public void test_XMLToken_newSetters_addAttributes1()
{
XMLTriple triple = new XMLTriple("test","","");
XMLAttributes attr = new XMLAttributes();
XMLToken token = new XMLToken(triple,attr);
XMLTriple xt2 = new XMLTriple("name3", "http://name3.org/", "p3");
int i = token.addAttr( "name1", "val1");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( token.getAttributesLength() == 1 );
assertTrue( token.isAttributesEmpty() == false );
assertTrue( ( "name1" != token.getAttrName(0) ) == false );
assertTrue( ( "val1" != token.getAttrValue(0) ) == false );
i = token.addAttr( "name2", "val2", "http://name1.org/", "p1");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( token.getAttributesLength() == 2 );
assertTrue( token.isAttributesEmpty() == false );
assertTrue( ( "name2" != token.getAttrName(1) ) == false );
assertTrue( ( "val2" != token.getAttrValue(1) ) == false );
assertTrue( ( "http://name1.org/" != token.getAttrURI(1) ) == false );
assertTrue( ( "p1" != token.getAttrPrefix(1) ) == false );
i = token.addAttr(xt2, "val2");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( token.getAttributesLength() == 3 );
assertTrue( token.isAttributesEmpty() == false );
assertTrue( ( "name3" != token.getAttrName(2) ) == false );
assertTrue( ( "val2" != token.getAttrValue(2) ) == false );
assertTrue( ( "http://name3.org/" != token.getAttrURI(2) ) == false );
assertTrue( ( "p3" != token.getAttrPrefix(2) ) == false );
xt2 = null;
triple = null;
attr = null;
token = null;
}
public void test_Node_clone()
{
XMLAttributes att = new XMLAttributes();
XMLTriple t = new XMLTriple("sarah", "http://foo.org/", "bar");
XMLToken token = new XMLToken(t,att,3,4);
XMLNode node = new XMLNode(token);
XMLNode child = new XMLNode();
node.addChild(child);
assertTrue( node.getNumChildren() == 1 );
assertTrue( node.getName() == "sarah" );
assertTrue( node.getURI() == "http://foo.org/" );
assertTrue( node.getPrefix() == "bar" );
assertTrue( node.isEnd() == false );
assertTrue( node.isEOF() == false );
assertTrue( node.getLine() == 3 );
assertTrue( node.getColumn() == 4 );
XMLNode node2 = (XMLNode) node.clone();
assertTrue( node2.getNumChildren() == 1 );
assertTrue( node2.getName() == "sarah" );
assertTrue( node2.getURI() == "http://foo.org/" );
assertTrue( node2.getPrefix() == "bar" );
assertTrue( node2.isEnd() == false );
assertTrue( node2.isEOF() == false );
assertTrue( node2.getLine() == 3 );
assertTrue( node2.getColumn() == 4 );
t = null;
token = null;
node = null;
node2 = null;
}
public void test_SyntaxChecker_validXHTML()
{
SBMLNamespaces NS24 = new SBMLNamespaces(2,4);
SBMLNamespaces NS31 = new SBMLNamespaces(3,1);
XMLToken toptoken;
XMLNode topnode;
XMLTriple toptriple = new XMLTriple("notes", "", "");
XMLToken token;
XMLNode node;
XMLTriple triple = new XMLTriple("p", "", "");
XMLAttributes att = new XMLAttributes();
XMLNamespaces ns = new XMLNamespaces();
ns.add( "http://www.w3.org/1999/xhtml", "");
XMLToken tt = new XMLToken("This is my text");
XMLNode n1 = new XMLNode(tt);
toptoken = new XMLToken(toptriple,att);
topnode = new XMLNode(toptoken);
token = new XMLToken(triple,att,ns);
node = new XMLNode(token);
node.addChild(n1);
topnode.addChild(node);
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,null) == true );
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == true );
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == true );
triple = new XMLTriple("html", "", "");
token = new XMLToken(triple,att,ns);
node = new XMLNode(token);
node.addChild(n1);
topnode.removeChild(0);
topnode.addChild(node);
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,null) == true );
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == false );
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == true );
triple = new XMLTriple("html", "", "");
ns.clear();
token = new XMLToken(triple,att,ns);
node = new XMLNode(token);
node.addChild(n1);
topnode.removeChild(0);
topnode.addChild(node);
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,null) == false );
