/*
* 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
ArraysASTPlugin::readMatrixRow(XMLInputStream& stream, const std::string& reqd_prefix,
const XMLToken& currentElement)
{
bool read = false;
stream.skipText();
const XMLToken nextElement = stream.peek();
const string& nextName = nextElement.getName();
unsigned int numChildren = determineNumChildren(stream, "matrixrow");
mVector = new ASTArraysVectorFunctionNode(AST_LINEAR_ALGEBRA_MATRIXROW_CONSTRUCTOR);
mVector->setExpectedNumChildren(numChildren);
// read attributes on this element here since we have already consumed
// the element
ExpectedAttributes expectedAttributes;
mVector->addExpectedAttributes(expectedAttributes, stream);
read = mVector->ASTBase::readAttributes(currentElement.getAttributes(),
expectedAttributes, stream, currentElement);
if (read == false)
{
mVector = NULL;
}
else
{
read = mVector->read(stream, reqd_prefix);
}
return read;
}
/**
* 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() );
}
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;
}
bool
AnalyticVolume::readOtherXML (XMLInputStream& stream)
{
bool read = false;
const string& name = stream.peek().getName();
if (name == "math")
{
const XMLToken elem = stream.peek();
const std::string prefix = checkMathMLNamespace(elem);
if (stream.getSBMLNamespaces() == NULL)
{
stream.setSBMLNamespaces(new SBMLNamespaces(getLevel(), getVersion()));
}
delete mMath;
mMath = readMathML(stream, prefix);
read = true;
}
if (SBase::readOtherXML(stream))
{
read = true;
}
return read;
}
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());
}
}
/*
* Subclasses should override this method to read (and store) XHTML,
* MathML, etc. directly from the XMLInputStream.
*
* @return true if the subclass read from the stream, false otherwise.
*/
bool
InitialAssignment::readOtherXML (XMLInputStream& stream)
{
bool read = false;
const string& name = stream.peek().getName();
if (name == "math")
{
// if this is level 1 there shouldnt be any math!!!
if (getLevel() == 1)
{
logError(NotSchemaConformant, getLevel(), getVersion(),
"SBML Level 1 does not support MathML.");
delete mMath;
return false;
}
if (mMath != NULL)
{
if (getLevel() < 3)
{
logError(NotSchemaConformant, getLevel(), getVersion(),
"Only one <math> element is permitted inside a "
"particular containing element.");
}
else
{
logError(OneMathElementPerInitialAssign, getLevel(), getVersion(),
"The <initialAssignment> with symbol '" + getSymbol() +
"' contains more than one <math> element.");
}
}
/* check for MathML namespace
* this may be explicitly declared here
* or implicitly declared on the whole document
*/
const XMLToken elem = stream.peek();
const std::string prefix = checkMathMLNamespace(elem);
delete mMath;
mMath = readMathML(stream, prefix);
if (mMath != NULL) mMath->setParentSBMLObject(this);
read = true;
}
/* ------------------------------
*
* (EXTENSION)
*
* ------------------------------ */
if ( SBase::readOtherXML(stream) )
read = true;
return read;
}
void
ASTCnBase::addExpectedAttributes(ExpectedAttributes& attributes,
XMLInputStream& stream)
{
ASTBase::addExpectedAttributes(attributes, stream);
if (stream.getSBMLNamespaces() != NULL
&& stream.getSBMLNamespaces()->getLevel() > 2)
{
attributes.add("units");
}
attributes.add("type");
}
bool
ASTArraysVectorFunctionNode::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;
unsigned int numChildrenAdded = 0;
while (stream.isGood() && numChildrenAdded < getExpectedNumChildren())// && 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 == true && addChild(child) == LIBSBML_OPERATION_SUCCESS)
{
numChildrenAdded++;
}
else
{
read = false;
break;
}
}
if (getExpectedNumChildren() == 0 && numChildrenAdded == 0)
{
read = true;
}
return read;
}
/*
* Subclasses should override this method to read (and store) XHTML,
* MathML, PolygonObject. directly from the XMLInputStream.
*
* @return true if the subclass read from the stream, false otherwise.
