COPASI API  4.40.278
Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | List of all members
CXMLParserData Class Reference

#include <CXMLParserData.h>

Public Types

typedef CLRenderInformationBase *(* CreateRenderInformation) (CXMLParserData *pData)
 

Public Member Functions

 CXMLParserData ()
 

Static Public Member Functions

static CLRenderInformationBase * createRenderInformation (CXMLParserData *pData)
 

Public Attributes

std::string CharacterData
 
std::string FunctionDescription
 
bool LocalRenderInformation
 
std::vector< std::pair< std::string, std::string > > mAssignments
 
std::map< size_t, std::string > mFunctionParameterKeyMap
 
std::map< std::string, CExpression * > mKey2ObjectiveFunction
 
CKeyFactory mKeyMap
 
std::stack< CModelParameterGroup * > ModelParameterGroupStack
 
CExpression * mpExpression
 
bool mPredefinedFunction
 
CAnnotation::UnsupportedAnnotation mUnsupportedAnnotations
 
CLBoundingBox * pBoundingBox
 
CLCompartmentGlyph * pCompartmentGlyph
 
CPlotDataChannelSpec * pCurrentChannelSpec
 
CLayout * pCurrentLayout
 
CModelParameter * pCurrentModelParameter
 
CCopasiParameter * pCurrentParameter
 
CPlotSpecification * pCurrentPlot
 
CPlotItem * pCurrentPlotItem
 
CCopasiTask * pCurrentTask
 
CUnitDefinition * pCurrentUnitDefinition
 
CLCurve * pCurve
 
CDataModel * pDataModel
 
CLDimensions * pDimensions
 
CLEllipse * pEllipse
 
CEvent * pEvent
 
CEventAssignment * pEventAssignment
 
CFunction * pFunction
 
CDataVectorN< CFunction > * pFunctionList
 
CFunctionParameter * pFunctionVariable
 
CLGeneralGlyph * pGeneralGlyph
 
CLGradientBase * pGradient
 
CLGroup * pGroup
 
SCopasiXMLGUI * pGUI
 
CLImage * pImage
 
CListOfLayouts * pLayoutList
 
CLLineEnding * pLineEnding
 
CLLineSegment * pLineSegment
 
std::vector< CLRenderPoint * > * pListOfCurveElements
 
CLMetabGlyph * pMetaboliteGlyph
 
CLMetabReferenceGlyph * pMetaboliteReferenceGlyph
 
CModel * pModel
 
COutputDefinitionVector * pPlotList
 
CLPolygon * pPolygon
 
CLPoint * pPosition
 
CReaction * pReaction
 
CLReactionGlyph * pReactionGlyph
 
CLRectangle * pRectangle
 
CLRenderCurve * pRenderCurve
 
CLRenderInformationBase * pRenderInformation
 
CReportDefinition * pReport
 
CReportDefinitionVector * pReportList
 
CLStyle * pStyle
 
CDataVectorN< CCopasiTask > * pTaskList
 
CLText * pText
 
CLTextGlyph * pTextGlyph
 
CUnitDefinitionDB * pUnitDefinitionImportList
 
CVersion * pVersion
 
std::map< std::string, std::vector< std::pair< std::vector< CRegisteredCommonName > *, size_t > > > reportReferenceMap
 
std::map< std::string, std::vector< const CDataObject * > > SourceParameterObjects
 
std::vector< CModelEntity * > StateVariableList
 
std::map< std::string, std::vector< CCopasiTask * > > taskReferenceMap
 
std::vector< std::string > UnmappedKeyParameters
 

Member Typedef Documentation

◆ CreateRenderInformation

typedef CLRenderInformationBase*(* CXMLParserData::CreateRenderInformation) (CXMLParserData *pData)

Constructor & Destructor Documentation

◆ CXMLParserData()

CXMLParserData::CXMLParserData ( )

Default Constructor

Member Function Documentation

◆ createRenderInformation()

CLRenderInformationBase * CXMLParserData::createRenderInformation ( CXMLParserData *  pData)
static

References CListOfLayouts::addGlobalRenderInformation(), CLayout::addLocalRenderInformation(), CListOfLayouts::getListOfGlobalRenderInformationObjects(), CLayout::getListOfLocalRenderInformationObjects(), LocalRenderInformation, pCurrentLayout, pLayoutList, and CDataVector< CType >::size().

