Detailed Description

An interface to an XML input stream.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

SBML content is serialized using XML; the resulting data can be stored and read to/from a file or data stream. Low-level XML parsers such as Xerces provide facilities to read XML data. To permit the use of different XML parsers (Xerces, Expat or libxml2), libSBML implements an abstraction layer. XMLInputStream and XMLOutputStream are two parts of that abstraction layer.

XMLInputStream is an interface to a file or text string containing XML. It wraps the content to be read, as well as the low-level XML parser to be used and an XMLErrorLog to record errors and other issues (if any arise). Internally, the content will be in the form of either a pointer to a file name or a character string; XMLInputStream knows the form of the content and acts appropriately. Other libSBML object classes use XMLInputStream as their interface for all read operations on the XML data. XMLInputStream provides the functionality to extract data in the form of XMLToken objects. It logs any errors encountered while reading. It also keeps track of whether a read operation has failed irrecoverably or determines whether it is safe to continue reading.

SBMLNamespaces objects can be associated with an XMLInputStream; this facilitates logging errors related to reading XML attributes and elements that may only be relevant to particular Level and Version combinations of SBML.

Note: The convenience of the XMLInputStream and XMLOutputStream abstraction may be useful for developers interested in creating parsers for other XML formats besides SBML. It can provide developers with a layer above more basic XML parsers, as well as some useful programmatic elements such as XMLToken, XMLError, etc.

See also: XMLOutputStream

Public Member Functions
bool	containsChild (const std::string &childName, const std::string &container)
	Predicate returning `true` if a child token of the specified type occurs within a given container element. More...

unsigned int	determineNumberChildren (const std::string elementName="")
	Returns the number of child tokens of the given element in this stream. More...

unsigned int	determineNumSpecificChildren (const std::string &childName, const std::string &container)
	Returns the number of child tokens of the specified type within a given container element. More...

const std::string &	getEncoding ()
	Returns the encoding of the XML stream. More...

XMLErrorLog *	getErrorLog ()
	Returns the XMLErrorLog used to log parsing problems. More...

SBMLNamespaces *	getSBMLNamespaces ()
	Returns the SBMLNamespaces object attached to this XMLInputStream. More...

const std::string &	getVersion ()
	Returns the version of the XML stream. More...

bool	isEOF () const
	Returns `true` if end of file (stream) has been reached. More...

bool	isError () const
	Returns `true` if a fatal error occurred while reading from this stream. More...

bool	isGood () const
	Returns `true` if the stream is in a good state. More...

XMLToken	next ()
	Returns the next token on this XML input stream. More...

const XMLToken &	peek ()
	Returns the next token without consuming it. More...

int	setErrorLog (XMLErrorLog *log)
	Sets the XMLErrorLog this stream will use to log errors. More...

void	setSBMLNamespaces (SBMLNamespaces *sbmlns)
	Sets the SBML namespaces associated with this XML input stream. More...

void	skipPastEnd (const XMLToken &element)
	Consume zero or more tokens up to and including the corresponding end element or EOF. More...

void	skipText ()
	Consume zero or more tokens up to but not including the next XML element or EOF. More...

std::string	toString ()
	Prints a string representation of the underlying token stream. More...

	XMLInputStream (const char content, bool isFile=true, const std::string library="", XMLErrorLog errorLog=NULL)
	Creates a new XMLInputStream. More...

virtual	~XMLInputStream ()
	Destroys this XMLInputStream. More...

Constructor & Destructor Documentation

XMLInputStream::XMLInputStream	(	const char *	content,
		bool	isFile = `true`,
		const std::string	library = `""`,
		XMLErrorLog *	errorLog = `NULL`
	)

Creates a new XMLInputStream.

Parameters

content	the source of the stream.
isFile	a boolean flag to indicate whether `content` is a file name. If `true`, `content` is assumed to be the file from which the XML content is to be read. If `false`, `content` is taken to be a string that is the content to be read.
library	the name of the parser library to use.
errorLog	the XMLErrorLog object to use.

virtual XMLInputStream::~XMLInputStream ( )

virtual

Destroys this XMLInputStream.

Member Function Documentation

bool XMLInputStream::containsChild	(	const std::string &	childName,
		const std::string &	container
	)

Predicate returning true if a child token of the specified type occurs within a given container element.

This method allows information from the input stream to be determined without the need to actually read and consume the tokens in the stream. It returns true if the childName element occurs at any point within the element specified by container.

Parameters

childName	a string representing the name of the child element whose presence is to be determined.
container	a string representing the name of the element for which the presence of the child element is to be determined.

