CAnnotation Class Reference

#include <CAnnotation.h>

Inheritance diagram for CAnnotation:

Collaboration diagram for CAnnotation:

Public Types
typedef std::map< std::string, std::string >	UnsupportedAnnotation

Public Member Functions
bool	addUnsupportedAnnotation (const std::string &name, const std::string &xml)
	CAnnotation ()
	CAnnotation (const CAnnotation &src)
virtual const std::string &	getKey () const
const std::string &	getMiriamAnnotation () const
const std::string &	getNotes () const
UnsupportedAnnotation &	getUnsupportedAnnotations ()
const UnsupportedAnnotation &	getUnsupportedAnnotations () const
bool	operator== (const CAnnotation &rhs) const
bool	removeUnsupportedAnnotation (const std::string &name)
bool	replaceUnsupportedAnnotation (const std::string &name, const std::string &xml)
void	setMiriamAnnotation (const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId)
void	setNotes (const std::string &notes)
virtual	~CAnnotation ()

Static Public Member Functions
static CAnnotation *	castObject (CCopasiObject *pObject)
static const CAnnotation *	castObject (const CCopasiObject *pObject)

Protected Attributes
std::string	mKey

Static Private Member Functions
static bool	isValidXML (const std::string &xml)

Private Attributes
std::string	mMiriamAnnotation
std::string	mNotes
UnsupportedAnnotation	mUnsupportedAnnotations
std::string	mXMLId

Detailed Description

Definition at line 14 of file CAnnotation.h.

Member Typedef Documentation

typedef std::map< std::string, std::string > CAnnotation::UnsupportedAnnotation

Definition at line 17 of file CAnnotation.h.

Constructor & Destructor Documentation

CAnnotation::CAnnotation

(

)

Default constructor

Definition at line 81 of file CAnnotation.cpp.

                        :
  mKey(""),
  mNotes(),
  mMiriamAnnotation(),
  mXMLId(),
  mUnsupportedAnnotations()
{}

CAnnotation::CAnnotation

(

const CAnnotation &

src

)

Copy constructor

Parameters

const

CAnnotation & src

Definition at line 89 of file CAnnotation.cpp.

                                               :
  mKey(""),
  mNotes(src.mNotes),
  mMiriamAnnotation(src.mMiriamAnnotation),
  mXMLId(src.mXMLId),
  mUnsupportedAnnotations(src.mUnsupportedAnnotations)
{}

CAnnotation::~CAnnotation ( )

virtual

Destructor

Definition at line 97 of file CAnnotation.cpp.

References CCopasiRootContainer::getKeyFactory(), mKey, and CKeyFactory::remove().

{
  CCopasiRootContainer::getKeyFactory()->remove(mKey);
}

Member Function Documentation

bool CAnnotation::addUnsupportedAnnotation	(	const std::string &	name,
		const std::string &	xml
	)

Add an unsupported annotation

Parameters

const	std::string & name
const	std::string & xml

Returns

bool success

Definition at line 211 of file CAnnotation.cpp.

References CCopasiMessage::ERROR, isValidXML(), MCAnnotation, and mUnsupportedAnnotations.

Referenced by SBMLImporter::importNotes().

{
  // The name must not be empty
  if (name == "")
    {
      CCopasiMessage(CCopasiMessage::ERROR, MCAnnotation + 7);
      return false;
    }

  // The name must be unique
  if (mUnsupportedAnnotations.find(name) != mUnsupportedAnnotations.end())
    {
      CCopasiMessage(CCopasiMessage::ERROR, MCAnnotation + 6, name.c_str());
      return false;
    }

  // We need to check whether we have valid XML.
  if (!isValidXML(xml))
    {
      CCopasiMessage(CCopasiMessage::ERROR, MCAnnotation + 5, name.c_str());
      return false;
    }

  mUnsupportedAnnotations[name] = xml;

  return true;
}

CAnnotation * CAnnotation::castObject ( CCopasiObject *  pObject )

static

Definition at line 32 of file CAnnotation.cpp.

Referenced by CMIRIAMInfo::load(), CQNotes::load(), CMIRIAMInfo::save(), CQNotes::save(), and CQMiriamWidget::showEvent().

