COPASI API
4.16.103
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#include <CMIRIAMResource.h>
Public Member Functions | |
void | addMIRIAMResource (CMIRIAMResource *pMIRIAMResource) |
bool | autoUpdateMIRIAMResources (CProcessReport *pProcessReport) |
CMIRIAMResources (const std::string &name="MIRIAM Resources", const CCopasiContainer *pParent=NULL) | |
CMIRIAMResources (const CMIRIAMResources &src, const CCopasiContainer *pParent=NULL) | |
CMIRIAMResources (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL) | |
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 () |
void | setMIRIAMUpdateFrequencyInDays (const size_t &days) |
bool | updateMIRIAMResources (CProcessReport *pProcessReport) |
bool | updateMIRIAMResourcesFromFile (CProcessReport *pProcessReport, const std::string &filename) |
virtual | ~CMIRIAMResources () |
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bool | addGroup (const std::string &name) |
bool | addParameter (const CCopasiParameter ¶meter) |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type) |
template<class CType > | |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value) |
void | addParameter (CCopasiParameter *pParameter) |
CCopasiParameterGroup * | assertGroup (const std::string &name) |
template<class CType > | |
CCopasiParameter * | assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue) |
index_iterator | beginIndex () const |
name_iterator | beginName () const |
CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL) | |
CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup") | |
void | clear () |
index_iterator | endIndex () const |
name_iterator | endName () const |
CCopasiParameterGroup * | getGroup (const std::string &name) |
const CCopasiParameterGroup * | getGroup (const std::string &name) const |
CCopasiParameterGroup * | getGroup (const size_t &index) |
const CCopasiParameterGroup * | getGroup (const size_t &index) const |
size_t | getIndex (const std::string &name) const |
std::string | getKey (const std::string &name) const |
std::string | getKey (const size_t &index) const |
virtual const std::string & | getName (const size_t &index) const |
virtual const CObjectInterface * | getObject (const CCopasiObjectName &cn) const |
CCopasiParameter * | getParameter (const std::string &name) |
const CCopasiParameter * | getParameter (const std::string &name) const |
CCopasiParameter * | getParameter (const size_t &index) |
const CCopasiParameter * | getParameter (const size_t &index) const |
CCopasiParameter::Type | getType (const std::string &name) const |
CCopasiParameter::Type | getType (const size_t &index) const |
std::string | getUniqueParameterName (const CCopasiParameter *pParameter) const |
const CCopasiParameter::Value & | getValue (const std::string &name) const |
const CCopasiParameter::Value & | getValue (const size_t &index) const |
CCopasiParameter::Value & | getValue (const std::string &name) |
CCopasiParameter::Value & | getValue (const size_t &index) |
CCopasiParameterGroup & | operator= (const CCopasiParameterGroup &rhs) |
virtual void | print (std::ostream *ostream) const |
bool | removeParameter (const std::string &name) |
bool | removeParameter (const size_t &index) |
template<class CType > | |
bool | setValue (const std::string &name, const CType &value) |
template<class CType > | |
bool | setValue (const size_t &index, const CType &value) |
size_t | size () const |
bool | swap (const size_t &iFrom, const size_t &iTo) |
bool | swap (index_iterator &from, index_iterator &to) |
virtual | ~CCopasiParameterGroup () |
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CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL) | |
CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CCopasiContainer *pParent=NULL, const std::string &objectType="Parameter") | |
virtual CCopasiObjectName | getCN () const |
virtual const std::string & | getKey () const |
virtual std::string | getObjectDisplayName (bool regular=true, bool richtext=false) const |
const CCopasiParameter::Type & | getType () const |
const Value & | getValue () const |
Value & | getValue () |
virtual void * | getValuePointer () const |
CCopasiObject * | getValueReference () const |
bool | isValidValue (const C_FLOAT64 &value) const |
bool | isValidValue (const C_INT32 &value) const |
bool | isValidValue (const unsigned C_INT32 &value) const |
bool | isValidValue (const bool &value) const |
bool | isValidValue (const std::string &value) const |
bool | isValidValue (const CCopasiObjectName &value) const |
bool | isValidValue (const std::vector< CCopasiParameter * > &value) const |
CCopasiParameter & | operator= (const CCopasiParameter &rhs) |
template<class CType > | |
bool | setValue (const CType &value) |
bool | setValue (const std::vector< CCopasiParameter * > &value) |
