CCopasiXML Class Reference

#include <CCopasiXML.h>

Inheritance diagram for CCopasiXML:

Collaboration diagram for CCopasiXML:

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 ()
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	fixBuild55 ()
void	fixBuild81 ()
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 CCopasiVector< CLGlobalRenderInformation > &list)
void	saveListOfLocalRenderInformation (const CCopasiVector< CLLocalRenderInformation > &list)
void	saveLocalRenderInformation (const CLLocalRenderInformation &renderInfo)
void	saveLocalStyle (const CLLocalStyle &style)
bool	saveModel ()
bool	saveModelParameter (const CModelParameter *pModelParameter)
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< CRegisteredObjectName > &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
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
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

Detailed Description

Definition at line 75 of file CCopasiXML.h.

Constructor & Destructor Documentation

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.

                      :
  CCopasiXMLInterface(),
  mpModel(NULL),
  mpFunctionList(NULL),
  mpTaskList(NULL),
  mpReportList(NULL),
  mpPlotList(NULL),
  mpGUI(NULL),
  mpLayoutList(NULL),
  mpDataModel(NULL),
  mMCXML21Issued(false)
{}

CCopasiXML::~CCopasiXML

(

)

Destructor

Definition at line 100 of file CCopasiXML.cpp.

{}

Member Function Documentation

bool CCopasiXML::buildFunctionList ( )

private

Build a list of functions.

Returns

bool success

Definition at line 1872 of file CCopasiXML.cpp.

References CCopasiRootContainer::getFunctionList(), CCopasiDataModel::getModel(), CFunctionDB::getUsedFunctions(), mpDataModel, and setFunctionList().

Referenced by save().

{
  bool success = true;

  CCopasiVectorN< CFunction > * pFunctionList
  = new CCopasiVectorN< CFunction >;

  *pFunctionList = CCopasiRootContainer::getFunctionList()->getUsedFunctions(this->mpDataModel->getModel());

  if (!setFunctionList(pFunctionList)) success = false;

  return success;
}

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

Definition at line 1886 of file CCopasiXML.cpp.

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

Referenced by load().

{
  if (mpTaskList == NULL) return;

  size_t Index = mpTaskList->getIndex("Parameter Estimation");

  if (Index == C_INVALID_INDEX) return;

  CFitTask * pTask = dynamic_cast< CFitTask * >((*mpTaskList)[Index]);

  if (pTask == NULL) return;

  pTask->fixBuild55();

  return;
}

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.

Definition at line 1903 of file CCopasiXML.cpp.

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

Referenced by load().

{
  if (mpTaskList == NULL) return;

  size_t Index = mpTaskList->getIndex("Scan");

  if (Index == C_INVALID_INDEX) return;

  CScanTask * pTask = dynamic_cast< CScanTask * >((*mpTaskList)[Index]);

  if (pTask == NULL) return;

  pTask->fixBuild81();

  return;
}

bool CCopasiXML::freeFunctionList

(

)

Free the function list.

Returns

bool success

Definition at line 282 of file CCopasiXML.cpp.

References mpFunctionList, and pdelete.

Referenced by save().

{
  pdelete(mpFunctionList);
  return true;
}

bool CCopasiXML::freeGUI

(

)

Free the GUI.

Returns

bool success

Definition at line 369 of file CCopasiXML.cpp.

References mpGUI, and pdelete.

Referenced by CCopasiDataModel::loadModel().

{
  pdelete(mpGUI);
  return true;
}

bool CCopasiXML::freeLayoutList

(

)

Free the layout list.

Returns

bool success

Definition at line 389 of file CCopasiXML.cpp.

References mpLayoutList, and pdelete.

Referenced by CCopasiDataModel::loadModel().

{
  pdelete(mpLayoutList);
  return true;
}

bool CCopasiXML::freeModel

(

)

Free the model.

Returns

bool success

Definition at line 264 of file CCopasiXML.cpp.

References mpModel, and pdelete.

Referenced by CCopasiDataModel::loadModel().

{
  pdelete(mpModel);
  return true;
}

bool CCopasiXML::freePlotList

(

)

Free the plot list.

Returns

bool success

Definition at line 331 of file CCopasiXML.cpp.

References mpPlotList, and pdelete.

Referenced by CCopasiDataModel::loadModel().

{
  pdelete(mpPlotList);
  return true;
}

bool CCopasiXML::freeReportList

(

)

Free the report list.

Returns

bool success

Definition at line 351 of file CCopasiXML.cpp.

References mpReportList, and pdelete.

Referenced by CCopasiDataModel::loadModel().

{
  pdelete(mpReportList);
  return true;
}

bool CCopasiXML::freeTaskList

(

)

Free the task list.

Returns

bool success

Definition at line 311 of file CCopasiXML.cpp.

References mpTaskList, and pdelete.

Referenced by CCopasiDataModel::loadModel().

{
  pdelete(mpTaskList);
  return true;
}

CCopasiVectorN< CFunction > * CCopasiXML::getFunctionList

(

)

const

Retrieve the function list.

Returns

CCopasiVectorN< CFunction > * pFunctionList

Definition at line 276 of file CCopasiXML.cpp.

References mpFunctionList.

{return mpFunctionList;}

SCopasiXMLGUI * CCopasiXML::getGUI

(

)

const

Retrieve the SCopasiXMLGUI.

Returns

SCopasiXMLGUI * pGUI

Definition at line 365 of file CCopasiXML.cpp.

References mpGUI.

{return mpGUI;}

CListOfLayouts * CCopasiXML::getLayoutList

(

)

const

Retrieve the layout list.

Returns

CListOfLayouts * layoutList

Definition at line 383 of file CCopasiXML.cpp.

References mpLayoutList.

Referenced by CCopasiDataModel::loadModel().

{return mpLayoutList;}

CModel * CCopasiXML::getModel

(

)

const

Retreive the model.

Returns

CModel * pModel

Definition at line 260 of file CCopasiXML.cpp.

References mpModel.

Referenced by CCopasiDataModel::loadModel().

{return mpModel;}

COutputDefinitionVector * CCopasiXML::getPlotList

(

)

const

Retrieve the plot list.

Returns

COutputDefinitionVector * plotList

Definition at line 325 of file CCopasiXML.cpp.

References mpPlotList.

Referenced by CCopasiDataModel::loadModel().

{return mpPlotList;}

CReportDefinitionVector * CCopasiXML::getReportList

(

)

const

Retrieve the report list.

Returns

CReportDefinitionVector * reportList

Definition at line 345 of file CCopasiXML.cpp.

References mpReportList.

Referenced by CCopasiDataModel::loadModel().

{return mpReportList;}

CCopasiVectorN< CCopasiTask > * CCopasiXML::getTaskList

(

)

const

Retrieve the task list.

Returns

CCopasiVectorN< CCopasiTask > * taskList

Definition at line 305 of file CCopasiXML.cpp.

References mpTaskList.

Referenced by CCopasiDataModel::loadModel().

{return mpTaskList;}

bool CCopasiXML::haveFunctionList

(

)

const

Retrieve whether the XML contains a function list.

Returns

bool haveFunctionList

Definition at line 279 of file CCopasiXML.cpp.

References mpFunctionList.

Referenced by save(), and saveFunctionList().

{return mpFunctionList != NULL;}

bool CCopasiXML::haveGUI

(

)

const

Retrieve whether the XML contains a GUI.

Returns

bool have GUI

Definition at line 367 of file CCopasiXML.cpp.

References mpGUI.

Referenced by saveGUI().

{return mpGUI != NULL;}

bool CCopasiXML::haveLayoutList

(

)

const

Retrieve whether the XML contains a layout list.

Returns

bool haveLayoutList

Definition at line 386 of file CCopasiXML.cpp.

References mpLayoutList.

Referenced by saveLayoutList().

{return mpLayoutList != NULL;}

bool CCopasiXML::haveModel

(

)

const

Retreive whether the XML contains a model.

Returns

bool have Model

Definition at line 262 of file CCopasiXML.cpp.

References mpModel.

Referenced by save(), and saveModel().

{return mpModel != NULL;}

bool CCopasiXML::havePlotList

(

)

const

Retrieve whether the XML contains a plot list.

Returns

bool havePlotList

Definition at line 328 of file CCopasiXML.cpp.

References mpPlotList.

Referenced by savePlotList().

{return mpPlotList != NULL;}

bool CCopasiXML::haveReportList

(

)

const

Retrieve whether the XML contains a report list.

Returns

bool haveReportList

Definition at line 348 of file CCopasiXML.cpp.

References mpReportList.

Referenced by saveReportList().

{return mpReportList != NULL;}

bool CCopasiXML::haveTaskList

(

)

const

Retrieve whether the XML contains a task list.

Returns

bool haveTaskList

Definition at line 308 of file CCopasiXML.cpp.

References mpTaskList.

Referenced by saveTaskList().

{return mpTaskList != NULL;}

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.

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().

{
  mPWD = relativeTo;

  is.imbue(std::locale::classic());
  is.precision(16);

  mpIstream = &is;
  bool success = true;
  bool done = false;

  CVersion FileVersion;
  CCopasiXMLParser Parser(FileVersion);

  Parser.setFunctionList(mpFunctionList);
  Parser.setGUI(mpGUI);
  Parser.setLayoutList(mpLayoutList);
  Parser.setDatamodel(this->mpDataModel);

#define BUFFER_SIZE 0xfffe
  char * pBuffer = new char[BUFFER_SIZE + 1];

  try
    {
      while (!done)
        {
          mpIstream->get(pBuffer, BUFFER_SIZE, 0);

          if (mpIstream->eof()) done = true;

          if (mpIstream->fail() && !done) fatalError();

          if (!Parser.parse(pBuffer, -1, done))
            {
              CCopasiMessage Message(CCopasiMessage::RAW, MCXML + 2,
                                     Parser.getCurrentLineNumber(),
                                     Parser.getCurrentColumnNumber(),
                                     Parser.getErrorString());
              done = true;
              success = false;
            }
        }
    }

  catch (...)
    {
      success = false;
    }

  delete [] pBuffer;
#undef BUFFER_SIZE

  mpModel = Parser.getModel();
  mpReportList = Parser.getReportList();
  mpTaskList = Parser.getTaskList();
  mpPlotList = Parser.getPlotList();
  mpLayoutList = Parser.getLayoutList();

  if (!success)
    {
      pdelete(mpModel);
      pdelete(mpReportList);
      pdelete(mpTaskList);
      pdelete(mpPlotList);
      pdelete(mpLayoutList);
    }

  // The range in which the fix needs to be applied
  if (36 <= FileVersion.getVersionDevel() && FileVersion.getVersionDevel() <= 58)
    {
      fixBuild55();
    }

  if (FileVersion.getVersionDevel() <= 81)
    {
      fixBuild81();
    }

  if (!CVersion::VERSION.isCompatible(FileVersion))
    CCopasiMessage(CCopasiMessage::WARNING, MCXML + 9, FileVersion.getVersion().c_str());

  return success;
}

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.

