COPASI API
4.16.103
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#include <CCopasiXML.h>
Public Member Functions | |
CCopasiXML () | |
bool | freeFunctionList () |
bool | freeGUI () |
bool | freeLayoutList () |
bool | freeModel () |
bool | freePlotList () |
bool | freeReportList () |
bool | freeTaskList () |
CCopasiVectorN< CFunction > * | getFunctionList () const |
SCopasiXMLGUI * | getGUI () const |
CListOfLayouts * | getLayoutList () const |
CModel * | getModel () const |
COutputDefinitionVector * | getPlotList () const |
CReportDefinitionVector * | getReportList () const |
CCopasiVectorN< 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) |
bool | setDatamodel (CCopasiDataModel *pDataModel) |
bool | setFunctionList (CCopasiVectorN< 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 (CCopasiVectorN< CCopasiTask > *pTaskList) |
~CCopasiXML () | |
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CCopasiXMLInterface () | |
bool | load (const std::string &fileName, const std::string &relativeTo) |
bool | save (const std::string &fileName, const std::string &relativeTo) |
virtual | ~CCopasiXMLInterface () |
Private Attributes | |
bool | mMCXML21Issued |
CCopasiDataModel * | mpDataModel |
CCopasiVectorN< CFunction > * | mpFunctionList |
SCopasiXMLGUI * | mpGUI |
CListOfLayouts * | mpLayoutList |
CModel * | mpModel |
COutputDefinitionVector * | mpPlotList |
CReportDefinitionVector * | mpReportList |
CCopasiVectorN< CCopasiTask > * | mpTaskList |
std::map< std::string, std::string > | mSBMLReference |
Additional Inherited Members | |
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enum | EncodingType { none = 0, standard, attribute, character } |
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static std::string | encode (const std::string &str, const EncodingType &type=standard) |
static std::string | utf8 (const std::string &str) |
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bool | endSaveElement (const std::string &name) |
bool | saveData (const std::string &data) |
bool | saveElement (const std::string &name, CXMLAttributeList &attributeList) |
bool | saveParameter (const CCopasiParameter ¶meter) |
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) |
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std::string | mIndent |
std::istream * | mpIstream |
std::ostream * | mpOstream |
std::string | mPWD |
Definition at line 75 of file CCopasiXML.h.
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
Definition at line 87 of file CCopasiXML.cpp.
CCopasiXML::~CCopasiXML | ( | ) |
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Build a list of functions.
Definition at line 1872 of file CCopasiXML.cpp.
References CCopasiRootContainer::getFunctionList(), CCopasiDataModel::getModel(), CFunctionDB::getUsedFunctions(), mpDataModel, and setFunctionList().
Referenced by save().
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Fix files written with Version 4.10.55, which wrote the square root of user defined weights for the parameter fitting task
Definition at line 1886 of file CCopasiXML.cpp.
References C_INVALID_INDEX, CFitTask::fixBuild55(), CCopasiVectorN< CType >::getIndex(), mpTaskList, and pTask.
Referenced by load().
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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.
Definition at line 1903 of file CCopasiXML.cpp.
References C_INVALID_INDEX, CScanTask::fixBuild81(), CCopasiVectorN< CType >::getIndex(), mpTaskList, and pTask.
Referenced by load().
bool CCopasiXML::freeFunctionList | ( | ) |
Free the function list.
Definition at line 282 of file CCopasiXML.cpp.
References mpFunctionList, and pdelete.
Referenced by save().
bool CCopasiXML::freeGUI | ( | ) |
Free the GUI.
Definition at line 369 of file CCopasiXML.cpp.
References mpGUI, and pdelete.
Referenced by CCopasiDataModel::loadModel().
bool CCopasiXML::freeLayoutList | ( | ) |
Free the layout list.
Definition at line 389 of file CCopasiXML.cpp.
References mpLayoutList, and pdelete.
Referenced by CCopasiDataModel::loadModel().
bool CCopasiXML::freeModel | ( | ) |
Free the model.
Definition at line 264 of file CCopasiXML.cpp.
References mpModel, and pdelete.
Referenced by CCopasiDataModel::loadModel().
bool CCopasiXML::freePlotList | ( | ) |
Free the plot list.
Definition at line 331 of file CCopasiXML.cpp.
References mpPlotList, and pdelete.
Referenced by CCopasiDataModel::loadModel().
bool CCopasiXML::freeReportList | ( | ) |
Free the report list.
Definition at line 351 of file CCopasiXML.cpp.
References mpReportList, and pdelete.
Referenced by CCopasiDataModel::loadModel().
bool CCopasiXML::freeTaskList | ( | ) |
Free the task list.
Definition at line 311 of file CCopasiXML.cpp.
References mpTaskList, and pdelete.
Referenced by CCopasiDataModel::loadModel().
CCopasiVectorN< CFunction > * CCopasiXML::getFunctionList | ( | ) | const |
Retrieve the function list.
Definition at line 276 of file CCopasiXML.cpp.
References mpFunctionList.
SCopasiXMLGUI * CCopasiXML::getGUI | ( | ) | const |
Retrieve the SCopasiXMLGUI.
Definition at line 365 of file CCopasiXML.cpp.
References mpGUI.
CListOfLayouts * CCopasiXML::getLayoutList | ( | ) | const |
Retrieve the layout list.
Definition at line 383 of file CCopasiXML.cpp.
References mpLayoutList.
Referenced by CCopasiDataModel::loadModel().
CModel * CCopasiXML::getModel | ( | ) | const |
Retreive the model.
Definition at line 260 of file CCopasiXML.cpp.
References mpModel.
Referenced by CCopasiDataModel::loadModel().
COutputDefinitionVector * CCopasiXML::getPlotList | ( | ) | const |
Retrieve the plot list.
Definition at line 325 of file CCopasiXML.cpp.
References mpPlotList.
Referenced by CCopasiDataModel::loadModel().
CReportDefinitionVector * CCopasiXML::getReportList | ( | ) | const |
Retrieve the report list.
Definition at line 345 of file CCopasiXML.cpp.
References mpReportList.
Referenced by CCopasiDataModel::loadModel().
CCopasiVectorN< CCopasiTask > * CCopasiXML::getTaskList | ( | ) | const |
Retrieve the task list.
Definition at line 305 of file CCopasiXML.cpp.
References mpTaskList.
Referenced by CCopasiDataModel::loadModel().
bool CCopasiXML::haveFunctionList | ( | ) | const |
Retrieve whether the XML contains a function list.
Definition at line 279 of file CCopasiXML.cpp.
References mpFunctionList.
Referenced by save(), and saveFunctionList().
bool CCopasiXML::haveGUI | ( | ) | const |
Retrieve whether the XML contains a GUI.
Definition at line 367 of file CCopasiXML.cpp.
References mpGUI.
Referenced by saveGUI().
bool CCopasiXML::haveLayoutList | ( | ) | const |
Retrieve whether the XML contains a layout list.
Definition at line 386 of file CCopasiXML.cpp.
References mpLayoutList.
Referenced by saveLayoutList().
bool CCopasiXML::haveModel | ( | ) | const |
Retreive whether the XML contains a model.
Definition at line 262 of file CCopasiXML.cpp.
References mpModel.
Referenced by save(), and saveModel().
bool CCopasiXML::havePlotList | ( | ) | const |
Retrieve whether the XML contains a plot list.
Definition at line 328 of file CCopasiXML.cpp.
References mpPlotList.
Referenced by savePlotList().
bool CCopasiXML::haveReportList | ( | ) | const |
Retrieve whether the XML contains a report list.
Definition at line 348 of file CCopasiXML.cpp.
References mpReportList.
Referenced by saveReportList().
bool CCopasiXML::haveTaskList | ( | ) | const |
Retrieve whether the XML contains a task list.
Definition at line 308 of file CCopasiXML.cpp.
References mpTaskList.
Referenced by saveTaskList().
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Load information from a given istream.
std::istream | & is |
const | std::string & pwd |
Implements CCopasiXMLInterface.
Definition at line 169 of file CCopasiXML.cpp.
References BUFFER_SIZE, fatalError, fixBuild55(), fixBuild81(), CExpatTemplate< CType >::getCurrentColumnNumber(), CExpatTemplate< CType >::getCurrentLineNumber(), CExpatTemplate< CType >::getErrorString(), CCopasiXMLParser::getLayoutList(), CCopasiXMLParser::getModel(), CCopasiXMLParser::getPlotList(), CCopasiXMLParser::getReportList(), CCopasiXMLParser::getTaskList(), CVersion::getVersion(), CVersion::getVersionDevel(), MCXML, mpDataModel, mpFunctionList, mpGUI, CCopasiXMLInterface::mpIstream, mpLayoutList, mpModel, mpPlotList, mpReportList, mpTaskList, CCopasiXMLInterface::mPWD, CExpatTemplate< CType >::parse(), pdelete, CCopasiMessage::RAW, CCopasiXMLParser::setDatamodel(), CCopasiXMLParser::setFunctionList(), CCopasiXMLParser::setGUI(), CCopasiXMLParser::setLayoutList(), CVersion::VERSION, and CCopasiMessage::WARNING.
