/*
* Creates a new XMLNode by reading XMLTokens from stream. The stream must
* be positioned on a start element (stream.peek().isStart() == true) and
* will be read until the matching end element is found.
*/
XMLNode::XMLNode (XMLInputStream& stream) : XMLToken( stream.next() )
{
if ( isEnd() ) return;
std::string s;
while ( stream.isGood() )
{
const XMLToken& next = stream.peek();
if ( next.isStart() )
{
addChild( XMLNode(stream) );
}
else if ( next.isText() )
{
s = trim(next.getCharacters());
if (s != "")
addChild( stream.next() );
else
stream.skipText();
}
else if ( next.isEnd() )
{
stream.next();
break;
}
}
}
bool
ASTCiNumberNode::read(XMLInputStream& stream, const std::string& reqd_prefix)
{
bool read = false;
const XMLToken element = stream.next ();
const string& nameE = element.getName();
ASTBase::checkPrefix(stream, reqd_prefix, element);
if (nameE != "ci")
{
#if 0
cout << "HELP\n";
#endif
return read;
}
ExpectedAttributes expectedAttributes;
addExpectedAttributes(expectedAttributes, stream);
read = readAttributes(element.getAttributes(), expectedAttributes,
stream, element);
const string name = trim( stream.next().getCharacters() );
setName((name));
ASTBase::setType(AST_NAME);
if (read == true)
stream.skipPastEnd(element);
return read;
}
bool
ASTCnBase::read(XMLInputStream& stream, const std::string& )
{
bool read = false;
const XMLToken element = stream.next ();
ExpectedAttributes expectedAttributes;
addExpectedAttributes(expectedAttributes, stream);
read = readAttributes(element.getAttributes(), expectedAttributes,
stream, element);
string prefix;
if (isSetUnits() == true)
{
prefix = element.getAttrPrefix(
element.getAttrIndex("units", stream.getSBMLNamespaces()->getURI()));
setUnitsPrefix(prefix);
}
//return ASTBase::read(stream, reqd_prefix);
return read;
}
/**
* 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() );
}
/*
* Reads other XML such as math/notes etc.
*/
bool
Uncertainty::readOtherXML(XMLInputStream& stream)
{
bool read = false;
const string& name = stream.peek().getName();
if (name == "UncertML")
{
const XMLToken& token = stream.next();
stream.skipText();
delete mUncertML;
XMLNode* xml = new XMLNode(stream);
mUncertML = new UncertMLNode(xml);
stream.skipPastEnd(token);
delete xml;
read = true;
}
if (SBase::readOtherXML(stream))
{
read = true;
}
return read;
}
bool
ASTSemanticsNode::read(XMLInputStream& stream, const std::string& reqd_prefix)
{
bool read = false;
ASTBase * child = NULL;
const XMLToken element = stream.peek ();
ASTBase::checkPrefix(stream, reqd_prefix, element);
const char* name;// = element.getName().c_str();
if (stream.isGood())// && stream.peek().isEndFor(element) == false)
{
stream.skipText();
name = stream.peek().getName().c_str();
if (representsNumber(ASTBase::getTypeFromName(name)) == true)
{
child = new ASTNumber();
}
else
{
child = new ASTFunction();
}
read = child->read(stream, reqd_prefix);
stream.skipText();
if (read == false || addChild(child) != LIBSBML_OPERATION_SUCCESS)
{
delete child;
child = NULL;
read = false;
}
}
unsigned int i = 0;
while ( i < getNumAnnotations())
{
if (stream.peek().getName() == "annotation"
|| stream.peek().getName() == "annotation-xml")
{
XMLNode semanticAnnotation = XMLNode(stream);
addSemanticsAnnotation(semanticAnnotation.clone());
i++;
}
else
{
stream.next();
}
}
return true;
}
bool
ASTBase::read(XMLInputStream& stream, const std::string& )
{
ExpectedAttributes expectedAttributes;
addExpectedAttributes(expectedAttributes, stream);
