CCopasiXMLParser::ReactionElement Class Reference

Inheritance diagram for CCopasiXMLParser::ReactionElement:

Collaboration diagram for CCopasiXMLParser::ReactionElement:

Public Member Functions
virtual void	end (const XML_Char *pszName)
	ReactionElement (CCopasiXMLParser &parser, SCopasiXMLParserCommon &common)
virtual void	start (const XML_Char *pszName, const XML_Char **papszAttrs)
virtual	~ReactionElement ()
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 {   Reaction = 0, MiriamAnnotation, Comment, ListOfUnsupportedAnnotations,   ListOfSubstrates, ListOfProducts, ListOfModifiers, ListOfConstants,   KineticLaw }

Private Attributes
std::string	mKey
KineticLawElement *	mpKineticLawElement
ListOfConstantsElement *	mpListOfConstantsElement
ListOfModifiersElement *	mpListOfModifiersElement
ListOfProductsElement *	mpListOfProductsElement
ListOfSubstratesElement *	mpListOfSubstratesElement

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 1123 of file CCopasiXMLParser.h.

Member Enumeration Documentation

enum CCopasiXMLParser::ReactionElement::Element

private

Enum of invoked parsers

Enumerator
Reaction
MiriamAnnotation
Comment
ListOfUnsupportedAnnotations
ListOfSubstrates
ListOfProducts
ListOfModifiers
ListOfConstants
KineticLaw

Definition at line 1131 of file CCopasiXMLParser.h.

    {
      Reaction = 0,
      MiriamAnnotation,
      Comment,
      ListOfUnsupportedAnnotations,
      ListOfSubstrates,
      ListOfProducts,
      ListOfModifiers,
      ListOfConstants,
      KineticLaw
    };

Constructor & Destructor Documentation

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

Constructor

Definition at line 3725 of file CCopasiXMLParser.cpp.

                                    :
  CXMLElementHandler< CCopasiXMLParser, SCopasiXMLParserCommon >(parser, common),
  mpListOfSubstratesElement(NULL),
  mpListOfProductsElement(NULL),
  mpListOfModifiersElement(NULL),
  mpListOfConstantsElement(NULL),
  mpKineticLawElement(NULL)
{}

CCopasiXMLParser::ReactionElement::~ReactionElement ( )

virtual

Destructor

Definition at line 3735 of file CCopasiXMLParser.cpp.

References pdelete.

{
  pdelete(mpListOfSubstratesElement);
  pdelete(mpListOfProductsElement);
  pdelete(mpListOfModifiersElement);
  pdelete(mpListOfConstantsElement);
  pdelete(mpKineticLawElement);
}

Member Function Documentation

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

virtual

End element handler

Parameters

const

XML_Char *pszName

Definition at line 3918 of file CCopasiXMLParser.cpp.

References SCopasiXMLParserCommon::CharacterData, CCopasiMessage::EXCEPTION, CReaction::getKey(), CAnnotation::getUnsupportedAnnotations(), CCopasiXMLParser::mCommon, MCXML, CExpatTemplate< CExpat >::mParser, SCopasiXMLParserCommon::pReaction, CAnnotation::setMiriamAnnotation(), CAnnotation::setNotes(), START_ELEMENT, and UNKNOWN_ELEMENT.

{
  switch (mCurrentElement)
    {
      case Reaction:

        if (strcmp(pszName, "Reaction"))
          CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 11,
                         pszName, "Reaction", 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());

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

      case Comment:

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

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

      case ListOfUnsupportedAnnotations:

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

        mCommon.pReaction->getUnsupportedAnnotations() = mParser.mListOfUnsupportedAnnotationsElement.getUnsupportedAnnotations();

        break;

      case ListOfSubstrates:

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

        break;

      case ListOfProducts:

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

        break;

      case ListOfModifiers:

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

        break;

      case ListOfConstants:

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

        break;

      case KineticLaw:

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

        break;

      case UNKNOWN_ELEMENT:
        break;

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

  mCurrentElement = Reaction;

  return;
}

void CCopasiXMLParser::ReactionElement::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 3744 of file CCopasiXMLParser.cpp.

References CCopasiVectorN< CType >::add(), CCopasiMessage::EXCEPTION, fatalError, CKeyFactory::get(), CModel::getReactions(), SCopasiXMLParserCommon::KeyMap, CCopasiXMLParser::mCommon, MCXML, CExpatTemplate< CExpat >::mParser, SCopasiXMLParserCommon::pModel, SCopasiXMLParserCommon::pReaction, CReaction::setFast(), CCopasiObject::setObjectName(), CReaction::setReversible(), CReaction::setSBMLId(), and UNKNOWN_ELEMENT.