{
  CModelEntity * pEntity = NULL;
  CEvent * pEvent = NULL;
  CReaction * pReaction = NULL;
  CFunction * pFunction = NULL;
  CModelParameterSet * pParameterSet = NULL;

  if ((pEntity = dynamic_cast< CModelEntity * >(pObject)) != NULL)
    return static_cast< CAnnotation * >(pEntity);

  if ((pEvent = dynamic_cast< CEvent * >(pObject)) != NULL)
    return static_cast< CAnnotation * >(pEvent);

  if ((pReaction = dynamic_cast< CReaction * >(pObject)) != NULL)
    return static_cast< CAnnotation * >(pReaction);

  if ((pParameterSet = dynamic_cast< CModelParameterSet * >(pObject)) != NULL)
    return static_cast< CAnnotation * >(pParameterSet);

  if ((pFunction = dynamic_cast< CFunction * >(pObject)) != NULL)
    return static_cast< CAnnotation * >(pFunction);

  return NULL;
}

const CAnnotation * CAnnotation::castObject ( const CCopasiObject *  pObject )

static

Definition at line 59 of file CAnnotation.cpp.

{
  const CModelEntity * pEntity = NULL;
  const CEvent * pEvent = NULL;
  const CReaction * pReaction = NULL;
  const CFunction * pFunction = NULL;

  if ((pEntity = dynamic_cast< const CModelEntity * >(pObject)) != NULL)
    return static_cast< const CAnnotation * >(pEntity);

  if ((pEvent = dynamic_cast< const CEvent * >(pObject)) != NULL)
    return static_cast< const CAnnotation * >(pEvent);

  if ((pReaction = dynamic_cast< const CReaction * >(pObject)) != NULL)
    return static_cast< const CAnnotation * >(pReaction);

  if ((pFunction = dynamic_cast< const CFunction * >(pObject)) != NULL)
    return static_cast< const CAnnotation * >(pFunction);

  return NULL;
}

const std::string & CAnnotation::getKey ( ) const

virtual

Retrieve the key

Returns

std::string key

Reimplemented in CModel, CEvent, CReaction, CModelEntity, CFunction, and CModelParameterSet.

Definition at line 103 of file CAnnotation.cpp.

References mKey.

Referenced by CFunction::getKey(), CModelEntity::getKey(), CReaction::getKey(), CEvent::getKey(), and CMIRIAMInfo::save().

{
  return mKey;
}

const std::string & CAnnotation::getMiriamAnnotation

(

)

const

Retrieve the RDF/XML representation of the MIRIAM annotation

Returns

const std::string & miriamAnnotation

Definition at line 117 of file CAnnotation.cpp.

References mMiriamAnnotation.

Referenced by CEvent::CEvent(), CFunction::CFunction(), CModelEntity::CModelEntity(), CReaction::CReaction(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateEvent(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CModelExpansion::duplicateReaction(), CQRDFTreeView::enterProtected(), CMIRIAMInfo::load(), CCopasiXML::saveAnnotation(), CQMiriamWidget::showEvent(), test000092::test_miriam_export_8(), test000092::test_miriam_export_9(), test000092::test_miriam_import_1(), and CSBMLExporter::updateMIRIAMAnnotation().

{return mMiriamAnnotation;}

const std::string & CAnnotation::getNotes

(

)

const

Retrieve the XHTML notes

Returns

const std::string & notes

Definition at line 124 of file CAnnotation.cpp.

References mNotes.

Referenced by CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateEvent(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CModelExpansion::duplicateReaction(), CModel::initObjects(), CQNotes::load(), CQNotes::save(), CCopasiXML::saveAnnotation(), and CSBMLExporter::setSBMLNotes().

{
  return mNotes;
}

CAnnotation::UnsupportedAnnotation & CAnnotation::getUnsupportedAnnotations

(

)

Retrieve the unsupported annotations in xml format.

Returns

std::map< std::string, std::string > & unsupportedAnnotations

Definition at line 201 of file CAnnotation.cpp.

References mUnsupportedAnnotations.