Referenced by CFunctionDB::load(), and CCopasiDataModel::loadModel().
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Save information to a given ostream.
std::ostream | & os |
const | std::string & relativeTo |
Implements CCopasiXMLInterface.
Definition at line 102 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), buildFunctionList(), CCopasiXMLInterface::endSaveElement(), freeFunctionList(), CVersion::getVersion(), haveFunctionList(), haveModel(), CCopasiXMLInterface::mpOstream, CCopasiXMLInterface::mPWD, saveFunctionList(), saveGUI(), saveLayoutList(), saveModel(), savePlotList(), saveReportList(), saveSBMLReference(), saveTaskList(), CCopasiXMLInterface::startSaveElement(), UTCTimeStamp(), and CVersion::VERSION.
Referenced by save_cps_model_to_stream().
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Saves the attributes for a 1D element
Definition at line 2342 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CLGraphicalPrimitive1D::getDashArray(), CLGraphicalPrimitive1D::getStroke(), CLGraphicalPrimitive1D::getStrokeWidth(), CLGraphicalPrimitive1D::isSetDashArray(), CLGraphicalPrimitive1D::isSetStroke(), CLGraphicalPrimitive1D::isSetStrokeWidth(), and saveTransformationAttributes().
Referenced by save2DAttributes(), saveRenderCurveElement(), and saveRenderTextElement().
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Saves the attributes for a 2D element
Definition at line 2380 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CLGraphicalPrimitive2D::EVENODD, CLGraphicalPrimitive2D::getFillColor(), CLGraphicalPrimitive2D::getFillRule(), CLGraphicalPrimitive2D::isSetFill(), CLGraphicalPrimitive2D::isSetFillRule(), CLGraphicalPrimitive2D::NONZERO, and save1DAttributes().
Referenced by saveEllipseElement(), saveGroupElement(), savePolygonElement(), and saveRectangleElement().
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Definition at line 922 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CAnnotation::getMiriamAnnotation(), CAnnotation::getNotes(), CAnnotation::getUnsupportedAnnotations(), CCopasiXMLInterface::mpOstream, CCopasiXMLInterface::saveXhtml(), CXMLAttributeList::setValue(), and CCopasiXMLInterface::startSaveElement().
Referenced by saveFunctionList(), and saveModel().
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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.
Definition at line 2505 of file CCopasiXML.cpp.
References CXMLAttributeList::add().
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Definition at line 1382 of file CCopasiXML.cpp.
References CCopasiXMLInterface::endSaveElement(), CLBoundingBox::getDimensions(), CLBoundingBox::getPosition(), saveDimensions(), savePosition(), and CCopasiXMLInterface::startSaveElement().
Referenced by saveLayoutList(), and saveLineEnding().
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Save a single color definition element.
Definition at line 2103 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CLColorDefinition::createValueString(), CLColorDefinition::getId(), and CCopasiXMLInterface::saveElement().
Referenced by saveRenderInformationDefinitionElements().
Definition at line 1390 of file CCopasiXML.cpp.
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().
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saves a vector of curve elements. This can be called from the polygon as well as the curve.
Definition at line 2718 of file CCopasiXML.cpp.
References CCopasiXMLInterface::endSaveElement(), saveRenderPoint(), and CCopasiXMLInterface::startSaveElement().
Referenced by savePolygonElement(), and saveRenderCurveElement().
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Definition at line 1373 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CXMLAttributeList::erase(), CLDimensions::getHeight(), CLDimensions::getWidth(), and CCopasiXMLInterface::saveElement().
Referenced by saveBoundingBox().
saves a single ellipse element.
Definition at line 2636 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CLEllipse::getCX(), CLEllipse::getCY(), CLEllipse::getCZ(), CLEllipse::getRX(), CLEllipse::getRY(), save2DAttributes(), CCopasiXMLInterface::saveElement(), and CLRelAbsVector::toString().
Referenced by saveTransformation2D().
