CBiologicalDescription Class Reference

#include <CBiologicalDescription.h>

Inheritance diagram for CBiologicalDescription:

Collaboration diagram for CBiologicalDescription:

Public Member Functions
	CBiologicalDescription (const std::string &objectName, const CCopasiContainer *pParent=NULL)
	CBiologicalDescription (const CRDFTriplet &triplet, const std::string &objectName="", const CCopasiContainer *pParent=NULL)
	CBiologicalDescription (const CBiologicalDescription &src, const CCopasiContainer *pParent=NULL)
void	clearInvalidEntries ()
const std::string &	getId () const
virtual const std::string &	getKey () const
const CMIRIAMResourceObject &	getMIRIAMResourceObject () const
std::string	getPredicate () const
std::string	getResource () const
const CRDFTriplet &	getTriplet () const
std::string	getURI () const
void	setId (const std::string &id)
void	setPredicate (const std::string &predicate)
void	setResource (const std::string &resource)
	~CBiologicalDescription ()
Public Member Functions inherited from CCopasiContainer
virtual bool	add (CCopasiObject *pObject, const bool &adopt=true)
	CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)
	CCopasiContainer (const CCopasiContainer &src, const CCopasiContainer *pParent=NULL)
virtual std::string	getChildObjectUnits (const CCopasiObject *pObject) const
virtual const CObjectInterface *	getObject (const CCopasiObjectName &cn) const
virtual const objectMap &	getObjects () const
virtual std::string	getUnits () const
virtual const CCopasiObject *	getValueObject () const
virtual bool	remove (CCopasiObject *pObject)
virtual	~CCopasiContainer ()
Public Member Functions inherited from CCopasiObject
void	addDirectDependency (const CCopasiObject *pObject)
	CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL)
void	clearDirectDependencies ()
void	clearRefresh ()
bool	dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const
void	getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const
virtual CCopasiObjectName	getCN () const
virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const
CCopasiContainer *	getObjectAncestor (const std::string &type) const
CCopasiDataModel *	getObjectDataModel ()
const CCopasiDataModel *	getObjectDataModel () const
virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const
const std::string &	getObjectName () const
CCopasiContainer *	getObjectParent () const
const std::string &	getObjectType () const
virtual const CObjectInterface::ObjectSet &	getPrerequisites () const
virtual Refresh *	getRefresh () const
UpdateMethod *	getUpdateMethod () const
virtual void *	getValuePointer () const
bool	hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const
bool	hasUpdateMethod () const
bool	isArray () const
bool	isContainer () const
bool	isDataModel () const
bool	isMatrix () const
bool	isNameVector () const
bool	isNonUniqueName () const
virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const
bool	isReference () const
bool	isRoot () const
bool	isSeparator () const
bool	isStaticString () const
bool	isValueBool () const
bool	isValueDbl () const
bool	isValueInt () const
bool	isValueInt64 () const
bool	isValueString () const
bool	isVector () const
virtual bool	mustBeDeleted (const DataObjectSet &deletedObjects) const
virtual void	print (std::ostream *ostream) const
void	removeDirectDependency (const CCopasiObject *pObject)
void	setDirectDependencies (const DataObjectSet &directDependencies)
bool	setObjectName (const std::string &name)
virtual bool	setObjectParent (const CCopasiContainer *pParent)
void	setObjectValue (const C_FLOAT64 &value)
void	setObjectValue (const C_INT32 &value)
void	setObjectValue (const bool &value)
template<class CType >
void	setRefresh (CType *pType, void(CType::*method)(void))
template<class CType >
void	setUpdateMethod (CType *pType, void(CType::*method)(const C_FLOAT64 &))
template<class CType >
void	setUpdateMethod (CType *pType, void(CType::*method)(const C_INT32 &))
template<class CType >
void	setUpdateMethod (CType *pType, void(CType::*method)(const bool &))
virtual	~CCopasiObject ()
Public Member Functions inherited from CObjectInterface
	CObjectInterface ()
virtual	~CObjectInterface ()

Private Attributes
std::string	mKey
CMIRIAMResourceObject	mResource
CRDFTriplet	mTriplet

