blast_nascan.h File Reference

Routines for scanning nucleotide BLAST lookup tables. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/lookup_wrap.h>

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Typedefs
typedef Int4(*	TNaScanSubjectFunction) (const LookupTableWrap *lookup_wrap, const BLAST_SequenceBlk *subject, BlastOffsetPair *offset_pairs, Int4 max_hits, Int4 *scan_range)
	Generic prototype for nucleotide subject scanning routines. More...

Functions
void	BlastChooseNucleotideScanSubject (LookupTableWrap *lookup_wrap)
	Choose the most appropriate function to scan through nucleotide subject sequences. More...
void *	BlastChooseNucleotideScanSubjectAny (LookupTableWrap *lookup_wrap)
	Return the most generic function to scan through nucleotide subject sequences. More...

Detailed Description

Routines for scanning nucleotide BLAST lookup tables.

Definition in file blast_nascan.h.

Typedef Documentation

TNaScanSubjectFunction

typedef Int4(* TNaScanSubjectFunction) (const LookupTableWrap *lookup_wrap, const BLAST_SequenceBlk *subject, BlastOffsetPair *offset_pairs, Int4 max_hits, Int4 *scan_range)

Generic prototype for nucleotide subject scanning routines.

Definition at line 43 of file blast_nascan.h.

Function Documentation

BlastChooseNucleotideScanSubject()

void BlastChooseNucleotideScanSubject

(

LookupTableWrap *

lookup_wrap

)

Choose the most appropriate function to scan through nucleotide subject sequences.

Parameters

lookup_wrap

Structure containing lookup table [in][out]

Definition at line 2982 of file blast_nascan.c.

References eNaHashLookupTable, eNaLookupTable, eSmallNaLookupTable, LookupTableWrap::lut_type, s_MBChooseScanSubject(), s_NaChooseScanSubject(), s_NaHashChooseScanSubject(), and s_SmallNaChooseScanSubject().

Referenced by TestFixture::RunScanSubject(), and s_BlastSetUpAuxStructures().

BlastChooseNucleotideScanSubjectAny()

void* BlastChooseNucleotideScanSubjectAny

(

LookupTableWrap *

lookup_wrap

)

Return the most generic function to scan through nucleotide subject sequences.

Parameters

lookup_wrap

Structure containing lookup table [in][out]

Definition at line 2994 of file blast_nascan.c.

References eNaHashLookupTable, eNaLookupTable, eSmallNaLookupTable, LookupTableWrap::lut_type, s_BlastNaHashScanSubject_Any(), s_BlastNaScanSubject_Any(), s_BlastSmallNaScanSubject_Any(), and s_MBScanSubject_Any().

Referenced by BlastNaWordFinder(), and JumperNaWordFinder().