1 
2 
3 MODULE = Wise2 PACKAGE = Wise2::ThreeStateModel
4 
5 void
6 force_global_model(tsm,prob_into_model)
7 	Wise2_ThreeStateModel * tsm
8 	double prob_into_model
9 	CODE:
10 	Wise2_force_global_model(tsm,prob_into_model);
11 
12 
13 
14 void
15 force_weighted_local_model(tsm,prob_into_model,ratio_start,ratio_end)
16 	Wise2_ThreeStateModel * tsm
17 	double prob_into_model
18 	double ratio_start
19 	double ratio_end
20 	CODE:
21 	Wise2_force_weighted_local_model(tsm,prob_into_model,ratio_start,ratio_end);
22 
23 
24 
25 Wise2_ThreeStateModel *
26 ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,gap,ext)
27 	Wise2_Protein * pro
28 	Wise2_CompMat * mat
29 	Wise2_RandomModel * rm
30 	int gap
31 	int ext
32 	CODE:
33 	RETVAL = Wise2_ThreeStateModel_from_half_bit_Sequence(pro,mat,rm,gap,ext);
34 	OUTPUT:
35 	RETVAL
36 
37 
38 
39 void
40 write_HMMer_1_7_ascii_ThreeStateModel(tsm,ofp)
41 	Wise2_ThreeStateModel * tsm
42 	FILE * ofp
43 	CODE:
44 	Wise2_write_HMMer_1_7_ascii_ThreeStateModel(tsm,ofp);
45 
46 
47 
48 Wise2_ThreeStateModel *
49 hard_link_ThreeStateModel(obj)
50 	Wise2_ThreeStateModel * obj
51 	CODE:
52 	RETVAL = Wise2_hard_link_ThreeStateModel(obj);
53 	OUTPUT:
54 	RETVAL
55 
56 
57 
58 Wise2_ThreeStateModel *
59 ThreeStateModel_alloc_std()
60 	CODE:
61 	RETVAL = Wise2_ThreeStateModel_alloc_std();
62 	OUTPUT:
63 	RETVAL
64 
65 
66 
67 boolean
68 set_name(obj,name)
69 	Wise2_ThreeStateModel * obj
70 	char * name
71 	CODE:
72 	RETVAL = Wise2_replace_name_ThreeStateModel(obj,Wise2_stringalloc(name));
73 	OUTPUT:
74 	RETVAL
75 
76 
77 
78 char *
79 name(obj)
80 	Wise2_ThreeStateModel * obj
81 	INIT:
82 	char * temp;
83 	CODE:
84 	temp = Wise2_stringalloc(Wise2_access_name_ThreeStateModel(obj));
85 	RETVAL = temp;
86 	OUTPUT:
87 	RETVAL
88 
89 
90 
91 Wise2_ThreeStateUnit *
92 unit(obj,i)
93 	Wise2_ThreeStateModel * obj
94 	int i
95 	INIT:
96 Wise2_ThreeStateUnit * temp;
97 	CODE:
98 	temp = Wise2_hard_link_ThreeStateUnit(Wise2_access_unit_ThreeStateModel(obj,i));
99 	RETVAL = temp;
100 	OUTPUT:
101 	RETVAL
102 
103 
104 
105 int
106 length_unit(obj)
107 	Wise2_ThreeStateModel * obj
108 	CODE:
109 	RETVAL = Wise2_length_unit_ThreeStateModel(obj);
110 	OUTPUT:
111 	RETVAL
112 
113 
114 
115 int
116 flush_unit(obj)
117 	Wise2_ThreeStateModel * obj
118 	CODE:
119 	RETVAL = Wise2_flush_ThreeStateModel(obj);
120 	OUTPUT:
121 	RETVAL
122 
123 
124 
125 boolean
126 add_unit(obj,add)
127 	Wise2_ThreeStateModel * obj
128 	Wise2_ThreeStateUnit * add
129 	CODE:
130 	RETVAL = Wise2_add_ThreeStateModel(obj,Wise2_hard_link_ThreeStateUnit(add));
131 	OUTPUT:
132 	RETVAL
133 
134 
135 
136 boolean
137 set_alphabet(obj,alphabet)
138 	Wise2_ThreeStateModel * obj
139 	char * alphabet
140 	CODE:
141 	RETVAL = Wise2_replace_alphabet_ThreeStateModel(obj,Wise2_stringalloc(alphabet));
142 	OUTPUT:
143 	RETVAL
144 
145 
146 
147 char *
148 alphabet(obj)
149 	Wise2_ThreeStateModel * obj
150 	INIT:
151 	char * temp;
152 	CODE:
153 	temp = Wise2_stringalloc(Wise2_access_alphabet_ThreeStateModel(obj));
154 	RETVAL = temp;
155 	OUTPUT:
156 	RETVAL
157 
158 
159 
160 boolean
161 set_accession(obj,accession)
162 	Wise2_ThreeStateModel * obj
163 	char * accession
164 	CODE:
165 	RETVAL = Wise2_replace_accession_ThreeStateModel(obj,Wise2_stringalloc(accession));
166 	OUTPUT:
167 	RETVAL
168 
169 
170 
171 char *
172 accession(obj)
173 	Wise2_ThreeStateModel * obj
174 	INIT:
