| #define DEFAULTGOP_N -1530 |
| #define DEFAULTGEP_N 0 |
| #define DEFAULTOFS_N -123 |
| #define DEFAULTPAMN 200 |
| |
| #define DEFAULTRNAGOP_N -1530 |
| #define DEFAULTRNAGEP_N 0 |
| #define DEFAULTRNATHR_N 0 |
| |
| // -h 0.11150 -> all positive |
| |
| double ribosum4[4][4] = |
| { |
| // a g c t |
| { 2.22, -1.46, -1.86, -1.39, }, // a |
| { -1.46, 1.03, -2.48, -1.74, }, // g |
| { -1.86, -2.48, 1.16, -1.05, }, // c |
| { -1.39, -1.74, -1.05, 1.65, }, // t |
| }; |
| |
| double ribosum16[16][16] = |
| { |
| // aa ag ac at ga gg gc gt ca cg cc ct ta tg tc tt |
| { -2.49, -8.24, -7.04, -4.32, -6.86, -8.39, -5.03, -5.84, -8.84, -4.68, -14.37, -12.64, -4.01, -6.16, -11.32, -9.05, }, // aa |
| { -8.24, -0.80, -8.89, -5.13, -8.61, -5.38, -5.77, -6.60, -10.41, -4.57, -14.53, -10.14, -5.43, -5.94, -8.87, -11.07, }, // ag |
| { -7.04, -8.89, -2.11, -2.04, -9.73, -11.05, -3.81, -4.72, -9.37, -5.86, -9.08, -10.45, -5.33, -6.93, -8.67, -7.83, }, // ac |
| { -4.32, -5.13, -2.04, 4.49, -5.33, -5.61, 2.70, 0.59, -5.56, 1.67, -6.71, -5.17, 1.61, -0.51, -4.81, -2.98, }, // at |
| { -6.86, -8.61, -9.73, -5.33, -1.05, -8.67, -4.88, -6.10, -7.98, -6.00, -12.43, -7.71, -5.85, -7.55, -6.63, -11.54, }, // ga |
| { -8.39, -5.38, -11.05, -5.61, -8.67, -1.98, -4.13, -5.77, -11.36, -4.66, -12.58, -13.69, -5.75, -4.27, -12.01, -10.79, }, // gg |
| { -5.03, -5.77, -3.81, 2.70, -4.88, -4.13, 5.62, 1.21, -5.95, 2.11, -3.70, -5.84, 1.60, -0.08, -4.49, -3.90, }, // gc |
| { -5.84, -6.60, -4.72, 0.59, -6.10, -5.77, 1.21, 3.47, -7.93, -0.27, -7.88, -5.61, -0.57, -2.09, -5.30, -4.45, }, // gt |
| { -8.84, -10.41, -9.37, -5.56, -7.98, -11.36, -5.95, -7.93, -5.13, -3.57, -10.45, -8.49, -2.42, -5.63, -7.08, -8.39, }, // ca |
| { -4.68, -4.57, -5.86, 1.67, -6.00, -4.66, 2.11, -0.27, -3.57, 5.36, -5.71, -4.96, 2.75, 1.32, -4.91, -3.67, }, // cg |
| { -14.37, -14.53, -9.08, -6.71, -12.43, -12.58, -3.70, -7.88, -10.45, -5.71, -3.59, -5.77, -6.88, -8.41, -7.40, -5.41, }, // cc |
| { -12.64, -10.14, -10.45, -5.17, -7.71, -13.69, -5.84, -5.61, -8.49, -4.96, -5.77, -2.28, -4.72, -7.36, -3.83, -5.21, }, // ct |
| { -4.01, -5.43, -5.33, 1.61, -5.85, -5.75, 1.60, -0.57, -2.42, 2.75, -6.88, -4.72, 4.97, 1.14, -2.98, -3.39, }, // ta |
| { -6.16, -5.94, -6.93, -0.51, -7.55, -4.27, -0.08, -2.09, -5.63, 1.32, -8.41, -7.36, 1.14, 3.36, -4.76, -4.28, }, // tg |
| { -11.32, -8.87, -8.67, -4.81, -6.63, -12.01, -4.49, -5.30, -7.08, -4.91, -7.40, -3.83, -2.98, -4.76, -3.21, -5.97, }, // tc |
| { -9.05, -11.07, -7.83, -2.98, -11.54, -10.79, -3.90, -4.45, -8.39, -3.67, -5.41, -5.21, -3.39, -4.28, -5.97, -0.02, }, // tt |
| }; |
| |
| int locpenaltyn = -1750; |
| char locaminon[] = "agctuAGCTUnNbdhkmnrsvwyx-O"; |
| char locgrpn[] = |
| { |
| 0, 1, 2, 3, 3, 0, 1, 2, 3, 3, |
| 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, |
| 5, 5, 5, 5, 5, 5 |
| }; |
| int exgpn = +00; |
| int locn_disn[26][26] = |
| /* u ha constants.c no nakade shori */ |
| /* 0 - 4 dake yomareru. */ |
| { |
| { |
| 1000, 600, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 600, 1000, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 1000, 600, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 600, 1000, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 500, 500, 0, 0, 0, 500, 500, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, -500, |
| }, |
| |
| { |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, |
| 0, 0, 0, 0, 0, 0, |
| }, |
| |
| { |
| -500, -500, -500, -500, -500, -500, -500, -500, -500, -500, |
| -500, -500, -500, -500, -500, -500, -500, -500, -500, -500, |
| -500, -500, -500, -500, 0, 500, |
| }, |
| }; |
