1 #ifndef _objblst3_ 2 #define _objblst3_ 3 4 #undef NLM_EXTERN 5 #ifdef NLM_IMPORT 6 #define NLM_EXTERN NLM_IMPORT 7 #else 8 #define NLM_EXTERN extern 9 #endif 10 11 12 #ifdef __cplusplus 13 extern "C" { /* } */ 14 #endif 15 16 17 /************************************************** 18 * 19 * Generated objects for Module NCBI-Blast 20 * Generated using ASNCODE Revision: 6.14 at Apr 16, 2002 11:50 AM 21 * 22 **************************************************/ 23 24 NLM_EXTERN Boolean LIBCALL 25 objblst3AsnLoad PROTO((void)); 26 27 28 /************************************************** 29 * 30 * BlastSearch 31 * 32 **************************************************/ 33 typedef struct struct_Blast_search { 34 Uint2 program; 35 /* following #defines are for enumerated type, not used by object loaders */ 36 #define Blast_search_program_blastn 0 37 #define Blast_search_program_blastp 1 38 #define Blast_search_program_blastx 2 39 #define Blast_search_program_tblastn 3 40 #define Blast_search_program_tblastx 4 41 42 struct struct_Bioseq PNTR query; 43 CharPtr database; 44 struct struct_Blast_parameters PNTR parameters; 45 ValNodePtr mask; 46 struct struct_Blast_matrix PNTR matrix; 47 Uint1 return_parts; 48 struct struct_Bioseq_set PNTR query_set; 49 } BlastSearch, PNTR BlastSearchPtr; 50 51 52 NLM_EXTERN BlastSearchPtr LIBCALL BlastSearchFree PROTO ((BlastSearchPtr )); 53 NLM_EXTERN BlastSearchPtr LIBCALL BlastSearchNew PROTO (( void )); 54 NLM_EXTERN BlastSearchPtr LIBCALL BlastSearchAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 55 NLM_EXTERN Boolean LIBCALL BlastSearchAsnWrite PROTO (( BlastSearchPtr , AsnIoPtr, AsnTypePtr)); 56 57 typedef ValNodePtr BlastRequestPtr; 58 typedef ValNode BlastRequest; 59 #define BlastRequest_init 1 60 #define BlastRequest_motd 2 61 #define BlastRequest_db_info 3 62 #define BlastRequest_db_info_specific 4 63 #define BlastRequest_matrix_get 5 64 #define BlastRequest_search 6 65 #define BlastRequest_db_seq_get 7 66 #define BlastRequest_db_redundant_ids_get 8 67 #define BlastRequest_db_redundant_descr_get 9 68 #define BlastRequest_fini 10 69 70 71 NLM_EXTERN BlastRequestPtr LIBCALL BlastRequestFree PROTO ((BlastRequestPtr )); 72 NLM_EXTERN BlastRequestPtr LIBCALL BlastRequestAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 73 NLM_EXTERN Boolean LIBCALL BlastRequestAsnWrite PROTO (( BlastRequestPtr , AsnIoPtr, AsnTypePtr)); 74 75 typedef ValNodePtr BlastResponsePtr; 76 typedef ValNode BlastResponse; 77 #define BlastResponse_init 1 78 #define BlastResponse_motd 2 79 #define BlastResponse_error 3 80 #define BlastResponse_db_seq_get 4 81 #define BlastResponse_db_redundant_ids_get 5 82 #define BlastResponse_db_redundant_descr_get 6 83 #define BlastResponse_db_info 7 84 #define BlastResponse_db_info_specific 8 85 #define BlastResponse_matrix 9 86 #define BlastResponse_alignment 10 87 #define BlastResponse_mask 11 88 #define BlastResponse_kablk 12 89 #define BlastResponse_parameters 13 90 #define BlastResponse_queued 14 91 #define BlastResponse_start 15 92 #define BlastResponse_progress 16 93 #define BlastResponse_done 17 94 #define BlastResponse_fini 18 95 #define BlastResponse_phialign 19 96 #define BlastResponse_parts 20 97 #define BlastResponse_mbalign 21 98 99 100 NLM_EXTERN BlastResponsePtr LIBCALL BlastResponseFree PROTO ((BlastResponsePtr )); 101 NLM_EXTERN BlastResponsePtr LIBCALL BlastResponseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 102 NLM_EXTERN Boolean LIBCALL BlastResponseAsnWrite PROTO (( BlastResponsePtr , AsnIoPtr, AsnTypePtr)); 103 104 105 106 /************************************************** 107 * 108 * BlastParameters 109 * 110 **************************************************/ 111 typedef struct struct_Blast_parameters { 112 Int4 first_threshold; 113 Int4 second_threshold; 114 ValNodePtr Cutoff_cutoff; 115 ValNodePtr Cutoff2_cutoff2; 116 Int4 hitlist_size; 117 Int4 nucl_penalty; 118 Int4 nucl_reward; 119 Int4 genetic_code; 120 Int4 db_genetic_code; 121 Int4 low_complexity_filtering; 122 Uint1 gapped_alignment; 123 Int4 gap_open; 124 Int4 gap_extend; 125 Int4 required_start; 126 Int4 required_end; 127 FloatHi ethresh; 128 Int4 max_num_passes; 129 Int4 pseudo_count_const; 130 CharPtr other_options; 131 ValNodePtr gilist; 132 CharPtr gifile; 133 CharPtr matrix; 134 CharPtr filter_string; 135 CharPtr entrez_query; 136 Int4 word_size; 137 Int4 db_length; 138 FloatHi searchsp_eff; 139 Int4 hsp_range_max; 140 Int4 block_width; 141 Uint1 perform_culling; 142 Int4 strand_option; 143 CharPtr phi_pattern; 144 Uint1 use_real_db_size; 145 Uint1 use_best_align; 146 Uint1 is_rps_blast; 147 Uint1 tweak_parameters; 148 Uint1 smith_waterman; 149 Uint1 is_megablast; 150 ValNodePtr query_lcase_mask; 151 Int4 is_ooframe; 152 Uint1 endpoint_results; 153 FloatHi percent_identity; 154 Int4 first_db_seq; 155 Int4 final_db_seq; 156 Int4 window_size; 157 Int4 mb_template_length; 158 Int4 mb_disc_type; 159 } BlastParameters, PNTR BlastParametersPtr; 160 161 162 NLM_EXTERN BlastParametersPtr LIBCALL BlastParametersFree PROTO ((BlastParametersPtr )); 163 NLM_EXTERN BlastParametersPtr LIBCALL BlastParametersNew PROTO (( void )); 164 NLM_EXTERN BlastParametersPtr LIBCALL BlastParametersAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 165 NLM_EXTERN Boolean LIBCALL BlastParametersAsnWrite PROTO (( BlastParametersPtr , AsnIoPtr, AsnTypePtr)); 166 167 168 #ifdef NLM_GENERATED_CODE_PROTO 169 170 typedef ValNodePtr Cutoff2_cutoff2Ptr; 171 typedef ValNode Cutoff2_cutoff2; 172 173 #endif /* NLM_GENERATED_CODE_PROTO */ 174 175 #define Cutoff2_cutoff2_evalue 1 176 #define Cutoff2_cutoff2_score 2 177 178 #ifdef NLM_GENERATED_CODE_PROTO 179 180 static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr )); 181 static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 182 static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr)); 183 184 #endif /* NLM_GENERATED_CODE_PROTO */ 185 186 187 #ifdef NLM_GENERATED_CODE_PROTO 188 189 typedef ValNodePtr Cutoff_cutoffPtr; 190 typedef ValNode Cutoff_cutoff; 191 192 #endif /* NLM_GENERATED_CODE_PROTO */ 193 194 #define Cutoff_cutoff_evalue 1 195 #define Cutoff_cutoff_score 