//Just create one Vertex SubExpressionGraph with this node
public override SubExpressionGraph Visit(AtomNode node)
{
var sub_graph = new SubExpressionGraph();
sub_graph.LastNode = node;
return(sub_graph);
}
public override void Visit(AtomNode node)
{
base.Visit(node);
if (!ReferenceEquals(node.VariableType, null))
{
node.VariableType.Accept(this);
}
}
/// <summary>Removes the specified <see cref="AtomNode"/> from this node.</summary>
/// <param name="node">The <see cref="AtomNode"/> to remove.</param>
/// <exception cref="ArgumentNullException"><paramref name="node"/> is null.</exception>
/// <exception cref="ArgumentException"><paramref name="node"/> cannot be removed.</exception>
public void Remove(AtomNode node)
{
if(node == null) throw new ArgumentNullException("node");
if(this.CanRemoveNode(node) == false) throw new ArgumentException(Errors.CannotRemoveNode, "node");
XElement element = (XElement)node;
if(element.Parent == this.Element)
element.Remove();
}
public SGChromosome Crossover(SGChromosome pair)
{
List <LinkEdge> childLinks = new List <LinkEdge>();
childLinks.AddRange(LinkEdge.ListClone(this.Molecule.LinkEdges.Take(this.Molecule.LinkEdges.Count / 2).ToList()));
childLinks.AddRange(LinkEdge.ListClone(pair.Molecule.LinkEdges.Skip(childLinks.Count).ToList()));
return(new SGChromosome(new MoleculeGraph(this.Molecule.Nomenclature, AtomNode.ListClone(this.Molecule.AtomNodes), childLinks)));
}
public Atom GetCollectionFromNode(AtomNode atom)
{
var collection = new Atom();
collection.AtomId = atom.AtomId;
collection.Octet = atom.Octet;
collection.Symbol = atom.Symbol;
return(collection);
}
public List <char> GetAtomsPart(string part)
{
var atoms = new List <char>();
foreach (var atom in part.Where(atom => AtomNode.IsAtom(atom) && !atoms.Contains(atom)))
{
atoms.Add(atom);
}
return(atoms);
}
//Replace IfNodes and link sub_graph of childs
public override SubExpressionGraph Visit(BlockExpressionNode node)
{
var sub_graph = new SubExpressionGraph();
var new_elements = new List <ExpressionNode>();
VariableDefNode t = new VariableDefNode();
t.ExpressionType = node.ExpressionType;
t.Name = "T" + temporary_counter;
AtomNode _0 = new AtomNode(node.ExpressionType);
_0.Value = "";
t.Value = _0;
VariableUseNode t_use = new VariableUseNode();
t_use.ExpressionType = node.ExpressionType;
t_use.Declaration = t;
t_use.Name = "T" + temporary_counter;
if (!ReferenceEquals(node.Elements, null))
{
int counter = 0;
foreach (var child in node.Elements)
{
if (!ReferenceEquals(child, null))
{
var child_graph = child.Accept(this);
if (child_graph == null)
{
throw new Exception("SubGraph of child is null");
}
new_elements.Add(GetUpdatedExpressionNodeValue(child, child_graph));
if (counter == node.Elements.Count() - 1)
{
OperatorNode _temp_assing = new OperatorNode();
_temp_assing.Operator = OperatorType.ASSIGN;
_temp_assing.Arguments = new List <ExpressionNode> {
t_use, child_graph.LastNode
};
child_graph.LastNode = _temp_assing;
}
child_graph = SubExpressionGraph.ConcatSubGraph(child_graph, SubExpressionGraph.CreateOneVertexSubGraph(child_graph.LastNode));
sub_graph = SubExpressionGraph.ConcatSubGraph(sub_graph, child_graph);
}
}
node.Elements = new_elements;
}
sub_graph.ContainsExtracted = true;
sub_graph.Temporary = t_use;
temporary_counter++;
