public void test_ASTNode_addChild1()
{
ASTNode node = new ASTNode();
ASTNode c1 = new ASTNode();
ASTNode c2 = new ASTNode();
ASTNode c1_1 = new ASTNode();
int i = 0;
node.setType(libsbml.AST_LOGICAL_AND);
c1.setName( "a");
c2.setName( "b");
node.addChild(c1);
node.addChild(c2);
assertTrue( node.getNumChildren() == 2 );
assertTrue(( "and(a, b)" == libsbml.formulaToString(node) ));
c1_1.setName( "d");
i = node.addChild(c1_1);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( node.getNumChildren() == 3 );
assertTrue(( "and(a, b, d)" == libsbml.formulaToString(node) ));
assertTrue(( "a" == node.getChild(0).getName() ));
assertTrue(( "b" == node.getChild(1).getName() ));
assertTrue(( "d" == node.getChild(2).getName() ));
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_SpeciesReference_setStoichiometryMath5()
{
SpeciesReference sr1 = new SpeciesReference(1,2);
StoichiometryMath sm = new StoichiometryMath(2,4);
ASTNode math = new ASTNode(libsbml.AST_TIMES);
ASTNode a = new ASTNode();
ASTNode b = new ASTNode();
a.setName( "a");
b.setName( "b");
math.addChild(a);
math.addChild(b);
sm.setMath(math);
int i = sr1.setStoichiometryMath(sm);
assertTrue( i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE );
assertEquals( false, sr1.isSetStoichiometryMath() );
sm = null;
sr1 = null;
}
public void test_KineticLaw_setMath2()
{
ASTNode math = new ASTNode(libsbml.AST_TIMES);
ASTNode a = new ASTNode();
a.setName( "a");
math.addChild(a);
int i = kl.setMath(math);
assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );
assertEquals( false, kl.isSetMath() );
math = null;
}
public void test_ASTNode_canonicalizeConstants()
{
ASTNode n = new ASTNode();
n.setName( "ExponentialE");
assertEquals( true, n.isName() );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_CONSTANT_E );
n.setType(libsbml.AST_NAME);
n.setName( "False");
assertEquals( true, n.isName() );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_CONSTANT_FALSE );
n.setType(libsbml.AST_NAME);
n.setName( "Pi");
assertEquals( true, n.isName() );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_CONSTANT_PI );
n.setType(libsbml.AST_NAME);
n.setName( "True");
assertEquals( true, n.isName() );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_CONSTANT_TRUE );
n.setType(libsbml.AST_NAME);
n.setName( "Foo");
assertEquals( true, n.isName() );
n.canonicalize();
assertEquals( true, n.isName() );
n = null;
}
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()
{
ASTNode n = new ASTNode();
n.setType(libsbml.AST_NAME_AVOGADRO);
n.setName( "NA");
assertTrue(( "NA" == n.getName() ));
double val = n.getReal();
assertTrue( val == 6.02214179e23 );
n = null;
}
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_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_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;
}
/// <summary>
///
/// </summary>
/// <param name="anASTNode"></param>
/// <returns></returns>
private ASTNode convertVariableName(ASTNode anASTNode)
{
long aNumChildren = anASTNode.getNumChildren();
if ( aNumChildren == 2 )
{
this.convertVariableName( anASTNode.getLeftChild() );
this.convertVariableName( anASTNode.getRightChild() );
}
else if ( aNumChildren == 1 )
{
this.convertVariableName( anASTNode.getLeftChild() );
}
else if ( aNumChildren == 0 )
{
if ( anASTNode.isNumber() )
{
}
else
{
string aName = anASTNode.getName();
int aType = this.getVariableType( aName );
//# Species
if ( aType == libsbml.libsbml.SBML_SPECIES )
{
string variableName = this.setSpeciesToVariableReference( aName , 0);
if( variableName != "" )
{
anASTNode.setName( variableName + ".Value" );
return anASTNode;
}
}
//# Parameter
else if ( aType == libsbml.libsbml.SBML_PARAMETER )
{
string variableName = this.setParameterToVariableReference( aName , 0);
if( variableName != "" )
{
anASTNode.setName( variableName + ".Value" );
return anASTNode;
}
}
//# Compartment
else if (aType == libsbml.libsbml.SBML_COMPARTMENT)
{
string variableName = this.setCompartmentToVariableReference(aName, 0);
