIAMInfo()

CMIRIAMInfo::~CMIRIAMInfo

(

)

References CAnnotation::freeMiriamInfo(), mpObject, mpRDFGraph, and pdelete.

Member Function Documentation

addDefaultCreatedDT()

bool CMIRIAMInfo::addDefaultCreatedDT

(

)

References empty(), getCreatedDT(), setCreatedDT(), and UTCTimeStamp().

Referenced by CDataModel::commonAfterLoad().

addDefaultCreator()

CCreator * CMIRIAMInfo::addDefaultCreator

(

bool

force = false

)

SMethod to add a creator based on user preferences. If the preferences or not set NULL is returned

Returns

CCreator * pCreator

References createCreator(), CDataVector< CType >::empty(), empty(), CRootContainer::getConfiguration(), getCreatedDT(), CConfigurationFile::getCurrentAuthorEmail(), CConfigurationFile::getCurrentAuthorFamilyName(), CConfigurationFile::getCurrentAuthorGivenName(), CConfigurationFile::getCurrentAuthorOrganization(), mCreators, CCreator::setEmail(), CCreator::setFamilyName(), CCreator::setGivenName(), and CCreator::setORG().

Referenced by CDataModel::commonAfterLoad().

applyData()

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

virtual

Apply the provided data to the object

Parameters

const

CData & data

Returns

bool success

Reimplemented from CDataContainer.

References CDataContainer::applyData(), CData::DATE, CData::getProperty(), CData::isSetProperty(), save(), setCreatedDT(), and CDataValue::toString().

createBiologicalDescription()

CBiologicalDescription * CMIRIAMInfo::createBiologicalDescription

(

)

References CDataVector< CType >::add(), CRDFGraph::addTriplet(), CRDFGraph::getAboutNode(), CRDFNode::getSubject(), mBiologicalDescriptions, mpRDFGraph, CRDFObject::RESOURCE, CRDFObject::setResource(), and CRDFObject::setType().

Referenced by CBiologicalDescription::fromData(), and SBMLImporter::importMIRIAM().

createCreator()

CCreator * CMIRIAMInfo::createCreator

(

const std::string &

objectName

)

References CDataVector< CType >::add(), CRDFGraph::addTriplet(), CRDFObject::BLANK_NODE, CRDFPredicate::dcterms_creator, CRDFGraph::generatedNodeId(), CRDFGraph::getAboutNode(), CRDFNode::getSubject(), CRDFPredicate::getURI(), mCreators, mpRDFGraph, CRDFObject::setBlankNodeId(), and CRDFObject::setType().

Referenced by addDefaultCreator(), and CCreator::fromData().

createModification()

CModification * CMIRIAMInfo::createModification

(

const std::string &

objectName

)

References CDataVector< CType >::add(), CRDFGraph::addTriplet(), CRDFObject::BLANK_NODE, CRDFPredicate::dcterms_modified, CRDFGraph::generatedNodeId(), CRDFGraph::getAboutNode(), CRDFNode::getSubject(), CRDFPredicate::getURI(), mModifications, mpRDFGraph, CRDFObject::setBlankNodeId(), CModification::setDate(), and CRDFObject::setType().

Referenced by CModification::fromData().

createReference()

CReference * CMIRIAMInfo::createReference

(

const std::string &

objectName

)

References CDataVector< CType >::add(), CRDFGraph::addTriplet(), CRDFObject::BLANK_NODE, CRDFPredicate::dcterms_bibliographicCitation, CRDFGraph::generatedNodeId(), CRDFGraph::getAboutNode(), CRDFNode::getSubject(), CRDFPredicate::getURI(), mpRDFGraph, mReferences, CRDFObject::setBlankNodeId(), and CRDFObject::setType().

Referenced by CReference::fromData().

createUndoData()

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

virtual

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

Reimplemented from CDataContainer.

