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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517
|
/* Functions that create, manipulate or act on MatchSummarySet
*
* Wise2_MatchSummarySet_from_AlnBlock_estwise
* Wise2_MatchSummarySet_from_AlnBlock_genewise
* Wise2_hard_link_MatchSummarySet
* Wise2_MatchSummarySet_alloc_std
* Wise2_access_ms_MatchSummarySet
* Wise2_length_ms_MatchSummarySet
* Wise2_flush_MatchSummarySet
* Wise2_add_MatchSummarySet
* Wise2_free_MatchSummarySet [destructor]
*
*/
/* Functions that create, manipulate or act on MatchSummary
*
* Wise2_hard_link_MatchSummary
* Wise2_MatchSummary_alloc
* Wise2_replace_bits_MatchSummary
* Wise2_access_bits_MatchSummary
* Wise2_replace_qname_MatchSummary
* Wise2_access_qname_MatchSummary
* Wise2_replace_tname_MatchSummary
* Wise2_access_tname_MatchSummary
* Wise2_replace_qstart_MatchSummary
* Wise2_access_qstart_MatchSummary
* Wise2_replace_qend_MatchSummary
* Wise2_access_qend_MatchSummary
* Wise2_replace_tstart_MatchSummary
* Wise2_access_tstart_MatchSummary
* Wise2_replace_tend_MatchSummary
* Wise2_access_tend_MatchSummary
* Wise2_replace_qintron_MatchSummary
* Wise2_access_qintron_MatchSummary
* Wise2_replace_qframeshift_MatchSummary
* Wise2_access_qframeshift_MatchSummary
* Wise2_replace_tintron_MatchSummary
* Wise2_access_tintron_MatchSummary
* Wise2_replace_tframeshift_MatchSummary
* Wise2_access_tframeshift_MatchSummary
* Wise2_free_MatchSummary [destructor]
*
*/
/* API for object MatchSummarySet */
/* Function: Wise2_MatchSummarySet_from_AlnBlock_estwise(alb,qname,offset,target)
*
* Descrip: Builds a MatchSummarySet from a
* EstWise alignment. this makes
* alot of assumptions about the labels
* setc in alb, so make sure it was a
* estwise alignment - however as you
* can notice this is exactly the same
* labels as found in genewise set
*
*
* Arg: alb Undocumented argument [Wise2_AlnBlock *]
* Arg: qname Undocumented argument [char *]
* Arg: offset Undocumented argument [int]
* Arg: target Undocumented argument [Wise2_Sequence *]
*
* Returns Undocumented return value [Wise2_MatchSummarySet *]
*
*/
Wise2_MatchSummarySet * Wise2_MatchSummarySet_from_AlnBlock_estwise( Wise2_AlnBlock * alb,char * qname,int offset,Wise2_Sequence * target);
/* Function: Wise2_MatchSummarySet_from_AlnBlock_genewise(alb,qname,protoff,target)
*
* Descrip: Builds a MatchSummarySet from a
* GeneWise alignment. this makes
* alot of assumptions about the labels
* setc in alb, so make sure it was a
* genewise alignment
*
*
* Arg: alb Undocumented argument [Wise2_AlnBlock *]
* Arg: qname Undocumented argument [char *]
* Arg: protoff Undocumented argument [int]
* Arg: target Undocumented argument [Wise2_Sequence *]
*
* Returns Undocumented return value [Wise2_MatchSummarySet *]
*
*/
Wise2_MatchSummarySet * Wise2_MatchSummarySet_from_AlnBlock_genewise( Wise2_AlnBlock * alb,char * qname,int protoff,Wise2_Sequence * target);
/* Function: Wise2_hard_link_MatchSummarySet(obj)
*
* Descrip: Bumps up the reference count of the object
* Meaning that multiple pointers can 'own' it
*
*
* Arg: obj Object to be hard linked [Wise2_MatchSummarySet *]
*
* Returns Undocumented return value [Wise2_MatchSummarySet *]
*
*/
Wise2_MatchSummarySet * Wise2_hard_link_MatchSummarySet( Wise2_MatchSummarySet * obj);
/* Function: Wise2_MatchSummarySet_alloc_std(void)
*
* Descrip: Equivalent to MatchSummarySet_alloc_len(MatchSummarySetLISTLENGTH)
*
*
*
* Returns Undocumented return value [Wise2_MatchSummarySet *]
*
*/
Wise2_MatchSummarySet * Wise2_MatchSummarySet_alloc_std();
/* Function: Wise2_access_ms_MatchSummarySet(obj,i)
*
* Descrip: Access members stored in the ms list
* For use principly by API functions
*
*
* Arg: obj Object holding the list [Wise2_MatchSummarySet *]
* Arg: i Position in the list [int]
*
* Returns Element of the list [Wise2_MatchSummary *]
*
*/
Wise2_MatchSummary * Wise2_access_ms_MatchSummarySet( Wise2_MatchSummarySet * obj,int i);
/* Function: Wise2_length_ms_MatchSummarySet(obj)
*
* Descrip: discover the length of the list
* For use principly by API functions
*
*
* Arg: obj Object holding the list [Wise2_MatchSummarySet *]
*
* Returns length of the list [int]
*
*/
int Wise2_length_ms_MatchSummarySet( Wise2_MatchSummarySet * obj);
/* Function: Wise2_flush_MatchSummarySet(obj)
*
* Descrip: Frees the list elements, sets length to 0