if( variableName != "" )
{
anASTNode.setName( variableName + ".Value" );
return anASTNode;
}
}
}
}
return anASTNode;
}
public void test_MathMLFormatter_csymbol_time()
{
string expected = wrapMathML(" <csymbol encoding=\"text\" " + "definitionURL=\"http://www.sbml.org/sbml/symbols/time\"> t </csymbol>\n");
N = new ASTNode(libsbml.AST_NAME_TIME);
N.setName("t");
S = libsbml.writeMathMLToString(N);
assertEquals( true, equals(expected,S) );
}
public void test_MathMLFormatter_csymbol_delay()
{
string expected = wrapMathML(" <apply>\n" +
" <csymbol encoding=\"text\" definitionURL=\"http://www.sbml.org/sbml/" +
"symbols/delay\"> my_delay </csymbol>\n" +
" <ci> x </ci>\n" +
" <cn> 0.1 </cn>\n" +
" </apply>\n");
N = libsbml.parseFormula("delay(x, 0.1)");
N.setName("my_delay");
S = libsbml.writeMathMLToString(N);
assertEquals( true, equals(expected,S) );
}
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_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_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_removeChild()
{
ASTNode node = new ASTNode();
ASTNode c1 = new ASTNode();
ASTNode c2 = new ASTNode();
int i = 0;
node.setType(libsbml.AST_PLUS);
c1.setName( "foo");
c2.setName( "foo2");
node.addChild(c1);
node.addChild(c2);
assertTrue( node.getNumChildren() == 2 );
i = node.removeChild(0);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( node.getNumChildren() == 1 );
i = node.removeChild(1);
assertTrue( i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE );
assertTrue( node.getNumChildren() == 1 );
i = node.removeChild(0);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( node.getNumChildren() == 0 );
node = null;
}
public void test_ASTNode_canonicalizeFunctions()
{
ASTNode n = new ASTNode(libsbml.AST_FUNCTION);
n.setName( "abs");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ABS );
n.setType(libsbml.AST_FUNCTION);
n.setName( "arccos");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCCOS );
n.setType(libsbml.AST_FUNCTION);
n.setName( "arccosh");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCCOSH );
n.setType(libsbml.AST_FUNCTION);
n.setName( "arccot");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCCOT );
n.setType(libsbml.AST_FUNCTION);
n.setName( "arccoth");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCCOTH );
n.setType(libsbml.AST_FUNCTION);
n.setName( "arccsc");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCCSC );
n.setType(libsbml.AST_FUNCTION);
n.setName( "arccsch");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCCSCH );
n.setType(libsbml.AST_FUNCTION);
n.setName( "arcsec");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCSEC );
n.setType(libsbml.AST_FUNCTION);
n.setName( "arcsech");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCSECH );
n.setType(libsbml.AST_FUNCTION);
n.setName( "arcsin");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCSIN );
n.setType(libsbml.AST_FUNCTION);
n.setName( "arcsinh");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCSINH );
n.setType(libsbml.AST_FUNCTION);
n.setName( "arctan");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCTAN );
n.setType(libsbml.AST_FUNCTION);
n.setName( "arctanh");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ARCTANH );
n.setType(libsbml.AST_FUNCTION);
n.setName( "ceiling");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_CEILING );
n.setType(libsbml.AST_FUNCTION);
n.setName( "cos");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_COS );
n.setType(libsbml.AST_FUNCTION);
n.setName( "cosh");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_COSH );
n.setType(libsbml.AST_FUNCTION);
n.setName( "cot");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_COT );
n.setType(libsbml.AST_FUNCTION);
n.setName( "coth");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_COTH );
n.setType(libsbml.AST_FUNCTION);
n.setName( "csc");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_CSC );
n.setType(libsbml.AST_FUNCTION);