return(sub_graph);
}
public void Formula4()
{
var c0 = new AtomNode("C");
var mole = new Molecule(c0);
for (int i = 0; i < 99; i++)
{
var c = new AtomNode("C");
mole.AddBondToLast(BondOrder.Single, c);
}
var formula = mole.GetMolecularFormula();
Assert.AreEqual("C100H202", formula);
}
public void Mr4()
{
var c0 = new AtomNode("C");
var mole = new Molecule(c0);
for (int i = 0; i < 99; i++)
{
var c = new AtomNode("C");
mole.AddBondToLast(BondOrder.Single, c);
}
var mass = float.Parse(mole.GetMolecularMass());
Assert.AreEqual(1402, mass);
}
//try to find definition type on base of Value
public override void Visit(AtomNode node)
{
base.Visit(node);
if (node.Value == null)
{
throw new TypeCheckException("Value is not set.");
}
HashSet <TypeNode> deducedType = deduceType(node.Value);
if (!deducedType.Contains(node.VariableType))
{
throw new TypeCheckException("Type of Const is not consistent with deduced Type.");
}
node.ExpressionType = node.VariableType;
}
public void Smiles3()
{
var c0 = new AtomNode("C");
var c1 = new AtomNode("C");
var c2 = new AtomNode("C");
var n = new AtomNode("N");
var mole = new Molecule(c0);
mole.AddBondToLast(BondOrder.Single, c1);
mole.AddBondToLast(BondOrder.Single, c2);
mole.AddBondToLast(BondOrder.Triple, n);
var smiles = mole.ToSMILES();
Assert.AreEqual("CCC#N", smiles);
}
public void Formula3()
{
var c0 = new AtomNode("C");
var c1 = new AtomNode("C");
var c2 = new AtomNode("C");
var n = new AtomNode("N");
var mole = new Molecule(c0);
mole.AddBondToLast(BondOrder.Single, c1);
mole.AddBondToLast(BondOrder.Single, c2);
mole.AddBondToLast(BondOrder.Triple, n);
var formula = mole.GetMolecularFormula();
Assert.AreEqual("C3H5N", formula);
}
public void Mr3()
{
var c0 = new AtomNode("C");
var c1 = new AtomNode("C");
var c2 = new AtomNode("C");
var n = new AtomNode("N");
var mole = new Molecule(c0);
mole.AddBondToLast(BondOrder.Single, c1);
mole.AddBondToLast(BondOrder.Single, c2);
mole.AddBondToLast(BondOrder.Triple, n);
var mass = float.Parse(mole.GetMolecularMass());
Assert.AreEqual(55, mass);
}
public void Smiles2()
{
var c0 = new AtomNode("C");
var c1 = new AtomNode("C");
var c2 = new AtomNode("C");
var c3 = new AtomNode("C");
var o = new AtomNode("O");
var mole = new Molecule(c0);
mole.AddBondToLast(BondOrder.Single, c1);
mole.AddBond(BondOrder.Single, c1, c2);
mole.AddBond(BondOrder.Single, c2, c3);
mole.AddBondToLast(BondOrder.Double, o);
var smiles = mole.ToSMILES();
Assert.AreEqual("CCCC=O", smiles);
}
public void Smiles4()
{
var c0 = new AtomNode("C");
var mole = new Molecule(c0);
var s = "C";
for (int i = 0; i < 20; i++)
{
var c = new AtomNode("C");
mole.AddBondToLast(BondOrder.Single, c);
s += "C";
}
var smiles = mole.ToSMILES();
Assert.AreEqual(s, smiles);
}
public void Formula2()
{
var c0 = new AtomNode("C");
var c1 = new AtomNode("C");
var c2 = new AtomNode("C");
var c3 = new AtomNode("C");
var o = new AtomNode("O");
var mole = new Molecule(c0);
mole.AddBondToLast(BondOrder.Single, c1);
mole.AddBond(BondOrder.Single, c1, c2);
mole.AddBond(BondOrder.Single, c2, c3);
mole.AddBondToLast(BondOrder.Double, o);
var formula = mole.GetMolecularFormula();
Assert.AreEqual("C4H8O", formula);
}
public void Mr2()
{
var c0 = new AtomNode("C");
var c1 = new AtomNode("C");
var c2 = new AtomNode("C");
