NCBI C++ ToolKit
hspfilter_collector.h
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1 /* $Id: hspfilter_collector.h 41998 2009-05-27 17:35:47Z camacho $
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26  * Author: Ning Ma
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29 
30 /** @file hspfilter_collector.h
31  * Implementation of a number of BlastHSPWriters to save hits from
32  * a BLAST search, and subsequently return them in sorted order.
33  */
34 
35 #ifndef ALGO_BLAST_CORE__HSPFILTER_COLLECTOR__H
36 #define ALGO_BLAST_CORE__HSPFILTER_COLLECTOR__H
37 
43 #include <connect/ncbi_core.h>
44 
45 #ifdef __cplusplus
46 extern "C" {
47 #endif
48 
49 /** Keeps prelim_hitlist_size and HitSavingOptions together. */
50 typedef struct BlastHSPCollectorParams {
51  EBlastProgramType program;/**< program type */
52  Int4 prelim_hitlist_size; /**< number of hits saved during preliminary
53  part of search. */
54  Int4 hsp_num_max; /**< number of HSPs to save per db sequence.*/
56 
57 /** Sets up parameter set for use by collector.
58  * @param program Blast program type.[in]
59  * @param hit_options field hitlist_size and hsp_num_max needed, a pointer to
60  * this structure will be stored on resulting structure.[in]
61  * @param ext_options field compositionBasedStats needed here. [in]
62  * @param scoring_options gapped_calculation needed here. [in]
63  * @return the pointer to the allocated parameter
64  */
68  Int4 compositionBasedStats,
69  Boolean gapped_calculation);
70 
71 /** Deallocates the BlastHSPCollectorParams structure passed in
72  * @param opts structure to deallocate [in]
73  * @return NULL
74  */
78 
79 /** WriterInfo to create a default writer: the collecter
80  * @param params The collector parameters.
81  * @return pointer to WriterInfo
82  */
86 
87 #ifdef __cplusplus
88 }
89 #endif
90 
91 #endif /* !ALGO_BLAST_CORE__HSPFILTER_COLLECTOR__H */
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
Definition: blast_export.h:65
Structures and API used for saving BLAST hits.
Declaration of ADT to filter and/or process HSPs in the BLAST engine.
The structures and functions in blast_options.
Definitions for various programs supported by core BLAST.
EBlastProgramType
Defines the engine's notion of the different applications of the BLAST algorithm.
Definition: blast_program.h:72
int32_t Int4
4-byte (32-bit) signed integer
Definition: ncbitype.h:102
struct BlastHSPCollectorParams BlastHSPCollectorParams
Keeps prelim_hitlist_size and HitSavingOptions together.
BlastHSPCollectorParams * BlastHSPCollectorParamsNew(const BlastHitSavingOptions *hit_options, Int4 compositionBasedStats, Boolean gapped_calculation)
Sets up parameter set for use by collector.
BlastHSPWriterInfo * BlastHSPCollectorInfoNew(BlastHSPCollectorParams *params)
WriterInfo to create a default writer: the collecter.
BlastHSPCollectorParams * BlastHSPCollectorParamsFree(BlastHSPCollectorParams *opts)
Deallocates the BlastHSPCollectorParams structure passed in.
Type and macro definitions from C toolkit that are not defined in C++ toolkit.
Uint1 Boolean
bool replacment for C
Definition: ncbi_std.h:94
Keeps prelim_hitlist_size and HitSavingOptions together.
EBlastProgramType program
program type
Int4 hsp_num_max
number of HSPs to save per db sequence.
Int4 prelim_hitlist_size
number of hits saved during preliminary part of search.
A wrap of data structure used to create a writer.
Options used when evaluating and saving hits These include: a.
Modified on Sun Apr 21 03:39:30 2024 by modify_doxy.py rev. 669887