#ifndef _objblst3_ #define _objblst3_ #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif #ifdef __cplusplus extern "C" { /* } */ #endif /************************************************** * * Generated objects for Module NCBI-Blast * Generated using ASNCODE Revision: 6.10 at Jan 5, 2001 12:44 PM * **************************************************/ NLM_EXTERN Boolean LIBCALL objblst3AsnLoad PROTO((void)); /************************************************** * * BlastSearch * **************************************************/ typedef struct struct_Blast_search { Uint2 program; /* following #defines are for enumerated type, not used by object loaders */ #define Blast_search_program_blastn 0 #define Blast_search_program_blastp 1 #define Blast_search_program_blastx 2 #define Blast_search_program_tblastn 3 #define Blast_search_program_tblastx 4 struct struct_Bioseq PNTR query; CharPtr database; struct struct_Blast_parameters PNTR parameters; ValNodePtr mask; struct struct_Blast_matrix PNTR matrix; Uint1 return_parts; struct struct_Bioseq_set PNTR query_set; } BlastSearch, PNTR BlastSearchPtr; NLM_EXTERN BlastSearchPtr LIBCALL BlastSearchFree PROTO ((BlastSearchPtr )); NLM_EXTERN BlastSearchPtr LIBCALL BlastSearchNew PROTO (( void )); NLM_EXTERN BlastSearchPtr LIBCALL BlastSearchAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastSearchAsnWrite PROTO (( BlastSearchPtr , AsnIoPtr, AsnTypePtr)); typedef ValNodePtr BlastRequestPtr; typedef ValNode BlastRequest; #define BlastRequest_init 1 #define BlastRequest_motd 2 #define BlastRequest_db_info 3 #define BlastRequest_db_info_specific 4 #define BlastRequest_matrix_get 5 #define BlastRequest_search 6 #define BlastRequest_db_seq_get 7 #define BlastRequest_db_redundant_ids_get 8 #define BlastRequest_db_redundant_descr_get 9 #define BlastRequest_fini 10 NLM_EXTERN BlastRequestPtr LIBCALL BlastRequestFree PROTO ((BlastRequestPtr )); NLM_EXTERN BlastRequestPtr LIBCALL BlastRequestAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastRequestAsnWrite PROTO (( BlastRequestPtr , AsnIoPtr, AsnTypePtr)); typedef ValNodePtr BlastResponsePtr; typedef ValNode BlastResponse; #define BlastResponse_init 1 #define BlastResponse_motd 2 #define BlastResponse_error 3 #define BlastResponse_db_seq_get 4 #define BlastResponse_db_redundant_ids_get 5 #define BlastResponse_db_redundant_descr_get 6 #define BlastResponse_db_info 7 #define BlastResponse_db_info_specific 8 #define BlastResponse_matrix 9 #define BlastResponse_alignment 10 #define BlastResponse_mask 11 #define BlastResponse_kablk 12 #define BlastResponse_parameters 13 #define BlastResponse_queued 14 #define BlastResponse_start 15 #define BlastResponse_progress 16 #define BlastResponse_done 17 #define BlastResponse_fini 18 #define BlastResponse_phialign 19 #define BlastResponse_parts 20 #define BlastResponse_mbalign 21 NLM_EXTERN BlastResponsePtr LIBCALL BlastResponseFree PROTO ((BlastResponsePtr )); NLM_EXTERN BlastResponsePtr LIBCALL BlastResponseAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastResponseAsnWrite PROTO (( BlastResponsePtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * BlastParameters * **************************************************/ typedef struct struct_Blast_parameters { Int4 first_threshold; Int4 second_threshold; ValNodePtr Cutoff_cutoff; ValNodePtr Cutoff2_cutoff2; Int4 hitlist_size; Int4 nucl_penalty; Int4 nucl_reward; Int4 genetic_code; Int4 db_genetic_code; Int4 low_complexity_filtering; Uint1 gapped_alignment; Int4 gap_open; Int4 gap_extend; Int4 required_start; Int4 required_end; FloatHi ethresh; Int4 max_num_passes; Int4 pseudo_count_const; CharPtr other_options; ValNodePtr gilist; CharPtr gifile; CharPtr matrix; CharPtr filter_string; CharPtr entrez_query; Int4 word_size; Int4 db_length; FloatHi searchsp_eff; Int4 hsp_range_max; Int4 block_width; Uint1 