/** @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;
}
void
CompSBasePlugin::createListOfReplacedElements()
{
if (mListOfReplacedElements==NULL) {
COMP_CREATE_NS(compns, getSBMLNamespaces());
mListOfReplacedElements = new ListOfReplacedElements(compns);
mListOfReplacedElements->connectToParent(getParentSBMLObject());
delete compns;
}
}
ReplacedBy*
CompSBasePlugin::createReplacedBy()
{
if (mReplacedBy!=NULL) {
delete mReplacedBy;
}
COMP_CREATE_NS(compns, getSBMLNamespaces());
mReplacedBy = new ReplacedBy(compns);
mReplacedBy->connectToParent(getParentSBMLObject());
delete compns;
return mReplacedBy;
}
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());
}
}
CompSBasePlugin::CompSBasePlugin(const CompSBasePlugin& orig)
: SBasePlugin(orig)
, mListOfReplacedElements(NULL)
, mReplacedBy(NULL)
{
if (orig.isSetReplacedBy()) {
mReplacedBy = orig.mReplacedBy->clone();
mReplacedBy->connectToParent(getParentSBMLObject());
}
if (orig.getNumReplacedElements() > 0) {
createListOfReplacedElements();
for (unsigned int re=0; re<orig.getNumReplacedElements(); re++) {
mListOfReplacedElements->append(orig.getReplacedElement(re));
}
}
connectToChild();
}
CompSBasePlugin&
CompSBasePlugin::operator=(const CompSBasePlugin& orig)
{
if(&orig!=this)
{
SBasePlugin::operator =(orig);
if (orig.getNumReplacedElements() > 0) {
createListOfReplacedElements();
for (unsigned int re=0; re<orig.getNumReplacedElements(); re++) {
mListOfReplacedElements->append(orig.getReplacedElement(re));
}
}
if (orig.mReplacedBy != NULL) {
mReplacedBy=orig.mReplacedBy->clone();
mReplacedBy->connectToParent(getParentSBMLObject());
}
}
return *this;
}
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;
}
}
/** @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 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 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());
}
}
}