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == false );
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == false );
}
public void test_XMLToken_newSetters_addAttributes2()
{
XMLTriple triple = new XMLTriple("test","","");
XMLToken token = new XMLToken(triple);
XMLTriple xt2 = new XMLTriple("name3", "http://name3.org/", "p3");
int i = token.addAttr( "name1", "val1");
assertTrue( i == libsbml.LIBSBML_INVALID_XML_OPERATION );
assertTrue( token.getAttributesLength() == 0 );
assertTrue( token.isAttributesEmpty() == true );
i = token.addAttr( "name2", "val2", "http://name1.org/", "p1");
assertTrue( i == libsbml.LIBSBML_INVALID_XML_OPERATION );
assertTrue( token.getAttributesLength() == 0 );
assertTrue( token.isAttributesEmpty() == true );
i = token.addAttr(xt2, "val2");
assertTrue( i == libsbml.LIBSBML_INVALID_XML_OPERATION );
assertTrue( token.getAttributesLength() == 0 );
assertTrue( token.isAttributesEmpty() == true );
xt2 = null;
triple = null;
token = null;
}
public void test_CVTerm_createFromNode()
{
XMLAttributes xa;
XMLTriple qual_triple = new XMLTriple("is", "", "bqbiol");
XMLTriple bag_triple = new XMLTriple();
XMLTriple li_triple = new XMLTriple();
XMLAttributes att = new XMLAttributes();
att.add( "", "This is my resource");
XMLAttributes att1 = new XMLAttributes();
XMLToken li_token = new XMLToken(li_triple,att);
XMLToken bag_token = new XMLToken(bag_triple,att1);
XMLToken qual_token = new XMLToken(qual_triple,att1);
XMLNode li = new XMLNode(li_token);
XMLNode bag = new XMLNode(bag_token);
XMLNode node = new XMLNode(qual_token);
bag.addChild(li);
node.addChild(bag);
CVTerm term = new CVTerm(node);
assertTrue( term != null );
assertTrue( term.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER );
assertTrue( term.getBiologicalQualifierType() == libsbml.BQB_IS );
xa = term.getResources();
assertTrue( xa.getLength() == 1 );
assertTrue(( "rdf:resource" == xa.getName(0) ));
assertTrue(( "This is my resource" == xa.getValue(0) ));
qual_triple = null;
bag_triple = null;
li_triple = null;
li_token = null;
bag_token = null;
qual_token = null;
att = null;
att1 = null;
term = null;
node = null;
bag = null;
li = null;
}
/** */
/* 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;
}
/** */
/* 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();
}
public void test_SBase_appendAnnotation()
{
XMLToken token;
XMLNode node;
XMLToken token1;
XMLNode node1;
XMLToken token_top;
XMLNode node_top;
XMLTriple triple = new XMLTriple("any", "", "pr");
XMLAttributes att = new XMLAttributes();
XMLNamespaces ns = new XMLNamespaces();
ns.add("http://www.any", "pr");
XMLToken token_top1;
XMLNode node_top1;
XMLTriple triple1 = new XMLTriple("anyOther", "", "prOther");
XMLNamespaces ns1 = new XMLNamespaces();
ns1.add("http://www.any.other", "prOther");
token = new XMLToken("This is a test note");
node = new XMLNode(token);
token1 = new XMLToken("This is additional");
node1 = new XMLNode(token1);
token_top = new XMLToken(triple, att, ns);
node_top = new XMLNode(token_top);
node_top.addChild(node);
token_top1 = new XMLToken(triple1, att, ns1);
node_top1 = new XMLNode(token_top1);
node_top1.addChild(node1);
int i = S.setAnnotation(node_top);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
i = S.appendAnnotation(node_top1);
XMLNode t1 = S.getAnnotation();
assertTrue( t1.getNumChildren() == 2 );
assertTrue(( "This is a test note" == t1.getChild(0).getChild(0).getCharacters() ));
assertTrue(( "This is additional" == t1.getChild(1).getChild(0).getCharacters() ));
}
/**
* Creates a new XMLNode by copying token.
*
* @param token XMLToken to be copied to XMLNode
*/
public XMLNode(XMLToken token)
: this(libsbmlPINVOKE.new_XMLNode__SWIG_1(XMLToken.getCPtr(token)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
/**
* Consume zero or more tokens up to and including the corresponding end
* element or EOF.
*
* @param element the element whose end will be sought in the input stream.
