1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
|
MODULE = Wise2 PACKAGE = Wise2::CodonTable
Wise2_CodonTable *
read_CodonTable_file(file)
char * file
CODE:
RETVAL = Wise2_read_CodonTable_file(file);
OUTPUT:
RETVAL
Wise2_CodonTable *
read_CodonTable(ifp)
FILE * ifp
CODE:
RETVAL = Wise2_read_CodonTable(ifp);
OUTPUT:
RETVAL
aa
aminoacid_from_seq(ct,seq)
Wise2_CodonTable * ct
char * seq
CODE:
RETVAL = Wise2_aminoacid_from_seq(ct,seq);
OUTPUT:
RETVAL
aa
aminoacid_from_codon(ct,c)
Wise2_CodonTable * ct
codon c
CODE:
RETVAL = Wise2_aminoacid_from_codon(ct,c);
OUTPUT:
RETVAL
boolean
is_stop_codon(c,ct)
codon c
Wise2_CodonTable * ct
CODE:
RETVAL = Wise2_is_stop_codon(c,ct);
OUTPUT:
RETVAL
boolean
is_valid_aminoacid(ct,c)
Wise2_CodonTable * ct
char c
CODE:
RETVAL = Wise2_is_valid_aminoacid(ct,c);
OUTPUT:
RETVAL
Wise2_CodonTable *
hard_link_CodonTable(obj)
Wise2_CodonTable * obj
CODE:
RETVAL = Wise2_hard_link_CodonTable(obj);
OUTPUT:
RETVAL
Wise2_CodonTable *
alloc()
CODE:
RETVAL = Wise2_CodonTable_alloc();
OUTPUT:
RETVAL
boolean
set_name(obj,name)
Wise2_CodonTable * obj
char * name
CODE:
RETVAL = Wise2_replace_name_CodonTable(obj,Wise2_stringalloc(name));
OUTPUT:
RETVAL
char *
name(obj)
Wise2_CodonTable * obj
INIT:
char * temp;
CODE:
temp = Wise2_stringalloc(Wise2_access_name_CodonTable(obj));
RETVAL = temp;
OUTPUT:
RETVAL
Wise2_CodonTable *
new(class)
char * class
PPCODE:
Wise2_CodonTable * out;
out = Wise2_CodonTable_alloc();
ST(0) = sv_newmortal();
sv_setref_pv(ST(0),class,(void*)out);
XSRETURN(1);
void
DESTROY(obj)
Wise2_CodonTable * obj
CODE:
Wise2_free_CodonTable(obj);
MODULE = Wise2 PACKAGE = Wise2
boolean
is_non_ambiguous_codon_seq(seq)
char * seq
CODE:
RETVAL = Wise2_is_non_ambiguous_codon_seq(seq);
OUTPUT:
RETVAL
codon
codon_from_base4_codon(c)
int c
CODE:
RETVAL = Wise2_codon_from_base4_codon(c);
OUTPUT:
RETVAL
int
base4_codon_from_codon(c)
codon c
CODE:
RETVAL = Wise2_base4_codon_from_codon(c);
OUTPUT:
RETVAL
boolean
has_random_bases(c)
codon c
CODE:
RETVAL = Wise2_has_random_bases(c);
OUTPUT:
RETVAL
codon
permute_possible_random_bases(c,one,two,three)
codon c
base one
base two
base three
CODE:
RETVAL = Wise2_permute_possible_random_bases(c,one,two,three);
OUTPUT:
RETVAL
base
base_from_codon(c,pos)
codon c
int pos
CODE:
RETVAL = Wise2_base_from_codon(c,pos);
OUTPUT:
RETVAL
codon
codon_from_seq(seq)
char * seq
CODE:
RETVAL = Wise2_codon_from_seq(seq);
OUTPUT:
RETVAL
int
base4_codon_from_seq(seq)
char * seq
CODE:
RETVAL = Wise2_base4_codon_from_seq(seq);
OUTPUT:
RETVAL
char
char_from_base(b)
base b
CODE:
RETVAL = Wise2_char_from_base(b);
OUTPUT:
RETVAL
base
base_from_char(c)
char c
CODE:
RETVAL = Wise2_base_from_char(c);
OUTPUT:
RETVAL
char
char_complement_base(c)
char c
CODE:
RETVAL = Wise2_char_complement_base(c);
OUTPUT:
RETVAL
base
complement_base(b)
base b
CODE:
RETVAL = Wise2_complement_base(b);
OUTPUT:
RETVAL
|
