COPASI API  4.40.278
CBiologicalDescription Class Reference

#include <CBiologicalDescription.h>

Inheritance diagram for CBiologicalDescription:
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Public Member Functions

virtual bool applyData (const CData &data, CUndoData::CChangeSet &changes)
 
 CBiologicalDescription (const CBiologicalDescription &src, const CDataContainer *pParent)
 
 CBiologicalDescription (const CRDFTriplet &triplet, const std::string &objectName="", const CDataContainer *pParent=NO_PARENT)
 
 CBiologicalDescription (const std::string &objectName, const CDataContainer *pParent=NO_PARENT)
 
void clearInvalidEntries ()
 
virtual void createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
 
virtual void destruct ()
 
const std::string & getId () const
 
virtual const std::string & getKey () const
 
const CMIRIAMResourceObjectgetMIRIAMResourceObject () const
 
std::string getPredicate () const
 
std::string getResource () const
 
const CRDFTripletgetTriplet () const
 
std::string getURI () const
 
void setId (const std::string &id)
 
void setPredicate (const std::string &predicate)
 
void setResource (const std::string &resource)
 
virtual CData toData () const
 
 ~CBiologicalDescription ()
 
- 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 CObjectInterfacegetObject (const CCommonName &cn) const override
 
virtual objectMapgetObjects ()
 
virtual const objectMapgetObjects () const
 
virtual const std::string getUnits () const override
 
virtual const CDataObjectgetValueObject () const override
 
virtual CUndoObjectInterfaceinsert (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 CCommonName getCN () const override
 
virtual const CDataObjectgetDataObject () const override
 
CDataContainergetObjectAncestor (const std::string &type) const
 
CDataModelgetObjectDataModel () const
 
virtual std::string getObjectDisplayName () const override
 
const CObjectInterfacegetObjectFromCN (const CCommonName &cn) const
 
const std::string & getObjectName () const
 
CDataContainergetObjectParent () const
 
const std::string & getObjectType () const
 
virtual const CObjectInterface::ObjectSetgetPrerequisites () const override
 
virtual const CValiditygetValidity () 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 ()
 

Static Public Member Functions

static CBiologicalDescriptionfromData (const CData &data, CUndoObjectInterface *pParent)
 
- Static Public Member Functions inherited from CDataContainer
static CDataContainerfromData (const CData &data, CUndoObjectInterface *pParent)
 
- Static Public Member Functions inherited from CDataObject
static CDataObjectfromData (const CData &data, CUndoObjectInterface *pParent)
 
static void sanitizeObjectName (std::string &name)
 
- Static Public Member Functions inherited from CObjectInterface
static const CDataObjectDataObject (const CObjectInterface *pInterface)
 
static CObjectInterfaceGetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName)
 
- Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType * fromData (const CData &, CUndoObjectInterface *)
 

Private Attributes

std::string mKey
 
CMIRIAMResourceObject mResource
 
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 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

◆ CBiologicalDescription() [1/3]

CBiologicalDescription::CBiologicalDescription ( const std::string &  objectName,
const CDataContainer pParent = NO_PARENT 
)

Default constructor

Parameters
conststd::string & objectName
constCDataContainer * pParent (default: NULL)

◆ CBiologicalDescription() [2/3]

CBiologicalDescription::CBiologicalDescription ( const CRDFTriplet triplet,
const std::string &  objectName = "",
const CDataContainer pParent = NO_PARENT 
)

Specific constructor

Parameters
constCRDFTriplet & triplet
conststd::string & objectName (default: "")
constCDataContainer * pParent (default: NULL)

◆ CBiologicalDescription() [3/3]

CBiologicalDescription::CBiologicalDescription ( const CBiologicalDescription src,
const CDataContainer pParent 
)

Copy constructor

Parameters
const CBiologicalDescription &src
constCDataContainer * pParent (default: NULL)

◆ ~CBiologicalDescription()

CBiologicalDescription::~CBiologicalDescription ( )

Member Function Documentation

◆ applyData()

bool CBiologicalDescription::applyData ( const CData data,
CUndoData::CChangeSet changes 
)
virtual

◆ clearInvalidEntries()

void CBiologicalDescription::clearInvalidEntries ( )

◆ createUndoData()

void CBiologicalDescription::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
constCUndoData::Type & type
constCData & oldData (default: empty data)
constCCore::Framework & framework (default: CCore::Framework::ParticleNumbers)
Returns
CUndoData undoData

Reimplemented from CDataContainer.

References CUndoData::addProperty(), CUndoData::CHANGE, CDataContainer::createUndoData(), CUndoData::empty(), getId(), getPredicate(), CData::getProperty(), getResource(), CData::MIRIAM_ID, CData::MIRIAM_PREDICATE, CData::MIRIAM_RESOURCE, CData::OBJECT_HASH, CData::OBJECT_INDEX, CUndoData::removeProperty(), and toData().

