#include <CConfigurationFile.h>

Inheritance diagram for CConfigurationFile:

Classes
class	CXML

Public Member Functions
	CConfigurationFile (const CConfigurationFile &src, const CDataContainer *pParent)

	CConfigurationFile (const std::string &name="Configuration", const CDataContainer *pParent=NO_PARENT)

bool	displayPopulations () const

virtual bool	elevateChildren ()

bool	enableAdditionalOptimizationParameters () const

const std::string	getApplicationFont () const

CCheckForUpdates &	getCheckForUpdates ()

const std::string &	getCurrentAuthorEmail () const

const std::string &	getCurrentAuthorFamilyName () const

const std::string &	getCurrentAuthorGivenName () const

const std::string &	getCurrentAuthorOrganization () const

bool	getDisableJIT () const

C_INT32	getDoublePrecision () const

const std::string	getProxyPassword () const

C_INT32	getProxyPort () const

const std::string	getProxyServer () const

const std::string	getProxyUser () const

CRecentFiles &	getRecentFiles ()

CMIRIAMResources &	getRecentMIRIAMResources ()

CRecentFiles &	getRecentSBMLFiles ()

CRecentFiles &	getRecentSEDMLFiles ()

const std::string	getWorkingDirectory () const

virtual bool	load ()

bool	normalizePerExperiment () const

const CConfigurationFile &	operator= (const CConfigurationFile &rhs)

const CConfigurationFile &	operator= (const CCopasiParameterGroup &rhs)

bool	resizeToContents () const

virtual bool	save ()

void	setApplicationFont (const std::string &applicationFont)

void	setCurrentAuthorEmail (const std::string &CurrentAuthorEmail)

void	setCurrentAuthorFamilyName (const std::string &CurrentAuthorFamilyName)

void	setCurrentAuthorGivenName (const std::string &CurrentAuthorGivenName)

void	setCurrentAuthorOrganization (const std::string &CurrentAuthorOrganization)

void	setDisableJIT (bool disableJIT)

void	setDisplayPopulations (bool flag)

void	setDoublePrecision (C_INT32 precision)

void	setEnableAdditionalOptimizationParameters (bool enableAdditionalOptimizationParameters)

void	setNormalizePerExperiment (bool flag)

void	setProxyPassword (const std::string &proxyPassword)

void	setProxyPort (C_INT32 proxyPort)

void	setProxyServer (const std::string &proxyServer)

void	setProxyUser (const std::string &proxyUser)

void	setRecentMIRIAMResources (const CMIRIAMResources &miriamResources)

void	setResizeToContents (bool flag)

void	setUseAdvancedEditing (bool useAdvancedEditing)

void	setUseAdvancedSliders (bool useAdvancedSliders)

void	setUseOpenGL (bool useOpenGL)

void	setValidateUnits (bool validateUnits)

void	setWorkingDirectory (const std::string &workingDirectory)

bool	showItemIssues (CIssue::eKind kind) const

bool	useAdvancedEditing () const

bool	useAdvancedSliders () const

bool	useOpenGL () const

bool	validateUnits () const

virtual	~CConfigurationFile ()

Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)

void	addParameter (CCopasiParameter *pParameter)

bool	addParameter (const CCopasiParameter &parameter)

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 ()

Private Member Functions
void	initializeParameter ()

Private Attributes
std::string *	mpApplicationFont

CCheckForUpdates *	mpCheckForUpdates

std::string *	mpCurrentAuthorEmail

std::string *	mpCurrentAuthorFamilyName

std::string *	mpCurrentAuthorGivenName

std::string *	mpCurrentAuthorOrganization

bool *	mpDisableJIT

CCopasiParameterGroup *	mpDisplayIssueKinds

CCopasiParameterGroup *	mpDisplayIssueSeverity

bool *	mpDisplayPopulations

bool *	mpEnableAdditionalOptimizationParameters

bool *	mpNormalizePerExperiment

C_INT32 *	mpPrecision

std::string *	mpProxyPass

C_INT32 *	mpProxyPort

std::string *	mpProxyServer

std::string *	mpProxyUser

CRecentFiles *	mpRecentFiles

CMIRIAMResources *	mpRecentMIRIAMResources

CRecentFiles *	mpRecentSBMLFiles

CRecentFiles *	mpRecentSEDMLFiles

bool *	mpResizeToContents

bool *	mpUseAdvancedEditing

bool *	mpUseAdvancedSliders

bool *	mpUseOpenGL

bool *	mpValidateUnits

std::string *	mpWorkingDirectory

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 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 *)