2 196 197 #ifdef NLM_GENERATED_CODE_PROTO 198 199 static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr )); 200 static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 201 static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr)); 202 203 #endif /* NLM_GENERATED_CODE_PROTO */ 204 205 206 207 /************************************************** 208 * 209 * BlastMatrix 210 * 211 **************************************************/ 212 typedef struct struct_Blast_matrix { 213 Uint1 is_protein; 214 CharPtr name; 215 ValNodePtr comments; 216 Int4 row_length; 217 Int4 column_length; 218 ValNodePtr scores; 219 FloatHi karlinK; 220 ValNodePtr posFreqs; 221 } BlastMatrix, PNTR BlastMatrixPtr; 222 223 224 NLM_EXTERN BlastMatrixPtr LIBCALL BlastMatrixFree PROTO ((BlastMatrixPtr )); 225 NLM_EXTERN BlastMatrixPtr LIBCALL BlastMatrixNew PROTO (( void )); 226 NLM_EXTERN BlastMatrixPtr LIBCALL BlastMatrixAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 227 NLM_EXTERN Boolean LIBCALL BlastMatrixAsnWrite PROTO (( BlastMatrixPtr , AsnIoPtr, AsnTypePtr)); 228 229 230 231 /************************************************** 232 * 233 * BlastDbinfo 234 * 235 **************************************************/ 236 typedef struct struct_Blast_dbinfo { 237 struct struct_Blast_dbinfo PNTR next; 238 Uint1 is_protein; 239 CharPtr name; 240 CharPtr definition; 241 CharPtr date; 242 Int4 total_length; 243 Int4 number_seqs; 244 } BlastDbinfo, PNTR BlastDbinfoPtr; 245 246 247 NLM_EXTERN BlastDbinfoPtr LIBCALL BlastDbinfoFree PROTO ((BlastDbinfoPtr )); 248 NLM_EXTERN BlastDbinfoPtr LIBCALL BlastDbinfoNew PROTO (( void )); 249 NLM_EXTERN BlastDbinfoPtr LIBCALL BlastDbinfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 250 NLM_EXTERN Boolean LIBCALL BlastDbinfoAsnWrite PROTO (( BlastDbinfoPtr , AsnIoPtr, AsnTypePtr)); 251 252 253 254 /************************************************** 255 * 256 * BlastMask 257 * 258 **************************************************/ 259 typedef struct struct_Blast_mask { 260 ValNodePtr location; 261 Uint2 frame; 262 /* following #defines are for enumerated type, not used by object loaders */ 263 #define Blast_mask_frame_notset 0 264 #define Blast_mask_frame_plus1 1 265 #define Blast_mask_frame_plus2 2 266 #define Blast_mask_frame_plus3 3 267 #define Blast_mask_frame_minus1 4 268 #define Blast_mask_frame_minus2 5 269 #define Blast_mask_frame_minus3 6 270 271 } BlastMask, PNTR BlastMaskPtr; 272 273 274 NLM_EXTERN BlastMaskPtr LIBCALL BlastMaskFree PROTO ((BlastMaskPtr )); 275 NLM_EXTERN BlastMaskPtr LIBCALL BlastMaskNew PROTO (( void )); 276 NLM_EXTERN BlastMaskPtr LIBCALL BlastMaskAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 277 NLM_EXTERN Boolean LIBCALL BlastMaskAsnWrite PROTO (( BlastMaskPtr , AsnIoPtr, AsnTypePtr)); 278 279 280 281 /************************************************** 282 * 283 * BlastKABlk 284 * 285 **************************************************/ 286 typedef struct struct_Blast_KABlk { 287 FloatHi lambda; 288 FloatHi k; 289 FloatHi h; 290 Uint1 gapped; 291 } BlastKABlk, PNTR