References CUndoData::addProperty(), CUndoData::CHANGE, CDataContainer::createUndoData(), CData::DATE, getCreatedDT(), and CData::getProperty().

empty()

bool CMIRIAMInfo::empty

(

)

const

References CRDFGraph::empty(), and mpRDFGraph.

Referenced by addDefaultCreatedDT(), addDefaultCreator(), and CSBMLExporter::updateMIRIAMAnnotation().

getBiologicalDescriptions() [1/2]

CDataVector< CBiologicalDescription > & CMIRIAMInfo::getBiologicalDescriptions

(

)

References mBiologicalDescriptions.

Referenced by SBMLImporter::importMIRIAM(), and CSBMLExporter::updateMIRIAMAnnotation().

getBiologicalDescriptions() [2/2]

const CDataVector< CBiologicalDescription > & CMIRIAMInfo::getBiologicalDescriptions

(

)

const

References mBiologicalDescriptions.

getCreatedDT()

const std::string CMIRIAMInfo::getCreatedDT

(

)

const

References CRDFPredicate::dcterms_W3CDTF, CRDFNode::getFieldValue(), mCreated, and CRDFTriplet::pObject.

Referenced by addDefaultCreatedDT(), addDefaultCreator(), createUndoData(), toData(), and CSBMLExporter::updateMIRIAMAnnotation().

getCreators() [1/2]

CDataVector< CCreator > & CMIRIAMInfo::getCreators

(

)

References mCreators.

Referenced by CSBMLExporter::updateMIRIAMAnnotation().

getCreators() [2/2]

const CDataVector< CCreator > & CMIRIAMInfo::getCreators

(

)

const

References mCreators.

getKey()

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

virtual

Reimplemented from CDataObject.

References CDataObject::getKey(), CAnnotation::getKey(), and mpAnnotation.

getModifications() [1/2]

CDataVector< CModification > & CMIRIAMInfo::getModifications

(

)

References mModifications.

Referenced by CSBMLExporter::updateMIRIAMAnnotation().

getModifications() [2/2]

const CDataVector< CModification > & CMIRIAMInfo::getModifications

(

)

const

References mModifications.

getRDFGraph()

CRDFGraph * CMIRIAMInfo::getRDFGraph

(

)

References mpRDFGraph.

getReferences() [1/2]

CDataVector< CReference > & CMIRIAMInfo::getReferences

(

)

References mReferences.

Referenced by CSBMLExporter::updateMIRIAMAnnotation().

getReferences() [2/2]

const CDataVector< CReference > & CMIRIAMInfo::getReferences

(

)

const

References mReferences.

load()

void CMIRIAMInfo::load

(

CDataContainer *

pObject

)

References CDataContainer::add(), CAnnotation::castObject(), CRDFGraph::createAboutNode(), CRDFPredicate::dcterms_created, CRDFNode::getDescendantsWithPredicate(), CDataObject::getKey(), CAnnotation::getMiriamAnnotation(), CDataObject::getObjectParent(), CRDFNode::getPath(), CRDFParser::graphFromXml(), loadBiologicalDescriptions(), loadCreators(), loadModifications(), loadReferences(), mCreated, mpAnnotation, mpObject, mpRDFGraph, mTriplet, pdelete, and CRDFTriplet::pObject.

Referenced by CDataModel::commonAfterLoad(), SBMLImporter::importMIRIAM(), and CSBMLExporter::updateMIRIAMAnnotation().

loadBiologicalDescriptions()

void CMIRIAMInfo::loadBiologicalDescriptions

(

)

