/* =========================================================================== * * 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: mblast.h Author: Ilya Dondoshansky Contents: prototypes for "public" Mega BLAST functions (ones that other utilitiles may safely call). ******************************************************************************/ /* $Revision: 6.39 $ * $Log: mblast.h,v $ * Revision 6.39 2002/01/04 22:29:02 dondosha * Changed diagonal distance for hsp inclusion check from 10 to 6 * * Revision 6.38 2001/12/28 20:38:40 dondosha * Moved Mega BLAST related parameters into a separate structure * * Revision 6.37 2001/11/13 18:20:33 dondosha * Use GapxEditScript structure instead of edit_script_t in higher level function calls * * Revision 6.36 2001/09/18 16:49:25 dondosha * Removed unneeded functions, eliminated mbutils.h header * * Revision 6.35 2001/06/13 21:40:54 dondosha * Moved GetGisFromFile declaration from mblast.h to blast.h * * Revision 6.34 2001/05/04 15:55:21 dondosha * Take into account removal of short sequences in function BlastFillQueryOffsets * * Revision 6.33 2000/12/21 22:29:29 dondosha * Added prototype for MegaBlastGetHspPercentIdentity * * Revision 6.32 2000/10/31 15:06:16 dondosha * Added Boolean parameter to PrintMaskedSequence function * * Revision 6.31 2000/10/24 18:56:45 dondosha * Moved prototype of UniqueLocalId() to blast.h * * Revision 6.30 2000/10/19 16:02:29 dondosha * Changed MegaBlastGetPercentIdentity to MegaBlastGetNumIdentical * * Revision 6.29 2000/10/05 19:47:51 dondosha * Added prototype for MegaBlastSaveCurrentHitlist * * Revision 6.28 2000/08/30 22:08:45 dondosha * Added function BioseqMegaBlastEngineByLoc * * Revision 6.27 2000/08/25 17:00:17 dondosha * Added prototype for MegaBlastReevaluateWithAmbiguities * * Revision 6.26 2000/07/11 16:45:39 dondosha * Removed mask SeqLocPtr array from all related prototypes * * Revision 6.25 2000/07/08 20:44:12 vakatov * Get all "#include" out of the 'extern "C" { }' scope; other cleanup... * * Revision 6.24 2000/06/30 17:52:45 madden * Move AWAKE_THR_MIN_SIZE to blastdef.h * * Revision 6.23 2000/06/27 22:21:02 dondosha * Added 3 prototypes for masked query output * * Revision 6.22 2000/06/27 14:48:04 dondosha * Changed and added macros for testing HSP inclusion * * Revision 6.21 2000/05/26 19:21:39 dondosha * Added two defines for neighboring * * Revision 6.20 2000/05/12 19:40:17 dondosha * Added prototype for BinarySearchInt4; macro MB_HSP_CONTAINED * * Revision 6.19 2000/05/03 20:20:15 dondosha * Added prototype for MegaBlastGappedAlign * * Revision 6.18 2000/04/12 21:10:05 dondosha * Added MegaBlastGetPercentIdentity prototype * * Revision 6.17 2000/04/10 17:43:44 dondosha * Changed prototype for BlastNeedHumanRepeatFiltering * * Revision 6.16 2000/04/07 16:52:44 dondosha * Changed prototype for BioseqMegaBlastEngine, removed BioseqMegaBlastEngineByLoc, BlastSearchHandleResults * * Revision 6.15 2000/04/05 18:12:33 dondosha * Moved SeqIdSetDup to objloc.h * * Revision 6.14 2000/04/04 20:51:57 dondosha * No need for BlastAdjustHitOffsets prototype