BlastKABlkPtr; 292 293 294 NLM_EXTERN BlastKABlkPtr LIBCALL BlastKABlkFree PROTO ((BlastKABlkPtr )); 295 NLM_EXTERN BlastKABlkPtr LIBCALL BlastKABlkNew PROTO (( void )); 296 NLM_EXTERN BlastKABlkPtr LIBCALL BlastKABlkAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 297 NLM_EXTERN Boolean LIBCALL BlastKABlkAsnWrite PROTO (( BlastKABlkPtr , AsnIoPtr, AsnTypePtr)); 298 299 300 301 /************************************************** 302 * 303 * BlastError 304 * 305 **************************************************/ 306 typedef struct struct_Blast_error { 307 Uint2 level; 308 /* following #defines are for enumerated type, not used by object loaders */ 309 #define Blast_error_level_none 0 310 #define Blast_error_level_info 1 311 #define Blast_error_level_warn 2 312 #define Blast_error_level_error 3 313 #define Blast_error_level_fatal 4 314 315 CharPtr msg; 316 } BlastError, PNTR BlastErrorPtr; 317 318 319 NLM_EXTERN BlastErrorPtr LIBCALL BlastErrorFree PROTO ((BlastErrorPtr )); 320 NLM_EXTERN BlastErrorPtr LIBCALL BlastErrorNew PROTO (( void )); 321 NLM_EXTERN BlastErrorPtr LIBCALL BlastErrorAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 322 NLM_EXTERN Boolean LIBCALL BlastErrorAsnWrite PROTO (( BlastErrorPtr , AsnIoPtr, AsnTypePtr)); 323 324 325 326 /************************************************** 327 * 328 * BlastPhialign 329 * 330 **************************************************/ 331 typedef struct struct_Blast_phialign { 332 Int4 numaligns; 333 ValNodePtr seqloc; 334 } BlastPhialign, PNTR BlastPhialignPtr; 335 336 337 NLM_EXTERN BlastPhialignPtr LIBCALL BlastPhialignFree PROTO ((BlastPhialignPtr )); 338 NLM_EXTERN BlastPhialignPtr LIBCALL BlastPhialignNew PROTO (( void )); 339 NLM_EXTERN BlastPhialignPtr LIBCALL BlastPhialignAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 340 NLM_EXTERN Boolean LIBCALL BlastPhialignAsnWrite PROTO (( BlastPhialignPtr , AsnIoPtr, AsnTypePtr)); 341 342 343 344 /************************************************** 345 * 346 * BlastDbinfoGet 347 * 348 **************************************************/ 349 typedef struct struct_Blast_dbinfo_get { 350 CharPtr name; 351 Uint2 type; 352 /* following #defines are for enumerated type, not used by object loaders */ 353 #define Blast_dbinfo_get_type_unknown 0 354 #define Blast_dbinfo_get_type_protein 1 355 #define Blast_dbinfo_get_type_nucleotide 2 356 357 } BlastDbinfoGet, PNTR BlastDbinfoGetPtr; 358 359 360 NLM_EXTERN BlastDbinfoGetPtr LIBCALL BlastDbinfoGetFree PROTO ((BlastDbinfoGetPtr )); 361 NLM_EXTERN BlastDbinfoGetPtr LIBCALL BlastDbinfoGetNew PROTO (( void )); 362 NLM_EXTERN BlastDbinfoGetPtr LIBCALL BlastDbinfoGetAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 363 NLM_EXTERN Boolean LIBCALL BlastDbinfoGetAsnWrite PROTO (( BlastDbinfoGetPtr , AsnIoPtr, AsnTypePtr)); 364 365 366 367 /************************************************** 368 * 369 * BlastSeqId 370 * 371 **************************************************/ 372 typedef struct struct_Blast_seq_id { 373 Uint1 is_protein; 374 CharPtr database; 375 ValNodePtr