*/
bool
ParametricObject::readOtherXML (XMLInputStream& stream)
{
bool read = false;
const string& name = stream.peek().getName();
if (name == "PolygonObject")
{
delete mPolygonObject;
mPolygonObject = PolygonObject::readPolygonObject(stream);
if (mPolygonObject) mPolygonObject->setParentSBMLObject(this);
read = true;
}
/* ------------------------------
*
* (EXTENSION)
*
*------------------------------- */
if ( SBase::readOtherXML(stream) )
read = true;
return read;
}
bool
ArraysASTPlugin::read(XMLInputStream& stream, const std::string& reqd_prefix,
const XMLToken& currentElement)
{
bool read = false;
stream.skipText();
const string& currentName = currentElement.getName();
//ASTBase::checkPrefix(stream, reqd_prefix, currentElement);
// create appropriate sub class
if (currentName == "vector")
{
read = readVector(stream, reqd_prefix, currentElement);
}
#if (0)
else if (currentName == "matrix")
{
read = readMatrix(stream, reqd_prefix, currentElement);
}
else if (currentName == "matrixrow")
{
read = readMatrixRow(stream, reqd_prefix, currentElement);
}
#endif
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
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
ASTBase::read(XMLInputStream& stream, const std::string& )
{
ExpectedAttributes expectedAttributes;
addExpectedAttributes(expectedAttributes, stream);
const XMLToken element = stream.next ();
return readAttributes(element.getAttributes(), expectedAttributes,
stream, element);
}
LIBSBML_CPP_NAMESPACE_BEGIN
static unsigned int
determineNumChildren(XMLInputStream & stream, const std::string element = "")
{
unsigned int n = 0;
n = stream.determineNumberChildren(element);
return n;
}
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;
}
/*
* Subclasses should override this method to read (and store) XHTML,
* MathML, etc. directly from the XMLInputStream.
*
* @return true if the subclass read from the stream, false otherwise.
*/
bool
StoichiometryMath::readOtherXML (XMLInputStream& stream)
{
bool read = false;
const string& name = stream.peek().getName();
if (name == "math")
{
// if this is level 1 there shouldnt be any math!!!
if (getLevel() == 1)
{
logError(NotSchemaConformant, getLevel(), getVersion(),
"SBML Level 1 does not support MathML.");
delete mMath;
return false;
}
/* check for MathML namespace
* this may be explicitly declared here
* or implicitly declared on the whole document
*/
const XMLToken elem = stream.peek();
const std::string prefix = checkMathMLNamespace(elem);
delete mMath;
mMath = readMathML(stream, prefix);
if (mMath) mMath->setParentSBMLObject(this);
read = true;
}
/* ------------------------------
*
* (EXTENSION)
*
* ------------------------------ */
if ( SBase::readOtherXML(stream) )
read = true;
return read;
}
/*
* 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
SedSetValue::readOtherXML (XMLInputStream& stream)
{
bool read = false;
const string& name = stream.peek().getName();
if (name == "math")
{
const XMLToken elem = stream.peek();
const std::string prefix = checkMathMLNamespace(elem);
delete mMath;
mMath = readMathML(stream, prefix);
read = true;
}
if (SedBase::readOtherXML(stream))
{
read = true;
}
return read;
}
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
Uncertainty::readOtherXML(XMLInputStream& stream)
{
const string& name = stream.peek().getName();
if (name == "UncertML")
{
delete mUncertML;
XMLNode * xml = new XMLNode(stream);
mUncertML = new UncertMLNode(xml);
delete xml;
return true;
}
return false;
}
void
ASTCiNumberNode::addExpectedAttributes(ExpectedAttributes& attributes,
XMLInputStream& stream)
{
ASTBase::addExpectedAttributes(attributes, stream);
SBMLNamespaces * sbmlns = stream.getSBMLNamespaces();
if (sbmlns != NULL)
{
if (sbmlns->getLevel() > 2)
{
attributes.add("definitionURL");
}
else if (sbmlns->getLevel() == 2 && sbmlns->getVersion() == 5)
{
attributes.add("definitionURL");
}
}
}
bool
ASTBase::readAttributes(const XMLAttributes& attributes,
const ExpectedAttributes& expectedAttributes,
XMLInputStream& stream, const XMLToken& element)
{
bool read = true;
//
// check that all attributes are expected
//
for (int i = 0; i < attributes.getLength(); i++)
{
std::string name = attributes.getName(i);
std::string uri = attributes.getURI(i);
std::string prefix = attributes.getPrefix(i);
//
// To allow prefixed attribute whose namespace doesn't belong to
// core or extension package.
