CCopasiXMLParser::ModelElement Class Reference

Inheritance diagram for CCopasiXMLParser::ModelElement:

Collaboration diagram for CCopasiXMLParser::ModelElement:

Public Member Functions
virtual void	end (const XML_Char *pszName)
	ModelElement (CCopasiXMLParser &parser, SCopasiXMLParserCommon &common)
virtual void	start (const XML_Char *pszName, const XML_Char **papszAttrs)
virtual	~ModelElement ()
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 {   Model = 0, MiriamAnnotation, Comment, ListOfUnsupportedAnnotations,   InitialExpression, ListOfCompartments, ListOfMetabolites, ListOfModelValues,   ListOfReactions, ListOfEvents, ListOfModelParameterSets, StateTemplate,   InitialState }

Private Attributes
std::string	mKey

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 1801 of file CCopasiXMLParser.h.

Member Enumeration Documentation

enum CCopasiXMLParser::ModelElement::Element

private

Enum of invoked parsers

Enumerator
Model
MiriamAnnotation
Comment
ListOfUnsupportedAnnotations
InitialExpression
ListOfCompartments
ListOfMetabolites
ListOfModelValues
ListOfReactions
ListOfEvents
ListOfModelParameterSets
StateTemplate
InitialState

Definition at line 1809 of file CCopasiXMLParser.h.

    {
      Model = 0,
      MiriamAnnotation,
      Comment,
      ListOfUnsupportedAnnotations,
      InitialExpression,
      ListOfCompartments,
      ListOfMetabolites,
      ListOfModelValues,
      ListOfReactions,
      ListOfEvents,
      ListOfModelParameterSets,
      StateTemplate,
      InitialState
    };

Constructor & Destructor Documentation

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

Constructor

Definition at line 1608 of file CCopasiXMLParser.cpp.

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

CCopasiXMLParser::ModelElement::~ModelElement ( )

virtual

Destructor

Definition at line 1613 of file CCopasiXMLParser.cpp.

{
  deleteCurrentHandler();
}

Member Function Documentation

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

virtual

End element handler

Parameters

const

XML_Char *pszName

Definition at line 1834 of file CCopasiXMLParser.cpp.

References SCopasiXMLParserCommon::CharacterData, CCopasiMessage::EXCEPTION, CModel::getKey(), CCopasiMessage::getLastMessage(), CAnnotation::getUnsupportedAnnotations(), CCopasiXMLParser::mCommon, MCXML, CExpatTemplate< CExpat >::mParser, SCopasiXMLParserCommon::pModel, CModel::setCompileFlag(), CModelEntity::setInitialExpression(), CAnnotation::setMiriamAnnotation(), CAnnotation::setNotes(), CCopasiMessage::size(), START_ELEMENT, and UNKNOWN_ELEMENT.

{
  switch (mCurrentElement)
    {
      case Model:

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

        mCommon.pModel->setCompileFlag(true);

        mParser.popElementHandler();
        mCurrentElement = 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.pModel->setMiriamAnnotation(mCommon.CharacterData, mCommon.pModel->getKey(), mKey);
        mCommon.CharacterData = "";
        break;

      case Comment:

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

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

      case ListOfUnsupportedAnnotations:

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

        mCommon.pModel->getUnsupportedAnnotations() = mParser.mListOfUnsupportedAnnotationsElement.getUnsupportedAnnotations();
        break;

      case InitialExpression:

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

        {
          size_t Size = CCopasiMessage::size();

          mCommon.pModel->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();
        }

        // Old CopasiML files have the incorrect order and the comment may appear after
        // the initial expression. Therefore, we reset to MiriamAnnotation.
        mCurrentElement = MiriamAnnotation;
        break;

      case ListOfCompartments:

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

        deleteCurrentHandler();
        break;

      case ListOfMetabolites:

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

        deleteCurrentHandler();
        break;

      case ListOfModelValues:

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

        deleteCurrentHandler();
        break;

      case ListOfReactions:

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

        deleteCurrentHandler();
        break;

      case ListOfEvents:

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

        deleteCurrentHandler();
        break;

      case ListOfModelParameterSets:

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

        deleteCurrentHandler();
        mCurrentElement = Model; // This is possibly the last element.
        break;

      case StateTemplate:

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

        deleteCurrentHandler();
        break;

      case InitialState:

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

        deleteCurrentHandler();
        mCurrentElement = Model; // This is possibly the last element.
        break;

      case UNKNOWN_ELEMENT:
        mCurrentElement = mLastKnownElement;
        mCurrentElement = Model; // This is possibly the last element.
        break;

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

  return;
}

void CCopasiXMLParser::ModelElement::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 1618 of file CCopasiXMLParser.cpp.

References CModel::AreaUnitNames, C_FLOAT64, CModel::deterministic, CCopasiMessage::EXCEPTION, CModel::getModelParameterSets(), CModel::LengthUnitNames, CModel::m, CModel::m2, CCopasiXMLParser::mCommon, MCXML, CModel::min, CModel::ml, CModel::mMol, CModel::ModelTypeNames, CExpatTemplate< CExpat >::mParser, CModel::OldMinute, CModel::OldXML, SCopasiXMLParserCommon::pDataModel, SCopasiXMLParserCommon::pModel, CModel::QuantityUnitNames, CModel::QuantityUnitOldXMLNames, CModel::s, CModel::setAreaUnit(), CModel::setAvogadro(), CModel::setLengthUnit(), CModel::setModelType(), CCopasiObject::setObjectName(), CModel::setQuantityUnit(), CModel::setTimeUnit(), CModel::setVolumeUnit(), CModel::TimeUnitNames, toEnum(), UNKNOWN_ELEMENT, and CModel::VolumeUnitNames.