var c3 = new AtomNode("C");
var o = new AtomNode("O");
var mole = new Molecule(c0);
mole.AddBondToLast(BondOrder.Single, c1);
mole.AddBond(BondOrder.Single, c1, c2);
mole.AddBond(BondOrder.Single, c2, c3);
mole.AddBondToLast(BondOrder.Double, o);
var mass = float.Parse(mole.GetMolecularMass());
Assert.AreEqual(72, mass);
}
public void Formula5()
{
var c0 = new AtomNode("C");
var p = new AtomNode("P");
var h = new AtomNode("H");
var n = new AtomNode("N");
var o = new AtomNode("O");
var cl = new AtomNode("Cl");
var o2 = new AtomNode("O");
var mole = new Molecule(c0);
mole.AddBondToLast(BondOrder.Single, p);
mole.AddBondToLast(BondOrder.Single, cl);
mole.AddBond(BondOrder.Single, c0, h);
mole.AddBond(BondOrder.Single, p, n);
mole.AddBondToLast(BondOrder.Double, o);
mole.AddBond(BondOrder.Single, n, o2);
var formula = mole.GetMolecularFormula();
Assert.AreEqual("CH4PClNO2", formula);
}
public void Smiles5()
{
var c0 = new AtomNode("C");
var p = new AtomNode("P");
var h = new AtomNode("H");
var n = new AtomNode("N");
var o = new AtomNode("O");
var cl = new AtomNode("Cl");
var o2 = new AtomNode("O");
var mole = new Molecule(c0);
mole.AddBondToLast(BondOrder.Single, p);
mole.AddBondToLast(BondOrder.Single, cl);
mole.AddBond(BondOrder.Single, c0, h);
mole.AddBond(BondOrder.Single, p, n);
mole.AddBondToLast(BondOrder.Double, o);
mole.AddBond(BondOrder.Single, n, o2);
var smiles = mole.ToSMILES();
Assert.AreEqual("CP(Cl)(N(=O)(O))", smiles);
}
public void Mr5()
{
var c0 = new AtomNode("C");
var p = new AtomNode("P");
var h = new AtomNode("H");
var n = new AtomNode("N");
var o = new AtomNode("O");
var cl = new AtomNode("Cl");
var o2 = new AtomNode("O");
var mole = new Molecule(c0);
mole.AddBondToLast(BondOrder.Single, p);
mole.AddBondToLast(BondOrder.Single, cl);
mole.AddBond(BondOrder.Single, c0, h);
mole.AddBond(BondOrder.Single, p, n);
mole.AddBondToLast(BondOrder.Double, o);
mole.AddBond(BondOrder.Single, n, o2);
var mass = float.Parse(mole.GetMolecularMass());
Assert.AreEqual(128.5, mass);
}
public void Smiles1()
{
var c0 = new AtomNode("C");
var c1 = new AtomNode("C");
var c2 = new AtomNode("C");
var c3 = new AtomNode("C");
var c4 = new AtomNode("C");
var c5 = new AtomNode("C");
var h = new AtomNode("H");
var mole = new Molecule(c0);
mole.AddBondToLast(BondOrder.Single, c1);
mole.AddBond(BondOrder.Single, c1, c2);
mole.AddBond(BondOrder.Single, c2, c3);
mole.AddBondToLast(BondOrder.Single, c4);
mole.AddBondToLast(BondOrder.Single, c5);
mole.AddBondToLast(BondOrder.Single, c0);
mole.AddBondToLast(BondOrder.Single, h);
var smiles = mole.ToSMILES();
Assert.AreEqual("C1CCCCC1", smiles);
}
public void Formula1()
{
var c0 = new AtomNode("C");
var c1 = new AtomNode("C");
var c2 = new AtomNode("C");
var c3 = new AtomNode("C");
var c4 = new AtomNode("C");
var c5 = new AtomNode("C");
var h = new AtomNode("H");
var mole = new Molecule(c0);
mole.AddBondToLast(BondOrder.Single, c1);
mole.AddBond(BondOrder.Single, c1, c2);
mole.AddBond(BondOrder.Single, c2, c3);
mole.AddBondToLast(BondOrder.Single, c4);
mole.AddBondToLast(BondOrder.Single, c5);
mole.AddBondToLast(BondOrder.Single, c0);
mole.AddBondToLast(BondOrder.Single, h);
var formula = mole.GetMolecularFormula();
Assert.AreEqual("C6H12", formula);
}
public void Mr1()
{
var c0 = new AtomNode("C");
