/usr/include/ncbi/mblast.h is in libncbi6-dev 6.1.20110713-3ubuntu2.
This file is owned by root:root, with mode 0o644.
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*
* 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: 6.49 $
* $Log: mblast.h,v $
* Revision 6.49 2004/01/16 23:43:44 dondosha
* No more need for special argument for partial search: it is set in options
*
* Revision 6.48 2003/12/10 17:05:28 dondosha
* Added function ReevaluateScoreWithAmbiguities to reevaluate score for one HSP; use it after greedy traceback
*
* Revision 6.47 2003/10/29 17:47:00 dondosha
* Allow 2-stage greedy extension in megablast
*
* Revision 6.46 2002/09/03 13:52:45 kans
* added prototypes for MegaBlastWordFinder and MegaBlastGappedAlign for Mac compiler
*
* Revision 6.45 2002/08/30 15:46:36 dondosha
* Moved some prototypes to blastpri.h and to mblast.c
*
* Revision 6.44 2002/08/01 20:47:24 dondosha
* Prototypes changed for megablast functions related to traceback
*
* Revision 6.43 2002/07/17 22:12:58 dondosha
* Allow return without computing seqalign for partial search
*
* Revision 6.42 2002/06/11 14:44:47 dondosha
* Return status from some functions instead of search block pointer
*
* Revision 6.41 2002/04/09 18:21:00 dondosha
* Changed #ifdefs to conditionals, allowing different discontiguous templates in a single binary
*
* Revision 6.40 2002/02/15 23:30:39 dondosha
* Allow masked query output with masking by lower case
*
* 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 <ncbi.h>
#include <blastdef.h>
#include <blastpri.h>
#include <objcode.h>
#include <objseq.h>
#include <tofasta.h>
#include <seqport.h>
#include <ncbithr.h>
#include <dust.h>
#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));
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));
void
MegaBlastFillHspGapInfo PROTO((BLAST_HSPPtr hsp, GapXEditScriptPtr esp));
SeqAlignPtr
MegaBlastGapInfoToSeqAlign PROTO((BlastSearchBlkPtr search, Int4 subject_index,
Int2 query_index));
Int4
MegaBlastGetNumIdentical PROTO((Uint1Ptr query, Uint1Ptr subject,
Int4 q_start, Int4 s_start, Int4 length,
Boolean reverse));
Boolean ReevaluateScoreWithAmbiguities(BlastSearchBlkPtr search,
Uint1Ptr subject_start, BLAST_HSPPtr hsp);
Int2
MegaBlastReevaluateWithAmbiguities PROTO((BlastSearchBlkPtr search));
Int4 BinarySearchInt4 PROTO((Int4 n, Int4Ptr A, Int4 size));
SeqLocPtr MaskSeqLocFromSeqAlign PROTO((SeqAlignPtr seqalign));
void PrintMaskedSequence PROTO((BioseqPtr query_bsp, SeqLocPtr mask_slp,
FILE *fp, Int2 line_len, Boolean lcase_masking));
Int4 LIBCALL
MegaBlastSaveCurrentHitlist PROTO((BlastSearchBlkPtr search));
FloatLo
MegaBlastGetHspPercentIdentity PROTO((BlastSearchBlkPtr search, BLAST_HSPPtr hsp));
MegaBlastParameterBlkPtr
MegaBlastParameterBlkNew PROTO((BLAST_OptionsBlkPtr options));
Int4
MegaBlastWordFinder PROTO((BlastSearchBlkPtr search, LookupTablePtr lookup));
void PerformGreedyAlignmentWithTraceback(GapAlignBlkPtr gap_align,
GreedyAlignMemPtr gamp, BLAST_ScoreBlkPtr sbp);
#ifdef __cplusplus
}
#endif
#endif /* !__MBLAST__ */
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