CCopasiXMLParser::MetaboliteElement Class Reference

Inheritance diagram for CCopasiXMLParser::MetaboliteElement:

Collaboration diagram for CCopasiXMLParser::MetaboliteElement:

Public Member Functions
virtual void	end (const XML_Char *pszName)
	MetaboliteElement (CCopasiXMLParser &parser, SCopasiXMLParserCommon &common)
virtual void	start (const XML_Char *pszName, const XML_Char **papszAttrs)
virtual	~MetaboliteElement ()
Public Member Functions inherited from CXMLElementHandler< CCopasiXMLParser, SCopasiXMLParserCommon >
	CXMLElementHandler (CCopasiXMLParser &parser, SCopasiXMLParserCommon &common)
virtual void	end (const XML_Char *C_UNUSED(pszName))
virtual void	reset ()
virtual void	start (const XML_Char *C_UNUSED(pszName), const XML_Char **C_UNUSED(papszAttrs))
virtual	~CXMLElementHandler ()

Private Types
enum	Element {   Metabolite = 0, MiriamAnnotation, Comment, ListOfUnsupportedAnnotations,   Expression, InitialExpression }

Private Attributes
std::string	mKey
CMetab *	mpMetabolite

Additional Inherited Members
Protected Member Functions inherited from CXMLElementHandler< CCopasiXMLParser, SCopasiXMLParserCommon >
void	addFix (const std::string &key, CCopasiObject *pObject)
void	deleteCurrentHandler ()
Protected Attributes inherited from CXMLElementHandler< CCopasiXMLParser, SCopasiXMLParserCommon >
SCopasiXMLParserCommon &	mCommon
C_INT32	mCurrentElement
C_INT32	mLastKnownElement
CCopasiXMLParser &	mParser
CXMLElementHandler *	mpCurrentHandler

Detailed Description

Definition at line 1244 of file CCopasiXMLParser.h.

Member Enumeration Documentation

enum CCopasiXMLParser::MetaboliteElement::Element

private

Enum of invoked parsers

Enumerator
Metabolite
MiriamAnnotation
Comment
ListOfUnsupportedAnnotations
Expression
InitialExpression

Definition at line 1252 of file CCopasiXMLParser.h.

    {
      Metabolite = 0,
      MiriamAnnotation,
      Comment,
      ListOfUnsupportedAnnotations,
      Expression,
      InitialExpression
    };

Constructor & Destructor Documentation

CCopasiXMLParser::MetaboliteElement::MetaboliteElement	(	CCopasiXMLParser &	parser,
		SCopasiXMLParserCommon &	common
	)

Constructor

Definition at line 2526 of file CCopasiXMLParser.cpp.

                                    :
  CXMLElementHandler< CCopasiXMLParser, SCopasiXMLParserCommon >(parser, common),
  mpMetabolite(NULL)
{}

CCopasiXMLParser::MetaboliteElement::~MetaboliteElement ( )

virtual

Destructor

Definition at line 2532 of file CCopasiXMLParser.cpp.

{}

Member Function Documentation

void CCopasiXMLParser::MetaboliteElement::end ( const XML_Char *  pszName )

virtual

End element handler

Parameters

const

XML_Char *pszName

Definition at line 2652 of file CCopasiXMLParser.cpp.

References SCopasiXMLParserCommon::CharacterData, CCopasiMessage::EXCEPTION, CCopasiMessage::getLastMessage(), CCopasiXMLParser::mCommon, MCXML, CExpatTemplate< CExpat >::mParser, CCopasiMessage::size(), START_ELEMENT, and UNKNOWN_ELEMENT.

{
  switch (mCurrentElement)
    {
      case Metabolite:

        if (strcmp(pszName, "Metabolite"))
          CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 11,
                         pszName, "Metabolite", mParser.getCurrentLineNumber());

        mParser.popElementHandler();
        mLastKnownElement = START_ELEMENT;

        /* Tell the parent element we are done. */
        mParser.onEndElement(pszName);
        break;

      case MiriamAnnotation:

        if (strcmp(pszName, "MiriamAnnotation"))
          CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 11,
                         pszName, "MiriamAnnotation", mParser.getCurrentLineNumber());

        mpMetabolite->setMiriamAnnotation(mCommon.CharacterData, mpMetabolite->getKey(), mKey);
        mCommon.CharacterData = "";
        break;

      case Comment:

        if (strcmp(pszName, "Comment"))
          CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 11,
                         pszName, "Comment", mParser.getCurrentLineNumber());

        mpMetabolite->setNotes(mCommon.CharacterData);
        mCommon.CharacterData = "";
        break;

      case ListOfUnsupportedAnnotations:

        if (strcmp(pszName, "ListOfUnsupportedAnnotations"))
          CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 11,
                         pszName, "ListOfUnsupportedAnnotations", mParser.getCurrentLineNumber());

        mpMetabolite->getUnsupportedAnnotations() = mParser.mListOfUnsupportedAnnotationsElement.getUnsupportedAnnotations();

        break;

      case Expression:

        if (strcmp(pszName, "Expression"))
          CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 11,
                         pszName, "Expression", mParser.getCurrentLineNumber());

        {
          size_t Size = CCopasiMessage::size();

          mpMetabolite->setExpression(mCommon.CharacterData);

