public void test_Node_clone()
{
XMLAttributes att = new XMLAttributes();
XMLTriple t = new XMLTriple("sarah", "http://foo.org/", "bar");
XMLToken token = new XMLToken(t,att,3,4);
XMLNode node = new XMLNode(token);
XMLNode child = new XMLNode();
node.addChild(child);
assertTrue( node.getNumChildren() == 1 );
assertTrue( node.getName() == "sarah" );
assertTrue( node.getURI() == "http://foo.org/" );
assertTrue( node.getPrefix() == "bar" );
assertTrue( node.isEnd() == false );
assertTrue( node.isEOF() == false );
assertTrue( node.getLine() == 3 );
assertTrue( node.getColumn() == 4 );
XMLNode node2 = (XMLNode) node.clone();
assertTrue( node2.getNumChildren() == 1 );
assertTrue( node2.getName() == "sarah" );
assertTrue( node2.getURI() == "http://foo.org/" );
assertTrue( node2.getPrefix() == "bar" );
assertTrue( node2.isEnd() == false );
assertTrue( node2.isEOF() == false );
assertTrue( node2.getLine() == 3 );
assertTrue( node2.getColumn() == 4 );
t = null;
token = null;
node = null;
node2 = null;
}
public void test_XMLNode_addChild1()
{
XMLNode node = new XMLNode();
XMLNode node2 = new XMLNode();
int i = node.addChild(node2);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( node.getNumChildren() == 1 );
node = null;
node2 = null;
}
public void test_XMLNode_addChild3()
{
XMLTriple triple = new XMLTriple("test","","");
XMLNode node = new XMLNode(triple);
XMLNode node2 = new XMLNode();
int i = node.addChild(node2);
assertTrue( i == libsbml.LIBSBML_INVALID_XML_OPERATION );
assertTrue( node.getNumChildren() == 0 );
triple = null;
node = null;
node2 = null;
}
public void test_XMLNode_addChild2()
{
XMLTriple triple = new XMLTriple("test","","");
XMLAttributes attr = new XMLAttributes();
XMLNode node = new XMLNode(triple,attr);
XMLNode node2 = new XMLNode();
int i = node.addChild(node2);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( node.getNumChildren() == 1 );
triple = null;
attr = null;
node = null;
node2 = null;
}
public void test_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_CVTerm_createFromNode()
{
XMLAttributes xa;
XMLTriple qual_triple = new XMLTriple("is", "", "bqbiol");
XMLTriple bag_triple = new XMLTriple();
XMLTriple li_triple = new XMLTriple();
XMLAttributes att = new XMLAttributes();
att.add( "", "This is my resource");
XMLAttributes att1 = new XMLAttributes();
XMLToken li_token = new XMLToken(li_triple,att);
XMLToken bag_token = new XMLToken(bag_triple,att1);
XMLToken qual_token = new XMLToken(qual_triple,att1);
XMLNode li = new XMLNode(li_token);
XMLNode bag = new XMLNode(bag_token);
XMLNode node = new XMLNode(qual_token);
bag.addChild(li);
node.addChild(bag);
CVTerm term = new CVTerm(node);
assertTrue( term != null );
assertTrue( term.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER );
assertTrue( term.getBiologicalQualifierType() == libsbml.BQB_IS );
xa = term.getResources();
assertTrue( xa.getLength() == 1 );
assertTrue(( "rdf:resource" == xa.getName(0) ));
assertTrue(( "This is my resource" == xa.getValue(0) ));
qual_triple = null;
bag_triple = null;
li_triple = null;
li_token = null;
bag_token = null;
qual_token = null;
att = null;
att1 = null;
term = null;
node = null;
bag = null;
li = null;
}
public 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_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_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 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_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;
}
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_insert()
{
XMLAttributes attr = new XMLAttributes();
XMLTriple trp_p = new XMLTriple("parent","","");
XMLTriple trp_c1 = new XMLTriple("child1","","");
XMLTriple trp_c2 = new XMLTriple("child2","","");
