Public Class SequenceAlignment

    Private Sub Button1_Click(ByVal sender As System.Object, ByVal e As  _
                              System.EventArgs) Handles Button1.Click
        ‘declare Score variables
        Dim MatchScore As Integer = 5
        Dim MisMatchScore As Integer = 0.5
        Dim GapScore As Integer = -2

        ‘+======================================================================================+
        ‘initialization; set initial Score and get initial Pointer ‘left’ or ‘up’
        ‘on top columns and Rows on the left respectively
        ‘+======================================================================================+

        Dim Matrix(,) As Integer = New Integer(,) {} ‘Created a matrix to fill the score
        Dim RowColpointer(,) As String = New String(,) {} ‘Created another matrix
        ‘for the pointer to the left and up

        Dim J As Integer = 1 ‘matrix index j
        Dim I As Integer = 1 ‘matrix index i

        ‘(0, 0) of the matrix is score is set to 0 and pointer to ‘none’.
        ‘This position is the end during trace back.
        ‘Matrix(1, 0) = 0 ‘run time error
        ‘RowColpointer(1, 0) = “none” ‘ I am getting run time error!!!
        ‘Index was outside the bounds of the array!!!.

        ‘creates values for each column on top of the matrix except the 0,0
        For J = 1 To J <= Seq1.Text.Length
            Matrix(0, J) = GapScore * J ‘creates score on each column
            RowColpointer(0, J) = “left” ‘creates pointer on each column
        Next J

        ‘creates pointer for each row on the left except 0,0
        For I = 1 To J <= Seq2.Text.Length
            Matrix(I, 0) = GapScore * I ‘creates score on each row
            RowColpointer(I, 0) = “up” ‘creates pointer on each column
        Next I

        ‘==============================================================================+
        ‘fill matrix with scores and pointers
        ‘==============================================================================+
        Dim diagonal_score As Integer
        Dim left_score As Integer
        Dim up_score As Integer
        Dim letter1 As Integer
        Dim letter2 As Integer

        For I = 1 To I <= Seq2.Text.Length ‘looping through the entire matrix
            For J = 1 To Seq1.Text.Length

                ‘Calculate matchScore
                letter1 = Mid(Seq1.Text, J – 1, 1)
                letter2 = Mid(Seq2.Text, I – 1, 1)

                ‘condition set to generate diagonal score
                If letter1 = letter2 Then
                    diagonal_score = Matrix(I – 1, J – 1) + MatchScore
                Else : diagonal_score = Matrix(I – 1, J – 1) + MisMatchScore
                End If

                ‘Calculate gap scores
                up_score = Matrix(I – 1, J) + GapScore
                left_score = Matrix(I, J – 1) + GapScore

                ‘conditions to generate best score and pointers the entire matrix
                If diagonal_score >= up_score Then
                    If diagonal_score >= left_score Then
                        Matrix(I, J) = diagonal_score
                        RowColpointer(I, J) = “diagonal”
                    Else : Matrix(I, J) = left_score
                        RowColpointer(I, J) = “left”
                    End If

                    If up_score >= left_score Then
                        Matrix(I, J) = up_score
                        RowColpointer(I, J) = “up”
                    Else : Matrix(I, J) = left_score
                        RowColpointer(I, J) = “left”
                    End If
                End If
            Next J
        Next I

        ‘=======================================================================================+
        ‘trace back      
        ‘=======================================================================================+

        Dim align1 As String = ” ”
        Dim align2 As String = ” ”

        ‘starts at the last cell of the matrix
        J = Seq1.Text.Length ‘|
        I = Seq2.Text.Length ‘| to select the last cell in the matrix

        ‘when the trace back reaches ‘none’ it stops
        While (1)
            If RowColpointer(I, J) = “none” Then ‘//run time error
                ‘//Index was outside the bounds of the array.
            End If
        End While

        If RowColpointer(I, J) = “Diagonal” Then ‘//run time error
            ‘//Index was outside the bounds of the array.
            align1 = Mid(Seq1.Text, J – 1, 1)
            align2 = Mid(Seq2.Text, I – 2, 1)
            I -= 1
            J -= 1
        ElseIf RowColpointer(I, J) = “left” Then ‘//run time error
            ‘//Index was outside the bounds of the array.
            align1 = Mid(Seq1.Text, J – 1, 1)
            align2 = “-”
            J -= 1
        ElseIf Matrix(I, J) = “up” Then ‘//run time error
            ‘//Index was outside the bounds of the array.
            align1 = “-”
            align2 = Mid(Seq1.Text, I – 1, 1)
            I -= 1
        End If

        ‘since the trace back is performed backwards thorugh the sequence, the string is
        ‘generated in a reverse order. so the sequence should be arranged in a correct order
        StrReverse(align1)
        StrReverse(align2)

        ‘Disply in message box
        MessageBox.Show(align1 + “n”, align2 + “n”)

    End Sub

Private Sub Button2_Click(ByVal sender As System.Object, ByVal e _
                          As System.EventArgs) Handles Button2.Click
    Me.Close()

End Sub
End Class