perform_culling; Int4 strand_option; CharPtr phi_pattern; Uint1 use_real_db_size; Uint1 use_best_align; Uint1 is_rps_blast; Uint1 tweak_parameters; Uint1 smith_waterman; Uint1 is_megablast; ValNodePtr query_lcase_mask; Int4 is_ooframe; Uint1 endpoint_results; FloatHi percent_identity; } BlastParameters, PNTR BlastParametersPtr; NLM_EXTERN BlastParametersPtr LIBCALL BlastParametersFree PROTO ((BlastParametersPtr )); NLM_EXTERN BlastParametersPtr LIBCALL BlastParametersNew PROTO (( void )); NLM_EXTERN BlastParametersPtr LIBCALL BlastParametersAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastParametersAsnWrite PROTO (( BlastParametersPtr , AsnIoPtr, AsnTypePtr)); #ifdef NLM_GENERATED_CODE_PROTO typedef ValNodePtr Cutoff2_cutoff2Ptr; typedef ValNode Cutoff2_cutoff2; #endif /* NLM_GENERATED_CODE_PROTO */ #define Cutoff2_cutoff2_evalue 1 #define Cutoff2_cutoff2_score 2 #ifdef NLM_GENERATED_CODE_PROTO static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2Free PROTO ((Cutoff2_cutoff2Ptr )); static Cutoff2_cutoff2Ptr LIBCALL Cutoff2_cutoff2AsnRead PROTO (( AsnIoPtr, AsnTypePtr)); static Boolean LIBCALL Cutoff2_cutoff2AsnWrite PROTO (( Cutoff2_cutoff2Ptr , AsnIoPtr, AsnTypePtr)); #endif /* NLM_GENERATED_CODE_PROTO */ #ifdef NLM_GENERATED_CODE_PROTO typedef ValNodePtr Cutoff_cutoffPtr; typedef ValNode Cutoff_cutoff; #endif /* NLM_GENERATED_CODE_PROTO */ #define Cutoff_cutoff_evalue 1 #define Cutoff_cutoff_score 2 #ifdef NLM_GENERATED_CODE_PROTO static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffFree PROTO ((Cutoff_cutoffPtr )); static Cutoff_cutoffPtr LIBCALL Cutoff_cutoffAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); static Boolean LIBCALL Cutoff_cutoffAsnWrite PROTO (( Cutoff_cutoffPtr , AsnIoPtr, AsnTypePtr)); #endif /* NLM_GENERATED_CODE_PROTO */ /************************************************** * * BlastMatrix * **************************************************/ typedef struct struct_Blast_matrix { Uint1 is_protein; CharPtr name; ValNodePtr comments; Int4 row_length; Int4 column_length; ValNodePtr scores; FloatHi karlinK; ValNodePtr posFreqs; } BlastMatrix, PNTR BlastMatrixPtr; NLM_EXTERN BlastMatrixPtr LIBCALL BlastMatrixFree PROTO ((BlastMatrixPtr )); NLM_EXTERN BlastMatrixPtr LIBCALL BlastMatrixNew PROTO (( void )); NLM_EXTERN BlastMatrixPtr LIBCALL BlastMatrixAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastMatrixAsnWrite PROTO (( BlastMatrixPtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * BlastDbinfo * **************************************************/ typedef struct struct_Blast_dbinfo { struct struct_Blast_dbinfo PNTR next; Uint1 is_protein; CharPtr name; CharPtr definition; CharPtr date; Int4 total_length; Int4 number_seqs; } BlastDbinfo, PNTR BlastDbinfoPtr; NLM_EXTERN BlastDbinfoPtr LIBCALL BlastDbinfoFree PROTO ((BlastDbinfoPtr )); NLM_EXTERN BlastDbinfoPtr LIBCALL BlastDbinfoNew PROTO (( void )); NLM_EXTERN BlastDbinfoPtr LIBCALL BlastDbinfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastDbinfoAsnWrite PROTO (( BlastDbinfoPtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * BlastMask * **************************************************/ typedef struct struct_Blast_mask { ValNodePtr location; Uint2 frame; /* following #defines are for enumerated type, not used by object loaders */ #define Blast_mask_frame_notset 0 #define Blast_mask_frame_plus1 1 #define Blast_mask_frame_plus2 2 #define Blast_mask_frame_plus3 3 #define Blast_mask_frame_minus1 4 #define Blast_mask_frame_minus2 5 #define Blast_mask_frame_minus3 6 } BlastMask, PNTR BlastMaskPtr; NLM_EXTERN BlastMaskPtr LIBCALL BlastMaskFree PROTO ((BlastMaskPtr )); NLM_EXTERN BlastMaskPtr LIBCALL BlastMaskNew PROTO (( void )); NLM_EXTERN BlastMaskPtr LIBCALL BlastMaskAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastMaskAsnWrite PROTO (( BlastMaskPtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * BlastKABlk * **************************************************/ typedef struct struct_Blast_KABlk { FloatHi lambda; FloatHi k; FloatHi h; Uint1 gapped; } BlastKABlk, PNTR BlastKABlkPtr; NLM_EXTERN BlastKABlkPtr LIBCALL BlastKABlkFree PROTO ((BlastKABlkPtr )); NLM_EXTERN BlastKABlkPtr LIBCALL BlastKABlkNew PROTO (( void )); NLM_EXTERN BlastKABlkPtr LIBCALL BlastKABlkAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastKABlkAsnWrite PROTO (( BlastKABlkPtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * BlastError * **************************************************/ typedef struct struct_Blast_error { Uint2 level; /* following #defines are for enumerated type, not used by object loaders */ #define Blast_error_level_none 0 #define Blast_error_level_info 1 #define Blast_error_level_warn 2 #define Blast_error_level_error 3 #define Blast_error_level_fatal 4 CharPtr msg; } BlastError, PNTR BlastErrorPtr; NLM_EXTERN BlastErrorPtr LIBCALL BlastErrorFree PROTO ((BlastErrorPtr )); NLM_EXTERN BlastErrorPtr LIBCALL BlastErrorNew PROTO (( void )); NLM_EXTERN BlastErrorPtr LIBCALL BlastErrorAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastErrorAsnWrite PROTO (( BlastErrorPtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * BlastPhialign * **************************************************/ typedef struct struct_Blast_phialign { Int4 numaligns; ValNodePtr seqloc; } BlastPhialign, PNTR BlastPhialignPtr; NLM_EXTERN BlastPhialignPtr LIBCALL BlastPhialignFree PROTO ((BlastPhialignPtr )); NLM_EXTERN BlastPhialignPtr LIBCALL BlastPhialignNew PROTO (( void )); NLM_EXTERN BlastPhialignPtr LIBCALL BlastPhialignAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastPhialignAsnWrite PROTO (( BlastPhialignPtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * BlastDbinfoGet * **************************************************/ typedef struct struct_Blast_dbinfo_get { CharPtr name; Uint2 type; /* following #defines are for enumerated type, not used by object loaders */ #define Blast_dbinfo_get_type_unknown 0 #define Blast_dbinfo_get_type_protein 1 #define Blast_dbinfo_get_type_nucleotide 2 } BlastDbinfoGet, PNTR BlastDbinfoGetPtr; NLM_EXTERN BlastDbinfoGetPtr LIBCALL BlastDbinfoGetFree PROTO ((BlastDbinfoGetPtr )); NLM_EXTERN BlastDbinfoGetPtr LIBCALL BlastDbinfoGetNew PROTO (( void )); NLM_EXTERN BlastDbinfoGetPtr LIBCALL BlastDbinfoGetAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastDbinfoGetAsnWrite PROTO (( BlastDbinfoGetPtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * BlastSeqId * **************************************************/ typedef struct struct_Blast_seq_id { Uint1 is_protein; CharPtr database; ValNodePtr id; } BlastSeqId, PNTR BlastSeqIdPtr; NLM_EXTERN BlastSeqIdPtr LIBCALL BlastSeqIdFree PROTO ((BlastSeqIdPtr )); NLM_EXTERN BlastSeqIdPtr LIBCALL BlastSeqIdNew PROTO (( void )); NLM_EXTERN BlastSeqIdPtr LIBCALL BlastSeqIdAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastSeqIdAsnWrite PROTO (( BlastSeqIdPtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * BlastSequence * **************************************************/ typedef struct struct_Blast_sequence { struct struct_Blast_sequence PNTR next; struct struct_Seq_align PNTR align; ByteStorePtr db_seq; } BlastSequence, PNTR BlastSequencePtr; NLM_EXTERN BlastSequencePtr LIBCALL BlastSequenceFree PROTO ((BlastSequencePtr )); NLM_EXTERN BlastSequencePtr LIBCALL BlastSequenceNew PROTO (( void )); NLM_EXTERN BlastSequencePtr LIBCALL BlastSequenceAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastSequenceAsnWrite PROTO (( BlastSequencePtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * BlastParts * **************************************************/ typedef struct struct_Blast_parts { struct struct_Blast_parts PNTR next; CharPtr defline; struct