CMIRIAMResource Class Reference

#include <CMIRIAMResource.h>

Inheritance diagram for CMIRIAMResource:

Collaboration diagram for CMIRIAMResource:

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 ()
Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)
bool	addParameter (const CCopasiParameter &parameter)
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 ()
Public Member Functions inherited from CCopasiParameter
	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 ()
Public Member Functions inherited from CCopasiContainer
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 ()
Public Member Functions inherited from CCopasiObject
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 ()
Public Member Functions inherited from CObjectInterface
	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
Public Types inherited from CCopasiParameterGroup
typedef parameterGroup::iterator	index_iterator
typedef CCopasiContainer::objectMap::iterator	name_iterator
typedef std::vector < CCopasiParameter * >	parameterGroup
Public Types inherited from CCopasiParameter
enum	Type {   DOUBLE = 0, UDOUBLE, INT, UINT,   BOOL, GROUP, STRING, CN,   KEY, FILE, EXPRESSION, INVALID }
Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap
Public Types inherited from CCopasiObject
typedef std::set< const CCopasiObject * >	DataObjectSet
typedef std::vector< Refresh * >	DataUpdateSequence
Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet
typedef std::vector < CObjectInterface * >	UpdateSequence
Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())
static void	setRenameHandler (CRenameHandler *rh)
Static Public Attributes inherited from CCopasiParameter
static const std::string	TypeName []
static const char *	XMLType []
Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList
Protected Types inherited from CCopasiObject
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 }
Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()
Protected Member Functions inherited from CCopasiContainer
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 ()
Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()
	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)
Protected Attributes inherited from CCopasiParameter
std::string	mKey
CCopasiObject *	mpValueReference
size_t	mSize
Value	mValue
Protected Attributes inherited from CCopasiContainer
objectMap	mObjects
Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 33 of file CMIRIAMResource.h.

Constructor & Destructor Documentation

CMIRIAMResource::CMIRIAMResource	(	const std::string &	name = "MIRIAM Resource",
		const CCopasiContainer *	pParent = NULL
	)

Default constructor

Parameters

const	std::string & name (default: MIRIAM Resource)
const	CCopasiContainer * pParent (default: NULL)

Definition at line 470 of file CMIRIAMResource.cpp.

References initializeParameter().

                                                                   :
  CCopasiParameterGroup(name, pParent),
  mpDisplayName(NULL),
  mpURI(NULL),
  mpCitation(NULL),
  mpDeprecated(NULL)
{initializeParameter();}

CMIRIAMResource::CMIRIAMResource	(	const CMIRIAMResource &	src,
		const CCopasiContainer *	pParent = NULL
	)

Copy constructor

Parameters

const	CMIRIAMResource & src
const	CCopasiContainer * pParent (default: NULL)

Definition at line 479 of file CMIRIAMResource.cpp.

References initializeParameter().

                                                                  :
  CCopasiParameterGroup(src, pParent),
  mpDisplayName(NULL),
  mpURI(NULL),
  mpCitation(NULL),
  mpDeprecated(NULL)
{initializeParameter();}

CMIRIAMResource::CMIRIAMResource	(	const CCopasiParameterGroup &	group,
		const CCopasiContainer *	pParent = NULL
	)

Specific constructor

Parameters

const	CCopasiParameterGroup & group
const	CCopasiContainer * pParent (default: NULL)

Definition at line 488 of file CMIRIAMResource.cpp.

References initializeParameter().

                                                                  :
  CCopasiParameterGroup(group, pParent),
  mpDisplayName(NULL),
  mpURI(NULL),
  mpCitation(NULL),
  mpDeprecated(NULL)
{initializeParameter();}

CMIRIAMResource::~CMIRIAMResource ( )

virtual

Destructor

Definition at line 510 of file CMIRIAMResource.cpp.

{}

Member Function Documentation

void CMIRIAMResource::addDeprecatedURL

(

const std::string &

URL

)

Add a deprecated URL to the MIRIAM Resource

Parameters

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().

{mpDeprecated->addParameter("URL", CCopasiParameter::STRING, URL);}

std::string CMIRIAMResource::getIdentifiersOrgURL

(

)

const

Retrieve the identifiers.org URL of the MIRIAM Resource.

Returns

std::string URL

Definition at line 548 of file CMIRIAMResource.cpp.

References mpURI.

Referenced by CMIRIAMResources::createURIMap(), CMIRIAMResourceObject::extractId(), and CMIRIAMResourceObject::getIdentifiersOrgURL().

{
  return "http://identifiers.org/" + mpURI->substr(11);
}

const bool & CMIRIAMResource::getMIRIAMCitation

(

)

const

Retrieve whether the resource can be used as reference.

Returns

const bool & isCitation

Definition at line 562 of file CMIRIAMResource.cpp.

References mpCitation.

Referenced by CQMiriamWidget::updateResourcesList().

{return * mpCitation;}

const CCopasiParameterGroup & CMIRIAMResource::getMIRIAMDeprecated

(

)

const

Retrieve the deprecated URL of the MIRIAM Resource

Returns

const CCopasiParameterGroup & deprecatedURLs

Definition at line 568 of file CMIRIAMResource.cpp.

