bool
ASTUnaryFunctionNode::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();
setType(getTypeFromName(name));
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;
}
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
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;
}
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;
}
/*
* 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;
}
}
}
/*
* 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
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;
}
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
ASTLambdaFunctionNode::read(XMLInputStream& stream, const std::string& reqd_prefix)
{
bool read = false;
ASTBase * child = NULL;
const char* name;
unsigned int numBvars = getNumBvars();
unsigned int numChildrenAdded = 0;
// read in bvars
// these are functions as they will be created as ASTQualifierNodes
while(numChildrenAdded < numBvars)
{
child = new ASTFunction();
read = child->read(stream, reqd_prefix);
if (read == true && addChild(child, true) == LIBSBML_OPERATION_SUCCESS)
{
numChildrenAdded++;
}
else
{
delete child;
child = NULL;
read = false;
break;
}
}
// if we had no bvars to read mark read as true so we will continue
if (numBvars == 0)
{
read = true;
}
while (read == true && 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 (addChild(child) == LIBSBML_OPERATION_SUCCESS)
{
numChildrenAdded++;
read = true;
}
else
{
delete child;
child = NULL;
read = false;
break;
}
}
return read;
}