Referenced by RenderInformationHandler::processStart().

Member Data Documentation

◆ CharacterData

std::string CXMLParserData::CharacterData

Storage for a comment.

Referenced by AssignmentHandler::processEnd(), CharacterDataHandler::processEnd(), CommentHandler::processEnd(), CompartmentHandler::processEnd(), EventHandler::processEnd(), FunctionHandler::processEnd(), InitialStateHandler::processEnd(), MetaboliteHandler::processEnd(), MiriamAnnotationHandler::processEnd(), ModelHandler::processEnd(), ModelParameterHandler::processEnd(), ModelParameterSetHandler::processEnd(), ModelValueHandler::processEnd(), ParameterTextHandler::processEnd(), ReactionHandler::processEnd(), RenderTextHandler::processEnd(), ReportDefinitionHandler::processEnd(), ReportSectionHandler::processEnd(), TableHandler::processEnd(), UnitDefinitionHandler::processEnd(), and ObjectHandler::processStart().

◆ FunctionDescription

std::string CXMLParserData::FunctionDescription

The description of the function.

◆ LocalRenderInformation

bool CXMLParserData::LocalRenderInformation

Referenced by createRenderInformation(), ListOfLayoutsHandler::processEnd(), and ListOfLayoutsHandler::processStart().

◆ mAssignments

std::vector<std::pair<std::string, std::string> > CXMLParserData::mAssignments

Storage for assignments.

◆ mFunctionParameterKeyMap

std::map< size_t, std::string > CXMLParserData::mFunctionParameterKeyMap

A map of new function to old keys parameter definitions

Referenced by FunctionHandler::processEnd(), FunctionHandler::processStart(), and ParameterDescriptionHandler::processStart().

◆ mKey2ObjectiveFunction

std::map< std::string, CExpression * > CXMLParserData::mKey2ObjectiveFunction

A map of a key to the infix of the objective function. This is only needed for old files containing the objective function as part of the list of function definitions

Referenced by TaskHandler::processEnd(), and FunctionHandler::processStart().

◆ mKeyMap

CKeyFactory CXMLParserData::mKeyMap

A map relating CopasiXML function keys with internal keys

Referenced by CXMLHandler::addFix(), COPASIHandler::processEnd(), ModelHandler::processEnd(), UnitDefinitionHandler::processEnd(), AssignmentHandler::processStart(), CallParameterHandler::processStart(), CompartmentGlyphHandler::processStart(), KineticLawHandler::processStart(), MetaboliteGlyphHandler::processStart(), MetaboliteHandler::processStart(), MetaboliteReferenceGlyphHandler::processStart(), ModelParameterSetHandler::processStart(), ModifierHandler::processStart(), ParameterHandler::processStart(), ProductHandler::processStart(), ReactionGlyphHandler::processStart(), ReactionHandler::processStart(), SBMLMapHandler::processStart(), SliderHandler::processStart(), SourceParameterHandler::processStart(), StateTemplateVariableHandler::processStart(), StyleHandler::processStart(), SubstrateHandler::processStart(), and TextGlyphHandler::processStart().

◆ ModelParameterGroupStack

std::stack< CModelParameterGroup * > CXMLParserData::ModelParameterGroupStack

Stack of Model Parameter Groups which is needed since nesting of groups is possible.

Referenced by ModelParameterGroupHandler::processEnd(), ModelParameterSetHandler::processEnd(), ModelParameterGroupHandler::processStart(), ModelParameterHandler::processStart(), and ModelParameterSetHandler::processStart().

