public void test_L3_LocalParameter_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
LocalParameter p = new LocalParameter(sbmlns);
assertTrue( p.getTypeCode() == libsbml.SBML_LOCAL_PARAMETER );
assertTrue( p.getMetaId() == "" );
assertTrue( p.getNotes() == null );
assertTrue( p.getAnnotation() == null );
assertTrue( p.getLevel() == 3 );
assertTrue( p.getVersion() == 1 );
assertTrue( p.getNamespaces() != null );
assertTrue( p.getNamespaces().getLength() == 2 );
assertTrue( p.getId() == "" );
assertTrue( p.getName() == "" );
assertTrue( p.getUnits() == "" );
assertEquals( true, double.IsNaN(p.getValue()) );
assertEquals( false, p.isSetId() );
assertEquals( false, p.isSetName() );
assertEquals( false, p.isSetValue() );
assertEquals( false, p.isSetUnits() );
p = null;
}
public void test_Constraint_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,2);
sbmlns.addNamespaces(xmlns);
Constraint object1 = new Constraint(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_CONSTRAINT );
assertTrue( object1.getMetaId() == "" );
assertTrue( object1.getNotes() == null );
assertTrue( object1.getAnnotation() == null );
assertTrue( object1.getLevel() == 2 );
assertTrue( object1.getVersion() == 2 );
assertTrue( object1.getNamespaces() != null );
assertTrue( object1.getNamespaces().getLength() == 2 );
object1 = null;
}
public void test_Delay_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
Delay object1 = new Delay(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_DELAY );
assertTrue( object1.getMetaId() == "" );
assertTrue( object1.getNotes() == null );
assertTrue( object1.getAnnotation() == null );
assertTrue( object1.getLevel() == 2 );
assertTrue( object1.getVersion() == 1 );
assertTrue( object1.getNamespaces() != null );
assertTrue( object1.getNamespaces().getLength() == 2 );
object1 = null;
}
public void test_StoichiometryMath_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
StoichiometryMath object1 = new StoichiometryMath(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_STOICHIOMETRY_MATH );
assertTrue( object1.getMetaId() == "" );
assertTrue( object1.getNotes() == null );
assertTrue( object1.getAnnotation() == null );
assertTrue( object1.getLevel() == 2 );
assertTrue( object1.getVersion() == 1 );
assertTrue( object1.getNamespaces() != null );
assertTrue( object1.getNamespaces().getLength() == 2 );
object1 = null;
}
public void test_EventAssignment_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
EventAssignment object1 = new EventAssignment(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_EVENT_ASSIGNMENT );
assertTrue( object1.getMetaId() == "" );
assertTrue( object1.getNotes() == null );
assertTrue( object1.getAnnotation() == null );
assertTrue( object1.getLevel() == 2 );
assertTrue( object1.getVersion() == 1 );
assertTrue( object1.getNamespaces() != null );
assertTrue( object1.getNamespaces().getLength() == 2 );
object1 = null;
}
public void test_SpeciesType_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,2);
sbmlns.addNamespaces(xmlns);
SpeciesType object1 = new SpeciesType(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_SPECIES_TYPE );
assertTrue( object1.getMetaId() == "" );
assertTrue( object1.getNotes() == null );
assertTrue( object1.getAnnotation() == null );
assertTrue( object1.getLevel() == 2 );
assertTrue( object1.getVersion() == 2 );
assertTrue( object1.getNamespaces() != null );
assertTrue( object1.getNamespaces().getLength() == 2 );
object1 = null;
}
public void test_ModifierSpeciesReference_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
SBase object1 = new ModifierSpeciesReference(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_MODIFIER_SPECIES_REFERENCE );
assertTrue( object1.getMetaId() == "" );
assertTrue( object1.getNotes() == null );
assertTrue( object1.getAnnotation() == null );
assertTrue( object1.getLevel() == 2 );
assertTrue( object1.getVersion() == 1 );
assertTrue( object1.getNamespaces() != null );
XMLNamespaces n = object1.getNamespaces();
assertTrue( n.getLength() == 2 );
object1 = 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_L3_Event_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
Event e = new Event(sbmlns);
assertTrue( e.getTypeCode() == libsbml.SBML_EVENT );
assertTrue( e.getMetaId() == "" );
