public void test_Node_copyConstructor()
{
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 = new XMLNode(node);
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_Constraint_setMessage2()
{
XMLNode text = XMLNode.convertStringToXMLNode(" Some text ", null);
XMLTriple triple = new XMLTriple("p", "http://www.w3.org/1999/xhtml", "");
XMLAttributes att = new XMLAttributes();
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.w3.org/1999/xhtml", "");
XMLNode p = new XMLNode(triple, att, xmlns);
p.addChild(text);
XMLTriple triple1 = new XMLTriple("message", "", "");
XMLAttributes att1 = new XMLAttributes();
XMLNode node = new XMLNode(triple1, att1);
node.addChild(p);
int i = C.setMessage(node);
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(C.isSetMessage() == true);
i = C.unsetMessage();
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertEquals(false, C.isSetMessage());
if (C.getMessage() != null)
{
;
}
{
}
node = 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_XMLNode_removeChildren()
{
XMLNode node = new XMLNode();
XMLNode node2 = new XMLNode();
XMLNode node3 = new XMLNode();
node.addChild(node2);
node.addChild(node3);
assertTrue(node.getNumChildren() == 2);
int i = node.removeChildren();
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
assertTrue(node.getNumChildren() == 0);
node = null;
node2 = null;
node3 = null;
}
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;
}
public void test_XMLNode_create()
{
XMLNode node = new XMLNode();
assertTrue(node != null);
assertTrue(node.getNumChildren() == 0);
node = null;
node = new XMLNode();
assertTrue(node != null);
XMLNode node2 = new XMLNode();
assertTrue(node2 != null);
node.addChild(node2);
assertTrue(node.getNumChildren() == 1);
XMLNode node3 = new XMLNode();
assertTrue(node3 != null);
node.addChild(node3);
assertTrue(node.getNumChildren() == 2);
node = null;
node2 = null;
node3 = null;
}
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_Constraint_assignmentOperator()
{
Constraint o1 = new Constraint(2, 4);
o1.setMetaId("c");
assertTrue(o1.getMetaId() == "c");
XMLNode text = XMLNode.convertStringToXMLNode(" Some text ");
XMLTriple triple = new XMLTriple("p", "http://www.w3.org/1999/xhtml", "");
XMLAttributes att = new XMLAttributes();
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.w3.org/1999/xhtml");
XMLNode p = new XMLNode(triple, att, xmlns);
p.addChild(text);
XMLTriple triple1 = new XMLTriple("message", "", "");
XMLAttributes att1 = new XMLAttributes();
XMLNode message = new XMLNode(triple1, att1);
message.addChild(p);
ASTNode math = new ASTNode(libsbml.AST_CONSTANT_PI);
o1.setMath(math);
o1.setMessage(message);
math = null;
message = null;
XMLNode msg;
assertTrue(o1.getMath() != null);
msg = o1.getMessage();
assertTrue(msg != null);
Constraint o2 = new Constraint(2, 4);
o2 = o1;
assertTrue(o2.getMetaId() == "c");
assertTrue(o2.getMath() != null);
msg = o2.getMessage();
assertTrue(msg != null);
assertTrue(o2.getParentSBMLObject() == o1.getParentSBMLObject());
o2 = null;
o1 = 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;
}
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);
}
public void test_XMLNode_remove()
{
XMLAttributes attr = new XMLAttributes();
XMLTriple trp_p = new XMLTriple("parent", "", "");
XMLTriple trp_c1 = new XMLTriple("child1", "", "");
