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
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;
}
/**
* 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
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;
}
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());
}
}
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;
}
/*
* @return @c true if this XMLToken is an XML end element for the given XML
* start element, false otherwise.
*/
bool
XMLToken::isEndFor (const XMLToken& element) const
{
return
isEnd() &&
!isStart() &&
element.isStart() &&
element.getName() == getName() &&
element.getURI () == getURI ();
}
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
XMLTokenizer::containsChild(bool & valid,
const std::string& qualifier,
const std::string& container)
{
valid = false;
//unsigned int numQualifiers = 0;
size_t size = mTokens.size();
if (size < 2)
{
return false;
}
unsigned int index = 0;
//unsigned int depth = 0;
std::string name;
XMLToken next = mTokens.at(index);
name = next.getName();
while (index < size-2)
{
// skip any text elements
while(next.isText() == true && index < size-1)
{
index++;
next = mTokens.at(index);
}
if (next.getName() == qualifier)
{
valid = true;
return true;
}
index++;
if (index < size)
{
next = mTokens.at(index);
}
}
// we might have hit the end of the loop and the end of the correct tag
if (valid == false && index >= size-2)
{
valid = true;
}
return false;
}
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;
}
void
ASTBase::checkPrefix(XMLInputStream &stream, const std::string& reqd_prefix,
const XMLToken& element)
{
if (!reqd_prefix.empty())
{
std::string prefix = element.getPrefix();
if (prefix != reqd_prefix)
{
const string message = "Element <" + element.getName()
+ "> should have prefix \"" + reqd_prefix + "\".";
logError(stream, element, InvalidMathElement, message);
}
}
}
/*
* Consume zero or more XMLTokens up to and including the corresponding
* end XML element or EOF.
*/
void
XMLInputStream::skipPastEnd (const XMLToken& element)
{
if ( element.isEnd() ) return;
while ( isGood() && !peek().isEndFor(element) ) next();
next();
}
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;
}
LIBSBML_CPP_NAMESPACE_BEGIN
#ifdef __cplusplus
/**
* logs the given erroron the error log of the stream.
*
* @param stream the stream to log the error on
* @param element the element to log the error for
* @param code the error code to log
* @param msg optional message
*/
static void
logError (XMLInputStream* stream, const XMLToken& element, SBMLErrorCode_t code,
const std::string& msg = "")
{
if (&element == NULL || stream == NULL) return;
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());
}
}
/*
* Copy constructor; creates a copy of this XMLToken.
*/
XMLToken::XMLToken(const XMLToken& orig)
: mTriple()
, mAttributes()
, mNamespaces()
, mChars (orig.mChars)
, mIsStart (orig.mIsStart)
, mIsEnd (orig.mIsEnd)
, mIsText (orig.mIsText)
, mLine (orig.mLine)
, mColumn (orig.mColumn)
{
if (!orig.mTriple.isEmpty())
mTriple = XMLTriple(orig.getName(), orig.getURI(), orig.getPrefix());
if (!orig.mAttributes.isEmpty())
mAttributes = XMLAttributes(orig.getAttributes());
if (!orig.mNamespaces.isEmpty())
mNamespaces = XMLNamespaces(orig.getNamespaces());
}
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
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;
}
XMLTokenHandler::Result PrefsLoader::HandleToken(XMLToken &token)
{
switch (token.GetType())
{
case XMLToken::TYPE_STag:
case XMLToken::TYPE_ETag:
case XMLToken::TYPE_EmptyElemTag:
if (token.GetType() != XMLToken::TYPE_ETag)
{
HandleStartElement(token.GetName().GetLocalPart(), token.GetName().GetLocalPartLength(), token.GetAttributes(), token.GetAttributesCount());
}
if (token.GetType() != XMLToken::TYPE_STag)
HandleEndElement(token.GetName().GetLocalPart(), token.GetName().GetLocalPartLength());
}
return RESULT_OK;
}
/*
* Receive notification of character data inside an element.