anymore * * Revision 6.13 2000/04/04 16:11:16 dondosha * Added prototype for BlastNeedHumanRepeatFiltering * * Revision 6.12 2000/03/31 19:10:26 dondosha * Changed some names related to MegaBlast * * Revision 6.11 2000/03/29 22:09:11 dondosha * Added prototypes for gap info related functions * * Revision 6.10 2000/03/16 18:12:25 dondosha * Added prototype for SeqIdSetDup * * Revision 6.9 2000/03/13 21:09:46 dondosha * Added prototype for BlastSortUniqHspArray * * Revision 6.8 2000/03/08 20:50:17 madden * Remove prototype for BlastGetAllowedGis * * Revision 6.7 2000/03/03 18:08:52 dondosha * Added prototype for MegaBlastWordFinderDeallocate * * Revision 6.6 2000/03/02 17:22:26 dondosha * Added array of lower case mask SeqLocPtrs as parameter to several routines * * Revision 6.5 2000/02/24 17:49:17 dondosha * Added prototype for BlastAdjustHitOffsets * * Revision 6.4 2000/02/11 20:55:38 dondosha * Added prototypes for new word finder and extension routines * * Revision 6.3 2000/02/03 22:12:26 dondosha * Added header comments * * Revision 6.2 2000/02/02 15:04:14 dondosha * Removed unused routine ReapHitlistByContext * * */ #ifndef __MBLAST__ #define __MBLAST__ #include #include #include #include #include #include #include #include #include #include #include #include #include #ifdef __cplusplus extern "C" { #endif #define MB_DIAG_CLOSE 6 #define MB_DIAG_NEAR 30 #define MB_HSP_CLOSE(q1, q2, s1, s2, c) \ (ABS((q1-s1) - (q2-s2)) < c) #define MB_HSP_CONTAINED(qo1,qo2,qe2,so1,so2,se2,c) \ (qo1>=qo2 && qo1<=qe2 && so1>=so2 && so1<=se2 && \ MB_HSP_CLOSE(qo1,qo2,so1,so2,c)) #define MIN_NEIGHBOR_PERC_IDENTITY 96 #define MIN_NEIGHBOR_HSP_LENGTH 100 Int2 MegaBlastSetUpSearchInternalByLoc 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)))); SeqAlignPtr PNTR BioseqMegaBlastEngine PROTO((BioseqPtr PNTR bspp, 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 *results_callback)PROTO((VoidPtr Ptr)))); SeqAlignPtr PNTR BioseqMegaBlastEngineByLoc PROTO((SeqLocPtr slp, CharPtr progname, CharPtr database, BLAST_OptionsBlkPtr options, ValNodePtr *other_returns, ValNodePtr *error_returns, int (LIBCALLBACK *callback)(Int4 done, Int4 positives), SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, Int4 gi_list_total, int (LIBCALLBACK *results_callback)PROTO((VoidPtr Ptr)))); SeqAlignPtr PNTR BioseqMegaBlastEngineCore PROTO((BlastSearchBlkPtr search, BLAST_OptionsBlkPtr options)); BlastSearchBlkPtr BlastFillQueryOffsets PROTO((BlastSearchBlkPtr search, SeqLocPtr query_slp, Int4 wordsize)); Boolean MegaBlastGetFirstAndLastContext PROTO((CharPtr prog_name, SeqLocPtr query_slp, Int2Ptr first_context, Int2Ptr last_context, Uint1 strand_options)); Int4 SeqLocTotalLen PROTO((CharPtr prog_name, SeqLocPtr slp)); BlastSearchBlkPtr MegaBlastSetUpSearchWithReadDbInternal PROTO((SeqLocPtr query_slp, BioseqPtr query_bsp, CharPtr prog_name, Int4 qlen, CharPtr dbname, BLAST_OptionsBlkPtr options, int (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, Int4 gi_list_total, ReadDBFILEPtr rdfp)); SeqAlignPtr PNTR MegaBlastPackAlignmentsByQuery PROTO((BlastSearchBlkPtr search, SeqAlignPtr