var c1 = new AtomNode("C");
var c2 = new AtomNode("C");
var c3 = new AtomNode("C");
var c4 = new AtomNode("C");
var c5 = new AtomNode("C");
var h = new AtomNode("H");
var mole = new Molecule(c0);
mole.AddBondToLast(BondOrder.Single, c1);
mole.AddBond(BondOrder.Single, c1, c2);
mole.AddBond(BondOrder.Single, c2, c3);
mole.AddBondToLast(BondOrder.Single, c4);
mole.AddBondToLast(BondOrder.Single, c5);
mole.AddBondToLast(BondOrder.Single, c0);
mole.AddBondToLast(BondOrder.Single, h);
var mass = float.Parse(mole.GetMolecularMass());
Assert.AreEqual(84, mass);
}
public void Mutate(double rate)
{
double randonrate = _random.NextDouble();
if (randonrate < rate)
{
this.Molecule.LinkEdges.RemoveAt(_random.Next(this.Molecule.LinkEdges.Count));
bool create = false;
do
{
var atom1 = this.Molecule.AtomNodes[_random.Next(this.Molecule.AtomNodes.Count)];
var atom2 = this.Molecule.AtomNodes[_random.Next(this.Molecule.AtomNodes.Count)];
create = atom1.AtomId != atom2.AtomId;
if (create)
{
var from = new AtomNode(atom1.Symbol, atom1.AtomId);
var to = new AtomNode(atom2.Symbol, atom2.AtomId);
this.Molecule.LinkEdges.Add(new LinkEdge(from, to));
}
} while (!create);
this.CalcFitness();
}
}
//create cycle for while
public override SubExpressionGraph Visit(WhileNode node)
{
while_stack.Add(node);
var sub_graph = new SubExpressionGraph();
var begin_while = SubExpressionGraph.CreateOneVertexSubGraph(new BlockExpressionNode());
if (!ReferenceEquals(node.Condition, null))
{
node.Condition = ProcessSingleNode(node.Condition, ref sub_graph);
}
if (!ReferenceEquals(node.Body, null))
{
node.Body = ProcessSingleNode(node.Body, ref sub_graph);
}
if (node.HasElse)
{
node.Else = ProcessSingleNode(node.Else, ref sub_graph);
}
VariableDefNode t = new VariableDefNode();
t.ExpressionType = node.ExpressionType;
t.Name = "T" + temporary_counter;
AtomNode _0 = new AtomNode(node.ExpressionType);
_0.Value = "";
t.Value = _0;
VariableUseNode t_use = new VariableUseNode();
t_use.ExpressionType = node.ExpressionType;
t_use.Declaration = t;
t_use.Name = "T" + temporary_counter;
List <Vertex> while_graph_vertex = new List <Vertex>();
OperatorNode assign_body = new OperatorNode();
assign_body.Operator = OperatorType.ASSIGN;
assign_body.Arguments = new List <ExpressionNode> {
t_use, node.Body
};
ConditionalJumpVertex condition_vertex = new ConditionalJumpVertex(null, null, node.Condition);
while_graph_vertex.Add(condition_vertex);
OneJumpVertex body_vertex = new OneJumpVertex(condition_vertex, assign_body);
while_graph_vertex.Add(body_vertex);
OneJumpVertex end_while_vertex = new OneJumpVertex(null, t_use);
condition_vertex.TrueJump = body_vertex;
body_vertex.Jump = begin_while.Start;
if (node.HasElse)
{
OperatorNode assign_else = new OperatorNode();
assign_else.Operator = OperatorType.ASSIGN;
assign_else.Arguments = new List <ExpressionNode> {
t_use, node.Else
};
OneJumpVertex else_vertex = new OneJumpVertex(end_while_vertex, assign_else);
while_graph_vertex.Add(else_vertex);
condition_vertex.FalseJump = else_vertex;
}
else
{
condition_vertex.FalseJump = end_while_vertex;
}
while_graph_vertex.Add(end_while_vertex);
sub_graph = SubExpressionGraph.ConcatSubGraph(sub_graph, new SubExpressionGraph(condition_vertex, while_graph_vertex, end_while_vertex, true, null));
sub_graph.Temporary = t_use;
