CCopasiXMLInterface Class Reference

#include <CCopasiXMLInterface.h>

Inheritance diagram for CCopasiXMLInterface:

Collaboration diagram for CCopasiXMLInterface:

Classes
class	DBL

Public Types
enum	EncodingType { none = 0, standard, attribute, character }

Public Member Functions
	CCopasiXMLInterface ()
virtual bool	load (std::istream &is, const std::string &relativeTo)=0
bool	load (const std::string &fileName, const std::string &relativeTo)
virtual bool	save (std::ostream &os, const std::string &relativeTo)=0
bool	save (const std::string &fileName, const std::string &relativeTo)
virtual	~CCopasiXMLInterface ()

Static Public Member Functions
static std::string	encode (const std::string &str, const EncodingType &type=standard)
static std::string	utf8 (const std::string &str)

Protected Member Functions
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
std::string	mIndent
std::istream *	mpIstream
std::ostream *	mpOstream
std::string	mPWD

Detailed Description

Definition at line 85 of file CCopasiXMLInterface.h.

Member Enumeration Documentation

enum CCopasiXMLInterface::EncodingType

Enumeration of encoding type.

Enumerator
none
standard
attribute
character

Definition at line 91 of file CCopasiXMLInterface.h.

  {
    none = 0,
    standard,
    attribute,
    character
  };

Constructor & Destructor Documentation

CCopasiXMLInterface::CCopasiXMLInterface

(

)

Constructor.

Definition at line 271 of file CCopasiXMLInterface.cpp.

                                        :
  mpIstream(NULL),
  mpOstream(NULL),
  mIndent()
{}

CCopasiXMLInterface::~CCopasiXMLInterface ( )

virtual

Destructor.

Definition at line 277 of file CCopasiXMLInterface.cpp.

{}

Member Function Documentation

std::string CCopasiXMLInterface::encode ( const std::string &  str, const EncodingType &  type = standard  )

static

Encode a given string to a valid XML string

Parameters

const

std::string & str

Returns

std::string encoded

Definition at line 158 of file CCopasiXMLInterface.cpp.

References attribute, character, encodeATTRIBUTE(), encodeCHARACTER(), encodeNONE(), encodeSTD(), none, standard, and void().

Referenced by CXMLAttributeList::add(), CCopasiXMLParser::UnsupportedAnnotationElement::end(), CCopasiXMLParser::MiriamAnnotationElement::end(), CMathMl::fixName(), CCopasiXMLParser::onCharacterData(), saveData(), CXMLAttributeList::set(), CXMLAttributeList::setValue(), CCopasiXMLParser::UnsupportedAnnotationElement::start(), CCopasiXMLParser::CommentElement::start(), and CCopasiXMLParser::MiriamAnnotationElement::start().

{
  /* All COPASI std::strings and char are already UTF-8 encoded.*/
  std::string tmp = str;
  std::ostringstream xml;

  void (*encode)(const char & chr, std::ostringstream & xml) = encodeNONE;

  std::string::const_iterator it = str.begin();
  std::string::const_iterator end = str.end();

  switch (type)
    {
      case none:
        encode = encodeNONE;
        break;

      case standard:
        encode = encodeSTD;
        break;

      case attribute:
        encode = encodeATTRIBUTE;
        break;

      case character:
        encode = encodeCHARACTER;
        break;
    }

  for (; it != end; ++it)
    encode(*it, xml);

  return xml.str();
}

bool CCopasiXMLInterface::endSaveElement ( const std::string &  name )

protected

End saving an XML element to the ostream started by startSaveElement.

Parameters

const

std::string & name

Returns

bool success

Definition at line 368 of file CCopasiXMLInterface.cpp.

References mIndent, and mpOstream.

Referenced by CCopasiXML::save(), CCopasiXML::saveAnnotation(), CCopasiXML::saveBoundingBox(), CCopasiXML::saveCurve(), CCopasiXML::saveCurveElements(), CCopasiXML::saveFunctionList(), CCopasiXML::saveGlobalRenderInformation(), CCopasiXML::saveGlobalStyle(), CCopasiXML::saveGroupElement(), CCopasiXML::saveGUI(), CCopasiXML::saveLayoutList(), CCopasiXML::saveLinearGradient(), CCopasiXML::saveLineEnding(), CCopasiXML::saveListOfGlobalRenderInformation(), CCopasiXML::saveListOfLocalRenderInformation(), CCopasiXML::saveLocalRenderInformation(), CCopasiXML::saveLocalStyle(), CCopasiXML::saveModel(), CCopasiXML::saveModelParameter(), saveParameter(), CCopasiXML::savePlotList(), CCopasiXML::savePolygonElement(), CCopasiXML::saveRadialGradient(), CCopasiXML::saveRenderCurveElement(), CCopasiXML::saveRenderInformationDefinitionElements(), CCopasiXML::saveRenderTextElement(), CCopasiXML::saveReportList(), CCopasiXML::saveReportSection(), CCopasiXML::saveSBMLReference(), and CCopasiXML::saveTaskList().

{
  mIndent = mIndent.substr(0, mIndent.length() - 2);
  *mpOstream << mIndent << "</" << name << ">" << std::endl;

  return true;
}

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

pure virtual

Load information from a given istream.

Parameters

std::istream	& is
const	std::string & relativeTo

Returns

bool success

Implemented in CConfigurationFile::CXML, and CCopasiXML.

Referenced by load().

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

Load information from a file.

Parameters

const	std::string & fileName
const	std::string & relativeTo

Returns

bool success

Definition at line 279 of file CCopasiXMLInterface.cpp.

References CLocaleString::fromUtf8(), load(), and mPWD.

{
  mPWD = relativeTo;

  std::ifstream is(CLocaleString::fromUtf8(fileName).c_str());

  if (is.fail()) return false;

  return load(is, relativeTo);
}

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

pure virtual

Save information to a given ostream.

Parameters

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

Returns

bool success

Implemented in CConfigurationFile::CXML, and CCopasiXML.

Referenced by save().

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

Save information to a file.

Parameters

const	std::string & fileName
const	std::string & relativeTo

Returns

bool success

Definition at line 291 of file CCopasiXMLInterface.cpp.

References CLocaleString::fromUtf8(), mPWD, and save().

{
  mPWD = relativeTo;

  std::ofstream os(CLocaleString::fromUtf8(fileName).c_str());

  if (os.fail()) return false;

  if (!save(os, relativeTo)) return false;

  return true;
}

bool CCopasiXMLInterface::saveData ( const std::string &  data )

protected

Save CDATA to the ostream

Parameters

const

std::string & data

Returns

bool success

Definition at line 305 of file CCopasiXMLInterface.cpp.

References encode(), mIndent, and mpOstream.

Referenced by CCopasiXML::saveFunctionList(), CCopasiXML::saveModel(), CCopasiXML::saveModelParameter(), saveParameter(), CCopasiXML::saveRenderTextElement(), CCopasiXML::saveReportSection(), and saveXhtml().

{
  *mpOstream << mIndent << CCopasiXMLInterface::encode(data) << std::endl;

  return true;
}

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

protected

Save an XML element to the ostream

Parameters

const	std::string & name
CXMLAttributeList	& attributeList

Returns

bool success

Definition at line 339 of file CCopasiXMLInterface.cpp.

References mIndent, and mpOstream.

Referenced by CCopasiXML::saveColorDefinition(), CCopasiXML::saveDimensions(), CCopasiXML::saveEllipseElement(), CCopasiXML::saveFunctionList(), CCopasiXML::saveGradientStop(), CCopasiXML::saveGUI(), CCopasiXML::saveImageElement(), CCopasiXML::saveLayoutList(), CCopasiXML::saveModel(), CCopasiXML::saveModelParameter(), saveParameter(), CCopasiXML::savePlotList(), CCopasiXML::savePosition(), CCopasiXML::saveRectangleElement(), CCopasiXML::saveRenderPoint(), CCopasiXML::saveReportList(), CCopasiXML::saveReportSection(), CCopasiXML::saveSBMLReference(), and CCopasiXML::saveTaskList().

{
  *mpOstream << mIndent << "<" << name;
  *mpOstream << attributeList;
  *mpOstream << "/>" << std::endl;

  return true;
}

bool CCopasiXMLInterface::saveParameter ( const CCopasiParameter &  parameter )

protected

Save a Parameter.

Parameters

const

CCopasiParameter & parameter

Returns

bool success

Definition at line 376 of file CCopasiXMLInterface.cpp.

References CXMLAttributeList::add(), CCopasiParameter::BOOL, CCopasiParameter::CN, CCopasiParameter::DOUBLE, endSaveElement(), CCopasiParameter::EXPRESSION, CCopasiParameter::FILE, CDirEntry::fileName(), CCopasiObject::getObjectName(), CCopasiParameter::getType(), CCopasiParameter::getValue(), CCopasiParameter::GROUP, CCopasiParameter::INT, CCopasiParameter::INVALID, CDirEntry::isRelativePath(), CCopasiParameter::KEY, CDirEntry::makePathRelative(), mPWD, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pCN, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pEXPRESSION, CCopasiParameter::Value::pFILE, CCopasiParameter::Value::pGROUP, CCopasiParameter::Value::pINT, CCopasiParameter::Value::pKEY, CCopasiParameter::Value::pSTRING, CCopasiParameter::Value::pUDOUBLE, CCopasiParameter::Value::pUINT, saveData(), saveElement(), saveParameterGroup(), CXMLAttributeList::skip(), startSaveElement(), CCopasiParameter::STRING, CCopasiParameter::UDOUBLE, CCopasiParameter::UINT, and CCopasiParameter::XMLType.

Referenced by saveParameterGroup().

{
  bool success = true;

  CXMLAttributeList Attributes;
  std::string File;

  Attributes.add("name", parameter.getObjectName());

  CCopasiParameter::Type Type = parameter.getType();
  Attributes.add("type", CCopasiParameter::XMLType[Type]);

  switch (parameter.getType())
    {
      case CCopasiParameter::DOUBLE:
        Attributes.add("value", * parameter.getValue().pDOUBLE);

        if (!saveElement("Parameter", Attributes)) success = false;

        break;

      case CCopasiParameter::UDOUBLE:
        Attributes.add("value", * parameter.getValue().pUDOUBLE);

        if (!saveElement("Parameter", Attributes)) success = false;

        break;

      case CCopasiParameter::INT:
        Attributes.add("value", * parameter.getValue().pINT);

        if (!saveElement("Parameter", Attributes)) success = false;

        break;

      case CCopasiParameter::UINT:
        Attributes.add("value", * parameter.getValue().pUINT);

        if (!saveElement("Parameter", Attributes)) success = false;

        break;

      case CCopasiParameter::BOOL:
        Attributes.add("value", * parameter.getValue().pBOOL);

        if (!saveElement("Parameter", Attributes)) success = false;

        break;

      case CCopasiParameter::STRING:
        Attributes.add("value", * parameter.getValue().pSTRING);

        if (!saveElement("Parameter", Attributes)) success = false;

        break;

      case CCopasiParameter::KEY:
        Attributes.add("value", * parameter.getValue().pKEY);

        if (!saveElement("Parameter", Attributes)) success = false;

        break;

      case CCopasiParameter::FILE:
        File = * parameter.getValue().pFILE;

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

        Attributes.add("value", File);

        if (!saveElement("Parameter", Attributes)) success = false;

        break;

      case CCopasiParameter::CN:
        Attributes.add("value", * parameter.getValue().pCN);

        if (!saveElement("Parameter", Attributes)) success = false;

        break;

      case CCopasiParameter::EXPRESSION:

        if (!startSaveElement("ParameterText", Attributes)) success = false;

        if (!saveData(*parameter.getValue().pEXPRESSION)) success = false;

        if (!endSaveElement("ParameterText")) success = false;

        break;

      case CCopasiParameter::GROUP:
        Attributes.skip(1);

        if (!startSaveElement("ParameterGroup", Attributes)) success = false;

        if (!saveParameterGroup(* parameter.getValue().pGROUP)) success = false;

        if (!endSaveElement("ParameterGroup")) success = false;

        break;

      case CCopasiParameter::INVALID:
      default:
        success = false;
        break;
    }

  return success;
}

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

protected

Save a Parameter Group.

Parameters

const

CCopasiParameterGroup::parameterGroup & group

Returns

bool success

Definition at line 489 of file CCopasiXMLInterface.cpp.

References saveParameter().

Referenced by saveParameter(), CCopasiXML::savePlotList(), and CCopasiXML::saveTaskList().

{
  bool success = true;

  std::vector< CCopasiParameter * >::const_iterator it = group.begin();
  std::vector< CCopasiParameter * >::const_iterator end = group.end();

  for (; it != end; ++it)
    if (!saveParameter(**it)) success = false;

  return success;
}

bool CCopasiXMLInterface::saveXhtml ( const std::string &  xhtml )

protected

Save xhtml to the ostream

Parameters

const

std::string & xhtml

Returns

bool success

Definition at line 312 of file CCopasiXMLInterface.cpp.

References mIndent, mpOstream, and saveData().

Referenced by CCopasiXML::saveAnnotation(), and CCopasiXML::saveReportList().

{
  // if there is nothing to save bail
  if (xhtml.empty())
    return true;

  std::string::size_type start = xhtml.find_first_not_of("\x0a\x0d\t ");

  if (start != std::string::npos && xhtml[start] == '<')
    {
      std::string::size_type pos = xhtml.find('>');
      std::string FirstElement = xhtml.substr(0, pos);

      if (FirstElement.find("xmlns=\"http://www.w3.org/1999/xhtml\"") == std::string::npos
          && FirstElement.find("xmlns='http://www.w3.org/1999/xhtml'") == std::string::npos)
        FirstElement += " xmlns=\"http://www.w3.org/1999/xhtml\"";

      *mpOstream << mIndent << FirstElement << xhtml.substr(pos) << std::endl;
    }
  else
    {
      saveData(xhtml);
    }

  return true;
}

bool CCopasiXMLInterface::startSaveElement ( const std::string &  name )

protected

Start saving an XML element to the ostream. Call endSaveElement to conclude.

