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annotate mafft/core/DNA.h @ 18:e4d75f9efb90 draft

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planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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18
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1 #define DEFAULTGOP_N -1530
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2 #define DEFAULTGEP_N 0
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3 #define DEFAULTOFS_N -369
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4 #define DEFAULTPAMN 200
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5
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6 #define DEFAULTRNAGOP_N -1530
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7 #define DEFAULTRNAGEP_N 0
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8 #define DEFAULTRNATHR_N 0
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9
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10 // -h 0.11150 -> all positive
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11
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12 double ribosum4[4][4] =
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13 {
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14 // a g c t
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15 { 2.22, -1.46, -1.86, -1.39, }, // a
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16 { -1.46, 1.03, -2.48, -1.74, }, // g
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17 { -1.86, -2.48, 1.16, -1.05, }, // c
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18 { -1.39, -1.74, -1.05, 1.65, }, // t
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19 };
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20
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21 double ribosum16[16][16] =
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22 {
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23 // aa ag ac at ga gg gc gt ca cg cc ct ta tg tc tt
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24 { -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
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25 { -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
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26 { -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
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27 { -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
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28 { -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
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29 { -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
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30 { -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
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31 { -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
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32 { -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
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33 { -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
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34 { -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
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35 { -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
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36 { -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
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37 { -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
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38 { -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
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39 { -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
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40 };
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41
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42 int locpenaltyn = -1750;
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43 char locaminon[] = "agctuAGCTUnNbdhkmnrsvwyx-O";
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44 char locgrpn[] =
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45 {
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46 0, 1, 2, 3, 3, 0, 1, 2, 3, 3,
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47 4, 4, 5, 5, 5, 5, 5, 5, 5, 5,
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48 5, 5, 5, 5, 5, 5
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49 };
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50 int exgpn = +00;
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51 int locn_disn[26][26] =
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52 /* u ha constants.c no nakade shori */
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53 /* 0 - 4 dake yomareru. */
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54 {
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55 {
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56 1000, 600, 0, 0, 0, 0, 0, 0, 0, 0,
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57 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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58 0, 0, 0, 0, 0, -500,
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59 },
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60
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61 {
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62 600, 1000, 0, 0, 0, 0, 0, 0, 0, 0,
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63 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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64 0, 0, 0, 0, 0, -500,
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65 },
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66
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67 {
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68 0, 0, 1000, 600, 0, 0, 0, 0, 0, 0,
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69 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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70 0, 0, 0, 0, 0, -500,
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71 },
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72
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73 {
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74 0, 0, 600, 1000, 0, 0, 0, 0, 0, 0,
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75 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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76 0, 0, 0, 0, 0, -500,
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77 },
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78
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79 {
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80 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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81 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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82 0, 0, 0, 0, 0, -500,
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83 },
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84
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85 {
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86 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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87 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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88 0, 0, 0, 0, 0, -500,
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89 },
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90
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91 {
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92 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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93 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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94 0, 0, 0, 0, 0, -500,
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95 },
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96
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97 {
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98 0, 500, 500, 0, 0, 0, 500, 500, 0, 0,
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