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Save the list of functions.
Definition at line 1018 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CXMLAttributeList::erase(), CEvaluationTree::getInfix(), CFunction::getKey(), CFunctionParameter::getKey(), CCopasiObject::getObjectName(), CFunction::getSBMLId(), CEvaluationTree::getType(), CFunctionParameter::getUsage(), CFunction::getVariables(), haveFunctionList(), CFunction::isReversible(), mpFunctionList, mSBMLReference, CFunctionParameter::RoleNameXML, saveAnnotation(), CCopasiXMLInterface::saveData(), CCopasiXMLInterface::saveElement(), CXMLAttributeList::setValue(), CFunctionParameters::size(), CCopasiVector< T >::size(), CCopasiXMLInterface::startSaveElement(), TriFalse, TriTrue, TriUnspecified, and CEvaluationTree::XMLType.
Referenced by save().
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Saves a single global render information object.
Definition at line 1955 of file CCopasiXML.cpp.
References CCopasiXMLInterface::endSaveElement(), CLGlobalRenderInformation::getNumStyles(), CLGlobalRenderInformation::getStyle(), saveGlobalStyle(), saveRenderInformationAttributes(), saveRenderInformationDefinitionElements(), and CCopasiXMLInterface::startSaveElement().
Referenced by saveListOfGlobalRenderInformation().
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Saves a single local style element.
Definition at line 2253 of file CCopasiXML.cpp.
References CCopasiXMLInterface::endSaveElement(), saveStyleAttributes(), saveStyleElements(), and CCopasiXMLInterface::startSaveElement().
Referenced by saveGlobalRenderInformation().
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Adds the attributes common to radial and linear gradient.
Definition at line 2167 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CLGradientBase::getId(), CLGradientBase::getSpreadMethod(), CLGradientBase::PAD, CLGradientBase::REFLECT, and CLGradientBase::REPEAT.
Referenced by saveLinearGradient(), and saveRadialGradient().
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Saves the elements that are common to linear and radial gradients.
Definition at line 2191 of file CCopasiXML.cpp.
References CLGradientBase::getGradientStop(), CLGradientBase::getNumGradientStops(), and saveGradientStop().
Referenced by saveLinearGradient(), and saveRadialGradient().
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Saves a single gradient stop element.
Definition at line 2207 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CLGradientStop::getOffset(), CLGradientStop::getStopColor(), CCopasiXMLInterface::saveElement(), and CLRelAbsVector::toString().
Referenced by saveGradientElements().
Saves a group element.
Definition at line 2293 of file CCopasiXML.cpp.
References CCopasiXMLInterface::endSaveElement(), save2DAttributes(), saveTransformation2D(), and CCopasiXMLInterface::startSaveElement().
Referenced by saveLineEnding(), saveStyleElements(), and saveTransformation2D().
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Save GUI information
Definition at line 1779 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CSlider::convertScaleToScaleName(), CCopasiXMLInterface::endSaveElement(), CSlider::getAssociatedEntityKey(), CSlider::getKey(), CSlider::getMaxValue(), CSlider::getMinValue(), CSlider::getScaling(), SCopasiXMLGUI::getSliderList(), CSlider::getSliderObjectCN(), CSlider::getSliderType(), CSlider::getSliderValue(), CSlider::getTickFactor(), CSlider::getTickNumber(), haveGUI(), mpGUI, CCopasiXMLInterface::saveElement(), CXMLAttributeList::setValue(), CCopasiVector< T >::size(), CCopasiXMLInterface::startSaveElement(), and CSlider::TypeName.
Referenced by save().
saves a single image element.
Definition at line 2580 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CLImage::getHeight(), CLImage::getImageReference(), CLImage::getWidth(), CLImage::getX(), CLImage::getY(), CLImage::getZ(), CCopasiXMLInterface::saveElement(), saveTransformationAttributes(), and CLRelAbsVector::toString().
Referenced by saveTransformation2D().
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Save the list of layout.
Definition at line 1431 of file CCopasiXML.cpp.
