/* =========================================================================== * * 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: blast.h Author: Tom Madden Contents: prototypes for "public" BLAST functions (ones that other utilitiles may safely call). ******************************************************************************/ /* $Revision: 6.48 $ * $Log: blast.h,v $ * Revision 6.48 2001/07/09 15:12:47 shavirin * Functions BLbasicSmithWatermanScoreOnly() and BLSmithWatermanFindStart() * used to calculate Smith-waterman alignments on low level become external. * * Revision 6.47 2001/06/18 16:09:25 dondosha * Added prototype for PrintTabularOutputHeader * * Revision 6.46 2001/06/13 21:40:54 dondosha * Moved GetGisFromFile declaration from mblast.h to blast.h * * Revision 6.45 2001/04/16 21:28:11 dondosha * Added function BlastPruneSeqAlignByEvalueRange * * Revision 6.44 2001/04/12 21:34:50 dondosha * Added function BlastPruneSeqAlignByGiList * * Revision 6.43 2001/04/06 18:15:08 madden * Move UNIX-specific stuff (HeyIAmInMemory) to bqueue.[ch] * * Revision 6.42 2001/02/07 21:10:10 dondosha * Added prototypes of Blast Engine functions with callback * * Revision 6.41 2001/01/16 23:16:51 dondosha * Added 2 arguments and several options to parse_blast_options * * Revision 6.40 2001/01/09 20:10:39 shavirin * Added sorting of all hits in result_struct for every element in * results. Added function RPSResultHspScoreCmp. * * Revision 6.39 2000/11/02 20:16:34 dondosha * Added prototypes for BlastTwoSequencesByLocWithCallback and BlastTwoSequencesWithCallback * * Revision 6.38 2000/10/31 16:30:58 shavirin * Function BLASTSetUpSearchInternalByLoc became external. * * Revision 6.37 2000/10/26 18:52:42 dondosha * Added prototype for MegaBlastPrintReference * * Revision 6.36 2000/10/24 19:00:39 dondosha * Removed UniqueLocalId() prototype - goes to sequtil.h * * Revision 6.35 2000/10/24 18:57:22 dondosha * Added prototype of UniqueLocalId(), removed from mblast.h * * Revision 6.34 2000/08/31 16:27:20 shavirin * Added definition of the function BlastSequenceBlkDestruct(). * * Revision 6.33 2000/07/12 23:07:30 kans * reverse_seq moved from pseed3.c to blastool.c, placed in blast.h header, called by gapxdrop.c * * Revision 6.32 2000/07/07 21:20:07 vakatov * Get all "#include" out of the 'extern "C" { }' scope! * * Revision 6.31 2000/06/20 15:50:45 shavirin * Added new functions: BLASTAddBlastDBTitleToSeqAnnot and * BLASTGetDatabaseTitleFromSeqAnnot(). * * Revision 6.30 2000/06/14 22:21:57 dondosha * Added prototypes for BlastQuerySequenceSetUp and BlastSequencesOnTheFlyEx * * Revision 6.29 2000/04/28 19:49:36 shavirin * Added definition of the function DefineToFrame(). * * Revision 6.28 2000/03/31 17:01:26 dondosha * Added explanation for use of blastx in two sequences search * * Revision 6.27 2000/03/24 17:01:27 kans * added BLASTUpdateSeqIdInSeqInt - needed to compile blastall.c on Mac, which requires prototypes * * Revision 6.26 2000/02/23 20:37:45 dondosha * Added prototype for MegaBlastBuildLookupTable and BlastNtWordExtend * * Revision 6.25 2000/02/11 16:40:53 egorov * The parse_blast_options