1 | /* This file has been generated from |
---|
2 | * default.xs and |
---|
3 | * ptype.header |
---|
4 | */ |
---|
5 | |
---|
6 | /* -------------------------------------------------------------------------------- |
---|
7 | * File : default.xs |
---|
8 | * Purpose : some input for arb_proto_2_xsub unit-test |
---|
9 | * -------------------------------------------------------------------------------- */ |
---|
10 | |
---|
11 | #ifndef __cplusplus |
---|
12 | #error please compile as C++ |
---|
13 | #endif |
---|
14 | |
---|
15 | #include "XSUB.h" |
---|
16 | |
---|
17 | static GB_shell4perl perl_shell; |
---|
18 | |
---|
19 | /* -------------------------------------------------------------------------------- |
---|
20 | * the following functions are hand-coded in ARB.default.xs: |
---|
21 | */ |
---|
22 | |
---|
23 | MODULE = FAKE PACKAGE = ARB PREFIX = P2A_ |
---|
24 | PROTOTYPES: ENABLE |
---|
25 | |
---|
26 | |
---|
27 | MODULE = FAKE PACKAGE = BIO PREFIX = P2AT_ |
---|
28 | |
---|
29 | |
---|
30 | # -------------------------------------------------------------------------------- |
---|
31 | # functions below are auto-generated by ../../../PERLTOOLS/arb_proto_2_xsub.cxx |
---|
32 | # using prototypes from ptype.header |
---|
33 | # -------------------------------------------------------------------------------- |
---|
34 | |
---|
35 | # -------------------------------------------------------------------------------- |
---|
36 | MODULE = ARB PACKAGE = ARB PREFIX = P2A_ |
---|
37 | |
---|
38 | char * |
---|
39 | P2A_get_type_name(gbd) |
---|
40 | GBDATA *gbd |
---|
41 | |
---|
42 | CODE: |
---|
43 | RETVAL = const_cast<char *>(GB_get_type_name(gbd)); |
---|
44 | |
---|
45 | OUTPUT: |
---|
46 | RETVAL |
---|
47 | |
---|
48 | |
---|
49 | void |
---|
50 | P2A_dump_db_path(gbd) |
---|
51 | GBDATA *gbd |
---|
52 | |
---|
53 | PPCODE: |
---|
54 | GB_dump_db_path(gbd); |
---|
55 | |
---|
56 | |
---|
57 | char * |
---|
58 | P2A_fix_database(gb_main) |
---|
59 | GBDATA *gb_main |
---|
60 | |
---|
61 | CODE: |
---|
62 | RETVAL = const_cast<char *>(GB_fix_database(gb_main)); |
---|
63 | |
---|
64 | OUTPUT: |
---|
65 | RETVAL |
---|
66 | |
---|
67 | |
---|
68 | void |
---|
69 | P2A_set_verbose() |
---|
70 | |
---|
71 | PPCODE: |
---|
72 | GB_set_verbose(); |
---|
73 | |
---|
74 | |
---|
75 | void |
---|
76 | P2A_set_next_main_idx(idx) |
---|
77 | long idx |
---|
78 | |
---|
79 | PPCODE: |
---|
80 | GB_set_next_main_idx(idx); |
---|
81 | |
---|
82 | |
---|
83 | GBDATA * |
---|
84 | P2A_open(path, opent) |
---|
85 | char *path |
---|
86 | char *opent |
---|
87 | |
---|
88 | CODE: |
---|
89 | RETVAL = GB_open(const_cast<const char *>(path), const_cast<const char *>(opent)); |
---|
90 | |
---|
91 | OUTPUT: |
---|
92 | RETVAL |
---|
93 | |
---|
94 | |
---|
95 | char * |
---|
96 | P2A_delete_database(filename) |
---|
97 | char *filename |
---|
98 | |
---|
99 | CODE: |
---|
100 | RETVAL = const_cast<char *>(GB_delete_database(const_cast<const char *>(filename))); |
---|
101 | |
---|
102 | OUTPUT: |
---|
103 | RETVAL |
---|
104 | |
---|
105 | |
---|
106 | char * |
---|
107 | P2A_set_cache_size(gbd, size) |
---|
108 | GBDATA *gbd |
---|
109 | size_t size |
---|
110 | |
---|
111 | CODE: |
---|
112 | freeset(static_pntr, GB_set_cache_size(gbd, size)); |
---|
113 | RETVAL = static_pntr; |
---|
114 | |
---|
115 | OUTPUT: |
---|
116 | RETVAL |
