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COPASI API
4.40.278
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#include <CMIRIAMResource.h>
Public Member Functions | |
| void | addMIRIAMResource (CMIRIAMResource *pMIRIAMResource) |
| CMIRIAMResources (const CCopasiParameterGroup &group, const CDataContainer *pParent) | |
| CMIRIAMResources (const CMIRIAMResources &src, const CDataContainer *pParent) | |
| CMIRIAMResources (const std::string &name="MIRIAM Resources", const CDataContainer *pParent=NO_PARENT) | |
| virtual bool | elevateChildren () |
| const unsigned C_INT32 & | getMIRIAMLastUpdateDate () const |
| const CMIRIAMResource & | getMIRIAMResource (const size_t index) const |
| size_t | getMIRIAMResourceIndex (const std::string &URI) const |
| const CMIRIAMResources & | getMIRIAMResources () const |
| const unsigned C_INT32 & | getMIRIAMUpdateFrequency () const |
| size_t | getResourceIndexFromDisplayName (const std::string &displayName) const |
| const CCopasiParameterGroup & | getResourceList () const |
| void | initializeParameter () |
| const CMIRIAMResources & | operator= (const CCopasiParameterGroup &rhs) |
| void | setMIRIAMUpdateFrequencyInDays (const size_t &days) |
| bool | updateMIRIAMResourcesFromFile (CProcessReport *pProcessReport, const std::string &filename) |
| virtual | ~CMIRIAMResources () |
Public Member Functions inherited from CCopasiParameterGroup | |
| bool | addGroup (const std::string &name) |
| void | addParameter (CCopasiParameter *pParameter) |
| bool | addParameter (const CCopasiParameter ¶meter) |
| bool | addParameter (const std::string &name, const CCopasiParameter::Type type, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All) |
| template<class CType > | |
| bool | addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All) |
| virtual bool | applyData (const CData &data, CUndoData::CChangeSet &changes) |
| CCopasiParameterGroup * | assertGroup (const std::string &name, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All) |
| template<class CType > | |
| CType * | assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All) |
| index_iterator | beginIndex () const |
| const_name_iterator | beginName () const |
| CCopasiParameterGroup (const CCopasiParameterGroup &src, const CDataContainer *pParent=NULL) | |
| CCopasiParameterGroup (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="ParameterGroup") | |
| void | clear () |
| virtual void | createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const |
| index_iterator | endIndex () const |
| const_name_iterator | endName () const |
| CCopasiParameterGroup & | getElementTemplates () |
| const CCopasiParameterGroup & | getElementTemplates () const |
| CCopasiParameterGroup * | getGroup (const size_t &index) |
| const CCopasiParameterGroup * | getGroup (const size_t &index) const |
| CCopasiParameterGroup * | getGroup (const std::string &name) |
| const CCopasiParameterGroup * | getGroup (const std::string &name) const |
| virtual size_t | getIndex (const CDataObject *pObject) const |
| size_t | getIndex (const std::string &name) const |
| std::string | getKey (const size_t &index) const |
| std::string | getKey (const std::string &name) const |
| virtual const std::string & | getName (const size_t &index) const |
| virtual const CObjectInterface * | getObject (const CCommonName &cn) const |
| CCopasiParameter * | getParameter (const size_t &index) |
| const CCopasiParameter * | getParameter (const size_t &index) const |
| CCopasiParameter * | getParameter (std::string name) |
| const CCopasiParameter * | getParameter (std::string name) const |
| CCopasiParameter::Type | getType (const size_t &index) const |
| CCopasiParameter::Type | getType (const std::string &name) const |
| std::string | getUniqueParameterName (const CCopasiParameter *pParameter) const |
| template<class CType > | |
| CType & | getValue (const size_t &index) |
| template<class CType > | |
| const CType & | getValue (const size_t &index) const |
| template<class CType > | |
| CType & | getValue (const std::string &name) |
| template<class CType > | |
| const CType & | getValue (const std::string &name) const |
| bool | haveTemplate () const |
| virtual CUndoObjectInterface * | insert (const CData &data) |
| CCopasiParameterGroup & | operator= (const CCopasiParameterGroup &rhs) |
| virtual void | print (std::ostream *ostream) const |
| virtual bool | remove (CDataObject *pObject) |
| bool | removeParameter (CCopasiParameter *pParameter) |
| bool | removeParameter (const size_t &index) |
| bool | removeParameter (const std::string &name) |
| virtual void | setUserInterfaceFlag (const UserInterfaceFlag &flag) |
| template<class CType > | |
| bool | setValue (const size_t &index, const CType &value) |
