public void test_element_bug_csymbol_delay_1()
{
string s = wrapMathML("<apply>" +
" <csymbol encoding='text' definitionURL='http://www.sbml.org/sbml/" +
"symbols/delay'> my_delay </csymbol>" +
" <ci> x </ci>" +
" <cn> 0.1 </cn>" +
"</apply>\n");
N = libsbml.readMathMLFromString(s);
assertTrue( N != null );
assertTrue( N.getType() == libsbml.AST_FUNCTION_DELAY );
assertTrue(( "my_delay" == N.getName() ));
assertTrue( N.getNumChildren() == 2 );
ASTNode c = N.getLeftChild();
assertTrue( c != null );
assertTrue( c.getType() == libsbml.AST_NAME );
assertTrue(( "x" == c.getName() ));
assertTrue( c.getNumChildren() == 0 );
c = N.getRightChild();
assertTrue( c != null );
assertTrue( c.getType() == libsbml.AST_REAL );
assertTrue( c.getReal() == 0.1 );
assertTrue( c.getNumChildren() == 0 );
}
public void test_element_bug_apply_ci_1()
{
string s = wrapMathML("<apply>" +
" <ci> Y </ci>" +
" <cn> 1 </cn>" +
"</apply>");
N = libsbml.readMathMLFromString(s);
assertTrue( N != null );
assertTrue( N.getType() == libsbml.AST_FUNCTION );
assertTrue(( "Y" == N.getName() ));
assertTrue( N.getNumChildren() == 1 );
ASTNode c = N.getLeftChild();
assertTrue( c != null );
assertTrue( c.getType() == libsbml.AST_REAL );
assertTrue( c.getReal() == 1 );
assertTrue( c.getNumChildren() == 0 );
}
public void test_element_bug_apply_ci_2()
{
string s = wrapMathML("<apply>" +
" <ci> Y </ci>" +
" <csymbol encoding='text' " +
" definitionURL='http://www.sbml.org/sbml/symbols/time'> t </csymbol>" +
"</apply>");
N = libsbml.readMathMLFromString(s);
assertTrue( N != null );
assertTrue( N.getType() == libsbml.AST_FUNCTION );
assertTrue(( "Y" == N.getName() ));
assertTrue( N.getNumChildren() == 1 );
ASTNode c = N.getLeftChild();
assertTrue( c != null );
assertTrue( c.getType() == libsbml.AST_NAME_TIME );
assertTrue(( "t" == c.getName() ));
assertTrue( c.getNumChildren() == 0 );
}
public void test_ASTNode_setCharacter()
{
ASTNode node = new ASTNode();
node.setName( "foo");
assertTrue( node.getType() == libsbml.AST_NAME );
assertTrue( node.getCharacter() == '\0' );
assertTrue(( "foo" == node.getName() ));
assertTrue( node.getInteger() == 0 );
assertTrue( node.getReal() == 0 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 1 );
node.setCharacter( '+');
assertTrue( node.getType() == libsbml.AST_PLUS );
assertTrue( node.getCharacter() == '+' );
assertTrue( node.getName() == null );
assertTrue( node.getInteger() == 0 );
assertTrue( node.getReal() == 0 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 1 );
node.setCharacter( '-');
assertTrue( node.getType() == libsbml.AST_MINUS );
assertTrue( node.getCharacter() == '-' );
assertTrue( node.getName() == null );
assertTrue( node.getInteger() == 0 );
assertTrue( node.getReal() == 0 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 1 );
node.setCharacter( '*');
assertTrue( node.getType() == libsbml.AST_TIMES );
assertTrue( node.getCharacter() == '*' );
assertTrue( node.getName() == null );
assertTrue( node.getInteger() == 0 );
assertTrue( node.getReal() == 0 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 1 );
node.setCharacter( '/');
assertTrue( node.getType() == libsbml.AST_DIVIDE );
assertTrue( node.getCharacter() == '/' );
assertTrue( node.getName() == null );
assertTrue( node.getInteger() == 0 );
assertTrue( node.getReal() == 0 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 1 );
node.setCharacter( '^');
assertTrue( node.getType() == libsbml.AST_POWER );
