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NCBI C++ ToolKit: src/algo/blast/core/phi_extend.c Source File

first_offset = 0;

(first_offset < last_offset)

offset_pairs, max_hits);

(hit_index = 0; hit_index < hits; ++hit_index) {

void Blast_UngappedStatsUpdate(BlastUngappedStats *ungapped_stats, Int4 total_hits, Int4 extended_hits, Int4 saved_hits)

Fill data in the ungapped hits diagnostics structure.

Boolean BLAST_SaveInitialHit(BlastInitHitList *init_hitlist, Int4 q_off, Int4 s_off, BlastUngappedData *ungapped_data)

Save the initial hit data into the initial hit list structure.

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

Int2 PHIBlastWordFinder(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)

WordFinder type function for PHI BLAST.

static Int2 s_PHISaveInitialHit(BlastInitHitList *init_hitlist, BlastOffsetPair *offset_pair)

Saves a pattern hit in a BlastInitHitList.

Word finder for PHI-BLAST.

Pseudo lookup table structure and database scanning functions used in PHI-BLAST.

Int4 PHIBlastScanSubject(const LookupTableWrap *lookup_wrap, const BLAST_SequenceBlk *query_blk, const BLAST_SequenceBlk *subject, Int4 *offset, BlastOffsetPair *offset_pairs, Int4 array_size)

Scans the subject sequence from "offset" to the end of the sequence.

Structure to hold a sequence.

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.

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.

This symbol enables the verbose option in makeblastdb and other BLAST+ search command line applicatio...

Uint4 s_start

Start offset of pattern in subject.

Uint4 s_end

End offset of pattern in subject.

struct BlastOffsetPair::@7 phi_offsets

Pattern offsets in subject (PHI BLAST only)

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