1=head1 NAME 2 3matchsum module - part of the Wise2 package 4 5=head1 SYNOPSIS 6 7This module contains the following objects 8 9=over 10 11=item MatchSummarySet 12 13=item MatchSummary 14 15 16=back 17 18=head1 DESCRIPTION 19 20=head2 Object MatchSummarySet 21 22=over 23 24=item ms 25 26 Type [MatchSummary **] List No documentation 27 28 29 30=back 31 32This holds a set of MatchSummaries, 33 34 35 36=head2 Member functions of MatchSummarySet 37 38=over 39 40=item MatchSummarySet_from_AlnBlock_estwise 41 42&Wise2::MatchSummarySet::MatchSummarySet_from_AlnBlock_estwise(alb,qname,offset,target) 43 44 Builds a MatchSummarySet from a 45 EstWise alignment. this makes 46 alot of assumptions about the labels 47 setc in alb, so make sure it was a 48 estwise alignment - however as you 49 can notice this is exactly the same 50 labels as found in genewise set 51 52 53 54 Argument alb [UNKN ] Undocumented argument [AlnBlock *] 55 Argument qname [UNKN ] Undocumented argument [char *] 56 Argument offset [UNKN ] Undocumented argument [int] 57 Argument target [UNKN ] Undocumented argument [Sequence *] 58 Return [UNKN ] Undocumented return value [MatchSummarySet *] 59 60 61=item MatchSummarySet_from_AlnBlock_genewise 62 63&Wise2::MatchSummarySet::MatchSummarySet_from_AlnBlock_genewise(alb,qname,protoff,target) 64 65 Builds a MatchSummarySet from a 66 GeneWise alignment. this makes 67 alot of assumptions about the labels 68 setc in alb, so make sure it was a 69 genewise alignment 70 71 72 73 Argument alb [UNKN ] Undocumented argument [AlnBlock *] 74 Argument qname [UNKN ] Undocumented argument [char *] 75 Argument protoff [UNKN ] Undocumented argument [int] 76 Argument target [UNKN ] Undocumented argument [Sequence *] 77 Return [UNKN ] Undocumented return value [MatchSummarySet *] 78 79 80=item hard_link_MatchSummarySet 81 82&Wise2::MatchSummarySet::hard_link_MatchSummarySet(obj) 83 84 Bumps up the reference count of the object 85 Meaning that multiple pointers can 'own' it 86 87 88 89 Argument obj [UNKN ] Object to be hard linked [MatchSummarySet *] 90 Return [UNKN ] Undocumented return value [MatchSummarySet *] 91 92 93=item MatchSummarySet_alloc_std 94 95&Wise2::MatchSummarySet::MatchSummarySet_alloc_std(void) 96 97 Equivalent to MatchSummarySet_alloc_len(MatchSummarySetLISTLENGTH) 98 99 100 101 Return [UNKN ] Undocumented return value [MatchSummarySet *] 102 103 104=item ms 105 106&Wise2::MatchSummarySet::ms(obj,i) 107 108 Access members stored in the ms list 109 For use principly by API functions 110 111 112 113 Argument obj [UNKN ] Object holding the list [MatchSummarySet *] 114 Argument i [UNKN ] Position in the list [int] 115 Return [SOFT ] Element of the list [MatchSummary *] 116 117 118=item length_ms 119 120&Wise2::MatchSummarySet::length_ms(obj) 121 122 discover the length of the list 123 For use principly by API functions 124 125 126 127 Argument obj [UNKN ] Object holding the list [MatchSummarySet *] 128 Return [UNKN ] length of the list [int] 129 130 131=item flush_ms 132 133&Wise2::MatchSummarySet::flush_ms(obj) 134 135 Frees the list elements, sets length to 0 136 If you want to save some elements, use hard_link_xxx 137 to protect them from being actually destroyed in the free 138 139 140 141 Argument obj [UNKN ] Object which contains the list [MatchSummarySet *] 142 Return [UNKN ] Undocumented return value [int] 143 144 145=item add_ms 146 147&Wise2::MatchSummarySet::add_ms(obj,add) 148 149 Adds another object to the list. It will expand the list if necessary 150 151 152 153 Argument obj [UNKN ] Object which contains the list [MatchSummarySet *] 154 Argument add [OWNER] Object to add to the list [MatchSummary *] 155 Return [UNKN ] Undocumented return value [boolean] 156 157 158=back 159 160=head2 Object MatchSummary 161 162=over 163 164=item bits 165 166 Type [double] Scalar No documentation 167 168=item qname 169 170 Type [char *] Scalar No documentation 171 172=item tname 173 174 Type [char *] Scalar No documentation 175 176=item qstart 177 