Referenced by CCopasiXMLParser::ReactionElement::end(), CCopasiXMLParser::EventElement::end(), CCopasiXMLParser::ModelElement::end(), CCopasiXMLParser::FunctionElement::end(), CCopasiXML::saveAnnotation(), and CSBMLExporter::setSBMLNotes().

{
  return mUnsupportedAnnotations;
}

const CAnnotation::UnsupportedAnnotation & CAnnotation::getUnsupportedAnnotations

(

)

const

Definition at line 206 of file CAnnotation.cpp.

References mUnsupportedAnnotations.

{
  return mUnsupportedAnnotations;
}

bool CAnnotation::isValidXML ( const std::string &  xml )

staticprivate

Definition at line 275 of file CAnnotation.cpp.

References BUFFER_SIZE, CCopasiMessage::getLastMessage(), CExpatTemplate< CType >::parse(), and CCopasiMessage::size().

Referenced by addUnsupportedAnnotation(), and replaceUnsupportedAnnotation().

{
  std::istringstream XML;
  XML.str(xml);
  XML.imbue(std::locale::classic());
  XML.precision(16);

  bool done = false;

  CVersion Version;
  CCopasiXMLParser Parser(Version);

  size_t Size = CCopasiMessage::size();

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

  while (!done)
    {
      XML.get(pBuffer, BUFFER_SIZE, 0);

      if (XML.eof()) done = true;

      if (XML.fail() && !done)
        {
          done = true;
          return false;
        }

      if (!Parser.parse(pBuffer, -1, done))
        {
          done = true;
          return false;
        }
    }

  delete [] pBuffer;
#undef BUFFER_SIZE

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

  return true;
}

bool CAnnotation::operator==

(

const CAnnotation &

rhs

)

const

Comparison operator

Parameters

const

CAnnotation & rhs

Returns

bool equal

Definition at line 129 of file CAnnotation.cpp.

References CRDFUtilities::fixLocalFileAboutReference(), mMiriamAnnotation, mNotes, and mXMLId.

{
  if (mNotes != rhs.mNotes)
    return false;

  std::string Annotation = mMiriamAnnotation;
  CRDFUtilities::fixLocalFileAboutReference(Annotation, rhs.mXMLId, mXMLId);

  // We need to ignore white spaces when comparing.
  std::string::const_iterator it = Annotation.begin();
  std::string::const_iterator end = Annotation.end();
  std::string::const_iterator itRhs = rhs.mMiriamAnnotation.begin();
  std::string::const_iterator endRhs = rhs.mMiriamAnnotation.end();

  while (it != end && itRhs != endRhs)
    {
      if (*it == * itRhs)
        {
          ++it;
          ++itRhs;

          continue;
        }

      // Advance past white spaces
      while (it != end)
        {
          if (*it == '\x20' || *it == '\x09' || *it == '\x0d' || *it == '\x0a')
            {
              ++it;

              continue;
            }

          break;
        }

      // Advance past white spaces
      while (itRhs != endRhs)
        {
          if (*itRhs == '\x20' || *itRhs == '\x09' || *itRhs == '\x0d' || *itRhs == '\x0a')
            {
              ++itRhs;

              continue;
            }

          break;
        }

      if (it == end && itRhs == endRhs)
        {
          return true;
        }

      if (it == end || itRhs == endRhs)
        {
          return false;
        }

      if (*it != *itRhs)
        {
          return false;
        }

      ++it;
      ++itRhs;
    }

  return true;
}

bool CAnnotation::removeUnsupportedAnnotation

(

const std::string &

name

)

Remove an unsupported annotation

Parameters

const

std::string & name

Returns

bool success

Definition at line 260 of file CAnnotation.cpp.

References mUnsupportedAnnotations.

{
  UnsupportedAnnotation::iterator it = mUnsupportedAnnotations.find(name);

  if (it == mUnsupportedAnnotations.end())
    {
      return false;
    }

  mUnsupportedAnnotations.erase(it);

  return true;
}

bool CAnnotation::replaceUnsupportedAnnotation	(	const std::string &	name,
		const std::string &	xml
	)

Replace an unsupported annotation

Parameters

const	std::string & name
const	std::string & xml

Returns

bool success

Definition at line 239 of file CAnnotation.cpp.

References CCopasiMessage::ERROR, isValidXML(), MCAnnotation, and mUnsupportedAnnotations.

