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