175 	char * temp;
176 	CODE:
177 	temp = Wise2_stringalloc(Wise2_access_accession_ThreeStateModel(obj));
178 	RETVAL = temp;
179 	OUTPUT:
180 	RETVAL
181 
182 
183 
184 boolean
185 set_threshold(obj,threshold)
186 	Wise2_ThreeStateModel * obj
187 	double threshold
188 	CODE:
189 	RETVAL = Wise2_replace_threshold_ThreeStateModel(obj,threshold);
190 	OUTPUT:
191 	RETVAL
192 
193 
194 
195 double
196 threshold(obj)
197 	Wise2_ThreeStateModel * obj
198 	CODE:
199 	RETVAL = Wise2_access_threshold_ThreeStateModel(obj);
200 	OUTPUT:
201 	RETVAL
202 
203 
204 
205 boolean
206 set_rm(obj,rm)
207 	Wise2_ThreeStateModel * obj
208 	Wise2_RandomModel * rm
209 	CODE:
210 	RETVAL = Wise2_replace_rm_ThreeStateModel(obj,Wise2_hard_link_RandomModel(rm));
211 	OUTPUT:
212 	RETVAL
213 
214 
215 
216 Wise2_RandomModel *
217 rm(obj)
218 	Wise2_ThreeStateModel * obj
219 	INIT:
220 Wise2_RandomModel * temp;
221 	CODE:
222 	temp = Wise2_hard_link_RandomModel(Wise2_access_rm_ThreeStateModel(obj));
223 	RETVAL = temp;
224 	OUTPUT:
225 	RETVAL
226 
227 
228 
229 
230 Wise2_ThreeStateModel *
231 new(class)
232 	char * class
233 	PPCODE:
234 	Wise2_ThreeStateModel * out;
235 	out = Wise2_ThreeStateModel_alloc_std();
236 	ST(0) = sv_newmortal();
237 	sv_setref_pv(ST(0),class,(void*)out);
238 	XSRETURN(1);
239 
240 void
241 DESTROY(obj)
242 	Wise2_ThreeStateModel * obj
243 	CODE:
244 	Wise2_free_ThreeStateModel(obj);
245 
246 void
247 each_unit(obj)
248 	Wise2_ThreeStateModel * obj
249 	PPCODE:
250 	int i=0;
251 	int len;
252 	SV* temp;
253 	len = Wise2_length_unit_ThreeStateModel(obj);
254 	for(i=0;i<len;i++){
255 	  temp = sv_newmortal();
256 	  sv_setref_pv(temp, "Wise2::ThreeStateUnit", (void*) (Wise2_hard_link_ThreeStateUnit(Wise2_access_unit_ThreeStateModel(obj,i))));
257 	  XPUSHs(temp);
258 	  }
259 	XSRETURN(len);
260 
261 
262 
263 MODULE = Wise2 PACKAGE = Wise2::ThreeStateUnit
264 
265 Wise2_ThreeStateUnit *
266 hard_link_ThreeStateUnit(obj)
267 	Wise2_ThreeStateUnit * obj
268 	CODE:
269 	RETVAL = Wise2_hard_link_ThreeStateUnit(obj);
270 	OUTPUT:
271 	RETVAL
272 
273 
274 
275 Wise2_ThreeStateUnit *
276 alloc()
277 	CODE:
278 	RETVAL = Wise2_ThreeStateUnit_alloc();
279 	OUTPUT:
280 	RETVAL
281 
282 
283 
284 boolean
285 set_display_char(obj,display_char)
286 	Wise2_ThreeStateUnit * obj
287 	char display_char
288 	CODE:
289 	RETVAL = Wise2_replace_display_char_ThreeStateUnit(obj,display_char);
290 	OUTPUT:
291 	RETVAL
292 
293 
294 
295 char
296 display_char(obj)
297 	Wise2_ThreeStateUnit * obj
298 	CODE:
299 	RETVAL = Wise2_access_display_char_ThreeStateUnit(obj);
300 	OUTPUT:
301 	RETVAL
302 
303 
304 
305 
306 Wise2_ThreeStateUnit *
307 new(class)
308 	char * class
309 	PPCODE:
310 	Wise2_ThreeStateUnit * out;
311 	out = Wise2_ThreeStateUnit_alloc();
312 	ST(0) = sv_newmortal();
313 	sv_setref_pv(ST(0),class,(void*)out);
314 	XSRETURN(1);
315 
316 void
317 DESTROY(obj)
318 	Wise2_ThreeStateUnit * obj
319 	CODE:
320 	Wise2_free_ThreeStateUnit(obj);
321 
322 
323 
324 MODULE = Wise2 PACKAGE = Wise2
325 
326 Wise2_ThreeStateModel *
327 read_HMMer_1_7_ascii_file(filename)
328 	char * filename
329 	CODE:
330 	RETVAL = Wise2_read_HMMer_1_7_ascii_file(filename);
331 	OUTPUT:
332 	RETVAL
333 
334 
335 
336 Wise2_ThreeStateModel *
337 read_HMMer_1_7_ascii(ifp)
338 	FILE * ifp
339 	CODE:
340 	RETVAL = Wise2_read_HMMer_1_7_ascii(ifp);
341 	OUTPUT:
342 	RETVAL
343 
344 
345 
346