// $Id: sw_test.cs,v 1.8 2011/07/07 13:38:20 djg11 Exp $
// Basic, single-threaded sw code: hardwired input and no CRC on output.
//
using System;
using System.Text;
using KiwiSystem;



namespace SmithWaterman
{

    class Program
    {
        [Kiwi.OutputWordPort("phase")] static byte phase;
        [Kiwi.OutputWordPort("result")] static long result;
        [Kiwi.OutputWordPort("d_monitor")] static long d_monitor;


        [Kiwi.HardwareEntryPoint()]
        static void Main()
        {

            long i, j, d_loc, q_loc; long Ins_c, Del_c, H_temp;
            long[] d_index = new long[78];
            long[] q_index = new long[78];
            char [] aa = new char [] {'a','c','d','e','f','g','h','i','k','l','m','n','p','q','r','s','t','v','w','y'};

            long[,] Ins = new long[78, 78]; long[,] Del = new long[78, 78]; long[,] H = new long[78, 78]; long[,] Hg = new long[78, 78];

  /* Query Sequence = d1xpa_1 a.6.1.2 (134-210) from ASTRAL 1.67 40% */
  char[] query = new char []{'d','k','h','k','l','i','t','k','t','e','a','k','q','e','y','l','l','k','d','c','d','l','e','k','r','e','p','p','l','k','f','i','v','k','k','n','p','h','h','s','q','w','g','d','m','k','l','y','l','k','l','q','i','v','k','r','s','l','e','v','w','g','s','q','e','a','l','e','e','a','k','e','v','r','q','e','n'};
  /* Database Sequence =  d1jjcb2 a.6.1.1 (B:400-474) from ASTRAL 1.67 40% */
  char [] d = new char[] {'p','p','e','a','i','p','f','r','p','e','y','a','n','r','l','l','g','t','s','y','p','e','a','e','q','i','a','i','l','k','r','l','g','c','r','v','e','g','e','g','p','t','y','r','v','t','p','p','s','h','r','l','d','l','r','l','e','e','d','l','v','e','e','v','a','r','i','q','g','y','e','t','i','p','l'};
  /* Scoring Matrix (PAM 250) */
  int  [,] S = new int [20,20] {
  { 2, -2,  0,  0,  -4,   1,  -1,  -1,  -1,  -2,  -1,   0,   1,   0,  -2,   1,   1,   0,  -1,  -3},
  {-2, 12, -5, -5,  -4,  -3,  -3,  -2,  -5,  -6,  -5,  -4,  -3,  -5,  -4,   0,  -2,  -2,  -8,   0},
  { 0, -5,  4,  3,  -6,   1,   1,  -2,   0,  -4,  -3,   2,  -1,   2,  -1,   0,   0,  -2,  -7,  -4},
  { 0, -5,  3,  4,  -5,   0,   1,  -2,   0,  -3,  -2,   1,  -1,   2,  -1,   0,   0,  -2,  -7,  -4},
  {-4, -4, -6, -5,   9,  -5,  -2,   1,  -5,   2,   0,  -4,  -5,  -5,  -4,  -3,  -3,  -1,   0,   7},
  { 1, -3,  1,  0,  -5,   5,  -2,  -3,  -2,  -4,  -3,   0,  -1,  -1,  -3,   1,   0,  -1,  -7,  -5},
  {-1, -3,  1,  1,  -2,  -2,   6,  -2,   0,  -2,  -2,   2,   0,   3,   2,  -1,  -1,  -2,  -3,   0},
  {-1, -2, -2, -2,   1,  -3,  -2,   5,  -2,   2,   2,  -2,  -2,  -2,  -2,  -1,   0,   4,  -5,  -1},
  {-1, -5,  0,  0,  -5,  -2,   0,  -2,   5,  -3,   0,   1,  -1,   1,   3,   0,   0,  -2,  -3,  -4},
  {-2, -6, -4, -3,   2,  -4,  -2,   2,  -3,   6,   4,  -3,  -3,  -2,  -3,  -3,  -2,   2,  -2,  -1},
  {-1, -5, -3, -2,   0,  -3,  -2,   2,   0,   4,   6,  -2,  -2,  -1,   0,  -2,  -1,   2,  -4,  -2},
  { 0, -4,  2,  1,  -4,   0,   2,  -2,   1,  -3,  -2,   2,  -1,   1,   0,   1,   0,  -2,  -4,  -2},
  { 1, -3, -1, -1,  -5,  -1,   0,  -2,  -1,  -3,  -2,  -1,   6,   0,   0,   1,   0,  -1,  -6,  -5},
  { 0, -5,  2,  2,  -5,  -1,   3,  -2,   1,  -2,  -1,   1,   0,   4,   1,  -1,  -1,  -2,  -5,  -4},
  {-2, -4, -1, -1,  -4,  -3,   2,  -2,   3,  -3,   0,   0,   0,   1,   6,   0,  -1,  -2,   2,  -4},
  { 1,  0,  0,  0,  -3,   1,  -1,  -1,   0,  -3,  -2,   1,   1,  -1,   0,   2,   1,  -1,  -2,  -3},
  { 1, -2,  0,  0,  -3,   0,  -1,   0,   0,  -2,  -1,   0,   0,  -1,  -1,   1,   3,   0,  -5,  -3},
  { 0, -2, -2, -2,  -1,  -1,  -2,   4,  -2,   2,   2,  -2,  -1,  -2,  -2,  -1,   0,   4,  -6,  -2},
  {-6, -8, -7, -7,   0,  -7,  -3,  -5,  -3,  -2,  -4,  -4,  -6,  -5,   2,  -2,  -5,  -6,  17,   0},
  {-3,  0, -4, -4,   7,  -5,   0,  -1,  -4,  -1,  -2,  -2,  -5,  -4,  -4,  -3,  -3,  -2,   0,  10},
  };