*/
void
XMLTokenizer::characters (const XMLToken& data)
{
if (mInStart)
{
mInStart = false;
mTokens.push_back( mCurrent );
}
if (mInChars)
{
mCurrent.append( data.getCharacters() );
}
else
{
mInChars = true;
mCurrent = data;
}
}
/* virtual */ XMLTokenHandler::Result
WebFeedStorage::HandleToken(XMLToken &token)
{
OP_STATUS status = OpStatus::OK;
switch (token.GetType())
{
case XMLToken::TYPE_CDATA:
case XMLToken::TYPE_Text:
status = HandleTextToken(token);
break;
case XMLToken::TYPE_STag:
status = HandleStartTagToken(token);
break;
case XMLToken::TYPE_ETag:
status = HandleEndTagToken(token);
break;
case XMLToken::TYPE_EmptyElemTag:
status = HandleStartTagToken(token);
if (OpStatus::IsSuccess(status))
status = HandleEndTagToken(token);
break;
default:
break;
}
if (OpStatus::IsMemoryError(status))
return XMLTokenHandler::RESULT_OOM;
else if (OpStatus::IsError(status))
return XMLTokenHandler::RESULT_ERROR;
return XMLTokenHandler::RESULT_OK;
}
/* virtual */ XMLTokenHandler::Result
XMLToLanguageParserTokenHandler::HandleToken(XMLToken &token)
{
OP_STATUS status = OpStatus::OK;
OpStatus::Ignore(status);
if (finished)
return RESULT_OK;
if (ignore_element_depth != 0)
{
if (token.GetType() == XMLToken::TYPE_STag)
++ignore_element_depth;
else if (token.GetType() == XMLToken::TYPE_ETag)
--ignore_element_depth;
}
XMLParserImpl *xmlparser = (XMLParserImpl *) token.GetParser();
BOOL block = FALSE;
if (ignore_element_depth == 0)
{
#ifdef XML_ERRORS
XMLRange location;
#endif // XML_ERRORS
switch (token.GetType())
{
case XMLToken::TYPE_PI:
#ifdef XML_ERRORS
token.GetTokenRange(location);
parser->SetLocation(location);
#endif // XML_ERRORS
status = parser->AddProcessingInstruction(token.GetName().GetLocalPart(), token.GetName().GetLocalPartLength(), token.GetData(), token.GetDataLength());
break;
case XMLToken::TYPE_CDATA:
case XMLToken::TYPE_Text:
case XMLToken::TYPE_Comment:
{
XMLLanguageParser::CharacterDataType cdatatype = XMLLanguageParser::CHARACTERDATA_TEXT;
if (token.GetType() != XMLToken::TYPE_Comment)
if (token.GetType() == XMLToken::TYPE_CDATA)
cdatatype = XMLLanguageParser::CHARACTERDATA_CDATA_SECTION;
else if (token.GetLiteralIsWhitespace())
{
if (!entity_signalled)
/* Don't generate calls to the language parser before the
first call to StartEntity. */
break;
cdatatype = XMLLanguageParser::CHARACTERDATA_TEXT_WHITESPACE;
}
const uni_char *simplevalue;
uni_char *allocatedvalue;
if ((simplevalue = token.GetLiteralSimpleValue()) == 0)
{
simplevalue = allocatedvalue = token.GetLiteralAllocatedValue();
if (!allocatedvalue)
status = OpStatus::ERR_NO_MEMORY;
}
else
allocatedvalue = 0;
if (simplevalue)
{
#ifdef XML_ERRORS
token.GetTokenRange(location);
parser->SetLocation(location);
#endif // XML_ERRORS
if (token.GetType() == XMLToken::TYPE_Comment)
status = parser->AddComment(simplevalue, token.GetLiteralLength());
else
status = parser->AddCharacterData(cdatatype, simplevalue, token.GetLiteralLength());
OP_DELETEA(allocatedvalue);
}
break;
}
case XMLToken::TYPE_STag:
case XMLToken::TYPE_ETag:
case XMLToken::TYPE_EmptyElemTag:
if (!(xmlparser->GetCurrentEntityUrl() == current_entity_url) && xmlparser->GetCurrentEntityDepth() <= current_entity_depth)
status = parser->EndEntity();
if (OpStatus::IsSuccess(status) && (!(xmlparser->GetCurrentEntityUrl() == current_entity_url) || current_entity_url.IsEmpty() && !entity_signalled) && xmlparser->GetCurrentEntityDepth() > current_entity_depth)
{
status = parser->StartEntity(xmlparser->GetCurrentEntityUrl(), xmlparser->GetDocumentInformation(), xmlparser->GetCurrentEntityDepth() > 1);
entity_signalled = TRUE;
}
current_entity_url = xmlparser->GetCurrentEntityUrl();
current_entity_depth = xmlparser->GetCurrentEntityDepth();
if (token.GetType() != XMLToken::TYPE_ETag)
{
if (OpStatus::IsSuccess(status))
{
