COPASI API
4.16.103
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#include <CModelMIRIAMInfo.h>
Public Member Functions | |
CMIRIAMInfo () | |
CBiologicalDescription * | createBiologicalDescription () |
CCreator * | createCreator (const std::string &objectName) |
CModification * | createModification (const std::string &objectName) |
CReference * | createReference (const std::string &objectName) |
const CCopasiVector < CBiologicalDescription > & | getBiologicalDescriptions () const |
const std::string | getCreatedDT () const |
const CCopasiVector< CCreator > & | getCreators () const |
virtual const std::string & | getKey () const |
const CCopasiVector < CModification > & | getModifications () const |
CRDFGraph * | getRDFGraph () |
const CCopasiVector< CReference > & | getReferences () const |
void | load (const std::string &key="") |
void | loadBiologicalDescriptions () |
void | loadCreators () |
void | loadModifications () |
void | loadReferences () |
bool | removeBiologicalDescription (int position) |
bool | removeCreator (int position) |
bool | removeModification (int position) |
bool | removeReference (int position) |
bool | save () |
void | setCreatedDT (const std::string &dt) |
~CMIRIAMInfo () | |
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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 () |
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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 () |
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CObjectInterface () | |
virtual | ~CObjectInterface () |
Private Attributes | |
CCopasiVector < CBiologicalDescription > | mBiologicalDescriptions |
CRDFTriplet | mCreated |
CRDFObject | mCreatedObj |
CCopasiVector< CCreator > | mCreators |
std::string | mKey |
CCopasiVector< CModification > | mModifications |
CRDFGraph * | mpRDFGraph |
CCopasiVector< CReference > | mReferences |
CRDFTriplet | mTriplet |
Additional Inherited Members | |
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typedef std::multimap < std::string, CCopasiObject * > | objectMap |
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typedef std::set< const CCopasiObject * > | DataObjectSet |
typedef std::vector< Refresh * > | DataUpdateSequence |
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typedef std::set< const CObjectInterface * > | ObjectSet |
typedef std::vector < CObjectInterface * > | UpdateSequence |
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static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
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static const std::vector < CCopasiContainer * > | EmptyList |
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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 } |
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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 () |
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CCopasiObject () | |
CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | |
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objectMap | mObjects |
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static CRenameHandler * | smpRenameHandler = NULL |
CMIRIAMInfo: Stores all MIRIAM info for a Model.
Definition at line 38 of file CModelMIRIAMInfo.h.
CMIRIAMInfo::CMIRIAMInfo | ( | ) |
Definition at line 37 of file CModelMIRIAMInfo.cpp.
CMIRIAMInfo::~CMIRIAMInfo | ( | ) |
CBiologicalDescription * CMIRIAMInfo::createBiologicalDescription | ( | ) |
Definition at line 312 of file CModelMIRIAMInfo.cpp.
References CCopasiVector< T >::add(), CRDFGraph::addTriplet(), CRDFGraph::getAboutNode(), CRDFNode::getSubject(), mBiologicalDescriptions, mpRDFGraph, CRDFObject::RESOURCE, CRDFObject::setResource(), and CRDFObject::setType().
Referenced by CQBiologicalDescriptionDM::insertRows().
CCreator * CMIRIAMInfo::createCreator | ( | const std::string & | objectName | ) |
Definition at line 59 of file CModelMIRIAMInfo.cpp.
References CCopasiVector< T >::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 CQCreatorDM::insertRows().
CModification * CMIRIAMInfo::createModification | ( | const std::string & | objectName | ) |
Definition at line 248 of file CModelMIRIAMInfo.cpp.
References CCopasiVector< T >::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 CQModifiedDM::insertRows().
CReference * CMIRIAMInfo::createReference | ( | const std::string & | objectName | ) |
Definition at line 137 of file CModelMIRIAMInfo.cpp.
References CCopasiVector< T >::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 CQReferenceDM::insertRows().
const CCopasiVector< CBiologicalDescription > & CMIRIAMInfo::getBiologicalDescriptions | ( | ) | const |
Definition at line 309 of file CModelMIRIAMInfo.cpp.
References mBiologicalDescriptions.
Referenced by CQBiologicalDescriptionDM::data(), CQBiologicalDescriptionDM::removeRows(), CQBiologicalDescriptionDM::rowCount(), CQBiologicalDescriptionDM::setData(), CQMiriamWidget::slotBtnBrowseDescription(), and CSBMLExporter::updateMIRIAMAnnotation().
const std::string CMIRIAMInfo::getCreatedDT | ( | ) | const |
Definition at line 212 of file CModelMIRIAMInfo.cpp.
References CRDFPredicate::dcterms_W3CDTF, CRDFNode::getFieldValue(), mCreated, and CRDFTriplet::pObject.
Referenced by CQMiriamWidget::showEvent(), CQMiriamWidget::slotCreatedDTChanged(), CQMiriamWidget::update(), and CSBMLExporter::updateMIRIAMAnnotation().
const CCopasiVector< CCreator > & CMIRIAMInfo::getCreators | ( | ) | const |
Definition at line 56 of file CModelMIRIAMInfo.cpp.
References mCreators.
Referenced by CQCreatorDM::data(), CQCreatorDM::removeRows(), CQCreatorDM::rowCount(), CQCreatorDM::setData(), and CSBMLExporter::updateMIRIAMAnnotation().
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Reimplemented from CCopasiObject.
Definition at line 475 of file CModelMIRIAMInfo.cpp.
References mKey.
Referenced by CQMiriamWidget::update().
const CCopasiVector< CModification > & CMIRIAMInfo::getModifications | ( | ) | const |
Definition at line 245 of file CModelMIRIAMInfo.cpp.
References mModifications.
Referenced by CQModifiedDM::data(), CQModifiedDM::removeRows(), CQModifiedDM::rowCount(), CQModifiedDM::setData(), and CSBMLExporter::updateMIRIAMAnnotation().
CRDFGraph * CMIRIAMInfo::getRDFGraph | ( | ) |
const CCopasiVector< CReference > & CMIRIAMInfo::getReferences | ( | ) | const |
Definition at line 134 of file CModelMIRIAMInfo.cpp.
References mReferences.
Referenced by CQReferenceDM::data(), CQReferenceDM::removeRows(), CQReferenceDM::rowCount(), CQReferenceDM::setData(), CQMiriamWidget::slotBtnBrowseReference(), and CSBMLExporter::updateMIRIAMAnnotation().
void CMIRIAMInfo::load | ( | const std::string & | key = "" | ) |
Definition at line 399 of file CModelMIRIAMInfo.cpp.
References CAnnotation::castObject(), CRDFGraph::createAboutNode(), CRDFPredicate::dcterms_created, CKeyFactory::get(), CRDFNode::getDescendantsWithPredicate(), CCopasiObject::getKey(), CCopasiRootContainer::getKeyFactory(), CAnnotation::getMiriamAnnotation(), CRDFNode::getPath(), CRDFParser::graphFromXml(), loadBiologicalDescriptions(), loadCreators(), loadModifications(), loadReferences(), mCreated, mKey, mpRDFGraph, mTriplet, pdelete, and CRDFTriplet::pObject.
Referenced by CQMiriamWidget::showEvent(), test000092::test_miriam_export_8(), test000092::test_miriam_export_9(), test000092::test_miriam_import_1(), CQMiriamWidget::update(), and CSBMLExporter::updateMIRIAMAnnotation().
void CMIRIAMInfo::loadBiologicalDescriptions | ( | ) |
Definition at line 353 of file CModelMIRIAMInfo.cpp.
References CCopasiVector< T >::add(), CRDFPredicate::bqbiol_encodes, CRDFPredicate::bqbiol_hasPart, CRDFPredicate::bqbiol_hasVersion, CRDFPredicate::bqbiol_is, CRDFPredicate::bqbiol_isEncodedBy, CRDFPredicate::bqbiol_isHomologTo, CRDFPredicate::bqbiol_isPartOf, CRDFPredicate::bqbiol_isVersionOf, CRDFPredicate::bqbiol_occursIn, CRDFPredicate::bqmodel_is, CCopasiVector< T >::cleanup(), CRDFPredicate::copasi_encodes, CRDFPredicate::copasi_hasPart, CRDFPredicate::copasi_hasVersion, CRDFPredicate::copasi_is, CRDFPredicate::copasi_isEncodedBy, CRDFPredicate::copasi_isHomologTo, CRDFPredicate::copasi_isPartOf, CRDFPredicate::copasi_isVersionOf, CRDFPredicate::copasi_occursIn, CRDFPredicate::end, CRDFNode::getDescendantsWithPredicate(), CRDFNode::getPath(), mBiologicalDescriptions, mTriplet, and CRDFTriplet::pObject.
Referenced by load().
void CMIRIAMInfo::loadCreators | ( | ) |
Definition at line 102 of file CModelMIRIAMInfo.cpp.
References CCopasiVector< T >::add(), CCopasiVector< T >::cleanup(), CRDFPredicate::dc_creator, CRDFPredicate::dcterms_creator, CRDFPredicate::end, CRDFNode::getDescendantsWithPredicate(), CRDFNode::getPath(), mCreators, mTriplet, and CRDFTriplet::pObject.
Referenced by load().
void CMIRIAMInfo::loadModifications | ( | ) |
Definition at line 294 of file CModelMIRIAMInfo.cpp.
References CCopasiVector< T >::add(), CCopasiVector< T >::cleanup(), CRDFPredicate::dcterms_modified, CRDFNode::getDescendantsWithPredicate(), mModifications, mTriplet, and CRDFTriplet::pObject.
