XMLNode(XMLTriple triple, long line, long column) : this(libsbmlPINVOKE.new_XMLNode__SWIG_8(XMLTriple.getCPtr(triple), line, column), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
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;
}
XMLNode(XMLTriple triple, XMLAttributes attributes) : this(libsbmlPINVOKE.new_XMLNode__SWIG_7(XMLTriple.getCPtr(triple), XMLAttributes.getCPtr(attributes)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
public void test_XMLNode_clearAttributes()
{
XMLTriple triple = new XMLTriple("test","","");
XMLAttributes attr = new XMLAttributes();
XMLNode node = new XMLNode(triple,attr);
XMLTriple xt2 = new XMLTriple("name3", "http://name3.org/", "p3");
XMLTriple xt1 = new XMLTriple("name5", "http://name5.org/", "p5");
int i = node.addAttr( "name1", "val1");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( node.getAttributes().getLength() == 1 );
i = node.addAttr( "name2", "val2", "http://name1.org/", "p1");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( node.getAttributes().getLength() == 2 );
i = node.addAttr(xt2, "val2");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( node.getAttributes().getLength() == 3 );
i = node.addAttr( "name4", "val4");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( node.getAttributes().getLength() == 4 );
i = node.clearAttributes();
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( node.getAttributes().getLength() == 0 );
xt1 = null;
xt2 = null;
triple = null;
attr = null;
node = 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;
}
XMLTriple clone()
{
IntPtr cPtr = libsbmlPINVOKE.XMLTriple_clone(swigCPtr);
XMLTriple ret = (cPtr == IntPtr.Zero) ? null : new XMLTriple(cPtr, true);
return(ret);
}
XMLTriple(XMLTriple orig) : this(libsbmlPINVOKE.new_XMLTriple__SWIG_4(XMLTriple.getCPtr(orig)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
XMLNode(XMLTriple triple) : this(libsbmlPINVOKE.new_XMLNode__SWIG_10(XMLTriple.getCPtr(triple)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
XMLNode(XMLTriple triple, XMLAttributes attributes, XMLNamespaces namespaces, long line) : this(libsbmlPINVOKE.new_XMLNode__SWIG_3(XMLTriple.getCPtr(triple), XMLAttributes.getCPtr(attributes), XMLNamespaces.getCPtr(namespaces), line), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
void writeAttribute(XMLTriple triple, int value)
{
libsbmlPINVOKE.XMLOutputStream_writeAttribute__SWIG_14(swigCPtr, XMLTriple.getCPtr(triple), value);
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
void startEndElement(XMLTriple triple)
{
libsbmlPINVOKE.XMLOutputStream_startEndElement__SWIG_2(swigCPtr, XMLTriple.getCPtr(triple));
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
}
bool hasAttribute(XMLTriple triple)
{
bool ret = libsbmlPINVOKE.XMLAttributes_hasAttribute__SWIG_3(swigCPtr, XMLTriple.getCPtr(triple));
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
return(ret);
}
int getIndex(XMLTriple triple)
{
int ret = libsbmlPINVOKE.XMLAttributes_getIndex__SWIG_2(swigCPtr, XMLTriple.getCPtr(triple));
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
return(ret);
}
int add(XMLTriple triple, string value)
{
int ret = libsbmlPINVOKE.XMLAttributes_add__SWIG_3(swigCPtr, XMLTriple.getCPtr(triple), value);
if (libsbmlPINVOKE.SWIGPendingException.Pending)
{
throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
return(ret);
}
public void test_XMLNode_addChild3()
{
XMLTriple triple = new XMLTriple("test","","");
XMLNode node = new XMLNode(triple);
XMLNode node2 = new XMLNode();
int i = node.addChild(node2);
assertTrue( i == libsbml.LIBSBML_INVALID_XML_OPERATION );
assertTrue( node.getNumChildren() == 0 );
triple = null;
node = null;
node2 = null;
}
internal static HandleRef getCPtrAndDisown(XMLTriple obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return(ptr);
}
public void test_XMLNode_addChild2()
{
XMLTriple triple = new XMLTriple("test","","");
XMLAttributes attr = new XMLAttributes();
XMLNode node = new XMLNode(triple,attr);
XMLNode node2 = new XMLNode();
int i = node.addChild(node2);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( node.getNumChildren() == 1 );
triple = null;
attr = null;
node = null;
node2 = null;
}
public void test_XMLAttributes_add1()
{
XMLAttributes xa = new XMLAttributes();
XMLTriple xt2 = new XMLTriple("name2", "http://name2.org/", "p2");