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(), CCopasiObject::getObjectName(), CLGraphicalObject::getObjectRole(), CLMetabReferenceGlyph::getRole(), CLTextGlyph::getText(), CLDimensions::getWidth(), CLGraphicalObject::hasValidModelReference(), haveLayoutList(), CLTextGlyph::isTextSet(), MCXML, mMCXML21Issued, mpLayoutList, saveBoundingBox(), saveCurve(), CCopasiXMLInterface::saveElement(), saveListOfGlobalRenderInformation(), saveListOfLocalRenderInformation(), CLGraphicalObject::setModelObjectKey(), CLTextGlyph::setText(), CCopasiVector< T >::size(), CCopasiXMLInterface::startSaveElement(), CCopasiMessage::WARNING, and CLMetabReferenceGlyph::XMLRole.
Referenced by save().
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Saves a single linear gradient definition.
Definition at line 2114 of file CCopasiXML.cpp.
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().
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Saves a line ending definiton,
Definition at line 2215 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CLLineEnding::getBoundingBox(), CLLineEnding::getGroup(), CLLineEnding::getId(), CLLineEnding::getIsEnabledRotationalMapping(), saveBoundingBox(), saveGroupElement(), and CCopasiXMLInterface::startSaveElement().
Referenced by saveRenderInformationDefinitionElements().
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Saves the list of global render information objects.
Definition at line 1923 of file CCopasiXML.cpp.
References CCopasiXMLInterface::endSaveElement(), saveGlobalRenderInformation(), CCopasiVector< T >::size(), and CCopasiXMLInterface::startSaveElement().
Referenced by saveLayoutList().
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Saves the list of local render information objects.
Definition at line 1939 of file CCopasiXML.cpp.
References CCopasiXMLInterface::endSaveElement(), saveLocalRenderInformation(), CCopasiVector< T >::size(), and CCopasiXMLInterface::startSaveElement().
Referenced by saveLayoutList().
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Saves a single local render information object.
Definition at line 1984 of file CCopasiXML.cpp.
References CCopasiXMLInterface::endSaveElement(), CLLocalRenderInformation::getNumStyles(), CLLocalRenderInformation::getStyle(), saveLocalStyle(), saveRenderInformationAttributes(), saveRenderInformationDefinitionElements(), and CCopasiXMLInterface::startSaveElement().
Referenced by saveListOfLocalRenderInformation().
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Saves a single local style element.
Definition at line 2233 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CLStyle::createStringFromSet(), CCopasiXMLInterface::endSaveElement(), CLLocalStyle::getKeyList(), CLLocalStyle::getNumKeys(), saveStyleAttributes(), saveStyleElements(), and CCopasiXMLInterface::startSaveElement().
Referenced by saveLocalRenderInformation().
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Save the model.
Definition at line 395 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CModelParameterGroup::begin(), CCopasiVector< T >::begin(), CModelParameterGroup::end(), CCopasiVector< T >::end(), CCopasiXMLInterface::endSaveElement(), CXMLAttributeList::erase(), CModelEntity::FIXED, CModel::getAreaUnitName(), CEvent::getAssignments(), CModel::getAvogadro(), CReaction::getChemEq(), CMetab::getCompartment(), CModel::getCompartments(), CEvent::getDelayAssignment(), CEvent::getDelayExpression(), CCompartment::getDimensionality(), CStateTemplate::getEntities(), CModel::getEvents(), CModelEntity::getExpression(), CEvent::getFireAtInitialTime(), CReaction::getFunction(), CReaction::getFunctionParameters(), CModelEntity::getInitialExpression(), CModelParameterSet::getKey(), CFunction::getKey(), CModelEntity::getKey(), CReaction::getKey(), CEvent::getKey(), CCopasiParameterGroup::getKey(), CModel::getKey(), CModel::getLengthUnitName(), CModel::getMetabolites(), CModel::getModelParameterSet(), CModel::getModelParameterSets(), CModel::getModelType(), CModel::getModelValues(), CChemEq::getModifiers(), CCopasiParameterGroup::getName(), CCopasiObject::getObjectName(), CReaction::getParameterMappings(), CReaction::getParameters(), CEvent::getPersistentTrigger(), CChemEq::getProducts(), CModel::getQuantityUnitName(), CModel::getReactions(), CModelEntity::getSBMLId(), CEvent::getSBMLId(), CReaction::getSBMLId(), CModel::getStateTemplate(), CModelEntity::getStatus(), CChemEq::getSubstrates(), CModel::getTimeUnitName(), CEvent::getTriggerExpression(), CCopasiRootContainer::getUndefinedFunction(), CCopasiParameterGroup::getValue(), CModel::getVolumeUnitName(), haveModel(), CReaction::isFast(), CReaction::isReversible(), CCopasiXMLInterface::mIndent, CModel::ModelTypeNames, mpModel, CCopasiXMLInterface::mpOstream, mSBMLReference, CCopasiParameter::Value::pDOUBLE, CModelEntity::REACTIONS, saveAnnotation(), CCopasiXMLInterface::saveData(), CCopasiXMLInterface::saveElement(), saveModelParameter(), CXMLAttributeList::setValue(), CFunctionParameters::size(), CStateTemplate::size(), CCopasiVector< T >::size(), CCopasiParameterGroup::size(), CXMLAttributeList::skip(), CCopasiXMLInterface::startSaveElement(), and CModelEntity::XMLStatus.