*/
public void skipPastEnd(XMLToken element)
{
libsbmlPINVOKE.XMLInputStream_skipPastEnd(swigCPtr, XMLToken.getCPtr(element));
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
/**
* Returns the next token on this XML input stream.
*
* The token is consumed in the process.
*
* @return the next XMLToken, or an EOF token (i.e.,
* <code>XMLToken.isEOF() == true</code>).
*
* @see peek()
*/
public XMLToken next()
{
XMLToken ret = new XMLToken(libsbmlPINVOKE.XMLInputStream_next(swigCPtr), true);
return ret;
}
internal static HandleRef getCPtrAndDisown(XMLToken obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return ptr;
}
public void test_XMLToken_newSetters_setTriple1()
{
XMLTriple triple = new XMLTriple("test","","");
XMLToken token = new XMLToken();
int i = token.setTriple(triple);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue(( "test" == token.getName() ));
triple = null;
token = null;
}
public void test_XMLToken_newSetters_setNamespaces2()
{
int i;
XMLTriple triple = new XMLTriple("test","","");
XMLToken token = new XMLToken(triple);
XMLNamespaces ns = new XMLNamespaces();
assertTrue( token.getNamespacesLength() == 0 );
assertTrue( token.isNamespacesEmpty() == true );
ns.add( "http://test1.org/", "test1");
i = token.setNamespaces(ns);
assertTrue( i == libsbml.LIBSBML_INVALID_XML_OPERATION );
assertTrue( token.getNamespacesLength() == 0 );
assertTrue( token.isNamespacesEmpty() == true );
triple = null;
token = null;
ns = null;
}
public void test_XMLToken_newSetters_setEOF()
{
XMLToken token = new XMLToken();
assertTrue( token.isEnd() == false );
int i = token.setEOF();
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( token.isEnd() == false );
assertTrue( token.isStart() == false );
assertTrue( token.isText() == false );
token = null;
}
public void test_XMLToken_newSetters_setAttributes2()
{
int i ;
XMLTriple triple = new XMLTriple("test","","");
XMLToken token = new XMLToken(triple);
XMLAttributes nattr = new XMLAttributes();
XMLTriple xt1 = new XMLTriple("name1", "http://name1.org/", "p1");
nattr.add(xt1, "val1");
i = token.setAttributes(nattr);
assertTrue( i == libsbml.LIBSBML_INVALID_XML_OPERATION );
assertTrue( token.isAttributesEmpty() == true );
nattr = null;
triple = null;
token = null;
xt1 = null;
}
public void test_XMLToken_newSetters_setAttributes1()
{
XMLTriple triple = new XMLTriple("test","","");
XMLAttributes attr = new XMLAttributes();
XMLToken token = new XMLToken(triple,attr);
XMLAttributes nattr = new XMLAttributes();
XMLTriple xt1 = new XMLTriple("name1", "http://name1.org/", "p1");
nattr.add(xt1, "val1");
int i = token.setAttributes(nattr);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( token.isAttributesEmpty() == false );
nattr = null;
attr = null;
triple = null;
token = null;
xt1 = null;
}
public void test_XMLToken_newSetters_removeNamespaces1()
{
XMLTriple triple = new XMLTriple("test","","");
XMLAttributes attr = new XMLAttributes();
XMLToken token = new XMLToken(triple,attr);
token.addNamespace( "http://test1.org/", "test1");
assertTrue( token.getNamespacesLength() == 1 );
int i = token.removeNamespace( "test2");
assertTrue( i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE );
assertTrue( token.getNamespacesLength() == 1 );
i = token.removeNamespace( "test1");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( token.getNamespacesLength() == 0 );
token = null;
triple = null;
attr = null;
}
public void test_XMLToken_newSetters_removeAttributes1()
{
XMLTriple triple = new XMLTriple("test","","");
XMLAttributes attr = new XMLAttributes();
XMLToken token = new XMLToken(triple,attr);
XMLTriple xt2 = new XMLTriple("name3", "http://name3.org/", "p3");
XMLTriple xt1 = new XMLTriple("name5", "http://name5.org/", "p5");
int i = token.addAttr( "name1", "val1");
i = token.addAttr( "name2", "val2", "http://name1.org/", "p1");
i = token.addAttr(xt2, "val2");
i = token.addAttr( "name4", "val4");
assertTrue( token.getAttributes().getLength() == 4 );
i = token.removeAttr(7);
assertTrue( i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE );
i = token.removeAttr( "name7");
assertTrue( i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE );
i = token.removeAttr( "name7", "namespaces7");
assertTrue( i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE );
i = token.removeAttr(xt1);
assertTrue( i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE );
assertTrue( token.getAttributes().getLength() == 4 );
i = token.removeAttr(3);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( token.getAttributes().getLength() == 3 );
i = token.removeAttr( "name1");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( token.getAttributes().getLength() == 2 );
i = token.removeAttr( "name2", "http://name1.org/");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( token.getAttributes().getLength() == 1 );
i = token.removeAttr(xt2);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( token.getAttributes().getLength() == 0 );
xt1 = null;
xt2 = null;
triple = null;
attr = null;
token = null;
}
/**
* Predicate returning @c true or @c false depending on whether
* this XMLToken is an XML end element for the given start element.