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

Constructor & Destructor Documentation

◆ CConfigurationFile() [1/2]

CConfigurationFile::CConfigurationFile	(	const std::string &	name = `"Configuration"`,
		const CDataContainer *	pParent = `NO_PARENT`
	)

Default constructor

Parameters

const	std::string & name (default: Configuration)
const	CDataContainer * pParent (default: NULL)

References initializeParameter().

◆ CConfigurationFile() [2/2]

CConfigurationFile::CConfigurationFile	(	const CConfigurationFile &	src,
		const CDataContainer *	pParent
	)

Copy constructor

Parameters

const	CConfigurationFile & src
const	CDataContainer * pParent (default: NULL)

References initializeParameter().

◆ ~CConfigurationFile()

CConfigurationFile::~CConfigurationFile ( )

virtual

Destructor

Member Function Documentation

◆ displayPopulations()

bool CConfigurationFile::displayPopulations ( ) const

Returns: a flag on whether populations should be displayed during optimization / parameter estimation

References mpDisplayPopulations.

◆ elevateChildren()

bool CConfigurationFile::elevateChildren ( )

virtual

This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.

Returns: bool success

Reimplemented from CCopasiParameterGroup.

References CCopasiParameterGroup::getGroup(), mpCheckForUpdates, mpRecentFiles, mpRecentMIRIAMResources, mpRecentSBMLFiles, mpRecentSEDMLFiles, and CMIRIAMResourceObject::setMIRIAMResources().

Referenced by initializeParameter().

◆ enableAdditionalOptimizationParameters()

bool CConfigurationFile::enableAdditionalOptimizationParameters ( ) const

Returns: a flag on whether to enable additional parameters in optimization methods

References mpEnableAdditionalOptimizationParameters.

Referenced by setEnableAdditionalOptimizationParameters().

◆ getApplicationFont()

const std::string CConfigurationFile::getApplicationFont ( ) const

Retrieve the application font.

Returns: const std::string & applicationFont

References mpApplicationFont.

◆ getCheckForUpdates()

CCheckForUpdates & CConfigurationFile::getCheckForUpdates ( )

Returns: auto update settings

References mpCheckForUpdates.

◆ getCurrentAuthorEmail()

const std::string & CConfigurationFile::getCurrentAuthorEmail ( ) const

Retrieve the Current Author Email

Returns: const std::string & CurrentAuthorEmail

References mpCurrentAuthorEmail.

Referenced by CMIRIAMInfo::addDefaultCreator().

◆ getCurrentAuthorFamilyName()

const std::string & CConfigurationFile::getCurrentAuthorFamilyName ( ) const

Retrieve the Current Author Familyname

Returns: const std::string & CurrentAuthorFamilyName

References mpCurrentAuthorFamilyName.

Referenced by CMIRIAMInfo::addDefaultCreator().

◆ getCurrentAuthorGivenName()

const std::string & CConfigurationFile::getCurrentAuthorGivenName ( ) const

Retrieve the Current Author GivenName

Returns: const std::string & CurrentAuthorGivenName

References mpCurrentAuthorGivenName.

Referenced by CMIRIAMInfo::addDefaultCreator().

◆ getCurrentAuthorOrganization()

const std::string & CConfigurationFile::getCurrentAuthorOrganization ( ) const

Retrieve the Current Author Organization

Returns: const std::string & CurrentAuthorOrganization

References mpCurrentAuthorOrganization.

Referenced by CMIRIAMInfo::addDefaultCreator().

◆ getDisableJIT()

bool CConfigurationFile::getDisableJIT ( ) const

Return whether JIT is disabled

Returns: bool disbaleJIT

References mpDisableJIT.

