Smith-Waterman

/*
    You must run systolic array generation on this code in order to generate hardware.

    A is the two dimensional feedback table.
    T is the stream we are comparing against.
*/

void SmithWaterman(int** A, int* T)
{
    int i ;
    int j ;	

    const int S[11] = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 } ;

    // These constants are adjustable
    const int matchCost = 10 ;
    const int mismatchCost = 100 ;
    const int insertCost = 20 ;
    const int deleteCost = 200 ;

    int tmp ;
    int tmp2 ;
    int tmp3 ;

    L1: for(i = 0 ; i < 11 ; ++i)
    {
        for(j = 0 ; j < 11 ; ++j)
        {
            if(S[i] == T[j])
            {
                tmp = A[i - 1][j - 1] + matchCost ;
            }
            else
            {
                tmp = A[i - 1][j - 1] + mismatchCost ;
            }

            if(A[i - 1][j] + insertCost > A[i][j - 1] + deleteCost)
            {
                tmp2 = A[i - 1][j] + insertCost ;
            }
            else
            {
                tmp2 = A[i][j - 1] + deleteCost ;
            }

            if(tmp > tmp2)
            {
                tmp3 = tmp ;
            }
            else
            {
                tmp3 = tmp2 ;
            }

            if(tmp3 < 0)
            {
                A[i][j] = 0 ;
            }
            else
            {
                A[i][j] = tmp3 ;
            }
        }
    }
}