public float BuildSmithWaterman(string str1, string str2)
{
float[,] matrix = new float[str1.Length + 1, str2.Length + 1];
matrix[0, 0] = 0;
// fill first row and column with 0
for (int i = 1; i <= str1.Length; i++)
{
matrix[i, 0] = 0;
}
for (int j = 1; j <= str2.Length; j++)
{
matrix[0, j] = 0;
}
for (int i = 1; i <= str1.Length; i++)
{
for (int j = 1; j <= str2.Length; j++)
{
float matchCost = this.CostFunction.GetCost(str1, i - 1, str2, j - 1);
float scoreDiag = matrix[i - 1, j - 1]; // match/mismatch
float scoreUp = matrix[i - 1, j]; // deletion
float scoreLeft = matrix[i, j - 1]; // insertion
matrix[i, j] = MathExtension.Max(0,
scoreDiag + matchCost,
scoreLeft - this.gapCost,
scoreUp - this.gapCost);
}
}
return(matrix[str1.Length, str2.Length]);
}