Referenced by CJitCompiler::JitEnabled().

◆ getDoublePrecision()

C_INT32 CConfigurationFile::getDoublePrecision ( ) const

Returns: the double precision to be used when converting to string

References mpPrecision.

◆ getProxyPassword()

const std::string CConfigurationFile::getProxyPassword ( ) const

Retrieve the proxy user password

References mpProxyPass.

◆ getProxyPort()

C_INT32 CConfigurationFile::getProxyPort ( ) const

Retrieve the proxy port

References mpProxyPort.

◆ getProxyServer()

const std::string CConfigurationFile::getProxyServer ( ) const

Retrieve the proxy server

References mpProxyServer.

◆ getProxyUser()

const std::string CConfigurationFile::getProxyUser ( ) const

Retrieve the proxy user name

References mpProxyUser.

◆ getRecentFiles()

CRecentFiles & CConfigurationFile::getRecentFiles ( )

Retrieve the list of recent files

Returns: CRecentFiles & recentFiles

References mpRecentFiles.

◆ getRecentMIRIAMResources()

CMIRIAMResources & CConfigurationFile::getRecentMIRIAMResources ( )

Retrieve the list of recent MIRIAM Resources

Returns: CMIRIAMResources & recentMIRIAMResources

References mpRecentMIRIAMResources.

Referenced by CMIRIAMResources::isCitation().

◆ getRecentSBMLFiles()

CRecentFiles & CConfigurationFile::getRecentSBMLFiles ( )

Retrieve the list of recent SBML files

Returns: CRecentFiles & recentSBMLFiles

References mpRecentSBMLFiles.

◆ getRecentSEDMLFiles()

CRecentFiles & CConfigurationFile::getRecentSEDMLFiles ( )

Retrieve the list of recent SEDML files

Returns: CRecentFiles & recentSEDMLFiles

References mpRecentSEDMLFiles.

◆ getWorkingDirectory()

const std::string CConfigurationFile::getWorkingDirectory ( ) const

Retrieve the working directory

Returns: const std::string & workingDirectory

References mpWorkingDirectory.

◆ initializeParameter()

void CConfigurationFile::initializeParameter ( )

private

Allocates all group parameters and assures that they are properly initialized.

References CIssue::__SIZE, CCopasiParameterGroup::assertGroup(), CCopasiParameterGroup::assertParameter(), CCopasiParameter::basic, CCopasiParameterGroup::beginIndex(), CCopasiParameter::BOOL, CCopasiParameter::editable, elevateChildren(), CCopasiParameterGroup::endIndex(), CCopasiParameterGroup::getParameter(), CCopasiParameter::getUserInterfaceFlag(), CCopasiParameter::getValue(), CCopasiParameter::INT, CIssue::kindNames, mpApplicationFont, mpCurrentAuthorEmail, mpCurrentAuthorFamilyName, mpCurrentAuthorGivenName, mpCurrentAuthorOrganization, mpDisableJIT, mpDisplayIssueKinds, mpDisplayIssueSeverity, mpDisplayPopulations, mpEnableAdditionalOptimizationParameters, mpNormalizePerExperiment, mpPrecision, mpProxyPass, mpProxyPort, mpProxyServer, mpProxyUser, mpResizeToContents, mpUseAdvancedEditing, mpUseAdvancedSliders, mpUseOpenGL, mpValidateUnits, mpWorkingDirectory, CCopasiParameterGroup::removeParameter(), CCopasiParameter::setUserInterfaceFlag(), CIssue::severityNames, CCopasiParameter::STRING, and toEnum().

Referenced by CConfigurationFile(), load(), and operator=().

◆ load()

bool CConfigurationFile::load ( )

virtual

Load the configuration file.

Returns: bool success

References CConfigurationFile::CXML::getConfiguration(), CCopasiParameterGroup::getGroup(), CMIRIAMResources::getResourceList(), COptions::getValue(), initializeParameter(), CMIRIAMResources::initializeParameter(), mpRecentMIRIAMResources, CDirEntry::Separator, and CCopasiParameterGroup::size().

