COPASI API
4.16.103
|
#include <CBiologicalDescription.h>
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 () | |
![]() | |
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 () |
![]() | |
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 () |
![]() | |
CObjectInterface () | |
virtual | ~CObjectInterface () |
Private Attributes | |
std::string | mKey |
CMIRIAMResourceObject | mResource |
CRDFTriplet | mTriplet |
Additional Inherited Members | |
![]() | |
typedef std::multimap < std::string, CCopasiObject * > | objectMap |
![]() | |
typedef std::set< const CCopasiObject * > | DataObjectSet |
typedef std::vector< Refresh * > | DataUpdateSequence |
![]() | |
typedef std::set< const CObjectInterface * > | ObjectSet |
typedef std::vector < CObjectInterface * > | UpdateSequence |
![]() | |
static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
![]() | |
static const std::vector < CCopasiContainer * > | EmptyList |
![]() | |
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 } |
![]() | |
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 () |
![]() | |
CCopasiObject () | |
CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | |
![]() | |
objectMap | mObjects |
![]() | |
static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 21 of file CBiologicalDescription.h.
CBiologicalDescription::CBiologicalDescription | ( | const std::string & | objectName, |
const CCopasiContainer * | pParent = NULL |
||
) |
Default constructor
const | std::string & objectName |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 23 of file CBiologicalDescription.cpp.
CBiologicalDescription::CBiologicalDescription | ( | const CRDFTriplet & | triplet, |
const std::string & | objectName = "" , |
||
const CCopasiContainer * | pParent = NULL |
||
) |
Specific constructor
const | CRDFTriplet & triplet |
const | std::string & objectName (default: "") |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 31 of file CBiologicalDescription.cpp.
CBiologicalDescription::CBiologicalDescription | ( | const CBiologicalDescription & | src, |
const CCopasiContainer * | pParent = NULL |
||
) |
Copy constructor
const CBiologicalDescription & | src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 40 of file CBiologicalDescription.cpp.
CBiologicalDescription::~CBiologicalDescription | ( | ) |
Destructor
Definition at line 48 of file CBiologicalDescription.cpp.
References CCopasiRootContainer::getKeyFactory(), mKey, and CKeyFactory::remove().
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.
const std::string & CBiologicalDescription::getId | ( | ) | const |
Retrieve the identifier of the subject in the MIRIAM resource.
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().
|
virtual |
Retrieve the key of the object.
Reimplemented from CCopasiObject.
Definition at line 64 of file CBiologicalDescription.cpp.
References 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().
std::string CBiologicalDescription::getPredicate | ( | ) | const |
Retrieve the predicate, i.e. the relationship between the subject. and the MIRIAM resource.
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().
std::string CBiologicalDescription::getResource | ( | ) | const |
Retrieve the MIRIAM resource (database) describing the subject.
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().
const CRDFTriplet & CBiologicalDescription::getTriplet | ( | ) | const |
Retrieve the RDF triplet holding the description.
Definition at line 61 of file CBiologicalDescription.cpp.
References mTriplet.
Referenced by CMIRIAMInfo::removeBiologicalDescription(), and CSBMLExporter::updateMIRIAMAnnotation().
std::string CBiologicalDescription::getURI | ( | ) | const |
Retrieve the URI comprised of MIRIAM resource and id.
Definition at line 105 of file CBiologicalDescription.cpp.
References CMIRIAMResourceObject::getURI(), and mResource.
void CBiologicalDescription::setId | ( | const std::string & | id | ) |
Set the identifier of the subject in the MIRIAM resource.
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().
void CBiologicalDescription::setPredicate | ( | const std::string & | predicate | ) |
Set the predicate, i.e., relationship between the subject and the MIRIAM resource.
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().
void CBiologicalDescription::setResource | ( | const std::string & | resource | ) |
Set the MIRIAM resource (database) describing the subject.
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().
|
private |
The key of the object needed for the COPASI tables.
Definition at line 33 of file CBiologicalDescription.h.
Referenced by getKey(), and ~CBiologicalDescription().
|
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().
|
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().