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().

{
  mPWD = relativeTo;

  os.imbue(std::locale::classic());
  os.precision(16);

  mpOstream = &os;
  bool success = true;

  *mpOstream << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>"
             << std::endl;

  *mpOstream << "<!-- generated with COPASI "
             << CVersion::VERSION.getVersion()
             << " (http://www.copasi.org) at "
             << UTCTimeStamp()
             << " UTC -->"
             << std::endl;

  *mpOstream << "<?oxygen RNGSchema=\"http://www.copasi.org/static/schema/CopasiML.rng\" type=\"xml\"?>" << std::endl;

  CXMLAttributeList Attributes;
  Attributes.add("xmlns", "http://www.copasi.org/static/schema");
  Attributes.add("versionMajor", CVersion::VERSION.getVersionMajor());
  Attributes.add("versionMinor", CVersion::VERSION.getVersionMinor());
  Attributes.add("versionDevel", CVersion::VERSION.getVersionDevel());
  Attributes.add("copasiSourcesModified", CVersion::VERSION.isSourceModified());

  /*
  Attributes.add("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance");
  Attributes.add("xsi:noNamespaceSchemaLocation",
                 "http://www.copasi.org/static/schema/CopasiML.rng");
  */

  startSaveElement("COPASI", Attributes);

  if (haveModel() && !haveFunctionList())
    {
      if (!buildFunctionList()) success = false;

      if (!saveFunctionList()) success = false;

      if (!freeFunctionList()) success = false;
    }
  else if (!saveFunctionList()) success = false;

  if (!saveModel()) success = false;

  if (!saveTaskList()) success = false;

  if (!saveReportList()) success = false;

  if (!savePlotList()) success = false;

  if (!saveGUI()) success = false;

  if (!saveLayoutList()) success = false;

  if (!saveSBMLReference()) success = false;

  endSaveElement("COPASI");

  return success;
}

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

private

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().

{
  // first we go and add the transformation attributes because each 1D element is automatically a transformation element.
  saveTransformationAttributes(primitive, attributes);

  // stroke
  if (primitive.isSetStroke())
    {
      attributes.add("stroke", primitive.getStroke());
    }

  // stroke size
  if (primitive.isSetStrokeWidth())
    {
      std::ostringstream os;
      os << primitive.getStrokeWidth();
      attributes.add("stroke-width", os.str());
    }

  // stroke dash array
  if (primitive.isSetDashArray())
    {
      std::ostringstream os;
      size_t i, iMax = primitive.getDashArray().size();
      os << primitive.getDashArray()[0];

      for (i = 1; i < iMax; ++i)
        {
          os << ", " << primitive.getDashArray()[i];
        }

      attributes.add("stroke-dasharray", os.str());
    }
}

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

private

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().

{
  // first we go and add the 1D attributes because each 2D element is automatically a 1D element.
  save1DAttributes(primitive, attributes);

  // fill
  if (primitive.isSetFill())
    {
      attributes.add("fill", primitive.getFillColor());
    }

  // fill rule
  if (primitive.isSetFillRule())
    {
      switch (primitive.getFillRule())
        {
          case CLGraphicalPrimitive2D::EVENODD:
            attributes.add("fill-rule", "evenodd");
            break;

          case CLGraphicalPrimitive2D::NONZERO:
          default:
            attributes.add("fill-rule", "nonzero");
            break;
        }
    }
}

bool CCopasiXML::saveAnnotation ( const CAnnotation *  pAnnotation )

private

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().

{
  if (pAnnotation->getMiriamAnnotation() != "")
    {
      startSaveElement("MiriamAnnotation");
      *mpOstream << pAnnotation->getMiriamAnnotation() << std::endl;
      endSaveElement("MiriamAnnotation");
    }

  if (pAnnotation->getNotes() != "")
    {
      startSaveElement("Comment");
      saveXhtml(pAnnotation->getNotes());
      endSaveElement("Comment");
    }

  if (pAnnotation->getUnsupportedAnnotations().size() > 0)
    {
      startSaveElement("ListOfUnsupportedAnnotations");

      CAnnotation::UnsupportedAnnotation::const_iterator it = pAnnotation->getUnsupportedAnnotations().begin();
      CAnnotation::UnsupportedAnnotation::const_iterator end = pAnnotation->getUnsupportedAnnotations().end();

      CXMLAttributeList Attributes;
      Attributes.add("name", "");

      for (; it != end; ++it)
        {
          Attributes.setValue(0, it->first);

          startSaveElement("UnsupportedAnnotation", Attributes);
          *mpOstream << it->second << std::endl;
          endSaveElement("UnsupportedAnnotation");
        }

      endSaveElement("ListOfUnsupportedAnnotations");
    }

  return true;
}

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.

Definition at line 2505 of file CCopasiXML.cpp.

References CXMLAttributeList::add().

{
  // start head
  if (element.isSetStartHead())
    {
      attributes.add("startHead", element.getStartHead());
    }

  // start head
  if (element.isSetEndHead())
    {
      attributes.add("endHead", element.getEndHead());
    }
}

void CCopasiXML::saveBoundingBox ( const CLBoundingBox &  bb )

private

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().

{
  startSaveElement("BoundingBox");
  savePosition(bb.getPosition());
  saveDimensions(bb.getDimensions());
  endSaveElement("BoundingBox");
}

void CCopasiXML::saveColorDefinition ( const CLColorDefinition &  color )

private

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().

{
  CXMLAttributeList attributes;
  attributes.add("id", color.getId());
  attributes.add("value", color.createValueString());
  saveElement("ColorDefinition", attributes);
}

void CCopasiXML::saveCurve ( const CLCurve &  c )

private

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().

{
  CXMLAttributeList Attributes;
  startSaveElement("Curve");

  if (c.getNumCurveSegments() > 0)
    {
      startSaveElement("ListOfCurveSegments");
      size_t i, imax = c.getNumCurveSegments();

      for (i = 0; i < imax; ++i)
        {
          const CLLineSegment & cs = c.getCurveSegments()[i];

          Attributes.erase();

          if (cs.isBezier())
            Attributes.add("xsi:type", "CubicBezier");
          else
            Attributes.add("xsi:type", "LineSegment");

          startSaveElement("CurveSegment", Attributes);

          savePosition(cs.getStart(), "Start");
          savePosition(cs.getEnd(), "End");

          if (cs.isBezier())
            {
              savePosition(cs.getBase1(), "BasePoint1");
              savePosition(cs.getBase2(), "BasePoint2");
            }

          endSaveElement("CurveSegment");
        }

      endSaveElement("ListOfCurveSegments");
    }

  endSaveElement("Curve");
}

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.

Definition at line 2718 of file CCopasiXML.cpp.

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

Referenced by savePolygonElement(), and saveRenderCurveElement().

{
  startSaveElement("ListOfElements");
  size_t i, iMax = curveElements.size();

  for (i = 0; i < iMax; ++i)
    {
      saveRenderPoint(*curveElements[i]);
    }

  endSaveElement("ListOfElements");
}

void CCopasiXML::saveDimensions ( const CLDimensions &  d )

private

Definition at line 1373 of file CCopasiXML.cpp.

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

Referenced by saveBoundingBox().

{
  CXMLAttributeList Attributes;
  Attributes.erase();
  Attributes.add("width", d.getWidth());
  Attributes.add("height", d.getHeight());
  saveElement("Dimensions", Attributes);
}

void CCopasiXML::saveEllipseElement ( const CLEllipse &  ellipse )

private

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().

{
  CXMLAttributeList attributes;
  // first we add the attributes for a 2D object
  save2DAttributes(ellipse, attributes);
  // now we add the ellipse specific attributes
  attributes.add("cx", ellipse.getCX().toString());
  attributes.add("cy", ellipse.getCY().toString());

  if (ellipse.getCZ() != CLRelAbsVector(0.0, 0.0))
    {
      attributes.add("cz", ellipse.getCZ().toString());
    }

  if (ellipse.getRX() != CLRelAbsVector(0.0, 0.0))
    {
      attributes.add("rx", ellipse.getRX().toString());
    }

  if (ellipse.getRY() != CLRelAbsVector(0.0, 0.0))
    {
      attributes.add("ry", ellipse.getRY().toString());
    }

  saveElement("Ellipse", attributes);
}

bool CCopasiXML::saveFunctionList ( )

private

Save the list of functions.

Returns

bool success

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().

{
  bool success = true;

  if (!haveFunctionList()) return success;

  size_t i, imax = mpFunctionList->size();

  if (!imax) return success;

  CXMLAttributeList Attributes;
  CFunction * pFunction = NULL;

  startSaveElement("ListOfFunctions");

  for (i = 0; i < imax; i++)
    {
      pFunction = (*mpFunctionList)[i];

      Attributes.erase();
      Attributes.add("key", pFunction->getKey());
      Attributes.add("name", pFunction->getObjectName());
      Attributes.add("type", CEvaluationTree::XMLType[pFunction->getType()]);

      if (pFunction)
        {
          switch (pFunction->isReversible())
            {
              case TriUnspecified:
                Attributes.add("reversible", "unspecified");
                break;

              case TriFalse:
                Attributes.add("reversible", "false");
                break;

              case TriTrue:
                Attributes.add("reversible", "true");
                break;
            }

          if (pFunction->getSBMLId() != "")
            mSBMLReference[pFunction->getSBMLId()] = pFunction->getKey();
        }

      startSaveElement("Function", Attributes);

      saveAnnotation(pFunction);

      startSaveElement("Expression");
      saveData(pFunction->getInfix());
      endSaveElement("Expression");

      if (pFunction)
        {
          startSaveElement("ListOfParameterDescriptions");

          size_t j, jmax = pFunction->getVariables().size();
          CFunctionParameter * pParameter;

          Attributes.erase();
          Attributes.add("key", "");
          Attributes.add("name", "");
          Attributes.add("order", "");
          Attributes.add("role", "");

          for (j = 0; j < jmax; j++)
            {
              pParameter = pFunction->getVariables()[j];
              Attributes.setValue(0, pParameter->getKey());
              Attributes.setValue(1, pParameter->getObjectName());
              Attributes.setValue(2, j);
              Attributes.setValue(3, CFunctionParameter::RoleNameXML[pParameter->getUsage()]);

              saveElement("ParameterDescription", Attributes);
            }

          endSaveElement("ListOfParameterDescriptions");
        }

      endSaveElement("Function");
    }

  endSaveElement("ListOfFunctions");

  return success;
}

void CCopasiXML::saveGlobalRenderInformation ( const CLGlobalRenderInformation &  renderInfo )

private

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().