Referenced by CRootContainer::initializeChildren().

◆ normalizePerExperiment()

bool CConfigurationFile::normalizePerExperiment ( ) const

Returns: a flag on whether weights in Parameter Estimation should be normalized per experiment

References mpNormalizePerExperiment.

◆ operator=() [1/2]

const CConfigurationFile & CConfigurationFile::operator= ( const CConfigurationFile & rhs )

References operator=().

◆ operator=() [2/2]

const CConfigurationFile & CConfigurationFile::operator= ( const CCopasiParameterGroup & rhs )

Assignment operator

Parameters

const CCopasiParameterGroup & rhs

Returns: const CConfigurationFile & self

References initializeParameter(), and CCopasiParameterGroup::operator=().

Referenced by operator=().

◆ resizeToContents()

bool CConfigurationFile::resizeToContents ( ) const

Returns: a flag on whether the GUI should resize tables to contents

References mpResizeToContents.

◆ save()

bool CConfigurationFile::save ( )

virtual

Save the configuration file.

Returns: bool success

References CDirEntry::dirName(), COptions::getValue(), and CConfigurationFile::CXML::setConfiguration().

Referenced by CRootContainer::~CRootContainer().

◆ setApplicationFont()

void CConfigurationFile::setApplicationFont ( const std::string & applicationFont )

Set the applications font.

Parameters

const std::string & applicationFont

References mpApplicationFont.

◆ setCurrentAuthorEmail()

void CConfigurationFile::setCurrentAuthorEmail ( const std::string & CurrentAuthorEmail )

Set the Current Author Email.

Parameters

const std::string & CurrentAuthorEmail

References mpCurrentAuthorEmail.

◆ setCurrentAuthorFamilyName()

void CConfigurationFile::setCurrentAuthorFamilyName ( const std::string & CurrentAuthorFamilyName )

Set the Current Author Familyname.

Parameters

const std::string & CurrentAuthorFamilyName

References mpCurrentAuthorFamilyName.

◆ setCurrentAuthorGivenName()

void CConfigurationFile::setCurrentAuthorGivenName ( const std::string & CurrentAuthorGivenName )

Set the Current Author Given Name.

Parameters

const std::string & CurrentAuthorGivenName

References mpCurrentAuthorGivenName.

◆ setCurrentAuthorOrganization()

void CConfigurationFile::setCurrentAuthorOrganization ( const std::string & CurrentAuthorOrganization )

Set the Current Author Organization.

Parameters

const std::string & CurrentAuthorOrganization

References mpCurrentAuthorOrganization.

◆ setDisableJIT()

void CConfigurationFile::setDisableJIT ( bool disableJIT )

Sets the whether JIT compilation is diable

Parameters

bool	disableJIT

References mpDisableJIT.

◆ setDisplayPopulations()

void CConfigurationFile::setDisplayPopulations ( bool flag )

Set whether weights in Parameter Estimation should be normalized per experiment

References mpDisplayPopulations.

◆ setDoublePrecision()

void CConfigurationFile::setDoublePrecision ( C_INT32 precision )

sets the double precision to be used when converting numbers to string

References mpPrecision.

◆ setEnableAdditionalOptimizationParameters()

void CConfigurationFile::setEnableAdditionalOptimizationParameters ( bool enableAdditionalOptimizationParameters )

Set whether to enable additional parameters in optimization methods

References enableAdditionalOptimizationParameters(), and mpEnableAdditionalOptimizationParameters.

◆ setNormalizePerExperiment()

void CConfigurationFile::setNormalizePerExperiment ( bool flag )

Set whether weights in Parameter Estimation should be normalized per experiment

References mpNormalizePerExperiment.

◆ setProxyPassword()

void CConfigurationFile::setProxyPassword ( const std::string & proxyPassword )

Set the proxy user password.

Parameters

proxyPassword the proxy password

References mpProxyPass.

◆ setProxyPort()

void CConfigurationFile::setProxyPort ( C_INT32 proxyPort )

Set the proxy port.

