NCBI C++ ToolKit
aa_ungapped.h
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1 /* $Id: aa_ungapped.h 33815 2007-05-04 17:18:18Z kazimird $
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26 
27 /** @file aa_ungapped.h
28  * Protein ungapped extension code.
29  */
30 
31 #ifndef ALGO_BLAST_CORE__AA_UNGAPPED_H
32 #define ALGO_BLAST_CORE__AA_UNGAPPED_H
33 
41 
42 #ifdef __cplusplus
43 extern "C" {
44 #endif
45 
46 /** Scan a subject sequence for word hits (blastp)
47  *
48  * @param subject the subject sequence [in]
49  * @param query the query sequence [in]
50  * @param query_info concatenated query information [in]
51  * @param lookup the lookup table [in]
52  * @param matrix the substitution matrix [in]
53  * @param word_params word parameters, needed for cutoff and dropoff [in]
54  * @param ewp extend parameters, needed for diagonal tracking [in]
55  * @param offset_pairs Array for storing query and subject offsets. [in]
56  * @param offset_array_size the number of elements in each offset array [in]
57  * @param init_hitlist hsps resulting from the ungapped extension [out]
58  * @param ungapped_stats Various hit counts. Not filled if NULL [out]
59  */
62  BlastQueryInfo* query_info,
64  Int4** matrix,
65  const BlastInitialWordParameters* word_params,
66  Blast_ExtendWord* ewp,
67  BlastOffsetPair* NCBI_RESTRICT offset_pairs,
68  Int4 offset_array_size,
69  BlastInitHitList* init_hitlist,
70  BlastUngappedStats* ungapped_stats);
71 
72 /** Scan a subject sequence for word hits (rpsblast and rpstblastn)
73  *
74  * @param subject the subject sequence [in]
75  * @param query the query sequence [in]
76  * @param query_info concatenated query information [in]
77  * @param lookup the lookup table [in]
78  * @param matrix the substitution matrix [in]
79  * @param word_params word parameters, needed for cutoff and dropoff [in]
80  * @param ewp extend parameters, needed for diagonal tracking [in]
81  * @param offset_pairs Array for storing query and subject offsets. [in]
82  * @param offset_array_size the number of elements in each offset array [in]
83  * @param init_hitlist hsps resulting from the ungapped extension [out]
84  * @param ungapped_stats Various hit counts. Not filled if NULL [out]
85  */
88  BlastQueryInfo* query_info,
90  Int4** matrix,
91  const BlastInitialWordParameters* word_params,
92  Blast_ExtendWord* ewp,
93  BlastOffsetPair* NCBI_RESTRICT offset_pairs,
94  Int4 offset_array_size,
95  BlastInitHitList* init_hitlist,
96  BlastUngappedStats* ungapped_stats);
97 
98 #ifdef __cplusplus
99 }
100 #endif
101 
102 #endif /* !ALGO_BLAST_CORE__AA_UNGAPPED_H */
Int2 BlastAaWordFinder(BLAST_SequenceBlk *subject, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, LookupTableWrap *lookup, Int4 **matrix, const BlastInitialWordParameters *word_params, Blast_ExtendWord *ewp, BlastOffsetPair *offset_pairs, Int4 offset_array_size, BlastInitHitList *init_hitlist, BlastUngappedStats *ungapped_stats)
Scan a subject sequence for word hits (blastp)
Definition: aa_ungapped.c:200
Int2 BlastRPSWordFinder(BLAST_SequenceBlk *subject, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, LookupTableWrap *lookup, Int4 **matrix, const BlastInitialWordParameters *word_params, Blast_ExtendWord *ewp, BlastOffsetPair *offset_pairs, Int4 offset_array_size, BlastInitHitList *init_hitlist, BlastUngappedStats *ungapped_stats)
Scan a subject sequence for word hits (rpsblast and rpstblastn)
Definition: aa_ungapped.c:238
Various diagnostics (hit counts, etc.) returned from the BLAST engine.
Ungapped extension structures that are common to nucleotide and protein extension routines.
Structures and API used for saving BLAST hits.
Common definitions for protein and nucleotide lookup tables.
Structure and function definitions for BLAST parameter structures, which are internal to the CORE of ...
static int lookup(const char *name, const struct lookup_int *table)
Definition: attributes.c:50
#define NCBI_RESTRICT
int16_t Int2
2-byte (16-bit) signed integer
Definition: ncbitype.h:100
int32_t Int4
4-byte (32-bit) signed integer
Definition: ncbitype.h:102
Wrapper for all lookup tables used in BLAST.
Type and macro definitions from C toolkit that are not defined in C++ toolkit.
Structure to hold a sequence.
Definition: blast_def.h:242
Structure to hold all initial HSPs for a given subject sequence.
Definition: blast_extend.h:158
Parameter block that contains a pointer to BlastInitialWordOptions and the values derived from it.
The query related information.
Structure containing hit counts from the ungapped stage of a BLAST search.
Structure for keeping initial word extension information.
Definition: blast_extend.h:109
Wrapper structure for different types of BLAST lookup tables.
Definition: lookup_wrap.h:50
static string subject
static string query
This symbol enables the verbose option in makeblastdb and other BLAST+ search command line applicatio...
Definition: blast_def.h:141
Modified on Fri Sep 20 14:57:13 2024 by modify_doxy.py rev. 669887
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