XMLNode(XMLInputStream stream) : this(libsbmlPINVOKE.new_XMLNode__SWIG_14(XMLInputStream.getCPtr(stream)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
static ModelHistory parseRDFAnnotation(XMLNode annotation, string metaId, XMLInputStream stream)
{
IntPtr cPtr = libsbmlPINVOKE.RDFAnnotationParser_parseRDFAnnotation__SWIG_0(XMLNode.getCPtr(annotation), metaId, XMLInputStream.getCPtr(stream));
ModelHistory ret = (cPtr == IntPtr.Zero) ? null : new ModelHistory(cPtr, false);
return(ret);
}
void logError(XMLInputStream stream, XMLToken element, int code)
{
libsbmlPINVOKE.ASTBase_logError__SWIG_1(swigCPtr, XMLInputStream.getCPtr(stream), XMLToken.getCPtr(element), code);
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
void addExpectedAttributes(SWIGTYPE_p_ExpectedAttributes attributes, XMLInputStream stream)
{
libsbmlPINVOKE.ASTBase_addExpectedAttributes(swigCPtr, SWIGTYPE_p_ExpectedAttributes.getCPtr(attributes), XMLInputStream.getCPtr(stream));
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
bool read(XMLInputStream stream, string reqd_prefix, XMLToken currentElement)
{
bool ret = libsbmlPINVOKE.ASTBasePlugin_read(swigCPtr, XMLInputStream.getCPtr(stream), reqd_prefix, XMLToken.getCPtr(currentElement));
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
return(ret);
}
bool read(XMLInputStream stream)
{
bool ret = libsbmlPINVOKE.ASTBase_read__SWIG_1(swigCPtr, XMLInputStream.getCPtr(stream));
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
return(ret);
}
internal static HandleRef getCPtrAndDisown(XMLInputStream obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return(ptr);
}
internal static HandleRef getCPtr(XMLInputStream obj)
{
return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
}
internal static HandleRef getCPtr(XMLInputStream obj)
{
return((obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr);
}
/** */
/* libsbml-internal */
public bool read(XMLInputStream stream, string reqd_prefix, XMLToken currentElement)
{
bool ret = libsbmlPINVOKE.ASTBasePlugin_read(swigCPtr, XMLInputStream.getCPtr(stream), reqd_prefix, XMLToken.getCPtr(currentElement));
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
return ret;
}
/** */
/* libsbml-internal */
public new void addExpectedAttributes(SWIGTYPE_p_ExpectedAttributes attributes, XMLInputStream stream)
{
libsbmlPINVOKE.ASTBase_addExpectedAttributes(swigCPtr, SWIGTYPE_p_ExpectedAttributes.getCPtr(attributes), XMLInputStream.getCPtr(stream));
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
public static void parseRDFAnnotation(XMLNode annotation, CVTermList CVTerms, string metaId, XMLInputStream stream)
{
libsbmlPINVOKE.RDFAnnotationParser_parseRDFAnnotation__SWIG_4(XMLNode.getCPtr(annotation), CVTermList.getCPtr(CVTerms), metaId, XMLInputStream.getCPtr(stream));
}
public static void parseRDFAnnotation(XMLNode annotation, CVTermList CVTerms, string metaId, XMLInputStream stream)
{
libsbmlPINVOKE.RDFAnnotationParser_parseRDFAnnotation__SWIG_4(XMLNode.getCPtr(annotation), CVTermList.getCPtr(CVTerms), metaId, XMLInputStream.getCPtr(stream));
}
/**
* Parses an annotation into a ModelHistory class instance.
*
* This is used to take an annotation that has been read into an SBML
* model, identify the RDF elements representing model history
* information, and create a list of corresponding CVTerm objects.
*
* @param annotation XMLNode containing the annotation.
* @param stream optional XMLInputStream that facilitates error logging
* @param metaId optional metaId, if set only the rdf annotation for this metaId will be returned.
*
* @if notclike @note Because this is a @em static method, the non-C++
* language interfaces for libSBML will contain two variants. One will
* be a static method on the class (i.e., RDFAnnotationParser), and the
* other will be a standalone top-level function with the name
* RDFAnnotationParser_parseRDFAnnotation(). They are functionally
* identical. @endif
*
* @return a pointer to the ModelHistory created.
