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_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_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_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_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_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_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_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_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_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_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_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;
}
/// <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_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_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_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_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_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_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;
}
/// <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;
}
private static ASTNode setDelayType(ASTNode anASTNode)
{
long aNumChildren = anASTNode.getNumChildren();
if ( aNumChildren == 2 )
{
if ( anASTNode.isFunction() == true && anASTNode.getName() == "delay" )
anASTNode.setType( libsbml.libsbml.AST_FUNCTION_DELAY );
setDelayType(anASTNode.getLeftChild());
setDelayType(anASTNode.getRightChild());
}
else if ( aNumChildren == 1 )
setDelayType( anASTNode.getLeftChild() );
return anASTNode;
}