---|
117 | |
---|
118 | |
---|
119 | char * |
---|
120 | P2A_create_index(gbd, key, case_sens, estimated_size) |
---|
121 | GBDATA *gbd |
---|
122 | char *key |
---|
123 | char *case_sens |
---|
124 | long estimated_size |
---|
125 | |
---|
126 | CODE: |
---|
127 | RETVAL = const_cast<char *>(GB_create_index(gbd, const_cast<const char *>(key), GBP_charPtr_2_GB_CASE(const_cast<const char *>(case_sens)), estimated_size)); |
---|
128 | |
---|
129 | OUTPUT: |
---|
130 | RETVAL |
---|
131 | |
---|
132 | |
---|
133 | char * |
---|
134 | P2A_request_undo_type(gb_main, type) |
---|
135 | GBDATA *gb_main |
---|
136 | char *type |
---|
137 | |
---|
138 | CODE: |
---|
139 | RETVAL = const_cast<char *>(GB_request_undo_type(gb_main, GBP_charPtr_2_GB_UNDO_TYPE(const_cast<const char *>(type)))); |
---|
140 | |
---|
141 | OUTPUT: |
---|
142 | RETVAL |
---|
143 | |
---|
144 | |
---|
145 | char * |
---|
146 | P2A_get_requested_undo_type(gb_main) |
---|
147 | GBDATA *gb_main |
---|
148 | |
---|
149 | CODE: |
---|
150 | RETVAL = const_cast<char *>(GBP_GB_UNDO_TYPE_2_charPtr(GB_get_requested_undo_type(gb_main))); |
---|
151 | |
---|
152 | OUTPUT: |
---|
153 | RETVAL |
---|
154 | |
---|
155 | |
---|
156 | char * |
---|
157 | P2A_undo(gb_main, type) |
---|
158 | GBDATA *gb_main |
---|
159 | char *type |
---|
160 | |
---|
161 | CODE: |
---|
162 | RETVAL = const_cast<char *>(GB_undo(gb_main, GBP_charPtr_2_GB_UNDO_TYPE(const_cast<const char *>(type)))); |
---|
163 | |
---|
164 | OUTPUT: |
---|
165 | RETVAL |
---|
166 | |
---|
167 | |
---|
168 | GBDATA * |
---|
169 | P2A_find(gbd, key, gbs) |
---|
170 | GBDATA *gbd |
---|
171 | char *key |
---|
172 | char *gbs |
---|
173 | |
---|
174 | CODE: |
---|
175 | RETVAL = GB_find(gbd, const_cast<const char *>(key), GBP_charPtr_2_GB_SEARCH_TYPE(const_cast<const char *>(gbs))); |
---|
176 | |
---|
177 | OUTPUT: |
---|
178 | RETVAL |
---|
179 | |
---|
180 | |
---|
181 | GBDATA * |
---|
182 | P2A_find_string(gbd, key, str, case_sens, gbs) |
---|
183 | GBDATA *gbd |
---|
184 | char *key |
---|
185 | char *str |
---|
186 | char *case_sens |
---|
187 | char *gbs |
---|
188 | |
---|
189 | CODE: |
---|
190 | RETVAL = GB_find_string(gbd, const_cast<const char *>(key), const_cast<const char *>(str), GBP_charPtr_2_GB_CASE(const_cast<const char *>(case_sens)), GBP_charPtr_2_GB_SEARCH_TYPE(const_cast<const char *>(gbs))); |
---|
191 | |
---|
192 | OUTPUT: |
---|
193 | RETVAL |
---|
194 | |
---|
195 | |
---|
196 | char * |
---|
197 | P2A_command_interpreter(gb_main, str, commands, gbd, default_tree_name) |
---|
198 | GBDATA *gb_main |
---|
199 | char *str |
---|
200 | char *commands |
---|
201 | GBDATA *gbd |
---|
202 | char *default_tree_name |
---|
203 | |
---|
204 | CODE: |
---|
205 | freeset(static_pntr, GB_command_interpreter(gb_main, const_cast<const char *>(str), const_cast<const char *>(commands), gbd, const_cast<const char *>(default_tree_name))); |
---|
206 | RETVAL = static_pntr; |
---|
207 | |
---|
208 | OUTPUT: |
---|
209 | RETVAL |
---|
210 | |
---|
211 | |
---|
212 | GB_ULONG |
---|
213 | P2A_time_of_day() |
---|
214 | |
---|
215 | CODE: |
---|
216 | RETVAL = GB_time_of_day(); |
---|
217 | |
---|
218 | OUTPUT: |
---|
219 | RETVAL |
---|
220 | |
---|
221 | |
---|
222 | double |
---|
223 | P2A_atof(str) |
---|
224 | char *str |
---|
225 | |
---|
226 | CODE: |
---|
227 | RETVAL = GB_atof(const_cast<const char *>(str)); |
