/* * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * File Name: netblap3.h * * Author: Tom Madden * * Version Creation Date: 05/12/97 * * File Description: * Application Programming Interface (API) for BLAST network server * * RCS Modification History: * $Log: netblap3.h,v $ * Revision 1.27 2001/05/02 19:42:48 egorov * Make the NetBlastGetMatrix() external * * Revision 1.26 2000/11/16 22:25:39 dondosha * Added other_returns argument to BlastBioseq * * Revision 1.25 2000/09/28 16:44:31 dondosha * Changed prototype for MegaBlastSeqLocNetCore to return SeqAlignPtr * * Revision 1.24 2000/08/28 16:29:19 dondosha * Added definitions related to megablast * * Revision 1.23 2000/06/15 16:22:44 egorov * Make SubmitRequest() external * * Revision 1.22 2000/05/04 18:09:26 shavirin * Added new function BLASTGetUidsFromQuery(). * * Revision 1.21 1999/11/24 21:42:31 vakatov * Fixed for the C++ and/or MSVC DLL compilation * * Revision 1.20 1999/10/27 13:00:02 madden * Changes to return-parts * * Revision 1.19 1999/08/19 19:40:01 shavirin * Returned to previous version. * * Revision 1.16 1999/08/17 18:59:47 shavirin * Added definition of the function SeedBioseqNetCore. * * Revision 1.15 1999/04/21 20:54:47 madden * Make BlastBioseq non-private * * Revision 1.14 1999/04/20 14:51:36 madden * BlastBioseqNetCore and BlastSeqLocNetCore have return status * * Revision 1.13 1999/04/16 15:53:26 madden * Add TraditionalBlastReportExtra function * * Revision 1.12 1999/03/19 21:47:38 madden * Add Blast3GetDbinfo function * * Revision 1.11 1999/01/12 21:05:58 victorov * server will now report an error if the ni-queue if full * * Revision 1.10 1998/12/14 19:38:31 egorov * add file #defines * * Revision 1.9 1998/09/22 16:14:07 egorov * Add prototype for parametersToOptions() * * Revision 1.8 1998/09/01 20:17:04 madden * Fixed uninitialzed problem in BlastNetBioseqFetchDisable, changed prototype * * Revision 1.7 1998/05/08 21:41:47 vakatov * use NetProgressCallback in the function prototypes * * Revision 1.6 1998/05/08 20:56:23 madden * Fix PC compile warnings, rename callback * * Revision 1.5 1998/04/23 14:18:42 egorov * Add number_of_hits parameter to TraditionalBlastReportLoc * * Revision 1.4 1998/04/22 18:10:07 egorov * Add support for SeqLoc to blastcl3 * * Revision 1.3 1998/04/16 19:35:32 madden * Added Int4Ptr arg to TraditionalBlastReport specifying the numbers of hits * * Revision 1.2 1997/11/25 14:43:36 madden * Changes to allow iterative searches * * Revision 1.1 1997/10/08 19:27:22 madden * Network support for gapped blast * */ #ifndef _NETBLAP3_ #define _NETBLAP3_ 1 #include #include #include #include #include #include #include #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif #ifdef __cplusplus extern "C" { #endif /* BLAST Overview options, more appropriate somewhere else? */ #define BLAST_OVERVIEW_NONE 0 #define BLAST_OVERVIEW_1 1 typedef Boolean (LIBCALLBACK *NetProgressCallback)(BlastResponsePtr response, Boolean PNTR cancel); typedef struct _blastnet3h { NI_HandPtr svcp; } BlastNet3H, PNTR BlastNet3Hptr; typedef struct _blastnet3_block { BioseqPtr bsp; /* The query. */ Uint2 prog_type; /* blast[npx], tblast[nx] */ CharPtr dbname; /* Name of database. */ BlastParametersPtr parameters; BlastResponsePtr response; /* Response from server. */ SeqLocPtr mask; /* Sequence to be masked */ BlastNet3Hptr bl3hptr; /* BlastNet 3 handler returned from BlastInit. */ NetProgressCallback callback; BLAST_MatrixPtr blast_matrix; /* Matrix to be sent to server. */ BioseqSetPtr bsp_set; /* All queries if more than one */ } BlastNet3Block, PNTR BlastNet3BlockPtr; /* BlastNet3Hptr PNTR bl3hpp must not be NULL when this is called, it must be saved and used to call BlastBioseq, as well as BlastFini. BlastResponsePtr PNTR resp contains a response pointer of type BlastResponse_init. This function is MT-safe. */ NLM_EXTERN Boolean LIBCALL BlastInit(CharPtr program_name, BlastNet3Hptr PNTR bl3hpp, BlastResponsePtr PNTR resp); NLM_EXTERN SeqAlignPtr LIBCALL BlastBioseq(BlastNet3BlockPtr blnet3blkptr, ValNodePtr *error_returns, Boolean PNTR status, ValNodePtr *other_returns); /* The BlastNet3Hptr returned by BlastInitMt must be passed in. */ NLM_EXTERN Boolean LIBCALL BlastFini(BlastNet3Hptr bl3hptr); /* Function to get a Bioseq for a give SeqIdPtr. Should be used for BioseqFetch function. */ NLM_EXTERN BioseqPtr LIBCALL BlastGetBioseq(BlastNet3BlockPtr blnet3blkptr, SeqIdPtr sip); NLM_EXTERN BlastNet3BlockPtr LIBCALL BlastNet3BlockNew(CharPtr program, CharPtr dbname); NLM_EXTERN BlastNet3BlockPtr LIBCALL BlastNet3BlockDestruct(BlastNet3BlockPtr blnet); NLM_EXTERN CharPtr LIBCALL Blast3GetMotd(BlastNet3Hptr bl3hptr); NLM_EXTERN SeqLocPtr LIBCALL BlastGetMaskedLoc(BlastNet3BlockPtr blnet3blkptr); NLM_EXTERN Boolean LIBCALL BlastNetBioseqFetchEnable(BlastNet3Hptr bl3hp, CharPtr dbname, Boolean is_na, Boolean now); NLM_EXTERN void LIBCALL BlastNetBioseqFetchDisable(BlastNet3Hptr bl3hp, CharPtr dbname, Boolean is_na); NLM_EXTERN BlastParametersPtr LIBCALL BlastOptionsToParameters(BLAST_OptionsBlkPtr options); NLM_EXTERN CharPtr LIBCALL BlastGetParameterBuffer(BlastNet3BlockPtr blnet3blkptr); NLM_EXTERN BlastKABlkPtr LIBCALL BlastGetKaParams(BlastNet3BlockPtr blnet3blkptr, Boolean gapped); NLM_EXTERN BlastDbinfoPtr LIBCALL BlastRequestDbInfo(BlastNet3Hptr bl3hp, CharPtr database, Boolean is_prot); NLM_EXTERN BlastDbinfoPtr LIBCALL BlastGetDbInfo(BlastNet3BlockPtr blnet3blkptr); NLM_EXTERN TxDfDbInfoPtr LIBCALL NetDbinfo2TxDbinfo(BlastDbinfoPtr net_dbinfo); NLM_EXTERN Boolean LIBCALL TraditionalBlastReport(BioseqPtr bsp, BLAST_OptionsBlkPtr options, BlastNet3Hptr bl3hp, CharPtr program, CharPtr database, Boolean html, FILE *outfp, Boolean verbose, Uint4 print_options, Uint4 align_options, Int4 number_of_descriptions, Int4 number_of_alignments, Int4Ptr number_of_hits); NLM_EXTERN Boolean LIBCALL TraditionalBlastReportLoc(SeqLocPtr slp, BLAST_OptionsBlkPtr options, BlastNet3Hptr bl3hp, CharPtr program, CharPtr database, Boolean html, FILE *outfp, Boolean verbose, Uint4 print_options, Uint4 align_options, Int4 number_of_descriptions, Int4 number_of_alignments, Int4Ptr number_of_hits); NLM_EXTERN