n.setName( "csch");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_CSCH );
n.setType(libsbml.AST_FUNCTION);
n.setName( "exp");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_EXP );
n.setType(libsbml.AST_FUNCTION);
n.setName( "factorial");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_FACTORIAL );
n.setType(libsbml.AST_FUNCTION);
n.setName( "floor");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_FLOOR );
n.setType(libsbml.AST_FUNCTION);
n.setName( "lambda");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_LAMBDA );
n.setType(libsbml.AST_FUNCTION);
n.setName( "ln");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_LN );
n.setType(libsbml.AST_FUNCTION);
n.setName( "log");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_LOG );
n.setType(libsbml.AST_FUNCTION);
n.setName( "piecewise");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_PIECEWISE );
n.setType(libsbml.AST_FUNCTION);
n.setName( "power");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_POWER );
n.setType(libsbml.AST_FUNCTION);
n.setName( "root");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_ROOT );
n.setType(libsbml.AST_FUNCTION);
n.setName( "sec");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_SEC );
n.setType(libsbml.AST_FUNCTION);
n.setName( "sech");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_SECH );
n.setType(libsbml.AST_FUNCTION);
n.setName( "sin");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_SIN );
n.setType(libsbml.AST_FUNCTION);
n.setName( "sinh");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_SINH );
n.setType(libsbml.AST_FUNCTION);
n.setName( "tan");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_TAN );
n.setType(libsbml.AST_FUNCTION);
n.setName( "tanh");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION_TANH );
n.setType(libsbml.AST_FUNCTION);
n.setName( "Foo");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n = null;
}
public void test_ASTNode_replaceChild()
{
ASTNode node = new ASTNode();
ASTNode c1 = new ASTNode();
ASTNode c2 = new ASTNode();
ASTNode c3 = new ASTNode();
ASTNode newc = new ASTNode();
int i = 0;
node.setType(libsbml.AST_LOGICAL_AND);
c1.setName( "a");
c2.setName( "b");
c3.setName( "c");
node.addChild(c1);
node.addChild(c2);
node.addChild(c3);
assertTrue( node.getNumChildren() == 3 );
assertTrue(( "and(a, b, c)" == libsbml.formulaToString(node) ));
newc.setName( "d");
i = node.replaceChild(0,newc);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( node.getNumChildren() == 3 );
assertTrue(( "and(d, b, c)" == libsbml.formulaToString(node) ));
i = node.replaceChild(3,newc);
assertTrue( i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE );
assertTrue( node.getNumChildren() == 3 );
assertTrue(( "and(d, b, c)" == libsbml.formulaToString(node) ));
i = node.replaceChild(1,c1);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( node.getNumChildren() == 3 );
assertTrue(( "and(d, a, c)" == libsbml.formulaToString(node) ));
node = 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_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;
}
public void test_ASTNode_canonicalizeLogical()
{
ASTNode n = new ASTNode(libsbml.AST_FUNCTION);
n.setName( "and");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_LOGICAL_AND );
n.setType(libsbml.AST_FUNCTION);
n.setName( "not");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_LOGICAL_NOT );
n.setType(libsbml.AST_FUNCTION);
n.setName( "or");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_LOGICAL_OR );
n.setType(libsbml.AST_FUNCTION);
n.setName( "xor");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_LOGICAL_XOR );
n.setType(libsbml.AST_FUNCTION);
n = null;
}
public void test_KineticLaw_setMath1()
{
ASTNode math = new ASTNode(libsbml.AST_TIMES);
ASTNode a = new ASTNode();
ASTNode b = new ASTNode();
a.setName( "a");
b.setName( "b");
math.addChild(a);
math.addChild(b);
string formula;
ASTNode math1;
int i = kl.setMath(math);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertEquals( true, kl.isSetMath() );