References CDataVector< CType >::add(), CRDFPredicate::bqbiol_encodes, CRDFPredicate::bqbiol_hasPart, CRDFPredicate::bqbiol_hasProperty, CRDFPredicate::bqbiol_hasTaxon, CRDFPredicate::bqbiol_hasVersion, CRDFPredicate::bqbiol_is, CRDFPredicate::bqbiol_isEncodedBy, CRDFPredicate::bqbiol_isHomologTo, CRDFPredicate::bqbiol_isPartOf, CRDFPredicate::bqbiol_isPropertyOf, CRDFPredicate::bqbiol_isVersionOf, CRDFPredicate::bqbiol_occursIn, CRDFPredicate::bqmodel_hasInstance, CRDFPredicate::bqmodel_is, CRDFPredicate::bqmodel_isDerivedFrom, CRDFPredicate::bqmodel_isInstanceOf, CDataVector< CType >::cleanup(), CRDFPredicate::copasi_encodes, CRDFPredicate::copasi_hasPart, CRDFPredicate::copasi_hasVersion, CRDFPredicate::copasi_is, CRDFPredicate::copasi_isDescribedBy, CRDFPredicate::copasi_isEncodedBy, CRDFPredicate::copasi_isHomologTo, CRDFPredicate::copasi_isPartOf, CRDFPredicate::copasi_isVersionOf, CRDFPredicate::copasi_occursIn, CRDFPredicate::end, CRDFNode::getDescendantsWithPredicate(), CRDFNode::getPath(), CMIRIAMResources::isCitation(), mBiologicalDescriptions, mTriplet, CRDFTriplet::pObject, and CRDFPredicate::unknown.

Referenced by load().

loadCreators()

void CMIRIAMInfo::loadCreators

(

)

References CDataVector< CType >::add(), CDataVector< CType >::cleanup(), CRDFPredicate::dc_creator, CRDFPredicate::dcterms_creator, CRDFPredicate::end, CRDFNode::getDescendantsWithPredicate(), CRDFNode::getPath(), mCreators, mTriplet, and CRDFTriplet::pObject.

Referenced by load().

loadModifications()

void CMIRIAMInfo::loadModifications

(

)

References CDataVector< CType >::add(), CDataVector< CType >::cleanup(), CRDFPredicate::dcterms_modified, CRDFNode::getDescendantsWithPredicate(), mModifications, mTriplet, and CRDFTriplet::pObject.

Referenced by load().

loadReferences()

void CMIRIAMInfo::loadReferences

(

)

References CDataVector< CType >::add(), CRDFPredicate::bqbiol_isDescribedBy, CRDFPredicate::bqmodel_isDescribedBy, CDataVector< CType >::cleanup(), CRDFPredicate::dcterms_bibliographicCitation, CRDFPredicate::end, CRDFNode::getDescendantsWithPredicate(), CRDFNode::getPath(), mReferences, mTriplet, and CRDFTriplet::pObject.

Referenced by load().

removeBiologicalDescription()

bool CMIRIAMInfo::removeBiologicalDescription

(

CBiologicalDescription *

pBiologicalDescription

)

References CBiologicalDescription::getTriplet(), mBiologicalDescriptions, mpRDFGraph, CRDFTriplet::pObject, CRDFTriplet::Predicate, CRDFTriplet::pSubject, CDataVector< CType >::remove(), and CRDFGraph::removeTriplet().

Referenced by CBiologicalDescription::destruct().

removeCreator()

bool CMIRIAMInfo::removeCreator

(

CCreator *

pCreator

)

References CCreator::getTriplet(), CRDFPredicate::getURI(), mCreators, mpRDFGraph, CRDFTriplet::pObject, CRDFTriplet::Predicate, CRDFTriplet::pSubject, CDataVector< CType >::remove(), and CRDFGraph::removeTriplet().

Referenced by CCreator::destruct().

removeModification()

bool CMIRIAMInfo::removeModification

(

CModification *

pModified

)

References CModification::getTriplet(), CRDFPredicate::getURI(), mModifications, mpRDFGraph, CRDFTriplet::pObject, CRDFTriplet::Predicate, CRDFTriplet::pSubject, CDataVector< CType >::remove(), and CRDFGraph::removeTriplet().

