/** @cond doxygenLibsbmlInternal */
void ReferenceGlyph::readAttributes (const XMLAttributes& attributes,
const ExpectedAttributes& expectedAttributes)
{
const unsigned int sbmlLevel = getLevel ();
const unsigned int sbmlVersion = getVersion();
unsigned int numErrs;
/* look to see whether an unknown attribute error was logged
* during the read of the listOfReferenceGlyphs - which will have
* happened immediately prior to this read
*/
bool loSubGlyphs = false;
if (getParentSBMLObject() != NULL
&& getParentSBMLObject()->getElementName() == "listOfSubGlyphs")
{
loSubGlyphs = true;
}
if (getErrorLog() != NULL &&
static_cast<ListOfReferenceGlyphs*>(getParentSBMLObject())->size() < 2)
{
numErrs = getErrorLog()->getNumErrors();
for (int n = (int)numErrs-1; n >= 0; n--)
{
if (getErrorLog()->getError((unsigned int)n)->getErrorId() == UnknownPackageAttribute)
{
const std::string details =
getErrorLog()->getError((unsigned int)n)->getMessage();
getErrorLog()->remove(UnknownPackageAttribute);
if (loSubGlyphs == true)
{
getErrorLog()->logPackageError("layout",
LayoutLOSubGlyphAllowedAttribs,
getPackageVersion(), sbmlLevel, sbmlVersion, details, getLine(), getColumn());
}
else
{
getErrorLog()->logPackageError("layout",
LayoutLOReferenceGlyphAllowedAttribs,
getPackageVersion(), sbmlLevel, sbmlVersion, details, getLine(), getColumn());
}
}
else if (getErrorLog()->getError((unsigned int)n)->getErrorId() == UnknownCoreAttribute)
{
const std::string details =
getErrorLog()->getError((unsigned int)n)->getMessage();
getErrorLog()->remove(UnknownCoreAttribute);
if (loSubGlyphs == true)
{
getErrorLog()->logPackageError("layout",
LayoutLOSubGlyphAllowedAttribs,
getPackageVersion(), sbmlLevel, sbmlVersion, details, getLine(), getColumn());
}
else
{
getErrorLog()->logPackageError("layout",
LayoutLOReferenceGlyphAllowedAttribs,
getPackageVersion(), sbmlLevel, sbmlVersion, details, getLine(), getColumn());
}
}
}
}
GraphicalObject::readAttributes(attributes, expectedAttributes);
// look to see whether an unknown attribute error was logged
if (getErrorLog() != NULL)
{
numErrs = getErrorLog()->getNumErrors();
for (int n = (int)numErrs-1; n >= 0; n--)
{
if (getErrorLog()->getError((unsigned int)n)->getErrorId() == UnknownPackageAttribute)
{
const std::string details =
getErrorLog()->getError((unsigned int)n)->getMessage();
getErrorLog()->remove(UnknownPackageAttribute);
getErrorLog()->logPackageError("layout", LayoutREFGAllowedAttributes,
getPackageVersion(), sbmlLevel, sbmlVersion, details, getLine(), getColumn());
}
else if (getErrorLog()->getError((unsigned int)n)->getErrorId() == UnknownCoreAttribute)
{
const std::string details =
getErrorLog()->getError((unsigned int)n)->getMessage();
getErrorLog()->remove(UnknownCoreAttribute);
getErrorLog()->logPackageError("layout",
LayoutREFGAllowedCoreAttributes,
getPackageVersion(), sbmlLevel, sbmlVersion, details, getLine(), getColumn());
}
}
}
bool assigned = false;
//
// glyph SIdRef ( use = "required" )
//
assigned = attributes.readInto("glyph", mGlyph);
if (getErrorLog() != NULL)
{
if (assigned == true)
{
// check string is not empty and correct syntax
if (mGlyph.empty() == true)
{
logEmptyString(mGlyph, getLevel(), getVersion(), "<ReferenceGlyph>");
}
else if (SyntaxChecker::isValidSBMLSId(mGlyph) == false)
{
getErrorLog()->logPackageError("layout", LayoutREFGGlyphSyntax,
getPackageVersion(), sbmlLevel, sbmlVersion, "The glyph on the <"
+ getElementName() + "> is '" + mGlyph + "', which does not conform to the syntax.", getLine(), getColumn());
}
}
else
{
std::string message = "Layout attribute 'glyph' is missing.";
getErrorLog()->logPackageError("layout", LayoutREFGAllowedAttributes,
getPackageVersion(), sbmlLevel, sbmlVersion, message, getLine(), getColumn());
}
}
//
// reference SIdRef ( use = "optional" )