//
// (e.g. xsi:type attribute in Curve element in layout extension)
//
if (!prefix.empty())
{
if ( expectedAttributes.hasAttribute(prefix + ":" + name) ) continue;
}
if (!expectedAttributes.hasAttribute(name))
{
std::string message = "The attribute '" + name + "' is not permitted" +
" on a <" + element.getName() + "> element.";
if (name == "type")
{
logError(stream, element, DisallowedMathTypeAttributeUse, message);
}
else if (name == "encoding")
{
logError(stream, element, DisallowedMathMLEncodingUse, message);
}
else if (name == "definitionURL")
{
logError(stream, element, DisallowedDefinitionURLUse, message);
}
else if (name == "units")
{
if (stream.getSBMLNamespaces() != NULL
&& stream.getSBMLNamespaces()->getLevel() > 2)
{
logError(stream, element, DisallowedMathUnitsUse, message);
}
else
{
message = "The 'units' attribute was introduced in SBML Level 3.";
logError(stream, element, InvalidMathMLAttribute, message);
}
}
else
{
logError(stream, element, InvalidMathElement, message);
}
// not sufficient to make the read bad
//return false;
}
}
string id;
string className;
string style;
attributes.readInto( "id" , id );
attributes.readInto( "class" , className );
attributes.readInto( "style" , style );
if (!id.empty())
{
if (setId(id) != LIBSBML_OPERATION_SUCCESS)
{
read = false;
}
}
if (!className.empty())
{
if (setClass(className) != LIBSBML_OPERATION_SUCCESS)
{
read = false;
}
}
if (!style.empty())
{
if (setStyle(style) != LIBSBML_OPERATION_SUCCESS)
{
read = false;
}
}
unsigned int i = 0;
while (read == true && i < getNumPlugins())
{
read = getPlugin(i)->readAttributes(attributes, expectedAttributes,
stream, element, getExtendedType());
i++;
}
return read;
}
/** @cond doxygenLibsbmlInternal */
bool
FbcModelPlugin::readOtherXML (SBase* parentObject, XMLInputStream& stream)
{
#ifndef ANNOATION
return false;
#else
bool readAnnotationFromStream = false;
const string& name = stream.peek().getName();
if (!(name.empty()) && name != "annotation")
{
return readAnnotationFromStream;
}
try
{
XMLNode *pAnnotation = parentObject->getAnnotation();
FBC_CREATE_NS_WITH_VERSION(fbcns, getSBMLNamespaces(), getPackageVersion());
if (!pAnnotation)
{
//
// (NOTES)
//
// annotation element has not been parsed by the parent element
// (Model) of this plugin object, thus annotation element is
// parsed via the given XMLInputStream object in this block.
//
const string& name = stream.peek().getName();
if (name == "annotation")
{
pAnnotation = new XMLNode(stream);
parseFbcAnnotation(pAnnotation, mAssociations, fbcns);
if (mAssociations.size() > 0)
{
//
// Removes the annotation for layout extension from the annotation
// of parent element (pAnnotation) and then set the new annotation
// (newAnnotation) to the parent element.
//
XMLNode *newAnnotation = deleteFbcAnnotation(pAnnotation);
parentObject->setAnnotation(newAnnotation);
delete newAnnotation;
}
else
{
//
// No layout annotation is included in the read annotation
// (pAnnotation) and thus just set the annotation to the parent
// element.
//
parentObject->setAnnotation(pAnnotation);
}
delete pAnnotation;
readAnnotationFromStream = true;
}
}
else if (mAssociations.size() == 0)
{
//
// (NOTES)
//
// annotation element has been parsed by the parent element
// (Model) of this plugin object, thus the annotation element
// set to the above pAnnotation variable is parsed in this block.
//
parseFbcAnnotation(pAnnotation, mAssociations, fbcns);
if (mAssociations.size() > 0)
{
//
// Removes the annotation for layout extension from the annotation
// of parent element (pAnnotation) and then set the new annotation
// (newAnnotation) to the parent element.
//
XMLNode *newAnnotation = deleteFbcAnnotation(pAnnotation);
parentObject->setAnnotation(newAnnotation);
}
readAnnotationFromStream = true;
}
delete fbcns;
}
catch(...)
{
// an exception occured, most likely becase a namespace constructor
// threw an exception, catching this here, and return false, to indicate
// that the annotation wasn't read.