*
* @param element XMLToken, element for which query is made.
*
* @return @c true if this XMLToken is an XML end element for the given
* XMLToken start element, @c false otherwise.
*/
public bool isEndFor(XMLToken element)
{
bool ret = libsbmlPINVOKE.XMLToken_isEndFor(swigCPtr, XMLToken.getCPtr(element));
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
return ret;
}
internal static HandleRef getCPtr(XMLToken obj)
{
return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
}
public void test_XMLToken_newSetters_setTriple2()
{
int i;
XMLTriple triple = new XMLTriple("test","","");
XMLToken token = new XMLToken("This is text");
i = token.setTriple(triple);
assertTrue( i == libsbml.LIBSBML_INVALID_XML_OPERATION );
triple = null;
token = null;
}
/**
* Copy constructor; creates a copy of this XMLToken.
*
* @param orig the XMLToken object to copy.
*
* @throws XMLConstructorException
* Thrown if the argument @p orig is @c null.
*/
public XMLToken(XMLToken orig)
: this(libsbmlPINVOKE.new_XMLToken__SWIG_13(XMLToken.getCPtr(orig)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
public void test_SBase_appendNotes()
{
XMLToken token;
XMLNode node;
XMLToken token1;
XMLNode node1;
XMLNode node2;
XMLTriple triple = new XMLTriple("p", "", "");
XMLAttributes att = new XMLAttributes();
XMLNamespaces ns = new XMLNamespaces();
ns.add( "http://www.w3.org/1999/xhtml", "");
XMLToken token4 = new XMLToken("This is my text");
XMLNode node4 = new XMLNode(token4);
XMLToken token5 = new XMLToken("This is additional text");
XMLNode node5 = new XMLNode(token5);
token = new XMLToken(triple,att,ns);
node = new XMLNode(token);
node.addChild(node4);
int i = S.setNotes(node);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( S.isSetNotes() == true );
token1 = new XMLToken(triple,att,ns);
node1 = new XMLNode(token1);
node1.addChild(node5);
i = S.appendNotes(node1);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( S.isSetNotes() == true );
node2 = S.getNotes();
assertTrue( node2.getNumChildren() == 2 );
assertTrue(( "p" == node2.getChild(0).getName() ));
assertTrue( node2.getChild(0).getNumChildren() == 1 );
assertTrue(( "p" == node2.getChild(1).getName() ));
assertTrue( node2.getChild(1).getNumChildren() == 1 );
string chars1 = node2.getChild(0).getChild(0).getCharacters();
string chars2 = node2.getChild(1).getChild(0).getCharacters();
assertTrue(( "This is my text" == chars1 ));
assertTrue(( "This is additional text" == chars2 ));
node = null;
node1 = null;
}
/**
* Returns the next token @em without consuming it.
*
* A subsequent call to either peek() or next() will return the same token.
*
* @return the next XMLToken or EOF (XMLToken.isEOF() == true).
