31 #ifndef ALGO_BLAST_CORE__AA_UNGAPPED_H
32 #define ALGO_BLAST_CORE__AA_UNGAPPED_H
68 Int4 offset_array_size,
94 Int4 offset_array_size,
Int2 BlastAaWordFinder(BLAST_SequenceBlk *subject, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, LookupTableWrap *lookup, Int4 **matrix, const BlastInitialWordParameters *word_params, Blast_ExtendWord *ewp, BlastOffsetPair *offset_pairs, Int4 offset_array_size, BlastInitHitList *init_hitlist, BlastUngappedStats *ungapped_stats)
Scan a subject sequence for word hits (blastp)
Int2 BlastRPSWordFinder(BLAST_SequenceBlk *subject, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, LookupTableWrap *lookup, Int4 **matrix, const BlastInitialWordParameters *word_params, Blast_ExtendWord *ewp, BlastOffsetPair *offset_pairs, Int4 offset_array_size, BlastInitHitList *init_hitlist, BlastUngappedStats *ungapped_stats)
Scan a subject sequence for word hits (rpsblast and rpstblastn)
Various diagnostics (hit counts, etc.) returned from the BLAST engine.
Ungapped extension structures that are common to nucleotide and protein extension routines.
Structures and API used for saving BLAST hits.
Common definitions for protein and nucleotide lookup tables.
Structure and function definitions for BLAST parameter structures, which are internal to the CORE of ...
static int lookup(const char *name, const struct lookup_int *table)
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.
Type and macro definitions from C toolkit that are not defined in C++ toolkit.
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...