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
|
MODULE = Wise2 PACKAGE = Wise2::GenomicRegion
Wise2_GenomicRegion *
new_GenomicRegion(gen)
Wise2_Genomic * gen
CODE:
RETVAL = Wise2_new_GenomicRegion(gen);
OUTPUT:
RETVAL
Wise2_GenomicRegion *
read_EMBL_GenomicRegion_file(filename)
char * filename
CODE:
RETVAL = Wise2_read_EMBL_GenomicRegion_file(filename);
OUTPUT:
RETVAL
Wise2_GenomicRegion *
read_EMBL_GenomicRegion(ifp)
FILE * ifp
CODE:
RETVAL = Wise2_read_EMBL_GenomicRegion(ifp);
OUTPUT:
RETVAL
boolean
add_Gene_to_GenomicRegion(gr,gene)
Wise2_GenomicRegion * gr
Wise2_Gene * gene
CODE:
RETVAL = Wise2_add_Gene_to_GenomicRegion(gr,gene);
OUTPUT:
RETVAL
void
show_ace_GenomicRegion(gr,seq_name,ofp)
Wise2_GenomicRegion * gr
char * seq_name
FILE * ofp
CODE:
Wise2_show_ace_GenomicRegion(gr,seq_name,ofp);
void
show_pretty_GenomicRegion(gr,show_supporting,ofp)
Wise2_GenomicRegion * gr
boolean show_supporting
FILE * ofp
CODE:
Wise2_show_pretty_GenomicRegion(gr,show_supporting,ofp);
void
write_Diana_FT_GenomicRegion(gr,ofp)
Wise2_GenomicRegion * gr
FILE * ofp
CODE:
Wise2_write_Diana_FT_GenomicRegion(gr,ofp);
void
write_Embl_FT_GenomicRegion(gr,ofp)
Wise2_GenomicRegion * gr
FILE * ofp
CODE:
Wise2_write_Embl_FT_GenomicRegion(gr,ofp);
Wise2_GenomicRegion *
hard_link_GenomicRegion(obj)
Wise2_GenomicRegion * obj
CODE:
RETVAL = Wise2_hard_link_GenomicRegion(obj);
OUTPUT:
RETVAL
Wise2_GenomicRegion *
GenomicRegion_alloc_std()
CODE:
RETVAL = Wise2_GenomicRegion_alloc_std();
OUTPUT:
RETVAL
Wise2_Gene *
gene(obj,i)
Wise2_GenomicRegion * obj
int i
INIT:
Wise2_Gene * temp;
CODE:
temp = Wise2_hard_link_Gene(Wise2_access_gene_GenomicRegion(obj,i));
RETVAL = temp;
OUTPUT:
RETVAL
int
length_gene(obj)
Wise2_GenomicRegion * obj
CODE:
RETVAL = Wise2_length_gene_GenomicRegion(obj);
OUTPUT:
RETVAL
int
flush_gene(obj)
Wise2_GenomicRegion * obj
CODE:
RETVAL = Wise2_flush_GenomicRegion(obj);
OUTPUT:
RETVAL
boolean
add_gene(obj,add)
Wise2_GenomicRegion * obj
Wise2_Gene * add
CODE:
RETVAL = Wise2_add_GenomicRegion(obj,Wise2_hard_link_Gene(add));
OUTPUT:
RETVAL
boolean
set_genomic(obj,genomic)
Wise2_GenomicRegion * obj
Wise2_Genomic * genomic
CODE:
RETVAL = Wise2_replace_genomic_GenomicRegion(obj,Wise2_hard_link_Genomic(genomic));
OUTPUT:
RETVAL
Wise2_Genomic *
genomic(obj)
Wise2_GenomicRegion * obj
INIT:
Wise2_Genomic * temp;
CODE:
temp = Wise2_hard_link_Genomic(Wise2_access_genomic_GenomicRegion(obj));
RETVAL = temp;
OUTPUT:
RETVAL
Wise2_GenomicRegion *
new(class)
char * class
PPCODE:
Wise2_GenomicRegion * out;
out = Wise2_GenomicRegion_alloc_std();
ST(0) = sv_newmortal();
sv_setref_pv(ST(0),class,(void*)out);
XSRETURN(1);
void
DESTROY(obj)
Wise2_GenomicRegion * obj
CODE:
Wise2_free_GenomicRegion(obj);
void
each_gene(obj)
Wise2_GenomicRegion * obj
PPCODE:
int i=0;
int len;
SV* temp;
len = Wise2_length_gene_GenomicRegion(obj);
for(i=0;i<len;i++){
temp = sv_newmortal();
sv_setref_pv(temp, "Wise2::Gene", (void*) (Wise2_hard_link_Gene(Wise2_access_gene_GenomicRegion(obj,i))));
XPUSHs(temp);
}
XSRETURN(len);
MODULE = Wise2 PACKAGE = Wise2
|