◆ mpExpression

CExpression* CXMLParserData::mpExpression

Pointer to the currently processed expression. This is only needed for old files containing the objective function as part of the list of function definitions

Referenced by FunctionHandler::processEnd(), and FunctionHandler::processStart().

◆ mPredefinedFunction

bool CXMLParserData::mPredefinedFunction

Indicates whether the current function was already in the list;

Referenced by FunctionHandler::processEnd(), FunctionHandler::processStart(), and ParameterDescriptionHandler::processStart().

◆ mUnsupportedAnnotations

CAnnotation::UnsupportedAnnotation CXMLParserData::mUnsupportedAnnotations

Referenced by CompartmentHandler::processEnd(), EventHandler::processEnd(), FunctionHandler::processEnd(), MetaboliteHandler::processEnd(), ModelHandler::processEnd(), ModelParameterSetHandler::processEnd(), ModelValueHandler::processEnd(), ReactionHandler::processEnd(), UnitDefinitionHandler::processEnd(), UnsupportedAnnotationHandler::processEnd(), CompartmentHandler::processStart(), EventHandler::processStart(), FunctionHandler::processStart(), MetaboliteHandler::processStart(), ModelHandler::processStart(), ModelParameterSetHandler::processStart(), ModelValueHandler::processStart(), and ReactionHandler::processStart().

◆ pBoundingBox

CLBoundingBox* CXMLParserData::pBoundingBox

Referenced by BoundingBoxHandler::BoundingBoxHandler(), AdditionalGraphicalObjectHandler::processEnd(), BoundingBoxHandler::processEnd(), CompartmentGlyphHandler::processEnd(), LineEndingHandler::processEnd(), MetaboliteGlyphHandler::processEnd(), MetaboliteReferenceGlyphHandler::processEnd(), ReactionGlyphHandler::processEnd(), TextGlyphHandler::processEnd(), and BoundingBoxHandler::~BoundingBoxHandler().

◆ pCompartmentGlyph

CLCompartmentGlyph* CXMLParserData::pCompartmentGlyph

Referenced by CompartmentGlyphHandler::processEnd(), and CompartmentGlyphHandler::processStart().

◆ pCurrentChannelSpec

CPlotDataChannelSpec* CXMLParserData::pCurrentChannelSpec

Pointer to the currently processed channel.

Referenced by ChannelSpecHandler::processEnd(), and ChannelSpecHandler::processStart().

◆ pCurrentLayout

CLayout* CXMLParserData::pCurrentLayout

Pointer to the currently processed layout

Referenced by createRenderInformation(), LayoutHandler::processEnd(), AdditionalGraphicalObjectHandler::processStart(), CompartmentGlyphHandler::processStart(), LayoutHandler::processStart(), MetaboliteGlyphHandler::processStart(), ReactionGlyphHandler::processStart(), and TextGlyphHandler::processStart().

◆ pCurrentModelParameter

CModelParameter* CXMLParserData::pCurrentModelParameter

The currently handeled Model Parameter

Referenced by ModelParameterGroupHandler::processEnd(), ModelParameterHandler::processEnd(), ModelParameterSetHandler::processEnd(), and ModelParameterHandler::processStart().

◆ pCurrentParameter

CCopasiParameter* CXMLParserData::pCurrentParameter

Pointer to the currently processed parameter

Referenced by CXMLParser::getCurrentGroup(), ParameterGroupHandler::isUniqueParameter(), ParameterGroupHandler::processEnd(), ParameterTextHandler::processEnd(), PlotItemHandler::processEnd(), PlotSpecificationHandler::processEnd(), ParameterHandler::processStart(), and ParameterTextHandler::processStart().

◆ pCurrentPlot

CPlotSpecification* CXMLParserData::pCurrentPlot

Pointer to the currently processed plot

Referenced by PlotSpecificationHandler::processEnd(), PlotItemHandler::processStart(), and PlotSpecificationHandler::processStart().