virtual | ~CCopasiParameter () |
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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 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 const DataObjectSet & | getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const |
CCopasiContainer * | getObjectAncestor (const std::string &type) const |
CCopasiDataModel * | getObjectDataModel () |
const CCopasiDataModel * | getObjectDataModel () 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 |
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 |
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 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 | |
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typedef parameterGroup::iterator | index_iterator |
typedef CCopasiContainer::objectMap::iterator | name_iterator |
typedef std::vector < CCopasiParameter * > | parameterGroup |
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enum | Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID } |
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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::string | TypeName [] |
static const char * | XMLType [] |
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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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CCopasiParameterGroup () | |
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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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std::string | mKey |
CCopasiObject * | mpValueReference |
size_t | mSize |
Value | mValue |
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objectMap | mObjects |
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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 173 of file CMIRIAMResource.h.
CMIRIAMResources::CMIRIAMResources | ( | const std::string & | name = "MIRIAM Resources" , |
const CCopasiContainer * | pParent = NULL |
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Default constructor
const | std::string & name (default: MIRIAM Resources) |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 29 of file CMIRIAMResource.cpp.
References initializeParameter().
CMIRIAMResources::CMIRIAMResources | ( | const CMIRIAMResources & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CMIRIAMResources & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 37 of file CMIRIAMResource.cpp.
References initializeParameter().
CMIRIAMResources::CMIRIAMResources | ( | const CCopasiParameterGroup & | group, |
const CCopasiContainer * | pParent = NULL |
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Specific constructor
const | CCopasiParameterGroup & group |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 45 of file CMIRIAMResource.cpp.
References initializeParameter().
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void CMIRIAMResources::addMIRIAMResource | ( | CMIRIAMResource * | pMIRIAMResource | ) |
Add a MIRIAM Resource to the list of MIRIAM Resources
CMIRIAMResource | * pMIRIAMResource |
Definition at line 67 of file CMIRIAMResource.cpp.
References CCopasiParameterGroup::addParameter(), and mpMIRIAMResources.
bool CMIRIAMResources::autoUpdateMIRIAMResources | ( | CProcessReport * | pProcessReport | ) |
Automatically update the resources when the last update is older than the current date minus the update interval.
CProcessReport | * pProcessReport |
Definition at line 323 of file CMIRIAMResource.cpp.
References getActDateInSeconds(), mpLastUpdateDate, mpUpdateFrequency, and updateMIRIAMResources().
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Initialize the display name to resource index map
Definition at line 344 of file CMIRIAMResource.cpp.
References CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::endIndex(), CMIRIAMResource::getMIRIAMDisplayName(), getMIRIAMResource(), mDisplayName2Resource, and mpMIRIAMResources.
Referenced by initializeParameter(), updateMIRIAMResources(), and updateMIRIAMResourcesFromFile().
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Initialize the URI to resource index map
Definition at line 360 of file CMIRIAMResource.cpp.
References CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::endIndex(), CMIRIAMResource::getIdentifiersOrgURL(), CMIRIAMResource::getMIRIAMDeprecated(), CMIRIAMResource::getMIRIAMURI(), mpMIRIAMResources, and mURI2Resource.
Referenced by initializeParameter(), updateMIRIAMResources(), and updateMIRIAMResourcesFromFile().
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This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.
Reimplemented from CCopasiParameterGroup.
Definition at line 331 of file CMIRIAMResource.cpp.
References CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::endIndex(), and mpMIRIAMResources.
Referenced by initializeParameter(), updateMIRIAMResources(), and updateMIRIAMResourcesFromFile().
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Retrieve the current date ins seconds
Definition at line 320 of file CMIRIAMResource.cpp.
References C_INT32.
Referenced by autoUpdateMIRIAMResources(), initializeParameter(), and setMIRIAMLastUpdateDate().
const unsigned C_INT32 & CMIRIAMResources::getMIRIAMLastUpdateDate | ( | ) | const |
Retrieve the day the resources where last updated
Definition at line 78 of file CMIRIAMResource.cpp.
References mpLastUpdateDate.
const CMIRIAMResource & CMIRIAMResources::getMIRIAMResource | ( | const size_t | index | ) | const |
Retrieve the indexed resource
const | size_t index |
Definition at line 397 of file CMIRIAMResource.cpp.
References CCopasiParameterGroup::getGroup(), CCopasiRootContainer::getUnknownMiriamResource(), mpMIRIAMResources, and CCopasiParameterGroup::size().
Referenced by createDisplayNameMap(), CMIRIAMResourceObject::extractId(), CMIRIAMResourceObject::getDisplayName(), CMIRIAMResourceObject::getIdentifiersOrgURL(), CMIRIAMResourceObject::getURI(), and CQMiriamWidget::updateResourcesList().
size_t CMIRIAMResources::getMIRIAMResourceIndex | ( | const std::string & | URI | ) | const |
Retrieve the index of the resource with the given URI
const | std::string & URI |
Definition at line 405 of file CMIRIAMResource.cpp.
References C_INVALID_INDEX, and mURI2Resource.
Referenced by CMIRIAMResourceObject::getResource(), and CMIRIAMResourceObject::isValid().
const CMIRIAMResources & CMIRIAMResources::getMIRIAMResources | ( | ) | const |
Retrieve the list of MIRIAM Resources
Definition at line 72 of file CMIRIAMResource.cpp.
const unsigned C_INT32 & CMIRIAMResources::getMIRIAMUpdateFrequency | ( | ) | const |
Retrieve the of interval between updates
Definition at line 81 of file CMIRIAMResource.cpp.
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 |
Definition at line 430 of file CMIRIAMResource.cpp.
References C_INVALID_INDEX, and mDisplayName2Resource.
Referenced by CMIRIAMResourceObject::setDisplayName().
const CCopasiParameterGroup & CMIRIAMResources::getResourceList | ( | ) | const |
Retrieve the list of MIRIAM resource as a CCopasiParameterGroup
Definition at line 75 of file CMIRIAMResource.cpp.
References mpMIRIAMResources.
Referenced by CConfigurationFile::load(), and CQMiriamWidget::updateResourcesList().
void CMIRIAMResources::initializeParameter | ( | ) |
Allocates all group parameters and assures that they are properly initialized.
Definition at line 53 of file CMIRIAMResource.cpp.
References CCopasiParameterGroup::assertGroup(), CCopasiParameterGroup::assertParameter(), C_INT32, createDisplayNameMap(), createURIMap(), elevateChildren(), getActDateInSeconds(), CCopasiParameter::getValue(), mpLastUpdateDate, mpMIRIAMResources, mpUpdateFrequency, CCopasiParameter::Value::pUINT, and CCopasiParameter::UINT.
Referenced by CMIRIAMResources(), and CConfigurationFile::load().
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Set the last update date to the current time
Definition at line 314 of file CMIRIAMResource.cpp.
References getActDateInSeconds(), and mpLastUpdateDate.
Referenced by updateMIRIAMResources(), and updateMIRIAMResourcesFromFile().
void CMIRIAMResources::setMIRIAMUpdateFrequencyInDays | ( | const size_t & | days | ) |
Set the days between updates
const | size_t & days |
Definition at line 317 of file CMIRIAMResource.cpp.