const XMLToken element = stream.next ();
return readAttributes(element.getAttributes(), expectedAttributes,
stream, element);
}
bool
ASTCnExponentialNode::read(XMLInputStream& stream, const std::string& reqd_prefix)
{
bool read = false;
const XMLToken element = stream.peek ();
const string& name = element.getName();
ASTBase::checkPrefix(stream, reqd_prefix, element);
if (name != "cn")
{
#if 0
cout << "HELP\n";
#endif
return read;
}
ASTCnBase::read(stream, reqd_prefix);
std::string type;
element.getAttributes().readInto("type", type);
if (type == "e-notation")
{
double mantissa = 0;
long exponent = 0;
istringstream ismantissa;
istringstream isexponent;
ismantissa.str( stream.next().getCharacters() );
ismantissa >> mantissa;
if (stream.peek().getName() == "sep")
{
stream.next();
isexponent.str( stream.next().getCharacters() );
isexponent >> exponent;
}
bool
ASTCnRealNode::read(XMLInputStream& stream, const std::string& reqd_prefix)
{
bool read = false;
const XMLToken element = stream.peek ();
const string& name = element.getName();
ASTBase::checkPrefix(stream, reqd_prefix, element);
if (name != "cn")
{
#if 0
cout << "HELP\n";
#endif
return read;
}
ASTCnBase::read(stream, reqd_prefix);
std::string type = "real";
element.getAttributes().readInto("type", type);
if (type == "real")
{
double value = 0;
istringstream isreal;
isreal.str( stream.next().getCharacters() );
isreal >> value;
setReal(value);
ASTBase::setType(AST_REAL);
if (isreal.fail()
|| (util_isInf(getValue()) > 0)
|| (util_isInf(getValue()) < 0)
)
{
logError(stream, element, FailedMathMLReadOfDouble);
}
read = true;
}
bool
ASTCnIntegerNode::read(XMLInputStream& stream, const std::string& reqd_prefix)
{
bool read = false;
const XMLToken element = stream.peek ();
const string& name = element.getName();
ASTBase::checkPrefix(stream, reqd_prefix, element);
if (name != "cn")
{
cout << "HELP\n";
return read;
}
ASTCnBase::read(stream, reqd_prefix);
std::string type;
element.getAttributes().readInto("type", type);
if (type == "integer")
{
int value = 0;
istringstream isint;
isint.str( stream.next().getCharacters() );
isint >> value;
if (isint.fail())
{
logError(stream, element, FailedMathMLReadOfInteger);
}
else if ( sizeof(int) > 4 && ( (value > SBML_INT_MAX) || (value < SBML_INT_MIN) ) )
{
logError(stream, element, FailedMathMLReadOfInteger);
}
setInteger(value);
ASTBase::setType(AST_INTEGER);
read = true;
}
bool
ASTCSymbolDelayNode::read(XMLInputStream& stream, const std::string& reqd_prefix)
{
bool read = false;
XMLToken element = stream.peek ();
const string& nameE = element.getName();
if (nameE != "csymbol")
{
#if 0
cout << "HELP\n";
#endif
return read;
}
ASTBase::read(stream, reqd_prefix);
const string nameDelay = trim( stream.next().getCharacters() );
setName((nameDelay));
ASTBase::setType(AST_FUNCTION_DELAY);
stream.skipPastEnd(element);
const char * name;
ASTBase * child = NULL;
unsigned int numChildrenAdded = 0;
// catch if we do not have two children
if (getExpectedNumChildren() > 0)
{
while (stream.isGood() && numChildrenAdded < getExpectedNumChildren())
{
stream.skipText();
name = stream.peek().getName().c_str();
if (representsNumber(ASTBase::getTypeFromName(name)) == true)
{
child = new ASTNumber();
}
else
{
child = new ASTFunction();
}
read = child->read(stream, reqd_prefix);
stream.skipText();
if (read == true && addChild(child) == LIBSBML_OPERATION_SUCCESS)
{
numChildrenAdded++;
}
else
{
read = false;
break;
}
}
}
else
{
stream.skipPastEnd(element);
read = true;
}
return read;
}