◆ pCurrentPlotItem

CPlotItem* CXMLParserData::pCurrentPlotItem

Pointer to the currently processed plot item.

Referenced by ChannelSpecHandler::processEnd(), PlotItemHandler::processEnd(), and PlotItemHandler::processStart().

◆ pCurrentTask

CCopasiTask* CXMLParserData::pCurrentTask

Pointer to the currently processed task

Referenced by ParameterGroupHandler::processEnd(), TaskHandler::processEnd(), MethodHandler::processStart(), ReportTargetHandler::processStart(), and TaskHandler::processStart().

◆ pCurrentUnitDefinition

CUnitDefinition* CXMLParserData::pCurrentUnitDefinition

Referenced by UnitDefinitionHandler::processEnd(), and UnitDefinitionHandler::processStart().

◆ pCurve

CLCurve* CXMLParserData::pCurve

Referenced by CurveHandler::CurveHandler(), ListOfCurveSegmentsHandler::processEnd(), MetaboliteReferenceGlyphHandler::processEnd(), ReactionGlyphHandler::processEnd(), CurveHandler::processStart(), and CurveHandler::~CurveHandler().

◆ pDataModel

CDataModel* CXMLParserData::pDataModel

A pointer to the datamodel.

Referenced by COPASIHandler::processStart(), ModelHandler::processStart(), and CXMLParser::setDatamodel().

◆ pDimensions

CLDimensions* CXMLParserData::pDimensions

Referenced by DimensionsHandler::DimensionsHandler(), BoundingBoxHandler::processEnd(), LayoutHandler::processEnd(), DimensionsHandler::processStart(), and DimensionsHandler::~DimensionsHandler().

◆ pEllipse

CLEllipse* CXMLParserData::pEllipse

Referenced by GroupHandler::processEnd(), and EllipseHandler::processStart().

◆ pEvent

CEvent* CXMLParserData::pEvent

Pointer to the currently processed event

Referenced by EventHandler::processEnd(), AssignmentHandler::processStart(), and EventHandler::processStart().

◆ pEventAssignment

CEventAssignment* CXMLParserData::pEventAssignment

Pointer to the currently processed event assignment

Referenced by AssignmentHandler::processEnd(), and AssignmentHandler::processStart().

◆ pFunction

CFunction* CXMLParserData::pFunction

Pointer to the currently processed function.

Referenced by FunctionHandler::processEnd(), KineticLawHandler::processEnd(), FunctionHandler::processStart(), KineticLawHandler::processStart(), and ParameterDescriptionHandler::processStart().

◆ pFunctionList

CDataVectorN< CFunction >* CXMLParserData::pFunctionList

Pointer to a vector of functions which has been loaded or is to be saved. The ownership is handed to the user.

Referenced by COPASIHandler::processEnd(), FunctionHandler::processEnd(), FunctionHandler::processStart(), and CXMLParser::setFunctionList().

◆ pFunctionVariable

CFunctionParameter* CXMLParserData::pFunctionVariable

Pointer to the currently processed function.

Referenced by CallParameterHandler::processStart(), and SourceParameterHandler::processStart().

◆ pGeneralGlyph

CLGeneralGlyph* CXMLParserData::pGeneralGlyph

Referenced by AdditionalGraphicalObjectHandler::processEnd(), and AdditionalGraphicalObjectHandler::processStart().

◆ pGradient

CLGradientBase* CXMLParserData::pGradient

Referenced by LinearGradientHandler::processEnd(), RadialGradientHandler::processEnd(), GradientStopHandler::processStart(), LinearGradientHandler::processStart(), and RadialGradientHandler::processStart().

◆ pGroup

CLGroup* CXMLParserData::pGroup

Referenced by GroupHandler::processEnd(), LineEndingHandler::processEnd(), StyleHandler::processEnd(), and GroupHandler::processStart().

◆ pGUI

SCopasiXMLGUI* CXMLParserData::pGUI

Referenced by COPASIHandler::processEnd(), COPASIHandler::processStart(), SliderHandler::processStart(), and CXMLParser::setGUI().

