public void test_XMLToken_namespace_set_clear()
{
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");
ns.add("http://test2.org/", "test2");
ns.add("http://test3.org/", "test3");
ns.add("http://test4.org/", "test4");
ns.add("http://test5.org/", "test5");
token.setNamespaces(ns);
assertTrue(token.getNamespacesLength() == 5);
assertTrue(token.isNamespacesEmpty() == false);
assertTrue(("test1" != token.getNamespacePrefix(0)) == false);
assertTrue(("test2" != token.getNamespacePrefix(1)) == false);
assertTrue(("test3" != token.getNamespacePrefix(2)) == false);
assertTrue(("test4" != token.getNamespacePrefix(3)) == false);
assertTrue(("test5" != token.getNamespacePrefix(4)) == false);
assertTrue(("http://test1.org/" != token.getNamespaceURI(0)) == false);
assertTrue(("http://test2.org/" != token.getNamespaceURI(1)) == false);
assertTrue(("http://test3.org/" != token.getNamespaceURI(2)) == false);
assertTrue(("http://test4.org/" != token.getNamespaceURI(3)) == false);
assertTrue(("http://test5.org/" != token.getNamespaceURI(4)) == false);
token.clearNamespaces();
assertTrue(token.getNamespacesLength() == 0);
ns = null;
token = null;
triple = null;
attr = 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_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_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_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_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_L3_Compartment_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 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() == 3);
assertTrue(c.getVersion() == 1);
assertTrue(c.getNamespaces() != null);
assertTrue(c.getNamespaces().getLength() == 2);
assertTrue(c.getId() == "");
assertTrue(c.getName() == "");
assertTrue(c.getUnits() == "");
assertTrue(c.getOutside() == "");
assertEquals(true, isnan(c.getSpatialDimensionsAsDouble()));
assertEquals(true, isnan(c.getVolume()));
assertTrue(c.getConstant() == true);
assertEquals(false, c.isSetId());
assertEquals(false, c.isSetSpatialDimensions());
assertEquals(false, c.isSetName());
assertEquals(false, c.isSetSize());
assertEquals(false, c.isSetVolume());
assertEquals(false, c.isSetUnits());
assertEquals(false, c.isSetOutside());
assertEquals(false, c.isSetConstant());
c = null;
}
public void test_L3_Parameter_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1);
sbmlns.addNamespaces(xmlns);
Parameter p = new Parameter(sbmlns);
assertTrue(p.getTypeCode() == libsbml.SBML_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, isnan(p.getValue()));
assertTrue(p.getConstant() == true);
assertEquals(false, p.isSetId());
assertEquals(false, p.isSetName());
assertEquals(false, p.isSetValue());
assertEquals(false, p.isSetUnits());
assertEquals(false, p.isSetConstant());
p = 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_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_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_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_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_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_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_UnitDefinition_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2, 1);
sbmlns.addNamespaces(xmlns);
UnitDefinition object1 = new UnitDefinition(sbmlns);
assertTrue(object1.getTypeCode() == libsbml.SBML_UNIT_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_Priority_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1);
sbmlns.addNamespaces(xmlns);
Priority object1 = new Priority(sbmlns);
assertTrue(object1.getTypeCode() == libsbml.SBML_PRIORITY);
assertTrue(object1.getMetaId() == "");
assertTrue(object1.getNotes() == null);
assertTrue(object1.getAnnotation() == null);
assertTrue(object1.getLevel() == 3);
assertTrue(object1.getVersion() == 1);
assertTrue(object1.getNamespaces() != null);
assertTrue(object1.getNamespaces().getLength() == 2);
object1 = null;
}
public void test_RateRule_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2, 1);
sbmlns.addNamespaces(xmlns);
Rule object1 = new RateRule(sbmlns);
assertTrue(object1.getTypeCode() == libsbml.SBML_RATE_RULE);
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_Parameter_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2, 1);
sbmlns.addNamespaces(xmlns);
Parameter object1 = new Parameter(sbmlns);
assertTrue(object1.getTypeCode() == libsbml.SBML_PARAMETER);
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_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_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_KineticLaw_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2, 1);
sbmlns.addNamespaces(xmlns);
KineticLaw object1 = new KineticLaw(sbmlns);
assertTrue(object1.getTypeCode() == libsbml.SBML_KINETIC_LAW);
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_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_XMLNode_getters()
{
XMLToken token;
XMLNode node;
XMLTriple triple;
XMLAttributes attr;
XMLNamespaces NS;
NS = new XMLNamespaces();
NS.add("http://test1.org/", "test1");
token = new XMLToken("This is a test");
node = new XMLNode(token);
assertTrue(node != null);
assertTrue(node.getNumChildren() == 0);
assertTrue(("This is a test" != node.getCharacters()) == false);
assertTrue(node.getChild(1) != null);
attr = new XMLAttributes();
assertTrue(attr != null);
attr.add("attr2", "value");
triple = new XMLTriple("attr", "uri", "prefix");
token = new XMLToken(triple, attr);
assertTrue(token != null);
node = new XMLNode(token);
assertTrue(("attr" != node.getName()) == false);
assertTrue(("uri" != node.getURI()) == false);
assertTrue(("prefix" != node.getPrefix()) == false);
XMLAttributes returnattr = node.getAttributes();
assertTrue(("attr2" != returnattr.getName(0)) == false);
assertTrue(("value" != returnattr.getValue(0)) == false);
token = new XMLToken(triple, attr, NS);
node = new XMLNode(token);
XMLNamespaces returnNS = node.getNamespaces();
assertTrue(returnNS.getLength() == 1);
assertTrue(returnNS.isEmpty() == false);
triple = null;
token = null;
node = 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_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_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_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 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_XMLNamespaces_add()
{
assertTrue(NS.getLength() == 0);
assertTrue(NS.isEmpty() == true);
NS.add("http://test1.org/", "test1");
assertTrue(NS.getLength() == 1);
assertTrue(NS.isEmpty() == false);
NS.add("http://test2.org/", "test2");
assertTrue(NS.getLength() == 2);
assertTrue(NS.isEmpty() == false);
NS.add("http://test1.org/", "test1a");
assertTrue(NS.getLength() == 3);
assertTrue(NS.isEmpty() == false);
NS.add("http://test1.org/", "test1a");
assertTrue(NS.getLength() == 3);
assertTrue(NS.isEmpty() == false);
assertTrue(!(NS.getIndex("http://test1.org/") == -1));
}