Parameters

proxyPort the proxy port

References mpProxyPort.

◆ setProxyServer()

void CConfigurationFile::setProxyServer ( const std::string & proxyServer )

Set the proxy server.

Parameters

proxyServer the proxy server

References mpProxyServer.

◆ setProxyUser()

void CConfigurationFile::setProxyUser ( const std::string & proxyUser )

Set the proxy user name.

Parameters

proxyUser the proxy username

References mpProxyUser.

◆ setRecentMIRIAMResources()

void CConfigurationFile::setRecentMIRIAMResources ( const CMIRIAMResources & miriamResources )

References mpRecentMIRIAMResources.

◆ setResizeToContents()

void CConfigurationFile::setResizeToContents ( bool flag )

Set whether the GUI should resize tables to contents

References mpResizeToContents.

◆ setUseAdvancedEditing()

void CConfigurationFile::setUseAdvancedEditing ( bool useAdvancedEditing )

Set whether the advanced expression editing (i.e manually entering copasiobjects) is to be used (true), or not

References mpUseAdvancedEditing, and useAdvancedEditing().

◆ setUseAdvancedSliders()

void CConfigurationFile::setUseAdvancedSliders ( bool useAdvancedSliders )

Set whether the sliders should react to keyboard input / mouse interaction.

References mpUseAdvancedSliders, and useAdvancedSliders().

◆ setUseOpenGL()

void CConfigurationFile::setUseOpenGL ( bool useOpenGL )

Set whether the openGL based rendering is to be used (true), or the Qt based one.

References mpUseOpenGL, and useOpenGL().

◆ setValidateUnits()

void CConfigurationFile::setValidateUnits ( bool validateUnits )

Set whether unit validation should always be performed or not.

Parameters

bool	validateUnits

References mpValidateUnits, and validateUnits().

◆ setWorkingDirectory()

void CConfigurationFile::setWorkingDirectory ( const std::string & workingDirectory )

Set the working directory.

Parameters

const std::string & workingDirectory

References mpWorkingDirectory.

◆ showItemIssues()

bool CConfigurationFile::showItemIssues ( CIssue::eKind kind ) const

Show item issues

Returns: a flag indicating whether an icon and tooltip should be displayed for items.

References CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), and mpDisplayIssueKinds.

◆ useAdvancedEditing()

bool CConfigurationFile::useAdvancedEditing ( ) const

Returns: a flag on whether to use the advanced expression editing (i.e manually entering copasiobjects)

References mpUseAdvancedEditing.

Referenced by setUseAdvancedEditing().

◆ useAdvancedSliders()

bool CConfigurationFile::useAdvancedSliders ( ) const

Returns: a flag on whether the sliders should react to keyboard input / mouse interaction.

References mpUseAdvancedSliders.

Referenced by setUseAdvancedSliders().

◆ useOpenGL()

bool CConfigurationFile::useOpenGL ( ) const

Returns: a flag on whether to use the open GL based rendering, or the Qt based one

References mpUseOpenGL.

Referenced by setUseOpenGL().

◆ validateUnits()

bool CConfigurationFile::validateUnits ( ) const

Always perform unit validation

Returns: a flag indicating whether unit validation should always be performed

References mpValidateUnits.

Referenced by setValidateUnits().

Member Data Documentation

◆ mpApplicationFont

std::string* CConfigurationFile::mpApplicationFont

private

A pointer to the application font

Referenced by getApplicationFont(), initializeParameter(), and setApplicationFont().

◆ mpCheckForUpdates

CCheckForUpdates* CConfigurationFile::mpCheckForUpdates

private

A pointer to the update check configuration

Referenced by elevateChildren(), and getCheckForUpdates().

◆ mpCurrentAuthorEmail

std::string* CConfigurationFile::mpCurrentAuthorEmail

private

A pointer to the Email of the current author.

Referenced by getCurrentAuthorEmail(), initializeParameter(), and setCurrentAuthorEmail().

◆ mpCurrentAuthorFamilyName

std::string* CConfigurationFile::mpCurrentAuthorFamilyName

private

A pointer to the Familyname of the current author.

