#include <CCopasiXML.h>

Inheritance diagram for CCopasiXML:

Public Member Functions
	CCopasiXML ()

bool	freeFunctionList ()

bool	freeGUI ()

bool	freeLayoutList ()

bool	freeModel ()

bool	freePlotList ()

bool	freeReportList ()

bool	freeTaskList ()

CDataVectorN< CFunction > *	getFunctionList () const

SCopasiXMLGUI *	getGUI () const

CListOfLayouts *	getLayoutList () const

CModel *	getModel () const

COutputDefinitionVector *	getPlotList () const

CReportDefinitionVector *	getReportList () const

CDataVectorN< CCopasiTask > *	getTaskList () const

bool	haveFunctionList () const

bool	haveGUI () const

bool	haveLayoutList () const

bool	haveModel () const

bool	havePlotList () const

bool	haveReportList () const

bool	haveTaskList () const

virtual bool	load (std::istream &is, const std::string &pwd)

virtual bool	save (std::ostream &os, const std::string &relativeTo)

virtual bool	saveModelParameterSets (std::ostream &os, const std::string &relativeTo)

bool	saveUnitDefinitionList ()

bool	setDatamodel (CDataModel *pDataModel)

bool	setFunctionList (CDataVectorN< CFunction > *pFunctionList)

bool	setGUI (SCopasiXMLGUI *pGUI)

bool	setLayoutList (const CListOfLayouts &reportList)

bool	setModel (CModel *pModel)

bool	setPlotList (COutputDefinitionVector *pPlotList)

bool	setReportList (CReportDefinitionVector *pReportList)

bool	setTaskList (CDataVectorN< CCopasiTask > *pTaskList)

	~CCopasiXML ()

Public Member Functions inherited from CCopasiXMLInterface
	CCopasiXMLInterface ()

bool	load (const std::string &fileName, const std::string &relativeTo)

bool	save (const std::string &fileName, const std::string &relativeTo)

virtual	~CCopasiXMLInterface ()

Private Member Functions
bool	buildFunctionList ()

void	fixBuild113 ()

void	fixBuild171 ()

void	fixBuild18 ()

void	fixBuild55 ()

void	fixBuild81 ()

void	fixBuildBefore104 ()

void	mergeUnitDefinitions (CUnitDefinitionDB *pUnitDefImportList)

void	save1DAttributes (const CLGraphicalPrimitive1D &primitive, CXMLAttributeList &attributes)

void	save2DAttributes (const CLGraphicalPrimitive2D &primitive, CXMLAttributeList &attributes)

bool	saveAnnotation (const CAnnotation *pAnnotation)

template<typename HEADELEMENT >
void	saveArrowHeadAttributes (const HEADELEMENT &element, CXMLAttributeList &attributes)

void	saveBoundingBox (const CLBoundingBox &bb)

void	saveColorDefinition (const CLColorDefinition &color)

void	saveCurve (const CLCurve &c)

void	saveCurveElements (const std::vector< CLRenderPoint * > &curveElements)

void	saveDimensions (const CLDimensions &d)

void	saveEllipseElement (const CLEllipse &ellipse)

bool	saveFunctionList ()

void	saveGlobalRenderInformation (const CLGlobalRenderInformation &renderInfo)

void	saveGlobalStyle (const CLGlobalStyle &style)

void	saveGradientAttributes (const CLGradientBase &gradient, CXMLAttributeList &attributes)

void	saveGradientElements (const CLGradientBase &gradient)

void	saveGradientStop (const CLGradientStop &stop)

void	saveGroupElement (const CLGroup &group)

bool	saveGUI ()

void	saveImageElement (const CLImage &image)

bool	saveLayoutList ()

void	saveLinearGradient (const CLLinearGradient &gradient)

void	saveLineEnding (const CLLineEnding &lineEnding)

void	saveListOfGlobalRenderInformation (const CDataVector< CLGlobalRenderInformation > &list)

void	saveListOfLocalRenderInformation (const CDataVector< CLLocalRenderInformation > &list)

void	saveLocalRenderInformation (const CLLocalRenderInformation &renderInfo)

void	saveLocalStyle (const CLLocalStyle &style)

bool	saveModel ()

bool	saveModelParameter (const CModelParameter *pModelParameter)

void	saveModelParameterSets ()

bool	savePlotList ()

void	savePolygonElement (const CLPolygon &polygon)

void	savePosition (const CLPoint &p, const std::string &tag="Position")

void	saveRadialGradient (const CLRadialGradient &gradient)

void	saveRectangleElement (const CLRectangle &rectangle)

void	saveRenderCurveElement (const CLRenderCurve &curve)

void	saveRenderInformationAttributes (const CLRenderInformationBase &renderInfo, CXMLAttributeList &attributes)

void	saveRenderInformationDefinitionElements (const CLRenderInformationBase &renderInfo)

void	saveRenderPoint (const CLRenderPoint &point)

void	saveRenderTextElement (const CLText &text)

bool	saveReportList ()

bool	saveReportSection (const std::string &name, const std::vector< CRegisteredCommonName > &section)

bool	saveSBMLReference ()

void	saveStyleAttributes (const CLStyle &style, CXMLAttributeList &attributes)

void	saveStyleElements (const CLStyle &style)

bool	saveTaskList ()

template<typename TEXTELEMENT >
void	saveTextAttributes (const TEXTELEMENT &text, CXMLAttributeList &attributes)

void	saveTransformation2D (const CLTransformation2D &transformation)

void	saveTransformationAttributes (const CLTransformation2D &transformation, CXMLAttributeList &attributes)

Private Attributes
bool	mMCXML21Issued

CDataModel *	mpDataModel

CDataVectorN< CFunction > *	mpFunctionList

SCopasiXMLGUI *	mpGUI

CListOfLayouts *	mpLayoutList

CModel *	mpModel

COutputDefinitionVector *	mpPlotList

CReportDefinitionVector *	mpReportList

CDataVectorN< CCopasiTask > *	mpTaskList

std::map< std::string, std::string >	mSBMLReference

Additional Inherited Members
Public Types inherited from CCopasiXMLInterface
enum	EncodingType { none = 0 , standard , attribute , character }

Static Public Member Functions inherited from CCopasiXMLInterface
static std::string	encode (const std::string &str, const EncodingType &type=standard)

static std::string	utf8 (const std::string &str)