math1 = kl.getMath();
assertTrue( math1 != null );
formula = libsbml.formulaToString(math1);
assertTrue( formula != null );
assertTrue(( "a * b" == formula ));
math = null;
}
public void test_ASTNode_canonicalizeRelational()
{
ASTNode n = new ASTNode(libsbml.AST_FUNCTION);
n.setName( "eq");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_RELATIONAL_EQ );
n.setType(libsbml.AST_FUNCTION);
n.setName( "geq");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_RELATIONAL_GEQ );
n.setType(libsbml.AST_FUNCTION);
n.setName( "gt");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_RELATIONAL_GT );
n.setType(libsbml.AST_FUNCTION);
n.setName( "leq");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_RELATIONAL_LEQ );
n.setType(libsbml.AST_FUNCTION);
n.setName( "lt");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_RELATIONAL_LT );
n.setType(libsbml.AST_FUNCTION);
n.setName( "neq");
assertTrue( n.getType() == libsbml.AST_FUNCTION );
n.canonicalize();
assertTrue( n.getType() == libsbml.AST_RELATIONAL_NEQ );
n.setType(libsbml.AST_FUNCTION);
n = null;
}
/// <summary>
///
/// </summary>
/// <param name="anASTNode"></param>
/// <returns></returns>
private ASTNode convertVariableName(ASTNode anASTNode)
{
long aNumChildren = anASTNode.getNumChildren();
if ( aNumChildren == 2 )
{
this.convertVariableName( anASTNode.getLeftChild() );
this.convertVariableName( anASTNode.getRightChild() );
return anASTNode;
}
else if ( aNumChildren == 1 )
{
this.convertVariableName( anASTNode.getLeftChild() );
return anASTNode;
}
else if ( aNumChildren == 0 )
{
if ( anASTNode.isNumber() )
{
}
else
{
string aName = anASTNode.getName();
string variableName = "";
// Check Species
foreach(SpeciesStruct aSpecies in this.Model.SpeciesList)
{
if ( aSpecies.ID != aName && aSpecies.Name != aName)
continue;
// Check VariableReference
foreach(VariableReferenceStruct aVariableReference in this.VariableReferenceList)
if (aVariableReference.Variable.Split(':')[2] == aName)
variableName = aVariableReference.Name;
if (variableName == "")
{
string aModifierID = this.Model.getSpeciesReferenceID(aName);
VariableReferenceStruct varRef = new VariableReferenceStruct(
"C" + this.ModifierNumber.ToString(),
"Variable:" + aModifierID,
0);
this.VariableReferenceList.Add(varRef);
variableName = varRef.Name;
this.ModifierNumber++;
}
//string compartmentName = this.setCompartmentToVariableReference( aSpecies.Compartment );
//anASTNode.setType( libsbml.libsbml.AST_DIVIDE );
//anASTNode.addChild( new ASTNode( libsbml.libsbml.AST_NAME ) );
//anASTNode.addChild( new ASTNode( libsbml.libsbml.AST_NAME ) );
//anASTNode.getLeftChild().setName( variableName + ".Value" );
//anASTNode.getRightChild().setName( compartmentName + ".Value" ) ;
anASTNode.setName(variableName + ".Value");
return anASTNode;
}
// Check Parameters.
foreach(ParameterStruct aParameter in this.Model.ParameterList)
{
if (aParameter.ID != aName && aParameter.Name != aName)
continue;
foreach(VariableReferenceStruct aVariableReference in this.VariableReferenceList)
if (aVariableReference.Variable.Split(':')[2] == aName)
variableName = aVariableReference.Name;
if( variableName == "" )
{
VariableReferenceStruct varRef = new VariableReferenceStruct(
aName,
"Variable:/:" + aName,
0 );
this.VariableReferenceList.Add( varRef );
this.ParameterNumber++;
variableName = varRef.Name;
}
anASTNode.setName( variableName + ".Value" );
return anASTNode;
}
// if variableName == '':
variableName = this.setCompartmentToVariableReference( aName );
if (variableName != "")
anASTNode.setName( variableName + ".Value" );
}
}
return anASTNode;
}
public void test_SpeciesReference_setStoichiometryMath2()
{
StoichiometryMath sm = new StoichiometryMath(2,4);
ASTNode math = new ASTNode(libsbml.AST_TIMES);
ASTNode a = new ASTNode();
a.setName( "a");
math.addChild(a);
sm.setMath(math);
int i = sr.setStoichiometryMath(sm);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertEquals( true, sr.isSetStoichiometryMath() );
sm = null;
}