*
* @see next()
*/
public XMLToken peek()
{
XMLToken ret = new XMLToken(libsbmlPINVOKE.XMLInputStream_peek(swigCPtr), false);
return ret;
}
public void test_SBase_appendAnnotationString()
{
XMLToken token;
XMLNode node;
token = new XMLToken("This is a test note");
node = new XMLNode(token);
XMLToken token_top;
XMLNode node_top;
XMLTriple triple = new XMLTriple("any", "", "pr");
XMLAttributes att = new XMLAttributes();
XMLNamespaces ns = new XMLNamespaces();
ns.add("http://www.any", "pr");
token_top = new XMLToken(triple, att, ns);
node_top = new XMLNode(token_top);
node_top.addChild(node);
int i = S.setAnnotation(node_top);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
i = S.appendAnnotation("<prA:other xmlns:prA=\"http://some\">This is additional</prA:other>");
XMLNode t1 = S.getAnnotation();
assertTrue( t1.getNumChildren() == 2 );
assertTrue(( "This is a test note" == t1.getChild(0).getChild(0).getCharacters() ));
XMLNode c1 = t1.getChild(1);
assertTrue( c1.getNumChildren() == 1 );
assertTrue(( "This is additional" == c1.getChild(0).getCharacters() ));
}
public void test_XMLToken_newSetters_addNamespaces1()
{
XMLTriple triple = new XMLTriple("test","","");
XMLAttributes attr = new XMLAttributes();
XMLToken token = new XMLToken(triple,attr);
assertTrue( token.getNamespacesLength() == 0 );
assertTrue( token.isNamespacesEmpty() == true );
int i = token.addNamespace( "http://test1.org/", "test1");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( token.getNamespacesLength() == 1 );
assertTrue( token.isNamespacesEmpty() == false );
attr = null;
triple = null;
token = null;
}
public static int Main(string[] args)
{
if (args.Length != 2)
{
Console.WriteLine(" usage: addingEvidenceCodes_2 <input-filename> <output-filename>");
Console.WriteLine(" Adds controlled vocabulary term to a species");
Console.WriteLine();
return 2;
}
SBMLDocument d = libsbml.readSBML(args[0]);
long errors = d.getNumErrors();
if (errors > 0)
{
Console.WriteLine("Read Error(s):");
d.printErrors();
Console.WriteLine("Correct the above and re-run.");
}
else
{
long n = d.getModel().getNumSpecies();
if (n <= 0)
{
Console.WriteLine("Model has no species.\n Cannot add CV terms\n");
}
else
{
Species s = d.getModel().getSpecies(0);
/* check that the species has a metaid
* no CVTerms will be added if there is no metaid to reference
*/
if (!s.isSetMetaId())
s.setMetaId("metaid_0000052");
CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv1.setBiologicalQualifierType(libsbml.BQB_OCCURS_IN);
cv1.addResource("urn:miriam:obo.go:GO%3A0005764");
s.addCVTerm(cv1);
// now create the additional annotation
//<rdf:Statement>
// <rdf:subject rdf:resource="#metaid_0000052"/>
// <rdf:predicate rdf:resource="http://biomodels.net/biology-qualifiers/occursIn"/>
// <rdf:object rdf:resource="urn:miriam:obo.go:GO%3A0005764"/>
// <bqbiol:isDescribedBy>
// <rdf:Bag>
// <rdf:li rdf:resource="urn:miriam:obo.eco:ECO%3A0000004"/>
// <rdf:li rdf:resource="urn:miriam:pubmed:7017716"/>
// </rdf:Bag>
// </bqbiol:isDescribedBy>
//</rdf:Statement>
/* attributes */
XMLAttributes blank_att = new XMLAttributes();
XMLAttributes resource_att = new XMLAttributes();
/* create the outer statement node */
XMLTriple statement_triple = new XMLTriple("Statement",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
XMLToken statement_token = new XMLToken(statement_triple, blank_att);
XMLNode statement = new XMLNode(statement_token);
/*create the subject node */
XMLTriple subject_triple = new XMLTriple("subject",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.clear();
resource_att.add("rdf:resource", "#" + s.getMetaId());
XMLToken subject_token = new XMLToken(subject_triple, resource_att);
XMLNode subject = new XMLNode(subject_token);
/*create the predicate node */
XMLTriple predicate_triple = new XMLTriple("predicate",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.clear();
resource_att.add("rdf:resource",
"http://biomodels.net/biology-qualifiers/occursIn");
XMLToken predicate_token = new XMLToken(predicate_triple, resource_att);
XMLNode predicate = new XMLNode(predicate_token);
/*create the object node */
XMLTriple object_triple = new XMLTriple("object",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:obo.go:GO%3A0005764");
