include/algo/cobalt/kmercounts.hpp File Reference

#include <util/math/matrix.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objmgr/scope.hpp>
#include <algo/cobalt/base.hpp>
#include <algo/blast/core/blast_encoding.h>
#include <vector>
#include <stack>

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Classes
class	CSparseKmerCounts
	Kmer counts for alignment free sequence similarity computation implemented as a sparse vector. More...
struct	CSparseKmerCounts::SVectorElement
	Element of the sparse vector. More...
class	CKmerCountsException
	Exception class for Kmer counts. More...
class	TKmerMethods< TKmerCounts >
	Interface for computing and manipulating k-mer counts vectors that allows for different implementations of K-mer counts vectors. More...
Functions
static const string	kAlphabet10 ("IJLMV AST BDENZ KQR G FY P H C W")
static const string	kAlphabet15 ("ST IJV LM KR EQZ A G BD P N F Y H C W")
static void	BuildCompressedTranslation (const string &trans_string, vector< Uint1 > &trans_table, unsigned alphabet_len)
	Creates translation table for compressed alphabets.

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Function Documentation

static void BuildCompressedTranslation (  const string &  trans_string, vector< Uint1 > &  trans_table, unsigned  alphabet_len )  [static]

Creates translation table for compressed alphabets. Parameters: trans_string  String with groupped letters [in] trans_table  Translation table [out] alphabet_len  Number of letters in compressed alphabet Definition at line 279 of file kmercounts.hpp. References _ASSERT, and AMINOACID_TO_NCBISTDAA. Referenced by TKmerMethods< TKmerCounts >::SetParams().

static const string kAlphabet10 (  "IJLMV AST BDENZ KQR G FY P H C W"   )  [static]

Referenced by TKmerMethods< TKmerCounts >::SetParams().

static const string kAlphabet15 (  "ST IJV LM KR EQZ A G BD P N F Y H C W"   )  [static]

Referenced by TKmerMethods< TKmerCounts >::SetParams().

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