is made public. * * Revision 6.24 2000/02/01 18:04:59 dondosha * Added prototype for GreedyAlignMemAlloc * * Revision 6.23 2000/01/26 22:01:57 madden * Add function BlastGetProgramName * * Revision 6.22 2000/01/14 18:27:45 shavirin * Added definitions of WordExtend* functions. * * Revision 6.21 1999/12/29 18:55:29 shavirin * Added definition of non-static function BlastSequenceAddSequence(). * * Revision 6.20 1999/09/22 20:55:07 egorov * Add time measure stuff * * Revision 6.19 1999/07/01 13:03:24 sicotte * Updated for DenseDiag and Moved seqalign_reverse_strand from blastutl.c(blast.h) to SeqAlignListReverseStrand in salpedit.ch and fixed call in salutil.c * * Revision 6.18 1999/03/18 16:43:31 shavirin * Added definition of the function Boolean HeyIAmInMemory(Int4 program) * * Revision 6.17 1999/03/17 16:49:11 madden * Removed comment within comment * * Revision 6.16 1999/01/26 18:26:23 madden * Add updateLambdaK prototype * * Revision 6.15 1998/09/22 16:56:12 egorov * Add prototype for BlastErrorPrintExtra() * * Revision 6.14 1998/09/14 15:11:14 egorov * Add support for Int8 length databases; remove unused variables * * Revision 6.13 1998/08/25 14:16:23 madden * Added BlastGetPhiReference and BlastPrintPhiReference * * Revision 6.12 1998/06/12 16:08:49 madden * BlastHitRange stuff * * Revision 6.11 1998/05/22 20:20:37 madden * Added BlastTwoSequencesByLocEx and BlastTwoSequencesEx * * Revision 6.10 1998/05/01 18:34:37 egorov * Add new parametes to BLASTOptionSetGapParam() * * Revision 6.9 1998/03/24 15:38:22 madden * Use BlastDoubleInt4Ptr to keep track of gis and ordinal_ids * * Revision 6.8 1998/03/18 14:14:14 madden * Support random access by gi list * * Revision 6.7 1998/03/14 18:28:08 madden * Added BioseqBlastEngineEx * * Revision 6.6 1998/02/26 19:09:28 madden * Removed AdjustOffSetsInSeqAlign prototype * * Revision 6.5 1998/01/05 22:41:44 madden * Added seqalign_reverse_strand * * Revision 6.4 1997/12/10 22:41:20 madden * prototype for BlastGetProgramNumber * * Revision 6.3 1997/12/01 22:07:15 madden * Changed call to BLASTOptionValidateEx * * Revision 6.2 1997/11/18 22:23:17 madden * Added BLASTOptionSetGapParams * * Revision 6.1 1997/10/02 17:28:55 madden * Added prototype for BlastPrintVersionInfoEx * * Revision 6.0 1997/08/25 18:52:29 madden * Revision changed to 6.0 * * Revision 1.26 1997/07/22 17:21:55 madden * Added index callbacks to SetUp function prototypes * * Revision 1.25 1997/07/21 17:36:47 madden * Added BlastGetReleaseDate * * Revision 1.24 1997/07/18 20:55:25 madden * Added prototypes for BlastGetVersionNumber and BlastGetReference * * Revision 1.23 1997/07/14 16:15:09 madden * Added prototype for BlastErrorPrint * * Revision 1.22 1997/07/14 15:33:32 madden * Prototype for BLASTOptionValidateEx * * Revision 1.21 1997/07/11 19:29:08 madden * Added prototypes for BLASTSetUpSearchByLocWithReadDb and BioseqBlastEngineByLoc * * Revision 1.20 1997/06/20 13:11:53 madden * added prototype for AdjustOffSetsInSeqAlign * * Revision 1.19 1997/05/20 17:51:02 madden * Added prototypes for BLASTSetUpSearchByLoc, BlastTwoSequencesByLoc and BlastSequencesOnTheFlyByLoc * * Revision 1.18 1997/03/11 14:38:40 madden * Added BlastSequencesOnTheFly prototype. * * Revision 1.17 1997/03/07 21:58:36 madden * Added Boolean gapped argument to BLASTOptionNew. * * Revision 1.16 1997/03/03 21:48:52 madden * *** empty log message *** * * Revision 1.15 1997/03/03 14:48:57 madden * Changes prototype for SumBlastGetGappedAlignmentTraceback * * Revision 1.14 1997/02/26 20:37:31 madden * Added *error_returns to BioseqBlastEngine. * * Revision 1.13 1997/02/18 17:58:52 madden * Added BioseqBlastEngine. * * Revision 1.12 1997/02/10 20:03:58 madden * Added all_words to BLASTSetUpSearch. * * Revision 1.11 1997/02/05 19:54:59 madden * Removed defunct prototype. * * Revision 1.10 1997/02/03 13:02:12 madden * Added length to BLASTSubjectInfoNew call. * * Revision 1.9 1997/01/28 22:38:56 madden * Added function BLASTOptionValidate. * * Revision 1.8 1997/01/11 18:58:29 madden * Removed defunct PerformBlastSearch... functions. * * Revision 1.7 1996/12/23 22:02:05 madden * Changes to allow two sequences to be compared. * * Revision 1.6 1996/09/26 20:18:43 madden * Added prototype for ExperimentalLocalBlastSearch. * * Revision 1.5 1996/09/25 19:59:10 madden * Removed prototype for for GetParameterStack. * * Revision 1.4 1996/09/11 22:21:51 madden * *** empty log message *** * * Revision 1.3 1996/09/11 19:14:09 madden * Added BLAST_OptionsBlkPtr structure and use thereof. * * Revision 1.2 1996/08/23 16:30:54 shavirin * Fixed NT compiler warnings type mismatch * * Revision 1.1 1996/08/05 19:46:34 madden * Initial revision * * Revision 1.34 1996/08/02 14:20:06 madden * Add prototype for do_the_blast_run. * * Revision 1.33 1996/06/26 15:53:54 madden * Second dropoff score parameter added. * * Revision 1.32 1996/06/24 17:57:39 madden * Added dropoff_number_of_bits argument to SetUpBlastSearch. * * Revision 1.31 1996/06/20 16:15:57 madden * Replaced int's with Int4's. * * Revision 1.30 1996/06/19 14:19:12 madden * Changed prototypes for SetUpBlastSearch. * * Revision 1.29 1996/06/06 17:54:09 madden * number_of_bits added to SetUpBlastSearch and SetUpBlastSearchWithReadDb. * * Revision 1.28 1996/06/04 15:33:12 madden * Changed prototype for GetParameterStack. * * Revision 1.27 1996/05/28 14:12:53 madden * prototype for GetParameterStack changed. * * Revision 1.26 1996/05/16 19:50:15 madden * Added documentation block. * * Revision 1.25 1996/05/16 13:29:38 madden * Changed prototype for SetUpBlastSearchWithReadDb. * * Revision 1.24 1996/05/03 19:55:07 madden * *** empty log message *** * * Revision 1.23 1996/05/01 14:58:22 madden * Changed prototypes for SetUpBlastSearchWithReadDb * * Revision 1.22 1996/04/24 12:52:06 madden * wordsize new parameter for SetUpBlastSearch. * * Revision 1.21 1996/04/22 21:40:07 madden * New prototypes for performing blast searches. * * Revision 1.20 1996/04/03 19:15:28 madden * *** empty log message *** * * Revision 1.19 1996/03/29 21:26:01 madden * Added prototype for SortSeqAlignByPvalue. * * Revision 1.18 1996/03/29 14:08:40 madden * prototype for SetUpBlastSearchWithReadDb added. * * Revision 1.17 1996/03/27 23:19:24 madden * changed parameters for