Referenced by load().
void CMIRIAMInfo::loadReferences | ( | ) |
Definition at line 180 of file CModelMIRIAMInfo.cpp.
References CCopasiVector< T >::add(), CRDFPredicate::bqbiol_isDescribedBy, CRDFPredicate::bqmodel_isDescribedBy, CCopasiVector< T >::cleanup(), CRDFPredicate::dcterms_bibliographicCitation, CRDFPredicate::end, CRDFNode::getDescendantsWithPredicate(), CRDFNode::getPath(), mReferences, mTriplet, and CRDFTriplet::pObject.
Referenced by load().
bool CMIRIAMInfo::removeBiologicalDescription | ( | int | position | ) |
Definition at line 336 of file CModelMIRIAMInfo.cpp.
References CBiologicalDescription::getTriplet(), mBiologicalDescriptions, mpRDFGraph, CRDFTriplet::pObject, CRDFTriplet::Predicate, CRDFTriplet::pSubject, CCopasiVector< T >::remove(), and CRDFGraph::removeTriplet().
Referenced by CQBiologicalDescriptionDM::removeRows().
bool CMIRIAMInfo::removeCreator | ( | int | position | ) |
Definition at line 86 of file CModelMIRIAMInfo.cpp.
References CCreator::getTriplet(), CRDFPredicate::getURI(), mCreators, mpRDFGraph, CRDFTriplet::pObject, CRDFTriplet::Predicate, CRDFTriplet::pSubject, CCopasiVector< T >::remove(), and CRDFGraph::removeTriplet().
Referenced by CQCreatorDM::removeRows().
bool CMIRIAMInfo::removeModification | ( | int | position | ) |
Definition at line 278 of file CModelMIRIAMInfo.cpp.
References CModification::getTriplet(), CRDFPredicate::getURI(), mModifications, mpRDFGraph, CRDFTriplet::pObject, CRDFTriplet::Predicate, CRDFTriplet::pSubject, CCopasiVector< T >::remove(), and CRDFGraph::removeTriplet().
Referenced by CQModifiedDM::removeRows().
bool CMIRIAMInfo::removeReference | ( | int | position | ) |
Definition at line 164 of file CModelMIRIAMInfo.cpp.
References CReference::getTriplet(), CRDFPredicate::getURI(), mpRDFGraph, mReferences, CRDFTriplet::pObject, CRDFTriplet::Predicate, CRDFTriplet::pSubject, CCopasiVector< T >::remove(), and CRDFGraph::removeTriplet().
Referenced by CQReferenceDM::removeRows().
bool CMIRIAMInfo::save | ( | ) |
Definition at line 449 of file CModelMIRIAMInfo.cpp.
References CAnnotation::castObject(), CRDFGraph::clean(), CKeyFactory::get(), CAnnotation::getKey(), CCopasiRootContainer::getKeyFactory(), mKey, mpRDFGraph, CAnnotation::setMiriamAnnotation(), CRDFGraph::updateNamespaces(), and CRDFWriter::xmlFromGraph().
Referenced by CQMiriamWidget::leave().
void CMIRIAMInfo::setCreatedDT | ( | const std::string & | dt | ) |
Definition at line 220 of file CModelMIRIAMInfo.cpp.
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 CQMiriamWidget::slotCreatedDTChanged().
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Definition at line 46 of file CModelMIRIAMInfo.h.
Referenced by createBiologicalDescription(), getBiologicalDescriptions(), loadBiologicalDescriptions(), and removeBiologicalDescription().
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Definition at line 50 of file CModelMIRIAMInfo.h.
Referenced by getCreatedDT(), load(), and setCreatedDT().
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Definition at line 47 of file CModelMIRIAMInfo.h.
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Definition at line 43 of file CModelMIRIAMInfo.h.
Referenced by createCreator(), getCreators(), loadCreators(), and removeCreator().
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Definition at line 42 of file CModelMIRIAMInfo.h.
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Definition at line 45 of file CModelMIRIAMInfo.h.
Referenced by createModification(), getModifications(), loadModifications(), and removeModification().
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Definition at line 48 of file CModelMIRIAMInfo.h.
Referenced by createBiologicalDescription(), createCreator(), createModification(), createReference(), getRDFGraph(), load(), removeBiologicalDescription(), removeCreator(), removeModification(), removeReference(), save(), setCreatedDT(), and ~CMIRIAMInfo().
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Definition at line 44 of file CModelMIRIAMInfo.h.
Referenced by createReference(), getReferences(), loadReferences(), and removeReference().
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Definition at line 49 of file CModelMIRIAMInfo.h.
Referenced by load(), loadBiologicalDescriptions(), loadCreators(), loadModifications(), loadReferences(), and setCreatedDT().