*/
public static ModelHistory parseRDFAnnotation(XMLNode annotation, string metaId, XMLInputStream stream)
{
IntPtr cPtr = libsbmlPINVOKE.RDFAnnotationParser_parseRDFAnnotation__SWIG_0(XMLNode.getCPtr(annotation), metaId, XMLInputStream.getCPtr(stream));
ModelHistory ret = (cPtr == IntPtr.Zero) ? null : new ModelHistory(cPtr, false);
return ret;
}
public void test_RDFAnnotation_testMissingAbout()
{
string withAbout = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" +
" <rdf:Description rdf:about=\"#_000004\">\n" +
" <bqbiol:is>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n" +
" </rdf:Bag>\n" +
" </bqbiol:is>\n" +
" </rdf:Description>\n" +
" </rdf:RDF>\n" +
" </annotation>";
string emptyAbout = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" +
" <rdf:Description rdf:about=\"\">\n" +
" <bqbiol:is>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n" +
" </rdf:Bag>\n" +
" </bqbiol:is>\n" +
" </rdf:Description>\n" +
" </rdf:RDF>\n" +
" </annotation>";
string noAbout = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" +
" <rdf:Description>\n" +
" <bqbiol:is>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n" +
" </rdf:Bag>\n" +
" </bqbiol:is>\n" +
" </rdf:Description>\n" +
" </rdf:RDF>\n" +
" </annotation>";
CVTermList cvTerms = new CVTermList();
XMLInputStream stream = new XMLInputStream ( withAbout,false );
XMLNode node = new XMLNode ( stream );
RDFAnnotationParser.parseRDFAnnotation(node,cvTerms);
assertTrue( cvTerms.getSize() == 1 );
cvTerms = new CVTermList();
RDFAnnotationParser.parseRDFAnnotation(node,cvTerms );
assertTrue( cvTerms.getSize() == 1 );
cvTerms = null;
cvTerms = null;
cvTerms = new CVTermList();
XMLInputStream stream1 = new XMLInputStream ( emptyAbout,false );
XMLNode node1 = new XMLNode ( stream1 );
RDFAnnotationParser.parseRDFAnnotation(node1,cvTerms);
assertTrue( cvTerms.getSize() == 0 );
cvTerms = null;
cvTerms = null;
cvTerms = new CVTermList();
XMLInputStream stream2 = new XMLInputStream ( noAbout,false );
XMLNode node2 = new XMLNode ( stream2 );
RDFAnnotationParser.parseRDFAnnotation(node2,cvTerms);
assertTrue( cvTerms.getSize() == 0 );
cvTerms = null;
cvTerms = null;
}
internal static HandleRef getCPtrAndDisown(XMLInputStream obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return ptr;
}
/** */
/* libsbml-internal */
public new void logError(XMLInputStream stream, XMLToken element, int code)
{
libsbmlPINVOKE.ASTBase_logError__SWIG_1(swigCPtr, XMLInputStream.getCPtr(stream), XMLToken.getCPtr(element), code);
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
/** */
/* libsbml-internal */
public new bool read(XMLInputStream stream)
{
bool ret = libsbmlPINVOKE.ASTBase_read__SWIG_1(swigCPtr, XMLInputStream.getCPtr(stream));
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
return ret;
}
bool readAttributes(XMLAttributes attributes, SWIGTYPE_p_ExpectedAttributes expectedAttributes, XMLInputStream stream, XMLToken element)
{
bool ret = libsbmlPINVOKE.ASTBase_readAttributes(swigCPtr, XMLAttributes.getCPtr(attributes), SWIGTYPE_p_ExpectedAttributes.getCPtr(expectedAttributes), XMLInputStream.getCPtr(stream), XMLToken.getCPtr(element));
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
return(ret);
}
/** */
/* libsbml-internal */
public new bool readAttributes(XMLAttributes attributes, SWIGTYPE_p_ExpectedAttributes expectedAttributes, XMLInputStream stream, XMLToken element)
{
bool ret = libsbmlPINVOKE.ASTBase_readAttributes(swigCPtr, XMLAttributes.getCPtr(attributes), SWIGTYPE_p_ExpectedAttributes.getCPtr(expectedAttributes), XMLInputStream.getCPtr(stream), XMLToken.getCPtr(element));
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
return ret;
}
/**
* Creates a new XMLNode by reading XMLTokens from stream.
*
* The stream must be positioned on a start element
* (<code>stream.peek().isStart() == true</code>) and will be read until
* the matching end element is found.
*
* @param stream XMLInputStream from which XMLNode is to be created.
*/
/* libsbml-internal */
public XMLNode(XMLInputStream stream)
: this(libsbmlPINVOKE.new_XMLNode__SWIG_14(XMLInputStream.getCPtr(stream)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
/** */
/* libsbml-internal */
public bool read(XMLInputStream stream, string reqd_prefix)
{
bool ret = libsbmlPINVOKE.ASTNode_read__SWIG_0(swigCPtr, XMLInputStream.getCPtr(stream), reqd_prefix);
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
return ret;
}