| template<class CType > | |
| bool | setValue (const std::string &name, const CType &value) |
| size_t | size (const UserInterfaceFlag &require=UserInterfaceFlag::None, const UserInterfaceFlag &exclude=UserInterfaceFlag::None) const |
| bool | swap (const size_t &iFrom, const size_t &iTo) |
| bool | swap (index_iterator &from, index_iterator &to) |
| virtual CData | toData () const |
| virtual void | updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject) |
| virtual | ~CCopasiParameterGroup () |
Public Member Functions inherited from CCopasiParameter | |
| CCopasiParameter (const CCopasiParameter &src, const CDataContainer *pParent) | |
| CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="Parameter") | |
| virtual CCommonName | getCN () const override |
| template<class CType > | |
| const CType & | getDefault () const |
| virtual const std::string & | getKey () const override |
| virtual std::string | getObjectDisplayName () const override |
| const CCopasiParameter::Type & | getType () const |
| const UserInterfaceFlag & | getUserInterfaceFlag () const |
| template<class CType > | |
| std::vector< std::pair< CType, CType > > & | getValidValues () |
| template<class CType > | |
| const std::vector< std::pair< CType, CType > > & | getValidValues () const |
| void * | getValidValuesPointer () const |
| template<class CType > | |
| CType & | getValue () |
| template<class CType > | |
| const CType & | getValue () const |
| virtual void * | getValuePointer () const override |
| CDataObject * | getValueReference () const |
| bool | hasValidValues () const |
| bool | isBasic () const |
| bool | isDefault () const |
| bool | isEditable () const |
| bool | isUnsupported () const |
| bool | isValidValue (const bool &value) const |
| bool | isValidValue (const C_FLOAT64 &value) const |
| bool | isValidValue (const C_INT32 &value) const |
| bool | isValidValue (const CCommonName &value) const |
| template<class CType > | |
| bool | isValidValue (const CType &) const |
| bool | isValidValue (const std::string &value) const |
| bool | isValidValue (const std::vector< CCopasiParameter * > &value) const |
| bool | isValidValue (const unsigned C_INT32 &value) const |
| CCopasiParameter & | operator= (const CCopasiParameter &rhs) |
| template<class CType > | |
| bool | setDefault (const CType &defaultValue) |
| bool | setDefault (const std::vector< CCopasiParameter * > &defaultValue) |
| virtual bool | setObjectParent (const CDataContainer *pParent) override |
| template<class CType , class Enum > | |
| bool | setValidValues (const CEnumAnnotation< CType, Enum > &validValues) |
| template<class CType > | |
| bool | setValidValues (const std::vector< std::pair< CType, CType > > &validValues) |
| template<class CType > | |
| bool | setValue (const CType &value) |
| bool | setValue (const std::vector< CCopasiParameter * > &value) |
| virtual | ~CCopasiParameter () |
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 objectMap & | getObjects () |
| virtual const objectMap & | getObjects () const |
| virtual const std::string | getUnits () const override |
| virtual const CDataObject * | getValueObject () const override |
| void | objectRenamed (CDataObject *pObject, const std::string &oldName) |
| 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 const CDataObject * | getDataObject () const override |
| CDataContainer * | getObjectAncestor (const std::string &type) const |
| CDataModel * | getObjectDataModel () const |
| 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 |
| 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 |
| void | removeIssue (const CIssue &issue) |
| void | removeReference (const CDataContainer *pReference) |
| bool | setObjectName (const std::string &name) |
| 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 | ~CUndoObjectInterface () |
Static Public Member Functions | |
| static bool | isCitation (const std::string &uri) |
| static void | isCitation (void *pData, void *pCallee) |
Static Public Member Functions inherited from CCopasiParameter | |
| static void | allocateValidValues (const Type &type, void *&pValidValues) |
| static void | allocateValue (const Type &type, void *&pValue) |
| static void | assignValue (const Type &type, void *&pValue, const void *pNewValue) |
| static void | deleteValidValues (const Type &type, void *&pValidValues) |
| static void | deleteValue (const Type &type, void *&pValue) |
| static CCopasiParameter * | fromData (const CData &data, CUndoObjectInterface *pParent) |
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 *) |
Private Member Functions | |
| void | createDisplayNameMap () |
| void | createURIMap () |
| unsigned C_INT32 | getActDateInSeconds () |
| void | setMIRIAMLastUpdateDate () |