Protected Member Functions inherited from CCopasiXMLInterface
bool	endSaveElement (const std::string &name)

bool	saveData (const std::string &data)

bool	saveElement (const std::string &name, CXMLAttributeList &attributeList)

bool	saveParameter (const CCopasiParameter &parameter)

bool	saveParameterGroup (const std::vector< CCopasiParameter * > &group)

bool	saveXhtml (const std::string &xhtml)

bool	startSaveElement (const std::string &name)

bool	startSaveElement (const std::string &name, CXMLAttributeList &attributeList)

Protected Attributes inherited from CCopasiXMLInterface
std::string	mIndent

std::istream *	mpIstream

std::ostream *	mpOstream

std::string	mPWD

Constructor & Destructor Documentation

◆ CCopasiXML()

CCopasiXML::CCopasiXML ( )

Constructor

CCopasiXML class. This class implements a CCopasiXMLInterface to the COPASI XML specified in http://www.copasi.org/schema/copasi.xsd

Created for COPASI by Stefan Hoops 2003 Copyright Stefan Hoops

◆ ~CCopasiXML()

CCopasiXML::~CCopasiXML ( )

Destructor

Member Function Documentation

◆ buildFunctionList()

bool CCopasiXML::buildFunctionList ( )

private

Build a list of functions.

Returns: bool success

References CRootContainer::getFunctionList(), CDataModel::getModel(), CFunctionDB::getUsedFunctions(), mpDataModel, and setFunctionList().

Referenced by save().

◆ fixBuild113()

void CCopasiXML::fixBuild113 ( )

private

The default kinetic law unit type needs to be corrected in rare cases.

References CDataVector< CType >::begin(), CReaction::ConcentrationPerTime, CDataVector< CType >::end(), CModel::getReactions(), and mpModel.

Referenced by load().

◆ fixBuild171()

void CCopasiXML::fixBuild171 ( )

private

The object names no longer may have special character and are sanitized. This invalidates common names (CNs).

References CRegisteredCommonName::sanitizeObjectNames().

Referenced by load().

◆ fixBuild18()

void CCopasiXML::fixBuild18 ( )

private

Fix files written with Version 4.0.18, which used units Mol, etc., instead of mol, . . .

References CModel::getQuantityUnit(), mpModel, CCore::ParticleNumbers, and CModel::setQuantityUnit().

Referenced by load().

◆ fixBuild55()

void CCopasiXML::fixBuild55 ( )

private

Fix files written with Version 4.10.55, which wrote the square root of user defined weights for the parameter fitting task

References C_INVALID_INDEX, CFitTask::fixBuild55(), CDataVectorN< CType >::getIndex(), and mpTaskList.

Referenced by load().

◆ fixBuild81()

void CCopasiXML::fixBuild81 ( )

private

Fix files written with Version 4.12.81 and earlier, which wrote the exp(mean) and exp(std. deviation) for normal random distributions in the scan task.

References C_INVALID_INDEX, CScanTask::fixBuild81(), CDataVectorN< CType >::getIndex(), and mpTaskList.

Referenced by load().

◆ fixBuildBefore104()

void CCopasiXML::fixBuildBefore104 ( )

private

After Build 104, at least, we shouldn't see any "m" in place of "min" for timeUnit.

References CModel::getTimeUnit(), mpModel, and CModel::setTimeUnit().

Referenced by load().

◆ freeFunctionList()

bool CCopasiXML::freeFunctionList ( )

Free the function list.

Returns: bool success

References mpFunctionList, and pdelete.

Referenced by save().

◆ freeGUI()

bool CCopasiXML::freeGUI ( )

Free the GUI.

Returns: bool success

References mpGUI, and pdelete.

Referenced by CDataModel::loadModel().

◆ freeLayoutList()

bool CCopasiXML::freeLayoutList ( )

Free the layout list.

Returns: bool success

References mpLayoutList, and pdelete.

Referenced by CDataModel::loadModel().

◆ freeModel()

bool CCopasiXML::freeModel ( )

Free the model.

Returns: bool success

References mpModel, and pdelete.

Referenced by CDataModel::loadModel().

◆ freePlotList()

bool CCopasiXML::freePlotList ( )

Free the plot list.

Returns: bool success

References mpPlotList, and pdelete.

Referenced by CDataModel::loadModel().

◆ freeReportList()

bool CCopasiXML::freeReportList ( )

Free the report list.

Returns: bool success

References mpReportList, and pdelete.

Referenced by CDataModel::loadModel().

◆ freeTaskList()

bool CCopasiXML::freeTaskList ( )

Free the task list.

Returns: bool success

References mpTaskList, and pdelete.

Referenced by CDataModel::loadModel().

◆ getFunctionList()

CDataVectorN< CFunction > * CCopasiXML::getFunctionList ( ) const

Retrieve the function list.

Returns: CDataVectorN< CFunction > * pFunctionList

References mpFunctionList.

◆ getGUI()

SCopasiXMLGUI * CCopasiXML::getGUI ( ) const

Retrieve the SCopasiXMLGUI.

Returns: SCopasiXMLGUI * pGUI

References mpGUI.

◆ getLayoutList()

CListOfLayouts * CCopasiXML::getLayoutList ( ) const

Retrieve the layout list.

Returns: CListOfLayouts * layoutList

References mpLayoutList.

Referenced by CDataModel::loadModel().

◆ getModel()

CModel * CCopasiXML::getModel ( ) const

Retreive the model.

Returns: CModel * pModel

References mpModel.

Referenced by CDataModel::loadModel().

◆ getPlotList()

COutputDefinitionVector * CCopasiXML::getPlotList ( ) const

Retrieve the plot list.

Returns: COutputDefinitionVector * plotList

References mpPlotList.

Referenced by CDataModel::loadModel().

◆ getReportList()

CReportDefinitionVector * CCopasiXML::getReportList ( ) const

Retrieve the report list.

Returns: CReportDefinitionVector * reportList

References mpReportList.

Referenced by CDataModel::loadModel().

◆ getTaskList()

CDataVectorN< CCopasiTask > * CCopasiXML::getTaskList ( ) const

Retrieve the task list.

Returns: CDataVectorN< CCopasiTask > * taskList

References mpTaskList.

Referenced by CDataModel::loadModel().

◆ haveFunctionList()

bool CCopasiXML::haveFunctionList ( ) const

Retrieve whether the XML contains a function list.

Returns: bool haveFunctionList

References mpFunctionList.

Referenced by save(), and saveFunctionList().

◆ haveGUI()

bool CCopasiXML::haveGUI ( ) const

Retrieve whether the XML contains a GUI.

Returns: bool have GUI

References mpGUI.

Referenced by saveGUI().

