34 #ifndef ALGO_BLAST_CORE__NA_UNGAPPED__H
35 #define ALGO_BLAST_CORE__NA_UNGAPPED__H
Definitions used throughout BLAST.
Various diagnostics (hit counts, etc.) returned from the BLAST engine.
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
Ungapped extension structures that are common to nucleotide and protein extension routines.
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 ...
Definitions and functions associated with the BlastQueryInfo structure.
int16_t Int2
2-byte (16-bit) signed integer
int32_t Int4
4-byte (32-bit) signed integer
Wrapper for all lookup tables used in BLAST.
Int4(* TNaExtendFunction)(const BlastOffsetPair *offset_pairs, Int4 num_hits, const BlastInitialWordParameters *word_params, LookupTableWrap *lookup_wrap, BLAST_SequenceBlk *query, BLAST_SequenceBlk *subject, Int4 **matrix, BlastQueryInfo *query_info, Blast_ExtendWord *ewp, BlastInitHitList *init_hitlist, Int4 range)
Signature of function used to compute ungapped alignments.
void BlastChooseNaExtend(LookupTableWrap *lookup_wrap)
Choose the best routine to use for creating ungapped alignments.
Int2 BlastNaWordFinder(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)
Find all words for a given subject sequence and perform ungapped extensions, assuming ordinary blastn...
Int2 JumperNaWordFinder(BLAST_SequenceBlk *subject, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, LookupTableWrap *lookup_wrap, const BlastInitialWordParameters *word_params, const BlastScoringParameters *score_params, const BlastHitSavingParameters *hit_params, BlastOffsetPair *offset_pairs, MapperWordHits *word_hits, Int4 max_hits, BlastGapAlignStruct *gap_align, BlastInitHitList *init_hitlist, BlastHSPList **hsp_list_ptr, BlastUngappedStats *ungapped_stats, BlastGappedStats *gapped_stats)
struct MapperWordHits MapperWordHits
MapperWordHits * MapperWordHitsFree(MapperWordHits *wh)
MapperWordHits * MapperWordHitsNew(const BLAST_SequenceBlk *query, const BlastQueryInfo *query_info)
Int2 ShortRead_IndexedWordFinder(BLAST_SequenceBlk *subject, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, LookupTableWrap *lookup_wrap, const BlastInitialWordParameters *word_params, const BlastScoringParameters *score_params, const BlastHitSavingParameters *hit_params, BlastOffsetPair *offset_pairs, MapperWordHits *word_hits, Int4 max_hits, BlastGapAlignStruct *gap_align, BlastInitHitList *init_hitlist, BlastHSPList **hsp_list, BlastUngappedStats *ungapped_stats, BlastGappedStats *gapped_stats)
range(_Ty, _Ty) -> range< _Ty >
Type and macro definitions from C toolkit that are not defined in C++ toolkit.
Structure to hold a sequence.
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.
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.
Parameter block that contains a pointer to BlastInitialWordOptions and the values derived from it.
The query related information.
Scoring parameters block Contains scoring-related information that is actually used for the blast sea...
Structure containing hit counts from the ungapped stage of a BLAST search.
Structure for keeping initial word extension information.
Wrapper structure for different types of BLAST lookup tables.
Int4 num_arrays
number of pair_arrays
BlastOffsetPair ** pair_arrays
lists of word hits
Int4 * last_diag
diagnal for the last word hit for each query context
Int4 array_size
size of each array
Int4 * last_pos
subject position for the last word hit for each query context
Int4 * num
number of hits in the list
Int4 divisor
divisor used to find pair_arrays index based on query offset
This symbol enables the verbose option in makeblastdb and other BLAST+ search command line applicatio...