---|
228 | |
---|
229 | OUTPUT: |
---|
230 | RETVAL |
---|
231 | |
---|
232 | |
---|
233 | char * |
---|
234 | P2A_read_type(gbd) |
---|
235 | GBDATA *gbd |
---|
236 | |
---|
237 | CODE: |
---|
238 | RETVAL = const_cast<char *>(GBP_GB_TYPES_2_charPtr(GB_read_type(gbd))); |
---|
239 | |
---|
240 | OUTPUT: |
---|
241 | RETVAL |
---|
242 | |
---|
243 | |
---|
244 | GBDATA * |
---|
245 | P2A_create(father, key, type) |
---|
246 | GBDATA *father |
---|
247 | char *key |
---|
248 | char *type |
---|
249 | |
---|
250 | CODE: |
---|
251 | RETVAL = GB_create(father, const_cast<const char *>(key), GBP_charPtr_2_GB_TYPES(const_cast<const char *>(type))); |
---|
252 | |
---|
253 | OUTPUT: |
---|
254 | RETVAL |
---|
255 | |
---|
256 | |
---|
257 | # -------------------------------------------------------------------------------- |
---|
258 | MODULE = ARB PACKAGE = BIO PREFIX = P2AT_ |
---|
259 | |
---|
260 | bool |
---|
261 | P2AT_is_genome_db(gb_main, default_value) |
---|
262 | GBDATA *gb_main |
---|
263 | int default_value |
---|
264 | |
---|
265 | CODE: |
---|
266 | RETVAL = GEN_is_genome_db(gb_main, default_value); |
---|
267 | |
---|
268 | OUTPUT: |
---|
269 | RETVAL |
---|
270 | |
---|
271 | |
---|
272 | char * |
---|
273 | P2AT_origin_organism(gb_pseudo) |
---|
274 | GBDATA *gb_pseudo |
---|
275 | |
---|
276 | CODE: |
---|
277 | RETVAL = const_cast<char *>(GEN_origin_organism(gb_pseudo)); |
---|
278 | |
---|
279 | OUTPUT: |
---|
280 | RETVAL |
---|
281 | |
---|
282 | |
---|
283 | long |
---|
284 | P2AT_get_organism_count(gb_main) |
---|
285 | GBDATA *gb_main |
---|
286 | |
---|
287 | CODE: |
---|
288 | RETVAL = GEN_get_organism_count(gb_main); |
---|
289 | |
---|
290 | OUTPUT: |
---|
291 | RETVAL |
---|
292 | |
---|
293 | |
---|
294 | char * |
---|
295 | P2AT_global_gene_identifier(gb_gene, gb_organism) |
---|
296 | GBDATA *gb_gene |
---|
297 | GBDATA *gb_organism |
---|
298 | |
---|
299 | CODE: |
---|
300 | freeset(static_pntr, GEN_global_gene_identifier(gb_gene, gb_organism)); |
---|
301 | RETVAL = static_pntr; |
---|
302 | |
---|
303 | OUTPUT: |
---|
304 | RETVAL |
---|
305 | |
---|
306 | |
---|
307 | char * |
---|
308 | P2AT_check_arb_file(name) |
---|
309 | char *name |
---|
310 | |
---|
311 | CODE: |
---|
312 | RETVAL = const_cast<char *>(GBT_check_arb_file(const_cast<const char *>(name))); |
---|
313 | |
---|
314 | OUTPUT: |
---|
315 | RETVAL |
---|
316 | |
---|
317 | |
---|
318 | char * |
---|
319 | P2AT_get_type_of_changekey(gb_main, field_name, change_key_path) |
---|
320 | GBDATA *gb_main |
---|
321 | char *field_name |
---|
322 | char *change_key_path |
---|
323 | |
---|
324 | CODE: |
---|
325 | RETVAL = const_cast<char *>(GBP_GB_TYPES_2_charPtr(GBT_get_type_of_changekey(gb_main, const_cast<const char *>(field_name), const_cast<const char *>(change_key_path)))); |
---|
326 | |
---|
327 | OUTPUT: |
---|
328 | RETVAL |
---|
329 | |
---|
330 | |
---|
331 | char * |
---|
332 | P2AT_write_sequence(gb_data, ali_name, ali_len, sequence) |
---|
333 | GBDATA *gb_data |
---|
334 | char *ali_name |
---|
335 | long ali_len |
---|
336 | char *sequence |
---|
337 | |
---|
338 | CODE: |
---|
339 | RETVAL = const_cast<char *>(GBT_write_sequence(gb_data, const_cast<const char *>(ali_name), ali_len, const_cast<const char *>(sequence))); |
---|
340 | |
---|
341 | OUTPUT: |
---|
342 | RETVAL |
---|
343 | |
---|
344 | |
---|