Returns: boolean true if a child of type childName occurs within the container element, false otherwise.

Note: This method assumes the stream has been read up to and including the element container.

unsigned int XMLInputStream::determineNumberChildren ( const std::string elementName = "" )

Returns the number of child tokens of the given element in this stream.

This method allows information from the input stream to be determined without the need to actually read and consume the tokens in the stream. It returns the number of child elements of the element represented by the elementName, i.e., the number of child elements encountered before the closing tag for the elementName supplied.

If no elementName is supplied or it is an empty string, then as a special case, this method assumes the element is a MathML apply element followed by a function name.

Parameters

elementName a string representing the name of the element for which the number of children are to be determined.

Returns: an unsigned int giving the number of children of the elementName specified.

Note: This method assumes the stream has been read up to and including the element elementName.

unsigned int XMLInputStream::determineNumSpecificChildren	(	const std::string &	childName,
		const std::string &	container
	)

Returns the number of child tokens of the specified type within a given container element.

This method allows information from the input stream to be determined without the need to actually read and consume the tokens in the stream. It returns the number of child elements of the childName element within the element specified by container. In other words, it counts the number of childName elements encountered before the closing tag for the container supplied.

Parameters

childName	a string representing the name of the child element whose number is to be determined.
container	a string representing the name of the element for which the number of children are to be determined.

Returns: an unsigned int giving the number of children of type childName within the container element.

Note: This method assumes the stream has been read up to and including the element container.

const std::string& XMLInputStream::getEncoding ( )

Returns the encoding of the XML stream.

The encoding is indicated by the xml declaration at the

beginning of an XML document or data stream. The form of this declaration is

<?xml version="1.0" encoding="UTF-8"?>

Note that the SBML specifications require the use of UTF-8 encoding, so for SBML documents, the value returned by this method will always be the string "UTF-8".

Returns: the encoding of the XML stream.

See also: getVersion()

XMLErrorLog* XMLInputStream::getErrorLog ( )

Returns the XMLErrorLog used to log parsing problems.

Returns: the XMLErrorLog used to log XML parse errors and other validation errors (and messages).

SBMLNamespaces* XMLInputStream::getSBMLNamespaces ( )

Returns the SBMLNamespaces object attached to this XMLInputStream.

Returns: the SBMLNamespaces object or NULL if none has been set.

const std::string& XMLInputStream::getVersion ( )

Returns the version of the XML stream.

The version is indicated by the xml declaration at the

beginning of an XML document or data stream. The form of this declaration is

 <?xml version="1.0" encoding="UTF-8"?>

Note that the SBML specifications require the use of version 1.0, so for SBML documents, the value returned by this method will always be the string "1.0".

Returns: the version of the XML stream.

See also: getEncoding()

bool XMLInputStream::isEOF ( ) const

Returns true if end of file (stream) has been reached.

Returns: true if end of file (stream) has been reached, false otherwise.

bool XMLInputStream::isError ( ) const

Returns true if a fatal error occurred while reading from this stream.

Returns: true if a fatal error occurred while reading from this stream.

bool XMLInputStream::isGood ( ) const

Returns true if the stream is in a good state.

The definition of "good state" is that isEOF() and isError() both return false.

Returns: true if the stream is in a good state, false otherwise.

XMLToken XMLInputStream::next ( )

Returns the next token on this XML input stream.

The token is consumed in the process.

Returns: the next XMLToken, or an EOF token (i.e., XMLToken.isEOF() == true).

See also: peek()

const XMLToken& XMLInputStream::peek ( )

Returns the next token without consuming it.

A subsequent call to either peek() or next() will return the same token.

Returns: the next XMLToken or EOF (XMLToken.isEOF() == true).

See also: next()

int XMLInputStream::setErrorLog ( XMLErrorLog * log )

Sets the XMLErrorLog this stream will use to log errors.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

void XMLInputStream::setSBMLNamespaces ( SBMLNamespaces * sbmlns )

Sets the SBML namespaces associated with this XML input stream.

This allows this stream to reference the available SBML namespaces being read.

Parameters

sbmlns the list of namespaces to use.

void XMLInputStream::skipPastEnd ( const XMLToken & element )

Consume zero or more tokens up to and including the corresponding end element or EOF.

Parameters

element the element whose end will be sought in the input stream.

void XMLInputStream::skipText ( )

Consume zero or more tokens up to but not including the next XML element or EOF.

std::string XMLInputStream::toString ( )

Prints a string representation of the underlying token stream.

Returns: a string representing the underlying XML token stream.

Note: This method is intended for debugging purposes.

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation