/** @cond doxygenLibsbmlInternal */
SBase*
BoundingBox::createObject (XMLInputStream& stream)
{
const std::string& name = stream.peek().getName();
SBase* object = 0;
if (name == "dimensions")
{
if (getDimensionsExplicitlySet() == true)
{
getErrorLog()->logPackageError("layout", LayoutBBoxAllowedElements,
getPackageVersion(), getLevel(), getVersion(), "", getLine(), getColumn());
}
object = &mDimensions;
mDimensionsExplicitlySet = true;
}
else if ( name == "position" )
{
if (getPositionExplicitlySet() == true)
{
getErrorLog()->logPackageError("layout", LayoutBBoxAllowedElements,
getPackageVersion(), getLevel(), getVersion(), "", getLine(), getColumn());
}
object = &mPosition;
mPositionExplicitlySet = true;
}
return object;
}
/** @cond doxygenLibsbmlInternal */
SBase*
ReactionGlyph::createObject (XMLInputStream& stream)
{
const std::string& name = stream.peek().getName();
SBase* object = 0;
if (name == "listOfSpeciesReferenceGlyphs")
{
if (mSpeciesReferenceGlyphs.size() != 0)
{
getErrorLog()->logPackageError("layout", LayoutRGAllowedElements,
getPackageVersion(), getLevel(), getVersion(), "", getLine(), getColumn());
}
object = &mSpeciesReferenceGlyphs;
}
else if(name=="curve")
{
if (getCurveExplicitlySet() == true)
{
getErrorLog()->logPackageError("layout", LayoutRGAllowedElements,
getPackageVersion(), getLevel(), getVersion(), "", getLine(), getColumn());
}
object = &mCurve;
mCurveExplicitlySet = true;
}
else
{
object=GraphicalObject::createObject(stream);
}
return object;
}
QString DiagnosticsDialog::getBrowsers() const
{
#if defined(Q_OS_LINUX)
return getPackageVersion( QStringList() << "chromium-browser" << "firefox" << "MozillaFirefox");
#elif defined(Q_OS_MAC)
return getPackageVersion( QStringList() << "Google Chrome" << "Firefox" << "Safari" );
#endif
}
/** @cond doxygenLibsbmlInternal */
void BoundingBox::readAttributes (const XMLAttributes& attributes,
const ExpectedAttributes& expectedAttributes)
{
const unsigned int sbmlLevel = getLevel ();
const unsigned int sbmlVersion = getVersion();
unsigned int numErrs;
SBase::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", LayoutBBoxAllowedAttributes,
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",
LayoutBBoxAllowedCoreAttributes,
getPackageVersion(), sbmlLevel, sbmlVersion, details, getLine(), getColumn());
}
}
}
bool assigned = false;
//
// id SId ( use = "optional" )
//
assigned = attributes.readInto("id", mId);
if (assigned == true && getErrorLog() != NULL)
{
// check string is not empty and correct syntax
if (mId.empty() == true)
{
logEmptyString(mId, getLevel(), getVersion(), "<BoundingBox>");
}
else if (SyntaxChecker::isValidSBMLSId(mId) == false)
{
getErrorLog()->logPackageError("layout", LayoutSIdSyntax,
getPackageVersion(), sbmlLevel, sbmlVersion);
}
}
}
/** @cond doxygenLibsbmlInternal */
SBase*
CompSBasePlugin::createObject(XMLInputStream& stream)
{
SBase* object = 0;
const std::string& name = stream.peek().getName();
const XMLNamespaces& xmlns = stream.peek().getNamespaces();
const std::string& prefix = stream.peek().getPrefix();
const std::string& targetPrefix = (xmlns.hasURI(mURI)) ? xmlns.getPrefix(mURI) : mPrefix;
if (prefix == targetPrefix)
{
if ( name == "listOfReplacedElements" )
{
if (mListOfReplacedElements != NULL)
{
getErrorLog()->logPackageError("comp", CompOneListOfReplacedElements,
getPackageVersion(), getLevel(), getVersion());
}
createListOfReplacedElements();
object = mListOfReplacedElements;
if (targetPrefix.empty())
{
//
// (NOTE)
//
// A top-level element (listOfReplacedElements) of the comp extension is located
// in a default namespace, and thus xmlns=".." attribute must be added to
// the element.
// This is done by invoking SBMLDocument::enableDefaultNS() function with
// the two arguments (the URI of this package and true value).
//
mListOfReplacedElements->getSBMLDocument()->enableDefaultNS(mURI,true);
}
}
if ( name == "replacedBy" ) {
if (mReplacedBy != NULL)
{
if (mSBML != NULL && getErrorLog() != NULL)
{
getErrorLog()->logPackageError("comp", CompOneReplacedByElement,
getPackageVersion(), getLevel(), getVersion());
}
}
delete mReplacedBy;
COMP_CREATE_NS(compns, getSBMLNamespaces());
mReplacedBy = new ReplacedBy(compns);
object = mReplacedBy;
object->connectToParent(getParentSBMLObject());
delete compns;
}
}
return object;
}
int
CompSBasePlugin::addReplacedElement (const ReplacedElement* replacedElement)
{
if (replacedElement == NULL)
{
return LIBSBML_INVALID_OBJECT;
}
else if (!(replacedElement->hasRequiredAttributes()) || !(replacedElement->hasRequiredElements()))
{
return LIBSBML_INVALID_OBJECT;
}
else if (getLevel() != replacedElement->getLevel())
{
return LIBSBML_LEVEL_MISMATCH;
}
else if (getVersion() != replacedElement->getVersion())
{
return LIBSBML_VERSION_MISMATCH;
}
else if (getPackageVersion() != replacedElement->getPackageVersion())
{
return LIBSBML_PKG_VERSION_MISMATCH;
}
else
{
createListOfReplacedElements();
return mListOfReplacedElements->append(replacedElement);
}
}
/** @cond doxygenLibsbmlInternal */
SBase*
ListOfLineSegments::createObject (XMLInputStream& stream)
{
const std::string& name = stream.peek().getName();
SBase* object = 0;
if (name == "curveSegment")
{
std::string type = "LineSegment";
XMLTriple triple("type","http://www.w3.org/2001/XMLSchema-instance","xsi");
if (!stream.peek().getAttributes().readInto(triple, type))
{
//std::cout << "[DEBUG] ListOfLineSegments::createObject () :
// Failed to read xsi:type" << std::endl;
getErrorLog()->logPackageError("layout",
LayoutXsiTypeAllowedLocations,
getPackageVersion(), getLevel(), getVersion(), "", getLine(), getColumn());
return object;
}
//std::cout << "[DEBUG] ListOfLineSegments::createObject () : type "
// << type << std::endl;
LAYOUT_CREATE_NS(layoutns,this->getSBMLNamespaces());
if(type=="LineSegment")
{
object = new LineSegment(layoutns);
}
else if(type=="CubicBezier")
{
object = new CubicBezier(layoutns);
}
else
{
getErrorLog()->logPackageError("layout", LayoutXsiTypeSyntax,
getPackageVersion(), getLevel(), getVersion(), "", getLine(), getColumn());
}
delete layoutns;
}
if(object) appendAndOwn(object);
return object;
}
/** @cond doxygenLibsbmlInternal */
SBase*
CubicBezier::createObject (XMLInputStream& stream)
{
const std::string& name = stream.peek().getName();
SBase* object = 0;
if (name == "basePoint1")
{
if (getBasePt1ExplicitlySet() == true)
{
getErrorLog()->logPackageError("layout", LayoutCBezAllowedElements,
getPackageVersion(), getLevel(), getVersion(), "", getLine(), getColumn());
}
object = &mBasePoint1;
mBasePt1ExplicitlySet = true;
}
else if(name == "basePoint2")
{
if (getBasePt2ExplicitlySet() == true)
{
getErrorLog()->logPackageError("layout", LayoutCBezAllowedElements,
getPackageVersion(), getLevel(), getVersion(), "", getLine(), getColumn());
}
object = &mBasePoint2;
mBasePt2ExplicitlySet = true;
}
else
{
object = LineSegment::createObject(stream);
}
return object;
}
/** @cond doxygenLibsbmlInternal */
void Curve::readAttributes (const XMLAttributes& attributes,
const ExpectedAttributes& expectedAttributes)
{
const unsigned int sbmlLevel = getLevel ();
const unsigned int sbmlVersion = getVersion();
unsigned int numErrs;
SBase::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", LayoutCurveAllowedAttributes,
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",
LayoutCurveAllowedCoreAttributes,
getPackageVersion(), sbmlLevel, sbmlVersion, details, getLine(), getColumn());
}
}
}
}
/*
* Subclasses should override this method to read values from the given
* XMLAttributes set into their specific fields.
*/
void
SBasePlugin::readAttributes (const XMLAttributes& attributes,
const ExpectedAttributes& expectedAttributes)
{
if (&attributes == NULL || &expectedAttributes == NULL ) return;
const unsigned int sbmlLevel = getLevel ();
const unsigned int sbmlVersion = getVersion();
const unsigned int pkgVersion = getPackageVersion();
std::string element = (mParent) ? mParent->getElementName() : std::string();
//
// (NOTE)
//
// This function is just used to identify unexpected
// attributes with the prefix of the package.
//
#if 0
std::cout << "[DEBUG] SBasePlugin::readAttributes() " << element << std::endl;
#endif
//
// check that all attributes of this plugin object are expected
//
for (int i = 0; i < attributes.getLength(); i++)
{
std::string name = attributes.getName(i);
std::string uri = attributes.getURI(i);
#if 0
std::cout << "[DEBUG] SBasePlugin::readAttributes() name : " << name
<< " uri " << uri << std::endl;
#endif
if (uri != mURI) continue;
if (!expectedAttributes.hasAttribute(name))
{
logUnknownAttribute(name, sbmlLevel, sbmlVersion, pkgVersion, element);
}
}
}
/** @cond doxygenLibsbmlInternal */
SBase*
Curve::createObject (XMLInputStream& stream)
{
const std::string& name = stream.peek().getName();
SBase* object = 0;
if (name == "listOfCurveSegments")
{
if (mCurveSegments.size() != 0)
{
getErrorLog()->logPackageError("layout", LayoutCurveAllowedElements,
getPackageVersion(), getLevel(), getVersion(), "", getLine(), getColumn());
}
object = &mCurveSegments;
}
return object;
}
int
CompSBasePlugin::setReplacedBy (const ReplacedBy* replacedBy)
{
if (mReplacedBy == replacedBy)
{
return LIBSBML_OPERATION_SUCCESS;
}
else if (replacedBy == NULL)
{
if (mReplacedBy != NULL) delete mReplacedBy;
mReplacedBy = NULL;
return LIBSBML_OPERATION_SUCCESS;
}
else if (!replacedBy->hasRequiredAttributes() || !replacedBy->hasRequiredElements()) {
return LIBSBML_INVALID_OBJECT;
}
else if (getLevel() != replacedBy->getLevel())
{
return LIBSBML_LEVEL_MISMATCH;
}
else if (getVersion() != replacedBy->getVersion())
{
return LIBSBML_VERSION_MISMATCH;
}
else if (getPackageVersion() != replacedBy->getPackageVersion())
{
return LIBSBML_PKG_VERSION_MISMATCH;
}
else
{
if (mReplacedBy != NULL) delete mReplacedBy;
mReplacedBy = replacedBy->clone();
if (mReplacedBy == NULL) {
return LIBSBML_OPERATION_FAILED;
}
mReplacedBy->connectToParent(getParentSBMLObject());
return LIBSBML_OPERATION_SUCCESS;
}
}
void
CompSBasePlugin::logInvalidId(const std::string& attribute,
const std::string& wrongattribute)
{
if (&attribute == NULL || &wrongattribute == NULL) return;
bool knownelement = (getParentSBMLObject() == NULL);
std::ostringstream msg;
msg << "Setting the attribute '" << attribute << "' ";
if (knownelement) {
msg << "of a <" << getParentSBMLObject()->getElementName() << "> ";
}
msg << "in the " << getPackageName()
<< " package (version " << getPackageVersion() << ") to '" << wrongattribute
<< "' is illegal: the string is not a well-formed SId.";
SBMLErrorLog* errlog = getErrorLog();
if (errlog)
{
errlog->logError(NotSchemaConformant, getLevel(), getVersion(), msg.str());
}
}
/** @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());
}
}
}
/** @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);
}
}
}
DiagnosticsDialog::DiagnosticsDialog( QWidget *parent )
: QDialog( parent )
{
setupUi( this );
setAttribute( Qt::WA_DeleteOnClose, true );
QString info;
QTextStream s( &info );
s << "<b>" << tr("Locale:") << "</b> ";
QString locale = QLocale::c().name();
s << (locale == "C" ? "en_us" : locale) << "<br /><br />";
#if defined(Q_OS_LINUX)
QString package = getPackageVersion( QStringList() << "estonianidcard", false );
QString utility = getPackageVersion( QStringList() << "qesteidutil", false );
if ( !package.isEmpty() )
s << "<b>" << tr("ID-card package version:") << "</b> " << package << "<br />";
if ( !utility.isEmpty() )
s << "<b>" << tr("ID-card utility version:") << "</b> " << utility << "<br />";
#else
s << "<b>" << tr("ID-card utility version:") << "</b> " << QCoreApplication::applicationVersion() << "<br />";
#endif
s << "<b>" << tr("OS:") << "</b> ";
#if defined(Q_OS_LINUX)
QProcess p;
p.start( "lsb_release", QStringList() << "-s" << "-d" );
p.waitForReadyRead();
s << p.readAll();
#elif defined(Q_OS_MAC)
SInt32 major, minor, bugfix;
if( Gestalt(gestaltSystemVersionMajor, &major) == noErr &&
Gestalt(gestaltSystemVersionMinor, &minor) == noErr &&
Gestalt(gestaltSystemVersionBugFix, &bugfix) == noErr )
s << "Mac OS " << major << "." << minor << "." << bugfix;
else
s << "Mac OS 10.3";
#endif
s << " (" << QSysInfo::WordSize << ")<br />";
#if defined(Q_OS_LINUX)
s << "<b>" << tr("CPU:") << "</b> " << getProcessor() << "<br /><br />";
#endif
s << "<b>" << tr("Library paths:") << "</b> " << QCoreApplication::libraryPaths().join( ";" ) << "<br />";
s << "<b>" << tr("Libraries") << ":</b><br />";
#if defined(Q_OS_MAC)
QProcess p;
p.start( "/Library/OpenSC/bin/opensc-tool", QStringList() << "-i" );
p.waitForReadyRead();
s << p.readAll() << "<br />";
#elif defined(Q_OS_LINUX)
s << getPackageVersion( QStringList() << "openssl" << "libpcsclite1" << "opensc" );
#endif
s << "QT (" << qVersion() << ")<br />" << "<br />";
s << "<b>" << tr("PCSC service status: ") << "</b>" << " " << (isPCSCRunning() ? tr("Running") : tr("Not running")) << "<br /><br />";
s << "<b>" << tr("Card readers") << ":</b><br />" << getReaderInfo() << "<br />";
QString browsers = getBrowsers();
if ( !browsers.isEmpty() )
s << "<b>" << tr("Browsers:") << "</b><br />" << browsers << "<br /><br />";
diagnosticsText->setHtml( info );
}
/** @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);
}
}