Private Attributes | |
| std::map< std::string, size_t > | mDisplayName2Resource |
| unsigned C_INT32 * | mpLastUpdateDate |
| CCopasiParameterGroup * | mpMIRIAMResources |
| unsigned C_INT32 * | mpUpdateFrequency |
| std::map< std::string, size_t > | mURI2Resource |
Additional Inherited Members | |
Public Types inherited from CCopasiParameterGroup | |
| typedef CDataObjectMap::const_type_iterator< CCopasiParameter > | const_name_iterator |
| typedef std::vector< CCopasiParameter * > | elements |
| typedef elements::iterator | index_iterator |
| typedef CDataObjectMap::type_iterator< CCopasiParameter > | name_iterator |
Public Types inherited from CCopasiParameter | |
| enum class | eUserInterfaceFlag { editable , basic , unsupported , __SIZE } |
| enum class | Type { DOUBLE = 0 , UDOUBLE , INT , UINT , BOOL , GROUP , STRING , CN , KEY , FILE , EXPRESSION , INVALID , __SIZE } |
| typedef CFlags< eUserInterfaceFlag > | UserInterfaceFlag |
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 CCopasiParameter | |
| static const CEnumAnnotation< std::string, Type > | TypeName |
| static const CEnumAnnotation< std::string, Type > | XMLType |
Static Public Attributes inherited from CDataContainer | |
| static const CObjectInterface::ContainerList | EmptyList |
Protected Member Functions inherited from CCopasiParameterGroup | |
| CCopasiParameterGroup () | |
Protected Member Functions inherited from CCopasiParameter | |
| CCopasiParameter (const CCopasiParameter &src) | |
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 CCopasiParameter | |
| std::string | mKey |
| void * | mpDefault |
| void * | mpValidValues |
| void * | mpValue |
| CDataObject * | mpValueReference |
| UserInterfaceFlag | mUserInterfaceFlag |
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 |
| CMIRIAMResources::CMIRIAMResources | ( | const std::string & | name = "MIRIAM Resources", |
| const CDataContainer * | pParent = NO_PARENT |
||
| ) |
Default constructor
| const | std::string & name (default: MIRIAM Resources) |
| const | CDataContainer * pParent (default: NULL) |
References initializeParameter().
| CMIRIAMResources::CMIRIAMResources | ( | const CMIRIAMResources & | src, |
| const CDataContainer * | pParent | ||
| ) |
Copy constructor
| const | CMIRIAMResources & src |
| const | CDataContainer * pParent (default: NULL) |
References initializeParameter().
| CMIRIAMResources::CMIRIAMResources | ( | const CCopasiParameterGroup & | group, |
| const CDataContainer * | pParent | ||
| ) |
Specific constructor
| const | CCopasiParameterGroup & group |
| const | CDataContainer * pParent (default: NULL) |
References initializeParameter().
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virtual |
Destructor
| void CMIRIAMResources::addMIRIAMResource | ( | CMIRIAMResource * | pMIRIAMResource | ) |
Add a MIRIAM Resource to the list of MIRIAM Resources
| CMIRIAMResource | * pMIRIAMResource |
References CCopasiParameterGroup::addParameter(), and mpMIRIAMResources.
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private |
Initialize the display name to resource index map
References CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::endIndex(), CMIRIAMResource::getMIRIAMDisplayName(), getMIRIAMResource(), mDisplayName2Resource, and mpMIRIAMResources.
Referenced by initializeParameter(), and updateMIRIAMResourcesFromFile().
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private |
Initialize the URI to resource index map
References CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::endIndex(), CMIRIAMResource::getIdentifiersOrgURL(), CMIRIAMResource::getMIRIAMDeprecated(), CMIRIAMResource::getMIRIAMURI(), mpMIRIAMResources, and mURI2Resource.
Referenced by initializeParameter(), and updateMIRIAMResourcesFromFile().
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virtual |
This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.
Reimplemented from CCopasiParameterGroup.
References CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::endIndex(), and mpMIRIAMResources.
Referenced by initializeParameter(), and updateMIRIAMResourcesFromFile().
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private |
Retrieve the current date ins seconds
References C_INT32.
Referenced by initializeParameter(), and setMIRIAMLastUpdateDate().
| const unsigned C_INT32 & CMIRIAMResources::getMIRIAMLastUpdateDate | ( | ) | const |
Retrieve the day the resources where last updated
References mpLastUpdateDate.
| const CMIRIAMResource & CMIRIAMResources::getMIRIAMResource | ( | const size_t | index | ) | const |
Retrieve the indexed resource
| const | size_t index |
References CCopasiParameterGroup::getGroup(), CRootContainer::getUnknownMiriamResource(), mpMIRIAMResources, and CCopasiParameterGroup::size().
