NCBI C++ ToolKit
phi_gapalign.h
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1 /* $Id: phi_gapalign.h 41431 2009-03-27 15:03:32Z camacho $
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26  * Author: Ilya Dondoshansky
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29 
30 /** @file phi_gapalign.h
31  * Function prototypes used for PHI BLAST gapped extension and gapped extension
32  * with traceback.
33  */
34 
35 #ifndef ALGO_BLAST_CORE__PHI_GAPALIGN_H
36 #define ALGO_BLAST_CORE__PHI_GAPALIGN_H
37 
46 
47 #ifdef __cplusplus
48 extern "C" {
49 #endif
50 
51 /** Perform a gapped alignment with traceback for PHI BLAST
52  * @param query The query sequence [in]
53  * @param subject The subject sequence [in]
54  * @param gap_align The gapped alignment structure [in] [out]
55  * @param score_params Scoring parameters [in]
56  * @param q_start Offset in query where to start alignment [in]
57  * @param s_start Offset in subject where to start alignment [in]
58  * @param query_length Maximal allowed extension in query [in]
59  * @param subject_length Maximal allowed extension in subject [in]
60  * @param q_pat_length Length of this pattern in query. [in]
61  * @param s_pat_length Length of this pattern in subject. [in]
62  * @param pattern_blk Detailed pattern information. [in]
63  * @return Status, 0 on success, -1 on failure.
64  */
67  BlastGapAlignStruct* gap_align,
68  const BlastScoringParameters* score_params,
69  Int4 q_start, Int4 s_start, Int4 query_length, Int4 subject_length,
70  Int4 q_pat_length, Int4 s_pat_length,
71  SPHIPatternSearchBlk *pattern_blk);
72 
73 /** Preliminary gapped alignment for PHI BLAST.
74  * @param program_number Type of BLAST program [in]
75  * @param query The query sequence block [in]
76  * @param query_info Query information structure, containing offsets into
77  * the concatenated sequence [in]
78  * @param subject The subject sequence block [in]
79  * @param gap_align The auxiliary structure for gapped alignment [in]
80  * @param score_params Parameters related to scoring [in]
81  * @param ext_params Parameters related to extensions (not used) [in]
82  * @param hit_params Parameters related to saving hits [in]
83  * @param init_hitlist List of initial HSPs, including offset pairs and
84  * pattern match lengths [in]
85  * @param hsp_list_ptr Structure containing all saved HSPs [out]
86  * @param gapped_stats Return statistics (not filled if NULL) [out]
87  * @param fence_hit Not curently supported for PHI-blast but here
88  * for compatiability. Normally true here indicates that an
89  * overrun was detected. [out]
90  * @return Status, 0 on success, -1 on failure.
91  */
94  BLAST_SequenceBlk* query, BlastQueryInfo* query_info,
96  BlastGapAlignStruct* gap_align,
97  const BlastScoringParameters* score_params,
98  const BlastExtensionParameters* ext_params,
99  const BlastHitSavingParameters* hit_params,
100  BlastInitHitList* init_hitlist,
101  BlastHSPList** hsp_list_ptr, BlastGappedStats* gapped_stats,
102  Boolean * fence_hit);
103 
104 #ifdef __cplusplus
105 }
106 #endif
107 #endif /* !ALGO_BLAST_CORE__PHI_GAPALIGN_H */
Definitions used throughout BLAST.
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
Definition: blast_export.h:65
Structures and functions prototypes used for BLAST gapped extension.
Structures and API used for saving BLAST hits.
Structure and function definitions for BLAST parameter structures, which are internal to the CORE of ...
EBlastProgramType
Defines the engine's notion of the different applications of the BLAST algorithm.
Definition: blast_program.h:72
Definitions and functions associated with the BlastQueryInfo structure.
Definitions of structures used for saving traceback information.
uint8_t Uint1
1-byte (8-bit) unsigned integer
Definition: ncbitype.h:99
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
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
Functions for finding pattern matches in sequence (PHI-BLAST).
Int2 PHIGappedAlignmentWithTraceback(Uint1 *query, Uint1 *subject, BlastGapAlignStruct *gap_align, const BlastScoringParameters *score_params, Int4 q_start, Int4 s_start, Int4 query_length, Int4 subject_length, Int4 q_pat_length, Int4 s_pat_length, SPHIPatternSearchBlk *pattern_blk)
Perform a gapped alignment with traceback for PHI BLAST.
Definition: phi_gapalign.c:836
Int2 PHIGetGappedScore(EBlastProgramType program_number, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, BLAST_SequenceBlk *subject, BlastGapAlignStruct *gap_align, const BlastScoringParameters *score_params, const BlastExtensionParameters *ext_params, const BlastHitSavingParameters *hit_params, BlastInitHitList *init_hitlist, BlastHSPList **hsp_list_ptr, BlastGappedStats *gapped_stats, Boolean *fence_hit)
Preliminary gapped alignment for PHI BLAST.
Definition: phi_gapalign.c:739
Structure to hold a sequence.
Definition: blast_def.h:242
Computed values used as parameters for gapped alignments.
Structure supporting the gapped alignment.
Structure containing hit counts from the gapped stage of a BLAST search.
The structure to hold all HSPs for a given sequence after the gapped alignment.
Definition: blast_hits.h:153
Parameter block that contains a pointer to BlastHitSavingOptions and the values derived from it.
Structure to hold all initial HSPs for a given subject sequence.
Definition: blast_extend.h:158
The query related information.
Scoring parameters block Contains scoring-related information that is actually used for the blast sea...
Structure containing all auxiliary information needed in a pattern search.
Definition: pattern.h:155
static string subject
static string query
Modified on Sat May 25 14:22:25 2024 by modify_doxy.py rev. 669887