XMLToken object_token = new XMLToken(object_triple, resource_att);
XMLNode object_ = new XMLNode(object_token);
/* create the bqbiol node */
XMLTriple bqbiol_triple = new XMLTriple("isDescribedBy",
"http://biomodels.net/biology-qualifiers/",
"bqbiol");
XMLToken bqbiol_token = new XMLToken(bqbiol_triple, blank_att);
XMLNode bqbiol = new XMLNode(bqbiol_token);
/* create the bag node */
XMLTriple bag_triple = new XMLTriple("Bag",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
XMLToken bag_token = new XMLToken(bag_triple, blank_att);
XMLNode bag = new XMLNode(bag_token);
/* create each li node and add to the bag */
XMLTriple li_triple = new XMLTriple("li",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:obo.eco:ECO%3A0000004");
XMLToken li_token = new XMLToken(li_triple, resource_att);
li_token.setEnd();
XMLNode li = new XMLNode(li_token);
bag.addChild(li);
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:pubmed:7017716");
li_token = new XMLToken(li_triple, resource_att);
li_token.setEnd();
li = new XMLNode(li_token);
bag.addChild(li);
/* add the bag to bqbiol */
bqbiol.addChild(bag);
/* add subject, predicate, object and bqbiol to statement */
statement.addChild(subject);
statement.addChild(predicate);
statement.addChild(object_);
statement.addChild(bqbiol);
/* create a top-level RDF element
* this will ensure correct merging
*/
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
xmlns.add("http://purl.org/dc/elements/1.1/", "dc");
xmlns.add("http://purl.org/dc/terms/", "dcterms");
xmlns.add("http://www.w3.org/2001/vcard-rdf/3.0#", "vCard");
xmlns.add("http://biomodels.net/biology-qualifiers/", "bqbiol");
xmlns.add("http://biomodels.net/model-qualifiers/", "bqmodel");
XMLTriple RDF_triple = new XMLTriple("RDF",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdf");
XMLToken RDF_token = new XMLToken(RDF_triple, blank_att, xmlns);
XMLNode annotation = new XMLNode(RDF_token);
/* add the staement node to the RDF node */
annotation.addChild(statement);
s.appendAnnotation(annotation);
libsbml.writeSBML(d, args[1]);
}
}
return (int)errors;
}
/** */
/* libsbml-internal */
public string checkMathMLNamespace(XMLToken elem)
{
string ret = libsbmlPINVOKE.SBase_checkMathMLNamespace(swigCPtr, XMLToken.getCPtr(elem));
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
return ret;
}
public void test_SBase_appendNotes8()
{
XMLAttributes att = new XMLAttributes();
XMLNamespaces ns = new XMLNamespaces();
ns.add( "http://www.w3.org/1999/xhtml", "");
XMLTriple body_triple = new XMLTriple("body", "", "");
XMLTriple p_triple = new XMLTriple("p", "", "");
XMLToken body_token = new XMLToken(body_triple,att,ns);
XMLToken p_token = new XMLToken(p_triple,att);
XMLToken text_token = new XMLToken("This is my text");
XMLNode body_node = new XMLNode(body_token);
XMLNode p_node = new XMLNode(p_token);
XMLNode text_node = new XMLNode(text_token);
XMLToken p_token1 = new XMLToken(p_triple,att,ns);
XMLToken text_token1 = new XMLToken("This is more text");
XMLNode p_node1 = new XMLNode(p_token1);
XMLNode text_node1 = new XMLNode(text_token1);
XMLNode notes;
XMLNode child, child1;
p_node.addChild(text_node);
body_node.addChild(p_node);
p_node1.addChild(text_node1);
int i = S.setNotes(body_node);
i = S.appendNotes(p_node1);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
notes = S.getNotes();
assertTrue(( "notes" == notes.getName() ));
assertTrue( notes.getNumChildren() == 1 );
child = notes.getChild(0);
assertTrue(( "body" == child.getName() ));
assertTrue( child.getNumChildren() == 2 );
child1 = child.getChild(0);
assertTrue(( "p" == child1.getName() ));
assertTrue( child1.getNumChildren() == 1 );
child1 = child1.getChild(0);
assertTrue(( "This is my text" == child1.getCharacters() ));
assertTrue( child1.getNumChildren() == 0 );
child1 = child.getChild(1);
assertTrue(( "p" == child1.getName() ));
assertTrue( child1.getNumChildren() == 1 );
child1 = child1.getChild(0);
assertTrue(( "This is more text" == child1.getCharacters() ));
assertTrue( child1.getNumChildren() == 0 );
att = null;
ns = null;
body_triple = null;
p_triple = null;
body_token = null;
p_token = null;
text_token = null;
text_token1 = null;
p_token1 = null;
body_node = null;
p_node = null;
text_node = null;
p_node1 = null;
text_node1 = null;
}