178 Type [int] Scalar No documentation 179 180=item qend 181 182 Type [int] Scalar No documentation 183 184=item tstart 185 186 Type [int] Scalar No documentation 187 188=item tend 189 190 Type [int] Scalar No documentation 191 192=item qintron 193 194 Type [int] Scalar No documentation 195 196=item qframeshift 197 198 Type [int] Scalar No documentation 199 200=item tintron 201 202 Type [int] Scalar No documentation 203 204=item tframeshift 205 206 Type [int] Scalar No documentation 207 208 209 210=back 211 212A Match Summary has summary statistics 213for a single alignment, with the 214two start/end ranges and the number of 215introns and frameshifts for each 216sequence (obviously, if one is a protein 217then neither are valid!) 218 219 220 221=head2 Member functions of MatchSummary 222 223=over 224 225=item hard_link_MatchSummary 226 227&Wise2::MatchSummary::hard_link_MatchSummary(obj) 228 229 Bumps up the reference count of the object 230 Meaning that multiple pointers can 'own' it 231 232 233 234 Argument obj [UNKN ] Object to be hard linked [MatchSummary *] 235 Return [UNKN ] Undocumented return value [MatchSummary *] 236 237 238=item alloc 239 240&Wise2::MatchSummary::alloc(void) 241 242 Allocates structure: assigns defaults if given 243 244 245 246 Return [UNKN ] Undocumented return value [MatchSummary *] 247 248 249=item set_bits 250 251&Wise2::MatchSummary::set_bits(obj,bits) 252 253 Replace member variable bits 254 For use principly by API functions 255 256 257 258 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 259 Argument bits [OWNER] New value of the variable [double] 260 Return [SOFT ] member variable bits [boolean] 261 262 263=item bits 264 265&Wise2::MatchSummary::bits(obj) 266 267 Access member variable bits 268 For use principly by API functions 269 270 271 272 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 273 Return [SOFT ] member variable bits [double] 274 275 276=item set_qname 277 278&Wise2::MatchSummary::set_qname(obj,qname) 279 280 Replace member variable qname 281 For use principly by API functions 282 283 284 285 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 286 Argument qname [OWNER] New value of the variable [char *] 287 Return [SOFT ] member variable qname [boolean] 288 289 290=item qname 291 292&Wise2::MatchSummary::qname(obj) 293 294 Access member variable qname 295 For use principly by API functions 296 297 298 299 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 300 Return [SOFT ] member variable qname [char *] 301 302 303=item set_tname 304 305&Wise2::MatchSummary::set_tname(obj,tname) 306 307 Replace member variable tname 308 For use principly by API functions 309 310 311 312 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 313 Argument tname [OWNER] New value of the variable [char *] 314 Return [SOFT ] member variable tname [boolean] 315 316 317=item tname 318 319&Wise2::MatchSummary::tname(obj) 320 321 Access member variable tname 322 For use principly by API functions 323 324 325 326 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 327 Return [SOFT ] member variable tname [char *] 328 329 330=item set_qstart 331 332&Wise2::MatchSummary::set_qstart(obj,qstart) 333 334 Replace member variable qstart 335 For use principly by API functions 336 337 338 339 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 340 Argument qstart [OWNER] New value of the variable [int] 341 Return [SOFT ] member variable qstart [boolean] 342 343 344=item qstart 345 346&Wise2::MatchSummary::qstart(obj) 347 348 Access member variable qstart 349 For use principly by API functions 350 351 352 353 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 354 Return [SOFT ] member variable qstart [int] 355 356 357=item set_qend 358 359&Wise2::MatchSummary::set_qend(obj,qend) 360 361 Replace member variable qend 362 For use principly by API functions 363 364 365 366 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 367 Argument qend [OWNER] New value of the variable [int] 368 Return [SOFT ] member