Referenced by save().
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Save a model parameter
const | CModelParameter * pModelParameter |
Definition at line 963 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CModelParameter::getCN(), CModelParameter::getCompareResult(), CModelParameter::getInitialExpression(), CModelParameter::getSimulationType(), CModelParameter::getType(), CModelParameter::getValue(), CModelParameter::Group, CModelParameter::Missing, CModelParameter::ParticleNumbers, CModelParameter::Reaction, CCopasiXMLInterface::saveData(), CCopasiXMLInterface::saveElement(), CCopasiXMLInterface::startSaveElement(), CModelParameter::TypeNames, and CModelEntity::XMLStatus.
Referenced by saveModel().
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Save the list of plots.
Definition at line 1106 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CXMLAttributeList::erase(), CPlotItem::getChannels(), CPlotSpecification::getItems(), CPlotItem::getNumChannels(), CCopasiObject::getObjectName(), CPlotItem::getType(), havePlotList(), CPlotSpecification::isActive(), CPlotDataChannelSpec::max, CPlotDataChannelSpec::maxAutoscale, CPlotDataChannelSpec::min, CPlotDataChannelSpec::minAutoscale, mpPlotList, CCopasiXMLInterface::saveElement(), CCopasiXMLInterface::saveParameterGroup(), CCopasiVector< T >::size(), CCopasiXMLInterface::startSaveElement(), and CPlotItem::XMLType.
Referenced by save().
saves a single image element.
Definition at line 2690 of file CCopasiXML.cpp.
References CCopasiXMLInterface::endSaveElement(), CLPolygon::getListOfElements(), save2DAttributes(), saveCurveElements(), and CCopasiXMLInterface::startSaveElement().
Referenced by saveTransformation2D().
Definition at line 1364 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CXMLAttributeList::erase(), CLPoint::getX(), CLPoint::getY(), and CCopasiXMLInterface::saveElement().
Referenced by saveBoundingBox(), and saveCurve().
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Saves a single radial gradient definition.
Definition at line 2145 of file CCopasiXML.cpp.
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().
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saves a single rectangle element.
Definition at line 2603 of file CCopasiXML.cpp.
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().
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saves a single image element.
Definition at line 2703 of file CCopasiXML.cpp.
References CCopasiXMLInterface::endSaveElement(), save1DAttributes(), saveCurveElements(), and CCopasiXMLInterface::startSaveElement().
Referenced by saveTransformation2D().
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Saves the attributes that render information objects have in common.
Definition at line 2010 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CLRenderInformationBase::getBackgroundColor(), CLRenderInformationBase::getKey(), CLRenderInformationBase::getName(), and CLRenderInformationBase::getReferenceRenderInformationKey().
Referenced by saveGlobalRenderInformation(), and saveLocalRenderInformation().
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Saves color definitions, gradient definitions and line endings.
Saves color definitions , gradient definitions and line endings.
Definition at line 2045 of file CCopasiXML.cpp.
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().
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saves a single render point element.
Definition at line 2734 of file CCopasiXML.cpp.
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().
saves a single text element.
Definition at line 2666 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CLText::getX(), CLText::getY(), CLText::getZ(), save1DAttributes(), CCopasiXMLInterface::saveData(), CCopasiXMLInterface::startSaveElement(), and CLRelAbsVector::toString().
Referenced by saveTransformation2D().
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Save the list of reports.