assertTrue( node.getCharacter() == '^' );
assertTrue( node.getName() == null );
assertTrue( node.getInteger() == 0 );
assertTrue( node.getReal() == 0 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 1 );
node.setCharacter( '$');
assertTrue( node.getType() == libsbml.AST_UNKNOWN );
assertTrue( node.getCharacter() == '$' );
assertTrue( node.getName() == null );
assertTrue( node.getInteger() == 0 );
assertTrue( node.getReal() == 0 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 1 );
node = null;
}
public void test_ASTNode_avogadro_bug()
{
double val;
ASTNode n = new ASTNode();
n.setName( "NA");
n.setType(libsbml.AST_NAME_AVOGADRO);
assertTrue(( "NA" == n.getName() ));
val = n.getReal();
assertTrue( val == 6.02214179e23 );
assertTrue( n.isConstant() == true );
n = null;
}
public void test_element_csymbol_delay_1()
{
string s = wrapMathML("<csymbol encoding='text' " + "definitionURL='http://www.sbml.org/sbml/symbols/delay'> delay </csymbol>");
N = libsbml.readMathMLFromString(s);
assertTrue( N != null );
assertTrue( N.getType() == libsbml.AST_FUNCTION_DELAY );
assertTrue(( "delay" == N.getName() ));
assertTrue( N.getNumChildren() == 0 );
}
public void test_ASTNode_setName()
{
string name = "foo";
ASTNode node = new ASTNode();
assertTrue( node.getType() == libsbml.AST_UNKNOWN );
node.setName(name);
assertTrue( node.getType() == libsbml.AST_NAME );
assertTrue(( name == node.getName() ));
assertTrue( node.getCharacter() == '\0' );
assertTrue( node.getInteger() == 0 );
assertTrue( node.getReal() == 0 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 1 );
if (node.getName() == name);
{
}
node.setName(null);
assertTrue( node.getType() == libsbml.AST_NAME );
if (node.getName() != null);
{
}
node.setType(libsbml.AST_FUNCTION_COS);
assertTrue( node.getType() == libsbml.AST_FUNCTION_COS );
assertTrue(( "cos" == node.getName() ));
assertTrue( node.getCharacter() == '\0' );
assertTrue( node.getInteger() == 0 );
assertTrue( node.getReal() == 0 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 1 );
node.setType(libsbml.AST_PLUS);
node.setName(name);
assertTrue( node.getType() == libsbml.AST_NAME );
assertTrue(( name == node.getName() ));
assertTrue( node.getCharacter() == '+' );
assertTrue( node.getInteger() == 0 );
assertTrue( node.getReal() == 0 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 1 );
node = null;
}
public void test_ASTNode_deepCopy_2()
{
ASTNode node = new ASTNode();
ASTNode copy;
node.setName( "Foo");
assertTrue( node.getType() == libsbml.AST_NAME );
assertTrue(( "Foo" == node.getName() ));
assertTrue( node.getNumChildren() == 0 );
copy = node.deepCopy();
assertTrue( copy != node );
assertTrue( copy.getType() == libsbml.AST_NAME );
assertTrue(( "Foo" == copy.getName() ));
assertTrue( copy.getNumChildren() == 0 );
node = null;
copy = null;
}
public void test_ASTNode_deepCopy_4()
{
ASTNode node = new ASTNode(libsbml.AST_FUNCTION_ABS);
ASTNode copy;
node.setName( "ABS");
assertTrue( node.getType() == libsbml.AST_FUNCTION_ABS );
assertTrue(( "ABS" == node.getName() ));
assertTrue( node.getNumChildren() == 0 );
copy = node.deepCopy();
assertTrue( copy != node );
assertTrue( copy.getType() == libsbml.AST_FUNCTION_ABS );
assertTrue(( "ABS" == copy.getName() ));
assertTrue( copy.getNumChildren() == 0 );
node = null;
copy = null;
}
public void test_ASTNode_canonicalizeFunctionsL1()
{
ASTNode n = new ASTNode(libsbml.AST_FUNCTION);
ASTNode c;
n.setName( "acos");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCCOS );
n.setType(libsbml.AST_FUNCTION);
n.setName( "asin");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCSIN );
n.setType(libsbml.AST_FUNCTION);
n.setName( "atan");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCTAN );
n.setType(libsbml.AST_FUNCTION);
n.setName( "ceil");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_CEILING );
n.setType(libsbml.AST_FUNCTION);
n.setName( "pow");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_POWER );
n = null;
n = new ASTNode(libsbml.AST_FUNCTION);
n.setName( "log");
c = new ASTNode();
c.setName( "x");
n.addChild(c);
assertTrue( n.getType() == libsbml.AST_FUNCTION );
assertTrue( n.getNumChildren() == 1 );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_LN );
assertTrue( n.getNumChildren() == 1 );
n.setType(libsbml.AST_FUNCTION);
c = new ASTNode();
c.setName( "y");
n.addChild(c);
assertTrue( n.getType() == libsbml.AST_FUNCTION );
assertTrue( n.getNumChildren() == 2 );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_LOG );
n = null;
n = new ASTNode(libsbml.AST_FUNCTION);
n.setName( "log10");
c = new ASTNode();
c.setName( "x");
n.addChild(c);
assertTrue( n.getType() == libsbml.AST_FUNCTION );
assertTrue( n.getNumChildren() == 1 );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_LOG );
assertTrue( n.getNumChildren() == 2 );
c = n.getLeftChild();
assertTrue( c.getType() == libsbml.AST_INTEGER );
assertTrue( c.getInteger() == 10 );
c = n.getRightChild();
assertTrue( c.getType() == libsbml.AST_NAME );
assertTrue(( "x" == c.getName() ));
n = null;
n = new ASTNode(libsbml.AST_FUNCTION);
n.setName( "sqr");
c = new ASTNode();
c.setName( "x");
n.addChild(c);
assertTrue( n.getType() == libsbml.AST_FUNCTION );
assertTrue( n.getNumChildren() == 1 );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_POWER );
assertTrue( n.getNumChildren() == 2 );
c = n.getLeftChild();
assertTrue( c.getType() == libsbml.AST_NAME );
assertTrue(( "x" == c.getName() ));
c = n.getRightChild();
assertTrue( c.getType() == libsbml.AST_INTEGER );
assertTrue( c.getInteger() == 2 );
n = null;
n = new ASTNode(libsbml.AST_FUNCTION);
n.setName( "sqrt");
c = new ASTNode();
c.setName( "x");
n.addChild(c);
assertTrue( n.getType() == libsbml.AST_FUNCTION );
assertTrue( n.getNumChildren() == 1 );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ROOT );
assertTrue( n.getNumChildren() == 2 );
c = n.getLeftChild();
assertTrue( c.getType() == libsbml.AST_INTEGER );
assertTrue( c.getInteger() == 2 );
c = n.getRightChild();
assertTrue( c.getType() == libsbml.AST_NAME );
assertTrue(( "x" == c.getName() ));
n = null;
}
public void test_ASTNode_create()
{
ASTNode n = new ASTNode();
EventAssignment ea = new EventAssignment(2,4);
assertTrue( n.getType() == libsbml.AST_UNKNOWN );
assertTrue( n.getCharacter() == '\0' );
assertTrue( n.getName() == null );
assertTrue( n.getInteger() == 0 );
assertTrue( n.getExponent() == 0 );
assertTrue( n.getNumChildren() == 0 );
assertTrue( n.getParentSBMLObject() == null );
ea = null;
n = null;
}
public void test_ASTNode_setType()
{
ASTNode node = new ASTNode();
node.setName( "foo");
assertTrue( node.getType() == libsbml.AST_NAME );
node.setType(libsbml.AST_FUNCTION);
assertTrue( node.getType() == libsbml.AST_FUNCTION );
assertTrue(( "foo" == node.getName() ));
node.setType(libsbml.AST_NAME);
assertTrue( node.getType() == libsbml.AST_NAME );
assertTrue(( "foo" == node.getName() ));
node.setType(libsbml.AST_INTEGER);