seqalign)); Int2 LIBCALL MegaBlastSequenceAddSequence PROTO((BlastSequenceBlkPtr sequence_blk, Uint1Ptr sequence, Uint1Ptr sequence_start, Int4 length, Int4 original_length, Int4 effective_length)); int LIBCALLBACK compare PROTO((VoidPtr v1, VoidPtr v2)); Uint1Ptr GetPrivatTranslationTable PROTO((CharPtr genetic_code, Boolean reverse_complement)); BioseqPtr BlastMakeTempProteinBioseq PROTO((Uint1Ptr sequence, Int4 length, Uint1 alphabet)); VoidPtr index_proc PROTO((VoidPtr dummy)); CharPtr BlastConstructFilterString PROTO((Int4 filter_value)); int LIBCALLBACK evalue_compare_hits PROTO((VoidPtr v1, VoidPtr v2)); Int2 blast_set_parameters PROTO((BlastSearchBlkPtr search, Int4 dropoff_number_of_bits_1st_pass, Int4 dropoff_number_of_bits_2nd_pass, Nlm_FloatHi avglen, Nlm_FloatHi searchsp, Int4 window)); void HackSeqLocId PROTO((SeqLocPtr slp, SeqIdPtr id)); Uint1 FrameToDefine PROTO((Int2 frame)); Boolean BlastGetFirstAndLastContext PROTO((CharPtr prog_name, SeqLocPtr query_slp, Int2Ptr first_context, Int2Ptr last_context, Uint1 strand_options)); Int4 MegaBlastExtendHit PROTO((BlastSearchBlkPtr search, LookupTablePtr lookup, Int4 s_off, Int4 q_off)); Int2 MegaBlastNtWordExtend PROTO((BlastSearchBlkPtr search, Uint1Ptr subject0, Int4 q_off, Int4 s_off)); Int4 MegaBlastWordFinder PROTO((BlastSearchBlkPtr search, LookupTablePtr lookup)); /*void BlastAdjustHitOffsets PROTO((BlastSearchBlkPtr search));*/ void MegaBlastMaskTheResidues PROTO((Uint1Ptr buffer, Int4 max_length, Uint1 mask_residue, SeqLocPtr mask_slp, Boolean reverse, Int4 offset, Boolean lowercase_mask)); BLAST_WordFinderPtr MegaBlastWordFinderDeallocate PROTO((BLAST_WordFinderPtr wfp)); void BlastSortUniqHspArray PROTO((BLAST_HitListPtr hitlist)); void MegaBlastFillHspGapInfo PROTO((BLAST_HSPPtr hsp, GapXEditScriptPtr esp)); GapXEditScriptPtr MBToGapXEditScript PROTO((edit_script_t PNTR ed_script)); SeqAlignPtr MegaBlastSeqAlignFromResultHitlist PROTO((BlastSearchBlkPtr search, BLASTResultHitlistPtr result_hitlist, SeqIdPtr subject_id)); Boolean BlastNeedHumanRepeatFiltering PROTO((BlastDoubleInt4Ptr gi_list, Int4 gi_list_size, Uint4 query_gi)); Int4 MegaBlastGetNumIdentical PROTO((Uint1Ptr query, Uint1Ptr subject, Int4 q_start, Int4 s_start, Int4 length, Boolean reverse)); Int2 MegaBlastReevaluateWithAmbiguities PROTO((BlastSearchBlkPtr search, Int4 sequence_number)); Int4 MegaBlastGappedAlign PROTO((BlastSearchBlkPtr search)); Int4 BinarySearchInt4 PROTO((Int4 n, Int4Ptr A, Int4 size)); void BlastLCaseMaskTheResidues PROTO((Uint1Ptr buffer, Int4 max_length, SeqLocPtr mask_slp, Boolean reverse, Int4 offset)); SeqLocPtr MaskSeqLocFromSeqAlign PROTO((SeqAlignPtr seqalign)); void PrintMaskedSequence PROTO((BioseqPtr query_bsp, SeqLocPtr mask_slp, CharPtr file_name, Boolean first)); Int4 LIBCALL MegaBlastSaveCurrentHitlist PROTO((BlastSearchBlkPtr search)); FloatLo MegaBlastGetHspPercentIdentity PROTO((BlastSearchBlkPtr search, BLAST_HSPPtr hsp)); MegaBlastParameterBlkPtr MegaBlastParameterBlkNew PROTO((BLAST_OptionsBlkPtr options)); #ifdef __cplusplus } #endif #endif /* !__MBLAST__ */