References C_INT32, and mpUpdateFrequency.
bool CMIRIAMResources::updateMIRIAMResources | ( | CProcessReport * | pProcessReport | ) |
Update the MIRIAM resources
CProcessReport | * pProcessReport |
Definition at line 206 of file CMIRIAMResource.cpp.
References ArrayOf_USCORExsd_USCOREstring::__ptr, ArrayOf_USCORExsd_USCOREstring::__size, ns2__getDataTypeURIsResponse::_getDataTypeURIsReturn, CMIRIAMResource::addDeprecatedURL(), CProcessReport::addItem(), CCopasiParameterGroup::addParameter(), C_INT32, CCopasiParameterGroup::CCopasiParameterGroup(), createDisplayNameMap(), createURIMap(), elevateChildren(), CCopasiMessage::ERROR, CProcessReport::finishItem(), MiriamWebServicesSoapBindingProxy::getDataTypePattern(), MiriamWebServicesSoapBindingProxy::getDataTypesName(), ns2__getDataTypesNameResponse::getDataTypesNameReturn, MiriamWebServicesSoapBindingProxy::getDataTypeURI(), MiriamWebServicesSoapBindingProxy::getDataTypeURIs(), MCAnnotation, mpMIRIAMResources, pdelete, CProcessReport::progressItem(), CMIRIAMResource::setMIRIAMCitation(), CMIRIAMResource::setMIRIAMDisplayName(), setMIRIAMLastUpdateDate(), CMIRIAMResource::setMIRIAMPattern(), CMIRIAMResource::setMIRIAMURI(), CProcessReport::setName(), MiriamWebServicesSoapBindingProxy::soap_fault_detail(), MiriamWebServicesSoapBindingProxy::soap_fault_string(), and SOAP_OK.
Referenced by autoUpdateMIRIAMResources().
bool CMIRIAMResources::updateMIRIAMResourcesFromFile | ( | CProcessReport * | pProcessReport, |
const std::string & | filename | ||
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Update the MIRIAM resources using a local filename
CProcessReport | * pProcessReport |
Definition at line 84 of file CMIRIAMResource.cpp.
References CMIRIAMResource::addDeprecatedURL(), CProcessReport::addItem(), CCopasiParameterGroup::addParameter(), C_INT32, CCopasiParameterGroup::CCopasiParameterGroup(), createDisplayNameMap(), createURIMap(), elevateChildren(), mpMIRIAMResources, pdelete, CProcessReport::progressItem(), CMIRIAMResource::setMIRIAMCitation(), CMIRIAMResource::setMIRIAMDisplayName(), setMIRIAMLastUpdateDate(), CMIRIAMResource::setMIRIAMPattern(), and CMIRIAMResource::setMIRIAMURI().
Referenced by DataModelGUI::miriamDownloadFinished().
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A map from display name to resource index
Definition at line 340 of file CMIRIAMResource.h.
Referenced by createDisplayNameMap(), and getResourceIndexFromDisplayName().
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A pointer to the last update date.
Definition at line 325 of file CMIRIAMResource.h.
Referenced by autoUpdateMIRIAMResources(), getMIRIAMLastUpdateDate(), initializeParameter(), and setMIRIAMLastUpdateDate().
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A pointer to the group of MIRIAM resources
Definition at line 335 of file CMIRIAMResource.h.
Referenced by addMIRIAMResource(), createDisplayNameMap(), createURIMap(), elevateChildren(), getMIRIAMResource(), getResourceList(), initializeParameter(), updateMIRIAMResources(), and updateMIRIAMResourcesFromFile().
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A pointer to the update interval.
Definition at line 330 of file CMIRIAMResource.h.
Referenced by autoUpdateMIRIAMResources(), getMIRIAMUpdateFrequency(), initializeParameter(), and setMIRIAMUpdateFrequencyInDays().
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A map from URI to resource index
Definition at line 345 of file CMIRIAMResource.h.
Referenced by createURIMap(), and getMIRIAMResourceIndex().