◆ haveLayoutList()

bool CCopasiXML::haveLayoutList ( ) const

Retrieve whether the XML contains a layout list.

Returns: bool haveLayoutList

References mpLayoutList.

Referenced by saveLayoutList().

◆ haveModel()

bool CCopasiXML::haveModel ( ) const

Retreive whether the XML contains a model.

Returns: bool have Model

References mpModel.

Referenced by save(), saveModel(), and saveModelParameterSets().

◆ havePlotList()

bool CCopasiXML::havePlotList ( ) const

Retrieve whether the XML contains a plot list.

Returns: bool havePlotList

References mpPlotList.

Referenced by savePlotList().

◆ haveReportList()

bool CCopasiXML::haveReportList ( ) const

Retrieve whether the XML contains a report list.

Returns: bool haveReportList

References mpReportList.

Referenced by saveReportList().

◆ haveTaskList()

bool CCopasiXML::haveTaskList ( ) const

Retrieve whether the XML contains a task list.

Returns: bool haveTaskList

References mpTaskList.

Referenced by saveTaskList().

◆ load()

bool CCopasiXML::load	(	std::istream &	is,
		const std::string &	pwd
	)

virtual

Load information from a given istream.

Parameters

std::istream	& is
const	std::string & pwd

Returns: bool success

Implements CCopasiXMLInterface.

References BUFFER_SIZE, fatalError, fixBuild113(), fixBuild171(), fixBuild18(), fixBuild55(), fixBuild81(), fixBuildBefore104(), CExpatTemplate< CType >::getCurrentColumnNumber(), CExpatTemplate< CType >::getCurrentLineNumber(), CExpatTemplate< CType >::getErrorString(), CXMLParser::getLayoutList(), CXMLParser::getModel(), CXMLParser::getPlotList(), CXMLParser::getReportList(), CXMLParser::getTaskList(), CXMLParser::getUnitDefinitionImportList(), CVersion::getVersion(), CVersion::getVersionDevel(), MCXML, mergeUnitDefinitions(), mpDataModel, mpFunctionList, mpGUI, CCopasiXMLInterface::mpIstream, mpLayoutList, mpModel, mpPlotList, mpReportList, mpTaskList, CCopasiXMLInterface::mPWD, CExpatTemplate< CType >::parse(), pdelete, CCopasiMessage::RAW, CXMLParser::setDatamodel(), CXMLParser::setFunctionList(), CXMLParser::setGUI(), CXMLParser::setLayoutList(), CVersion::VERSION, and CCopasiMessage::WARNING.

Referenced by CFunctionDB::load(), and CDataModel::loadModel().

◆ mergeUnitDefinitions()

void CCopasiXML::mergeUnitDefinitions ( CUnitDefinitionDB * pUnitDefImportList )

private

Load in Unit Definitions we don't already have. Create new names and symbols for conflicts. Update model to use any created symbols.

References CUnitDefinitionDB::add(), CDataVector< CType >::begin(), C_INVALID_INDEX, CModel::changeUnitExpressionSymbols(), CUnitDefinitionDB::containsSymbol(), CDataVector< CType >::end(), CUnit::getExpression(), CDataVectorN< CType >::getIndex(), CCopasiMessage::getLastMessage(), CDataObject::getObjectName(), CUnitDefinition::getSymbol(), CRootContainer::getUnitList(), mpModel, CUnit::replaceSymbol(), CUnitDefinition::setExpression(), CUnitDefinition::setSymbol(), and CCopasiMessage::size().

Referenced by load().

◆ save()

bool CCopasiXML::save	(	std::ostream &	os,
		const std::string &	relativeTo
	)

virtual

Save information to a given ostream.

Parameters

std::ostream	& os
const	std::string & relativeTo

Returns: bool success

Implements CCopasiXMLInterface.

References CXMLAttributeList::add(), buildFunctionList(), CCopasiXMLInterface::endSaveElement(), freeFunctionList(), CVersion::getVersion(), haveFunctionList(), haveModel(), CCopasiXMLInterface::mpOstream, CCopasiXMLInterface::mPWD, saveFunctionList(), saveGUI(), saveLayoutList(), saveModel(), savePlotList(), saveReportList(), saveSBMLReference(), saveTaskList(), saveUnitDefinitionList(), CCopasiXMLInterface::startSaveElement(), UTCTimeStamp(), and CVersion::VERSION.

Referenced by CDataModel::saveModelToString().

◆ save1DAttributes()

void CCopasiXML::save1DAttributes	(	const CLGraphicalPrimitive1D &	primitive,
		CXMLAttributeList &	attributes
	)

private

Saves the attributes for a 1D element

References CXMLAttributeList::add(), CLGraphicalPrimitive1D::getDashArray(), CLGraphicalPrimitive1D::getStroke(), CLGraphicalPrimitive1D::getStrokeWidth(), CLGraphicalPrimitive1D::isSetDashArray(), CLGraphicalPrimitive1D::isSetStroke(), CLGraphicalPrimitive1D::isSetStrokeWidth(), and saveTransformationAttributes().

Referenced by save2DAttributes(), saveRenderCurveElement(), and saveRenderTextElement().

◆ save2DAttributes()

void CCopasiXML::save2DAttributes	(	const CLGraphicalPrimitive2D &	primitive,
		CXMLAttributeList &	attributes
	)

private

Saves the attributes for a 2D element

References CXMLAttributeList::add(), CLGraphicalPrimitive2D::EVENODD, CLGraphicalPrimitive2D::getFillColor(), CLGraphicalPrimitive2D::getFillRule(), CLGraphicalPrimitive2D::isSetFill(), CLGraphicalPrimitive2D::isSetFillRule(), CLGraphicalPrimitive2D::NONZERO, and save1DAttributes().

Referenced by saveEllipseElement(), saveGroupElement(), savePolygonElement(), and saveRectangleElement().

◆ saveAnnotation()

bool CCopasiXML::saveAnnotation ( const CAnnotation * pAnnotation )

private

References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CAnnotation::getMiriamAnnotation(), CAnnotation::getNotes(), CAnnotation::getUnsupportedAnnotations(), CCopasiXMLInterface::mpOstream, CCopasiXMLInterface::saveXhtml(), CXMLAttributeList::setValue(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveFunctionList(), saveModel(), saveModelParameterSets(), and saveUnitDefinitionList().

◆ saveArrowHeadAttributes()

template<typename HEADELEMENT >

void CCopasiXML::saveArrowHeadAttributes	(	const HEADELEMENT &	element,
		CXMLAttributeList &	attributes
	)

private

Saves the startHead and endHead attribute as found in group and curves. We write it as a template so that it can be used on curves and group elements.