assertTrue( node.getType() == libsbml.AST_INTEGER );
node.setType(libsbml.AST_REAL);
assertTrue( node.getType() == libsbml.AST_REAL );
node.setType(libsbml.AST_UNKNOWN);
assertTrue( node.getType() == libsbml.AST_UNKNOWN );
node.setType(libsbml.AST_PLUS);
assertTrue( node.getType() == libsbml.AST_PLUS );
assertTrue( node.getCharacter() == '+' );
node.setType(libsbml.AST_MINUS);
assertTrue( node.getType() == libsbml.AST_MINUS );
assertTrue( node.getCharacter() == '-' );
node.setType(libsbml.AST_TIMES);
assertTrue( node.getType() == libsbml.AST_TIMES );
assertTrue( node.getCharacter() == '*' );
node.setType(libsbml.AST_DIVIDE);
assertTrue( node.getType() == libsbml.AST_DIVIDE );
assertTrue( node.getCharacter() == '/' );
node.setType(libsbml.AST_POWER);
assertTrue( node.getType() == libsbml.AST_POWER );
assertTrue( node.getCharacter() == '^' );
node = null;
}
public void test_ASTNode_setReal()
{
ASTNode node = new ASTNode();
node.setName( "foo");
assertTrue( node.getType() == libsbml.AST_NAME );
node.setValue(32.1);
assertTrue( node.getType() == libsbml.AST_REAL );
assertTrue( node.getInteger() == 0 );
assertTrue( node.getName() == null );
assertTrue( node.getCharacter() == '\0' );
assertTrue( node.getReal() == 32.1 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 1 );
assertTrue( node.getMantissa() == 32.1 );
node.setValue(45,90);
assertTrue( node.getType() == libsbml.AST_RATIONAL );
assertTrue( node.getInteger() == 45 );
assertTrue( node.getName() == null );
assertTrue( node.getCharacter() == '\0' );
assertTrue( node.getReal() == 0.5 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 90 );
assertTrue( node.getMantissa() == 0 );
node.setValue(32.0,4);
assertTrue( node.getType() == libsbml.AST_REAL_E );
assertTrue( node.getInteger() == 0 );
assertTrue( node.getName() == null );
assertTrue( node.getCharacter() == '\0' );
assertTrue( node.getReal() == 320000 );
assertTrue( node.getExponent() == 4 );
assertTrue( node.getDenominator() == 1 );
assertTrue( node.getMantissa() == 32 );
node = null;
}
public void test_ASTNode_setName_override()
{
ASTNode node = new ASTNode(libsbml.AST_FUNCTION_SIN);
assertTrue(( "sin" == node.getName() ));
assertTrue( node.getType() == libsbml.AST_FUNCTION_SIN );
node.setName( "MySinFunc");
assertTrue(( "MySinFunc" == node.getName() ));
assertTrue( node.getType() == libsbml.AST_FUNCTION_SIN );
node.setName(null);
assertTrue(( "sin" == node.getName() ));
assertTrue( node.getType() == libsbml.AST_FUNCTION_SIN );
node = null;
}
public void test_element_ci_definitionURL()
{
string s = wrapMathML("<ci definitionURL=\"foobar\"> x </ci>");
N = libsbml.readMathMLFromString(s);
assertTrue( N != null );
assertTrue( N.getType() == libsbml.AST_NAME );
assertTrue(( "x" == N.getName() ));
assertTrue( N.getNumChildren() == 0 );
assertTrue( N.getDefinitionURL().getValue(0) == "foobar" );
}
public void test_ASTNode_freeName()
{
ASTNode node = new ASTNode();
int i = 0;
i = node.setName( "a");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue(( "a" == libsbml.formulaToString(node) ));
assertTrue(( "a" == node.getName() ));
i = node.freeName();
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( node.getName() == null );
i = node.freeName();
assertTrue( i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE );
assertTrue( node.getName() == null );
node.setType(libsbml.AST_UNKNOWN);
i = node.freeName();
assertTrue( i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE );
assertTrue( node.getName() == null );