* If you want to save some elements, use hard_link_xxx
* to protect them from being actually destroyed in the free
*
*
* Arg: obj Object which contains the list [Wise2_MatchSummarySet *]
*
* Returns Undocumented return value [int]
*
*/
int Wise2_flush_MatchSummarySet( Wise2_MatchSummarySet * obj);
/* Function: Wise2_add_MatchSummarySet(obj,add)
*
* Descrip: Adds another object to the list. It will expand the list if necessary
*
*
* Arg: obj Object which contains the list [Wise2_MatchSummarySet *]
* Arg: add Object to add to the list [Wise2_MatchSummary *]
*
* Returns Undocumented return value [boolean]
*
*/
boolean Wise2_add_MatchSummarySet( Wise2_MatchSummarySet * obj,Wise2_MatchSummary * add);
/* This is the destructor function, ie, call this to free object*/
/* Function: Wise2_free_MatchSummarySet(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj Object that is free'd [Wise2_MatchSummarySet *]
*
* Returns Undocumented return value [Wise2_MatchSummarySet *]
*
*/
Wise2_MatchSummarySet * Wise2_free_MatchSummarySet( Wise2_MatchSummarySet * obj);
/* API for object MatchSummary */
/* Function: Wise2_hard_link_MatchSummary(obj)
*
* Descrip: Bumps up the reference count of the object
* Meaning that multiple pointers can 'own' it
*
*
* Arg: obj Object to be hard linked [Wise2_MatchSummary *]
*
* Returns Undocumented return value [Wise2_MatchSummary *]
*
*/
Wise2_MatchSummary * Wise2_hard_link_MatchSummary( Wise2_MatchSummary * obj);
/* Function: Wise2_MatchSummary_alloc(void)
*
* Descrip: Allocates structure: assigns defaults if given
*
*
*
* Returns Undocumented return value [Wise2_MatchSummary *]
*
*/
Wise2_MatchSummary * Wise2_MatchSummary_alloc();
/* Function: Wise2_replace_bits_MatchSummary(obj,bits)
*
* Descrip: Replace member variable bits
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
* Arg: bits New value of the variable [double]
*
* Returns member variable bits [boolean]
*
*/
boolean Wise2_replace_bits_MatchSummary( Wise2_MatchSummary * obj,double bits);
/* Function: Wise2_access_bits_MatchSummary(obj)
*
* Descrip: Access member variable bits
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
*
* Returns member variable bits [double]
*
*/
double Wise2_access_bits_MatchSummary( Wise2_MatchSummary * obj);
/* Function: Wise2_replace_qname_MatchSummary(obj,qname)
*
* Descrip: Replace member variable qname
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
* Arg: qname New value of the variable [char *]
*
* Returns member variable qname [boolean]
*
*/
boolean Wise2_replace_qname_MatchSummary( Wise2_MatchSummary * obj,char * qname);
/* Function: Wise2_access_qname_MatchSummary(obj)
*
* Descrip: Access member variable qname
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
*
* Returns member variable qname [char *]
*
*/
char * Wise2_access_qname_MatchSummary( Wise2_MatchSummary * obj);
/* Function: Wise2_replace_tname_MatchSummary(obj,tname)
*
* Descrip: Replace member variable tname
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
* Arg: tname New value of the variable [char *]
*
* Returns member variable tname [boolean]
*
*/
boolean Wise2_replace_tname_MatchSummary( Wise2_MatchSummary * obj,char * tname);
/* Function: Wise2_access_tname_MatchSummary(obj)
*
* Descrip: Access member variable tname
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
*
* Returns member variable tname [char *]
*
*/
char * Wise2_access_tname_MatchSummary( Wise2_MatchSummary * obj);
/* Function: Wise2_replace_qstart_MatchSummary(obj,qstart)
*
* Descrip: Replace member variable qstart
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
* Arg: qstart New value of the variable [int]
*
* Returns member variable qstart [boolean]
*
*/
boolean Wise2_replace_qstart_MatchSummary( Wise2_MatchSummary * obj,int qstart);
/* Function: Wise2_access_qstart_MatchSummary(obj)
*
* Descrip: Access member variable qstart
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
*
* Returns member variable qstart [int]
*
*/
int Wise2_access_qstart_MatchSummary( Wise2_MatchSummary * obj);
/* Function: Wise2_replace_qend_MatchSummary(obj,qend)
*
* Descrip: Replace member variable qend
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
* Arg: qend New value of the variable [int]
*
* Returns member variable qend [boolean]
*
*/
boolean Wise2_replace_qend_MatchSummary( Wise2_MatchSummary * obj,int qend);