Additional Inherited Members
Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap
Public Types inherited from CCopasiObject
typedef std::set< const CCopasiObject * >	DataObjectSet
typedef std::vector< Refresh * >	DataUpdateSequence
Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet
typedef std::vector < CObjectInterface * >	UpdateSequence
Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())
static void	setRenameHandler (CRenameHandler *rh)
Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList
Protected Types inherited from CCopasiObject
enum	Flag {   Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8,   Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80,   ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800,   Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000,   Root = 0x10000, Gui = 0x20000 }
Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObject *	addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
template<class CType >
CCopasiObject *	addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
template<class CType >
CCopasiObject *	addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
void	initObjects ()
Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()
	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)
Protected Attributes inherited from CCopasiContainer
objectMap	mObjects
Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 21 of file CBiologicalDescription.h.

Constructor & Destructor Documentation

CBiologicalDescription::CBiologicalDescription	(	const std::string &	objectName,
		const CCopasiContainer *	pParent = NULL
	)

Default constructor

Parameters

const	std::string & objectName
const	CCopasiContainer * pParent (default: NULL)

Definition at line 23 of file CBiologicalDescription.cpp.

                                     :
  CCopasiContainer(objectName, pParent, "BiologicalDescription"),
  mTriplet(),
  mKey(CCopasiRootContainer::getKeyFactory()->add("BiologicalDescription", this)),
  mResource(NULL)
{}

CBiologicalDescription::CBiologicalDescription	(	const CRDFTriplet &	triplet,
		const std::string &	objectName = "",
		const CCopasiContainer *	pParent = NULL
	)

Specific constructor

Parameters

const	CRDFTriplet & triplet
const	std::string & objectName (default: "")
const	CCopasiContainer * pParent (default: NULL)

Definition at line 31 of file CBiologicalDescription.cpp.

                                     :
  CCopasiContainer(objectName, pParent, "BiologicalDescription"),
  mTriplet(triplet),
  mKey(CCopasiRootContainer::getKeyFactory()->add("BiologicalDescription", this)),
  mResource(mTriplet.pObject)
{}

CBiologicalDescription::CBiologicalDescription	(	const CBiologicalDescription &	src,
		const CCopasiContainer *	pParent = NULL
	)

Copy constructor

Parameters

const CBiologicalDescription &	src
const	CCopasiContainer * pParent (default: NULL)

Definition at line 40 of file CBiologicalDescription.cpp.

                                     :
  CCopasiContainer(src, pParent),
  mTriplet(src.mTriplet),
  mKey(CCopasiRootContainer::getKeyFactory()->add("Creator", this)),
  mResource(src.mResource)
{}

CBiologicalDescription::~CBiologicalDescription

(

)

Destructor

Definition at line 48 of file CBiologicalDescription.cpp.

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

{
  CCopasiRootContainer::getKeyFactory()->remove(mKey);
}

Member Function Documentation

void CBiologicalDescription::clearInvalidEntries

(

)

Convenience method removing invalid predicate, resource, and id combinations

Definition at line 108 of file CBiologicalDescription.cpp.

References CRDFPredicate::getURI(), CMIRIAMResourceObject::isValid(), mResource, mTriplet, CRDFTriplet::pObject, CRDFTriplet::Predicate, CRDFTriplet::pSubject, CRDFNode::removeEdge(), and CRDFPredicate::unknown.

{
  if ((mTriplet.Predicate == CRDFPredicate::unknown &&
       mTriplet.Predicate.getURI() == "") ||
      !mResource.isValid())
    {
      // Remove the edge with the predicate and object.
      mTriplet.pSubject->removeEdge(mTriplet.Predicate, mTriplet.pObject);
    }
}

const std::string & CBiologicalDescription::getId

(

)

const

Retrieve the identifier of the subject in the MIRIAM resource.

Returns

const std::string id

Definition at line 73 of file CBiologicalDescription.cpp.

References CMIRIAMResourceObject::getId(), and mResource.

Referenced by test000092::test_miriam_export_8(), and test000092::test_miriam_export_9().

{return mResource.getId();}

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

virtual

Retrieve the key of the object.

Returns

const std::string & key

Reimplemented from CCopasiObject.

Definition at line 64 of file CBiologicalDescription.cpp.

References mKey.

{return mKey;}

const CMIRIAMResourceObject & CBiologicalDescription::getMIRIAMResourceObject

(

)

const

Retrieve the MIRIAM resource object for this reference

Definition at line 56 of file CBiologicalDescription.cpp.

References mResource.

Referenced by CQMiriamWidget::slotBtnBrowseDescription(), and CSBMLExporter::updateMIRIAMAnnotation().

{
  return mResource;
}

std::string CBiologicalDescription::getPredicate

(

)

const

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

Returns

std::string predicate

Definition at line 67 of file CBiologicalDescription.cpp.

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

Referenced by test000092::test_miriam_export_8(), and test000092::test_miriam_export_9().

{return CRDFPredicate::getDisplayName(mTriplet.Predicate);}

std::string CBiologicalDescription::getResource

(

)

const

Retrieve the MIRIAM resource (database) describing the subject.

Returns

std::string resource

Definition at line 70 of file CBiologicalDescription.cpp.

References CMIRIAMResourceObject::getDisplayName(), and mResource.

Referenced by test000092::test_miriam_export_8(), and test000092::test_miriam_export_9().

{return mResource.getDisplayName();}

const CRDFTriplet & CBiologicalDescription::getTriplet

(

)

const

Retrieve the RDF triplet holding the description.

Returns

const CRDFTriplet & triplet

Definition at line 61 of file CBiologicalDescription.cpp.

References mTriplet.

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

{return mTriplet;}

std::string CBiologicalDescription::getURI

(

)

const

Retrieve the URI comprised of MIRIAM resource and id.

Returns

std::string uri

Definition at line 105 of file CBiologicalDescription.cpp.

References CMIRIAMResourceObject::getURI(), and mResource.

{return mResource.getURI();}

void CBiologicalDescription::setId

(

const std::string &

id

)

Set the identifier of the subject in the MIRIAM resource.

Parameters

const

std::string & id

Definition at line 99 of file CBiologicalDescription.cpp.

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

Referenced by test000092::test_miriam_export_8(), and test000092::test_miriam_export_9().

{
  mResource.setId(id);
  mTriplet.pObject->getObject().setResource(mResource.getURI(), false);
}

void CBiologicalDescription::setPredicate

(

const std::string &

predicate

)

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

Parameters

const

std::string & predicate

Definition at line 76 of file CBiologicalDescription.cpp.

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

Referenced by test000092::test_miriam_export_8(), and test000092::test_miriam_export_9().

{
  CRDFPredicate Predicate(CRDFPredicate::getPredicateFromDisplayName(predicate));

  if (Predicate == mTriplet.Predicate)
    return;

  // Add the edge with the new predicate without any object creation.
  mTriplet.pSubject->addEdge(Predicate, mTriplet.pObject);

  // Remove the edge with the predicate without destroying any objects.
  mTriplet.pSubject->removeEdge(mTriplet.Predicate, mTriplet.pObject);

  // Set the new predicate
  mTriplet.Predicate = Predicate;
}

void CBiologicalDescription::setResource

(

const std::string &

resource

)

Set the MIRIAM resource (database) describing the subject.

Parameters

const

std::string & predicate

Definition at line 93 of file CBiologicalDescription.cpp.

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

Referenced by test000092::test_miriam_export_8(), and test000092::test_miriam_export_9().

{
  mResource.setDisplayName(resource);
  mTriplet.pObject->getObject().setResource(mResource.getURI(), false);
}

Member Data Documentation

std::string CBiologicalDescription::mKey

private

The key of the object needed for the COPASI tables.

Definition at line 33 of file CBiologicalDescription.h.

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

CMIRIAMResourceObject CBiologicalDescription::mResource

private

MIRIAM resource for holding the database and Id.

Definition at line 38 of file CBiologicalDescription.h.

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

CRDFTriplet CBiologicalDescription::mTriplet

private

Triplet in the RDF graph representing the description.

Definition at line 28 of file CBiologicalDescription.h.

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

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

• CBiologicalDescription.h
• CBiologicalDescription.cpp