BOOL fragment_start = FALSE;
if (!fragment_found)
{
if (!fragment_id)
fragment_start = TRUE;
else
{
XMLToken::Attribute *attributes = token.GetAttributes();
unsigned attributes_count = token.GetAttributesCount();
unsigned fragment_id_length = uni_strlen(fragment_id);
for (unsigned index = 0; index < attributes_count; ++index)
if (attributes[index].GetId())
if (attributes[index].GetValueLength() == fragment_id_length && uni_strncmp(attributes[index].GetValue(), fragment_id, fragment_id_length) == 0)
{
fragment_start = TRUE;
break;
}
}
if (fragment_start)
fragment_found = TRUE;
}
#ifdef XML_ERRORS
token.GetTokenRange(location);
parser->SetLocation(location);
#endif // XML_ERRORS
BOOL ignore_element = FALSE;
status = parser->StartElement(token.GetName(), fragment_start, ignore_element);
if (ignore_element)
{
if (token.GetType() == XMLToken::TYPE_STag)
ignore_element_depth = 1;
}
else
{
XMLToken::Attribute *attributes = token.GetAttributes();
unsigned attributes_count = token.GetAttributesCount();
for (unsigned index = 0; OpStatus::IsSuccess(status) && index < attributes_count; ++index)
{
#ifdef XML_ERRORS
token.GetAttributeRange(location, index);
parser->SetLocation(location);
#endif // XML_ERRORS
XMLToken::Attribute &attribute = attributes[index];
status = parser->AddAttribute(attribute.GetName(), attribute.GetValue(), attribute.GetValueLength(), attribute.GetSpecified(), attribute.GetId());
}
if (OpStatus::IsSuccess(status))
status = parser->StartContent();
}
}
}
if (OpStatus::IsSuccess(status) && token.GetType() != XMLToken::TYPE_STag)
{
#ifdef XML_ERRORS
token.GetTokenRange(location);
parser->SetLocation(location);
#endif // XML_ERRORS
status = parser->EndElement(block, finished);
if (OpStatus::IsSuccess(status) && block)
parser->SetSourceCallback(&sourcecallbackimpl);
}
break;
case XMLToken::TYPE_Finished:
status = parser->EndEntity();
}
}
if (OpStatus::IsSuccess(status))
if (block)
return RESULT_BLOCK;
else
return RESULT_OK;
else if (OpStatus::IsMemoryError(status))
return RESULT_OOM;
else
return RESULT_ERROR;
}
OP_STATUS
WebFeedStorage::HandleStartTagToken(const XMLToken& token)
{
// Fetch information about the element.
const XMLCompleteNameN &elemname = token.GetName();
const uni_char *elm_name = elemname.GetLocalPart();
UINT elm_name_len = elemname.GetLocalPartLength();
if (STRN_MATCH(elm_name, "entry", elm_name_len))
{
OP_ASSERT(m_current_feed);
OP_ASSERT(!m_current_entry);
m_current_entry = OP_NEW(WebFeedEntry, (m_current_feed));
if (!m_current_entry)
return OpStatus::ERR_NO_MEMORY;
if (OpStatus::IsError(m_current_entry->Init()))
{
m_current_entry->DecRef();
return OpStatus::ERR_NO_MEMORY;
}
const XMLToken::Attribute *attrs = token.GetAttributes();
for (UINT i = 0; i < token.GetAttributesCount(); i++)
{
const uni_char *attr_name = attrs[i].GetName().GetLocalPart();
UINT attr_name_len = attrs[i].GetName().GetLocalPartLength();
const uni_char *attr_value = attrs[i].GetValue();
UINT attr_value_len = attrs[i].GetValueLength();
if (STRN_MATCH(attr_name, "id", attr_name_len))
{
OpString attr_val_str;
RETURN_IF_ERROR(attr_val_str.Set(attr_value, attr_value_len));
m_current_entry->SetId((OpFeedEntry::EntryId)uni_atoi(attr_val_str.CStr()));
}
else if (STRN_MATCH(attr_name, "keep", attr_name_len))
{
if (STRN_MATCH(attr_value, "yes", attr_value_len))
m_current_entry->SetKeep(TRUE);
}
else if (STRN_MATCH(attr_name, "read", attr_name_len))
{
if (STRN_MATCH(attr_value, "yes", attr_value_len))
m_current_entry->SetReadStatus(OpFeedEntry::STATUS_READ);
}
else if (STRN_MATCH(attr_name, "guid", attr_name_len))
{
OpString attr_val_str;
RETURN_IF_ERROR(attr_val_str.Set(attr_value, attr_value_len));
m_current_entry->SetGuid(attr_val_str.CStr());
}
}
}
else if (STRN_MATCH(elm_name, "feed", elm_name_len))
{
OP_ASSERT(!m_current_feed);
if (m_is_feed_file)
{
OP_STATUS status;
if (m_current_feed)
m_current_feed->DecRef();
m_current_feed = OP_NEW(WebFeed, ());
if (!m_current_feed)
return OpStatus::ERR_NO_MEMORY;
OP_ASSERT(m_current_stub);
if (m_current_stub)
status = m_current_feed->Init(m_current_stub);
else
return OpStatus::ERR;
if (OpStatus::IsError(status))
{
m_current_feed->DecRef();
m_current_feed = NULL;
return OpStatus::ERR_NO_MEMORY;
}
else
m_current_feed->IncRef();
}
else
{
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;
}
unsigned int
XMLTokenizer::determineNumberChildren(bool & valid, const std::string element)
{
valid = false;
unsigned int numChildren = 0;
std::string closingTag = element;
bool forcedElement = true;
if (closingTag.empty() == true)
{
closingTag = "apply";
forcedElement = false;
}
// if there is only one token there cannot be any children
size_t size = mTokens.size();
if (size < 2)
{
return numChildren;
}
// we assume that the first unread token is a
// function and that at some point in the
// list of tokens we will hit the end of the
// element for that function
// need to count the number of starts
unsigned int index = 0;
XMLToken firstUnread = mTokens.at(index);
while (firstUnread.isText() && index < size - 1)
{
// skip any text
index++;
firstUnread = mTokens.at(index);
}
// if we have an apply the firstToken should be a function
// that is both a start and an end
// unless we are reading a user function
// or a csymbol
// if the tag is not a start and an end this is an error
// we want to exit
// but be happy that the read is ok
// and the error gets logged elsewhere
if (closingTag == "apply")
{
std::string firstName = firstUnread.getName();
if (firstName != "ci" && firstName != "csymbol")
{
if (firstUnread.isStart() != true
|| (firstUnread.isStart() == true && firstUnread.isEnd() != true))
{
valid = true;
return numChildren;
}
}
}
index = 1;
if (forcedElement == true)
{
index = 0;
}
unsigned int depth = 0;
std::string name;
bool cleanBreak = false;
XMLToken next = mTokens.at(index);
while (index < size-2)
{
// skip any text elements
while(next.isText() == true && index < size-1)
{
index++;
next = mTokens.at(index);
}
if (next.isEnd() == true && next.getName() == closingTag)
{
valid = true;
break;
}
// iterate to first start element
while (next.isStart() == false && index < size-1)
{
index++;
next = mTokens.at(index);
}
// check we have not reached the end
// this would be a bad place if we have so set num children to zero
if (index == size)
{
numChildren = 0;
break;
}
// record the name of the start element
name = next.getName();
numChildren++;
// index++;
// check we have not reached the end
if (index + 1 == size)
{
numChildren = 0;
break;
}
else if (next.isEnd() == false)
{
index++;
if (index < size)
{
next = mTokens.at(index);
}
else
{
break;
}
}
// iterate to the end of </name>
// checking that we have not got a nested element <name></name>
cleanBreak = false;
while (index < size-1)
{
if (next.isStart() == true && next.isEnd() == false && next.getName() == name)
{
depth++;
}
if (next.isEnd() == true && next.getName() == name)
{
if (depth == 0)
{
cleanBreak = true;
break;
}
else
{
depth--;
}
}
index++;
next = mTokens.at(index);
}
index++;
if (index < size)
{
next = mTokens.at(index);
}
}
// we might have hit the end of the loop and the end of the correct tag
// but the loop hits before it can record that it was valid
if (valid == false && cleanBreak == true)
{
if (index >= size-2 && next.isEnd() == true && next.getName() == closingTag)
{
valid = true;
}
}
return numChildren;
}
unsigned int
XMLTokenizer::determineNumSpecificChildren(bool & valid,
const std::string& qualifier,
const std::string& container)
{
valid = false;
unsigned int numQualifiers = 0;
size_t size = mTokens.size();
if (size < 2)
{
return numQualifiers;
}
unsigned int depth = 0;
unsigned int index = 0;
std::string name;
std::string prevName = "";
std::string rogueTag = "";
XMLToken next = mTokens.at(index);
name = next.getName();
if (next.isStart() == true && next.isEnd() == true &&
name == qualifier && index < size)
{
numQualifiers++;
index++;
next = mTokens.at(index);
}
bool cleanBreak = false;
while (index < size-2)
{
// skip any text elements
while(next.isText() == true && index < size-1)
{
index++;
next = mTokens.at(index);
}
if (next.isEnd() == true)
{
if (next.getName() == container)
{
valid = true;
break;
}
//else if (!rogueTag.empty() && next.getName() == rogueTag)
//{
// index++;
// next = mTokens.at(index);
// break;
//}
}
// iterate to first start element
while (next.isStart() == false && index < size-1)
{
index++;
next = mTokens.at(index);
}
if (next.isStart() == true && next.isEnd() == true)
{
if (qualifier.empty() == true)
{
// if we are not looking for a specifc element then
// we may have a child that is a start and end
// such as <true/>
numQualifiers++;
}
index++;
if (index < size)
{
next = mTokens.at(index);
continue;
}
}
// check we have not reached the end
// this would be a bad place if we have so set num children to zero
if (index == size)
{
numQualifiers = 0;
break;
}
// record the name of the start element
name = next.getName();
// need to deal with the weird situation where someone has used a tag
// after the piece but before the next correct element
//if (container == "piecewise")
//{
// if (prevName == "piece")
// {
// if (name != "piece" && name != "otherwise")
// {
// rogueTag = name;
// index++;
// next = mTokens.at(index);
// continue;
// }
// }
//}
if (qualifier.empty() == true || name == qualifier)
{
numQualifiers++;
}
// index++;
// check we have not reached the end
if (index+1 == size)
{
numQualifiers = 0;
break;
}
else
{
index++;
next = mTokens.at(index);
}
// iterate to the end of </name>
// checking that we have not got a nested element <name></name>
cleanBreak = false;
while (index < size-1)
{
if (next.isStart() == true && next.getName() == name)
{
depth++;
}
if (next.isEnd() == true && next.getName() == name)
{
if (depth == 0)
{
cleanBreak = true;
break;
}
else
{
depth--;
}
}
index++;
if (index < size)
{
next = mTokens.at(index);
}
}
prevName = name;
index++;
if (index < size)
{
next = mTokens.at(index);
}
}
// we might have hit the end of the loop and the end of the correct tag
if (valid == false && cleanBreak == true)
{
if (index >= size-2 && next.isEnd() == true && next.getName() == container)
{
valid = true;
}
}
return numQualifiers;
}
/*
* 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)
{
if (getLevel() < 3)
{
logError(NotSchemaConformant, getLevel(), getVersion(),
"Only one <math> element is permitted inside a "
"particular containing element.");
}
else
{
logError(OneMathElementPerInitialAssign, getLevel(), getVersion());
}
}
/* check for MathML namespace
* this may be explicitly declared here
* or implicitly declared on the whole document
*/
const XMLToken elem = stream.peek();
unsigned int match = 0;
int n;
if (elem.getNamespaces().getLength() != 0)
{
for (n = 0; n < elem.getNamespaces().getLength(); n++)
{
if (!strcmp(elem.getNamespaces().getURI(n).c_str(), "http://www.w3.org/1998/Math/MathML"))
{
match = 1;
break;
}
}
}
if (match == 0)
{
if( mSBML->getNamespaces() != NULL)
/* check for implicit declaration */
{
for (n = 0; n < mSBML->getNamespaces()->getLength(); n++)
{
if (!strcmp(mSBML->getNamespaces()->getURI(n).c_str(),
"http://www.w3.org/1998/Math/MathML"))
{
match = 1;
break;
}
}
}
}
if (match == 0)
{
logError(InvalidMathElement);
}
delete mMath;
mMath = readMathML(stream);
if (mMath) mMath->setParentSBMLObject(this);
read = true;
}
return read;
}
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;
}
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;
}