  phase = 2;

  /* Convert residue characters to indices */
  for (d_loc=0; d_loc<75; d_loc++)
  {
    d_monitor = d_loc;
    for (j=0; j<20; j++)
      { 
        Kiwi.Pause();
	if (d[d_loc] == aa[j])
        d_index[d_loc] = j;
      }	
    for (q_loc=0; q_loc<77; q_loc++)
      for (j=0; j<20; j++)
        {
           Kiwi.Pause();
          if (query[q_loc] == aa[j]) q_index[q_loc] = j;
	}
   }

  phase = 4;

  /* Perhapse 640000ate calculation enough times to get good timing results */
 // for (i=1; i<640000; i++)

    /* Intialize Ins, Del, and H */
  for (d_loc=0; d_loc<75+1; d_loc++)
  {
      Kiwi.Pause();
      d_monitor = d_loc;
      Ins[d_loc,0] = 0;
      Del[d_loc,0] = 0;
      H[d_loc,0] = 0;
      Hg[d_loc,0] = - 10;
  }
  for (q_loc=1; q_loc<77+1; q_loc++) {
      Kiwi.Pause();
      Ins[0,q_loc] = 0;
      Del[0,q_loc] = 0;
      H[0,q_loc] = 0;
      Hg[0,q_loc] = - 10;
    }

  phase = 4;

  /* Do scoring */
  for (d_loc=0; d_loc<75; d_loc++)
  {
    d_monitor = d_loc;
    for (q_loc=0; q_loc<77; q_loc++) 
    {
        Kiwi.Pause();
        Ins_c = Ins[d_loc,q_loc+1] - 2;
        if (Hg[d_loc,q_loc+1] > Ins_c)
          Ins[d_loc+1,q_loc+1] = Hg[d_loc,q_loc+1];
        else
          Ins[d_loc+1,q_loc+1] = Ins_c;
        Del_c = Del[d_loc+1,q_loc] - 2;
        if (Hg[d_loc+1,q_loc] > Del_c)
          Del[d_loc+1,q_loc+1] = Hg[d_loc+1,q_loc];
        else
          Ins[d_loc+1,q_loc+1] = Del_c;
        if (Ins[d_loc,q_loc] > Del[d_loc,q_loc])
          H_temp = Ins[d_loc,q_loc];
        else
          H_temp = Del[d_loc,q_loc];
        if (H_temp < H[d_loc,q_loc])
          H_temp = H[d_loc,q_loc];
        H[d_loc+1,q_loc+1] = H_temp + S[q_index[q_loc],d_index[d_loc]];
        if (H[d_loc+1,q_loc+1] < 0)
          H[d_loc+1,q_loc+1] = 0;
        Hg[d_loc+1,q_loc+1] = H[d_loc+1,q_loc+1] - 10;
    }
  }
 
  phase = 6;
  Console.WriteLine("Scored h matrix");
 
  for (i = 0; i < 75; i++)
   {
     for (j = 0; j < 77; j++)
      {
        Kiwi.Pause();
        Console.Write("{0} {1} : {2}   ", i, j, H[i,j]);
        Console.WriteLine("");
        result = H[i,j];
	}
      }
  phase = 8;
    }
  }
}




// eof