PerformBlastSearch and Perform2PassBlastSearch. * * Revision 1.16 1996/03/26 19:36:42 madden * Changes to read databases formatted with formatdb. * * Revision 1.15 1996/03/25 16:34:19 madden * Changes to mimic old statistics. * * Revision 1.14 1996/02/28 21:36:54 madden * changes for discontiguous words. * * Revision 1.13 1996/02/15 15:22:52 madden * renamed Perform2HitBlastSearch to Perform2PassBlastSearch. * * Revision 1.12 1996/02/09 13:50:45 madden * Added prototype for Perform2HitBlastSearch. * * Revision 1.11 1996/02/05 18:46:30 madden * Added second threshold value to SetUpBlastSearch. * * Revision 1.10 1996/01/29 21:11:38 madden * Changes for MultipleHits BLAST. * * Revision 1.9 1996/01/23 16:31:23 madden * e_cutoff changed from BLAST_Score to double in SetUpBlastSearch. * * Revision 1.8 1996/01/17 23:18:01 madden * *** empty log message *** * * Revision 1.7 1996/01/17 17:00:24 madden * Added gap arguments to SetUpBlastSearch. * * Revision 1.6 1996/01/17 13:45:25 madden * Added "gap_decay_rate" to SetUpBlastSearch. * * Revision 1.5 1996/01/16 15:28:54 madden * Changed call to SetUpBlastSearch. * * Revision 1.4 1995/12/30 19:22:04 madden * Added prototype for PerformBlastSearch. * * Revision 1.3 1995/12/30 18:39:27 madden * Added prototype for SetUpBlastSearch. * * Revision 1.2 1995/12/19 22:31:05 madden * *** empty log message *** * * Revision 1.1 1995/12/08 15:48:23 madden * Initial revision * * */ #ifndef __BLAST__ #define __BLAST__ #include #include #ifdef __cplusplus extern "C" { #endif /* Call this function to allocate the "options" structure. The fields will be filled in with the default values, which depend on the program. */ BLAST_OptionsBlkPtr LIBCALL BLASTOptionNew PROTO((CharPtr progname, Boolean gapped)); BLAST_OptionsBlkPtr LIBCALL BLASTOptionDelete PROTO((BLAST_OptionsBlkPtr)); BLAST_OptionsBlkPtr LIBCALL BLASTOptionValidate PROTO((BLAST_OptionsBlkPtr options, CharPtr progname)); Int2 LIBCALL BLASTOptionValidateEx PROTO((BLAST_OptionsBlkPtr options, CharPtr progname, ValNodePtr PNTR error_return)); Int2 LIBCALL BLASTOptionSetGapParams PROTO((BLAST_OptionsBlkPtr options, CharPtr matrix, Int4 open, Int4 extended)); /* the setup functions, call before running blast. */ BlastSearchBlkPtr LIBCALL BLASTSetUpSearchWithReadDb PROTO((BioseqPtr query_bsp, CharPtr prog_name, Int4 qlen, CharPtr dbname, BLAST_OptionsBlkPtr options, int (LIBCALLBACK *index_callback)PROTO((Int4 done, Int4 positives)))); BlastSearchBlkPtr LIBCALL BLASTSetUpSearchWithReadDbEx PROTO((BioseqPtr query_bsp, CharPtr prog_name, Int4 qlen, CharPtr dbname, BLAST_OptionsBlkPtr options, int (LIBCALLBACK *index_callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, Int4 gi_list_total)); BlastSearchBlkPtr LIBCALL BLASTSetUpSearchByLocWithReadDb PROTO((SeqLocPtr slp, CharPtr prog_name, Int4 qlen, CharPtr dbname, BLAST_OptionsBlkPtr options, int (LIBCALLBACK *index_callback)PROTO((Int4 done, Int4 positives)))); BlastSearchBlkPtr LIBCALL BLASTSetUpSearchByLocWithReadDbEx PROTO((SeqLocPtr slp, CharPtr prog_name, Int4 qlen, CharPtr dbname, BLAST_OptionsBlkPtr options, int (LIBCALLBACK *index_callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, Int4 gi_list_total)); BlastSearchBlkPtr LIBCALL BLASTSetUpSearch PROTO((BioseqPtr query_bsp, CharPtr prog_name, Int4 qlen, Int8 dblen, BlastAllWordPtr all_words, BLAST_OptionsBlkPtr options, int (LIBCALLBACK *index_callback)PROTO((Int4 done, Int4 positives)))); BlastSearchBlkPtr LIBCALL BLASTSetUpSearchByLoc PROTO((SeqLocPtr query_slp, CharPtr prog_name, Int4 qlen, Int8 dblen, BlastAllWordPtr all_words, BLAST_OptionsBlkPtr options, int (LIBCALLBACK *index_callback)PROTO((Int4 done, Int4 positives)))); Int2 LIBCALL BLASTSetUpSearchInternalByLoc PROTO((BlastSearchBlkPtr search, SeqLocPtr query_slp, BioseqPtr query_bsp, CharPtr prog_name, Int4 qlen, BLAST_OptionsBlkPtr options, int (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)))); /* Use these function to perform the search. */ Int2 LIBCALL BLASTPerform2PassSearch PROTO((BlastSearchBlkPtr search, Int4 subject_length, Uint1Ptr subject_seq)); Int2 LIBCALL BLASTPerformFinalSearch PROTO((BlastSearchBlkPtr search, Int4 subject_length, Uint1Ptr subject_seq)); BLASTSubjectInfoPtr LIBCALL BLASTSubjectInfoNew PROTO((SeqIdPtr sip, CharPtr defline, Int4 length)); BLASTSubjectInfoPtr LIBCALL BLASTSubjectInfoDestruct PROTO((BLASTSubjectInfoPtr subject_info)); void LIBCALL do_the_blast_run PROTO((BlastSearchBlkPtr search)); Int2 LIBCALL BlastSequenceAddSequence PROTO((BlastSequenceBlkPtr sequence_blk, Uint1Ptr sequence, Uint1Ptr sequence_start, Int4 length, Int4 original_seq, Int4 effective_length)); BlastSequenceBlkPtr LIBCALL BlastSequenceBlkDestruct PROTO((BlastSequenceBlkPtr seq_blk)); void BLASTUpdateSeqIdInSeqInt(SeqLocPtr mask, SeqIdPtr sip); /* Blast two sequences and return a SeqAlign. For blastx program first sequence must be nucleotide, second protein. */ SeqAlignPtr LIBCALL BlastTwoSequences PROTO((BioseqPtr bsp1, BioseqPtr bsp2, CharPtr progname, BLAST_OptionsBlkPtr options)); SeqAlignPtr LIBCALL BlastTwoSequencesByLoc PROTO((SeqLocPtr slp1, SeqLocPtr slp2, CharPtr progname, BLAST_OptionsBlkPtr options)); SeqAlignPtr LIBCALL BlastTwoSequencesByLocEx PROTO((SeqLocPtr slp1, SeqLocPtr slp2, CharPtr progname, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns)); SeqAlignPtr LIBCALL BlastTwoSequencesByLocWithCallback PROTO((SeqLocPtr slp1, SeqLocPtr slp2, CharPtr progname, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, int (LIBCALLBACK *handle_results)PROTO((VoidPtr srch)))); SeqAlignPtr LIBCALL BlastTwoSequencesEx PROTO((BioseqPtr bsp1, BioseqPtr bsp2, CharPtr progname, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns)); SeqAlignPtr LIBCALL BlastTwoSequencesWithCallback PROTO((BioseqPtr bsp1, BioseqPtr bsp2, CharPtr progname, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, int (LIBCALLBACK *handle_results)PROTO((VoidPtr srch)))); SeqAlignPtr LIBCALL BlastSequencesOnTheFly PROTO((BlastSearchBlkPtr search, BioseqPtr subject_bsp)); SeqAlignPtr LIBCALL BlastSequencesOnTheFlyByLoc PROTO((BlastSearchBlkPtr search, SeqLocPtr subject_slp)); BlastSearchBlkPtr LIBCALL BlastQuerySequenceSetUp PROTO((BioseqPtr bsp, CharPtr progname, BLAST_OptionsBlkPtr options)); BlastSearchBlkPtr