◆ pImage

CLImage* CXMLParserData::pImage

Referenced by GroupHandler::processEnd(), and ImageHandler::processStart().

◆ pLayoutList

CListOfLayouts* CXMLParserData::pLayoutList

Pointer to a list of Layouts which has been loaded or is to be saved. The ownership is handed to the user.

Referenced by createRenderInformation(), CXMLParser::getLayoutList(), LayoutHandler::processEnd(), COPASIHandler::processStart(), and CXMLParser::setLayoutList().

◆ pLineEnding

CLLineEnding* CXMLParserData::pLineEnding

Referenced by LineEndingHandler::processEnd(), and LineEndingHandler::processStart().

◆ pLineSegment

CLLineSegment* CXMLParserData::pLineSegment

Referenced by ListOfCurveSegmentsHandler::ListOfCurveSegmentsHandler(), CubicBezierHandler::processEnd(), LineSegmentHandler::processEnd(), ListOfCurveSegmentsHandler::processEnd(), ListOfCurveSegmentsHandler::processStart(), CXMLParser::~CXMLParser(), and ListOfCurveSegmentsHandler::~ListOfCurveSegmentsHandler().

◆ pListOfCurveElements

std::vector<CLRenderPoint*>* CXMLParserData::pListOfCurveElements

Referenced by PolygonHandler::processStart(), RenderCurveElementHandler::processStart(), and RenderCurveHandler::processStart().

◆ pMetaboliteGlyph

CLMetabGlyph* CXMLParserData::pMetaboliteGlyph

Referenced by MetaboliteGlyphHandler::processEnd(), and MetaboliteGlyphHandler::processStart().

◆ pMetaboliteReferenceGlyph

CLMetabReferenceGlyph* CXMLParserData::pMetaboliteReferenceGlyph

Referenced by MetaboliteReferenceGlyphHandler::processEnd(), and MetaboliteReferenceGlyphHandler::processStart().

◆ pModel

CModel* CXMLParserData::pModel

The model which is build during parsing.

Referenced by CXMLParser::getModel(), ModelHandler::processEnd(), CompartmentHandler::processStart(), EventHandler::processStart(), MetaboliteHandler::processStart(), ModelHandler::processStart(), ModelParameterSetHandler::processStart(), ModelValueHandler::processStart(), ReactionHandler::processStart(), and TaskHandler::processStart().

◆ pPlotList

COutputDefinitionVector* CXMLParserData::pPlotList

Pointer to a vector of plots which has been loaded or is to be saved. The ownership is handed to the user.

Referenced by CXMLParser::getPlotList(), PlotSpecificationHandler::processEnd(), and COPASIHandler::processStart().

◆ pPolygon

CLPolygon* CXMLParserData::pPolygon

Referenced by GroupHandler::processEnd(), and PolygonHandler::processStart().

◆ pPosition

CLPoint* CXMLParserData::pPosition

Referenced by PointHandler::PointHandler(), BoundingBoxHandler::processEnd(), CubicBezierHandler::processEnd(), LineSegmentHandler::processEnd(), PointHandler::processStart(), and PointHandler::~PointHandler().

◆ pReaction

CReaction* CXMLParserData::pReaction

Pointer to the currently processed reaction.

Referenced by KineticLawHandler::processEnd(), ReactionHandler::processEnd(), ConstantHandler::processStart(), KineticLawHandler::processStart(), ModifierHandler::processStart(), ProductHandler::processStart(), ReactionHandler::processStart(), and SubstrateHandler::processStart().

◆ pReactionGlyph

CLReactionGlyph* CXMLParserData::pReactionGlyph

Referenced by ReactionGlyphHandler::processEnd(), MetaboliteReferenceGlyphHandler::processStart(), and ReactionGlyphHandler::processStart().

◆ pRectangle

CLRectangle* CXMLParserData::pRectangle

Referenced by GroupHandler::processEnd(), and RectangleHandler::processStart().