struct_Blast_sequence PNTR sequence; } BlastParts, PNTR BlastPartsPtr; NLM_EXTERN BlastPartsPtr LIBCALL BlastPartsFree PROTO ((BlastPartsPtr )); NLM_EXTERN BlastPartsPtr LIBCALL BlastPartsNew PROTO (( void )); NLM_EXTERN BlastPartsPtr LIBCALL BlastPartsAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastPartsAsnWrite PROTO (( BlastPartsPtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * BlastQueued * **************************************************/ typedef struct struct_Blast_Queued { Int4 length; } BlastQueued, PNTR BlastQueuedPtr; NLM_EXTERN BlastQueuedPtr LIBCALL BlastQueuedFree PROTO ((BlastQueuedPtr )); NLM_EXTERN BlastQueuedPtr LIBCALL BlastQueuedNew PROTO (( void )); NLM_EXTERN BlastQueuedPtr LIBCALL BlastQueuedAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastQueuedAsnWrite PROTO (( BlastQueuedPtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * BlastProgress * **************************************************/ typedef struct struct_Blast_Progress { Int4 completed; } BlastProgress, PNTR BlastProgressPtr; NLM_EXTERN BlastProgressPtr LIBCALL BlastProgressFree PROTO ((BlastProgressPtr )); NLM_EXTERN BlastProgressPtr LIBCALL BlastProgressNew PROTO (( void )); NLM_EXTERN BlastProgressPtr LIBCALL BlastProgressAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastProgressAsnWrite PROTO (( BlastProgressPtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * BlastDefline * **************************************************/ typedef struct struct_Blast_defline { struct struct_Blast_defline PNTR next; ValNodePtr id; CharPtr defline; } BlastDefline, PNTR BlastDeflinePtr; NLM_EXTERN BlastDeflinePtr LIBCALL BlastDeflineFree PROTO ((BlastDeflinePtr )); NLM_EXTERN BlastDeflinePtr LIBCALL BlastDeflineNew PROTO (( void )); NLM_EXTERN BlastDeflinePtr LIBCALL BlastDeflineAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastDeflineAsnWrite PROTO (( BlastDeflinePtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * BlastVersion * **************************************************/ typedef struct struct_Blast_version { CharPtr version; CharPtr date; } BlastVersion, PNTR BlastVersionPtr; NLM_EXTERN BlastVersionPtr LIBCALL BlastVersionFree PROTO ((BlastVersionPtr )); NLM_EXTERN BlastVersionPtr LIBCALL BlastVersionNew PROTO (( void )); NLM_EXTERN BlastVersionPtr LIBCALL BlastVersionAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL BlastVersionAsnWrite PROTO (( BlastVersionPtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * MegaBlastHit * **************************************************/ typedef struct struct_MegaBlast_hit { struct struct_MegaBlast_hit PNTR next; CharPtr id1; CharPtr id2; Int4 query_offset; Int4 subject_offset; Int4 query_end; Int4 subject_end; Int4 score; } MegaBlastHit, PNTR MegaBlastHitPtr; NLM_EXTERN MegaBlastHitPtr LIBCALL MegaBlastHitFree PROTO ((MegaBlastHitPtr )); NLM_EXTERN MegaBlastHitPtr LIBCALL MegaBlastHitNew PROTO (( void )); NLM_EXTERN MegaBlastHitPtr LIBCALL MegaBlastHitAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL MegaBlastHitAsnWrite PROTO (( MegaBlastHitPtr , AsnIoPtr, AsnTypePtr)); /************************************************** * * MegaBlastResults * **************************************************/ typedef struct struct_MegaBlast_results { struct struct_MegaBlast_hit PNTR mbhits; } MegaBlastResults, PNTR MegaBlastResultsPtr; NLM_EXTERN MegaBlastResultsPtr LIBCALL MegaBlastResultsFree PROTO ((MegaBlastResultsPtr )); NLM_EXTERN MegaBlastResultsPtr LIBCALL MegaBlastResultsNew PROTO (( void )); NLM_EXTERN MegaBlastResultsPtr LIBCALL MegaBlastResultsAsnRead PROTO (( AsnIoPtr, AsnTypePtr)); NLM_EXTERN Boolean LIBCALL MegaBlastResultsAsnWrite PROTO (( MegaBlastResultsPtr , AsnIoPtr, AsnTypePtr)); #ifdef __cplusplus /* { */ } #endif #endif /* _objblst3_ */ #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif