COPASI API
4.16.103
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#include <CMIRIAMResource.h>
Public Member Functions | |
void | addDeprecatedURL (const std::string &URL) |
CMIRIAMResource (const std::string &name="MIRIAM Resource", const CCopasiContainer *pParent=NULL) | |
CMIRIAMResource (const CMIRIAMResource &src, const CCopasiContainer *pParent=NULL) | |
CMIRIAMResource (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL) | |
std::string | getIdentifiersOrgURL () const |
const bool & | getMIRIAMCitation () const |
const CCopasiParameterGroup & | getMIRIAMDeprecated () const |
const std::string & | getMIRIAMDisplayName () const |
const CMIRIAMResource & | getMIRIAMMIRIAMResource () const |
const std::string & | getMIRIAMPattern () const |
const std::string & | getMIRIAMURI () const |
void | setMIRIAMCitation (const bool &isCitation) |
void | setMIRIAMDisplayName (const std::string &displayName) |
void | setMIRIAMPattern (const std::string &pattern) |
void | setMIRIAMURI (const std::string &URI) |
virtual | ~CMIRIAMResource () |
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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 () |
virtual bool | elevateChildren () |
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 | initializeParameter () |
Private Attributes | |
bool * | mpCitation |
CCopasiParameterGroup * | mpDeprecated |
std::string * | mpDisplayName |
std::string * | mpPattern |
std::string * | mpURI |
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 33 of file CMIRIAMResource.h.
CMIRIAMResource::CMIRIAMResource | ( | const std::string & | name = "MIRIAM Resource" , |
const CCopasiContainer * | pParent = NULL |
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Default constructor
const | std::string & name (default: MIRIAM Resource) |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 470 of file CMIRIAMResource.cpp.
References initializeParameter().
CMIRIAMResource::CMIRIAMResource | ( | const CMIRIAMResource & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CMIRIAMResource & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 479 of file CMIRIAMResource.cpp.
References initializeParameter().
CMIRIAMResource::CMIRIAMResource | ( | const CCopasiParameterGroup & | group, |
const CCopasiContainer * | pParent = NULL |
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Specific constructor
const | CCopasiParameterGroup & group |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 488 of file CMIRIAMResource.cpp.
References initializeParameter().
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void CMIRIAMResource::addDeprecatedURL | ( | const std::string & | URL | ) |
Add a deprecated URL to the MIRIAM Resource
const | std::string & URL |
Definition at line 565 of file CMIRIAMResource.cpp.
References CCopasiParameterGroup::addParameter(), mpDeprecated, and CCopasiParameter::STRING.
Referenced by CMIRIAMResources::updateMIRIAMResources(), and CMIRIAMResources::updateMIRIAMResourcesFromFile().
std::string CMIRIAMResource::getIdentifiersOrgURL | ( | ) | const |
Retrieve the identifiers.org URL of the MIRIAM Resource.
Definition at line 548 of file CMIRIAMResource.cpp.
References mpURI.
Referenced by CMIRIAMResources::createURIMap(), CMIRIAMResourceObject::extractId(), and CMIRIAMResourceObject::getIdentifiersOrgURL().
const bool & CMIRIAMResource::getMIRIAMCitation | ( | ) | const |
Retrieve whether the resource can be used as reference.
Definition at line 562 of file CMIRIAMResource.cpp.
References mpCitation.
Referenced by CQMiriamWidget::updateResourcesList().
const CCopasiParameterGroup & CMIRIAMResource::getMIRIAMDeprecated | ( | ) | const |
Retrieve the deprecated URL of the MIRIAM Resource
Definition at line 568 of file CMIRIAMResource.cpp.
References mpDeprecated.
Referenced by CMIRIAMResources::createURIMap().
const std::string & CMIRIAMResource::getMIRIAMDisplayName | ( | ) | const |
Retrieve the Display Name of the MIRIAM Resource.
Definition at line 539 of file CMIRIAMResource.cpp.
References mpDisplayName.