int i = xa.add( "name1", "val1", "http://name1.org/", "p1");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
i = xa.add(xt2, "val2");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( xa.getLength() == 2 );
assertTrue( xa.isEmpty() == false );
i = xa.add( "noprefix", "val3");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( xa.getLength() == 3 );
assertTrue( xa.isEmpty() == false );
xa = null;
xt2 = 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_XMLTriple_create()
{
XMLTriple t = new XMLTriple();
assertTrue( t != null );
assertTrue( t.isEmpty() != false );
t = null;
t = new XMLTriple("attr", "uri", "prefix");
assertTrue( ( "attr" != t.getName() ) == false );
assertTrue( ( "uri" != t.getURI() ) == false );
assertTrue( ( "prefix" != t.getPrefix() ) == false );
assertTrue( ( "prefix:attr" != t.getPrefixedName() ) == false );
assertTrue( t.isEmpty() == false );
t = null;
t = new XMLTriple("attr", "uri", "");
assertTrue( ( "attr" != t.getName() ) == false );
assertTrue( ( "uri" != t.getURI() ) == false );
assertTrue( t.getPrefix() == "" );
assertTrue( ( "attr" != t.getPrefixedName() ) == false );
assertTrue( t.isEmpty() == false );
t = 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;
}
/**
* Return the index of an attribute with the given XMLTriple.
*
* @param triple an XMLTriple, the XML triple of the attribute for which
* the index is required.
*
* @return the index of an attribute with the given XMLTriple, or <code>-1</code> if not present.
*/
public int getAttrIndex(XMLTriple triple)
{
int ret = libsbmlPINVOKE.XMLToken_getAttrIndex__SWIG_2(swigCPtr, XMLTriple.getCPtr(triple));
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
return ret;
}
/**
* Adds an attribute with the given XMLTriple/value pair to the attribute set
* in this XMLToken.
* Nothing will be done if this XMLToken is not a start element.
*
* @note if local name with the same namespace URI already exists in the
* attribute set, its value and prefix will be replaced.
*
* @param triple an XMLTriple, the XML triple of the attribute.
* @param value a string, the value of the attribute.
*
* @return integer value indicating success/failure of the
* function. The possible values
* returned by this function are:
* @li @link libsbmlcs#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
* @li @link libsbmlcs#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION@endlink
*/
public int addAttr(XMLTriple triple, string value)
{
int ret = libsbmlPINVOKE.XMLToken_addAttr__SWIG_3(swigCPtr, XMLTriple.getCPtr(triple), value);
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
return ret;
}
/**
* Sets the XMLTripe (name, uri and prefix) of this XML element.
* Nothing will be done if this XML element is a text node.
*
* @param triple XMLTriple to be added to this XML element.
*
* @return integer value indicating success/failure of the
* function. The possible values
* returned by this function are:
* @li @link libsbmlcs#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
* @li @link libsbmlcs#LIBSBML_OPERATION_FAILED LIBSBML_OPERATION_FAILED@endlink
* @li @link libsbmlcs#LIBSBML_INVALID_XML_OPERATION LIBSBML_INVALID_XML_OPERATION@endlink
* @li @link libsbmlcs#LIBSBML_INVALID_OBJECT LIBSBML_INVALID_OBJECT@endlink
*/
public int setTriple(XMLTriple triple)
{
int ret = libsbmlPINVOKE.XMLToken_setTriple(swigCPtr, XMLTriple.getCPtr(triple));
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
return ret;
}
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;
}
/**
* Creates an end element XMLNode.
*
* @param triple XMLTriple.
* @param line a long integer, the line number (default = 0).
* @param column a long integer, the column number (default = 0).
*
* @ifnot hasDefaultArgs @htmlinclude warn-default-args-in-docs.html @endif
*/
public XMLNode(XMLTriple triple, long line, long column)
: this(libsbmlPINVOKE.new_XMLNode__SWIG_8(XMLTriple.getCPtr(triple), line, column), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
/**
* Creates a new start element XMLNode with the given set of attributes and
* namespace declarations.
*
* @param triple XMLTriple.
* @param attributes XMLAttributes, the attributes to set.
* @param namespaces XMLNamespaces, the namespaces to set.
* @param line a long integer, the line number (default = 0).
* @param column a long integer, the column number (default = 0).