XMLTriple trp_c2 = new XMLTriple("child2", "", "");
XMLTriple trp_c3 = new XMLTriple("child3", "", "");
XMLTriple trp_c4 = new XMLTriple("child4", "", "");
XMLTriple trp_c5 = new XMLTriple("child5", "", "");
XMLNode p = new XMLNode(trp_p, attr);
XMLNode c1 = new XMLNode(trp_c1, attr);
XMLNode c2 = new XMLNode(trp_c2, attr);
XMLNode c3 = new XMLNode(trp_c3, attr);
XMLNode c4 = new XMLNode(trp_c4, attr);
XMLNode c5 = new XMLNode(trp_c5, attr);
XMLNode r;
p.addChild(c1);
p.addChild(c2);
p.addChild(c3);
p.addChild(c4);
p.addChild(c5);
r = p.removeChild(5);
assertTrue(r == null);
r = p.removeChild(1);
assertTrue(p.getNumChildren() == 4);
assertTrue(("child2" != r.getName()) == false);
r = null;
r = p.removeChild(3);
assertTrue(p.getNumChildren() == 3);
assertTrue(("child5" != r.getName()) == false);
r = null;
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 2);
assertTrue(("child1" != r.getName()) == false);
r = null;
r = p.removeChild(1);
assertTrue(p.getNumChildren() == 1);
assertTrue(("child4" != r.getName()) == false);
r = null;
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 0);
assertTrue(("child3" != r.getName()) == false);
r = null;
p.addChild(c1);
p.addChild(c2);
p.addChild(c3);
p.addChild(c4);
p.addChild(c5);
r = p.removeChild(4);
assertTrue(p.getNumChildren() == 4);
assertTrue(("child5" != r.getName()) == false);
r = null;
r = p.removeChild(3);
assertTrue(p.getNumChildren() == 3);
assertTrue(("child4" != r.getName()) == false);
r = null;
r = p.removeChild(2);
assertTrue(p.getNumChildren() == 2);
assertTrue(("child3" != r.getName()) == false);
r = null;
r = p.removeChild(1);
assertTrue(p.getNumChildren() == 1);
assertTrue(("child2" != r.getName()) == false);
r = null;
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 0);
assertTrue(("child1" != r.getName()) == false);
r = null;
p.addChild(c1);
p.addChild(c2);
p.addChild(c3);
p.addChild(c4);
p.addChild(c5);
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 4);
assertTrue(("child1" != r.getName()) == false);
r = null;
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 3);
assertTrue(("child2" != r.getName()) == false);
r = null;
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 2);
assertTrue(("child3" != r.getName()) == false);
r = null;
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 1);
assertTrue(("child4" != r.getName()) == false);
r = null;
r = p.removeChild(0);
assertTrue(p.getNumChildren() == 0);
assertTrue(("child5" != r.getName()) == false);
r = null;
p.addChild(c1);
p.addChild(c2);
p.addChild(c3);
p.addChild(c4);
p.addChild(c5);
r = p.removeChild(0);
assertTrue(("child1" != r.getName()) == false);
p.insertChild(0, r);
assertTrue(p.getNumChildren() == 5);
assertTrue(("child1" != p.getChild(0).getName()) == false);
r = null;
r = p.removeChild(1);
assertTrue(("child2" != r.getName()) == false);
p.insertChild(1, r);
assertTrue(p.getNumChildren() == 5);
assertTrue(("child2" != p.getChild(1).getName()) == false);
r = null;
r = p.removeChild(2);
assertTrue(("child3" != r.getName()) == false);
p.insertChild(2, r);
assertTrue(p.getNumChildren() == 5);
assertTrue(("child3" != p.getChild(2).getName()) == false);
r = null;
r = p.removeChild(3);
assertTrue(("child4" != r.getName()) == false);
p.insertChild(3, r);
assertTrue(p.getNumChildren() == 5);
assertTrue(("child4" != p.getChild(3).getName()) == false);
r = null;
r = p.removeChild(4);
assertTrue(("child5" != r.getName()) == false);
p.insertChild(4, r);
assertTrue(p.getNumChildren() == 5);
assertTrue(("child5" != p.getChild(4).getName()) == false);
r = null;
p = null;
c1 = null;
c2 = null;
c3 = null;
c4 = null;
c5 = null;
attr = null;
trp_p = null;
trp_c1 = null;
trp_c2 = null;
trp_c3 = null;
trp_c4 = null;
trp_c5 = null;
}
public void test_XMLNode_insert()
{
XMLAttributes attr = new XMLAttributes();
XMLTriple trp_p = new XMLTriple("parent", "", "");
XMLTriple trp_c1 = new XMLTriple("child1", "", "");
XMLTriple trp_c2 = new XMLTriple("child2", "", "");
XMLTriple trp_c3 = new XMLTriple("child3", "", "");
XMLTriple trp_c4 = new XMLTriple("child4", "", "");
XMLTriple trp_c5 = new XMLTriple("child5", "", "");
XMLNode p = new XMLNode(trp_p, attr);
XMLNode c1 = new XMLNode(trp_c1, attr);
XMLNode c2 = new XMLNode(trp_c2, attr);
XMLNode c3 = new XMLNode(trp_c3, attr);
XMLNode c4 = new XMLNode(trp_c4, attr);
XMLNode c5 = new XMLNode(trp_c5, attr);
p.addChild(c2);
p.addChild(c4);
p.insertChild(0, c1);
p.insertChild(2, c3);
p.insertChild(4, c5);
assertTrue(p.getNumChildren() == 5);
assertTrue(("child1" != p.getChild(0).getName()) == false);
assertTrue(("child2" != p.getChild(1).getName()) == false);
assertTrue(("child3" != p.getChild(2).getName()) == false);
assertTrue(("child4" != p.getChild(3).getName()) == false);
assertTrue(("child5" != p.getChild(4).getName()) == false);
p.removeChildren();
p.insertChild(0, c1);
p.insertChild(0, c2);
p.insertChild(0, c3);
p.insertChild(0, c4);
p.insertChild(0, c5);
assertTrue(p.getNumChildren() == 5);
assertTrue(("child5" != p.getChild(0).getName()) == false);
assertTrue(("child4" != p.getChild(1).getName()) == false);
assertTrue(("child3" != p.getChild(2).getName()) == false);
assertTrue(("child2" != p.getChild(3).getName()) == false);
assertTrue(("child1" != p.getChild(4).getName()) == false);
p.removeChildren();
p.insertChild(1, c1);
p.insertChild(2, c2);
p.insertChild(3, c3);
p.insertChild(4, c4);
p.insertChild(5, c5);
assertTrue(p.getNumChildren() == 5);
assertTrue(("child1" != p.getChild(0).getName()) == false);
assertTrue(("child2" != p.getChild(1).getName()) == false);
assertTrue(("child3" != p.getChild(2).getName()) == false);
assertTrue(("child4" != p.getChild(3).getName()) == false);
assertTrue(("child5" != p.getChild(4).getName()) == false);
p.removeChildren();
XMLNode tmp;
tmp = p.insertChild(0, c1);
assertTrue(("child1" != tmp.getName()) == false);
tmp = p.insertChild(0, c2);
assertTrue(("child2" != tmp.getName()) == false);
tmp = p.insertChild(0, c3);
assertTrue(("child3" != tmp.getName()) == false);
tmp = p.insertChild(0, c4);
assertTrue(("child4" != tmp.getName()) == false);
tmp = p.insertChild(0, c5);
assertTrue(("child5" != tmp.getName()) == false);
p.removeChildren();
tmp = p.insertChild(1, c1);
assertTrue(("child1" != tmp.getName()) == false);
tmp = p.insertChild(2, c2);
assertTrue(("child2" != tmp.getName()) == false);
tmp = p.insertChild(3, c3);
assertTrue(("child3" != tmp.getName()) == false);
tmp = p.insertChild(4, c4);
assertTrue(("child4" != tmp.getName()) == false);
tmp = p.insertChild(5, c5);
assertTrue(("child5" != tmp.getName()) == false);
p = null;
c1 = null;
c2 = null;
c3 = null;
c4 = null;
c5 = null;
attr = null;
trp_p = null;
trp_c1 = null;
trp_c2 = null;
trp_c3 = null;
trp_c4 = null;
trp_c5 = null;
}