References CXMLAttributeList::add().

◆ saveBoundingBox()

void CCopasiXML::saveBoundingBox ( const CLBoundingBox & bb )

private

References CCopasiXMLInterface::endSaveElement(), CLBoundingBox::getDimensions(), CLBoundingBox::getPosition(), saveDimensions(), savePosition(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveLayoutList(), and saveLineEnding().

◆ saveColorDefinition()

void CCopasiXML::saveColorDefinition ( const CLColorDefinition & color )

private

Save a single color definition element.

References CXMLAttributeList::add(), CLColorDefinition::createValueString(), CLColorDefinition::getId(), and CCopasiXMLInterface::saveElement().

Referenced by saveRenderInformationDefinitionElements().

◆ saveCurve()

void CCopasiXML::saveCurve ( const CLCurve & c )

private

References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CXMLAttributeList::erase(), CLLineSegment::getBase1(), CLLineSegment::getBase2(), CLCurve::getCurveSegments(), CLLineSegment::getEnd(), CLCurve::getNumCurveSegments(), CLLineSegment::getStart(), CLLineSegment::isBezier(), savePosition(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveLayoutList().

◆ saveCurveElements()

void CCopasiXML::saveCurveElements ( const std::vector< CLRenderPoint * > & curveElements )

private

saves a vector of curve elements. This can be called from the polygon as well as the curve.

References CCopasiXMLInterface::endSaveElement(), saveRenderPoint(), and CCopasiXMLInterface::startSaveElement().

Referenced by savePolygonElement(), and saveRenderCurveElement().

◆ saveDimensions()

void CCopasiXML::saveDimensions ( const CLDimensions & d )

private

References CXMLAttributeList::add(), CXMLAttributeList::erase(), CLDimensions::getHeight(), CLDimensions::getWidth(), and CCopasiXMLInterface::saveElement().

Referenced by saveBoundingBox().

◆ saveEllipseElement()

void CCopasiXML::saveEllipseElement ( const CLEllipse & ellipse )

private

saves a single ellipse element.

References CXMLAttributeList::add(), CLEllipse::getCX(), CLEllipse::getCY(), CLEllipse::getCZ(), CLEllipse::getRX(), CLEllipse::getRY(), save2DAttributes(), CCopasiXMLInterface::saveElement(), and CLRelAbsVector::toString().

Referenced by saveTransformation2D().

◆ saveFunctionList()

bool CCopasiXML::saveFunctionList ( )

private

◆ saveGlobalRenderInformation()

void CCopasiXML::saveGlobalRenderInformation ( const CLGlobalRenderInformation & renderInfo )

private

Saves a single global render information object.

References CCopasiXMLInterface::endSaveElement(), CLGlobalRenderInformation::getNumStyles(), CLGlobalRenderInformation::getStyle(), saveGlobalStyle(), saveRenderInformationAttributes(), saveRenderInformationDefinitionElements(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveListOfGlobalRenderInformation().

◆ saveGlobalStyle()

void CCopasiXML::saveGlobalStyle ( const CLGlobalStyle & style )

private

Saves a single local style element.

References CCopasiXMLInterface::endSaveElement(), saveStyleAttributes(), saveStyleElements(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveGlobalRenderInformation().

◆ saveGradientAttributes()

void CCopasiXML::saveGradientAttributes	(	const CLGradientBase &	gradient,
		CXMLAttributeList &	attributes
	)

private

Adds the attributes common to radial and linear gradient.

References CXMLAttributeList::add(), CLGradientBase::getId(), CLGradientBase::getSpreadMethod(), CLGradientBase::PAD, CLGradientBase::REFLECT, and CLGradientBase::REPEAT.

Referenced by saveLinearGradient(), and saveRadialGradient().

◆ saveGradientElements()

void CCopasiXML::saveGradientElements ( const CLGradientBase & gradient )

private

Saves the elements that are common to linear and radial gradients.

References CLGradientBase::getGradientStop(), CLGradientBase::getNumGradientStops(), and saveGradientStop().

Referenced by saveLinearGradient(), and saveRadialGradient().

◆ saveGradientStop()

void CCopasiXML::saveGradientStop ( const CLGradientStop & stop )

private

Saves a single gradient stop element.

References CXMLAttributeList::add(), CLGradientStop::getOffset(), CLGradientStop::getStopColor(), CCopasiXMLInterface::saveElement(), and CLRelAbsVector::toString().

Referenced by saveGradientElements().

◆ saveGroupElement()

void CCopasiXML::saveGroupElement ( const CLGroup & group )

private

Saves a group element.

References CCopasiXMLInterface::endSaveElement(), CLGroup::getElement(), CLGroup::getNumElements(), save2DAttributes(), saveTransformation2D(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveLineEnding(), saveStyleElements(), and saveTransformation2D().

◆ saveGUI()

bool CCopasiXML::saveGUI ( )

private

◆ saveImageElement()

void CCopasiXML::saveImageElement ( const CLImage & image )

private

saves a single image element.

References CXMLAttributeList::add(), CLImage::getHeight(), CLImage::getImageReference(), CLImage::getWidth(), CLImage::getX(), CLImage::getY(), CLImage::getZ(), CCopasiXMLInterface::saveElement(), saveTransformationAttributes(), and CLRelAbsVector::toString().

Referenced by saveTransformation2D().

◆ saveLayoutList()

bool CCopasiXML::saveLayoutList ( )

private

Save the list of layout.

Returns: bool success

References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CXMLAttributeList::erase(), CLGraphicalObject::getBoundingBox(), CLGlyphWithCurve::getCurve(), CLayout::getDimensions(), CLTextGlyph::getGraphicalObjectKey(), CLDimensions::getHeight(), CLayout::getKey(), CLGraphicalObject::getKey(), CLayout::getListOfCompartmentGlyphs(), CLayout::getListOfGeneralGlyphs(), CListOfLayouts::getListOfGlobalRenderInformationObjects(), CLayout::getListOfLocalRenderInformationObjects(), CLayout::getListOfMetaboliteGlyphs(), CLReactionGlyph::getListOfMetabReferenceGlyphs(), CLayout::getListOfReactionGlyphs(), CLayout::getListOfTextGlyphs(), CLMetabReferenceGlyph::getMetabGlyphKey(), CLGraphicalObject::getModelObjectKey(), CLCurve::getNumCurveSegments(), CDataObject::getObjectName(), CLGraphicalObject::getObjectRole(), CLMetabReferenceGlyph::getRole(), CLTextGlyph::getText(), CLDimensions::getWidth(), CLGraphicalObject::hasValidModelReference(), haveLayoutList(), CLBoundingBox::isEmpty(), CLTextGlyph::isTextSet(), MCXML, mMCXML21Issued, mpLayoutList, saveBoundingBox(), saveCurve(), CCopasiXMLInterface::saveElement(), saveListOfGlobalRenderInformation(), saveListOfLocalRenderInformation(), CDataVector< CType >::size(), CCopasiXMLInterface::startSaveElement(), CCopasiMessage::WARNING, and CLMetabReferenceGlyph::XMLRole.

