NCBI C++ ToolKit
mb_indexed_lookup.h
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1 /* $Id: mb_indexed_lookup.h 55125 2012-07-18 17:07:15Z morgulis $
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26  * Author: Aleksandr Morgulis
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29 
30 /** @file mb_indexed_lookup.h
31  * Declarations for functions that extract hits from indexed blast
32  * databases (specialized for megablast)
33  */
34 
35 #ifndef __MB_INDEXED_LOOKUP__
36 #define __MB_INDEXED_LOOKUP__
37 
40 
41 #ifdef __cplusplus
42 extern "C" {
43 #endif
44 
45 #define LAST_VOL_IDX_INIT (-1)
46 #define LAST_VOL_IDX_NULL (-2)
47 
48 enum EOidState {
52 };
53 
54 /** Function pointer type to retrieve hits from an indexed database */
55 typedef unsigned long (*T_MB_IdbGetResults)(/* void * idb, */Int4 oid, Int4 chunk,
56  BlastInitHitList * init_hitlist);
57 
58 /** Function pointer type to check index seeds availability for oid. */
59 typedef int (*T_MB_IdbCheckOid)( Int4 oid, Int4 * last_vol_id );
60 
61 /** Function pointer type to indicate end of preliminary search by the
62  thread to the indexing library.
63 */
64 typedef void (*T_MB_IdxEndSearchIndication)( Int4 last_vol_id );
65 
66 /** Finds all runs of a specified number of exact matches between
67  * two nucleotide sequences. Assumes the subject sequence is part
68  * of a previously indexed database
69  * @param subject The subject sequence [in]
70  * @param query Ignored
71  * @param query_info Ignored
72  * @param lookup_wrap Pointer to the (wrapper) lookup table structure [in]
73  * @param matrix Ignored
74  * @param word_params Ignored
75  * @param ewp Ignored
76  * @param offset_pairs Ignored
77  * @param max_hits Ignored
78  * @param init_hitlist Structure to hold all hits information. Has to be
79  * allocated up front [out]
80  * @param ungapped_stats Ignored
81  */
85  BlastQueryInfo * query_info,
86  LookupTableWrap * lookup_wrap,
87  Int4 ** matrix,
88  const BlastInitialWordParameters * word_params,
89  Blast_ExtendWord * ewp,
90  BlastOffsetPair * offset_pairs,
91  Int4 max_hits,
92  BlastInitHitList * init_hitlist,
93  BlastUngappedStats * ungapped_stats );
94 
95 #ifdef __cplusplus
96 }
97 #endif
98 
99 #endif /* __MB_INDEXED_LOOKUP__ */
Ungapped extension structures that are common to nucleotide and protein extension routines.
Structure and function definitions for BLAST parameter structures, which are internal to the CORE of ...
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
unsigned int
A callback function used to compare two keys in a database.
Definition: types.hpp:1210
int(* T_MB_IdbCheckOid)(Int4 oid, Int4 *last_vol_id)
Function pointer type to check index seeds availability for oid.
void(* T_MB_IdxEndSearchIndication)(Int4 last_vol_id)
Function pointer type to indicate end of preliminary search by the thread to the indexing library.
unsigned long(* T_MB_IdbGetResults)(Int4 oid, Int4 chunk, BlastInitHitList *init_hitlist)
Function pointer type to retrieve hits from an indexed database.
EOidState
@ eHasResults
@ eNotIndexed
@ eNoResults
Int2 MB_IndexedWordFinder(BLAST_SequenceBlk *subject, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, LookupTableWrap *lookup_wrap, Int4 **matrix, const BlastInitialWordParameters *word_params, Blast_ExtendWord *ewp, BlastOffsetPair *offset_pairs, Int4 max_hits, BlastInitHitList *init_hitlist, BlastUngappedStats *ungapped_stats)
Finds all runs of a specified number of exact matches between two nucleotide sequences.
Definition: na_ungapped.c:1697
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 Thu May 23 12:26:52 2024 by modify_doxy.py rev. 669887