XMLTriple trp_c3 = new XMLTriple("child3","","");
XMLTriple trp_c4 = new XMLTriple("child4","","");
XMLTriple trp_c5 = new XMLTriple("child5","","");
XMLNode p = new XMLNode(trp_p,attr);
XMLNode c1 = new XMLNode(trp_c1,attr);
XMLNode c2 = new XMLNode(trp_c2,attr);
XMLNode c3 = new XMLNode(trp_c3,attr);
XMLNode c4 = new XMLNode(trp_c4,attr);
XMLNode c5 = new XMLNode(trp_c5,attr);
p.addChild(c2);
p.addChild(c4);
p.insertChild(0,c1);
p.insertChild(2,c3);
p.insertChild(4,c5);
assertTrue( p.getNumChildren() == 5 );
assertTrue( ( "child1" != p.getChild(0).getName() ) == false );
assertTrue( ( "child2" != p.getChild(1).getName() ) == false );
assertTrue( ( "child3" != p.getChild(2).getName() ) == false );
assertTrue( ( "child4" != p.getChild(3).getName() ) == false );
assertTrue( ( "child5" != p.getChild(4).getName() ) == false );
p.removeChildren();
p.insertChild(0,c1);
p.insertChild(0,c2);
p.insertChild(0,c3);
p.insertChild(0,c4);
p.insertChild(0,c5);
assertTrue( p.getNumChildren() == 5 );
assertTrue( ( "child5" != p.getChild(0).getName() ) == false );
assertTrue( ( "child4" != p.getChild(1).getName() ) == false );
assertTrue( ( "child3" != p.getChild(2).getName() ) == false );
assertTrue( ( "child2" != p.getChild(3).getName() ) == false );
assertTrue( ( "child1" != p.getChild(4).getName() ) == false );
p.removeChildren();
p.insertChild(1,c1);
p.insertChild(2,c2);
p.insertChild(3,c3);
p.insertChild(4,c4);
p.insertChild(5,c5);
assertTrue( p.getNumChildren() == 5 );
assertTrue( ( "child1" != p.getChild(0).getName() ) == false );
assertTrue( ( "child2" != p.getChild(1).getName() ) == false );
assertTrue( ( "child3" != p.getChild(2).getName() ) == false );
assertTrue( ( "child4" != p.getChild(3).getName() ) == false );
assertTrue( ( "child5" != p.getChild(4).getName() ) == false );
p.removeChildren();
XMLNode tmp;
tmp = p.insertChild(0,c1);
assertTrue( ( "child1" != tmp.getName() ) == false );
tmp = p.insertChild(0,c2);
assertTrue( ( "child2" != tmp.getName() ) == false );
tmp = p.insertChild(0,c3);
assertTrue( ( "child3" != tmp.getName() ) == false );
tmp = p.insertChild(0,c4);
assertTrue( ( "child4" != tmp.getName() ) == false );
tmp = p.insertChild(0,c5);
assertTrue( ( "child5" != tmp.getName() ) == false );
p.removeChildren();
tmp = p.insertChild(1,c1);
assertTrue( ( "child1" != tmp.getName() ) == false );
tmp = p.insertChild(2,c2);
assertTrue( ( "child2" != tmp.getName() ) == false );
tmp = p.insertChild(3,c3);
assertTrue( ( "child3" != tmp.getName() ) == false );
tmp = p.insertChild(4,c4);
assertTrue( ( "child4" != tmp.getName() ) == false );
tmp = p.insertChild(5,c5);
assertTrue( ( "child5" != tmp.getName() ) == false );
p = null;
c1 = null;
c2 = null;
c3 = null;
c4 = null;
c5 = null;
attr = null;
trp_p = null;
trp_c1 = null;
trp_c2 = null;
trp_c3 = null;
trp_c4 = null;
trp_c5 = null;
}
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_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);
S.setNotes (p_node);
S.appendNotes (html_node1);
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_XMLNode_remove()
{
XMLAttributes attr = new XMLAttributes();
XMLTriple trp_p = new XMLTriple("parent","","");
XMLTriple trp_c1 = new XMLTriple("child1","","");
XMLTriple trp_c2 = new XMLTriple("child2","","");
XMLTriple trp_c3 = new XMLTriple("child3","","");
XMLTriple trp_c4 = new XMLTriple("child4","","");
XMLTriple trp_c5 = new XMLTriple("child5","","");
XMLNode p = new XMLNode(trp_p,attr);
XMLNode c1 = new XMLNode(trp_c1,attr);
XMLNode c2 = new XMLNode(trp_c2,attr);
XMLNode c3 = new XMLNode(trp_c3,attr);
XMLNode c4 = new XMLNode(trp_c4,attr);
XMLNode c5 = new XMLNode(trp_c5,attr);
XMLNode r;
p.addChild(c1);