id; 376 } BlastSeqId, PNTR BlastSeqIdPtr; 377 378 379 NLM_EXTERN BlastSeqIdPtr LIBCALL BlastSeqIdFree PROTO ((BlastSeqIdPtr )); 380 NLM_EXTERN BlastSeqIdPtr LIBCALL BlastSeqIdNew PROTO (( void )); 381 NLM_EXTERN BlastSeqIdPtr LIBCALL BlastSeqIdAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 382 NLM_EXTERN Boolean LIBCALL BlastSeqIdAsnWrite PROTO (( BlastSeqIdPtr , AsnIoPtr, AsnTypePtr)); 383 384 385 386 /************************************************** 387 * 388 * BlastSequence 389 * 390 **************************************************/ 391 typedef struct struct_Blast_sequence { 392 struct struct_Blast_sequence PNTR next; 393 struct struct_Seq_align PNTR align; 394 ByteStorePtr db_seq; 395 } BlastSequence, PNTR BlastSequencePtr; 396 397 398 NLM_EXTERN BlastSequencePtr LIBCALL BlastSequenceFree PROTO ((BlastSequencePtr )); 399 NLM_EXTERN BlastSequencePtr LIBCALL BlastSequenceNew PROTO (( void )); 400 NLM_EXTERN BlastSequencePtr LIBCALL BlastSequenceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 401 NLM_EXTERN Boolean LIBCALL BlastSequenceAsnWrite PROTO (( BlastSequencePtr , AsnIoPtr, AsnTypePtr)); 402 403 404 405 /************************************************** 406 * 407 * BlastParts 408 * 409 **************************************************/ 410 typedef struct struct_Blast_parts { 411 struct struct_Blast_parts PNTR next; 412 CharPtr defline; 413 struct struct_Blast_sequence PNTR sequence; 414 } BlastParts, PNTR BlastPartsPtr; 415 416 417 NLM_EXTERN BlastPartsPtr LIBCALL BlastPartsFree PROTO ((BlastPartsPtr )); 418 NLM_EXTERN BlastPartsPtr LIBCALL BlastPartsNew PROTO (( void )); 419 NLM_EXTERN BlastPartsPtr LIBCALL BlastPartsAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 420 NLM_EXTERN Boolean LIBCALL BlastPartsAsnWrite PROTO (( BlastPartsPtr , AsnIoPtr, AsnTypePtr)); 421 422 423 424 /************************************************** 425 * 426 * BlastQueued 427 * 428 **************************************************/ 429 typedef struct struct_Blast_Queued { 430 Int4 length; 431 } BlastQueued, PNTR BlastQueuedPtr; 432 433 434 NLM_EXTERN BlastQueuedPtr LIBCALL BlastQueuedFree PROTO ((BlastQueuedPtr )); 435 NLM_EXTERN BlastQueuedPtr LIBCALL BlastQueuedNew PROTO (( void )); 436 NLM_EXTERN BlastQueuedPtr LIBCALL BlastQueuedAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 437 NLM_EXTERN Boolean LIBCALL BlastQueuedAsnWrite PROTO (( BlastQueuedPtr , AsnIoPtr, AsnTypePtr)); 438 439 440 441 /************************************************** 442 * 443 * BlastProgress 444 * 445 **************************************************/ 446 typedef struct struct_Blast_Progress { 447 Int4 completed; 448 } BlastProgress, PNTR BlastProgressPtr; 449 450 451 NLM_EXTERN BlastProgressPtr LIBCALL BlastProgressFree PROTO ((BlastProgressPtr )); 452 NLM_EXTERN BlastProgressPtr LIBCALL BlastProgressNew PROTO (( void )); 453 NLM_EXTERN BlastProgressPtr LIBCALL BlastProgressAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 454 NLM_EXTERN Boolean LIBCALL BlastProgressAsnWrite PROTO (( BlastProgressPtr , AsnIoPtr, AsnTypePtr)); 