{
  // first we create the attributes that are common to all render information objects
  CXMLAttributeList attributes;
  saveRenderInformationAttributes(renderInfo, attributes);
  startSaveElement("RenderInformation", attributes);
  // now we save the definition that are the same for all render information objects
  saveRenderInformationDefinitionElements(renderInfo);
  // last we save the global styles
  size_t i, iMax = renderInfo.getNumStyles();

  if (iMax > 0)
    {
      startSaveElement("ListOfStyles");

      for (i = 0; i < iMax; ++i)
        {
          saveGlobalStyle(*(dynamic_cast<const CLGlobalStyle*>(renderInfo.getStyle(i))));
        }

      endSaveElement("ListOfStyles");
    }

  endSaveElement("RenderInformation");
}

void CCopasiXML::saveGlobalStyle ( const CLGlobalStyle &  style )

private

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().

{
  // first we create the attributes
  CXMLAttributeList attributes;
  saveStyleAttributes(style, attributes);
  startSaveElement("Style", attributes);
  saveStyleElements(style);
  endSaveElement("Style");
}

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

private

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().

{
  attributes.add("id", gradient.getId());

  switch (gradient.getSpreadMethod())
    {
      case CLGradientBase::REPEAT:
        attributes.add("spreadMethod", "repeat");
        break;

      case CLGradientBase::REFLECT:
        attributes.add("spreadMethod", "reflect");
        break;

      case CLGradientBase::PAD:
      default:
        attributes.add("spreadMethod", "pad");
        break;
    }
}

void CCopasiXML::saveGradientElements ( const CLGradientBase &  gradient )

private

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().

{
  size_t i, iMax = gradient.getNumGradientStops();

  if (iMax > 0)
    {
      for (i = 0; i < iMax; ++i)
        {
          saveGradientStop(*(gradient.getGradientStop(i)));
        }
    }
}

void CCopasiXML::saveGradientStop ( const CLGradientStop &  stop )

private

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().

{
  CXMLAttributeList attributes;
  attributes.add("offset", stop.getOffset().toString());
  attributes.add("stop-color", stop.getStopColor());
  saveElement("Stop", attributes);
}

void CCopasiXML::saveGroupElement ( const CLGroup &  group )

private

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().

{
  CXMLAttributeList attributes;
  save2DAttributes(group, attributes);
  saveTextAttributes<CLGroup>(group, attributes);
  saveArrowHeadAttributes<CLGroup>(group, attributes);
  startSaveElement("Group", attributes);
  size_t i, iMax = group.getNumElements();

  if (iMax > 0)
    {
      for (i = 0; i < iMax; ++i)
        {
          saveTransformation2D(*dynamic_cast<const CLTransformation2D*>(group.getElement(i)));
        }
    }

  endSaveElement("Group");
}

bool CCopasiXML::saveGUI ( )

private

Save GUI information

Returns

bool success

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().

{
  bool success = true;

  if (!haveGUI()) return success;

  startSaveElement("GUI");

  if (mpGUI->getSliderList() && mpGUI->getSliderList()->size())
    {
      startSaveElement("ListOfSliders");

      CSlider * pSlider;
      CXMLAttributeList Attributes;

      Attributes.add("key", "");
      Attributes.add("associatedEntityKey", "");
      Attributes.add("objectCN", "");
      Attributes.add("objectType", "");
      Attributes.add("objectValue", "");
      Attributes.add("minValue", "");
      Attributes.add("maxValue", "");
      Attributes.add("tickNumber", "");
      Attributes.add("tickFactor", "");
      Attributes.add("scaling", "");

      size_t i, imax = mpGUI->getSliderList()->size();

      for (i = 0; i < imax; i++)
        {
          pSlider = (*mpGUI->getSliderList())[i];
          Attributes.setValue(0, pSlider->getKey());
          Attributes.setValue(1, pSlider->getAssociatedEntityKey());
          Attributes.setValue(2, pSlider->getSliderObjectCN());
          Attributes.setValue(3, CSlider::TypeName[pSlider->getSliderType()]);
          Attributes.setValue(4, pSlider->getSliderValue());
          Attributes.setValue(5, pSlider->getMinValue());
          Attributes.setValue(6, pSlider->getMaxValue());
          Attributes.setValue(7, pSlider->getTickNumber());
          Attributes.setValue(8, pSlider->getTickFactor());
          Attributes.setValue(9, pSlider->convertScaleToScaleName(pSlider->getScaling()));
          saveElement("Slider", Attributes);
        }

      endSaveElement("ListOfSliders");
    }

  endSaveElement("GUI");

  return success;
}

void CCopasiXML::saveImageElement ( const CLImage &  image )

private

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().

{
  CXMLAttributeList attributes;
  // first we add the attributes for a transformation
  saveTransformationAttributes(image, attributes);
  // now we add the image specific attributes
  attributes.add("x", image.getX().toString());
  attributes.add("y", image.getY().toString());

  if (image.getZ() != CLRelAbsVector(0.0, 0.0))
    {
      attributes.add("z", image.getZ().toString());
    }

  attributes.add("width", image.getWidth().toString());
  attributes.add("height", image.getHeight().toString());
  attributes.add("href", image.getImageReference());
  saveElement("Image", attributes);
}

bool CCopasiXML::saveLayoutList ( )

private

Save the list of layout.

Returns

bool success

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().

{
  bool success = true;

  if (!haveLayoutList()) return success;

  size_t i, imax = mpLayoutList->size();

  if (!imax) return success;

  CXMLAttributeList Attributes;
  CLayout * pLayout = NULL;
  Attributes.add("xmlns:xsi", "http://www.w3.org/2001/XMLSchema-instance");
  startSaveElement("ListOfLayouts", Attributes);

  for (i = 0; i < imax; i++)
    {
      pLayout = (*mpLayoutList)[i];

      Attributes.erase();
      Attributes.add("key", pLayout->getKey());
      Attributes.add("name", pLayout->getObjectName());
      startSaveElement("Layout", Attributes);

      Attributes.erase();
      Attributes.add("width", pLayout->getDimensions().getWidth());
      Attributes.add("height", pLayout->getDimensions().getHeight());
      saveElement("Dimensions", Attributes);

      size_t j, jmax;

      //compartment glyphs
      if (pLayout->getListOfCompartmentGlyphs().size() > 0)
        {
          startSaveElement("ListOfCompartmentGlyphs");

          jmax = pLayout->getListOfCompartmentGlyphs().size();

          for (j = 0; j < jmax; ++j)
            {
              CLCompartmentGlyph* cg = pLayout->getListOfCompartmentGlyphs()[j];
              Attributes.erase();
              Attributes.add("key", cg->getKey());
              Attributes.add("name", cg->getObjectName());

              if (!cg->getModelObjectKey().empty() && cg->hasValidModelReference())
                {
                  Attributes.add("compartment", cg->getModelObjectKey());
                }
              else
                {
                  // we set the model reference to the empty string so that
                  // the warnings message only appears on the first save operation
                  cg->setModelObjectKey("");

                  if (!this->mMCXML21Issued)
                    {
                      CCopasiMessage(CCopasiMessage::WARNING, MCXML + 21);
                      this->mMCXML21Issued = true;
                    }

                  // Bug 1973: we still write out the attribute, so that older
                  //           versions of COPASI do not refuse to read the model
                  Attributes.add("metabolite", "");
                }

              if (cg->getObjectRole().find_first_not_of(" \t\r\n") != std::string::npos)
                {
                  Attributes.add("objectRole", cg->getObjectRole());
                }

              startSaveElement("CompartmentGlyph", Attributes);

              saveBoundingBox(cg->getBoundingBox());

              endSaveElement("CompartmentGlyph");
            }

          endSaveElement("ListOfCompartmentGlyphs");
        }

      //species glyphs
      if (pLayout->getListOfMetaboliteGlyphs().size() > 0)
        {
          startSaveElement("ListOfMetabGlyphs");

          jmax = pLayout->getListOfMetaboliteGlyphs().size();

          for (j = 0; j < jmax; ++j)
            {
              CLMetabGlyph* cg = pLayout->getListOfMetaboliteGlyphs()[j];
              Attributes.erase();
              Attributes.add("key", cg->getKey());
              Attributes.add("name", cg->getObjectName());

              if (!cg->getModelObjectKey().empty() && cg->hasValidModelReference())
                {
                  Attributes.add("metabolite", cg->getModelObjectKey());
                }
              else
                {
                  // we set the model reference to the empty string so that
                  // the warnings message only appears on the first save operation
                  cg->setModelObjectKey("");

                  if (!this->mMCXML21Issued)
                    {
                      CCopasiMessage(CCopasiMessage::WARNING, MCXML + 21);
                      this->mMCXML21Issued = true;
                    }

                  // Bug 1973: we still write out the attribute, so that older
                  //           versions of COPASI do not refuse to read the model
                  Attributes.add("metabolite", "");
                }

              if (cg->getObjectRole().find_first_not_of(" \t\r\n") != std::string::npos)
                {
                  Attributes.add("objectRole", cg->getObjectRole());
                }

              startSaveElement("MetaboliteGlyph", Attributes);

              saveBoundingBox(cg->getBoundingBox());

              endSaveElement("MetaboliteGlyph");
            }

          endSaveElement("ListOfMetabGlyphs");
        }

      //reaction glyphs
      if (pLayout->getListOfReactionGlyphs().size() > 0)
        {
          startSaveElement("ListOfReactionGlyphs");

          jmax = pLayout->getListOfReactionGlyphs().size();

          for (j = 0; j < jmax; ++j)
            {
              CLReactionGlyph* cg = pLayout->getListOfReactionGlyphs()[j];
              Attributes.erase();
              Attributes.add("key", cg->getKey());
              Attributes.add("name", cg->getObjectName());

              if (!cg->getModelObjectKey().empty() && cg->hasValidModelReference())
                {
                  Attributes.add("reaction", cg->getModelObjectKey());
                }
              else
                {
                  // we set the model reference to the empty string so that
                  // the warnings message only appears on the first save operation
                  cg->setModelObjectKey("");

                  if (!this->mMCXML21Issued)
                    {
                      CCopasiMessage(CCopasiMessage::WARNING, MCXML + 21);
                      this->mMCXML21Issued = true;
                    }
                }

              if (cg->getObjectRole().find_first_not_of(" \t\r\n") != std::string::npos)
                {
                  Attributes.add("objectRole", cg->getObjectRole());
                }

              startSaveElement("ReactionGlyph", Attributes);

              if (cg->getCurve().getNumCurveSegments() == 0)
                saveBoundingBox(cg->getBoundingBox());
              else
                saveCurve(cg->getCurve());

              // metab reference glyphs
              startSaveElement("ListOfMetaboliteReferenceGlyphs");
              size_t k, kmax = cg->getListOfMetabReferenceGlyphs().size();

              for (k = 0; k < kmax; ++k)
                {
                  CLMetabReferenceGlyph * mrg = cg->getListOfMetabReferenceGlyphs()[k];
                  Attributes.erase();
                  Attributes.add("key", mrg->getKey());
                  Attributes.add("name", mrg->getObjectName());
                  Attributes.add("metaboliteGlyph", mrg->getMetabGlyphKey());
                  //Attributes.add("metaboliteReference", mrg->getXXX());
                  Attributes.add("role", CLMetabReferenceGlyph::XMLRole[mrg->getRole()]);

                  if (mrg->getObjectRole().find_first_not_of(" \t\r\n") != std::string::npos)
                    {
                      Attributes.add("objectRole", mrg->getObjectRole());
                    }

                  startSaveElement("MetaboliteReferenceGlyph", Attributes);

                  if (mrg->getCurve().getNumCurveSegments() == 0)
                    saveBoundingBox(mrg->getBoundingBox());
                  else
                    saveCurve(mrg->getCurve());

                  endSaveElement("MetaboliteReferenceGlyph");
                }

              endSaveElement("ListOfMetaboliteReferenceGlyphs");

              endSaveElement("ReactionGlyph");
            }

          endSaveElement("ListOfReactionGlyphs");
        }

      //text Glyphs
      if (pLayout->getListOfTextGlyphs().size() > 0)
        {
          startSaveElement("ListOfTextGlyphs");

          jmax = pLayout->getListOfTextGlyphs().size();

          for (j = 0; j < jmax; ++j)
            {
              CLTextGlyph* cg = pLayout->getListOfTextGlyphs()[j];
              // we only export the text glyph if it either has a text
              // or a valid originOfText
              std::string id = cg->getModelObjectKey();

              if (cg->isTextSet() || id.find_first_not_of(" \t\r\n") != std::string::npos)
                {
                  Attributes.erase();
                  Attributes.add("key", cg->getKey());
                  Attributes.add("name", cg->getObjectName());
                  Attributes.add("graphicalObject", cg->getGraphicalObjectKey());

                  if (cg->isTextSet())
                    {
                      Attributes.add("text", cg->getText());
                    }
                  else
                    {
                      // check if the object actually exists
                      if (cg->hasValidModelReference())
                        {
                          Attributes.add("originOfText", id);
                        }
                      else
                        {
                          // set the text to unset instead
                          Attributes.add("text", "unset");
                          // set the invalid key to the empty string
                          cg->setModelObjectKey("");
                          cg->setText("unset");

                          if (!this->mMCXML21Issued)
                            {
                              CCopasiMessage(CCopasiMessage::WARNING, MCXML + 21);
                              this->mMCXML21Issued = true;
                            }
                        }
                    }

                  if (cg->getObjectRole().find_first_not_of(" \t\r\n") != std::string::npos)
                    {
                      Attributes.add("objectRole", cg->getObjectRole());
                    }

                  startSaveElement("TextGlyph", Attributes);

                  saveBoundingBox(cg->getBoundingBox());

                  endSaveElement("TextGlyph");
                }
            }

          endSaveElement("ListOfTextGlyphs");
        }

      //additional graphical objects
      if (pLayout->getListOfGeneralGlyphs().size() > 0)
        {
          startSaveElement("ListOfAdditionalGraphicalObjects");

          jmax = pLayout->getListOfGeneralGlyphs().size();

          for (j = 0; j < jmax; ++j)
            {
              CLGeneralGlyph* cg = pLayout->getListOfGeneralGlyphs()[j];
              Attributes.erase();
              Attributes.add("key", cg->getKey());
              Attributes.add("name", cg->getObjectName());

              if (!cg->getModelObjectKey().empty() && cg->hasValidModelReference())
                {
                  Attributes.add("reference", cg->getModelObjectKey());
                }
              else
                {
                  // we set the model reference to the empty string so that
                  // the warnings message only appears on the first save operation
                  cg->setModelObjectKey("");

                  //a general glyph does not necessarily have a model reference.
                  //so no warning is issued
                  /*if (!this->mMCXML21Issued)
                    {
                      CCopasiMessage(CCopasiMessage::WARNING, MCXML + 21);
                      this->mMCXML21Issued = true;
                    }*/
                }

              if (cg->getObjectRole().find_first_not_of(" \t\r\n") != std::string::npos)
                {
                  Attributes.add("objectRole", cg->getObjectRole());
                }

              startSaveElement("AdditionalGraphicalObject", Attributes);

              //if (cg->getCurve().getNumCurveSegments() == 0)
              saveBoundingBox(cg->getBoundingBox());
              //else
              //  saveCurve(cg->getCurve());

              // reference glyphs

              endSaveElement("AdditionalGraphicalObject");
            }

          endSaveElement("ListOfAdditionalGraphicalObjects");
        }

      // save the local render information
      if (pLayout->getListOfLocalRenderInformationObjects().size() > 0)
        {
          saveListOfLocalRenderInformation(pLayout->getListOfLocalRenderInformationObjects());
        }

      endSaveElement("Layout");
    }

  // save the global render information list
  if (mpLayoutList->getListOfGlobalRenderInformationObjects().size() > 0)
    {
      saveListOfGlobalRenderInformation(mpLayoutList->getListOfGlobalRenderInformationObjects());
    }

  endSaveElement("ListOfLayouts");

  return success;
}

void CCopasiXML::saveLinearGradient ( const CLLinearGradient &  gradient )

private

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().

{
  CXMLAttributeList attributes;
  // first we create the common attributes
  saveGradientAttributes(gradient, attributes);
  // now we add the attributes specific to the radial gradient
  attributes.add("x1", gradient.getXPoint1().toString());
  attributes.add("y1", gradient.getYPoint1().toString());

  if (gradient.getZPoint1() != CLRelAbsVector(0.0, 0.0))
    {
      attributes.add("z1", gradient.getZPoint1().toString());
    }

  attributes.add("x2", gradient.getXPoint2().toString());
  attributes.add("y2", gradient.getYPoint2().toString());

  if (gradient.getZPoint2() != CLRelAbsVector(0.0, 0.0))
    {
      attributes.add("z2", gradient.getZPoint2().toString());
    }

  startSaveElement("LinearGradient", attributes);
  // save the gradient stops
  saveGradientElements(gradient);
  endSaveElement("LinearGradient");
}

void CCopasiXML::saveLineEnding ( const CLLineEnding &  lineEnding )

private

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().

{
  // create the attributes
  CXMLAttributeList attributes;
  attributes.add("id", lineEnding.getId());
  attributes.add("enableRotationalMapping", lineEnding.getIsEnabledRotationalMapping() ? std::string("true") : std::string("false"));
  startSaveElement("LineEnding", attributes);
  // a line ending has a bounding box
  saveBoundingBox(*(lineEnding.getBoundingBox()));
  // and a group element
  assert(lineEnding.getGroup() != NULL);
  saveGroupElement(*lineEnding.getGroup());
  endSaveElement("LineEnding");
}

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

private

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().

{
  startSaveElement("ListOfGlobalRenderInformation");
  size_t i, iMax = list.size();

  for (i = 0; i < iMax; ++i)
    {
      saveGlobalRenderInformation(*list[i]);
    }

  endSaveElement("ListOfGlobalRenderInformation");
}

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

private

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().

{
  startSaveElement("ListOfRenderInformation");
  size_t i, iMax = list.size();

  for (i = 0; i < iMax; ++i)
    {
      saveLocalRenderInformation(*list[i]);
    }

  endSaveElement("ListOfRenderInformation");
}

void CCopasiXML::saveLocalRenderInformation ( const CLLocalRenderInformation &  renderInfo )

private

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().

{
  // first we create the attributes that are common to all render information objects
  CXMLAttributeList attributes;
  saveRenderInformationAttributes(renderInfo, attributes);
  startSaveElement("RenderInformation", attributes);
  // now we save the definition that are the same for all render information objects
  saveRenderInformationDefinitionElements(renderInfo);
  // last we save the global styles
  size_t i, iMax = renderInfo.getNumStyles();

  if (iMax > 0)
    {
      startSaveElement("ListOfStyles");

      for (i = 0; i < iMax; ++i)
        {
          saveLocalStyle(*(dynamic_cast<const CLLocalStyle*>(renderInfo.getStyle(i))));
        }

      endSaveElement("ListOfStyles");
    }

  endSaveElement("RenderInformation");
}

void CCopasiXML::saveLocalStyle ( const CLLocalStyle &  style )

private

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().

{
  // first we create the attributes
  CXMLAttributeList attributes;
  saveStyleAttributes(style, attributes);

  // now we add the attributes that are specific to local styles
  if (style.getNumKeys() > 0)
    {
      attributes.add("keyList", CLStyle::createStringFromSet(style.getKeyList()));
    }

  startSaveElement("Style", attributes);
  saveStyleElements(style);
  endSaveElement("Style");
}

bool CCopasiXML::saveModel ( )

private

Save the model.

Returns

bool success

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().

{
  bool success = true;

  if (!haveModel()) return success;

  CXMLAttributeList Attributes;
  Attributes.add("key", mpModel->getKey());
  Attributes.add("name", mpModel->getObjectName());
  Attributes.add("simulationType", CModelEntity::XMLStatus[mpModel->getStatus()]);
  Attributes.add("timeUnit", mpModel->getTimeUnitName());
  Attributes.add("volumeUnit", mpModel->getVolumeUnitName());
  Attributes.add("areaUnit", mpModel->getAreaUnitName());
  Attributes.add("lengthUnit", mpModel->getLengthUnitName());
  Attributes.add("quantityUnit", mpModel->getQuantityUnitName());
  Attributes.add("type", CModel::ModelTypeNames[mpModel->getModelType()]);
  Attributes.add("avogadroConstant", mpModel->getAvogadro());

  // This is now optional
  // Attributes.add("stateVariable",
  //                mpModel->getStateTemplate().getKey(mpModel->getKey()));

  startSaveElement("Model", Attributes);

  saveAnnotation(mpModel);

  if (mpModel->getInitialExpression() != "")
    {
      startSaveElement("InitialExpression");
      saveData(mpModel->getInitialExpression());
      endSaveElement("InitialExpression");
    }

  size_t i, imax;

  // Compartment
  if ((imax = mpModel->getCompartments().size()) > 0)
    {
      startSaveElement("ListOfCompartments");

      Attributes.erase();
      Attributes.add("key", "");
      Attributes.add("name", "");
      Attributes.add("simulationType", "");
      Attributes.add("dimensionality", "");

      size_t i, imax = mpModel->getCompartments().size();

      for (i = 0; i < imax; i++)
        {
          CCompartment * pComp = mpModel->getCompartments()[i];

          Attributes.setValue(0, pComp->getKey());
          Attributes.setValue(1, pComp->getObjectName());
          CModelEntity::Status SimulationType = pComp->getStatus();
          Attributes.setValue(2, CModelEntity::XMLStatus[SimulationType]);
          Attributes.setValue(3, pComp->getDimensionality());

          startSaveElement("Compartment", Attributes);

          saveAnnotation(pComp);

          if (SimulationType != CModelEntity::FIXED &&
              pComp->getExpression() != "")
            {
              startSaveElement("Expression");
              saveData(pComp->getExpression());
              endSaveElement("Expression");
            }

          if (pComp->getInitialExpression() != "")
            {
              startSaveElement("InitialExpression");
              saveData(pComp->getInitialExpression());
              endSaveElement("InitialExpression");
            }

          endSaveElement("Compartment");

          if (pComp->getSBMLId() != "")
            mSBMLReference[pComp->getSBMLId()] = pComp->getKey();
        }

      endSaveElement("ListOfCompartments");
    }

  // Metabolites (aka. Species)
  if ((imax = mpModel->getMetabolites().size()) > 0)
    {
      startSaveElement("ListOfMetabolites");

      Attributes.erase();
      Attributes.add("key", "");
      Attributes.add("name", "");
      Attributes.add("simulationType", "");
      Attributes.add("compartment", "");

      for (i = 0; i < imax; i++)
        {
          CMetab * pMetab = mpModel->getMetabolites()[i];

          Attributes.setValue(0, pMetab->getKey());
          Attributes.setValue(1, pMetab->getObjectName());
          CModelEntity::Status SimulationType = pMetab->getStatus();
          Attributes.setValue(2, CModelEntity::XMLStatus[SimulationType]);
          Attributes.setValue(3, pMetab->getCompartment()->getKey());

          startSaveElement("Metabolite", Attributes);

          saveAnnotation(pMetab);

          if (SimulationType != CModelEntity::FIXED &&
              SimulationType != CModelEntity::REACTIONS &&
              pMetab->getExpression() != "")
            {
              startSaveElement("Expression");
              saveData(pMetab->getExpression());
              endSaveElement("Expression");
            }

          if (pMetab->getInitialExpression() != "")
            {
              startSaveElement("InitialExpression");
              saveData(pMetab->getInitialExpression());
              endSaveElement("InitialExpression");
            }

          endSaveElement("Metabolite");

          if (pMetab->getSBMLId() != "")
            mSBMLReference[pMetab->getSBMLId()] = pMetab->getKey();
        }

      endSaveElement("ListOfMetabolites");
    }

  // Model Values (aka. Global Quantities)
  if ((imax = mpModel->getModelValues().size()) > 0)
    {
      startSaveElement("ListOfModelValues");

      Attributes.erase();
      Attributes.add("key", "");
      Attributes.add("name", "");
      Attributes.add("simulationType", "");

      for (i = 0; i < imax; i++)
        {
          CModelValue * pMV = mpModel->getModelValues()[i];

          Attributes.setValue(0, pMV->getKey());
          Attributes.setValue(1, pMV->getObjectName());
          CModelEntity::Status SimulationType = pMV->getStatus();
          Attributes.setValue(2, CModelEntity::XMLStatus[SimulationType]);

          startSaveElement("ModelValue", Attributes);

          saveAnnotation(pMV);

          if (SimulationType != CModelEntity::FIXED &&
              pMV->getExpression() != "")
            {
              startSaveElement("Expression");
              saveData(pMV->getExpression());
              endSaveElement("Expression");
            }

          if (pMV->getInitialExpression() != "")
            {
              startSaveElement("InitialExpression");
              saveData(pMV->getInitialExpression());
              endSaveElement("InitialExpression");
            }

          endSaveElement("ModelValue");

          if (pMV->getSBMLId() != "")
            mSBMLReference[pMV->getSBMLId()] = pMV->getKey();
        }

      endSaveElement("ListOfModelValues");
    }

  // Reactions
  if ((imax = mpModel->getReactions().size()) > 0)
    {
      startSaveElement("ListOfReactions");

      CXMLAttributeList Attr;
      const CCopasiVector< CChemEqElement > * pReactantList;
      size_t j, jmax;

      std::vector< const CCopasiObject * > ObjectList;
      size_t k, kmax;

      Attributes.erase();
      Attributes.add("key", "");
      Attributes.add("name", "");
      Attributes.add("reversible", "");
      Attributes.add("fast", "");

      for (i = 0; i < imax; i++)
        {
          CReaction * pReaction = mpModel->getReactions()[i];

          Attributes.setValue(0, pReaction->getKey());
          Attributes.setValue(1, pReaction->getObjectName());
          Attributes.setValue(2, pReaction->isReversible() ? "true" : "false");
          Attributes.setValue(3, pReaction->isFast() ? "true" : "false");

          if (pReaction->getSBMLId() != "")
            mSBMLReference[pReaction->getSBMLId()] = pReaction->getKey();

          startSaveElement("Reaction", Attributes);

          saveAnnotation(pReaction);

          Attr.erase();
          Attr.add("metabolite", "");
          Attr.add("stoichiometry", "");

          pReactantList = & pReaction->getChemEq().getSubstrates();

          if ((jmax = pReactantList->size()) > 0)
            {
              startSaveElement("ListOfSubstrates");

              for (j = 0; j < jmax; j++)
                {
                  Attr.setValue(0, (*pReactantList)[j]->getMetaboliteKey());
                  Attr.setValue(1, (*pReactantList)[j]->getMultiplicity());

                  saveElement("Substrate", Attr);
                }

              endSaveElement("ListOfSubstrates");
            }

          //startSaveElement("ListOfProducts"); // this seems to belong further down

          pReactantList = & pReaction->getChemEq().getProducts();

          if ((jmax = pReactantList->size()) > 0)
            {
              startSaveElement("ListOfProducts"); //this seems to belong here

              for (j = 0; j < jmax; j++)
                {
                  Attr.setValue(0, (*pReactantList)[j]->getMetaboliteKey());
                  Attr.setValue(1, (*pReactantList)[j]->getMultiplicity());

                  saveElement("Product", Attr);
                }

              endSaveElement("ListOfProducts");
            }

          pReactantList = & pReaction->getChemEq().getModifiers();

          if ((jmax = pReactantList->size()) > 0)
            {
              startSaveElement("ListOfModifiers");

              for (j = 0, jmax = pReactantList->size(); j < jmax; j++)
                {
                  Attr.setValue(0, (*pReactantList)[j]->getMetaboliteKey());
                  Attr.setValue(1, (*pReactantList)[j]->getMultiplicity());

                  saveElement("Modifier", Attr);
                }

              endSaveElement("ListOfModifiers");
            }

          const CCopasiParameterGroup * pParamList;

          pParamList = & pReaction->getParameters();

          if ((jmax = pParamList->size()) > 0)
            {
              startSaveElement("ListOfConstants");

              Attr.erase();
              Attr.add("key", "");
              Attr.add("name", "");
              Attr.add("value", "");

              for (j = 0; j < jmax; j++)
                {
                  Attr.setValue(0, pParamList->getKey(j));
                  Attr.setValue(1, pParamList->getName(j));
                  Attr.setValue(2, * pParamList->getValue(j).pDOUBLE);

                  saveElement("Constant", Attr);
                }

              endSaveElement("ListOfConstants");
            }

          if (pReaction->getFunction() != CCopasiRootContainer::getUndefinedFunction())
            {
              Attr.erase();
              Attr.add("function", pReaction->getFunction()->getKey());
              startSaveElement("KineticLaw", Attr);

              if ((jmax = pReaction->getFunctionParameters().size()))
                {
                  startSaveElement("ListOfCallParameters");
                  const std::vector< std::vector<std::string> > & rMap =
                    pReaction->getParameterMappings();

                  for (j = 0; j < jmax; j++)
                    {
                      Attr.erase();
                      Attr.add("functionParameter",
                               pReaction->
                               getFunction()->getVariables()[j]->getKey());

                      startSaveElement("CallParameter", Attr);

                      Attr.erase();
                      Attr.add("reference", "");

                      for (k = 0, kmax = rMap[j].size(); k < kmax; k++)
                        {
                          Attr.setValue(0, rMap[j][k]);
                          saveElement("SourceParameter", Attr);
                        }

                      endSaveElement("CallParameter");
                    }

                  endSaveElement("ListOfCallParameters");
                }

              endSaveElement("KineticLaw");
            }

          endSaveElement("Reaction");
        }

      endSaveElement("ListOfReactions");
    }

  // Events (added 07.04.08)
  if ((imax = mpModel->getEvents().size()) > 0)
    {
      startSaveElement("ListOfEvents");

      Attributes.erase();
      Attributes.add("key", "");
      Attributes.add("name", "");
      Attributes.add("delayAssignment", "");
      Attributes.add("fireAtInitialTime", "");
      Attributes.add("persistentTrigger", "");

      for (i = 0; i < imax; i++)
        {
          CEvent * pEvent = mpModel->getEvents()[i];

          Attributes.setValue(0, pEvent->getKey());
          Attributes.setValue(1, pEvent->getObjectName());

          if (pEvent->getDelayExpression() != "")
            {
              Attributes.setValue(2, pEvent->getDelayAssignment() ? "true" : "false");
            }
          else
            {
              Attributes.skip(2);
            }

          Attributes.setValue(3, pEvent->getFireAtInitialTime());
          Attributes.setValue(4, pEvent->getPersistentTrigger());

          startSaveElement("Event", Attributes);

          saveAnnotation(pEvent);

          if (pEvent->getTriggerExpression() != "")
            {
              startSaveElement("TriggerExpression");
              saveData(pEvent->getTriggerExpression());
              endSaveElement("TriggerExpression");
            }

          if (pEvent->getDelayExpression() != "")
            {
              startSaveElement("DelayExpression");
              saveData(pEvent->getDelayExpression());
              endSaveElement("DelayExpression");
            }

          const CCopasiVectorN< CEventAssignment > & Assignments = pEvent->getAssignments();

          if (Assignments.size() > 0)
            {
              startSaveElement("ListOfAssignments");

              CXMLAttributeList Attr;
              Attr.add("targetKey", "");

              CCopasiVectorN< CEventAssignment >::const_iterator it = Assignments.begin();
              CCopasiVectorN< CEventAssignment >::const_iterator end = Assignments.end();

              for (; it != end; ++it)
                {
                  Attr.setValue(0, (*it)->getTargetKey());

                  startSaveElement("Assignment", Attr);

                  startSaveElement("Expression");
                  saveData((*it)->getExpression());
                  endSaveElement("Expression");

                  endSaveElement("Assignment");
                }

              endSaveElement("ListOfAssignments");
            }

          endSaveElement("Event");

          if (pEvent->getSBMLId() != "")
            mSBMLReference[pEvent->getSBMLId()] = pEvent->getKey();
        }

      endSaveElement("ListOfEvents");
    }

  // Save the model parameter sets
  Attributes.erase();
  const CModelParameterSet * pSet = & mpModel->getModelParameterSet();
  Attributes.add("activeSet", pSet->getKey());

  startSaveElement("ListOfModelParameterSets", Attributes);

  Attributes.erase();
  Attributes.add("key", "");
  Attributes.add("name", "");

  pSet = & mpModel->getModelParameterSet();

  Attributes.setValue(0, pSet->getKey());
  Attributes.setValue(1, pSet->getObjectName());

  startSaveElement("ModelParameterSet", Attributes);

  saveAnnotation(pSet);

  CModelParameterGroup::const_iterator itSet = pSet->begin();
  CModelParameterGroup::const_iterator endSet = pSet->end();

  for (; itSet != endSet; ++itSet)
    {
      saveModelParameter(*itSet);
    }

  endSaveElement("ModelParameterSet");

  imax = mpModel->getModelParameterSets().size();

  for (i = 0; i < imax; i++)
    {
      pSet = mpModel->getModelParameterSets()[i];

      Attributes.setValue(0, pSet->getKey());
      Attributes.setValue(1, pSet->getObjectName());

      startSaveElement("ModelParameterSet", Attributes);

      saveAnnotation(pSet);

      itSet = pSet->begin();
      endSet = pSet->end();

      for (; itSet != endSet; ++itSet)
        {
          saveModelParameter(*itSet);
        }

      endSaveElement("ModelParameterSet");
    }

  endSaveElement("ListOfModelParameterSets");

  // The State an state Template is only save for backwards compatibility
  startSaveElement("StateTemplate");

  Attributes.erase();
  // This is now optional.
  // Attributes.add("key", "");
  Attributes.add("objectReference", "");
  std::pair< std::string, std::string > Variable;

  CModelEntity *const* ppEntity = mpModel->getStateTemplate().getEntities();
  CModelEntity *const* ppEntityEnd = ppEntity + mpModel->getStateTemplate().size();

  for (; ppEntity != ppEntityEnd; ++ppEntity)
    {
      Attributes.setValue(0, (*ppEntity)->getKey());

      saveElement("StateTemplateVariable", Attributes);
    }

  endSaveElement("StateTemplate");

  Attributes.erase();
  Attributes.add("type", "initialState");
  startSaveElement("InitialState", Attributes);
  *mpOstream << mIndent;
  ppEntity = mpModel->getStateTemplate().getEntities();

  for (; ppEntity != ppEntityEnd; ++ppEntity)
    {
      *mpOstream << (DBL)(*ppEntity)->getInitialValue() << " ";
    }

  *mpOstream << std::endl;

  endSaveElement("InitialState");

  endSaveElement("Model");

  return success;
}

bool CCopasiXML::saveModelParameter ( const CModelParameter *  pModelParameter )

private

Save a model parameter

Parameters

const

CModelParameter * pModelParameter

Returns

bool success

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().

{
  // We do not save model parameters which are marked missing to preserve
  // their missing state.
  if (pModelParameter->getCompareResult() == CModelParameter::Missing)
    {
      return true;
    }

  bool success = true;

  CXMLAttributeList Attributes;

  if (pModelParameter->getType() != CModelParameter::Reaction &&
      pModelParameter->getType() != CModelParameter::Group)
    {
      Attributes.add("cn", pModelParameter->getCN());
      Attributes.add("value", pModelParameter->getValue(CModelParameter::ParticleNumbers));
      Attributes.add("type", CModelParameter::TypeNames[pModelParameter->getType()]);
      Attributes.add("simulationType", CModelEntity::XMLStatus[pModelParameter->getSimulationType()]);

      if (pModelParameter->getInitialExpression() != "")
        {
          startSaveElement("ModelParameter", Attributes);
          startSaveElement("InitialExpression");
          saveData(pModelParameter->getInitialExpression());
          endSaveElement("InitialExpression");
          endSaveElement("ModelParameter");
        }
      else
        {
          saveElement("ModelParameter", Attributes);
        }
    }
  else
    {
      Attributes.add("cn", pModelParameter->getCN());
      Attributes.add("type", CModelParameter::TypeNames[pModelParameter->getType()]);

      startSaveElement("ModelParameterGroup", Attributes);

      CModelParameterGroup::const_iterator it = static_cast< const CModelParameterGroup * >(pModelParameter)->begin();
      CModelParameterGroup::const_iterator end = static_cast< const CModelParameterGroup * >(pModelParameter)->end();

      for (; it != end; ++it)
        {
          success &= saveModelParameter(*it);
        }

      endSaveElement("ModelParameterGroup");
    }

  return success;
}

bool CCopasiXML::savePlotList ( )

private

Save the list of plots.

Returns

bool success

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().

{
  //std::cerr << "Saving plot list. " << std::endl;
  bool success = true;

  if (!havePlotList())
    {
      //std::cerr << "No plot list defined." << std::endl;
      return success;
    }

  size_t i, imax = mpPlotList->size();

  //std::cerr << "Saving " << imax << " plots." << std::endl;
  if (!imax) return success;

  CXMLAttributeList Attributes;

  startSaveElement("ListOfPlots");

  for (i = 0; i < imax; i++)
    {
      const CPlotSpecification* pPlot = (*mpPlotList)[i];

      Attributes.erase();
      Attributes.add("name", pPlot->getObjectName());
      Attributes.add("type", CPlotSpecification::XMLType[pPlot->getType()]);
      Attributes.add("active", pPlot->isActive());
      startSaveElement("PlotSpecification", Attributes);
      saveParameterGroup(* pPlot->CCopasiParameter::getValue().pGROUP);
      startSaveElement("ListOfPlotItems");
      size_t j, jmax = pPlot->getItems().size();

      //std::cerr << "Saving " << jmax << "PlotItems." << std::endl;
      for (j = 0; j < jmax; j++)
        {
          const CPlotItem* pPlotItem = pPlot->getItems()[j];
          Attributes.erase();
          Attributes.add("name", pPlotItem->getObjectName());
          Attributes.add("type", CPlotItem::XMLType[pPlotItem->getType()]);
          startSaveElement("PlotItem", Attributes);
          saveParameterGroup(* pPlotItem->CCopasiParameter::getValue().pGROUP);
          startSaveElement("ListOfChannels");
          size_t k, kmax = pPlotItem->getNumChannels();

          //std::cerr << "Saving " << kmax << " Channels." << std::endl;
          for (k = 0; k < kmax; k++)
            {
              const CPlotDataChannelSpec pDataChannelSpec = pPlotItem->getChannels()[k];
              Attributes.erase();
              Attributes.add("cn", pDataChannelSpec);

              if (!pDataChannelSpec.minAutoscale)
                {
                  Attributes.add("min", pDataChannelSpec.min);
                }

              if (!pDataChannelSpec.maxAutoscale)
                {
                  Attributes.add("max", pDataChannelSpec.max);
                }

              saveElement("ChannelSpec", Attributes);
            }

          endSaveElement("ListOfChannels");
          endSaveElement("PlotItem");
        }

      endSaveElement("ListOfPlotItems");
      endSaveElement("PlotSpecification");
    }

  endSaveElement("ListOfPlots");
  return success;
}

void CCopasiXML::savePolygonElement ( const CLPolygon &  polygon )

private

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().

{
  CXMLAttributeList attributes;
  // first we add the attributes for a 2D object
  save2DAttributes(polygon, attributes);
  startSaveElement("Polygon", attributes);
  saveCurveElements(*polygon.getListOfElements());
  endSaveElement("Polygon");
}

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

private

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().

{
  CXMLAttributeList Attributes;
  Attributes.erase();
  Attributes.add("x", p.getX());
  Attributes.add("y", p.getY());
  saveElement(tag, Attributes);
}

void CCopasiXML::saveRadialGradient ( const CLRadialGradient &  gradient )

private

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().

{
  CXMLAttributeList attributes;
  // first we create the common attributes
  saveGradientAttributes(gradient, attributes);
  // now we add the attributes specific to the radial gradient
  attributes.add("cx", gradient.getCenterX().toString());
  attributes.add("cy", gradient.getCenterY().toString());
  attributes.add("cz", gradient.getCenterZ().toString());
  attributes.add("r", gradient.getRadius().toString());
  attributes.add("fx", gradient.getFocalPointX().toString());
  attributes.add("fy", gradient.getFocalPointY().toString());
  attributes.add("fz", gradient.getFocalPointZ().toString());
  startSaveElement("RadialGradient", attributes);
  // save the gradient stops
  saveGradientElements(gradient);
  endSaveElement("RadialGradient");
}

void CCopasiXML::saveRectangleElement ( const CLRectangle &  rectangle )

private

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().

{
  CXMLAttributeList attributes;
  // first we add the attributes for a 2D object
  save2DAttributes(rectangle, attributes);
  // now we add the rectangle specific attributes
  attributes.add("x", rectangle.getX().toString());
  attributes.add("y", rectangle.getY().toString());

  if (rectangle.getZ() != CLRelAbsVector(0.0, 0.0))
    {
      attributes.add("z", rectangle.getZ().toString());
    }

  attributes.add("width", rectangle.getWidth().toString());
  attributes.add("height", rectangle.getHeight().toString());

  if (rectangle.getRadiusX() != CLRelAbsVector(0.0, 0.0))
    {
      attributes.add("rx", rectangle.getRadiusX().toString());
    }

  if (rectangle.getRadiusY() != CLRelAbsVector(0.0, 0.0))
    {
      attributes.add("ry", rectangle.getRadiusY().toString());
    }

  saveElement("Rectangle", attributes);
}

void CCopasiXML::saveRenderCurveElement ( const CLRenderCurve &  curve )

private

saves a single image element.

Definition at line 2703 of file CCopasiXML.cpp.

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

Referenced by saveTransformation2D().

{
  CXMLAttributeList attributes;
  // first we add the attributes for a 1D object
  save1DAttributes(curve, attributes);
  // next we add the arrow head attributes
  saveArrowHeadAttributes<CLRenderCurve>(curve, attributes);
  startSaveElement("Curve", attributes);
  saveCurveElements(*curve.getListOfCurveElements());
  endSaveElement("Curve");
}

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

private

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().

{
  // save the key
  attributes.add("key", renderInfo.getKey());
  // save the name
  std::string s = renderInfo.getName();
  const char* ws = " \t\n\r";

  if (s.find_first_not_of(ws) != std::string::npos)
    {
      attributes.add("name", s);
    }

  // save the background color
  s = renderInfo.getBackgroundColor();

  if (s.find_first_not_of(ws) != std::string::npos)
    {
      // save the name
      attributes.add("backgroundColor", s);
    }

  // save the reference render information key
  s = renderInfo.getReferenceRenderInformationKey();

  if (s.find_first_not_of(ws) != std::string::npos)
    {
      // save the name
      attributes.add("referenceRenderInformation", s);
    }
}

void CCopasiXML::saveRenderInformationDefinitionElements ( const CLRenderInformationBase &  renderInfo )

private

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().

{
  size_t i, iMax = renderInfo.getNumColorDefinitions();

  if (iMax > 0)
    {
      startSaveElement("ListOfColorDefinitions");

      for (i = 0; i < iMax; ++i)
        {
          saveColorDefinition(*(renderInfo.getColorDefinition(i)));
        }

      endSaveElement("ListOfColorDefinitions");
    }

  iMax = renderInfo.getNumGradientDefinitions();

  if (iMax > 0)
    {
      startSaveElement("ListOfGradientDefinitions");
      const CLGradientBase* pGradient = NULL;

      for (i = 0; i < iMax; ++i)
        {
          pGradient = renderInfo.getGradientDefinition(i);

          if (dynamic_cast<const CLRadialGradient*>(pGradient))
            {
              saveRadialGradient(*static_cast<const CLRadialGradient*>(pGradient));
            }
          else if (dynamic_cast<const CLLinearGradient*>(pGradient))
            {
              saveLinearGradient(*static_cast<const CLLinearGradient*>(pGradient));
            }
        }

      endSaveElement("ListOfGradientDefinitions");
    }

  iMax = renderInfo.getNumLineEndings();

  if (iMax > 0)
    {
      startSaveElement("ListOfLineEndings");

      for (i = 0; i < iMax; ++i)
        {
          saveLineEnding(*(renderInfo.getLineEnding(i)));
        }

      endSaveElement("ListOfLineEndings");
    }
}

void CCopasiXML::saveRenderPoint ( const CLRenderPoint &  point )

private

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().

{
  CXMLAttributeList attributes;
  attributes.add("x", point.x().toString());
  attributes.add("y", point.y().toString());

  if (point.z() != CLRelAbsVector(0.0, 0.0))
    {
      attributes.add("z", point.z().toString());
    }

  const CLRenderCubicBezier* pCB = dynamic_cast<const CLRenderCubicBezier*>(&point);

  if (pCB != NULL)
    {
      attributes.add("basePoint1_x", pCB->basePoint1_X().toString());
      attributes.add("basePoint1_y", pCB->basePoint1_Y().toString());

      if (pCB->basePoint1_Z() != CLRelAbsVector(0.0, 0.0))
        {
          attributes.add("basePoint1_z", pCB->basePoint1_Z().toString());
        }

      attributes.add("basePoint2_x", pCB->basePoint2_X().toString());
      attributes.add("basePoint2_y", pCB->basePoint2_Y().toString());

      if (pCB->basePoint2_Z() != CLRelAbsVector(0.0, 0.0))
        {
          attributes.add("basePoint2_z", pCB->basePoint2_Z().toString());
        }
    }

  saveElement("Element", attributes);
}

void CCopasiXML::saveRenderTextElement ( const CLText &  text )

private

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().

{
  CXMLAttributeList attributes;
  // first we add the attributes for a 1D object
  save1DAttributes(text, attributes);
  // save text attributes
  attributes.add("x", text.getX().toString());
  attributes.add("y", text.getY().toString());

  if (text.getZ() != CLRelAbsVector(0.0, 0.0))
    {
      attributes.add("z", text.getZ().toString());
    }

  // next we add the text specific attributes
  saveTextAttributes<CLText>(text, attributes);
  startSaveElement("Text", attributes);
  saveData(text.getText());
  endSaveElement("Text");
}

bool CCopasiXML::saveReportList ( )

private

Save the list of reports.

Returns

bool success

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().

{
  bool success = true;

  if (!haveReportList()) return success;

  size_t i, imax = mpReportList->size();

  if (!imax) return success;

  CXMLAttributeList Attributes;
  CReportDefinition * pReport = NULL;

  startSaveElement("ListOfReports");

  for (i = 0; i < imax; i++)
    {
      pReport = (*mpReportList)[i];

      Attributes.erase();
      Attributes.add("key", pReport->getKey());
      Attributes.add("name", pReport->getObjectName());
      Attributes.add("taskType", CCopasiTask::XMLType[pReport->getTaskType()]);
      Attributes.add("separator", pReport->getSeparator().getStaticString());
      Attributes.add("precision", pReport->getPrecision());

      startSaveElement("Report", Attributes);

      startSaveElement("Comment");
      saveXhtml(pReport->getComment());
      endSaveElement("Comment");

      if (pReport->isTable())
        {
          Attributes.erase();
          Attributes.add("printTitle", pReport->getTitle());
          startSaveElement("Table", Attributes);

          const std::vector <CRegisteredObjectName> & Table = * pReport->getTableAddr();
          size_t j, jmax = Table.size();

          Attributes.erase();
          Attributes.add("cn", "");

          for (j = 0; j < jmax; j++)
            {
              Attributes.setValue(0, Table[j]);
              saveElement("Object", Attributes);
            }

          endSaveElement("Table");
        }
      else
        {
          saveReportSection("Header", * pReport->getHeaderAddr());
          saveReportSection("Body", * pReport->getBodyAddr());
          saveReportSection("Footer", * pReport->getFooterAddr());
        }

      endSaveElement("Report");
    }

  endSaveElement("ListOfReports");

  return success;
}

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

private

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

Parameters

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

Returns

bool success

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().

{
  CXMLAttributeList Attributes;
  Attributes.add("NoName", "");

  size_t j, jmax = section.size();

  if (jmax)
    {
      startSaveElement(name);

      for (j = 0; j < jmax; j++)
        {
          if (section[j].getObjectType() == "html")
            {
              //Write in Text
              startSaveElement("html");
              Attributes.set(0, "xmlns", "http://www.w3.org/1999/xhtml");
              startSaveElement("body", Attributes);
              saveData(section[j].getObjectName()); //TODO check
              endSaveElement("body");
              endSaveElement("html");
            }
          else
            {
              //Write in Object
              Attributes.set(0, "cn", section[j]);
              saveElement("Object", Attributes);
            }
        }

      endSaveElement(name);
    }

  return true;
}

bool CCopasiXML::saveSBMLReference ( )

private

Save the SBML reference information

Returns

bool success

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().

{
  // if there is no model, there are no SBML references to save,
  // so no reason to fail saving at this point
  if (!this->mpDataModel) return true;

  if (this->mpDataModel->getSBMLFileName() == "" ||
      mSBMLReference.size() == 0)
    return true;

  CXMLAttributeList Attributes;

  std::string SBMLFile = this->mpDataModel->getSBMLFileName();

  if (!CDirEntry::isRelativePath(SBMLFile) &&
      !CDirEntry::makePathRelative(SBMLFile, mPWD))
    SBMLFile = CDirEntry::fileName(SBMLFile);

  Attributes.add("file", SBMLFile);

  startSaveElement("SBMLReference", Attributes);
  Attributes.erase();
  Attributes.add("SBMLid", "");
  Attributes.add("COPASIkey", "");

  std::map<std::string, std::string>::const_iterator it = mSBMLReference.begin();
  std::map<std::string, std::string>::const_iterator end = mSBMLReference.end();

  for (; it != end; ++it)
    {
      Attributes.setValue(0, it->first);
      Attributes.setValue(1, it->second);

      saveElement("SBMLMap", Attributes);
    }

  endSaveElement("SBMLReference");

  return true;
}

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

private

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().

{
  attributes.add("key", style.getKey());

  if (style.getNumRoles() > 0)
    {
      attributes.add("roleList", CLStyle::createStringFromSet(style.getRoleList()));
    }

  if (style.getNumTypes() > 0)
    {
      attributes.add("typeList", CLStyle::createStringFromSet(style.getTypeList()));
    }
}

void CCopasiXML::saveStyleElements ( const CLStyle &  style )

private

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().