variable qend [boolean] 369 370 371=item qend 372 373&Wise2::MatchSummary::qend(obj) 374 375 Access member variable qend 376 For use principly by API functions 377 378 379 380 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 381 Return [SOFT ] member variable qend [int] 382 383 384=item set_tstart 385 386&Wise2::MatchSummary::set_tstart(obj,tstart) 387 388 Replace member variable tstart 389 For use principly by API functions 390 391 392 393 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 394 Argument tstart [OWNER] New value of the variable [int] 395 Return [SOFT ] member variable tstart [boolean] 396 397 398=item tstart 399 400&Wise2::MatchSummary::tstart(obj) 401 402 Access member variable tstart 403 For use principly by API functions 404 405 406 407 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 408 Return [SOFT ] member variable tstart [int] 409 410 411=item set_tend 412 413&Wise2::MatchSummary::set_tend(obj,tend) 414 415 Replace member variable tend 416 For use principly by API functions 417 418 419 420 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 421 Argument tend [OWNER] New value of the variable [int] 422 Return [SOFT ] member variable tend [boolean] 423 424 425=item tend 426 427&Wise2::MatchSummary::tend(obj) 428 429 Access member variable tend 430 For use principly by API functions 431 432 433 434 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 435 Return [SOFT ] member variable tend [int] 436 437 438=item set_qintron 439 440&Wise2::MatchSummary::set_qintron(obj,qintron) 441 442 Replace member variable qintron 443 For use principly by API functions 444 445 446 447 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 448 Argument qintron [OWNER] New value of the variable [int] 449 Return [SOFT ] member variable qintron [boolean] 450 451 452=item qintron 453 454&Wise2::MatchSummary::qintron(obj) 455 456 Access member variable qintron 457 For use principly by API functions 458 459 460 461 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 462 Return [SOFT ] member variable qintron [int] 463 464 465=item set_qframeshift 466 467&Wise2::MatchSummary::set_qframeshift(obj,qframeshift) 468 469 Replace member variable qframeshift 470 For use principly by API functions 471 472 473 474 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 475 Argument qframeshift [OWNER] New value of the variable [int] 476 Return [SOFT ] member variable qframeshift [boolean] 477 478 479=item qframeshift 480 481&Wise2::MatchSummary::qframeshift(obj) 482 483 Access member variable qframeshift 484 For use principly by API functions 485 486 487 488 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 489 Return [SOFT ] member variable qframeshift [int] 490 491 492=item set_tintron 493 494&Wise2::MatchSummary::set_tintron(obj,tintron) 495 496 Replace member variable tintron 497 For use principly by API functions 498 499 500 501 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 502 Argument tintron [OWNER] New value of the variable [int] 503 Return [SOFT ] member variable tintron [boolean] 504 505 506=item tintron 507 508&Wise2::MatchSummary::tintron(obj) 509 510 Access member variable tintron 511 For use principly by API functions 512 513 514 515 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 516 Return [SOFT ] member variable tintron [int] 517 518 519=item set_tframeshift 520 521&Wise2::MatchSummary::set_tframeshift(obj,tframeshift) 522 523 Replace member variable tframeshift 524 For use principly by API functions 525 526 527 528 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 529 Argument tframeshift [OWNER] New value of the variable [int] 530 Return [SOFT ] member variable tframeshift [boolean] 531 532 533=item tframeshift 534 535&Wise2::MatchSummary::tframeshift(obj) 536 537 Access member variable tframeshift 538 For use principly by API functions 539 540 541 542 Argument obj [UNKN ] Object holding the variable [MatchSummary *] 543 Return [SOFT ] member variable tframeshift [int] 544 545 546=back 547 548