1=head1 NAME 2 3pfamhmmer1db module - part of the Wise2 package 4 5=head1 SYNOPSIS 6 7This module contains the following objects 8 9=over 10 11=item PfamHmmer1DB 12 13=item PfamHmmer1Entry 14 15 16=back 17 18=head1 DESCRIPTION 19 20=head2 Object PfamHmmer1DB 21 22=over 23 24=item en 25 26 Type [PfamHmmer1Entry **] List No documentation 27 28=item dirname 29 30 Type [char *] Scalar directory name with the models 31 32=item cur 33 34 Type [int] Scalar No documentation 35 36=item def 37 38 Type [RandomModel *] Scalar default random model 39 40 41 42=back 43 44 45Pfam Hmmer1db is a wrapper around a Pfam Hmmer database. This is file 46called HMM.s in a directory which has appropiate .HMM and .random 47files 48 49Although this DB will be phased out, it is still around for a while. 50 51This wont be used directly, but rather in a threestatedb model. 52It does not implement a full dynamite style db stream. rather it expects 53threestatedb to prod it in the correct manner. 54 55 56 57 58=head2 Member functions of PfamHmmer1DB 59 60=over 61 62=item hard_link_PfamHmmer1DB 63 64&Wise2::PfamHmmer1DB::hard_link_PfamHmmer1DB(obj) 65 66 Bumps up the reference count of the object 67 Meaning that multiple pointers can 'own' it 68 69 70 71 Argument obj [UNKN ] Object to be hard linked [PfamHmmer1DB *] 72 Return [UNKN ] Undocumented return value [PfamHmmer1DB *] 73 74 75=item PfamHmmer1DB_alloc_std 76 77&Wise2::PfamHmmer1DB::PfamHmmer1DB_alloc_std(void) 78 79 Equivalent to PfamHmmer1DB_alloc_len(PfamHmmer1DBLISTLENGTH) 80 81 82 83 Return [UNKN ] Undocumented return value [PfamHmmer1DB *] 84 85 86=item en 87 88&Wise2::PfamHmmer1DB::en(obj,i) 89 90 Access members stored in the en list 91 For use principly by API functions 92 93 94 95 Argument obj [UNKN ] Object holding the list [PfamHmmer1DB *] 96 Argument i [UNKN ] Position in the list [int] 97 Return [SOFT ] Element of the list [PfamHmmer1Entry *] 98 99 100=item length_en 101 102&Wise2::PfamHmmer1DB::length_en(obj) 103 104 discover the length of the list 105 For use principly by API functions 106 107 108 109 Argument obj [UNKN ] Object holding the list [PfamHmmer1DB *] 110 Return [UNKN ] length of the list [int] 111 112 113=item flush_en 114 115&Wise2::PfamHmmer1DB::flush_en(obj) 116 117 Frees the list elements, sets length to 0 118 If you want to save some elements, use hard_link_xxx 119 to protect them from being actually destroyed in the free 120 121 122 123 Argument obj [UNKN ] Object which contains the list [PfamHmmer1DB *] 124 Return [UNKN ] Undocumented return value [int] 125 126 127=item add_en 128 129&Wise2::PfamHmmer1DB::add_en(obj,add) 130 131 Adds another object to the list. It will expand the list if necessary 132 133 134 135 Argument obj [UNKN ] Object which contains the list [PfamHmmer1DB *] 136 Argument add [OWNER] Object to add to the list [PfamHmmer1Entry *] 137 Return [UNKN ] Undocumented return value [boolean] 138 139 140=item set_dirname 141 142&Wise2::PfamHmmer1DB::set_dirname(obj,dirname) 143 144 Replace member variable dirname 145 For use principly by API functions 146 147 148 149 Argument obj [UNKN ] Object holding the variable [PfamHmmer1DB *] 150 Argument dirname [OWNER] New value of the variable [char *] 151 Return [SOFT ] member variable dirname [boolean] 152 153 154=item dirname 155 156&Wise2::PfamHmmer1DB::dirname(obj) 157 158 Access member variable dirname 159 For use principly by API functions 160 161 162 163 Argument obj [UNKN ] Object holding the variable [PfamHmmer1DB *] 164 Return [SOFT ] member variable dirname [char *] 165 166 167=item set_cur 168 169&Wise2::PfamHmmer1DB::set_cur(obj,cur) 170 171 Replace member variable cur 172 For use principly by API functions 173 174 175 176 Argument obj [UNKN ] Object holding the variable [PfamHmmer1DB *] 177 Argument cur [OWNER] New value of the variable [int] 178 Return [SOFT ] member variable cur [boolean] 179 180 181=item cur 182 183&Wise2::PfamHmmer1DB::cur(obj) 184 185 Access member variable cur 186 For use principly by API functions 187 188 189 190 Argument obj [UNKN ] Object holding the variable [PfamHmmer1DB *] 191 Return [SOFT ] member variable cur [int] 192 193 194=item set_def 195 196&Wise2::PfamHmmer1DB::set_def(obj,def) 197 198 Replace member variable def 