public static void Traceback_Step(Cell[,] Matrix, string Sq1, string Sq2, List<char> Seq1, List<char> Seq2)
{
//List<char> Seq1 = new List<char>();
//List<char> Seq2 = new List<char>();
Cell CurrentCell = Matrix[Sq2.Length - 1, Sq1.Length - 1];
while (CurrentCell.CellPointer != null)
{
if (CurrentCell.Type == Cell.PrevcellType.Diagonal)
{
Seq1.Add(Sq1[CurrentCell.CellColumn]);
Seq2.Add(Sq2[CurrentCell.CellRow]);
}
if (CurrentCell.Type == Cell.PrevcellType.Left)
{
Seq1.Add(Sq1[CurrentCell.CellColumn]);
Seq2.Add('-');
}
if (CurrentCell.Type == Cell.PrevcellType.Above)
{
Seq1.Add('-');
Seq2.Add(Sq2[CurrentCell.CellRow]);
}
CurrentCell = CurrentCell.CellPointer;
}
}
public static Cell[,] Intialization_Step(string Seq1, string Seq2,int Sim,int NonSimilar,int Gap)
{
int M = Seq1.Length;//Length+1//-AAA
int N = Seq2.Length;//Length+1//-AAA
Cell[,] Matrix = new Cell[N, M];
//Intialize the first Row With Gap Penality Equal To i*Gap
for (int i = 0; i < Matrix.GetLength(1); i++)
{
Matrix[0, i] = new Cell(0, i, i*Gap);
}
//Intialize the first Column With Gap Penality Equal To i*Gap
for (int i = 0; i < Matrix.GetLength(0); i++)
{
Matrix[i, 0] = new Cell(i, 0, i*Gap);
}
// Fill Matrix with each cell has a value result from method Get_Max
for (int j = 1; j < Matrix.GetLength(0); j++)
{
for (int i = 1; i < Matrix.GetLength(1); i++)
{
Matrix[j, i] = Get_Max(i, j, Seq1, Seq2, Matrix,Sim,NonSimilar,Gap);
}
}
return Matrix;
}
public static Cell Get_Max(int i, int j, string Seq1, string Seq2, Cell[,] Matrix,int Similar,int NonSimilar,int GapPenality)
{
Cell Temp = new Cell();
int Sim;
int Gap = GapPenality;
if (Seq1[i] == Seq2[j])
Sim = Similar;
else
Sim = NonSimilar;
int M1, M2, M3;
M1 = Matrix[j - 1, i - 1].CellScore + Sim;
M2 = Matrix[j, i - 1].CellScore + Gap;
M3 = Matrix[j - 1, i].CellScore + Gap;
int max = M1 >= M2 ? M1 : M2;
int Mmax = M3 >= max ? M3 : max;
if (Mmax == M1)
{ Temp = new Cell(j, i, M1, Matrix[j - 1, i - 1], Cell.PrevcellType.Diagonal); }
else
{
if (Mmax == M2)
{ Temp = new Cell(j, i, M2, Matrix[j, i - 1], Cell.PrevcellType.Left); }
else
{
if (Mmax == M3)
{ Temp = new Cell(j, i, M3, Matrix[j - 1, i], Cell.PrevcellType.Above); }
}
}
return Temp;
}
public Cell(int row, int Col, int sco, Cell Prev)
{
this.Column = Col;
this.row = row;
this.Score = sco;
this.Prevoius_Cell = Prev;
}
public Cell(int row, int Col, int sco, Cell Prev, PrevcellType PType)
{
this.Column = Col;
this.row = row;
this.Score = sco;
this.Prevoius_Cell = Prev;
this.PCType = PType;
}