Definition at line 1297 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CXMLAttributeList::erase(), CReportDefinition::getBodyAddr(), CReportDefinition::getComment(), CReportDefinition::getFooterAddr(), CReportDefinition::getHeaderAddr(), CReportDefinition::getKey(), CCopasiObject::getObjectName(), CReportDefinition::getPrecision(), CReportDefinition::getSeparator(), CCopasiStaticString::getStaticString(), CReportDefinition::getTableAddr(), CReportDefinition::getTaskType(), CReportDefinition::getTitle(), haveReportList(), CReportDefinition::isTable(), mpReportList, CCopasiXMLInterface::saveElement(), saveReportSection(), CCopasiXMLInterface::saveXhtml(), CXMLAttributeList::setValue(), CCopasiVector< T >::size(), CCopasiXMLInterface::startSaveElement(), and CCopasiTask::XMLType.
Referenced by save().
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Save a Report Section such as Header, Body or Footer.
const | std::string & name |
const | std::vector <CCopasiObjectName> & section |
Definition at line 1259 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CCopasiXMLInterface::saveData(), CCopasiXMLInterface::saveElement(), CXMLAttributeList::set(), and CCopasiXMLInterface::startSaveElement().
Referenced by saveReportList().
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Save the SBML reference information
Definition at line 1831 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CCopasiXMLInterface::endSaveElement(), CXMLAttributeList::erase(), CDirEntry::fileName(), CCopasiDataModel::getSBMLFileName(), CDirEntry::isRelativePath(), CDirEntry::makePathRelative(), mpDataModel, CCopasiXMLInterface::mPWD, mSBMLReference, CCopasiXMLInterface::saveElement(), CXMLAttributeList::setValue(), and CCopasiXMLInterface::startSaveElement().
Referenced by save().
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Adds the attributes common to both style types.
Definition at line 2266 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CLStyle::createStringFromSet(), CLStyle::getKey(), CLStyle::getNumRoles(), CLStyle::getNumTypes(), CLStyle::getRoleList(), and CLStyle::getTypeList().
Referenced by saveGlobalStyle(), and saveLocalStyle().
Saves the elements common to both style types.
Definition at line 2284 of file CCopasiXML.cpp.
References CLStyle::getGroup(), and saveGroupElement().
Referenced by saveGlobalStyle(), and saveLocalStyle().
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Save the list of tasks.
Definition at line 1184 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CReport::append(), CReport::confirmOverwrite(), CCopasiXMLInterface::endSaveElement(), CXMLAttributeList::erase(), CDirEntry::fileName(), CReportDefinition::getKey(), CCopasiTask::getKey(), CCopasiTask::getMethod(), CCopasiObject::getObjectName(), CCopasiTask::getProblem(), CCopasiTask::getReport(), CReport::getReportDefinition(), CCopasiMethod::getSubType(), CReport::getTarget(), CCopasiTask::getType(), haveTaskList(), CDirEntry::isRelativePath(), CCopasiTask::isScheduled(), CCopasiTask::isUpdateModel(), CDirEntry::makePathRelative(), mpTaskList, CCopasiXMLInterface::mPWD, pTask, CCopasiXMLInterface::saveElement(), CCopasiXMLInterface::saveParameterGroup(), CCopasiVector< T >::size(), CCopasiXMLInterface::startSaveElement(), CCopasiMethod::XMLSubType, and CCopasiTask::XMLType.
Referenced by save().
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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.
Definition at line 2413 of file CCopasiXML.cpp.
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.
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Saves a class that is subclasses from Transformation2D. This covers images, curves, rectangles, ellipses, polygons, text elements and groups.
Definition at line 2524 of file CCopasiXML.cpp.
References saveEllipseElement(), saveGroupElement(), saveImageElement(), savePolygonElement(), saveRectangleElement(), saveRenderCurveElement(), and saveRenderTextElement().
Referenced by saveGroupElement().
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Saves the attributes for a transformation.
Definition at line 2316 of file CCopasiXML.cpp.
References CXMLAttributeList::add(), CLTransformation2D::get2DTransformationString(), CLTransformation::get3DTransformationString(), CLTransformation::is2DTransformation(), CLTransformation::isIdentityMatrix(), and CLTransformation::isSetMatrix().
Referenced by save1DAttributes(), and saveImageElement().
bool CCopasiXML::setDatamodel | ( | CCopasiDataModel * | pDataModel | ) |
Set the datamodel.
CCopasiDataModel* | pDataModel |
Definition at line 299 of file CCopasiXML.cpp.
References mpDataModel.
Referenced by CCopasiDataModel::loadModel(), save_cps_model_to_stream(), and CCopasiDataModel::saveModel().
bool CCopasiXML::setFunctionList | ( | CCopasiVectorN< CFunction > * | pFunctionList | ) |
Set the function list.
