COPASI API
4.16.103
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#include <CConfigurationFile.h>
Classes | |
class | CXML |
Public Member Functions | |
CConfigurationFile (const std::string &name="Configuration", const CCopasiContainer *pParent=NULL) | |
CConfigurationFile (const CConfigurationFile &src, const CCopasiContainer *pParent=NULL) | |
CConfigurationFile (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL) | |
virtual bool | elevateChildren () |
const std::string | getApplicationFont () const |
CRecentFiles & | getRecentFiles () |
CMIRIAMResources & | getRecentMIRIAMResources () |
CRecentFiles & | getRecentSBMLFiles () |
CRecentFiles & | getRecentSEDMLFiles () |
const std::string | getWorkingDirectory () const |
virtual bool | load () |
bool | normalizePerExperiment () const |
virtual bool | save () |
void | setApplicationFont (const std::string &applicationFont) |
void | setNormalizePerExperiment (bool flag) |
void | setRecentMIRIAMResources (const CMIRIAMResources &miriamResources) |
void | setUseAdvancedEditing (bool useAdvancedEditing) |
void | setUseAdvancedSliders (bool useAdvancedSliders) |
void | setUseOpenGL (bool useOpenGL) |
void | setValidateUnits (bool validateUnits) |
void | setWorkingDirectory (const std::string &workingDirectory) |
bool | useAdvancedEditing () const |
bool | useAdvancedSliders () const |
bool | useOpenGL () const |
bool | validateUnits () const |
virtual | ~CConfigurationFile () |
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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 | initializeParameter () |
Private Attributes | |
std::string * | mpApplicationFont |
bool * | mpNormalizePerExperiment |
CRecentFiles * | mpRecentFiles |
CMIRIAMResources * | mpRecentMIRIAMResources |
CRecentFiles * | mpRecentSBMLFiles |
CRecentFiles * | mpRecentSEDMLFiles |
bool * | mpUseAdvancedEditing |
bool * | mpUseAdvancedSliders |
bool * | mpUseOpenGL |
bool * | mpValidateUnits |
std::string * | mpWorkingDirectory |
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 83 of file CConfigurationFile.h.
CConfigurationFile::CConfigurationFile | ( | const std::string & | name = "Configuration" , |
const CCopasiContainer * | pParent = NULL |
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Default constructor
const | std::string & name (default: Configuration) |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 102 of file CConfigurationFile.cpp.
References initializeParameter().
CConfigurationFile::CConfigurationFile | ( | const CConfigurationFile & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CConfigurationFile & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 118 of file CConfigurationFile.cpp.
References initializeParameter().
CConfigurationFile::CConfigurationFile | ( | const CCopasiParameterGroup & | group, |
const CCopasiContainer * | pParent = NULL |
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Specific constructor
const | CCopasiParameterGroup & group |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 134 of file CConfigurationFile.cpp.
References initializeParameter().
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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 153 of file CConfigurationFile.cpp.
References CCopasiParameterGroup::getGroup(), mpRecentFiles, mpRecentMIRIAMResources, mpRecentSBMLFiles, mpRecentSEDMLFiles, and CMIRIAMResourceObject::setMIRIAMResources().
Referenced by initializeParameter().
const std::string CConfigurationFile::getApplicationFont | ( | ) | const |
Retrieve the application font.
Definition at line 273 of file CConfigurationFile.cpp.
References mpApplicationFont.
Referenced by CopasiUI3Window::setApplicationFont().
CRecentFiles & CConfigurationFile::getRecentFiles | ( | ) |
Retrieve the list of recent files
Definition at line 257 of file CConfigurationFile.cpp.
References mpRecentFiles.
Referenced by CQPreferenceDialog::init(), DataModelGUI::loadModelFinished(), CopasiUI3Window::refreshRecentFileMenu(), DataModelGUI::saveModelFinished(), CQPreferenceDialog::slotBtnOk(), and CopasiUI3Window::slotOpenRecentFile().