◆ destruct()

void CBiologicalDescription::destruct ( )
virtual

◆ fromData()

CBiologicalDescription * CBiologicalDescription::fromData ( const CData data,
CUndoObjectInterface pParent 
)
static

Static method to create a CDataObject based on the provided data

Parameters
constCData & data
Returns
CBiologicalDescription * pDataObject

References CMIRIAMInfo::createBiologicalDescription(), CDataObject::getObjectAncestor(), and CDataContainer::remove().

◆ getId()

const std::string & CBiologicalDescription::getId ( ) const

Retrieve the identifier of the subject in the MIRIAM resource.

Returns
const std::string id

References CMIRIAMResourceObject::getId(), and mResource.

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

◆ getKey()

const std::string & CBiologicalDescription::getKey ( ) const
virtual

Retrieve the key of the object.

Returns
const std::string & key

Reimplemented from CDataObject.

References mKey.

◆ getMIRIAMResourceObject()

const CMIRIAMResourceObject & CBiologicalDescription::getMIRIAMResourceObject ( ) const

Retrieve the MIRIAM resource object for this reference

References mResource.

Referenced by CSBMLExporter::updateMIRIAMAnnotation().

◆ getPredicate()

std::string CBiologicalDescription::getPredicate ( ) const

Retrieve the predicate, i.e. the relationship between the subject. and the MIRIAM resource.

Returns
std::string predicate

References CRDFPredicate::getDisplayName(), mTriplet, and CRDFTriplet::Predicate.

Referenced by createUndoData(), and toData().

◆ getResource()

std::string CBiologicalDescription::getResource ( ) const

Retrieve the MIRIAM resource (database) describing the subject.

Returns
std::string resource

References CMIRIAMResourceObject::getDisplayName(), and mResource.

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

◆ getTriplet()

const CRDFTriplet & CBiologicalDescription::getTriplet ( ) const

Retrieve the RDF triplet holding the description.

Returns
const CRDFTriplet & triplet

References mTriplet.

Referenced by CMIRIAMInfo::removeBiologicalDescription(), and CSBMLExporter::updateMIRIAMAnnotation().

◆ getURI()

std::string CBiologicalDescription::getURI ( ) const

Retrieve the URI comprised of MIRIAM resource and id.

Returns
std::string uri

References CMIRIAMResourceObject::getURI(), and mResource.

◆ setId()

void CBiologicalDescription::setId ( const std::string &  id)

Set the identifier of the subject in the MIRIAM resource.

Parameters
conststd::string & id

References CRDFNode::getObject(), CMIRIAMResourceObject::getURI(), mResource, mTriplet, CRDFTriplet::pObject, CMIRIAMResourceObject::setId(), and CRDFObject::setResource().

Referenced by applyData(), and SBMLImporter::importMIRIAM().

◆ setPredicate()

void CBiologicalDescription::setPredicate ( const std::string &  predicate)

Set the predicate, i.e., relationship between the subject and the MIRIAM resource.

Parameters
conststd::string & predicate

References CRDFNode::addEdge(), CRDFPredicate::getPredicateFromDisplayName(), mTriplet, CRDFTriplet::pObject, CRDFTriplet::Predicate, CRDFTriplet::pSubject, and CRDFNode::removeEdge().

Referenced by applyData(), and SBMLImporter::importMIRIAM().

◆ setResource()

void CBiologicalDescription::setResource ( const std::string &  resource)

Set the MIRIAM resource (database) describing the subject.

Parameters
conststd::string & predicate

References CRDFNode::getObject(), CMIRIAMResourceObject::getURI(), mResource, mTriplet, CRDFTriplet::pObject, CMIRIAMResourceObject::setDisplayName(), and CRDFObject::setResource().

Referenced by applyData(), and SBMLImporter::importMIRIAM().

◆ toData()

CData CBiologicalDescription::toData ( ) const
virtual

Member Data Documentation

◆ mKey

std::string CBiologicalDescription::mKey
private

The key of the object needed for the COPASI tables.

Referenced by getKey(), and ~CBiologicalDescription().

◆ mResource

CMIRIAMResourceObject CBiologicalDescription::mResource
private

MIRIAM resource for holding the database and Id.

Referenced by clearInvalidEntries(), getId(), getMIRIAMResourceObject(), getResource(), getURI(), setId(), and setResource().

◆ mTriplet

CRDFTriplet CBiologicalDescription::mTriplet
private

Triplet in the RDF graph representing the description.

Referenced by clearInvalidEntries(), getPredicate(), getTriplet(), setId(), setPredicate(), and setResource().


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