temporary_counter++;
if (while_for_loop_control.ContainsKey(LoopControlMode.LCM_BREAK) && while_for_loop_control[LoopControlMode.LCM_BREAK].ContainsKey(node))
{
foreach (var loop_control_vertex in while_for_loop_control[LoopControlMode.LCM_BREAK][node])
{
((OneJumpVertex)loop_control_vertex).Jump = sub_graph.End;
}
}
if (while_for_loop_control.ContainsKey(LoopControlMode.LCM_CONTINUE) && while_for_loop_control[LoopControlMode.LCM_CONTINUE].ContainsKey(node))
{
foreach (var loop_control_vertex in while_for_loop_control[LoopControlMode.LCM_CONTINUE][node])
{
((OneJumpVertex)loop_control_vertex).Jump = sub_graph.Start;
}
}
while_stack.Remove(node);
return(sub_graph);
}
//Create diamond graph with CondtionVertex, mark flag IF
public override SubExpressionGraph Visit(IfNode node)
{
var sub_graph = new SubExpressionGraph();
if (!ReferenceEquals(node.Condition, null))
{
node.Condition = ProcessSingleNode(node.Condition, ref sub_graph);
}
if (!ReferenceEquals(node.Then, null))
{
node.Then = ProcessSingleNode(node.Then, ref sub_graph);
}
if (node.HasElse)
{
node.Else = ProcessSingleNode(node.Else, ref sub_graph);
}
VariableDefNode t = new VariableDefNode();
t.ExpressionType = node.ExpressionType;
t.Name = "T" + temporary_counter;
AtomNode _0 = new AtomNode(node.ExpressionType);
_0.Value = "";
t.Value = _0;
VariableUseNode t_use = new VariableUseNode();
t_use.ExpressionType = node.ExpressionType;
t_use.Declaration = t;
t_use.Name = "T" + temporary_counter;
OperatorNode assign_then = new OperatorNode();
assign_then.Operator = OperatorType.ASSIGN;
assign_then.Arguments = new List <ExpressionNode> {
t_use, node.Then
};
OneJumpVertex then_vertex = new OneJumpVertex(null, assign_then);
OneJumpVertex end_if = new OneJumpVertex(null, t_use);
ConditionalJumpVertex condition_vertex = new ConditionalJumpVertex(then_vertex, end_if, node.Condition);
var vertex_in_if = new List <Vertex> {
condition_vertex, then_vertex
};
if (node.HasElse)
{
OperatorNode assign_else = new OperatorNode();
assign_else.Operator = OperatorType.ASSIGN;
assign_else.Arguments = new List <ExpressionNode> {
t_use, node.Else
};
OneJumpVertex else_vertex = new OneJumpVertex(null, assign_else);
condition_vertex.FalseJump = else_vertex;
else_vertex.Jump = end_if;
vertex_in_if.Add(else_vertex);
}
else
{
condition_vertex.FalseJump = end_if;
}
vertex_in_if.Add(end_if);
var if_sub_graph = new SubExpressionGraph(condition_vertex, vertex_in_if, end_if, true, null);
sub_graph = SubExpressionGraph.ConcatSubGraph(sub_graph, if_sub_graph);
sub_graph.Temporary = t_use;
temporary_counter++;
return(sub_graph);
}
public override void Visit(IfNode node)
{
base.Visit(node);
if (changed_nodes.ContainsKey(node.Condition))
{
node.Condition = changed_nodes[node.Condition];
}
if (changed_nodes.ContainsKey(node.Then))
{
node.Then = changed_nodes[node.Then];
}
if (changed_nodes.ContainsKey(node.Else))
{
node.Else = changed_nodes[node.Else];
}
VariableDefNode t = new VariableDefNode();
t.Name = "T" + temporary_counter;
AtomNode _0 = new AtomNode(NamedTypeNode.IntType());
_0.Value = "0";
t.Value = _0;
VariableUseNode t_use = new VariableUseNode();
t_use.Declaration = t;
t_use.Name = "T" + temporary_counter;
OperatorNode assign_then = new OperatorNode();
assign_then.Operator = OperatorType.ASSIGN;