assertTrue( e.getNotes() == null );
assertTrue( e.getAnnotation() == null );
assertTrue( e.getLevel() == 3 );
assertTrue( e.getVersion() == 1 );
assertTrue( e.getNamespaces() != null );
assertTrue( e.getNamespaces().getLength() == 2 );
assertTrue( e.getId() == "" );
assertTrue( e.getName() == "" );
assertTrue( e.getUseValuesFromTriggerTime() == true );
assertEquals( false, e.isSetId() );
assertEquals( false, e.isSetName() );
assertEquals( false, e.isSetUseValuesFromTriggerTime() );
e = null;
}
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() ));
}
public void test_L3_Reaction_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
Reaction r = new Reaction(sbmlns);
assertTrue( r.getTypeCode() == libsbml.SBML_REACTION );
assertTrue( r.getMetaId() == "" );
assertTrue( r.getNotes() == null );
assertTrue( r.getAnnotation() == null );
assertTrue( r.getLevel() == 3 );
assertTrue( r.getVersion() == 1 );
assertTrue( r.getNamespaces() != null );
assertTrue( r.getNamespaces().getLength() == 2 );
assertTrue( r.getId() == "" );
assertTrue( r.getName() == "" );
assertTrue( r.getCompartment() == "" );
assertTrue( r.getFast() == false );
assertTrue( r.getReversible() == true );
assertEquals( false, r.isSetId() );
assertEquals( false, r.isSetName() );
assertEquals( false, r.isSetCompartment() );
assertEquals( false, r.isSetFast() );
assertEquals( false, r.isSetReversible() );
r = null;
}
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;
}
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;
}
public void test_FunctionDefinition_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
FunctionDefinition object1 = new FunctionDefinition(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_FUNCTION_DEFINITION );
assertTrue( object1.getMetaId() == "" );
assertTrue( object1.getNotes() == null );
assertTrue( object1.getAnnotation() == null );
assertTrue( object1.getLevel() == 2 );
assertTrue( object1.getVersion() == 1 );
assertTrue( object1.getNamespaces() != null );
assertTrue( object1.getNamespaces().getLength() == 2 );
object1 = null;
}
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 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_L3_Unit_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
Unit u = new Unit(sbmlns);
assertTrue( u.getTypeCode() == libsbml.SBML_UNIT );
assertTrue( u.getMetaId() == "" );
assertTrue( u.getNotes() == null );
assertTrue( u.getAnnotation() == null );
assertTrue( u.getLevel() == 3 );
assertTrue( u.getVersion() == 1 );
assertTrue( u.getNamespaces() != null );
assertTrue( u.getNamespaces().getLength() == 2 );
assertTrue( u.getKind() == libsbml.UNIT_KIND_INVALID );
assertEquals( true, isnan(u.getExponentAsDouble()) );
assertEquals( true, isnan(u.getMultiplier()) );
assertEquals( false, u.isSetKind() );
assertEquals( false, u.isSetExponent() );
assertEquals( false, u.isSetMultiplier() );
assertEquals( false, u.isSetScale() );
u = null;
}
public void test_XMLToken_newSetters_setNamespaces1()
{
XMLTriple triple = new XMLTriple("test","","");
XMLAttributes attr = new XMLAttributes();
XMLToken token = new XMLToken(triple,attr);
XMLNamespaces ns = new XMLNamespaces();
assertTrue( token.getNamespacesLength() == 0 );
assertTrue( token.isNamespacesEmpty() == true );
ns.add( "http://test1.org/", "test1");
int i = token.setNamespaces(ns);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( token.getNamespacesLength() == 1 );
assertTrue( token.isNamespacesEmpty() == false );
attr = null;
triple = null;
token = null;
ns = null;
}
public void test_WriteSBML_Constraint_full()
{
D.setLevelAndVersion(2,2,false);
string expected = "<constraint sboTerm=\"SBO:0000064\">\n" +
" <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n" +
" <apply>\n" +
" <leq/>\n" +
" <ci> P1 </ci>\n" +
" <ci> t </ci>\n" +
" </apply>\n" +
" </math>\n" +
" <message>\n" +
" <p xmlns=\"http://www.w3.org/1999/xhtml\"> Species P1 is out of range </p>\n" +
" </message>\n" +
"</constraint>";
Constraint c = D.createModel().createConstraint();
ASTNode node = libsbml.parseFormula("leq(P1,t)");
c.setMath(node);
c.setSBOTerm(64);
XMLNode text = XMLNode.convertStringToXMLNode(" Species P1 is out of range ");
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);
c.setMessage(message);
assertEquals( true, equals(expected,c.toSBML()) );
}
public void test_AlgebraicRule_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,3);
sbmlns.addNamespaces(xmlns);
Rule r = new AlgebraicRule(sbmlns);
assertTrue( r.getTypeCode() == libsbml.SBML_ALGEBRAIC_RULE );
assertTrue( r.getMetaId() == "" );
assertTrue( r.getNotes() == null );
assertTrue( r.getAnnotation() == null );
assertTrue( r.getLevel() == 2 );
assertTrue( r.getVersion() == 3 );
assertTrue( r.getNamespaces() != null );
assertTrue( r.getNamespaces().getLength() == 2 );
r = null;
}
public void test_NS_copyConstructor()
{
XMLNamespaces ns = new XMLNamespaces();
ns.add("http://test1.org/", "test1");
assertTrue( ns.getLength() == 1 );
assertTrue( ns.isEmpty() == false );
assertTrue( ns.getPrefix(0) == "test1" );
assertTrue( ns.getURI("test1") == "http://test1.org/" );
XMLNamespaces ns2 = new XMLNamespaces(ns);
assertTrue( ns2.getLength() == 1 );
assertTrue( ns2.isEmpty() == false );
assertTrue( ns2.getPrefix(0) == "test1" );
assertTrue( ns2.getURI("test1") == "http://test1.org/" );
ns2 = null;
ns = 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_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_Compartment_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
Compartment c = new Compartment(sbmlns);
assertTrue( c.getTypeCode() == libsbml.SBML_COMPARTMENT );
assertTrue( c.getMetaId() == "" );
assertTrue( c.getNotes() == null );
assertTrue( c.getAnnotation() == null );
assertTrue( c.getLevel() == 2 );
assertTrue( c.getVersion() == 1 );
assertTrue( c.getNamespaces() != null );
assertTrue( c.getNamespaces().getLength() == 2 );
assertTrue( c.getName() == "" );
assertTrue( c.getSpatialDimensions() == 3 );
assertTrue( c.getConstant() == true );
c = null;
}
public void test_L3_SpeciesReference_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
SpeciesReference sr = new SpeciesReference(sbmlns);
assertTrue( sr.getTypeCode() == libsbml.SBML_SPECIES_REFERENCE );
assertTrue( sr.getMetaId() == "" );
assertTrue( sr.getNotes() == null );
assertTrue( sr.getAnnotation() == null );
assertTrue( sr.getLevel() == 3 );
assertTrue( sr.getVersion() == 1 );
assertTrue( sr.getNamespaces() != null );
assertTrue( sr.getNamespaces().getLength() == 2 );
assertTrue( sr.getId() == "" );
assertTrue( sr.getName() == "" );
assertTrue( sr.getSpecies() == "" );
assertEquals( true, isnan(sr.getStoichiometry()) );
assertTrue( sr.getConstant() == false );
assertEquals( false, sr.isSetId() );
assertEquals( false, sr.isSetName() );
assertEquals( false, sr.isSetSpecies() );
assertEquals( false, sr.isSetStoichiometry() );
assertEquals( false, sr.isSetConstant() );
sr = null;
}
public void test_L3_Species_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
Species s = new Species(sbmlns);
assertTrue( s.getTypeCode() == libsbml.SBML_SPECIES );
assertTrue( s.getMetaId() == "" );
assertTrue( s.getNotes() == null );
assertTrue( s.getAnnotation() == null );
assertTrue( s.getLevel() == 3 );
assertTrue( s.getVersion() == 1 );
assertTrue( s.getNamespaces() != null );
assertTrue( s.getNamespaces().getLength() == 2 );
assertTrue( s.getId() == "" );
assertTrue( s.getName() == "" );
assertTrue( s.getCompartment() == "" );
assertEquals( true, isnan(s.getInitialAmount()) );
assertEquals( true, isnan(s.getInitialConcentration()) );
assertTrue( s.getSubstanceUnits() == "" );
assertTrue( s.getHasOnlySubstanceUnits() == false );
assertTrue( s.getBoundaryCondition() == false );
assertTrue( s.getConstant() == false );
assertTrue( s.getConversionFactor() == "" );
assertEquals( false, s.isSetId() );
assertEquals( false, s.isSetName() );
assertEquals( false, s.isSetCompartment() );
assertEquals( false, s.isSetInitialAmount() );
assertEquals( false, s.isSetInitialConcentration() );
assertEquals( false, s.isSetSubstanceUnits() );
assertEquals( false, s.isSetHasOnlySubstanceUnits() );
assertEquals( false, s.isSetBoundaryCondition() );
assertEquals( false, s.isSetConstant() );
assertEquals( false, s.isSetConversionFactor() );
s = null;
}
public void test_SBase_setNamespaces()
{
XMLNamespaces ns = new XMLNamespaces();
ns.add("url", "name");
int i = S.setNamespaces(ns);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( (S).getNamespaces().getLength() == 1 );
i = S.setNamespaces(null);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( (S).getNamespaces() == null );
}
public void test_SBase_setNotes1()
{
XMLAttributes att = new XMLAttributes();
XMLNamespaces ns = new XMLNamespaces();
ns.add( "http://www.w3.org/1999/xhtml", "");
XMLTriple html_triple = new XMLTriple("html", "", "");
XMLTriple head_triple = new XMLTriple("head", "", "");
XMLTriple title_triple = new XMLTriple("title", "", "");
XMLTriple body_triple = new XMLTriple("body", "", "");
XMLTriple p_triple = new XMLTriple("p", "", "");
XMLToken html_token = new XMLToken(html_triple,att,ns);
XMLToken head_token = new XMLToken(head_triple,att);
XMLToken title_token = new XMLToken(title_triple,att);
XMLToken body_token = new XMLToken(body_triple,att);
XMLToken p_token = new XMLToken(p_triple,att);
XMLToken text_token = new XMLToken("This is my text");
XMLNode html_node = new XMLNode(html_token);
XMLNode head_node = new XMLNode(head_token);
XMLNode title_node = new XMLNode(title_token);
XMLNode body_node = new XMLNode(body_token);
XMLNode p_node = new XMLNode(p_token);
XMLNode text_node = new XMLNode(text_token);
XMLNode notes;
XMLNode child;
p_node.addChild(text_node);
body_node.addChild(p_node);
head_node.addChild(title_node);
html_node.addChild(head_node);
html_node.addChild(body_node);
int i = S.setNotes(html_node);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
notes = S.getNotes();
assertTrue(( "notes" == notes.getName() ));
assertTrue( notes.getNumChildren() == 1 );
child = notes.getChild(0);
assertTrue(( "html" == child.getName() ));
assertTrue( child.getNumChildren() == 2 );
child = child.getChild(1);
assertTrue(( "body" == child.getName() ));
assertTrue( child.getNumChildren() == 1 );
child = child.getChild(0);
assertTrue(( "p" == child.getName() ));
assertTrue( child.getNumChildren() == 1 );
child = child.getChild(0);
assertTrue(( "This is my text" == child.getCharacters() ));
assertTrue( child.getNumChildren() == 0 );
att = null;
ns = null;
html_triple = null;
head_triple = null;
body_triple = null;
p_triple = null;
html_token = null;
head_token = null;
body_token = null;
p_token = null;
text_token = null;
html_node = null;
head_node = null;
body_node = null;
p_node = null;
text_node = null;
}
public void test_L3_Model_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3,1);
sbmlns.addNamespaces(xmlns);
Model m = new Model(sbmlns);
assertTrue( m.getTypeCode() == libsbml.SBML_MODEL );
assertTrue( m.getMetaId() == "" );
assertTrue( m.getNotes() == null );
assertTrue( m.getAnnotation() == null );
assertTrue( m.getLevel() == 3 );
assertTrue( m.getVersion() == 1 );
assertTrue( m.getNamespaces() != null );
assertTrue( m.getNamespaces().getLength() == 2 );
assertTrue( m.getId() == "" );
assertTrue( m.getName() == "" );
assertTrue( m.getSubstanceUnits() == "" );
assertTrue( m.getTimeUnits() == "" );
assertTrue( m.getVolumeUnits() == "" );
assertTrue( m.getAreaUnits() == "" );
assertTrue( m.getLengthUnits() == "" );
assertTrue( m.getConversionFactor() == "" );
assertEquals( false, m.isSetId() );
assertEquals( false, m.isSetName() );
assertEquals( false, m.isSetSubstanceUnits() );
assertEquals( false, m.isSetTimeUnits() );
assertEquals( false, m.isSetVolumeUnits() );
assertEquals( false, m.isSetAreaUnits() );
assertEquals( false, m.isSetLengthUnits() );
assertEquals( false, m.isSetConversionFactor() );
m = null;
}
public void test_SBase_setNotes()
{
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);
token = new XMLToken(triple,att,ns);
node = new XMLNode(token);
node.addChild(n1);
int i = S.setNotes(node);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( S.isSetNotes() == true );
i = S.unsetNotes();
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( S.isSetNotes() == false );
token = new XMLToken("This is a test note");
node = new XMLNode(token);
i = S.setNotes(node);
assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );
assertTrue( S.isSetNotes() == false );
token = new XMLToken(triple,att,ns);
node = new XMLNode(token);
node.addChild(n1);
i = S.setNotes(node);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( S.isSetNotes() == true );
i = S.setNotes((XMLNode)null);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( S.isSetNotes() == false );
node = null;
}