Referenced by getCurrentAuthorFamilyName(), initializeParameter(), and setCurrentAuthorFamilyName().

◆ mpCurrentAuthorGivenName

std::string* CConfigurationFile::mpCurrentAuthorGivenName

private

A pointer to the Given name of the current author.

Referenced by getCurrentAuthorGivenName(), initializeParameter(), and setCurrentAuthorGivenName().

◆ mpCurrentAuthorOrganization

std::string* CConfigurationFile::mpCurrentAuthorOrganization

private

A pointer to the Organization of the current author.

Referenced by getCurrentAuthorOrganization(), initializeParameter(), and setCurrentAuthorOrganization().

◆ mpDisableJIT

bool* CConfigurationFile::mpDisableJIT

private

A pointer indicating whether to disable JIT compilation even if it is available

Referenced by getDisableJIT(), initializeParameter(), and setDisableJIT().

◆ mpDisplayIssueKinds

CCopasiParameterGroup* CConfigurationFile::mpDisplayIssueKinds

private

A pointer to a group indicating which kinds of issues should be displayed.

Referenced by initializeParameter(), and showItemIssues().

◆ mpDisplayIssueSeverity

CCopasiParameterGroup* CConfigurationFile::mpDisplayIssueSeverity

private

A pointer indicating the severity level of issues to be displayed.

Referenced by initializeParameter().

◆ mpDisplayPopulations

bool* CConfigurationFile::mpDisplayPopulations

private

A pointer indicating whether to display the population visualization window

Referenced by displayPopulations(), initializeParameter(), and setDisplayPopulations().

◆ mpEnableAdditionalOptimizationParameters

bool* CConfigurationFile::mpEnableAdditionalOptimizationParameters

private

A pointer to a flag indicating whether to enable additional parameters in optimization methods

Referenced by enableAdditionalOptimizationParameters(), initializeParameter(), and setEnableAdditionalOptimizationParameters().

◆ mpNormalizePerExperiment

bool* CConfigurationFile::mpNormalizePerExperiment

private

A pointer indicating whether to experiments should be normalized by default

Referenced by initializeParameter(), normalizePerExperiment(), and setNormalizePerExperiment().

◆ mpPrecision

C_INT32* CConfigurationFile::mpPrecision

private

a pointer to the double precision requested when converting numbers to string

Referenced by getDoublePrecision(), initializeParameter(), and setDoublePrecision().

◆ mpProxyPass

std::string* CConfigurationFile::mpProxyPass

private

A pointer to the proxy password.

Referenced by getProxyPassword(), initializeParameter(), and setProxyPassword().

◆ mpProxyPort

C_INT32* CConfigurationFile::mpProxyPort

private

A pointer to the proxy port.

Referenced by getProxyPort(), initializeParameter(), and setProxyPort().

◆ mpProxyServer

std::string* CConfigurationFile::mpProxyServer

private

A pointer to the proxy server.

Referenced by getProxyServer(), initializeParameter(), and setProxyServer().

◆ mpProxyUser

std::string* CConfigurationFile::mpProxyUser

private

A pointer to the proxy user name.

Referenced by getProxyUser(), initializeParameter(), and setProxyUser().

◆ mpRecentFiles

CRecentFiles* CConfigurationFile::mpRecentFiles

private

A pointer to the list of recent files

Referenced by elevateChildren(), and getRecentFiles().

◆ mpRecentMIRIAMResources

CMIRIAMResources* CConfigurationFile::mpRecentMIRIAMResources

private

A pointer to the list of MIRIAM Resources

Referenced by elevateChildren(), getRecentMIRIAMResources(), load(), and setRecentMIRIAMResources().

◆ mpRecentSBMLFiles

CRecentFiles* CConfigurationFile::mpRecentSBMLFiles

private

A pointer to the list of recent files

Referenced by elevateChildren(), and getRecentSBMLFiles().

◆ mpRecentSEDMLFiles

CRecentFiles* CConfigurationFile::mpRecentSEDMLFiles

private

A pointer to the list of recent files

Referenced by elevateChildren(), and getRecentSEDMLFiles().