{
  const char * Name;
  const char * timeUnit;
  CModel::TimeUnit TimeUnit;
  const char * volumeUnit;
  CModel::VolumeUnit VolumeUnit;
  const char * areaUnit;
  CModel::AreaUnit AreaUnit;
  const char * lengthUnit;
  CModel::LengthUnit LengthUnit;
  const char * quantityUnit;
  CModel::QuantityUnit QuantityUnit;
  CModel::ModelType ModelType;
  C_FLOAT64 Avogadro;

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

  switch (mCurrentElement)
    {
      case Model:

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

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

        timeUnit = mParser.getAttributeValue("timeUnit", papszAttrs);
        TimeUnit = toEnum(timeUnit, CModel::TimeUnitNames, CModel::OldMinute);

        if (TimeUnit == CModel::OldMinute)
          {
            if (strcmp(timeUnit, "m"))
              TimeUnit = CModel::s;
            else
              TimeUnit = CModel::min;
          }

        volumeUnit = mParser.getAttributeValue("volumeUnit", papszAttrs);
        VolumeUnit = toEnum(volumeUnit, CModel::VolumeUnitNames, CModel::ml);

        //the next 2 attributes are introduced in Build 31, they have a default for
        //reading older cps files
        areaUnit = mParser.getAttributeValue("areaUnit", papszAttrs, "m\xc2\xb2");
        AreaUnit = toEnum(areaUnit, CModel::AreaUnitNames, CModel::m2);

        lengthUnit = mParser.getAttributeValue("lengthUnit", papszAttrs, "m");
        LengthUnit = toEnum(lengthUnit, CModel::LengthUnitNames, CModel::m);

        quantityUnit = mParser.getAttributeValue("quantityUnit", papszAttrs);
        QuantityUnit = toEnum(quantityUnit, CModel::QuantityUnitNames, CModel::OldXML);

        if (QuantityUnit == CModel::OldXML)
          QuantityUnit = toEnum(quantityUnit, CModel::QuantityUnitOldXMLNames, CModel::mMol);

        ModelType = toEnum(mParser.getAttributeValue("type", papszAttrs, "deterministic"),
                           CModel::ModelTypeNames, CModel::deterministic);

        Avogadro = CCopasiXMLInterface::DBL(mParser.getAttributeValue("avogadroConstant", papszAttrs, "6.0221415e23"));

        if (!mCommon.pModel) mCommon.pModel = new CModel(mCommon.pDataModel);

        // We remove the default parameter set:
        mCommon.pModel->getModelParameterSets().CCopasiVector< CModelParameterSet >::remove((size_t) 0);

        addFix(mKey, mCommon.pModel);
        mCommon.pModel->setObjectName(Name);
        mCommon.pModel->setTimeUnit(TimeUnit);
        mCommon.pModel->setVolumeUnit(VolumeUnit);
        mCommon.pModel->setAreaUnit(AreaUnit);
        mCommon.pModel->setLengthUnit(LengthUnit);
        mCommon.pModel->setQuantityUnit(QuantityUnit);
        mCommon.pModel->setModelType(ModelType);
        mCommon.pModel->setAvogadro(Avogadro);

        return;
        break;

      case MiriamAnnotation:

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

        break;

      case Comment:

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

        break;

      case ListOfUnsupportedAnnotations:

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

        break;

      case InitialExpression:

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

        break;

      case ListOfCompartments:

        if (!strcmp(pszName, "ListOfCompartments"))
          {
            mpCurrentHandler = new ListOfCompartmentsElement(mParser, mCommon);
            mLastKnownElement = mCurrentElement;
          }

        break;

      case ListOfMetabolites:

        if (!strcmp(pszName, "ListOfMetabolites"))
          {
            mpCurrentHandler = new ListOfMetabolitesElement(mParser, mCommon);
            mLastKnownElement = mCurrentElement;
          }

        break;

      case ListOfModelValues:

        if (!strcmp(pszName, "ListOfModelValues"))
          {
            mpCurrentHandler = new ListOfModelValuesElement(mParser, mCommon);
            mLastKnownElement = mCurrentElement;
          }

        break;

      case ListOfReactions:

        if (!strcmp(pszName, "ListOfReactions"))
          {
            mpCurrentHandler = new ListOfReactionsElement(mParser, mCommon);
            mLastKnownElement = mCurrentElement;
          }

        break;

      case ListOfEvents:

        if (!strcmp(pszName, "ListOfEvents"))
          {
            mpCurrentHandler = new ListOfEventsElement(mParser, mCommon);
            mLastKnownElement = mCurrentElement;
          }

        break;

      case ListOfModelParameterSets:

        if (!strcmp(pszName, "ListOfModelParameterSets"))
          {
            mpCurrentHandler = new ListOfModelParameterSetsElement(mParser, mCommon);
            mLastKnownElement = mCurrentElement;
          }

        break;

      case StateTemplate:

        if (!strcmp(pszName, "StateTemplate"))
          {
            mpCurrentHandler = new StateTemplateElement(mParser, mCommon);
            mLastKnownElement = mCurrentElement;
          }

        break;

      case InitialState:

        if (!strcmp(pszName, "InitialState"))
          {
            mpCurrentHandler = new InitialStateElement(mParser, mCommon);
            mLastKnownElement = mCurrentElement;
          }

        break;

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

  if (mpCurrentHandler)
    mParser.pushElementHandler(mpCurrentHandler);

  mParser.onStartElement(pszName, papszAttrs);

  return;
}

Member Data Documentation

std::string CCopasiXMLParser::ModelElement::mKey

private

The key in the CopasiML file

Definition at line 1829 of file CCopasiXMLParser.h.

---

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

• CCopasiXMLParser.h
• CCopasiXMLParser.cpp