public void test_SpeciesReference_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,1);
sbmlns.addNamespaces(xmlns);
SpeciesReference object1 = new SpeciesReference(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_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 );
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_CompartmentType_createWithNS()
{
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add( "http://www.sbml.org", "testsbml");
SBMLNamespaces sbmlns = new SBMLNamespaces(2,2);
sbmlns.addNamespaces(xmlns);
CompartmentType object1 = new CompartmentType(sbmlns);
assertTrue( object1.getTypeCode() == libsbml.SBML_COMPARTMENT_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_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_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_SyntaxChecker_validXHTML()
{
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);
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(node,null) == false );
triple = new XMLTriple("html", "", "");
ns.clear();
token = new XMLToken(triple,att,ns);
node = new XMLNode(token);
node.addChild(n1);
assertTrue( SyntaxChecker.hasExpectedXHTMLSyntax(node,null) == 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_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_XMLNode_createElement()
{
XMLTriple triple;
XMLAttributes attr;
XMLNamespaces ns;
XMLNode snode, enode, tnode;
XMLAttributes cattr;
string name = "test";
string uri = "http://test.org/";
string prefix = "p";
string text = "text node";
triple = new XMLTriple(name,uri,prefix);
ns = new XMLNamespaces();
attr = new XMLAttributes();
ns.add(uri,prefix);
attr.add("id", "value",uri,prefix);
snode = new XMLNode(triple,attr,ns);
assertTrue( snode != null );
assertTrue( snode.getNumChildren() == 0 );
assertTrue( ( name != snode.getName() ) == false );
assertTrue( ( prefix != snode.getPrefix() ) == false );
assertTrue( ( uri != snode.getURI() ) == false );
assertTrue( snode.isElement() == true );
assertTrue( snode.isStart() == true );
assertTrue( snode.isEnd() == false );
assertTrue( snode.isText() == false );
snode.setEnd();
assertTrue( snode.isEnd() == true );
snode.unsetEnd();
assertTrue( snode.isEnd() == false );
cattr = snode.getAttributes();
assertTrue( cattr != null );
assertTrue( ( "id" != cattr.getName(0) ) == false );
assertTrue( ( "value" != cattr.getValue(0) ) == false );
assertTrue( ( prefix != cattr.getPrefix(0) ) == false );
assertTrue( ( uri != cattr.getURI(0) ) == false );
triple = null;
attr = null;
ns = null;
snode = null;
attr = new XMLAttributes();
attr.add("id", "value");
triple = new XMLTriple(name, "", "");
snode = new XMLNode(triple,attr);
assertTrue( snode != null );
assertTrue( snode.getNumChildren() == 0 );
assertTrue( ( "test" != snode.getName() ) == false );
assertTrue( snode.getPrefix() == "" );
assertTrue( snode.getURI() == "" );
assertTrue( snode.isElement() == true );
assertTrue( snode.isStart() == true );
assertTrue( snode.isEnd() == false );
assertTrue( snode.isText() == false );
cattr = snode.getAttributes();
assertTrue( cattr != null );
assertTrue( ( "id" != cattr.getName(0) ) == false );
assertTrue( ( "value" != cattr.getValue(0) ) == false );
assertTrue( cattr.getPrefix(0) == "" );
assertTrue( cattr.getURI(0) == "" );
enode = new XMLNode(triple);
assertTrue( enode != null );
assertTrue( enode.getNumChildren() == 0 );
assertTrue( ( "test" != enode.getName() ) == false );
assertTrue( enode.getPrefix() == "" );
assertTrue( enode.getURI() == "" );
assertTrue( enode.isElement() == true );
assertTrue( enode.isStart() == false );
assertTrue( enode.isEnd() == true );
assertTrue( enode.isText() == false );
tnode = new XMLNode(text);
assertTrue( tnode != null );
assertTrue( ( text != tnode.getCharacters() ) == false );
assertTrue( tnode.getNumChildren() == 0 );
assertTrue( tnode.getName() == "" );
assertTrue( tnode.getPrefix() == "" );
assertTrue( tnode.getURI() == "" );
assertTrue( tnode.isElement() == false );
assertTrue( tnode.isStart() == false );
assertTrue( tnode.isEnd() == false );
assertTrue( tnode.isText() == true );
triple = null;
attr = null;
snode = null;
enode = null;
tnode = null;
}
public void test_Constraint_setMessage()
{
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);
C.setMessage(node);
assertTrue( C.getMessage() != node );
assertTrue( C.isSetMessage() == true );