/* Function: Wise2_access_qend_MatchSummary(obj)
*
* Descrip: Access member variable qend
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
*
* Returns member variable qend [int]
*
*/
int Wise2_access_qend_MatchSummary( Wise2_MatchSummary * obj);
/* Function: Wise2_replace_tstart_MatchSummary(obj,tstart)
*
* Descrip: Replace member variable tstart
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
* Arg: tstart New value of the variable [int]
*
* Returns member variable tstart [boolean]
*
*/
boolean Wise2_replace_tstart_MatchSummary( Wise2_MatchSummary * obj,int tstart);
/* Function: Wise2_access_tstart_MatchSummary(obj)
*
* Descrip: Access member variable tstart
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
*
* Returns member variable tstart [int]
*
*/
int Wise2_access_tstart_MatchSummary( Wise2_MatchSummary * obj);
/* Function: Wise2_replace_tend_MatchSummary(obj,tend)
*
* Descrip: Replace member variable tend
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
* Arg: tend New value of the variable [int]
*
* Returns member variable tend [boolean]
*
*/
boolean Wise2_replace_tend_MatchSummary( Wise2_MatchSummary * obj,int tend);
/* Function: Wise2_access_tend_MatchSummary(obj)
*
* Descrip: Access member variable tend
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
*
* Returns member variable tend [int]
*
*/
int Wise2_access_tend_MatchSummary( Wise2_MatchSummary * obj);
/* Function: Wise2_replace_qintron_MatchSummary(obj,qintron)
*
* Descrip: Replace member variable qintron
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
* Arg: qintron New value of the variable [int]
*
* Returns member variable qintron [boolean]
*
*/
boolean Wise2_replace_qintron_MatchSummary( Wise2_MatchSummary * obj,int qintron);
/* Function: Wise2_access_qintron_MatchSummary(obj)
*
* Descrip: Access member variable qintron
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
*
* Returns member variable qintron [int]
*
*/
int Wise2_access_qintron_MatchSummary( Wise2_MatchSummary * obj);
/* Function: Wise2_replace_qframeshift_MatchSummary(obj,qframeshift)
*
* Descrip: Replace member variable qframeshift
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
* Arg: qframeshift New value of the variable [int]
*
* Returns member variable qframeshift [boolean]
*
*/
boolean Wise2_replace_qframeshift_MatchSummary( Wise2_MatchSummary * obj,int qframeshift);
/* Function: Wise2_access_qframeshift_MatchSummary(obj)
*
* Descrip: Access member variable qframeshift
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
*
* Returns member variable qframeshift [int]
*
*/
int Wise2_access_qframeshift_MatchSummary( Wise2_MatchSummary * obj);
/* Function: Wise2_replace_tintron_MatchSummary(obj,tintron)
*
* Descrip: Replace member variable tintron
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
* Arg: tintron New value of the variable [int]
*
* Returns member variable tintron [boolean]
*
*/
boolean Wise2_replace_tintron_MatchSummary( Wise2_MatchSummary * obj,int tintron);
/* Function: Wise2_access_tintron_MatchSummary(obj)
*
* Descrip: Access member variable tintron
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
*
* Returns member variable tintron [int]
*
*/
int Wise2_access_tintron_MatchSummary( Wise2_MatchSummary * obj);
/* Function: Wise2_replace_tframeshift_MatchSummary(obj,tframeshift)
*
* Descrip: Replace member variable tframeshift
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
* Arg: tframeshift New value of the variable [int]
*
* Returns member variable tframeshift [boolean]
*
*/
boolean Wise2_replace_tframeshift_MatchSummary( Wise2_MatchSummary * obj,int tframeshift);
/* Function: Wise2_access_tframeshift_MatchSummary(obj)
*
* Descrip: Access member variable tframeshift
* For use principly by API functions
*
*
* Arg: obj Object holding the variable [Wise2_MatchSummary *]
*
* Returns member variable tframeshift [int]
*
*/
int Wise2_access_tframeshift_MatchSummary( Wise2_MatchSummary * obj);
/* This is the destructor function, ie, call this to free object*/
/* Function: Wise2_free_MatchSummary(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj Object that is free'd [Wise2_MatchSummary *]
*
* Returns Undocumented return value [Wise2_MatchSummary *]
*
*/
Wise2_MatchSummary * Wise2_free_MatchSummary( Wise2_MatchSummary * obj);
|