CMIRIAMResources & CConfigurationFile::getRecentMIRIAMResources | ( | ) |
Retrieve the list of recent MIRIAM Resources
Definition at line 267 of file CConfigurationFile.cpp.
References mpRecentMIRIAMResources.
Referenced by CQMiriamWidget::updateResourcesList().
CRecentFiles & CConfigurationFile::getRecentSBMLFiles | ( | ) |
Retrieve the list of recent SBML files
Definition at line 260 of file CConfigurationFile.cpp.
References mpRecentSBMLFiles.
Referenced by DataModelGUI::exportSBMLFinished(), DataModelGUI::importSBMLFinished(), CQPreferenceDialog::init(), CopasiUI3Window::refreshRecentSBMLFileMenu(), CQPreferenceDialog::slotBtnOk(), and CopasiUI3Window::slotOpenRecentSBMLFile().
CRecentFiles & CConfigurationFile::getRecentSEDMLFiles | ( | ) |
Retrieve the list of recent SEDML files
Definition at line 264 of file CConfigurationFile.cpp.
References mpRecentSEDMLFiles.
const std::string CConfigurationFile::getWorkingDirectory | ( | ) | const |
Retrieve the web working directory
Definition at line 328 of file CConfigurationFile.cpp.
References mpWorkingDirectory.
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Allocates all group parameters and assures that they are properly initialized.
Definition at line 181 of file CConfigurationFile.cpp.
References CCopasiParameterGroup::assertGroup(), CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, elevateChildren(), CCopasiParameter::getValue(), mpApplicationFont, mpNormalizePerExperiment, mpUseAdvancedEditing, mpUseAdvancedSliders, mpUseOpenGL, mpValidateUnits, mpWorkingDirectory, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pSTRING, and CCopasiParameter::STRING.
Referenced by CConfigurationFile(), and load().
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Load the configuration file.
Definition at line 216 of file CConfigurationFile.cpp.
References CConfigurationFile::CXML::getConfiguration(), CCopasiParameterGroup::getGroup(), CMIRIAMResources::getResourceList(), COptions::getValue(), initializeParameter(), CMIRIAMResources::initializeParameter(), mpRecentMIRIAMResources, CDirEntry::Separator, and CCopasiParameterGroup::size().
bool CConfigurationFile::normalizePerExperiment | ( | ) | const |
Definition at line 313 of file CConfigurationFile.cpp.
References mpNormalizePerExperiment.
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Save the configuration file.
Definition at line 202 of file CConfigurationFile.cpp.
References COptions::getValue(), and CConfigurationFile::CXML::setConfiguration().
Referenced by CopasiUI3Window::slotUpdateMIRIAMFinished(), and CCopasiRootContainer::~CCopasiRootContainer().
void CConfigurationFile::setApplicationFont | ( | const std::string & | applicationFont | ) |
Set the applications font.
const | std::string & applicationFont |
Definition at line 278 of file CConfigurationFile.cpp.
References mpApplicationFont.
Referenced by CopasiUI3Window::setApplicationFont(), and CopasiUI3Window::slotFontSelection().
void CConfigurationFile::setNormalizePerExperiment | ( | bool | flag | ) |
Set whether weights in Parameter Estimation should be normalized per experiment
Definition at line 318 of file CConfigurationFile.cpp.
References mpNormalizePerExperiment.
void CConfigurationFile::setRecentMIRIAMResources | ( | const CMIRIAMResources & | miriamResources | ) |
Definition at line 270 of file CConfigurationFile.cpp.
References mpRecentMIRIAMResources.
void CConfigurationFile::setUseAdvancedEditing | ( | bool | useAdvancedEditing | ) |
Set whether the advanced expression editing (i.e manually entering copasiobjects) is to be used (true), or not
Definition at line 308 of file CConfigurationFile.cpp.
References mpUseAdvancedEditing, and useAdvancedEditing().
void CConfigurationFile::setUseAdvancedSliders | ( | bool | useAdvancedSliders | ) |
Set whether the sliders should react to keyboard input / mouse interaction.
Definition at line 298 of file CConfigurationFile.cpp.
