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comparison 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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17:836fa4fe9494 18:e4d75f9efb90
1 #define DEFAULTGOP_N -1530
2 #define DEFAULTGEP_N 0
3 #define DEFAULTOFS_N -369
4 #define DEFAULTPAMN 200
5
6 #define DEFAULTRNAGOP_N -1530
7 #define DEFAULTRNAGEP_N 0
8 #define DEFAULTRNATHR_N 0
9
10 // -h 0.11150 -> all positive
11
12 double ribosum4[4][4] =
13 {
14 // a g c t
15 { 2.22, -1.46, -1.86, -1.39, }, // a
16 { -1.46, 1.03, -2.48, -1.74, }, // g
17 { -1.86, -2.48, 1.16, -1.05, }, // c
18 { -1.39, -1.74, -1.05, 1.65, }, // t
19 };
20
21 double ribosum16[16][16] =
22 {
23 // aa ag ac at ga gg gc gt ca cg cc ct ta tg tc tt
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
40 };
41
42 int locpenaltyn = -1750;
43 char locaminon[] = "agctuAGCTUnNbdhkmnrsvwyx-O";
44 char locgrpn[] =
45 {
46 0, 1, 2, 3, 3, 0, 1, 2, 3, 3,
47 4, 4, 5, 5, 5, 5, 5, 5, 5, 5,
48 5, 5, 5, 5, 5, 5
49 };
50 int exgpn = +00;
51 int locn_disn[26][26] =
52 /* u ha constants.c no nakade shori */
53 /* 0 - 4 dake yomareru. */
54 {
55 {
56 1000, 600, 0, 0, 0, 0, 0, 0, 0, 0,
57 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
58 0, 0, 0, 0, 0, -500,
59 },
60
61 {
62 600, 1000, 0, 0, 0, 0, 0, 0, 0, 0,
63 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
64 0, 0, 0, 0, 0, -500,
65 },
66
67 {
68 0, 0, 1000, 600, 0, 0, 0, 0, 0, 0,
69 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
70 0, 0, 0, 0, 0, -500,
71 },
72
73 {
74 0, 0, 600, 1000, 0, 0, 0, 0, 0, 0,
75 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
76 0, 0, 0, 0, 0, -500,
77 },
78
79 {
80 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
81 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
82 0, 0, 0, 0, 0, -500,
83 },
84
85 {
86 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
87 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
88 0, 0, 0, 0, 0, -500,
89 },
90
91 {
92 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
93 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
94 0, 0, 0, 0, 0, -500,
95 },
96
97 {
98 0, 500, 500, 0, 0, 0, 500, 500, 0, 0,
99 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
100 0, 0, 0, 0, 0, -500,
101 },
102
103 {
104 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
105 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
106 0, 0, 0, 0, 0, -500,
107 },
108
109 {
110 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
111 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
112 0, 0, 0, 0, 0, -500,
113 },
114
115 {
116 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
117 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
118 0, 0, 0, 0, 0, -500,
119 },
120
121 {
122 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
123 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
124 0, 0, 0, 0, 0, -500,
125 },
126
127 {
128 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
129 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
130 0, 0, 0, 0, 0, -500,
131 },
132
133 {
134 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
135 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
136 0, 0, 0, 0, 0, -500,
137 },
138
139 {
140 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
141 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
142 0, 0, 0, 0, 0, -500,
143 },
144
145 {
146 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
147 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
148 0, 0, 0, 0, 0, -500,
149 },
150
151 {
152 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
153 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
154 0, 0, 0, 0, 0, -500,
155 },
156
157 {
158 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
159 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
160 0, 0, 0, 0, 0, -500,
161 },
162
163 {
164 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
165 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
166 0, 0, 0, 0, 0, -500,
167 },
168
169 {
170 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
171 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
172 0, 0, 0, 0, 0, -500,
173 },
174
175 {
176 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
177 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
178 0, 0, 0, 0, 0, -500,
179 },
180
181 {
182 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
183 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
184 0, 0, 0, 0, 0, -500,
185 },
186
187 {
188 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
189 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
190 0, 0, 0, 0, 0, -500,
191 },
192
193 {
194 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
195 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
196 0, 0, 0, 0, 0, -500,
197 },
198
199 {
200 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
201 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
202 0, 0, 0, 0, 0, 0,
203 },
204
205 {
206 -500, -500, -500, -500, -500, -500, -500, -500, -500, -500,
207 -500, -500, -500, -500, -500, -500, -500, -500, -500, -500,
208 -500, -500, -500, -500, 0, 500,
209 },
210 };