LIBCALL BlastSequencesOnTheFlyEx PROTO((BlastSearchBlkPtr search, BioseqPtr subject_bsp)); SeqAlignPtr LIBCALL SumBlastGetGappedAlignmentTraceback PROTO((BlastSearchBlkPtr search, Int4 hit_number, Boolean reverse, Boolean ordinal_number, Uint1Ptr subject, Int4 subject_length)); /* Performs a complete BLAST search and returns a SeqAnlign. */ SeqAlignPtr LIBCALL BioseqBlastEngine PROTO((BioseqPtr bsp, CharPtr progname, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, int (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)))); SeqAlignPtr LIBCALL BioseqBlastEngineWithCallback PROTO((BioseqPtr bsp, CharPtr progname, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, int (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), int (LIBCALLBACK *handle_results)PROTO((VoidPtr srch)))); SeqAlignPtr LIBCALL BioseqBlastEngineEx PROTO((BioseqPtr bsp, CharPtr progname, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, int (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, Int4 gi_list_total)); SeqAlignPtr LIBCALL BioseqBlastEngineByLoc PROTO((SeqLocPtr slp, CharPtr progname, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, int (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)))); SeqAlignPtr LIBCALL BioseqBlastEngineByLocEx PROTO((SeqLocPtr slp, CharPtr progname, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, int (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, Int4 gi_list_total)); SeqAlignPtr LIBCALL BioseqBlastEngineByLocWithCallback PROTO((SeqLocPtr slp, CharPtr progname, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, int (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, Int4 gi_list_total, int (LIBCALLBACK *handle_results)PROTO((VoidPtr srch)))); /* Prints error messages. */ void LIBCALL BlastErrorPrint PROTO((ValNodePtr error_return)); void LIBCALL BlastErrorPrintExtra PROTO((ValNodePtr error_return, Boolean errpostex, FILE* fp)); /* Prints some header information. */ CharPtr LIBCALL BlastGetVersionNumber PROTO((void)); CharPtr LIBCALL BlastGetReference PROTO((Boolean html)); Boolean LIBCALL BlastPrintReference PROTO((Boolean html, Int4 line_length, FILE *outfp)); Boolean LIBCALL MegaBlastPrintReference PROTO((Boolean html, Int4 line_length, FILE *outfp)); CharPtr LIBCALL BlastGetPhiReference PROTO((Boolean html)); Boolean LIBCALL BlastPrintPhiReference PROTO((Boolean html, Int4 line_length, FILE *outfp)); Boolean BlastPrintVersionInfo PROTO((CharPtr program, Boolean html, FILE *outfp)); Boolean BlastPrintVersionInfoEx PROTO((CharPtr program, Boolean html, CharPtr version, CharPtr date, FILE *outfp)); CharPtr LIBCALL BlastGetReleaseDate PROTO((void)); Uint1 LIBCALL BlastGetProgramNumber PROTO((CharPtr blast_program)); CharPtr LIBCALL BlastGetProgramName PROTO((Uint1 number)); BlastHitRangePtr LIBCALL BlastHitRangeDestruct PROTO((BlastHitRangePtr old)); BlastHitRangePtr LIBCALL BlastHitRangeNew PROTO((Int4 total)); BlastHitRangePtr LIBCALL BioseqHitRangeEngineCore PROTO((BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options)); SeqLocPtr LIBCALL BioseqHitRangeEngineByLoc PROTO((SeqLocPtr slp, CharPtr