void
ASTBase::logError (XMLInputStream& stream, const XMLToken& element, SBMLErrorCode_t code,
const std::string& msg)
{
SBMLNamespaces* ns = stream.getSBMLNamespaces();
if (ns != NULL)
{
static_cast <SBMLErrorLog*>
(stream.getErrorLog())->logError(
code,
ns->getLevel(),
ns->getVersion(),
msg,
element.getLine(),
element.getColumn());
}
else
{
static_cast <SBMLErrorLog*>
(stream.getErrorLog())->logError(
code,
SBML_DEFAULT_LEVEL,
SBML_DEFAULT_VERSION,
msg,
element.getLine(),
element.getColumn());
}
}
/**
* Sets the type of an ASTNode based on the given MathML <cn> element.
* Errors will be logged in the stream's SBMLErrorLog object.
*/
static void
setTypeCN (ASTNode& node, const XMLToken& element, XMLInputStream& stream)
{
string type = "real";
element.getAttributes().readInto("type", type);
// here is the only place we might encounter the sbml:units attribute
string units = "";
element.getAttributes().readInto("units", units);
if (type == "real")
{
double value = 0;
istringstream isreal;
isreal.str( stream.next().getCharacters() );
isreal >> value;
node.setValue(value);
if (isreal.fail()
|| node.isInfinity()
|| node.isNegInfinity()
)
{
static_cast <SBMLErrorLog*>
(stream.getErrorLog())->logError(FailedMathMLReadOfDouble,
stream.getSBMLNamespaces()->getLevel(),
stream.getSBMLNamespaces()->getVersion());
}
}
/**
* Sets the type of an ASTNode based on the given MathML <ci> element.
* Errors will be logged in the stream's SBMLErrorLog object.
*/
static void
setTypeCI (ASTNode& node, const XMLToken& element, XMLInputStream& stream)
{
if (element.getName() == "csymbol")
{
string url;
element.getAttributes().readInto("definitionURL", url);
if ( url == URL_DELAY ) node.setType(AST_FUNCTION_DELAY);
else if ( url == URL_TIME ) node.setType(AST_NAME_TIME);
else if ( url == URL_AVOGADRO ) node.setType(AST_NAME_AVOGADRO);
else
{
static_cast <SBMLErrorLog*>
(stream.getErrorLog())->logError(BadCsymbolDefinitionURLValue,
stream.getSBMLNamespaces()->getLevel(),
stream.getSBMLNamespaces()->getVersion());
}
}
else if (element.getName() == "ci")
{
node.setDefinitionURL(element.getAttributes());
}
const string name = trim( stream.next().getCharacters() );
node.setName( name.c_str() );
}