//
assigned = attributes.readInto("reference", mReference);
if (assigned == true && getErrorLog() != NULL)
{
// check string is not empty and correct syntax
if (mReference.empty() == true)
{
logEmptyString(mReference, getLevel(), getVersion(), "<ReferenceGlyph>");
}
else if (SyntaxChecker::isValidSBMLSId(mReference) == false)
{
getErrorLog()->logPackageError("layout", LayoutREFGReferenceSyntax,
getPackageVersion(), sbmlLevel, sbmlVersion, "The reference on the <"
+ getElementName() + "> is '" + mReference + "', which does not conform to the syntax.", getLine(), getColumn());
}
}
//
// role string ( use = "optional" )
//
std::string role;
assigned = attributes.readInto("role", role);
if (assigned == true)
{
// check string is not empty
if (role.empty() == true && getErrorLog() != NULL)
{
logEmptyString(role, getLevel(), getVersion(), "<ReferenceGlyph>");
}
this->setRole(role);
}
}
/** @cond doxygenLibsbmlInternal */
void GeneralGlyph::readAttributes (const XMLAttributes& attributes,
const ExpectedAttributes& expectedAttributes)
{
const unsigned int sbmlLevel = getLevel ();
const unsigned int sbmlVersion = getVersion();
unsigned int numErrs;
/* look to see whether an unknown attribute error was logged
* during the read of the listOfAdditionalGraphicalObjects - which will have
* happened immediately prior to this read
*/
bool loSubGlyphs = false;
if (getParentSBMLObject() != NULL
&& getParentSBMLObject()->getElementName() == "listOfSubGlyphs")
{
loSubGlyphs = true;
}
if (getErrorLog() != NULL &&
static_cast<ListOfGraphicalObjects*>(getParentSBMLObject())->size() < 2)
{
numErrs = getErrorLog()->getNumErrors();
for (int n = numErrs-1; n >= 0; n--)
{
if (getErrorLog()->getError(n)->getErrorId() == UnknownPackageAttribute)
{
const std::string details =
getErrorLog()->getError(n)->getMessage();
getErrorLog()->remove(UnknownPackageAttribute);
if (loSubGlyphs == true)
{
getErrorLog()->logPackageError("layout",
LayoutLOSubGlyphAllowedAttribs,
getPackageVersion(), sbmlLevel, sbmlVersion, details);
}
else
{
getErrorLog()->logPackageError("layout",
LayoutLOAddGOAllowedAttribut,
getPackageVersion(), sbmlLevel, sbmlVersion, details);
}
}
else if (getErrorLog()->getError(n)->getErrorId() == UnknownCoreAttribute)
{
const std::string details =
getErrorLog()->getError(n)->getMessage();
getErrorLog()->remove(UnknownCoreAttribute);
if (loSubGlyphs == true)
{
getErrorLog()->logPackageError("layout",
LayoutLOSubGlyphAllowedAttribs,
getPackageVersion(), sbmlLevel, sbmlVersion, details);
}
else
{
getErrorLog()->logPackageError("layout",
LayoutLOAddGOAllowedAttribut,
getPackageVersion(), sbmlLevel, sbmlVersion, details);
}
}
}
}
GraphicalObject::readAttributes(attributes, expectedAttributes);
// look to see whether an unknown attribute error was logged
if (getErrorLog() != NULL)
{
numErrs = getErrorLog()->getNumErrors();
for (int n = numErrs-1; n >= 0; n--)
{
if (getErrorLog()->getError(n)->getErrorId() == UnknownPackageAttribute)
{
const std::string details =
getErrorLog()->getError(n)->getMessage();
getErrorLog()->remove(UnknownPackageAttribute);
getErrorLog()->logPackageError("layout", LayoutGGAllowedAttributes,
getPackageVersion(), sbmlLevel, sbmlVersion, details);
}
else if (getErrorLog()->getError(n)->getErrorId() == UnknownCoreAttribute)
{
const std::string details =
getErrorLog()->getError(n)->getMessage();
getErrorLog()->remove(UnknownCoreAttribute);
getErrorLog()->logPackageError("layout", LayoutGGAllowedCoreAttributes,
getPackageVersion(), sbmlLevel, sbmlVersion, details);
}
}
}
bool assigned = false;
//
// reference SIdRef ( use = "optional" )
//
assigned = attributes.readInto("reference", mReference);
if (assigned == true)
{
// check string is not empty and correct syntax
if (mReference.empty() == true)
{