Boolean LIBCALL TraditionalBlastReportExtra(BioseqPtr bsp, BLAST_OptionsBlkPtr options, BlastNet3Hptr bl3hp, CharPtr program, CharPtr database, Boolean html, FILE *outfp, Boolean verbose, Uint4 print_options, Uint4 align_options, Int4 number_of_descriptions, Int4 number_of_alignments, Int4Ptr number_of_hits, Uint4 overview); NLM_EXTERN Boolean LIBCALL TraditionalBlastReportLocExtra(SeqLocPtr slp, BLAST_OptionsBlkPtr options, BlastNet3Hptr bl3hp, CharPtr program, CharPtr database, Boolean html, FILE *outfp, Boolean verbose, Uint4 print_options, Uint4 align_options, Int4 number_of_descriptions, Int4 number_of_alignments, Int4Ptr number_of_hits, Uint4 overview); NLM_EXTERN SeqAlignPtr LIBCALL BlastBioseqNet(BlastNet3Hptr bl3hp, BioseqPtr bsp, CharPtr program, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, NetProgressCallback callback); NLM_EXTERN SeqAlignPtr LIBCALL BlastSeqLocNet(BlastNet3Hptr bl3hp, SeqLocPtr slp, CharPtr program, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, NetProgressCallback callback); NLM_EXTERN SeqAlignPtr LIBCALL BlastBioseqNetCore(BlastNet3Hptr bl3hp, BioseqPtr bsp, CharPtr program, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, NetProgressCallback callback, BLAST_MatrixPtr blast_matrix, Boolean PNTR status); NLM_EXTERN SeqAlignPtr LIBCALL BlastSeqLocNetCore(BlastNet3Hptr bl3hp, SeqLocPtr slp, CharPtr program, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, NetProgressCallback callback, BLAST_MatrixPtr blast_matrix, Boolean PNTR status); NLM_EXTERN SeqAlignPtr LIBCALL MegaBlastSeqLocNetCore(BlastNet3Hptr bl3hp, SeqLocPtr slp, CharPtr program, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, NetProgressCallback callback, Boolean PNTR status); NLM_EXTERN BlastPhialignPtr LIBCALL SeedBioseqNetCore(BlastNet3Hptr bl3hp, BioseqPtr bsp, CharPtr program, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, NetProgressCallback callback, BLAST_MatrixPtr blast_matrix, Boolean PNTR ret_status, ValNodePtr PNTR vnp); NLM_EXTERN BlastPartsPtr LIBCALL BlastBioseqNetReturnParts(BlastNet3Hptr bl3hp, BioseqPtr bsp, CharPtr program, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, NetProgressCallback callback, BLAST_MatrixPtr blast_matrix, Boolean PNTR ret_status); NLM_EXTERN BLAST_MatrixPtr LIBCALL BlastNetMatrixToBlastMatrix(BlastMatrixPtr net_matrix); NLM_EXTERN BlastMatrixPtr LIBCALL BlastMatrixToBlastNetMatrix(BLAST_MatrixPtr matrix); NLM_EXTERN BLAST_OptionsBlkPtr parametersToOptions (BlastParametersPtr parameters, CharPtr program, ValNodePtr PNTR error_returns); NLM_EXTERN BlastDbinfoPtr LIBCALL Blast3GetDbinfo(BlastNet3Hptr bl3hptr); NLM_EXTERN Int4 BLASTGetUidsFromQuery(CharPtr query, Int4Ptr PNTR uids, Boolean is_na, Boolean count_only); NLM_EXTERN Boolean SubmitRequest PROTO((BlastNet3Hptr bl3hptr, BlastRequestPtr blreqp, BlastResponsePtr PNTR response, NetProgressCallback callback, Boolean reestablish)); NLM_EXTERN BlastMatrixPtr LIBCALL NetBlastGetMatrix(BlastNet3BlockPtr blnet3blkptr); #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif /* NETBLAP3 */