          // Remove error messages created by setExpression as this may fail
          // due to incomplete model specification at this time.
          while (CCopasiMessage::size() > Size)
            CCopasiMessage::getLastMessage();
        }

        break;

      case InitialExpression:

        if (strcmp(pszName, "InitialExpression"))
          CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 11,
                         pszName, "InitialExpression", mParser.getCurrentLineNumber());

        {
          size_t Size = CCopasiMessage::size();

          mpMetabolite->setInitialExpression(mCommon.CharacterData);

          // Remove error messages created by setExpression as this may fail
          // due to incomplete model specification at this time.
          while (CCopasiMessage::size() > Size)
            CCopasiMessage::getLastMessage();
        }

        break;

      case UNKNOWN_ELEMENT:
        break;

      default:
        CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 11,
                       pszName, "???", mParser.getCurrentLineNumber());
        break;
    }

  mCurrentElement = Metabolite;
  return;
}

void CCopasiXMLParser::MetaboliteElement::start ( const XML_Char *  pszName, const XML_Char **  papszAttrs  )

virtual

Start element handler

Parameters

const	XML_Char *pszName
const	XML_Char **papszAttrs

Definition at line 2535 of file CCopasiXMLParser.cpp.

References CCopasiVector< T >::add(), CCompartment::addMetabolite(), CCopasiMessage::EXCEPTION, fatalError, CKeyFactory::get(), CModel::getMetabolites(), SCopasiXMLParserCommon::KeyMap, CCopasiXMLParser::mCommon, MCXML, CExpatTemplate< CExpat >::mParser, SCopasiXMLParserCommon::pModel, CModelEntity::REACTIONS, toEnum(), UNKNOWN_ELEMENT, and CModelEntity::XMLStatus.

{
  CCompartment * pCompartment = NULL;
  const char * Name;
  const char * simulationType;
  CModelEntity::Status SimulationType;
  const char reactions[] = "reactions";
  const char * Compartment;

  mpCurrentHandler = NULL;
  mCurrentElement = mLastKnownElement;

  while (mpCurrentHandler == NULL)
    {
      mCurrentElement++; /* We should always be on the next element */

      switch (mCurrentElement)
        {
          case Metabolite:

            if (strcmp(pszName, "Metabolite"))
              CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 10,
                             pszName, "Metabolite", mParser.getCurrentLineNumber());

            mKey = mParser.getAttributeValue("key", papszAttrs);
            Name = mParser.getAttributeValue("name", papszAttrs);

            simulationType = mParser.getAttributeValue("simulationType", papszAttrs, false);

            // We need to handle old files which used the attribute status.
            if (!simulationType)
              {
                simulationType = mParser.getAttributeValue("status", papszAttrs, false);

                if (!simulationType) // status and simulationType are both missing
                  simulationType = mParser.getAttributeValue("simulationType", papszAttrs);
                else if (!strcmp(simulationType, "variable")) // reactions was named variable
                  simulationType = reactions;
              }

            SimulationType = toEnum(simulationType, CModelEntity::XMLStatus, CModelEntity::REACTIONS);
            Compartment = mParser.getAttributeValue("compartment", papszAttrs);

            mpMetabolite = new CMetab();
            addFix(mKey, mpMetabolite);
            mpMetabolite->setObjectName(Name);
            mpMetabolite->setStatus(SimulationType);

            pCompartment =
              dynamic_cast< CCompartment* >(mCommon.KeyMap.get(Compartment));

            if (!pCompartment) fatalError();

            pCompartment->addMetabolite(mpMetabolite);
            mCommon.pModel->getMetabolites().add(mpMetabolite);

            mLastKnownElement = mCurrentElement;
            return;

          case MiriamAnnotation:

            if (!strcmp(pszName, "MiriamAnnotation"))
              mpCurrentHandler = &mParser.mMiriamAnnotationElement;

            break;

          case Comment:

            if (!strcmp(pszName, "Comment"))
              {
                mpCurrentHandler = &mParser.mCommentElement;
                mLastKnownElement = mCurrentElement;
              }

            break;

          case ListOfUnsupportedAnnotations:

            if (!strcmp(pszName, "ListOfUnsupportedAnnotations"))
              mpCurrentHandler = &mParser.mListOfUnsupportedAnnotationsElement;

            break;

          case Expression:

            if (!strcmp(pszName, "Expression"))
              mpCurrentHandler = &mParser.mCharacterDataElement;

            break;

          case InitialExpression:

            if (!strcmp(pszName, "InitialExpression"))
              mpCurrentHandler = &mParser.mCharacterDataElement;

            break;

          default:
            mCurrentElement = UNKNOWN_ELEMENT;
            mpCurrentHandler = &mParser.mUnknownElement;
            break;
        }
    }

  mParser.pushElementHandler(mpCurrentHandler);

  if (mpCurrentHandler != &mParser.mUnknownElement)
    {
      mLastKnownElement = mCurrentElement;
    }

  mParser.onStartElement(pszName, papszAttrs);

  return;
}

Member Data Documentation

std::string CCopasiXMLParser::MetaboliteElement::mKey

private

The key in the CopasiML file

Definition at line 1298 of file CCopasiXMLParser.h.

CMetab* CCopasiXMLParser::MetaboliteElement::mpMetabolite

private

A pointer to the current metabolite.

Definition at line 1293 of file CCopasiXMLParser.h.

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

• CCopasiXMLParser.h
• CCopasiXMLParser.cpp