include/algo/blast/core/lookup_util.h File Reference

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Detailed Description

Utility functions for lookup table generation.

Definition in file lookup_util.h.

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

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Functions
Int4	iexp (Int4 x, Int4 n)
	Integer exponentiation using right to left binary algorithm.
Int4	ilog2 (Int4 x)
	Integer base two logarithm.
void	debruijn (Int4 n, Int4 k, Uint1 *output, Uint1 *alphabet)
	generates a de Bruijn sequence containing all substrings of length n over an alphabet of size k.
Int4	EstimateNumTableEntries (BlastSeqLoc *location, Int4 *max_off)
	Given a list of query locations, estimate the number of words that would need to be added to a lookup table.

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Function Documentation

void debruijn (  Int4  n, Int4  k, Uint1 *  output, Uint1 *  alphabet )

generates a de Bruijn sequence containing all substrings of length n over an alphabet of size k. if alphabet is not NULL, use it as a translation table for the output. expects that "output" has already been allocated and is at least k^n in size. Parameters: n  the number of letters in each word k  the size of the alphabet output  the output sequence alphabet  optional translation alphabet Definition at line 175 of file lookup_util.c. References fkm(), and sfree. Referenced by AalookupTestFixture::GetSeqBlk().

Int4 EstimateNumTableEntries (  BlastSeqLoc *  location, Int4 *  max_off )

Given a list of query locations, estimate the number of words that would need to be added to a lookup table. The estimate is currently intended for nucleotide locations, and ignores ambiguities and the actual width of a lookup table word Parameters: location  A linked list of locations to index [in] max_off  upper bound on the largest query offset to be indexed [out] Returns: The approximate number of lookup table entries Definition at line 195 of file lookup_util.c. References SSeqRange::left, MAX, BlastSeqLoc::next, SSeqRange::right, and BlastSeqLoc::ssr. Referenced by LookupTableWrapInit().

Int4 iexp (  Int4  x, Int4  n )

Integer exponentiation using right to left binary algorithm. See knuth TAOCP vol. 2, section 4.6.3. Parameters: x  x n  n Returns: x to the n-th power Definition at line 52 of file lookup_util.c. Referenced by BlastCompressedAaLookupTableNew(), and AalookupTestFixture::GetSeqBlk().

Int4 ilog2 (  Int4  x  )

Integer base two logarithm. Parameters: x  x Returns: lg(x) Definition at line 76 of file lookup_util.c. Referenced by BlastAaLookupTableNew(), BlastMBLookupTableNew(), and RPSLookupTableNew().

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