Referenced by save().

◆ saveLinearGradient()

void CCopasiXML::saveLinearGradient ( const CLLinearGradient & gradient )

private

Saves a single linear gradient definition.

References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CLLinearGradient::getXPoint1(), CLLinearGradient::getXPoint2(), CLLinearGradient::getYPoint1(), CLLinearGradient::getYPoint2(), CLLinearGradient::getZPoint1(), CLLinearGradient::getZPoint2(), saveGradientAttributes(), saveGradientElements(), CCopasiXMLInterface::startSaveElement(), and CLRelAbsVector::toString().

Referenced by saveRenderInformationDefinitionElements().

◆ saveLineEnding()

void CCopasiXML::saveLineEnding ( const CLLineEnding & lineEnding )

private

Saves a line ending definiton,

References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CLLineEnding::getBoundingBox(), CLLineEnding::getGroup(), CLLineEnding::getId(), CLLineEnding::getIsEnabledRotationalMapping(), saveBoundingBox(), saveGroupElement(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveRenderInformationDefinitionElements().

◆ saveListOfGlobalRenderInformation()

void CCopasiXML::saveListOfGlobalRenderInformation ( const CDataVector< CLGlobalRenderInformation > & list )

private

Saves the list of global render information objects.

References CCopasiXMLInterface::endSaveElement(), saveGlobalRenderInformation(), CDataVector< CType >::size(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveLayoutList().

◆ saveListOfLocalRenderInformation()

void CCopasiXML::saveListOfLocalRenderInformation ( const CDataVector< CLLocalRenderInformation > & list )

private

Saves the list of local render information objects.

References CCopasiXMLInterface::endSaveElement(), saveLocalRenderInformation(), CDataVector< CType >::size(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveLayoutList().

◆ saveLocalRenderInformation()

void CCopasiXML::saveLocalRenderInformation ( const CLLocalRenderInformation & renderInfo )

private

Saves a single local render information object.

References CCopasiXMLInterface::endSaveElement(), CLLocalRenderInformation::getNumStyles(), CLLocalRenderInformation::getStyle(), saveLocalStyle(), saveRenderInformationAttributes(), saveRenderInformationDefinitionElements(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveListOfLocalRenderInformation().

◆ saveLocalStyle()

void CCopasiXML::saveLocalStyle ( const CLLocalStyle & style )

private

Saves a single local style element.

References CXMLAttributeList::add(), CLStyle::createStringFromSet(), CCopasiXMLInterface::endSaveElement(), CLLocalStyle::getKeyList(), CLLocalStyle::getNumKeys(), saveStyleAttributes(), saveStyleElements(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveLocalRenderInformation().

◆ saveModel()

bool CCopasiXML::saveModel ( )

private

Save the model.

Returns: bool success

References CXMLAttributeList::add(), CVectorCore< CType >::array(), CDataVector< CType >::begin(), C_FLOAT64, CDataVector< CType >::end(), CCopasiXMLInterface::endSaveElement(), CXMLAttributeList::erase(), CModelEntity::FIXED, CModel::getAreaUnitName(), CEvent::getAssignments(), CModel::getAvogadro(), CReaction::getChemEq(), CDataObject::getCN(), CMetab::getCompartment(), CModel::getCompartments(), CEvent::getDelayAssignment(), CEvent::getDelayExpression(), CCompartment::getDimensionality(), CStateTemplate::getEntities(), CModel::getEvents(), CModelEntity::getExpression(), CEvent::getFireAtInitialTime(), CReaction::getFunction(), CReaction::getFunctionParameters(), CModelEntity::getInitialExpression(), CDataObject::getKey(), CFunction::getKey(), CEvent::getKey(), CModel::getKey(), CReaction::getKey(), CModelEntity::getKey(), CCopasiParameterGroup::getKey(), CReaction::getKineticLawUnitType(), CModel::getLengthUnitName(), CModel::getMetabolites(), CModel::getModelType(), CModel::getModelValues(), CChemEq::getModifiers(), CCopasiParameterGroup::getName(), CModelEntity::getNoiseExpression(), CReaction::getNoiseExpression(), CDataObject::getObjectDataModel(), CDataObject::getObjectName(), CReaction::getParameterObjects(), CReaction::getParameters(), CEvent::getPersistentTrigger(), CEvent::getPriorityExpression(), CChemEq::getProducts(), CModel::getQuantityUnitName(), CModel::getReactions(), CEvent::getSBMLId(), CModelEntity::getSBMLId(), CReaction::getSBMLId(), CReaction::getScalingCompartment(), CModel::getStateTemplate(), CModelEntity::getStatus(), CChemEq::getSubstrates(), CModel::getTimeUnitName(), CEvent::getTriggerExpression(), CRootContainer::getUndefinedFunction(), CModelEntity::getUnitExpression(), CCopasiParameterGroup::getValue(), CFunction::getVariables(), CModel::getVolumeUnitName(), CModelEntity::hasNoise(), CReaction::hasNoise(), haveModel(), CReaction::isFast(), CReaction::isReversible(), CReaction::KineticLawUnitTypeName, CCopasiXMLInterface::mIndent, CModel::ModelTypeNames, mpModel, CCopasiXMLInterface::mpOstream, mSBMLReference, CModelEntity::REACTIONS, saveAnnotation(), CCopasiXMLInterface::saveData(), CCopasiXMLInterface::saveElement(), saveModelParameterSets(), CXMLAttributeList::setValue(), CDataVector< CType >::size(), CFunctionParameters::size(), CStateTemplate::size(), CCopasiParameterGroup::size(), CXMLAttributeList::skip(), CCopasiXMLInterface::startSaveElement(), and CModelEntity::XMLStatus.

Referenced by save().