readAnnotationFromStream = false;
}
return readAnnotationFromStream;
#endif
}
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;
}
bool
ASTNaryFunctionNode::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();
int type = getTypeFromName(name);
setType(type);
ASTBase::read(stream, reqd_prefix);
unsigned int numChildrenAdded = 0;
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
{
delete child;
child = NULL;
read = false;
break;
}
}
}
else
{
stream.skipPastEnd(element);
read = true;
}
if (read == true && type == AST_FUNCTION_ROOT
&& getExpectedNumChildren() == 1
&& ASTFunctionBase::getChild(0)->getType() != AST_QUALIFIER_DEGREE)
{
/* HACK TO REPLICATE OLD BEHAVIOUR */
/* we need to add the qualifier child for the degree 2 */
ASTFunction * degree = new ASTFunction(AST_QUALIFIER_DEGREE);
ASTNumber * int2 = new ASTNumber(AST_INTEGER);
int2->setInteger(2);
degree->addChild(int2->deepCopy());
this->prependChild(degree->deepCopy());
delete int2;
delete degree;
}
//if (read == false)
//{
// stream.skipPastEnd(element);
//}
return read;
}
/*
* Subclasses should override this method to read (and store) XHTML,
* MathML, etc. directly from the XMLInputStream.
*
* @return true if the subclass read from the stream, false otherwise.
*/
bool
Rule::readOtherXML (XMLInputStream& stream)
{
bool read = false;
const string& name = stream.peek().getName();
if (name == "math")
{
// if this is level 1 there shouldnt be any math!!!
if (getLevel() == 1)
{
logError(NotSchemaConformant, getLevel(), getVersion(),
"SBML Level 1 does not support MathML.");
delete mMath;
return false;
}
if (mMath != NULL)
{
if (getLevel() < 3)
{
logError(NotSchemaConformant, getLevel(), getVersion(),
"Only one <math> element is permitted inside a "
"particular containing element.");
}
else
{
std::string details;
if (isAssignment() == true)
{
details = "The <assignmentRule> with variable '" + getVariable() +"'";
}
else if (isRate() == true)
{
details = "The <rateRule> with variable '" + getVariable() +"'";
}
else
{
details = "The <algebraicRule>";
}
details += " contains more than one <math> element.";
logError(OneMathElementPerRule, getLevel(), getVersion(), details);
}
}
delete mMath;
/* check for MathML namespace
* this may be explicitly declared here
* or implicitly declared on the whole document
*/
const XMLToken elem = stream.peek();
const std::string prefix = checkMathMLNamespace(elem);
mMath = readMathML(stream, prefix);
if (mMath != NULL) mMath->setParentSBMLObject(this);
read = true;
}
/* ------------------------------
*
* (EXTENSION)
*
* ------------------------------ */
if ( SBase::readOtherXML(stream) )
read = true;
return read;
}
/*
* Subclasses should override this method to read (and store) XHTML,
* MathML, etc. directly from the XMLInputStream.
*
* @return true if the subclass read from the stream, false otherwise.
*/
bool
Constraint::readOtherXML (XMLInputStream& stream)
{
bool read = false;
const string& name = stream.peek().getName();
if (name == "math")
{
// if this is level 1 there shouldnt be any math!!!
if (getLevel() == 1)
{
logError(NotSchemaConformant, getLevel(), getVersion(),
"SBML Level 1 does not support MathML.");
delete mMath;
return false;
}
if (mMath)
{
if (getLevel() < 3)
{
logError(NotSchemaConformant, getLevel(), getVersion(),
"Only one <math> element is permitted inside a "
"particular containing element.");
}
else
{
logError(OneMathElementPerConstraint, getLevel(), getVersion(),
"The <constraint> contains more than one <math> element.");
}
}
// If there's a <message>, it's supposed to show up first
if (mMessage && getLevel() == 2) logError(IncorrectOrderInConstraint);
/* check for MathML namespace
* this may be explicitly declared here
* or implicitly declared on the whole document
*/
const XMLToken elem = stream.peek();
const std::string prefix = checkMathMLNamespace(elem);
delete mMath;
mMath = readMathML(stream, prefix);
if (mMath) mMath->setParentSBMLObject(this);
read = true;
}
else if (name == "message")
{
if (mMessage)
{
if (getLevel() < 3)
{
logError(NotSchemaConformant, getLevel(), getVersion(),
"Only one <message> element is permitted inside a "
"particular containing element.");
}
else
{
logError(OneMessageElementPerConstraint, getLevel(), getVersion());
}
}
delete mMessage;
mMessage = new XMLNode(stream);
//
// checks if the given default namespace (if any) is a valid
// SBML namespace
//
const XMLNamespaces &xmlns = mMessage->getNamespaces();
checkDefaultNamespace(&xmlns,"message");
if (getSBMLDocument() != NULL)
{
if (getSBMLDocument()->getNumErrors() == 0)
{
checkXHTML(mMessage);
}
}
read = true;
}
/* ------------------------------
*
* (EXTENSION)
*
* ------------------------------ */
if ( SBase::readOtherXML(stream) )
read = true;
return read;
}