Referenced by CMIRIAMResources::createDisplayNameMap(), and CQMiriamWidget::updateResourcesList().
const CMIRIAMResource & CMIRIAMResource::getMIRIAMMIRIAMResource | ( | ) | const |
Retrieve the list of MIRIAM Resource.
Definition at line 533 of file CMIRIAMResource.cpp.
const std::string & CMIRIAMResource::getMIRIAMPattern | ( | ) | const |
Retrieve the Pattern of the MIRIAM Resource.
Definition at line 556 of file CMIRIAMResource.cpp.
References mpPattern.
const std::string & CMIRIAMResource::getMIRIAMURI | ( | ) | const |
Retrieve the URI of the MIRIAM Resource.
Definition at line 545 of file CMIRIAMResource.cpp.
References mpURI.
Referenced by CMIRIAMResources::createURIMap(), and CMIRIAMResourceObject::extractId().
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Allocates all group parameters and assures that they are properly initialized.
Definition at line 497 of file CMIRIAMResource.cpp.
References CCopasiParameterGroup::assertGroup(), CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, CCopasiParameter::getValue(), mpCitation, mpDeprecated, mpDisplayName, mpPattern, mpURI, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pSTRING, and CCopasiParameter::STRING.
Referenced by CMIRIAMResource().
void CMIRIAMResource::setMIRIAMCitation | ( | const bool & | isCitation | ) |
Set whether the resource can be used as reference.
const | bool & isCitation |
Definition at line 559 of file CMIRIAMResource.cpp.
References mpCitation.
Referenced by CMIRIAMResources::updateMIRIAMResources(), and CMIRIAMResources::updateMIRIAMResourcesFromFile().
void CMIRIAMResource::setMIRIAMDisplayName | ( | const std::string & | displayName | ) |
Set the Display Name of the MIRIAM Resource.
const | std::string & DisplayName |
Definition at line 536 of file CMIRIAMResource.cpp.
References mpDisplayName.
Referenced by CCopasiRootContainer::initializeChildren(), CMIRIAMResources::updateMIRIAMResources(), and CMIRIAMResources::updateMIRIAMResourcesFromFile().
void CMIRIAMResource::setMIRIAMPattern | ( | const std::string & | pattern | ) |
Set the Pattern of the MIRIAM Resource.
const | std::string & Pattern |
Definition at line 553 of file CMIRIAMResource.cpp.
References mpPattern.
Referenced by CMIRIAMResources::updateMIRIAMResources(), and CMIRIAMResources::updateMIRIAMResourcesFromFile().
void CMIRIAMResource::setMIRIAMURI | ( | const std::string & | URI | ) |
Set the URI of the MIRIAM Resource.
const | std::string & URI |
Definition at line 542 of file CMIRIAMResource.cpp.
References mpURI.
Referenced by CCopasiRootContainer::initializeChildren(), CMIRIAMResources::updateMIRIAMResources(), and CMIRIAMResources::updateMIRIAMResourcesFromFile().
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A pointer to a bool indication the the resource an be used as reference
Definition at line 163 of file CMIRIAMResource.h.
Referenced by getMIRIAMCitation(), initializeParameter(), and setMIRIAMCitation().
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A parameter group holding all deprecated URIs
Definition at line 168 of file CMIRIAMResource.h.
Referenced by addDeprecatedURL(), getMIRIAMDeprecated(), and initializeParameter().
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The name used in the GUI
Definition at line 148 of file CMIRIAMResource.h.
Referenced by getMIRIAMDisplayName(), initializeParameter(), and setMIRIAMDisplayName().
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A pointer to the pattern
Definition at line 158 of file CMIRIAMResource.h.
Referenced by getMIRIAMPattern(), initializeParameter(), and setMIRIAMPattern().
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A pointer to the URI
Definition at line 153 of file CMIRIAMResource.h.
Referenced by getIdentifiersOrgURL(), getMIRIAMURI(), initializeParameter(), and setMIRIAMURI().