199 For use principly by API functions 200 201 202 203 Argument obj [UNKN ] Object holding the variable [PfamHmmer1DB *] 204 Argument def [OWNER] New value of the variable [RandomModel *] 205 Return [SOFT ] member variable def [boolean] 206 207 208=item def 209 210&Wise2::PfamHmmer1DB::def(obj) 211 212 Access member variable def 213 For use principly by API functions 214 215 216 217 Argument obj [UNKN ] Object holding the variable [PfamHmmer1DB *] 218 Return [SOFT ] member variable def [RandomModel *] 219 220 221=back 222 223=head2 Object PfamHmmer1Entry 224 225=over 226 227=item entryname 228 229 Type [char *] Scalar No documentation 230 231=item is_random 232 233 Type [boolean] Scalar No documentation 234 235=item is_hmmls 236 237 Type [boolean] Scalar No documentation 238 239=item bits_cutoff 240 241 Type [double] Scalar No documentation 242 243 244 245=back 246 247No documentation for PfamHmmer1Entry 248 249=head2 Member functions of PfamHmmer1Entry 250 251=over 252 253=item hard_link_PfamHmmer1Entry 254 255&Wise2::PfamHmmer1Entry::hard_link_PfamHmmer1Entry(obj) 256 257 Bumps up the reference count of the object 258 Meaning that multiple pointers can 'own' it 259 260 261 262 Argument obj [UNKN ] Object to be hard linked [PfamHmmer1Entry *] 263 Return [UNKN ] Undocumented return value [PfamHmmer1Entry *] 264 265 266=item alloc 267 268&Wise2::PfamHmmer1Entry::alloc(void) 269 270 Allocates structure: assigns defaults if given 271 272 273 274 Return [UNKN ] Undocumented return value [PfamHmmer1Entry *] 275 276 277=item set_entryname 278 279&Wise2::PfamHmmer1Entry::set_entryname(obj,entryname) 280 281 Replace member variable entryname 282 For use principly by API functions 283 284 285 286 Argument obj [UNKN ] Object holding the variable [PfamHmmer1Entry *] 287 Argument entryname [OWNER] New value of the variable [char *] 288 Return [SOFT ] member variable entryname [boolean] 289 290 291=item entryname 292 293&Wise2::PfamHmmer1Entry::entryname(obj) 294 295 Access member variable entryname 296 For use principly by API functions 297 298 299 300 Argument obj [UNKN ] Object holding the variable [PfamHmmer1Entry *] 301 Return [SOFT ] member variable entryname [char *] 302 303 304=item set_is_random 305 306&Wise2::PfamHmmer1Entry::set_is_random(obj,is_random) 307 308 Replace member variable is_random 309 For use principly by API functions 310 311 312 313 Argument obj [UNKN ] Object holding the variable [PfamHmmer1Entry *] 314 Argument is_random [OWNER] New value of the variable [boolean] 315 Return [SOFT ] member variable is_random [boolean] 316 317 318=item is_random 319 320&Wise2::PfamHmmer1Entry::is_random(obj) 321 322 Access member variable is_random 323 For use principly by API functions 324 325 326 327 Argument obj [UNKN ] Object holding the variable [PfamHmmer1Entry *] 328 Return [SOFT ] member variable is_random [boolean] 329 330 331=item set_is_hmmls 332 333&Wise2::PfamHmmer1Entry::set_is_hmmls(obj,is_hmmls) 334 335 Replace member variable is_hmmls 336 For use principly by API functions 337 338 339 340 Argument obj [UNKN ] Object holding the variable [PfamHmmer1Entry *] 341 Argument is_hmmls [OWNER] New value of the variable [boolean] 342 Return [SOFT ] member variable is_hmmls [boolean] 343 344 345=item is_hmmls 346 347&Wise2::PfamHmmer1Entry::is_hmmls(obj) 348 349 Access member variable is_hmmls 350 For use principly by API functions 351 352 353 354 Argument obj [UNKN ] Object holding the variable [PfamHmmer1Entry *] 355 Return [SOFT ] member variable is_hmmls [boolean] 356 357 358=item set_bits_cutoff 359 360&Wise2::PfamHmmer1Entry::set_bits_cutoff(obj,bits_cutoff) 361 362 Replace member variable bits_cutoff 363 For use principly by API functions 364 365 366 367 Argument obj [UNKN ] Object holding the variable [PfamHmmer1Entry *] 368 Argument bits_cutoff [OWNER] New value of the variable [double] 369 Return [SOFT ] member variable bits_cutoff [boolean] 370 371 372=item bits_cutoff 373 374&Wise2::PfamHmmer1Entry::bits_cutoff(obj) 375 376 Access member variable bits_cutoff 377 For use principly by API functions 378 379 380 381 Argument obj [UNKN ] Object holding the variable [PfamHmmer1Entry *] 382 Return [SOFT ] member variable bits_cutoff [double] 383 384 385=back 386 387