◆ saveModelParameter()

bool CCopasiXML::saveModelParameter ( const CModelParameter * pModelParameter )

private

Save a model parameter

Parameters

const CModelParameter * pModelParameter

Returns: bool success

References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CModelParameter::getCN(), CModelParameter::getCompareResult(), CModelParameter::getInitialExpression(), CModelParameter::getSimulationType(), CModelParameter::getType(), CModelParameter::getValue(), CModelParameter::Group, CModelParameter::Missing, CCore::ParticleNumbers, CModelParameter::Reaction, CCopasiXMLInterface::saveData(), CCopasiXMLInterface::saveElement(), CCopasiXMLInterface::startSaveElement(), CModelParameter::TypeNames, and CModelEntity::XMLStatus.

Referenced by saveModelParameterSets().

◆ saveModelParameterSets() [1/2]

void CCopasiXML::saveModelParameterSets ( )

private

Save the model parameter sets to stream

References CXMLAttributeList::add(), CModelParameterSet::begin(), CModelParameterSet::end(), CCopasiXMLInterface::endSaveElement(), CXMLAttributeList::erase(), CModel::getActiveModelParameterSet(), CModelParameterSet::getKey(), CModel::getModelParameterSets(), CDataObject::getObjectName(), mpModel, saveAnnotation(), saveModelParameter(), CXMLAttributeList::setValue(), CDataVector< CType >::size(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveModel(), and saveModelParameterSets().

◆ saveModelParameterSets() [2/2]

bool CCopasiXML::saveModelParameterSets	(	std::ostream &	os,
		const std::string &	relativeTo
	)

virtual

Save information to a given ostream.

Parameters

std::ostream	& os
const	std::string & relativeTo

Returns: bool success

References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CModel::getAreaUnitName(), CModel::getAvogadro(), CModel::getKey(), CModel::getLengthUnitName(), CModel::getModelType(), CDataObject::getObjectName(), CModel::getQuantityUnitName(), CModelEntity::getStatus(), CModel::getTimeUnitName(), CVersion::getVersion(), CModel::getVolumeUnitName(), haveModel(), CModel::ModelTypeNames, mpModel, CCopasiXMLInterface::mpOstream, CCopasiXMLInterface::mPWD, saveModelParameterSets(), CCopasiXMLInterface::startSaveElement(), UTCTimeStamp(), CVersion::VERSION, and CModelEntity::XMLStatus.

Referenced by CDataModel::saveModelParameterSets().

◆ savePlotList()

bool CCopasiXML::savePlotList ( )

private

◆ savePolygonElement()

void CCopasiXML::savePolygonElement ( const CLPolygon & polygon )

private

saves a single image element.

References CCopasiXMLInterface::endSaveElement(), CLPolygon::getListOfElements(), save2DAttributes(), saveCurveElements(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveTransformation2D().

◆ savePosition()

void CCopasiXML::savePosition	(	const CLPoint &	p,
		const std::string &	tag = `"Position"`
	)

private

References CXMLAttributeList::add(), CXMLAttributeList::erase(), CLPoint::getX(), CLPoint::getY(), and CCopasiXMLInterface::saveElement().

Referenced by saveBoundingBox(), and saveCurve().

◆ saveRadialGradient()

void CCopasiXML::saveRadialGradient ( const CLRadialGradient & gradient )

private

Saves a single radial gradient definition.

References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CLRadialGradient::getCenterX(), CLRadialGradient::getCenterY(), CLRadialGradient::getCenterZ(), CLRadialGradient::getFocalPointX(), CLRadialGradient::getFocalPointY(), CLRadialGradient::getFocalPointZ(), CLRadialGradient::getRadius(), saveGradientAttributes(), saveGradientElements(), CCopasiXMLInterface::startSaveElement(), and CLRelAbsVector::toString().

Referenced by saveRenderInformationDefinitionElements().

◆ saveRectangleElement()

void CCopasiXML::saveRectangleElement ( const CLRectangle & rectangle )

private

saves a single rectangle element.

References CXMLAttributeList::add(), CLRectangle::getHeight(), CLRectangle::getRadiusX(), CLRectangle::getRadiusY(), CLRectangle::getWidth(), CLRectangle::getX(), CLRectangle::getY(), CLRectangle::getZ(), save2DAttributes(), CCopasiXMLInterface::saveElement(), and CLRelAbsVector::toString().

Referenced by saveTransformation2D().

◆ saveRenderCurveElement()

void CCopasiXML::saveRenderCurveElement ( const CLRenderCurve & curve )

private

saves a single image element.

References CCopasiXMLInterface::endSaveElement(), CLRenderCurve::getListOfCurveElements(), save1DAttributes(), saveCurveElements(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveTransformation2D().

◆ saveRenderInformationAttributes()

void CCopasiXML::saveRenderInformationAttributes	(	const CLRenderInformationBase &	renderInfo,
		CXMLAttributeList &	attributes
	)

private

Saves the attributes that render information objects have in common.

References CXMLAttributeList::add(), CLRenderInformationBase::getBackgroundColor(), CLRenderInformationBase::getKey(), CLRenderInformationBase::getName(), and CLRenderInformationBase::getReferenceRenderInformationKey().

Referenced by saveGlobalRenderInformation(), and saveLocalRenderInformation().

◆ saveRenderInformationDefinitionElements()

void CCopasiXML::saveRenderInformationDefinitionElements ( const CLRenderInformationBase & renderInfo )

private

Saves color definitions, gradient definitions and line endings.

Saves color definitions , gradient definitions and line endings.

References CCopasiXMLInterface::endSaveElement(), CLRenderInformationBase::getColorDefinition(), CLRenderInformationBase::getGradientDefinition(), CLRenderInformationBase::getLineEnding(), CLRenderInformationBase::getNumColorDefinitions(), CLRenderInformationBase::getNumGradientDefinitions(), CLRenderInformationBase::getNumLineEndings(), saveColorDefinition(), saveLinearGradient(), saveLineEnding(), saveRadialGradient(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveGlobalRenderInformation(), and saveLocalRenderInformation().

◆ saveRenderPoint()

void CCopasiXML::saveRenderPoint ( const CLRenderPoint & point )

private

saves a single render point element.

References CXMLAttributeList::add(), CLRenderCubicBezier::basePoint1_X(), CLRenderCubicBezier::basePoint1_Y(), CLRenderCubicBezier::basePoint1_Z(), CLRenderCubicBezier::basePoint2_X(), CLRenderCubicBezier::basePoint2_Y(), CLRenderCubicBezier::basePoint2_Z(), CCopasiXMLInterface::saveElement(), CLRelAbsVector::toString(), CLRenderPoint::x(), CLRenderPoint::y(), and CLRenderPoint::z().