p.addChild(c2);
p.addChild(c3);
p.addChild(c4);
p.addChild(c5);
r = p.removeChild(5);
assertTrue( r == null );
r = p.removeChild(1);
assertTrue( p.getNumChildren() == 4 );
assertTrue( ( "child2" != r.getName() ) == false );
r = null;
r = p.removeChild(3);
assertTrue( p.getNumChildren() == 3 );
assertTrue( ( "child5" != r.getName() ) == false );
r = null;
r = p.removeChild(0);
assertTrue( p.getNumChildren() == 2 );
assertTrue( ( "child1" != r.getName() ) == false );
r = null;
r = p.removeChild(1);
assertTrue( p.getNumChildren() == 1 );
assertTrue( ( "child4" != r.getName() ) == false );
r = null;
r = p.removeChild(0);
assertTrue( p.getNumChildren() == 0 );
assertTrue( ( "child3" != r.getName() ) == false );
r = null;
p.addChild(c1);
p.addChild(c2);
p.addChild(c3);
p.addChild(c4);
p.addChild(c5);
r = p.removeChild(4);
assertTrue( p.getNumChildren() == 4 );
assertTrue( ( "child5" != r.getName() ) == false );
r = null;
r = p.removeChild(3);
assertTrue( p.getNumChildren() == 3 );
assertTrue( ( "child4" != r.getName() ) == false );
r = null;
r = p.removeChild(2);
assertTrue( p.getNumChildren() == 2 );
assertTrue( ( "child3" != r.getName() ) == false );
r = null;
r = p.removeChild(1);
assertTrue( p.getNumChildren() == 1 );
assertTrue( ( "child2" != r.getName() ) == false );
r = null;
r = p.removeChild(0);
assertTrue( p.getNumChildren() == 0 );
assertTrue( ( "child1" != r.getName() ) == false );
r = null;
p.addChild(c1);
p.addChild(c2);
p.addChild(c3);
p.addChild(c4);
p.addChild(c5);
r = p.removeChild(0);
assertTrue( p.getNumChildren() == 4 );
assertTrue( ( "child1" != r.getName() ) == false );
r = null;
r = p.removeChild(0);
assertTrue( p.getNumChildren() == 3 );
assertTrue( ( "child2" != r.getName() ) == false );
r = null;
r = p.removeChild(0);
assertTrue( p.getNumChildren() == 2 );
assertTrue( ( "child3" != r.getName() ) == false );
r = null;
r = p.removeChild(0);
assertTrue( p.getNumChildren() == 1 );
assertTrue( ( "child4" != r.getName() ) == false );
r = null;
r = p.removeChild(0);
assertTrue( p.getNumChildren() == 0 );
assertTrue( ( "child5" != r.getName() ) == false );
r = null;
p.addChild(c1);
p.addChild(c2);
p.addChild(c3);
p.addChild(c4);
p.addChild(c5);
r = p.removeChild(0);
assertTrue( ( "child1" != r.getName() ) == false );
p.insertChild(0,r);
assertTrue( p.getNumChildren() == 5 );
assertTrue( ( "child1" != p.getChild(0).getName() ) == false );
r = null;
r = p.removeChild(1);
assertTrue( ( "child2" != r.getName() ) == false );
p.insertChild(1,r);
assertTrue( p.getNumChildren() == 5 );
assertTrue( ( "child2" != p.getChild(1).getName() ) == false );
r = null;
r = p.removeChild(2);
assertTrue( ( "child3" != r.getName() ) == false );
p.insertChild(2,r);
assertTrue( p.getNumChildren() == 5 );
assertTrue( ( "child3" != p.getChild(2).getName() ) == false );
r = null;
r = p.removeChild(3);
assertTrue( ( "child4" != r.getName() ) == false );
p.insertChild(3,r);
assertTrue( p.getNumChildren() == 5 );
assertTrue( ( "child4" != p.getChild(3).getName() ) == false );
r = null;
r = p.removeChild(4);
assertTrue( ( "child5" != r.getName() ) == false );
p.insertChild(4,r);
assertTrue( p.getNumChildren() == 5 );
assertTrue( ( "child5" != p.getChild(4).getName() ) == false );
r = null;
p = null;
c1 = null;
c2 = null;
c3 = null;
c4 = null;
c5 = null;
attr = null;
trp_p = null;
trp_c1 = null;
trp_c2 = null;
trp_c3 = null;
trp_c4 = null;
trp_c5 = null;
}
public void test_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;
}
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_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;
}
/**
*
* Creates an SBML model represented in "7.2 Example involving units"
* in the SBML Level 2 Version 4 Specification.
