1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
|
/* $Id: blast_aascan.h,v 1.6 2010/07/23 14:36:34 kazimird Exp $
* ===========================================================================
*
* 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 blast_aascan.h
* Routines for creating protein BLAST lookup tables.
* Contains definitions and prototypes for the lookup
* table scanning phase of blastp and RPS blast.
*/
#ifndef ALGO_BLAST_CORE__BLAST_AASCAN__H
#define ALGO_BLAST_CORE__BLAST_AASCAN__H
#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/lookup_wrap.h>
#ifdef __cplusplus
extern "C" {
#endif
/** Generic prototype for nucleotide subject scanning routines */
typedef Int4 (*TAaScanSubjectFunction)(const LookupTableWrap* lookup_wrap,
const BLAST_SequenceBlk* subject,
BlastOffsetPair* NCBI_RESTRICT offset_pairs,
Int4 max_hits,
Int4 * s_range);
/** Choose the most appropriate function to scan through
* protein subject sequences
* @param lookup_wrap Structure containing lookup table [in][out]
*/
NCBI_XBLAST_EXPORT
void BlastChooseProteinScanSubject(LookupTableWrap *lookup_wrap);
/**
* Scans the RPS query sequence from "offset" to the end of the sequence.
* Copies at most array_size hits.
* Returns the number of hits found.
* If there isn't enough room to copy all the hits, return early, and update
* "offset".
*
* @param lookup_wrap the lookup table [in]
* @param sequence the subject sequence [in]
* @param offset the offset in the subject at which to begin scanning [in/out]
* @return The number of hits found.
*/
NCBI_XBLAST_EXPORT
Int4 BlastRPSScanSubject(const LookupTableWrap* lookup_wrap,
const BLAST_SequenceBlk *sequence,
Int4* offset);
#ifdef __cplusplus
}
#endif
#endif /* !ALGO_BLAST_CORE__BLAST_AASCAN__H */
|