Referenced by saveCurveElements().

◆ saveRenderTextElement()

void CCopasiXML::saveRenderTextElement ( const CLText & text )

private

saves a single text element.

References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CLText::getText(), CLText::getX(), CLText::getY(), CLText::getZ(), save1DAttributes(), CCopasiXMLInterface::saveData(), CCopasiXMLInterface::startSaveElement(), and CLRelAbsVector::toString().

Referenced by saveTransformation2D().

◆ saveReportList()

bool CCopasiXML::saveReportList ( )

private

Save the list of reports.

Returns: bool success

Referenced by save().

◆ saveReportSection()

bool CCopasiXML::saveReportSection	(	const std::string &	name,
		const std::vector< CRegisteredCommonName > &	section
	)

private

Save a Report Section such as Header, Body or Footer.

Parameters

const	std::string & name
const	std::vector <CCommonName> & section

Returns: bool success

References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CCopasiXMLInterface::saveElement(), CCopasiXMLInterface::saveXhtml(), CXMLAttributeList::set(), and CCopasiXMLInterface::startSaveElement().

Referenced by saveReportList().

◆ saveSBMLReference()

bool CCopasiXML::saveSBMLReference ( )

private

Save the SBML reference information

Returns: bool success

References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CXMLAttributeList::erase(), CDirEntry::fileName(), CDataModel::getSBMLFileName(), CDirEntry::isRelativePath(), CDirEntry::makePathRelative(), mpDataModel, CCopasiXMLInterface::mPWD, mSBMLReference, CCopasiXMLInterface::saveElement(), CXMLAttributeList::setValue(), and CCopasiXMLInterface::startSaveElement().

Referenced by save().

◆ saveStyleAttributes()

void CCopasiXML::saveStyleAttributes	(	const CLStyle &	style,
		CXMLAttributeList &	attributes
	)

private

Adds the attributes common to both style types.

References CXMLAttributeList::add(), CLStyle::createStringFromSet(), CLStyle::getKey(), CLStyle::getNumRoles(), CLStyle::getNumTypes(), CLStyle::getRoleList(), and CLStyle::getTypeList().

Referenced by saveGlobalStyle(), and saveLocalStyle().

◆ saveStyleElements()

void CCopasiXML::saveStyleElements ( const CLStyle & style )

private

Saves the elements common to both style types.

References CLStyle::getGroup(), and saveGroupElement().

Referenced by saveGlobalStyle(), and saveLocalStyle().

◆ saveTaskList()

bool CCopasiXML::saveTaskList ( )

private

Save the list of tasks.

Returns: bool success

References CXMLAttributeList::add(), CReport::append(), CReport::confirmOverwrite(), CCopasiXMLInterface::endSaveElement(), CXMLAttributeList::erase(), CReportDefinition::getKey(), CCopasiTask::getKey(), CCopasiTask::getMethod(), CDataObject::getObjectName(), CCopasiTask::getProblem(), CCopasiTask::getReport(), CReport::getReportDefinition(), CCopasiMethod::getSubType(), CReport::getTarget(), CCopasiTask::getType(), haveTaskList(), CDirEntry::isRelativePath(), CCopasiTask::isScheduled(), CCopasiTask::isUpdateModel(), CDirEntry::makePathRelative(), CTaskEnum::MethodXML, mpTaskList, CCopasiXMLInterface::mPWD, CCopasiXMLInterface::saveElement(), CCopasiXMLInterface::saveParameterGroup(), CDataVector< CType >::size(), CCopasiXMLInterface::startSaveElement(), CTaskEnum::TaskXML, and CCopasiMessage::WARNING.

Referenced by save().

◆ saveTextAttributes()

template<typename TEXTELEMENT >

void CCopasiXML::saveTextAttributes	(	const TEXTELEMENT &	text,
		CXMLAttributeList &	attributes
	)

private

Saves the attributes for a text element. We make this a template so that we can use it for a group as well as a text element.

References CXMLAttributeList::add(), CLText::ANCHOR_BOTTOM, CLText::ANCHOR_END, CLText::ANCHOR_MIDDLE, CLText::ANCHOR_START, CLText::ANCHOR_TOP, CLText::STYLE_ITALIC, and CLText::WEIGHT_BOLD.

◆ saveTransformation2D()

void CCopasiXML::saveTransformation2D ( const CLTransformation2D & transformation )

private

Saves a class that is subclasses from Transformation2D. This covers images, curves, rectangles, ellipses, polygons, text elements and groups.

References saveEllipseElement(), saveGroupElement(), saveImageElement(), savePolygonElement(), saveRectangleElement(), saveRenderCurveElement(), and saveRenderTextElement().

Referenced by saveGroupElement().

◆ saveTransformationAttributes()

void CCopasiXML::saveTransformationAttributes	(	const CLTransformation2D &	transformation,
		CXMLAttributeList &	attributes
	)

private

Saves the attributes for a transformation.

References CXMLAttributeList::add(), CLTransformation2D::get2DTransformationString(), CLTransformation::get3DTransformationString(), CLTransformation::is2DTransformation(), CLTransformation::isIdentityMatrix(), and CLTransformation::isSetMatrix().

Referenced by save1DAttributes(), and saveImageElement().

◆ saveUnitDefinitionList()

bool CCopasiXML::saveUnitDefinitionList ( )

Save the Unit Definition list.

Returns: bool success

References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CXMLAttributeList::erase(), CUnit::getExpression(), CUnitDefinition::getKey(), CDataObject::getObjectName(), CUnitDefinition::getSymbol(), CRootContainer::getUnitList(), CModel::getUnitSymbolUsage(), CUnitDefinition::isReadOnly(), mpModel, saveAnnotation(), CCopasiXMLInterface::saveData(), CDataVector< CType >::size(), and CCopasiXMLInterface::startSaveElement().

Referenced by save().

◆ setDatamodel()

bool CCopasiXML::setDatamodel ( CDataModel * pDataModel )

Set the datamodel.

Parameters

CDataModel* pDataModel

Returns: bool success

References mpDataModel.

Referenced by CDataModel::loadModel(), CDataModel::saveModel(), and CDataModel::saveModelToString().

◆ setFunctionList()

bool CCopasiXML::setFunctionList ( CDataVectorN< CFunction > * pFunctionList )

Set the function list.

Parameters

CopasiVectorN< CFunction > * pFunctionList

Returns: bool success

References mpFunctionList.

Referenced by buildFunctionList(), CFunctionDB::load(), CDataModel::loadModel(), and CFunctionDB::save().