assign_then.Arguments = new List <ExpressionNode> {
t_use, node.Then
};
OneJumpVertex then_vertex = new OneJumpVertex(null, assign_then);
graph_vertex.Add(then_vertex);
ConditionalJumpVertex condition_vertex = new ConditionalJumpVertex(then_vertex, null, node.Condition);
graph_vertex.Add(condition_vertex);
AddNextJump(condition_vertex);
nodes_to_next_jmp.Add(then_vertex);
if (node.HasElse)
{
OperatorNode assign_else = new OperatorNode();
assign_else.Operator = OperatorType.ASSIGN;
assign_else.Arguments = new List <ExpressionNode> {
t_use, node.Else
};
OneJumpVertex else_vertex = new OneJumpVertex(null, assign_else);
graph_vertex.Add(else_vertex);
nodes_to_next_jmp.Add(else_vertex);
condition_vertex.FalseJump = else_vertex;
}
else
{
nodes_to_next_jmp.Add(condition_vertex);
}
changed_nodes[node] = t_use;
temporary_counter++;
}
public virtual T Visit(AtomNode node)
{
return(Visit(node as ExpressionNode));
}
public ComparisonNode(AtomNode left, AtomNode right, string op)
{
_left = left;
_right = right;
_op = op;
}
/// <summary>Returns a value indicating whether the specified <see cref="AtomNode"/> can be removed.</summary>
/// <param name="node">The <see cref="AtomNode"/> to test.</param>
/// <returns>True if the specified <see cref="AtomNode"/> can be removed; otherwise, false.</returns>
protected override bool CanRemoveNode(AtomNode node)
{
return (node is AtomId || node is AtomTitle || node is AtomUpdated) == false;
}
public virtual void Visit(AtomNode node)
{
Visit(node as ExpressionNode);
}
/// <summary>Returns a value indicating whether the specified <see cref="AtomNode"/> can be added.</summary>
/// <param name="node">The <see cref="AtomNode"/> to test.</param>
/// <returns>True if the specified <see cref="AtomNode"/> can be added; otherwise, false.</returns>
protected override bool CanAddNode(AtomNode node)
{
return base.CanAddNode(node) || node is AtomEntry;
}
/// <summary>When overridden in a derived class, returns a value indicating whether the specified <see cref="AtomNode"/> can be removed.</summary> /// <param name="node">The <see cref="AtomNode"/> to test.</param> /// <returns>True if the specified <see cref="AtomNode"/> can be removed; otherwise, false.</returns> protected abstract bool CanRemoveNode(AtomNode node);
/// <summary>When overridden in a derived class, returns a value indicating whether the specified <see cref="AtomNode"/> can be added.</summary> /// <param name="node">The <see cref="AtomNode"/> to test.</param> /// <returns>True if the specified <see cref="AtomNode"/> can be added; otherwise, false.</returns> protected abstract bool CanAddNode(AtomNode node);
/// <summary>Adds the specified <see cref="AtomNode"/> to this node.</summary>
/// <param name="node">The <see cref="AtomNode"/> to add.</param>
/// <exception cref="ArgumentNullException"><paramref name="node"/> is null.</exception>
/// <exception cref="ArgumentException"><paramref name="node"/> cannot be added.</exception>
public void Add(AtomNode node)
{
if(node == null) throw new ArgumentNullException("node");
if(this.CanAddNode(node) == false) throw new ArgumentException(Errors.CannotAddNode, "node");
this.Element.Add((XElement)node);
}
public IBoundScope <TItem> GetScope(AtomNode node, IScope <TItem> parentScope)
{
// Ignore atom nodes
return(null);
}