Parameters

const

std::string & name

Returns

bool success

Definition at line 349 of file CCopasiXMLInterface.cpp.

References mIndent, and mpOstream.

Referenced by CCopasiXML::save(), CCopasiXML::saveAnnotation(), CCopasiXML::saveBoundingBox(), CCopasiXML::saveCurve(), CCopasiXML::saveCurveElements(), CCopasiXML::saveFunctionList(), CCopasiXML::saveGlobalRenderInformation(), CCopasiXML::saveGlobalStyle(), CCopasiXML::saveGroupElement(), CCopasiXML::saveGUI(), CCopasiXML::saveLayoutList(), CCopasiXML::saveLinearGradient(), CCopasiXML::saveLineEnding(), CCopasiXML::saveListOfGlobalRenderInformation(), CCopasiXML::saveListOfLocalRenderInformation(), CCopasiXML::saveLocalRenderInformation(), CCopasiXML::saveLocalStyle(), CCopasiXML::saveModel(), CCopasiXML::saveModelParameter(), saveParameter(), CCopasiXML::savePlotList(), CCopasiXML::savePolygonElement(), CCopasiXML::saveRadialGradient(), CCopasiXML::saveRenderCurveElement(), CCopasiXML::saveRenderInformationDefinitionElements(), CCopasiXML::saveRenderTextElement(), CCopasiXML::saveReportList(), CCopasiXML::saveReportSection(), CCopasiXML::saveSBMLReference(), and CCopasiXML::saveTaskList().

{
  *mpOstream << mIndent << "<" << name << ">" << std::endl;

  mIndent += "  ";
  return true;
}

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

protected

Start saving an XML element to the ostream. Call endSaveElement to conclude.

Parameters

const	std::string & name
CXMLAttributeList	& attributeList

Returns

bool success

Definition at line 357 of file CCopasiXMLInterface.cpp.

References mIndent, and mpOstream.

{
  *mpOstream << mIndent << "<" << name;
  *mpOstream << attributeList;
  *mpOstream << ">" << std::endl;

  mIndent += "  ";
  return true;
}

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

static

Encode a given string to a valid XML string

Parameters

const

C_FLOAT64 & dbl

Returns

std::string encoded Encode a given string to a utf-8 string

Parameters

const

std::string & str

Returns

std::string encoded

Definition at line 245 of file CCopasiXMLInterface.cpp.

Referenced by CMIRIAMResourceObject::unescapeId().

{
  std::ostringstream utf8;

  /* Based on RFC 2279.
     Since every string within COPASI is treated as latin1 and input
     is only obtained through QT and Expat which will provide latin1
     encoded strings the below should suffice. */
  size_t i, imax;

  for (i = 0, imax = str.length(); i < imax; i++)
    {
      const unsigned char Char = str[i];

      if (Char < 0x80)
        utf8 << Char;
      else
        {
          utf8 << (unsigned char)(0xc0 + ((Char >> 6) & 0x03));
          utf8 << (unsigned char)(0x80 + (Char & 0x3f));
        }
    }

  return utf8.str();
}

Member Data Documentation

std::string CCopasiXMLInterface::mIndent

protected

Indent

Definition at line 133 of file CCopasiXMLInterface.h.

Referenced by endSaveElement(), saveData(), saveElement(), CCopasiXML::saveModel(), saveXhtml(), and startSaveElement().

std::istream* CCopasiXMLInterface::mpIstream

protected

A pointer to the input stream

Definition at line 123 of file CCopasiXMLInterface.h.

Referenced by CCopasiXML::load().

std::ostream* CCopasiXMLInterface::mpOstream

protected

A pointer to the output stream

Definition at line 128 of file CCopasiXMLInterface.h.

Referenced by endSaveElement(), CCopasiXML::save(), CCopasiXML::saveAnnotation(), saveData(), saveElement(), CCopasiXML::saveModel(), saveXhtml(), and startSaveElement().

std::string CCopasiXMLInterface::mPWD

protected

The filename if available

Definition at line 138 of file CCopasiXMLInterface.h.

Referenced by CCopasiXML::load(), load(), CCopasiXML::save(), save(), saveParameter(), CCopasiXML::saveSBMLReference(), and CCopasiXML::saveTaskList().

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

• CCopasiXMLInterface.h
• CCopasiXMLInterface.cpp