Referenced by CModification::destruct().

removeReference()

bool CMIRIAMInfo::removeReference

(

CReference *

pReference

)

References CReference::getTriplet(), CRDFPredicate::getURI(), mpRDFGraph, mReferences, CRDFTriplet::pObject, CRDFTriplet::Predicate, CRDFTriplet::pSubject, CDataVector< CType >::remove(), and CRDFGraph::removeTriplet().

Referenced by CReference::destruct().

save()

bool CMIRIAMInfo::save

(

)

References CRDFGraph::clean(), CAnnotation::getKey(), mpAnnotation, mpRDFGraph, CAnnotation::setMiriamAnnotation(), CRDFGraph::updateNamespaces(), and CRDFWriter::xmlFromGraph().

Referenced by CBiologicalDescription::applyData(), CCreator::applyData(), applyData(), CModification::applyData(), CReference::applyData(), CDataModel::commonAfterLoad(), CBiologicalDescription::destruct(), CCreator::destruct(), CModification::destruct(), CReference::destruct(), and SBMLImporter::importMIRIAM().

setCreatedDT()

void CMIRIAMInfo::setCreatedDT

(

const std::string &

dt

)

References CRDFGraph::addTriplet(), CRDFObject::BLANK_NODE, CRDFPredicate::dcterms_created, CRDFPredicate::dcterms_W3CDTF, CRDFGraph::generatedNodeId(), CRDFNode::getPath(), CRDFNode::getSubject(), CRDFPredicate::getURI(), mCreated, mpRDFGraph, mTriplet, CRDFTriplet::pObject, CRDFObject::setBlankNodeId(), CRDFNode::setFieldValue(), and CRDFObject::setType().

Referenced by addDefaultCreatedDT(), and applyData().

toData()

CData CMIRIAMInfo::toData ( ) const

virtual

Retrieve the data describing the object

Returns

CData data

Reimplemented from CDataContainer.

References CData::addProperty(), CData::DATE, getCreatedDT(), and CDataContainer::toData().

Member Data Documentation

mBiologicalDescriptions

CDataVector<CBiologicalDescription> CMIRIAMInfo::mBiologicalDescriptions

private

Referenced by createBiologicalDescription(), getBiologicalDescriptions(), loadBiologicalDescriptions(), and removeBiologicalDescription().

mCreated

CRDFTriplet CMIRIAMInfo::mCreated

private

Referenced by getCreatedDT(), load(), and setCreatedDT().

mCreatedObj

CRDFObject CMIRIAMInfo::mCreatedObj

private

mCreators

CDataVector<CCreator> CMIRIAMInfo::mCreators

private

Referenced by addDefaultCreator(), createCreator(), getCreators(), loadCreators(), and removeCreator().

mModifications

CDataVector<CModification> CMIRIAMInfo::mModifications

private

Referenced by createModification(), getModifications(), loadModifications(), and removeModification().

mpAnnotation

CAnnotation* CMIRIAMInfo::mpAnnotation

private

Referenced by getKey(), load(), and save().

mpObject

CDataContainer* CMIRIAMInfo::mpObject

private

Referenced by load(), and ~CMIRIAMInfo().

mpRDFGraph

CRDFGraph* CMIRIAMInfo::mpRDFGraph

private

Referenced by createBiologicalDescription(), createCreator(), createModification(), createReference(), empty(), getRDFGraph(), load(), removeBiologicalDescription(), removeCreator(), removeModification(), removeReference(), save(), setCreatedDT(), and ~CMIRIAMInfo().

mReferences

CDataVector<CReference> CMIRIAMInfo::mReferences

private

Referenced by createReference(), getReferences(), loadReferences(), and removeReference().

mTriplet

CRDFTriplet CMIRIAMInfo::mTriplet

private

Referenced by load(), loadBiologicalDescriptions(), loadCreators(), loadModifications(), loadReferences(), and setCreatedDT().

---

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

• CModelMIRIAMInfo.h
• CModelMIRIAMInfo.cpp