455 456 457 458 /************************************************** 459 * 460 * BlastDefline 461 * 462 **************************************************/ 463 typedef struct struct_Blast_defline { 464 struct struct_Blast_defline PNTR next; 465 ValNodePtr id; 466 CharPtr defline; 467 } BlastDefline, PNTR BlastDeflinePtr; 468 469 470 NLM_EXTERN BlastDeflinePtr LIBCALL BlastDeflineFree PROTO ((BlastDeflinePtr )); 471 NLM_EXTERN BlastDeflinePtr LIBCALL BlastDeflineNew PROTO (( void )); 472 NLM_EXTERN BlastDeflinePtr LIBCALL BlastDeflineAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 473 NLM_EXTERN Boolean LIBCALL BlastDeflineAsnWrite PROTO (( BlastDeflinePtr , AsnIoPtr, AsnTypePtr)); 474 475 476 477 /************************************************** 478 * 479 * BlastVersion 480 * 481 **************************************************/ 482 typedef struct struct_Blast_version { 483 CharPtr version; 484 CharPtr date; 485 } BlastVersion, PNTR BlastVersionPtr; 486 487 488 NLM_EXTERN BlastVersionPtr LIBCALL BlastVersionFree PROTO ((BlastVersionPtr )); 489 NLM_EXTERN BlastVersionPtr LIBCALL BlastVersionNew PROTO (( void )); 490 NLM_EXTERN BlastVersionPtr LIBCALL BlastVersionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 491 NLM_EXTERN Boolean LIBCALL BlastVersionAsnWrite PROTO (( BlastVersionPtr , AsnIoPtr, AsnTypePtr)); 492 493 494 495 /************************************************** 496 * 497 * MegaBlastHit 498 * 499 **************************************************/ 500 typedef struct struct_MegaBlast_hit { 501 struct struct_MegaBlast_hit PNTR next; 502 CharPtr id1; 503 CharPtr id2; 504 Int4 query_offset; 505 Int4 subject_offset; 506 Int4 query_end; 507 Int4 subject_end; 508 Int4 score; 509 } MegaBlastHit, PNTR MegaBlastHitPtr; 510 511 512 NLM_EXTERN MegaBlastHitPtr LIBCALL MegaBlastHitFree PROTO ((MegaBlastHitPtr )); 513 NLM_EXTERN MegaBlastHitPtr LIBCALL MegaBlastHitNew PROTO (( void )); 514 NLM_EXTERN MegaBlastHitPtr LIBCALL MegaBlastHitAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 515 NLM_EXTERN Boolean LIBCALL MegaBlastHitAsnWrite PROTO (( MegaBlastHitPtr , AsnIoPtr, AsnTypePtr)); 516 517 518 519 /************************************************** 520 * 521 * MegaBlastResults 522 * 523 **************************************************/ 524 typedef struct struct_MegaBlast_results { 525 struct struct_MegaBlast_hit PNTR mbhits; 526 } MegaBlastResults, PNTR MegaBlastResultsPtr; 527 528 529 NLM_EXTERN MegaBlastResultsPtr LIBCALL MegaBlastResultsFree PROTO ((MegaBlastResultsPtr )); 530 NLM_EXTERN MegaBlastResultsPtr LIBCALL MegaBlastResultsNew PROTO (( void )); 531 NLM_EXTERN MegaBlastResultsPtr LIBCALL MegaBlastResultsAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); 532 NLM_EXTERN Boolean LIBCALL MegaBlastResultsAsnWrite PROTO (( MegaBlastResultsPtr , AsnIoPtr, AsnTypePtr)); 533 534 #ifdef __cplusplus 535 /* { */ } 536 #endif 537 538 #endif /* _objblst3_ */ 539 540 #undef NLM_EXTERN 541 #ifdef NLM_EXPORT 542 #define NLM_EXTERN NLM_EXPORT 543 #else 544 #define NLM_EXTERN 545 #endif 546 547