progname, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, int (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, Int4 gi_list_total)); SeqLocPtr LIBCALL BioseqHitRangeEngine PROTO((BioseqPtr bsp, CharPtr progname, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, int (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, Int4 gi_list_total)); BLAST_ExtendWordParamsPtr BLAST_ExtendWordParamsNew (Int4 qlen, Boolean multiple_hits, Int4 window_size); BLAST_ExtendWordPtr BLAST_ExtendWordNew (BLAST_ExtendWordParamsPtr ewp_params); BLAST_ExtendWordPtr LIBCALL BLAST_ExtendWordDestruct (BLAST_ExtendWordPtr ewp); void LIBCALL updateLambdaK PROTO((BlastMatrixRescalePtr matrix_rescale, Boolean position_dependent)); BlastSearchBlkPtr GreedyAlignMemAlloc PROTO((BlastSearchBlkPtr search)); Boolean parse_blast_options(BLAST_OptionsBlkPtr options, CharPtr string_options, CharPtr PNTR error_message, CharPtr PNTR database, Int4Ptr descriptions, Int4Ptr alignments); Int2 BlastNtWordExtend PROTO((BlastSearchBlkPtr search, Int4 q_off, Int4 s_off, BLAST_Diag real_diag, Int2 context)); Boolean MegaBlastBuildLookupTable PROTO((BlastSearchBlkPtr search)); Int2 DefineToFrame PROTO((Uint1 define)); CharPtr BLASTGetDatabaseTitleFromSeqAnnot PROTO((SeqAnnotPtr seqannot)); void BLASTAddBlastDBTitleToSeqAnnot PROTO((SeqAnnotPtr seqannot, CharPtr title)); Int4 reverse_seq (Uint1 *seq, Uint1 *pos, Uint1 *target); int LIBCALLBACK RPSResultHspScoreCmp(VoidPtr v1, VoidPtr v2); SeqAlignPtr BlastPruneSeqAlignByGiList PROTO((SeqAlignPtr seqalign, Int4Ptr gi_list, Int4 gi_list_total)); SeqAlignPtr BlastPruneSeqAlignByEvalueRange PROTO((SeqAlignPtr seqalign, FloatHi expect_low, FloatHi expect_high)); BlastDoubleInt4Ptr GetGisFromFile PROTO((CharPtr file_name, Int4Ptr gi_list_size)); void PrintTabularOutputHeader PROTO((CharPtr blast_database, BioseqPtr query_bsp, SeqLocPtr query_slp, CharPtr blast_program, Int4 iteration, Boolean believe_query, FILE *outfp)); /* ------ Functions related to Smith-Waterman algorithm ------ */ Nlm_FloatHi BLbasicSmithWatermanScoreOnly(Uint1 * matchSeq, Int4 matchSeqLength, Uint1 *query, Int4 queryLength, BLAST_Score **matrix, Int4 gapOpen, Int4 gapExtend, Int4 *matchSeqEnd, Int4 *queryEnd, Int4 *score, BLAST_KarlinBlkPtr kbp, Nlm_FloatHi effSearchSpace, Boolean positionSpecific); Int4 BLSmithWatermanFindStart(Uint1 * matchSeq, Int4 matchSeqLength, Uint1 *query, Int4 queryLength, BLAST_Score **matrix, Int4 gapOpen, Int4 gapExtend, Int4 matchSeqEnd, Int4 queryEnd, Int4 score, Int4 *matchSeqStart, Int4 *queryStart, Boolean positionSpecific); /* ----------------------------------------------------------- */ /* DEBUG */ /* time mesuaring utilities */ /* #define BLAST_TIMER */ #ifdef BLAST_TIMER clock_t last_clock; #define start_timer last_clock = clock(); #define stop_timer(msg) { \ clock_t current_clock = clock(), since; \ since = current_clock - last_clock; \ fprintf(stderr, "TIME [%s] - %5.2f\n", msg, ((double) since) / CLOCKS_PER_SEC); \ last_clock = current_clock; \ } #else #define start_timer ; #define stop_timer ; #endif /* end of DEBUG block */ #ifdef __cplusplus } #endif #endif /* !__BLAST__ */