C.setMessage(C.getMessage());
assertTrue( C.getMessage() != node );
assertTrue( C.getMessageString() != null );
C.unsetMessage();
assertEquals( false, C.isSetMessage() );
if (C.getMessage() != null);
{
}
node = 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_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_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_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_SBase_appendNotes5()
{
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 p_token1 = new XMLToken(p_triple,att,ns);
XMLToken text_token = new XMLToken("This is my text");
XMLNode p_node = new XMLNode(p_token1);
XMLNode text_node = new XMLNode(text_token);
XMLToken text_token1 = new XMLToken("This is more text");
XMLNode html_node1 = new XMLNode(html_token);
XMLNode head_node1 = new XMLNode(head_token);
XMLNode title_node1 = new XMLNode(title_token);
XMLNode body_node1 = new XMLNode(body_token);
XMLNode p_node1 = new XMLNode(p_token);
XMLNode text_node1 = new XMLNode(text_token1);
XMLNode notes;
XMLNode child, child1;
p_node.addChild(text_node);
p_node1.addChild(text_node1);
body_node1.addChild(p_node1);
head_node1.addChild(title_node1);
html_node1.addChild(head_node1);
html_node1.addChild(body_node1);
int i = S.setNotes(p_node);
i = S.appendNotes(html_node1);
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() == 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;
html_triple = null;
head_triple = null;
body_triple = null;
p_triple = null;
body_token = null;
p_token = null;
p_token1 = null;
text_token = null;
text_token1 = null;
p_node = null;
text_node = null;
html_node1 = null;
head_node1 = null;
body_node1 = null;
p_node1 = null;
text_node1 = 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_namespace_set_clear()
{
XMLTriple triple = new XMLTriple("test","","");
XMLAttributes attr = new XMLAttributes();
XMLNode node = new XMLNode(triple,attr);
XMLNamespaces ns = new XMLNamespaces();
assertTrue( node.getNamespacesLength() == 0 );
assertTrue( node.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");
node.setNamespaces(ns);
assertTrue( node.getNamespacesLength() == 5 );
assertTrue( node.isNamespacesEmpty() == false );
assertTrue( ( "test1" != node.getNamespacePrefix(0) ) == false );
assertTrue( ( "test2" != node.getNamespacePrefix(1) ) == false );
assertTrue( ( "test3" != node.getNamespacePrefix(2) ) == false );
assertTrue( ( "test4" != node.getNamespacePrefix(3) ) == false );
assertTrue( ( "test5" != node.getNamespacePrefix(4) ) == false );
assertTrue( ( "http://test1.org/" != node.getNamespaceURI(0) ) == false );
assertTrue( ( "http://test2.org/" != node.getNamespaceURI(1) ) == false );
assertTrue( ( "http://test3.org/" != node.getNamespaceURI(2) ) == false );
assertTrue( ( "http://test4.org/" != node.getNamespaceURI(3) ) == false );
assertTrue( ( "http://test5.org/" != node.getNamespaceURI(4) ) == false );
node.clearNamespaces();
assertTrue( node.getNamespacesLength() == 0 );
assertTrue( node.isAttributesEmpty() != false );
ns = null;
node = null;
triple = null;
attr = 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);
S.setNotes(node);
assertTrue( S.isSetNotes() == true );
token1 = new XMLToken(triple,att,ns);
node1 = new XMLNode(token1);
node1.addChild(node5);
S.appendNotes(node1);
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_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_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_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_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_XMLToken_newSetters_setNamespaces2()
{
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");
int 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_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_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_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_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);
S.setNotes(body_node);
S.appendNotes(p_node1);
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_Constraint_copyConstructor()
{
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(o1);
assertTrue( o2.getMetaId() == "c" );
assertTrue( o2.getMath() != null );
msg = o2.getMessage();
assertTrue( msg != null );
assertTrue( o2.getParentSBMLObject() == o1.getParentSBMLObject() );
o2 = null;
o1 = null;
}