◆ setGUI()

bool CCopasiXML::setGUI ( SCopasiXMLGUI * pGUI )

Set the GUI.

Parameters

SCopasiXMLGUI *pGUI

Returns: bool success

References mpGUI.

Referenced by CDataModel::loadModel(), CDataModel::saveModel(), and CDataModel::saveModelToString().

◆ setLayoutList()

bool CCopasiXML::setLayoutList ( const CListOfLayouts & reportList )

Set the layout list.

Parameters

const CListOfLayouts & reportList

Returns: bool success

References mpLayoutList.

Referenced by CDataModel::saveModel(), and CDataModel::saveModelToString().

◆ setModel()

bool CCopasiXML::setModel ( CModel * pModel )

Set the model.

Parameters

CModel * pModel

Returns: bool success

References mpModel.

Referenced by CDataModel::saveModel(), CDataModel::saveModelParameterSets(), and CDataModel::saveModelToString().

◆ setPlotList()

bool CCopasiXML::setPlotList ( COutputDefinitionVector * pPlotList )

Set the plot list.

Parameters

COutputDefinitionVector * pPlotList

Returns: bool success

References mpPlotList.

Referenced by CDataModel::saveModel(), and CDataModel::saveModelToString().

◆ setReportList()

bool CCopasiXML::setReportList ( CReportDefinitionVector * pReportList )

Set the report list.

Parameters

CReportDefinitionVector *pReportList

Returns: bool success

References mpReportList.

Referenced by CDataModel::saveModel(), and CDataModel::saveModelToString().

◆ setTaskList()

bool CCopasiXML::setTaskList ( CDataVectorN< CCopasiTask > * pTaskList )

Set the task list.

Parameters

CDataVectorN< CCopasiTask > *pTaskList

Returns: bool success

References mpTaskList.

Referenced by CDataModel::saveModel(), and CDataModel::saveModelToString().

Member Data Documentation

◆ mMCXML21Issued

bool CCopasiXML::mMCXML21Issued

private

Remember if we already issued MCXML21

Referenced by saveLayoutList().

◆ mpDataModel

CDataModel* CCopasiXML::mpDataModel

private

Pointer to the datamodel

Referenced by buildFunctionList(), load(), saveSBMLReference(), and setDatamodel().

◆ mpFunctionList

CDataVectorN< CFunction >* CCopasiXML::mpFunctionList

private

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

Referenced by freeFunctionList(), getFunctionList(), haveFunctionList(), load(), saveFunctionList(), and setFunctionList().

◆ mpGUI

SCopasiXMLGUI* CCopasiXML::mpGUI

private

Pointer to a GUI related information, which has been loaded or is to be saved. The ownership is handed to the user.

Referenced by freeGUI(), getGUI(), haveGUI(), load(), saveGUI(), and setGUI().

◆ mpLayoutList

CListOfLayouts* CCopasiXML::mpLayoutList

private

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

Referenced by freeLayoutList(), getLayoutList(), haveLayoutList(), load(), saveLayoutList(), and setLayoutList().

◆ mpModel

CModel* CCopasiXML::mpModel

private

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

Referenced by fixBuild113(), fixBuild18(), fixBuildBefore104(), freeModel(), getModel(), haveModel(), load(), mergeUnitDefinitions(), saveModel(), saveModelParameterSets(), saveUnitDefinitionList(), and setModel().

◆ mpPlotList

COutputDefinitionVector* CCopasiXML::mpPlotList

private

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

Referenced by freePlotList(), getPlotList(), havePlotList(), load(), savePlotList(), and setPlotList().

◆ mpReportList

CReportDefinitionVector* CCopasiXML::mpReportList

private

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

Referenced by freeReportList(), getReportList(), haveReportList(), load(), saveReportList(), and setReportList().

◆ mpTaskList

CDataVectorN< CCopasiTask >* CCopasiXML::mpTaskList

private

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

Referenced by fixBuild55(), fixBuild81(), freeTaskList(), getTaskList(), haveTaskList(), load(), saveTaskList(), and setTaskList().

◆ mSBMLReference

std::map< std::string, std::string > CCopasiXML::mSBMLReference

private

SBML Reference

Referenced by saveFunctionList(), saveModel(), and saveSBMLReference().

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ CCopasiXML()

◆ ~CCopasiXML()

Member Function Documentation

◆ buildFunctionList()

◆ fixBuild113()

◆ fixBuild171()

◆ fixBuild18()

◆ fixBuild55()

◆ fixBuild81()

◆ fixBuildBefore104()

◆ freeFunctionList()

◆ freeGUI()

◆ freeLayoutList()

◆ freeModel()

◆ freePlotList()

◆ freeReportList()

◆ freeTaskList()

◆ getFunctionList()

◆ getGUI()

◆ getLayoutList()

◆ getModel()

◆ getPlotList()

◆ getReportList()

◆ getTaskList()

◆ haveFunctionList()

◆ haveGUI()

◆ haveLayoutList()

◆ haveModel()

◆ havePlotList()

◆ haveReportList()

◆ haveTaskList()

◆ load()

◆ mergeUnitDefinitions()

◆ save()

◆ save1DAttributes()

◆ save2DAttributes()

◆ saveAnnotation()

◆ saveArrowHeadAttributes()

◆ saveBoundingBox()

◆ saveColorDefinition()

◆ saveCurve()

◆ saveCurveElements()

◆ saveDimensions()

◆ saveEllipseElement()

◆ saveFunctionList()

◆ saveGlobalRenderInformation()

◆ saveGlobalStyle()

◆ saveGradientAttributes()

◆ saveGradientElements()

◆ saveGradientStop()

◆ saveGroupElement()

◆ saveGUI()

◆ saveImageElement()

◆ saveLayoutList()

◆ saveLinearGradient()

◆ saveLineEnding()

◆ saveListOfGlobalRenderInformation()

◆ saveListOfLocalRenderInformation()

◆ saveLocalRenderInformation()

◆ saveLocalStyle()

◆ saveModel()

◆ saveModelParameter()

◆ saveModelParameterSets() [1/2]

◆ saveModelParameterSets() [2/2]

◆ savePlotList()

◆ savePolygonElement()

◆ savePosition()

◆ saveRadialGradient()

◆ saveRectangleElement()

◆ saveRenderCurveElement()

◆ saveRenderInformationAttributes()

◆ saveRenderInformationDefinitionElements()

◆ saveRenderPoint()

◆ saveRenderTextElement()

◆ saveReportList()