*
* @ifnot hasDefaultArgs @htmlinclude warn-default-args-in-docs.html @endif
*/
public XMLNode(XMLTriple triple, XMLAttributes attributes, XMLNamespaces namespaces, long line)
: this(libsbmlPINVOKE.new_XMLNode__SWIG_3(XMLTriple.getCPtr(triple), XMLAttributes.getCPtr(attributes), XMLNamespaces.getCPtr(namespaces), line), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
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;
}
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_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 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;
}
/**
* Removes a specific attribute from this list of attributes.
*
* @param triple an XMLTriple describing the attribute to be removed.
*
*
* @return integer value indicating success/failure of the
* function. @if clike The value is drawn from the
* enumeration #OperationReturnValues_t. @endif The possible values
* returned by this function are:
* @li @link libsbml#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
* @li @link libsbml#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE@endlink
*
* The value @link libsbml#LIBSBML_INDEX_EXCEEDS_SIZE LIBSBML_INDEX_EXCEEDS_SIZE@endlink is returned if there is no attribute matching
* the properties of the given @p triple.
*
* @see remove(int n)
* @see remove(string name, string uri)
*/
public int remove(XMLTriple triple)
{
int ret = libsbmlPINVOKE.XMLAttributes_remove__SWIG_3(swigCPtr, XMLTriple.getCPtr(triple));
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
return ret;
}
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;
}
/**
* Return a value of an attribute with the given XMLTriple.
*
* @param triple an XMLTriple, the XML triple of the attribute whose
* value is required.
*
* @return The attribute value as a string.
*
* @note If an attribute with the
* given XMLTriple does not exist, an empty string will be returned.
* Use XMLToken::hasAttr(@if java XMLTriple@endif)
* to test for attribute existence.
*/
public string getAttrValue(XMLTriple triple)
{
string ret = libsbmlPINVOKE.XMLToken_getAttrValue__SWIG_3(swigCPtr, XMLTriple.getCPtr(triple));
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
return ret;
}
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;
}
internal static HandleRef getCPtr(XMLTriple obj)
{
return((obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr);
}
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;
}
/**
* Predicate returning @c true or @c false depending on whether
* an attribute with the given XML triple exists in the attribute set in
* this XMLToken
*
* @param triple an XMLTriple, the XML triple of the attribute
*
* @return @c true if an attribute with the given XML triple exists
* in the attribute set in this XMLToken, @c false otherwise.
*
*/
public bool hasAttr(XMLTriple triple)
{
bool ret = libsbmlPINVOKE.XMLToken_hasAttr__SWIG_3(swigCPtr, XMLTriple.getCPtr(triple));
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
return ret;
}
/**
* Creates a start element XMLNode with the given set of attributes.
*
* @param triple XMLTriple.
* @param attributes XMLAttributes, the attributes to set.
* @param line a long integer, the line number (default = 0).
* @param column a long integer, the column number (default = 0).
*
* @ifnot hasDefaultArgs @htmlinclude warn-default-args-in-docs.html @endif
*/
public XMLNode(XMLTriple triple, XMLAttributes attributes)
: this(libsbmlPINVOKE.new_XMLNode__SWIG_7(XMLTriple.getCPtr(triple), XMLAttributes.getCPtr(attributes)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
/**
* Creates a start element XMLToken with the given set of attributes.
*
* @param triple XMLTriple.
* @param attributes XMLAttributes, the attributes to set.
* @param line a long integer, the line number (default = 0).
* @param column a long integer, the column number (default = 0).
*
* @ifnot hasDefaultArgs @htmlinclude warn-default-args-in-docs.html @endif
*/
public XMLToken(XMLTriple triple, XMLAttributes attributes, long line)
: this(libsbmlPINVOKE.new_XMLToken__SWIG_5(XMLTriple.getCPtr(triple), XMLAttributes.getCPtr(attributes), line), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
/**
* Creates an end element XMLNode.
*
* @param triple XMLTriple.
* @param line a long integer, the line number (default = 0).
* @param column a long integer, the column number (default = 0).
*
* @ifnot hasDefaultArgs @htmlinclude warn-default-args-in-docs.html @endif
*/
public XMLNode(XMLTriple triple)
: this(libsbmlPINVOKE.new_XMLNode__SWIG_10(XMLTriple.getCPtr(triple)), true)
{
if (libsbmlPINVOKE.SWIGPendingException.Pending) throw libsbmlPINVOKE.SWIGPendingException.Retrieve();
}
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;
}