Referenced by createDisplayNameMap(), CMIRIAMResourceObject::extractId(), CMIRIAMResourceObject::getDisplayName(), CMIRIAMResourceObject::getIdentifiersOrgURL(), CMIRIAMResourceObject::getURI(), and isCitation().
| size_t CMIRIAMResources::getMIRIAMResourceIndex | ( | const std::string & | URI | ) | const |
Retrieve the index of the resource with the given URI
| const | std::string & URI |
References C_INVALID_INDEX, and mURI2Resource.
Referenced by CMIRIAMResourceObject::getResource(), isCitation(), and CMIRIAMResourceObject::isValid().
| const CMIRIAMResources & CMIRIAMResources::getMIRIAMResources | ( | ) | const |
Retrieve the list of MIRIAM Resources
| const unsigned C_INT32 & CMIRIAMResources::getMIRIAMUpdateFrequency | ( | ) | const |
Retrieve the of interval between updates
References mpUpdateFrequency.
| size_t CMIRIAMResources::getResourceIndexFromDisplayName | ( | const std::string & | displayName | ) | const |
Retrieve the index of the resource with the given display name
| const | std::string & displayName |
References C_INVALID_INDEX, and mDisplayName2Resource.
Referenced by CMIRIAMResourceObject::setDisplayName().
| const CCopasiParameterGroup & CMIRIAMResources::getResourceList | ( | ) | const |
Retrieve the list of MIRIAM resource as a CCopasiParameterGroup
References mpMIRIAMResources.
Referenced by CConfigurationFile::load().
| void CMIRIAMResources::initializeParameter | ( | ) |
Allocates all group parameters and assures that they are properly initialized.
References CCopasiParameterGroup::assertGroup(), CCopasiParameterGroup::assertParameter(), C_INT32, createDisplayNameMap(), createURIMap(), elevateChildren(), getActDateInSeconds(), mpLastUpdateDate, mpMIRIAMResources, mpUpdateFrequency, and CCopasiParameter::UINT.
Referenced by CMIRIAMResources(), CConfigurationFile::load(), and operator=().
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static |
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static |
References CRDFPredicate::rdf_li.
Referenced by CMIRIAMInfo::loadBiologicalDescriptions().
| const CMIRIAMResources & CMIRIAMResources::operator= | ( | const CCopasiParameterGroup & | rhs | ) |
Assignment operator
| const | CCopasiParameterGroup & rhs |
References initializeParameter(), and CCopasiParameterGroup::operator=().
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private |
Set the last update date to the current time
References getActDateInSeconds(), and mpLastUpdateDate.
Referenced by updateMIRIAMResourcesFromFile().
| void CMIRIAMResources::setMIRIAMUpdateFrequencyInDays | ( | const size_t & | days | ) |
Set the days between updates
| const | size_t & days |
References C_INT32, and mpUpdateFrequency.
| bool CMIRIAMResources::updateMIRIAMResourcesFromFile | ( | CProcessReport * | pProcessReport, |
| const std::string & | filename | ||
| ) |
Update the MIRIAM resources using a local filename
| CProcessReport | * pProcessReport |
References CMIRIAMResource::addDeprecatedURL(), CProcessReport::addItem(), CCopasiParameterGroup::addParameter(), C_INT32, CCopasiParameterGroup::CCopasiParameterGroup(), createDisplayNameMap(), createURIMap(), elevateChildren(), CProcessReport::finishItem(), mpMIRIAMResources, pdelete, CProcessReport::progressItem(), CMIRIAMResource::setMIRIAMCitation(), CMIRIAMResource::setMIRIAMDisplayName(), setMIRIAMLastUpdateDate(), CMIRIAMResource::setMIRIAMNamespaceEmbeddedInPattern(), CMIRIAMResource::setMIRIAMPattern(), and CMIRIAMResource::setMIRIAMURI().
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A map from display name to resource index
Referenced by createDisplayNameMap(), and getResourceIndexFromDisplayName().
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A pointer to the last update date.
Referenced by getMIRIAMLastUpdateDate(), initializeParameter(), and setMIRIAMLastUpdateDate().
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private |
A pointer to the group of MIRIAM resources
Referenced by addMIRIAMResource(), createDisplayNameMap(), createURIMap(), elevateChildren(), getMIRIAMResource(), getResourceList(), initializeParameter(), and updateMIRIAMResourcesFromFile().
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A pointer to the update interval.
Referenced by getMIRIAMUpdateFrequency(), initializeParameter(), and setMIRIAMUpdateFrequencyInDays().
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A map from URI to resource index
Referenced by createURIMap(), and getMIRIAMResourceIndex().