◆ mpResizeToContents

bool* CConfigurationFile::mpResizeToContents

private

A pointer indicating whether the GUI should resize tables to contents

Referenced by initializeParameter(), resizeToContents(), and setResizeToContents().

◆ mpUseAdvancedEditing

bool* CConfigurationFile::mpUseAdvancedEditing

private

A pointer indicating whether to use the advanced editing

Referenced by initializeParameter(), setUseAdvancedEditing(), and useAdvancedEditing().

◆ mpUseAdvancedSliders

bool* CConfigurationFile::mpUseAdvancedSliders

private

A pointer indicating whether the sliders should react to keyboard input / mouse interaction.

Referenced by initializeParameter(), setUseAdvancedSliders(), and useAdvancedSliders().

◆ mpUseOpenGL

bool* CConfigurationFile::mpUseOpenGL

private

A pointer indicating whether to use the OpenGL rendering, or the Qt based one

Referenced by initializeParameter(), setUseOpenGL(), and useOpenGL().

◆ mpValidateUnits

bool* CConfigurationFile::mpValidateUnits

private

A pointer indicating whether units will always be validated

Referenced by initializeParameter(), setValidateUnits(), and validateUnits().

◆ mpWorkingDirectory

std::string* CConfigurationFile::mpWorkingDirectory

private

A pointer to the last used working directory of the GUI.

Referenced by getWorkingDirectory(), initializeParameter(), and setWorkingDirectory().

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

Classes

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ CConfigurationFile() [1/2]

◆ CConfigurationFile() [2/2]

◆ ~CConfigurationFile()

Member Function Documentation

◆ displayPopulations()

◆ elevateChildren()

◆ enableAdditionalOptimizationParameters()

◆ getApplicationFont()

◆ getCheckForUpdates()

◆ getCurrentAuthorEmail()

◆ getCurrentAuthorFamilyName()

◆ getCurrentAuthorGivenName()

◆ getCurrentAuthorOrganization()

◆ getDisableJIT()

◆ getDoublePrecision()

◆ getProxyPassword()

◆ getProxyPort()

◆ getProxyServer()

◆ getProxyUser()

◆ getRecentFiles()

◆ getRecentMIRIAMResources()

◆ getRecentSBMLFiles()

◆ getRecentSEDMLFiles()

◆ getWorkingDirectory()

◆ initializeParameter()

◆ load()

◆ normalizePerExperiment()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ resizeToContents()

◆ save()

◆ setApplicationFont()

◆ setCurrentAuthorEmail()

◆ setCurrentAuthorFamilyName()

◆ setCurrentAuthorGivenName()

◆ setCurrentAuthorOrganization()

◆ setDisableJIT()

◆ setDisplayPopulations()

◆ setDoublePrecision()

◆ setEnableAdditionalOptimizationParameters()

◆ setNormalizePerExperiment()

◆ setProxyPassword()

◆ setProxyPort()

◆ setProxyServer()

◆ setProxyUser()

◆ setRecentMIRIAMResources()

◆ setResizeToContents()

◆ setUseAdvancedEditing()

◆ setUseAdvancedSliders()

◆ setUseOpenGL()

◆ setValidateUnits()

◆ setWorkingDirectory()

◆ showItemIssues()

◆ useAdvancedEditing()

◆ useAdvancedSliders()

◆ useOpenGL()

◆ validateUnits()

Member Data Documentation

◆ mpApplicationFont

◆ mpCheckForUpdates

◆ mpCurrentAuthorEmail

◆ mpCurrentAuthorFamilyName

◆ mpCurrentAuthorGivenName

◆ mpCurrentAuthorOrganization

◆ mpDisableJIT

◆ mpDisplayIssueKinds

◆ mpDisplayIssueSeverity

◆ mpDisplayPopulations

◆ mpEnableAdditionalOptimizationParameters

◆ mpNormalizePerExperiment

◆ mpPrecision

◆ mpProxyPass

◆ mpProxyPort

◆ mpProxyServer