*
*/
private static SBMLDocument createExampleInvolvingUnits()
{
int level = Level;
int version = Version;
//---------------------------------------------------------------------------
//
// Creates an SBMLDocument object
//
//---------------------------------------------------------------------------
SBMLDocument sbmlDoc = new SBMLDocument(level, version);
// Adds the namespace for XHTML to the SBMLDocument object. We need this
// because we will add notes to the model. (By default, the SBML document
// created by SBMLDocument only declares the SBML XML namespace.)
sbmlDoc.getNamespaces().add("http://www.w3.org/1999/xhtml", "xhtml");
//---------------------------------------------------------------------------
//
// Creates a Model object inside the SBMLDocument object.
//
//---------------------------------------------------------------------------
Model model = sbmlDoc.createModel();
model.setId("unitsExample");
//---------------------------------------------------------------------------
//
// Creates UnitDefinition objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointers (reused more than once below).
UnitDefinition unitdef;
Unit unit;
//---------------------------------------------------------------------------
// (UnitDefinition1) Creates an UnitDefinition object ("substance").
//
// This has the effect of redefining the default unit of subtance for the
// whole model.
//---------------------------------------------------------------------------
unitdef = model.createUnitDefinition();
unitdef.setId("substance");
// Creates an Unit inside the UnitDefinition object
unit = unitdef.createUnit();
unit.setKind(libsbml.UNIT_KIND_MOLE);
unit.setScale(-3);
//--------------------------------------------------------------------------------
// (UnitDefinition2) Creates an UnitDefinition object ("mmls")
//--------------------------------------------------------------------------------
// Note that we can reuse the pointers 'unitdef' and 'unit' because the
// actual UnitDefinition object (along with the Unit objects within it)
// is already attached to the Model object.
unitdef = model.createUnitDefinition();
unitdef.setId("mmls");
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef.createUnit();
unit.setKind(libsbml.UNIT_KIND_MOLE);
unit.setScale(-3);
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef.createUnit();
unit.setKind(libsbml.UNIT_KIND_LITRE);
unit.setExponent(-1);
// Creates an Unit inside the UnitDefinition object ("mmls")
unit = unitdef.createUnit();
unit.setKind(libsbml.UNIT_KIND_SECOND);
unit.setExponent(-1);
//--------------------------------------------------------------------------------
// (UnitDefinition3) Creates an UnitDefinition object ("mml")
//--------------------------------------------------------------------------------
unitdef = model.createUnitDefinition();
unitdef.setId("mml");
// Creates an Unit inside the UnitDefinition object ("mml")
unit = unitdef.createUnit();
unit.setKind(libsbml.UNIT_KIND_MOLE);
unit.setScale(-3);
// Creates an Unit inside the UnitDefinition object ("mml")
unit = unitdef.createUnit();
unit.setKind(libsbml.UNIT_KIND_LITRE);
unit.setExponent(-1);
//---------------------------------------------------------------------------
//
// Creates a Compartment object inside the Model object.
//
//---------------------------------------------------------------------------
Compartment comp;
string compName = "cell";
// Creates a Compartment object ("cell")
comp = model.createCompartment();
comp.setId(compName);
// Sets the "size" attribute of the Compartment object.
//
// The units of this Compartment object is the default SBML
// units of volume (litre), and thus we don't have to explicitly invoke
// setUnits("litre") function to set the default units.
//
comp.setSize(1);
//---------------------------------------------------------------------------
//
// Creates Species objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointer (reused more than once below).
Species sp;
//---------------------------------------------------------------------------
// (Species1) Creates a Species object ("x0")
//---------------------------------------------------------------------------
sp = model.createSpecies();
sp.setId("x0");
// Sets the "compartment" attribute of the Species object to identify the
// compartnet in which the Species object located.
sp.setCompartment(compName);
// Sets the "initialConcentration" attribute of the Species object.
//
// The units of this Species object is determined by two attributes of this
// Species object ("substanceUnits" and "hasOnlySubstanceUnits") and the
// "spatialDimensions" attribute of the Compartment object ("cytosol") in which
// this species object is located.
// Since the default values are used for "substanceUnits" (substance (mole))
// and "hasOnlySubstanceUnits" (false) and the value of "spatialDimension" (3)
// is greater than 0, the units of this Species object is moles/liters .