◆ pRenderCurve

CLRenderCurve* CXMLParserData::pRenderCurve

Referenced by GroupHandler::processEnd(), and RenderCurveHandler::processStart().

◆ pRenderInformation

CLRenderInformationBase* CXMLParserData::pRenderInformation

Referenced by ColorDefinitionHandler::processStart(), LinearGradientHandler::processStart(), LineEndingHandler::processStart(), RadialGradientHandler::processStart(), RenderInformationHandler::processStart(), and StyleHandler::processStart().

◆ pReport

CReportDefinition* CXMLParserData::pReport

Pointer to the currently processed report

Referenced by ReportDefinitionHandler::processEnd(), TableHandler::processEnd(), ReportDefinitionHandler::processStart(), ReportSectionHandler::processStart(), and TableHandler::processStart().

◆ pReportList

CReportDefinitionVector* CXMLParserData::pReportList

Pointer to a vector of reports which has been loaded or is to be saved. The ownership is handed to the user.

Referenced by CXMLParser::getReportList(), COPASIHandler::processStart(), and ReportDefinitionHandler::processStart().

◆ pStyle

CLStyle* CXMLParserData::pStyle

Referenced by StyleHandler::processEnd(), and StyleHandler::processStart().

◆ pTaskList

CDataVectorN< CCopasiTask >* CXMLParserData::pTaskList

Pointer to a vector of tasks which has been loaded or is to be saved. The ownership is handed to the user.

Referenced by CXMLParser::getTaskList(), COPASIHandler::processStart(), and TaskHandler::processStart().

◆ pText

CLText* CXMLParserData::pText

Referenced by GroupHandler::processEnd(), RenderTextHandler::processEnd(), and RenderTextHandler::processStart().

◆ pTextGlyph

CLTextGlyph* CXMLParserData::pTextGlyph

Referenced by TextGlyphHandler::processEnd(), and TextGlyphHandler::processStart().

◆ pUnitDefinitionImportList

CUnitDefinitionDB* CXMLParserData::pUnitDefinitionImportList

Referenced by CXMLParser::getUnitDefinitionImportList(), COPASIHandler::processStart(), UnitDefinitionHandler::processStart(), and CXMLParser::~CXMLParser().

◆ pVersion

CVersion* CXMLParserData::pVersion

The version of the parsed file

Referenced by CXMLParser::CXMLParser(), COPASIHandler::processStart(), and EventHandler::processStart().

◆ reportReferenceMap

std::map<std::string , std::vector < std::pair < std::vector < CRegisteredCommonName > *, size_t > > > CXMLParserData::reportReferenceMap

A map that stores a vector of pairs of header,body or footer addresses with the index together with the key to the reference.

Referenced by COPASIHandler::processEnd().

◆ SourceParameterObjects

std::map< std::string, std::vector< const CDataObject * > > CXMLParserData::SourceParameterObjects

The keys of the source parameters for a call parameter.

Referenced by KineticLawHandler::processEnd(), and SourceParameterHandler::processStart().

◆ StateVariableList

std::vector< CModelEntity * > CXMLParserData::StateVariableList

A map relating StateVariables to model entities.

Referenced by InitialStateHandler::processEnd(), StateTemplateHandler::processStart(), and StateTemplateVariableHandler::processStart().

◆ taskReferenceMap

std::map<std::string , std::vector < CCopasiTask* > > CXMLParserData::taskReferenceMap

A map that stores a vector of tasks that reference a certain key together with the key to the reference.

Referenced by COPASIHandler::processEnd(), and ReportTargetHandler::processStart().

◆ UnmappedKeyParameters

std::vector< std::string > CXMLParserData::UnmappedKeyParameters

Vector of parameters of type key which could not be updated due to missing target objects at time of read.

Referenced by COPASIHandler::processEnd(), ParameterGroupHandler::processEnd(), and ParameterHandler::processStart().

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