References mpDeprecated.

Referenced by CMIRIAMResources::createURIMap().

{return * mpDeprecated;}

const std::string & CMIRIAMResource::getMIRIAMDisplayName

(

)

const

Retrieve the Display Name of the MIRIAM Resource.

Returns

const std::string & DisplayName

Definition at line 539 of file CMIRIAMResource.cpp.

References mpDisplayName.

Referenced by CMIRIAMResources::createDisplayNameMap(), and CQMiriamWidget::updateResourcesList().

{return *mpDisplayName;}

const CMIRIAMResource & CMIRIAMResource::getMIRIAMMIRIAMResource

(

)

const

Retrieve the list of MIRIAM Resource.

Returns

const CMIRIAMResource & MIRIAMResource

Definition at line 533 of file CMIRIAMResource.cpp.

{return * this;}

const std::string & CMIRIAMResource::getMIRIAMPattern

(

)

const

Retrieve the Pattern of the MIRIAM Resource.

Returns

std::string & Pattern

Definition at line 556 of file CMIRIAMResource.cpp.

References mpPattern.

{return * mpPattern;}

const std::string & CMIRIAMResource::getMIRIAMURI

(

)

const

Retrieve the URI of the MIRIAM Resource.

Returns

const std::string & URI

Definition at line 545 of file CMIRIAMResource.cpp.

References mpURI.

Referenced by CMIRIAMResources::createURIMap(), and CMIRIAMResourceObject::extractId().

{return * mpURI;}

void CMIRIAMResource::initializeParameter ( )

private

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().

{
  mpDisplayName = assertParameter("DisplayName", CCopasiParameter::STRING,
                                  (std::string) "")->getValue().pSTRING;
  mpURI = assertParameter("URI", CCopasiParameter::STRING,
                          (std::string) "")->getValue().pSTRING;
  mpPattern = assertParameter("Pattern", CCopasiParameter::STRING,
                              (std::string) "")->getValue().pSTRING;
  mpCitation = assertParameter("Citation", CCopasiParameter::BOOL,
                               false)->getValue().pBOOL;
  mpDeprecated = assertGroup("Deprecated");
}

void CMIRIAMResource::setMIRIAMCitation

(

const bool &

isCitation

)

Set whether the resource can be used as reference.

Parameters

const

bool & isCitation

Definition at line 559 of file CMIRIAMResource.cpp.

References mpCitation.

Referenced by CMIRIAMResources::updateMIRIAMResources(), and CMIRIAMResources::updateMIRIAMResourcesFromFile().

{*mpCitation = citation;}

void CMIRIAMResource::setMIRIAMDisplayName

(

const std::string &

displayName

)

Set the Display Name of the MIRIAM Resource.

Parameters

const

std::string & DisplayName

Definition at line 536 of file CMIRIAMResource.cpp.

References mpDisplayName.

Referenced by CCopasiRootContainer::initializeChildren(), CMIRIAMResources::updateMIRIAMResources(), and CMIRIAMResources::updateMIRIAMResourcesFromFile().

{*mpDisplayName = displayName;}

void CMIRIAMResource::setMIRIAMPattern

(

const std::string &

pattern

)

Set the Pattern of the MIRIAM Resource.

Parameters

const

std::string & Pattern

Definition at line 553 of file CMIRIAMResource.cpp.

References mpPattern.

Referenced by CMIRIAMResources::updateMIRIAMResources(), and CMIRIAMResources::updateMIRIAMResourcesFromFile().

{*mpPattern = pattern;}

void CMIRIAMResource::setMIRIAMURI

(

const std::string &

URI

)

Set the URI of the MIRIAM Resource.

Parameters

const

std::string & URI

Definition at line 542 of file CMIRIAMResource.cpp.

References mpURI.

Referenced by CCopasiRootContainer::initializeChildren(), CMIRIAMResources::updateMIRIAMResources(), and CMIRIAMResources::updateMIRIAMResourcesFromFile().

{*mpURI = URI;}

Member Data Documentation

bool* CMIRIAMResource::mpCitation

private

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().

CCopasiParameterGroup* CMIRIAMResource::mpDeprecated

private

A parameter group holding all deprecated URIs

Definition at line 168 of file CMIRIAMResource.h.

Referenced by addDeprecatedURL(), getMIRIAMDeprecated(), and initializeParameter().

std::string* CMIRIAMResource::mpDisplayName

private

The name used in the GUI

Definition at line 148 of file CMIRIAMResource.h.

Referenced by getMIRIAMDisplayName(), initializeParameter(), and setMIRIAMDisplayName().

std::string* CMIRIAMResource::mpPattern

private

A pointer to the pattern

Definition at line 158 of file CMIRIAMResource.h.

Referenced by getMIRIAMPattern(), initializeParameter(), and setMIRIAMPattern().

std::string* CMIRIAMResource::mpURI

private

A pointer to the URI

Definition at line 153 of file CMIRIAMResource.h.

Referenced by getIdentifiersOrgURL(), getMIRIAMURI(), initializeParameter(), and setMIRIAMURI().

---

The documentation for this class was generated from the following files:

• CMIRIAMResource.h
• CMIRIAMResource.cpp