{
  // We need to check whether we have valid XML.
  if (!isValidXML(xml))
    {
      CCopasiMessage(CCopasiMessage::ERROR, MCAnnotation + 5, name.c_str());
      return false;
    }

  // The annotation must exist
  if (mUnsupportedAnnotations.find(name) == mUnsupportedAnnotations.end())
    {
      CCopasiMessage(CCopasiMessage::ERROR, MCAnnotation + 8, name.c_str());
      return false;
    }

  mUnsupportedAnnotations[name] = xml;

  return true;
}

void CAnnotation::setMiriamAnnotation	(	const std::string &	miriamAnnotation,
		const std::string &	newId,
		const std::string &	oldId
	)

Set the RDF/XML representation of the MIRIAM annotation

Parameters

const	std::string & miriamAnnotation
const	std::string & newId
const	std::string & oldId

Definition at line 108 of file CAnnotation.cpp.

References CRDFUtilities::fixLocalFileAboutReference(), mMiriamAnnotation, and mXMLId.

Referenced by CEvent::CEvent(), CFunction::CFunction(), CModelEntity::CModelEntity(), CReaction::CReaction(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateEvent(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CModelExpansion::duplicateReaction(), CCopasiXMLParser::ModelParameterSetElement::end(), CCopasiXMLParser::ReactionElement::end(), CCopasiXMLParser::EventElement::end(), CCopasiXMLParser::ModelElement::end(), CCopasiXMLParser::FunctionElement::end(), SBMLImporter::importMIRIAM(), CMIRIAMInfo::save(), CQMiriamWidget::showEvent(), and test000092::test_miriam_export_7().

{
  mMiriamAnnotation = miriamAnnotation;
  mXMLId = newId;
  CRDFUtilities::fixLocalFileAboutReference(mMiriamAnnotation, newId, oldId);
}

void CAnnotation::setNotes

(

const std::string &

notes

)

Set the XHTML Notes

Parameters

const

std::string & notes

Definition at line 120 of file CAnnotation.cpp.

References mNotes.

Referenced by CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateEvent(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CModelExpansion::duplicateReaction(), CCopasiXMLParser::ReactionElement::end(), CCopasiXMLParser::EventElement::end(), CCopasiXMLParser::ModelElement::end(), CCopasiXMLParser::FunctionElement::end(), SBMLImporter::importNotes(), CModel::load(), and CQNotes::save().

{
  mNotes = notes;
}

Member Data Documentation

std::string CAnnotation::mKey

protected

Key of the model entity. It is stored here, but constructed in the derived classes.

Definition at line 119 of file CAnnotation.h.

Referenced by CCompartment::CCompartment(), CEvent::CEvent(), CFunction::CFunction(), CMetab::CMetab(), CModelEntity::CModelEntity(), CMetab::compile(), CReaction::CReaction(), getKey(), CModel::getKey(), CModel::initObjects(), ~CAnnotation(), CCompartment::~CCompartment(), CEvent::~CEvent(), CFunction::~CFunction(), CMetab::~CMetab(), CModel::~CModel(), and CReaction::~CReaction().

std::string CAnnotation::mMiriamAnnotation

private

MIRIAM compliant annotation in RDF/XML format

Definition at line 130 of file CAnnotation.h.

Referenced by getMiriamAnnotation(), operator==(), and setMiriamAnnotation().

std::string CAnnotation::mNotes

private

Notes in XHTML format

Definition at line 125 of file CAnnotation.h.

Referenced by getNotes(), operator==(), and setNotes().

UnsupportedAnnotation CAnnotation::mUnsupportedAnnotations

private

The annotations which are not supported by COPASI. Note, the name is enforced to be unique.

Definition at line 141 of file CAnnotation.h.

Referenced by addUnsupportedAnnotation(), getUnsupportedAnnotations(), removeUnsupportedAnnotation(), and replaceUnsupportedAnnotation().

std::string CAnnotation::mXMLId

private

The XMLId used in the about statement

Definition at line 135 of file CAnnotation.h.

Referenced by operator==(), and setMiriamAnnotation().

---

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

• CAnnotation.h
• CAnnotation.cpp