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; }