References mpUseAdvancedSliders, and useAdvancedSliders().
void CConfigurationFile::setUseOpenGL | ( | bool | useOpenGL | ) |
Set whether the openGL based rendering is to be used (true), or the Qt based one.
Definition at line 288 of file CConfigurationFile.cpp.
References mpUseOpenGL, and useOpenGL().
void CConfigurationFile::setValidateUnits | ( | bool | validateUnits | ) |
Set whether unit validation should always be performed or not.
bool | validateUnits |
Definition at line 338 of file CConfigurationFile.cpp.
References mpValidateUnits, and validateUnits().
void CConfigurationFile::setWorkingDirectory | ( | const std::string & | workingDirectory | ) |
Set the working directory.
const | std::string & workingDirectory |
Definition at line 333 of file CConfigurationFile.cpp.
References mpWorkingDirectory.
Referenced by CopasiFileDialog::getOpenFileName(), CopasiFileDialog::getSaveFileName(), and CopasiFileDialog::openExampleDir().
bool CConfigurationFile::useAdvancedEditing | ( | ) | const |
Definition at line 303 of file CConfigurationFile.cpp.
References mpUseAdvancedEditing.
Referenced by CQExpressionWidget::getExpression(), CQExpressionWidget::keyPressEvent(), and setUseAdvancedEditing().
bool CConfigurationFile::useAdvancedSliders | ( | ) | const |
Definition at line 293 of file CConfigurationFile.cpp.
References mpUseAdvancedSliders.
Referenced by setUseAdvancedSliders(), and SliderDialog::sliderValueChanged().
bool CConfigurationFile::useOpenGL | ( | ) | const |
Definition at line 283 of file CConfigurationFile.cpp.
References mpUseOpenGL.
Referenced by setUseOpenGL().
bool CConfigurationFile::validateUnits | ( | ) | const |
Always perform unit validation
Definition at line 323 of file CConfigurationFile.cpp.
References mpValidateUnits.
Referenced by setValidateUnits().
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A pointer to the application font
Definition at line 329 of file CConfigurationFile.h.
Referenced by getApplicationFont(), initializeParameter(), and setApplicationFont().
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A pointer indicating whether to experiments should be normalized by default
Definition at line 355 of file CConfigurationFile.h.
Referenced by initializeParameter(), normalizePerExperiment(), and setNormalizePerExperiment().
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A pointer to the list of recent files
Definition at line 308 of file CConfigurationFile.h.
Referenced by elevateChildren(), and getRecentFiles().
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A pointer to the list of MIRIAM Resources
Definition at line 324 of file CConfigurationFile.h.
Referenced by elevateChildren(), getRecentMIRIAMResources(), load(), and setRecentMIRIAMResources().
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A pointer to the list of recent files
Definition at line 313 of file CConfigurationFile.h.
Referenced by elevateChildren(), and getRecentSBMLFiles().
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A pointer to the list of recent files
Definition at line 319 of file CConfigurationFile.h.
Referenced by elevateChildren(), and getRecentSEDMLFiles().
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A pointer indicating whether to use the advanced editing
Definition at line 350 of file CConfigurationFile.h.
Referenced by initializeParameter(), setUseAdvancedEditing(), and useAdvancedEditing().
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A pointer indicating whether the sliders should react to keyboard input / mouse interaction.
Definition at line 345 of file CConfigurationFile.h.
Referenced by initializeParameter(), setUseAdvancedSliders(), and useAdvancedSliders().
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A pointer indicating whether to use the OpenGL rendering, or the Qt based one
Definition at line 339 of file CConfigurationFile.h.
Referenced by initializeParameter(), setUseOpenGL(), and useOpenGL().
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A pointer indicating whether units will always be validated
Definition at line 334 of file CConfigurationFile.h.
Referenced by initializeParameter(), setValidateUnits(), and validateUnits().
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A pointer to the last used working directory of the GUI.
Definition at line 360 of file CConfigurationFile.h.
Referenced by getWorkingDirectory(), initializeParameter(), and setWorkingDirectory().