{
  CCompartment * pCompartment;
  const char * Name;
  const char * Compartment; // Default Compartment_00
  const char * reversible;
  bool Reversible;
  const char * fast;
  bool Fast;
  const char * SBMLId;

  mCurrentElement = mLastKnownElement;
  mpCurrentHandler = NULL;

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

      switch (mCurrentElement)
        {
          case Reaction:

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

            mKey = mParser.getAttributeValue("key", papszAttrs);
            Name = mParser.getAttributeValue("name", papszAttrs);
            Compartment = mParser.getAttributeValue("compartment", papszAttrs,
                                                    "Compartment_00");

            reversible = mParser.getAttributeValue("reversible", papszAttrs);
            Reversible = mParser.toBool(reversible);

            fast = mParser.getAttributeValue("fast", papszAttrs, "false");
            Fast = mParser.toBool(fast);

            mCommon.pReaction = new CReaction();
            addFix(mKey, mCommon.pReaction);
            mCommon.pReaction->setObjectName(Name);
            mCommon.pReaction->setReversible(Reversible);
            mCommon.pReaction->setFast(Fast);
            SBMLId = mParser.getAttributeValue("sbmlid", papszAttrs, "");

            if (std::string(SBMLId) != std::string(""))
              {
                mCommon.pReaction->setSBMLId(SBMLId);
              }

            if (strcmp(Compartment, "Compartment_00")) //TODO necessary?
              {
                pCompartment =
                  dynamic_cast< CCompartment* >(mCommon.KeyMap.get(Compartment));

                if (!pCompartment) fatalError();

                //mCommon.pReaction->setCompartment(pCompartment);
              }

            mCommon.pModel->getReactions().add(mCommon.pReaction, true);

            mLastKnownElement = Reaction;
            return;
            break;

          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 ListOfSubstrates:

            if (!strcmp(pszName, "ListOfSubstrates"))
              {
                /* If we do not have a function element handler we create one. */
                if (!mpListOfSubstratesElement)
                  mpListOfSubstratesElement =
                    new ListOfSubstratesElement(mParser, mCommon);

                mpCurrentHandler = mpListOfSubstratesElement;
              }

            break;

          case ListOfProducts:

            if (!strcmp(pszName, "ListOfProducts"))
              {
                if (!mpListOfProductsElement)
                  mpListOfProductsElement =
                    new ListOfProductsElement(mParser, mCommon);

                mpCurrentHandler = mpListOfProductsElement;
              }

            break;

          case ListOfModifiers:

            if (!strcmp(pszName, "ListOfModifiers"))
              {
                if (!mpListOfModifiersElement)
                  mpListOfModifiersElement =
                    new ListOfModifiersElement(mParser, mCommon);

                mpCurrentHandler = mpListOfModifiersElement;
              }

            break;

          case ListOfConstants:

            if (!strcmp(pszName, "ListOfConstants"))
              {
                if (!mpListOfConstantsElement)
                  mpListOfConstantsElement =
                    new ListOfConstantsElement(mParser, mCommon);

                mpCurrentHandler = mpListOfConstantsElement;
              }

            break;

          case KineticLaw:

            if (!strcmp(pszName, "KineticLaw"))
              {
                if (!mpKineticLawElement)
                  mpKineticLawElement = new KineticLawElement(mParser, mCommon);

                mpCurrentHandler = mpKineticLawElement;
              }

            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::ReactionElement::mKey

private

The key in the CopasiML gile

Definition at line 1172 of file CCopasiXMLParser.h.

KineticLawElement* CCopasiXMLParser::ReactionElement::mpKineticLawElement

private

Pointer to ListOfConstantsElement element handler.

Definition at line 1167 of file CCopasiXMLParser.h.

ListOfConstantsElement* CCopasiXMLParser::ReactionElement::mpListOfConstantsElement

private

Pointer to ListOfConstantsElement element handler.

Definition at line 1162 of file CCopasiXMLParser.h.

ListOfModifiersElement* CCopasiXMLParser::ReactionElement::mpListOfModifiersElement

private

Pointer to ListOfModifiersElement element handler.

Definition at line 1157 of file CCopasiXMLParser.h.

ListOfProductsElement* CCopasiXMLParser::ReactionElement::mpListOfProductsElement

private

Pointer to ListOfProductsElement element handler.

Definition at line 1152 of file CCopasiXMLParser.h.

ListOfSubstratesElement* CCopasiXMLParser::ReactionElement::mpListOfSubstratesElement

private

Pointer to ListOfSubstratesElement element handler.

Definition at line 1147 of file CCopasiXMLParser.h.

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

• CCopasiXMLParser.h
• CCopasiXMLParser.cpp