CopasiVectorN< | CFunction > * pFunctionList |
Definition at line 270 of file CCopasiXML.cpp.
References mpFunctionList.
Referenced by buildFunctionList(), CFunctionDB::load(), CCopasiDataModel::loadModel(), and CFunctionDB::save().
bool CCopasiXML::setGUI | ( | SCopasiXMLGUI * | pGUI | ) |
Set the GUI.
SCopasiXMLGUI | *pGUI |
Definition at line 359 of file CCopasiXML.cpp.
References mpGUI.
Referenced by CCopasiDataModel::loadModel(), save_cps_model_to_stream(), and CCopasiDataModel::saveModel().
bool CCopasiXML::setLayoutList | ( | const CListOfLayouts & | reportList | ) |
Set the layout list.
const | CListOfLayouts & reportList |
Definition at line 377 of file CCopasiXML.cpp.
References mpLayoutList.
Referenced by save_cps_model_to_stream(), and CCopasiDataModel::saveModel().
bool CCopasiXML::setModel | ( | CModel * | pModel | ) |
Set the model.
CModel | * pModel |
Definition at line 254 of file CCopasiXML.cpp.
References mpModel.
Referenced by save_cps_model_to_stream(), and CCopasiDataModel::saveModel().
bool CCopasiXML::setPlotList | ( | COutputDefinitionVector * | pPlotList | ) |
Set the plot list.
COutputDefinitionVector | * pPlotList |
Definition at line 319 of file CCopasiXML.cpp.
References mpPlotList.
Referenced by save_cps_model_to_stream(), and CCopasiDataModel::saveModel().
bool CCopasiXML::setReportList | ( | CReportDefinitionVector * | pReportList | ) |
Set the report list.
CReportDefinitionVector | *pReportList |
Definition at line 339 of file CCopasiXML.cpp.
References mpReportList.
Referenced by save_cps_model_to_stream(), and CCopasiDataModel::saveModel().
bool CCopasiXML::setTaskList | ( | CCopasiVectorN< CCopasiTask > * | pTaskList | ) |
Set the task list.
CCopasiVectorN< | CCopasiTask > *pTaskList |
Definition at line 288 of file CCopasiXML.cpp.
References mpTaskList.
Referenced by save_cps_model_to_stream(), and CCopasiDataModel::saveModel().
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Remember if we already issued MCXML21
Definition at line 604 of file CCopasiXML.h.
Referenced by saveLayoutList().
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Pointer to the datamodel
Definition at line 599 of file CCopasiXML.h.
Referenced by buildFunctionList(), load(), saveSBMLReference(), and setDatamodel().
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Pointer to a vector of functions which has been loaded or is to be saved. The ownership is handed to the user.
Definition at line 559 of file CCopasiXML.h.
Referenced by freeFunctionList(), getFunctionList(), haveFunctionList(), load(), saveFunctionList(), and setFunctionList().
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Pointer to a vector of plots which has been loaded or is to be saved. The ownership is handed to the user.
Definition at line 589 of file CCopasiXML.h.
Referenced by freeLayoutList(), getLayoutList(), haveLayoutList(), load(), saveLayoutList(), and setLayoutList().
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Pointer to a model which has been loaded or is to be saved. The ownership is handed to the user.
Definition at line 553 of file CCopasiXML.h.
Referenced by freeModel(), getModel(), haveModel(), load(), saveModel(), and setModel().
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Pointer to a vector of plots which has been loaded or is to be saved. The ownership is handed to the user.
Definition at line 577 of file CCopasiXML.h.
Referenced by freePlotList(), getPlotList(), havePlotList(), load(), savePlotList(), and setPlotList().
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Pointer to a vector of reports which has been loaded or is to be saved. The ownership is handed to the user.
Definition at line 571 of file CCopasiXML.h.
Referenced by freeReportList(), getReportList(), haveReportList(), load(), saveReportList(), and setReportList().
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Pointer to a vector of tasks which has been loaded or is to be saved. The ownership is handed to the user.
Definition at line 565 of file CCopasiXML.h.
Referenced by fixBuild55(), fixBuild81(), freeTaskList(), getTaskList(), haveTaskList(), load(), saveTaskList(), and setTaskList().
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SBML Reference
Definition at line 594 of file CCopasiXML.h.
Referenced by saveFunctionList(), saveModel(), and saveSBMLReference().