//
sp.setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species2) Creates a Species object ("x1")
//---------------------------------------------------------------------------
sp = model.createSpecies();
sp.setId("x1");
sp.setCompartment(compName);
sp.setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species3) Creates a Species object ("s1")
//---------------------------------------------------------------------------
sp = model.createSpecies();
sp.setCompartment(compName);
sp.setId("s1");
sp.setInitialConcentration(1);
//---------------------------------------------------------------------------
// (Species4) Creates a Species object ("s2")
//---------------------------------------------------------------------------
sp = model.createSpecies();
sp.setCompartment(compName);
sp.setId("s2");
sp.setInitialConcentration(1);
//---------------------------------------------------------------------------
//
// Creates global Parameter objects inside the Model object.
//
//---------------------------------------------------------------------------
Parameter para;
// Creates a Parameter ("vm")
para = model.createParameter();
para.setId("vm");
para.setValue(2);
para.setUnits("mmls");
// Creates a Parameter ("km")
para = model.createParameter();
para.setId("km");
para.setValue(2);
para.setUnits("mml");
//---------------------------------------------------------------------------
//
// Creates Reaction objects inside the Model object.
//
//---------------------------------------------------------------------------
// Temporary pointers.
Reaction reaction;
SpeciesReference spr;
KineticLaw kl;
//---------------------------------------------------------------------------
// (Reaction1) Creates a Reaction object ("v1").
//---------------------------------------------------------------------------
reaction = model.createReaction();
reaction.setId("v1");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v1").
//---------------------------------------------------------------------------
// (Reactant1) Creates a Reactant object that references Species "x0"
// in the model.
spr = reaction.createReactant();
spr.setSpecies("x0");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v1").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "s1" in the model.
spr = reaction.createProduct();
spr.setSpecies("s1");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v1").
//---------------------------------------------------------------------------
kl = reaction.createKineticLaw();
// Creates a <notes> element in the KineticLaw object.
// Here we illustrate how to do it using a literal string. This requires
// known the required syntax of XHTML and the requirements for SBML <notes>
// elements. Later below, we show how to create notes using objects instead
// of strings.
string notesString = "<xhtml:p> ((vm * s1)/(km + s1)) * cell </xhtml:p>";
kl.setNotes(notesString);
//---------------------------------------------------------------------------
// Creates an ASTNode object which represents the following KineticLaw object.
//
// <math xmlns=\"http://www.w3.org/1998/Math/MathML\">
// <apply>
// <times/>
// <apply>
// <divide/>
// <apply>
// <times/>
// <ci> vm </ci>
// <ci> s1 </ci>
// </apply>
// <apply>
// <plus/>
// <ci> km </ci>
// <ci> s1 </ci>
// </apply>
// </apply>
// <ci> cell </ci>
// </apply>
// </math>
//---------------------------------------------------------------------------
//
// In the following code, ASTNode objects, which construct an ASTNode tree
// of the above math, are created and added in the order of preorder traversal
// of the tree (i.e. the order corresponds to the nested structure of the above
// MathML elements), and thus the following code maybe a bit more efficient but
// maybe a bit difficult to read.
//
ASTNode astMath = new ASTNode(libsbml.AST_TIMES);
astMath.addChild(new ASTNode(libsbml.AST_DIVIDE));
ASTNode astDivide = astMath.getLeftChild();
astDivide.addChild(new ASTNode(libsbml.AST_TIMES));
ASTNode astTimes = astDivide.getLeftChild();
astTimes.addChild(new ASTNode(libsbml.AST_NAME));
astTimes.getLeftChild().setName("vm");
astTimes.addChild(new ASTNode(libsbml.AST_NAME));
astTimes.getRightChild().setName("s1");
astDivide.addChild(new ASTNode(libsbml.AST_PLUS));
ASTNode astPlus = astDivide.getRightChild();
astPlus.addChild(new ASTNode(libsbml.AST_NAME));
astPlus.getLeftChild().setName("km");
astPlus.addChild(new ASTNode(libsbml.AST_NAME));
astPlus.getRightChild().setName("s1");
astMath.addChild(new ASTNode(libsbml.AST_NAME));
astMath.getRightChild().setName("cell");
//---------------------------------------------
//
// set the Math element
//
//------------------------------------------------
kl.setMath(astMath);
//---------------------------------------------------------------------------
// (Reaction2) Creates a Reaction object ("v2").
//---------------------------------------------------------------------------
reaction = model.createReaction();
reaction.setId("v2");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v2").
//---------------------------------------------------------------------------
// (Reactant2) Creates a Reactant object that references Species "s1"
// in the model.
spr = reaction.createReactant();
spr.setSpecies("s1");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v2").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "s2" in the model.
spr = reaction.createProduct();
spr.setSpecies("s2");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v2").
