/// <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_ASTNode_no_children()
{
ASTNode node = new ASTNode();
assertTrue( node.getNumChildren() == 0 );
assertTrue( node.getLeftChild() == null );
assertTrue( node.getRightChild() == null );
assertTrue( node.getChild(0) == null );
node = null;
}
public void test_ASTNode_one_child()
{
ASTNode node = new ASTNode();
ASTNode child = new ASTNode();
node.addChild(child);
assertTrue( node.getNumChildren() == 1 );
assertTrue( node.getLeftChild() == child );
assertTrue( node.getRightChild() == null );
assertTrue( node.getChild(0) == child );
assertTrue( node.getChild(1) == null );
node = null;
}
public void test_ASTNode_children()
{
ASTNode parent = new ASTNode();
ASTNode left = new ASTNode();
ASTNode right = new ASTNode();
ASTNode right2 = new ASTNode();
parent.setType(libsbml.AST_PLUS);
left.setValue(1);
right.setValue(2);
right2.setValue(3);
parent.addChild(left);
parent.addChild(right);
assertTrue( parent.getNumChildren() == 2 );
assertTrue( left.getNumChildren() == 0 );
assertTrue( right.getNumChildren() == 0 );
assertTrue( parent.getLeftChild() == left );
assertTrue( parent.getRightChild() == right );
assertTrue( parent.getChild(0) == left );
assertTrue( parent.getChild(1) == right );
assertTrue( parent.getChild(2) == null );
parent.addChild(right2);
assertTrue( parent.getNumChildren() == 3 );
assertTrue( left.getNumChildren() == 0 );
assertTrue( right.getNumChildren() == 0 );
assertTrue( right2.getNumChildren() == 0 );
assertTrue( parent.getLeftChild() == left );
assertTrue( parent.getRightChild() == right2 );
assertTrue( parent.getChild(0) == left );
assertTrue( parent.getChild(1) == right );
assertTrue( parent.getChild(2) == right2 );
assertTrue( parent.getChild(3) == null );
parent = null;
}
public void test_ASTNode_deepCopy_1()
{
ASTNode node = new ASTNode();
ASTNode child, copy;
node.setCharacter( '+');
node.addChild(new ASTNode());
node.addChild(new ASTNode());
node.getLeftChild().setValue(1);
node.getRightChild().setValue(2);
assertTrue( node.getType() == libsbml.AST_PLUS );
assertTrue( node.getCharacter() == '+' );
assertTrue( node.getNumChildren() == 2 );
child = node.getLeftChild();
assertTrue( child.getType() == libsbml.AST_INTEGER );
assertTrue( child.getInteger() == 1 );
assertTrue( child.getNumChildren() == 0 );
child = node.getRightChild();
assertTrue( child.getType() == libsbml.AST_INTEGER );
assertTrue( child.getInteger() == 2 );
assertTrue( child.getNumChildren() == 0 );
copy = node.deepCopy();
assertTrue( copy != node );
assertTrue( copy.getType() == libsbml.AST_PLUS );
assertTrue( copy.getCharacter() == '+' );
assertTrue( copy.getNumChildren() == 2 );
child = copy.getLeftChild();
assertTrue( child != node.getLeftChild() );
assertTrue( child.getType() == libsbml.AST_INTEGER );
assertTrue( child.getInteger() == 1 );
assertTrue( child.getNumChildren() == 0 );
child = copy.getRightChild();
assertTrue( child != node.getRightChild() );
assertTrue( child.getType() == libsbml.AST_INTEGER );
assertTrue( child.getInteger() == 2 );
assertTrue( child.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_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_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_csymbol_1()
{
string s = wrapMathML("<apply>" +
" <gt/>" +
" <csymbol encoding='text' " +
" definitionURL='http://www.sbml.org/sbml/symbols/time'>time</csymbol>" +
" <cn>5000</cn>" +
"</apply>");
N = libsbml.readMathMLFromString(s);
assertTrue( N != null );
assertTrue( N.getType() == libsbml.AST_RELATIONAL_GT );
assertTrue( N.getNumChildren() == 2 );
ASTNode c = N.getLeftChild();
assertTrue( c != null );
assertTrue( c.getType() == libsbml.AST_NAME_TIME );
assertTrue(( "time" == c.getName() ));
assertTrue( c.getNumChildren() == 0 );
c = N.getRightChild();
assertTrue( c != null );
assertTrue( c.getType() == libsbml.AST_REAL );
assertTrue( c.getReal() == 5000 );
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_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 );
}
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;
}