{
  assert(style.getGroup() != NULL);
  saveGroupElement(*(style.getGroup()));
}

bool CCopasiXML::saveTaskList ( )

private

Save the list of tasks.

Returns

bool success

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().

{
  bool success = true;

  if (!haveTaskList()) return success;

  size_t i, imax = mpTaskList->size();

  if (!imax) return success;

  CXMLAttributeList Attributes;
  CCopasiTask * pTask = NULL;

  startSaveElement("ListOfTasks");

  for (i = 0; i < imax; i++)
    {
      pTask = (*mpTaskList)[i];

      Attributes.erase();
      Attributes.add("key", pTask->getKey());
      Attributes.add("name", pTask->getObjectName());
      Attributes.add("type", CCopasiTask::XMLType[pTask->getType()]);
      Attributes.add("scheduled", pTask->isScheduled() ? "true" : "false");
      Attributes.add("updateModel", pTask->isUpdateModel() ? "true" : "false");

      startSaveElement("Task", Attributes);

      // Report Element
      CReport & tReport = pTask->getReport();

      if (tReport.getReportDefinition())
        {
          Attributes.erase();
          Attributes.add("reference", tReport.getReportDefinition()->getKey());

          std::string Target = tReport.getTarget();

          if (!CDirEntry::isRelativePath(Target) &&
              !CDirEntry::makePathRelative(Target, mPWD))
            Target = CDirEntry::fileName(Target);

          Attributes.add("target", Target);
          Attributes.add("append", tReport.append());
          Attributes.add("confirmOverwrite", tReport.confirmOverwrite());
          saveElement("Report", Attributes);
        }

      //Problem Element
      CCopasiProblem *tProblem = pTask->getProblem();

      Attributes.erase();
      startSaveElement("Problem");
      saveParameterGroup(* tProblem->CCopasiParameter::getValue().pGROUP);
      endSaveElement("Problem");

      // Method Element
      CCopasiMethod *tMethod = pTask->getMethod();

      Attributes.erase();
      Attributes.add("name", tMethod->CCopasiParameter::getObjectName());
      Attributes.add("type", CCopasiMethod::XMLSubType[tMethod->getSubType()]);
      startSaveElement("Method", Attributes);
      saveParameterGroup(* tMethod->CCopasiParameter::getValue().pGROUP);
      endSaveElement("Method");

      endSaveElement("Task");
    }

  endSaveElement("ListOfTasks");

  return success;
}

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.

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.

{
  // text size
  if (text.isSetFontSize())
    {
      attributes.add("font-size", text.getFontSize().toString());
    }

  // font family
  if (text.isSetFontFamily())
    {
      attributes.add("font-family", text.getFontFamily());
    }

  // font weight
  if (text.isSetFontWeight())
    {
      switch (text.getFontWeight())
        {
          case CLText::WEIGHT_BOLD:
            attributes.add("font-weight", "bold");
            break;

          default:
            break;
        }
    }

  // font style
  if (text.isSetFontStyle())
    {
      switch (text.getFontStyle())
        {
          case CLText::STYLE_ITALIC:
            attributes.add("font-style", "italic");
            break;

          default:
            break;
        }
    }

  // text anchor
  if (text.isSetTextAnchor())
    {
      switch (text.getTextAnchor())
        {
          case CLText::ANCHOR_MIDDLE:
            attributes.add("text-anchor", "middle");
            break;

          case CLText::ANCHOR_END:
            attributes.add("text-anchor", "end");
            break;

          case CLText::ANCHOR_START:
            attributes.add("text-anchor", "start");
            break;

          default:
            break;
        }
    }

  // vertical text anchor
  if (text.isSetVTextAnchor())
    {
      switch (text.getVTextAnchor())
        {
          case CLText::ANCHOR_MIDDLE:
            attributes.add("vtext-anchor", "middle");
            break;

          case CLText::ANCHOR_BOTTOM:
            attributes.add("vtext-anchor", "bottom");
            break;

          case CLText::ANCHOR_TOP:
            attributes.add("vtext-anchor", "top");
            break;

          default:
            break;
        }
    }
}

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.

Definition at line 2524 of file CCopasiXML.cpp.

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

Referenced by saveGroupElement().

{
  if (dynamic_cast<const CLGraphicalPrimitive1D*>(&transformation))
    {
      if (dynamic_cast<const CLRenderCurve*>(&transformation))
        {
          saveRenderCurveElement(static_cast<const CLRenderCurve&>(transformation));
        }
      else if (dynamic_cast<const CLGraphicalPrimitive2D*>(&transformation))
        {
          if (dynamic_cast<const CLRectangle*>(&transformation))
            {
              saveRectangleElement(static_cast<const CLRectangle&>(transformation));
            }
          else if (dynamic_cast<const CLEllipse*>(&transformation))
            {
              saveEllipseElement(static_cast<const CLEllipse&>(transformation));
            }
          else if (dynamic_cast<const CLPolygon*>(&transformation))
            {
              savePolygonElement(static_cast<const CLPolygon&>(transformation));
            }
          else if (dynamic_cast<const CLGroup*>(&transformation))
            {
              saveGroupElement(static_cast<const CLGroup&>(transformation));
            }
          else
            {
              // we should never end up here.
              assert(false);
            }
        }
      else if (dynamic_cast<const CLText*>(&transformation))
        {
          saveRenderTextElement(static_cast<const CLText&>(transformation));
        }
      else
        {
          // we should never end up here.
          assert(false);
        }
    }
  else if (dynamic_cast<const CLImage*>(&transformation))
    {
      saveImageElement(static_cast<const CLImage&>(transformation));
    }
  else
    {
      // we should never end up here.
      assert(false);
    }
}

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

private

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().

{
  // transformation
  if (!transformation.isIdentityMatrix())
    {
      // check if it is a 2D or a 3D transformation
      if (transformation.is2DTransformation())
        {
          if (transformation.isSetMatrix())
            {
              attributes.add("transform", transformation.get2DTransformationString());
            }
        }
      else
        {
          if (transformation.isSetMatrix())
            {
              attributes.add("transform", transformation.get3DTransformationString());
            }
        }
    }
}

bool CCopasiXML::setDatamodel

(

CCopasiDataModel *

pDataModel

)

Set the datamodel.

Parameters

CCopasiDataModel*

pDataModel

Returns

bool success

Definition at line 299 of file CCopasiXML.cpp.

References mpDataModel.

Referenced by CCopasiDataModel::loadModel(), save_cps_model_to_stream(), and CCopasiDataModel::saveModel().

{
  this->mpDataModel = pDataModel;
  return true;
}

bool CCopasiXML::setFunctionList

(

CCopasiVectorN< CFunction > *

pFunctionList

)

Set the function list.

Parameters

CopasiVectorN<

CFunction > * pFunctionList

Returns

bool success

Definition at line 270 of file CCopasiXML.cpp.

References mpFunctionList.

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

{
  mpFunctionList = pFunctionList;
  return true;
}

bool CCopasiXML::setGUI

(

SCopasiXMLGUI *

pGUI

)

Set the GUI.

Parameters

SCopasiXMLGUI

*pGUI

Returns

bool success

Definition at line 359 of file CCopasiXML.cpp.

References mpGUI.

Referenced by CCopasiDataModel::loadModel(), save_cps_model_to_stream(), and CCopasiDataModel::saveModel().

{
  mpGUI = pGUI;
  return true;
}

bool CCopasiXML::setLayoutList

(

const CListOfLayouts &

reportList

)

Set the layout list.

Parameters

const

CListOfLayouts & reportList

Returns

bool success

Definition at line 377 of file CCopasiXML.cpp.

References mpLayoutList.

Referenced by save_cps_model_to_stream(), and CCopasiDataModel::saveModel().

{
  mpLayoutList = const_cast<CListOfLayouts *>(&layoutList);
  return true;
}

bool CCopasiXML::setModel

(

CModel *

pModel

)

Set the model.

Parameters

CModel

* pModel

Returns

bool success

Definition at line 254 of file CCopasiXML.cpp.

References mpModel.

Referenced by save_cps_model_to_stream(), and CCopasiDataModel::saveModel().

{
  mpModel = pModel;
  return true;
}

bool CCopasiXML::setPlotList

(

COutputDefinitionVector *

pPlotList

)

Set the plot list.

Parameters

COutputDefinitionVector

* pPlotList

Returns

bool success

Definition at line 319 of file CCopasiXML.cpp.

References mpPlotList.

Referenced by save_cps_model_to_stream(), and CCopasiDataModel::saveModel().

{
  mpPlotList = pPlotList;
  return true;
}

bool CCopasiXML::setReportList

(

CReportDefinitionVector *

pReportList

)

Set the report list.

Parameters

CReportDefinitionVector

*pReportList

Returns

bool success

Definition at line 339 of file CCopasiXML.cpp.

References mpReportList.

Referenced by save_cps_model_to_stream(), and CCopasiDataModel::saveModel().

{
  mpReportList = pReportList;
  return true;
}

bool CCopasiXML::setTaskList

(

CCopasiVectorN< CCopasiTask > *

pTaskList

)

Set the task list.

Parameters

CCopasiVectorN<

CCopasiTask > *pTaskList

Returns

bool success

Definition at line 288 of file CCopasiXML.cpp.

References mpTaskList.

Referenced by save_cps_model_to_stream(), and CCopasiDataModel::saveModel().

{
  mpTaskList = pTaskList;
  return true;
}

Member Data Documentation

bool CCopasiXML::mMCXML21Issued

private

Remember if we already issued MCXML21

Definition at line 604 of file CCopasiXML.h.

Referenced by saveLayoutList().

CCopasiDataModel* CCopasiXML::mpDataModel

private

Pointer to the datamodel

Definition at line 599 of file CCopasiXML.h.

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

CCopasiVectorN< 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.

Definition at line 559 of file CCopasiXML.h.

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

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.

Definition at line 583 of file CCopasiXML.h.

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

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.

Definition at line 589 of file CCopasiXML.h.

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

CModel* CCopasiXML::mpModel

private

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().

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.

Definition at line 577 of file CCopasiXML.h.

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

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.

Definition at line 571 of file CCopasiXML.h.

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

CCopasiVectorN< 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.

Definition at line 565 of file CCopasiXML.h.

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

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

private

SBML Reference

Definition at line 594 of file CCopasiXML.h.

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

---

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

• CCopasiXML.h
• CCopasiXML.cpp