//---------------------------------------------------------------------------
kl = reaction.createKineticLaw();
// Sets a notes (by XMLNode) to the KineticLaw object.
//
// The following code is an alternative to using setNotes(const string&).
// The equivalent code would be like this:
//
// notesString = "<xhtml:p>((vm * s2)/(km + s2))*cell</xhtml:p>";
// kl.setNotes(notesString);
// Creates an XMLNode of start element (<xhtml:p>) without attributes.
XMLNode notesXMLNode = new XMLNode(
new XMLTriple("p", "", "xhtml"),
new XMLAttributes());
// Adds a text element to the start element.
notesXMLNode.addChild(new XMLNode(" ((vm * s2)/(km + s2)) * cell "));
// Adds it to the kineticLaw object.
kl.setNotes(notesXMLNode);
//---------------------------------------------------------------------------
// Sets a math (ASTNode object) to the KineticLaw object.
//---------------------------------------------------------------------------
// To create mathematical expressions, one would typically construct
// an ASTNode tree as the above example code which creates a math of another
// KineticLaw object. Here, to save some space and illustrate another approach
// of doing it, we will write out the formula in MathML form and then use a
// libSBML convenience function to create the ASTNode tree for us.
// (This is a bit dangerous; it's very easy to make mistakes when writing MathML
// by hand, so in a real program, we would not really want to do it this way.)
string mathXMLString = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
+ " <apply>"
+ " <times/>"
+ " <apply>"
+ " <divide/>"
+ " <apply>"
+ " <times/>"
+ " <ci> vm </ci>"
+ " <ci> s2 </ci>"
+ " </apply>"
+ " <apply>"
+ " <plus/>"
+ " <ci> km </ci>"
+ " <ci> s2 </ci>"
+ " </apply>"
+ " </apply>"
+ " <ci> cell </ci>"
+ " </apply>"
+ "</math>";
astMath = libsbml.readMathMLFromString(mathXMLString);
kl.setMath(astMath);
//---------------------------------------------------------------------------
// (Reaction3) Creates a Reaction object ("v3").
//---------------------------------------------------------------------------
reaction = model.createReaction();
reaction.setId("v3");
//---------------------------------------------------------------------------
// Creates Reactant objects inside the Reaction object ("v3").
//---------------------------------------------------------------------------
// (Reactant2) Creates a Reactant object that references Species "s2"
// in the model.
spr = reaction.createReactant();
spr.setSpecies("s2");
//---------------------------------------------------------------------------
// Creates a Product object inside the Reaction object ("v3").
//---------------------------------------------------------------------------
// Creates a Product object that references Species "x1" in the model.
spr = reaction.createProduct();
spr.setSpecies("x1");
//---------------------------------------------------------------------------
// Creates a KineticLaw object inside the Reaction object ("v3").
//---------------------------------------------------------------------------
kl = reaction.createKineticLaw();
// Sets a notes (by string) to the KineticLaw object.
notesString = "<xhtml:p> ((vm * x1)/(km + x1)) * cell </xhtml:p>";
kl.setNotes(notesString);
//---------------------------------------------------------------------------
// Sets a math (ASTNode object) to the KineticLaw object.
//---------------------------------------------------------------------------
mathXMLString = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"
+ " <apply>"
+ " <times/>"
+ " <apply>"
+ " <divide/>"
+ " <apply>"
+ " <times/>"
+ " <ci> vm </ci>"
+ " <ci> x1 </ci>"
+ " </apply>"
+ " <apply>"
+ " <plus/>"
+ " <ci> km </ci>"
+ " <ci> x1 </ci>"
+ " </apply>"
+ " </apply>"
+ " <ci> cell </ci>"
+ " </apply>"
+ "</math>";
astMath = libsbml.readMathMLFromString(mathXMLString);
kl.setMath(astMath);
// Returns the created SBMLDocument object.
// The returned object must be explicitly deleted by the caller,
// otherwise memory leak will happen.
return sbmlDoc;
}
public void test_XMLNode_create()
{
XMLNode node = new XMLNode();
assertTrue( node != null );
assertTrue( node.getNumChildren() == 0 );
node = null;
node = new XMLNode();
assertTrue( node != null );
XMLNode node2 = new XMLNode();
assertTrue( node2 != null );
node.addChild(node2);
assertTrue( node.getNumChildren() == 1 );
XMLNode node3 = new XMLNode();
assertTrue( node3 != null );
node.addChild(node3);
assertTrue( node.getNumChildren() == 2 );
node = null;
node2 = null;
node3 = null;
}