logEmptyString(mReference, getLevel(), getVersion(), "<GeneralGlyph>");
}
else if (SyntaxChecker::isValidSBMLSId(mReference) == false)
{
getErrorLog()->logPackageError("layout", LayoutGGReferenceSyntax,
getPackageVersion(), sbmlLevel, sbmlVersion);
}
}
}
/** @cond doxygenLibsbmlInternal */
void SpeciesGlyph::readAttributes (const XMLAttributes& attributes,
const ExpectedAttributes& expectedAttributes)
{
const unsigned int sbmlLevel = getLevel ();
const unsigned int sbmlVersion = getVersion();
unsigned int numErrs;
/* look to see whether an unknown attribute error was logged
* during the read of the listOfSpeciesGlyphs - which will have
* happened immediately prior to this read
*/
bool loSubGlyphs = false;
if (getParentSBMLObject() != NULL
&& getParentSBMLObject()->getElementName() == "listOfSubGlyphs")
{
loSubGlyphs = true;
}
if (getErrorLog() != NULL &&
static_cast<ListOfSpeciesGlyphs*>(getParentSBMLObject())->size() < 2)
{
numErrs = getErrorLog()->getNumErrors();
for (int n = (int)numErrs-1; n >= 0; n--)
{
if (getErrorLog()->getError((unsigned int)n)->getErrorId() == UnknownPackageAttribute)
{
const std::string details =
getErrorLog()->getError((unsigned int)n)->getMessage();
getErrorLog()->remove(UnknownPackageAttribute);
if (loSubGlyphs == true)
{
getErrorLog()->logPackageError("layout",
LayoutLOSubGlyphAllowedAttribs,
getPackageVersion(), sbmlLevel, sbmlVersion, details, getLine(), getColumn());
}
else
{
getErrorLog()->logPackageError("layout",
LayoutLOSpeciesGlyphAllowedAttributes,
getPackageVersion(), sbmlLevel, sbmlVersion, details, getLine(), getColumn());
}
}
else if (getErrorLog()->getError((unsigned int)n)->getErrorId() == UnknownCoreAttribute)
{
const std::string details =
getErrorLog()->getError((unsigned int)n)->getMessage();
getErrorLog()->remove(UnknownCoreAttribute);
if (loSubGlyphs == true)
{
getErrorLog()->logPackageError("layout",
LayoutLOSubGlyphAllowedAttribs,
getPackageVersion(), sbmlLevel, sbmlVersion, details, getLine(), getColumn());
}
else
{
getErrorLog()->logPackageError("layout",
LayoutLOSpeciesGlyphAllowedAttributes,
getPackageVersion(), sbmlLevel, sbmlVersion, details, getLine(), getColumn());
}
}
}
}
GraphicalObject::readAttributes(attributes, expectedAttributes);
// look to see whether an unknown attribute error was logged
if (getErrorLog() != NULL)
{
numErrs = getErrorLog()->getNumErrors();
for (int n = (int)numErrs-1; n >= 0; n--)
{
if (getErrorLog()->getError((unsigned int)n)->getErrorId() == UnknownPackageAttribute)
{
const std::string details =
getErrorLog()->getError((unsigned int)n)->getMessage();
getErrorLog()->remove(UnknownPackageAttribute);
getErrorLog()->logPackageError("layout", LayoutSGAllowedAttributes,
getPackageVersion(), sbmlLevel, sbmlVersion, details, getLine(), getColumn());
}
else if (getErrorLog()->getError((unsigned int)n)->getErrorId() == UnknownCoreAttribute)
{
const std::string details =
getErrorLog()->getError((unsigned int)n)->getMessage();
getErrorLog()->remove(UnknownCoreAttribute);
getErrorLog()->logPackageError("layout", LayoutSGAllowedCoreAttributes,
getPackageVersion(), sbmlLevel, sbmlVersion, details, getLine(), getColumn());
}
}
}
bool assigned = false;
//
// species SIdRef ( use = "optional" )
//
assigned = attributes.readInto("species", mSpecies);
if (assigned == true && getErrorLog() != NULL)
{
// check string is not empty and correct syntax
if (mSpecies.empty() == true)
{
logEmptyString(mSpecies, getLevel(), getVersion(), "<SpeciesGlyph>");
}
else if (SyntaxChecker::isValidSBMLSId(mSpecies) == false)
{
getErrorLog()->logPackageError("layout", LayoutSGSpeciesSyntax,
getPackageVersion(), sbmlLevel, sbmlVersion, "The species on the <"
+ getElementName() + "> is '" + mSpecies + "', which does not conform to the syntax.", getLine(), getColumn());
}
}
}