node = null;
}
public void test_element_ci_surrounding_spaces_bug()
{
string s = wrapMathML(" <ci> s </ci> ");
N = libsbml.readMathMLFromString(s);
assertTrue( N != null );
assertTrue( N.getType() == libsbml.AST_NAME );
assertTrue(( "s" == N.getName() ));
assertTrue( N.getNumChildren() == 0 );
}
public void test_ASTNode_getName()
{
ASTNode n = new ASTNode();
n.setName( "foo");
assertTrue(( "foo" == n.getName() ));
n.setType(libsbml.AST_NAME_TIME);
assertTrue(( "foo" == n.getName() ));
n.setName(null);
assertTrue( n.getName() == null );
n.setType(libsbml.AST_CONSTANT_E);
assertTrue(( "exponentiale" == n.getName() ));
n.setType(libsbml.AST_CONSTANT_FALSE);
assertTrue(( "false" == n.getName() ));
n.setType(libsbml.AST_CONSTANT_PI);
assertTrue(( "pi" == n.getName() ));
n.setType(libsbml.AST_CONSTANT_TRUE);
assertTrue(( "true" == n.getName() ));
n.setType(libsbml.AST_LAMBDA);
assertTrue(( "lambda" == n.getName() ));
n.setType(libsbml.AST_FUNCTION);
n.setName( "f");
assertTrue(( "f" == n.getName() ));
n.setType(libsbml.AST_FUNCTION_DELAY);
assertTrue(( "f" == n.getName() ));
n.setName(null);
assertTrue(( "delay" == n.getName() ));
n.setType(libsbml.AST_FUNCTION);
assertTrue( n.getName() == null );
n.setType(libsbml.AST_FUNCTION_ABS);
assertTrue(( "abs" == n.getName() ));
n.setType(libsbml.AST_FUNCTION_ARCCOS);
assertTrue(( "arccos" == n.getName() ));
n.setType(libsbml.AST_FUNCTION_TAN);
assertTrue(( "tan" == n.getName() ));
n.setType(libsbml.AST_FUNCTION_TANH);
assertTrue(( "tanh" == n.getName() ));
n.setType(libsbml.AST_LOGICAL_AND);
assertTrue(( "and" == n.getName() ));
n.setType(libsbml.AST_LOGICAL_NOT);
assertTrue(( "not" == n.getName() ));
n.setType(libsbml.AST_LOGICAL_OR);
assertTrue(( "or" == n.getName() ));
n.setType(libsbml.AST_LOGICAL_XOR);
assertTrue(( "xor" == n.getName() ));
n.setType(libsbml.AST_RELATIONAL_EQ);
assertTrue(( "eq" == n.getName() ));
n.setType(libsbml.AST_RELATIONAL_GEQ);
assertTrue(( "geq" == n.getName() ));
n.setType(libsbml.AST_RELATIONAL_LT);
assertTrue(( "lt" == n.getName() ));
n.setType(libsbml.AST_RELATIONAL_NEQ);
assertTrue(( "neq" == n.getName() ));
n = null;
}
public void test_element_csymbol_time()
{
string s = wrapMathML("<csymbol encoding='text' " + "definitionURL='http://www.sbml.org/sbml/symbols/time'> t </csymbol>");
N = libsbml.readMathMLFromString(s);
assertTrue( N != null );
assertTrue( N.getType() == libsbml.AST_NAME_TIME );
assertTrue(( "t" == N.getName() ));
assertTrue( N.getNumChildren() == 0 );
}
public void test_ASTNode_setInteger()
{
ASTNode node = new ASTNode();
node.setName( "foo");
assertTrue( node.getType() == libsbml.AST_NAME );
assertTrue(( "foo" == node.getName() ));
assertTrue( node.getCharacter() == '\0' );
assertTrue( node.getInteger() == 0 );
assertTrue( node.getReal() == 0 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 1 );
node.setValue(3.2);
assertTrue( node.getType() == libsbml.AST_REAL );
assertTrue( node.getInteger() == 0 );
assertTrue( node.getName() == null );
assertTrue( node.getCharacter() == '\0' );
assertTrue( node.getReal() == 3.2 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 1 );
node.setValue(321);
assertTrue( node.getType() == libsbml.AST_INTEGER );
assertTrue( node.getInteger() == 321 );
assertTrue( node.getName() == null );
assertTrue( node.getCharacter() == '\0' );
assertTrue( node.getReal() == 0 );
assertTrue( node.getExponent() == 0 );
assertTrue( node.getDenominator() == 1 );
node = null;
}