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NCBI C++ ToolKit: TKmerMethods< TKmerCounts
Search Toolkit Book for TKmerMethods
Interface for computing and manipulating k-mer counts vectors that allows for different implementations of K-mer counts vectors. More...
#include <algo/cobalt/kmercounts.hpp>
static void SetParams (unsigned kmer_len, unsigned alphabet_size) Set default counts vector parameters. More...
static void BuildCompressedTranslation (ECompressedAlphabet alph_index, vector< Uint1 > &trans_table, unsigned alphabet_len) Creates translation table for compressed alphabets. More...
static void SetParams (unsigned kmer_len, ECompressedAlphabet alph) Set default counts vector parameters for use with compressed alphabet. More...
static void ComputeCounts (const vector< CRef< objects::CSeq_loc > > &seqs, objects::CScope &scope, vector< TKmerCounts > &counts) Create k-mer counts vectors for given sequences. More...
static void ComputeDistMatrix (const vector< TKmerCounts > &counts, double(*fsim)(const TKmerCounts &, const TKmerCounts &), TDistMatrix &dmat) Compute matrix of distances between given counts vectors. More...
static void ComputeDistMatrix (const vector< TKmerCounts > &counts, TDistMatrix &dmat, double(*fsim)(const TKmerCounts &, const TKmerCounts &, double, double), const vector< double > &normalizers) Compute matrix of distances between given list of counts vectors using distance function with additional normalizing values. More...
static void ComputeDistMatrix (const vector< TKmerCounts > &counts, EDistMeasures dist_method, TDistMatrix &dmat) Compute distance matrix for given counts vectors and distance measure. More...
static unique_ptr< TDistMatrix > ComputeDistMatrix (const vector< TKmerCounts > &counts, EDistMeasures dist_method) Compute distance matrix for given counts vectors and distance measure and avoid copying. More...
static CRef< CLinks > ComputeDistLinks (const vector< TKmerCounts > &counts, EDistMeasures dist_method, double max_dist) Compute distances between k-mer counts as graph where nodes are sequences and edges represent distances. More...
template<class TKmerCounts>
class TKmerMethods< TKmerCounts >
Interface for computing and manipulating k-mer counts vectors that allows for different implementations of K-mer counts vectors.
Definition at line 425 of file kmercounts.hpp.
◆ TDistMatrix ◆ ECompressedAlphabet
template<class TKmerCounts >
Enumerator eRegular eSE_V10 eSE_B15 eFirstCompressed eLastAlphabet
Definition at line 428 of file kmercounts.hpp.
◆ EDistMeasures
template<class TKmerCounts >
Enumerator eFractionCommonKmersGlobal eFractionCommonKmersLocal
Definition at line 434 of file kmercounts.hpp.
◆ BuildCompressedTranslation()
template<class TKmerCounts >
◆ ComputeCounts()
template<class TKmerCounts >
static void TKmerMethods< TKmerCounts >::ComputeCounts ( const vector< CRef< objects::CSeq_loc > > & seqs, objects::CScope & scope, vector< TKmerCounts > & counts ) inlinestatic ◆ ComputeDistLinks()
template<class TKmerCounts >
Compute distances between k-mer counts as graph where nodes are sequences and edges represent distances.
Distances above given threshold will not have edges.
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Parameters
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counts List of k-mer counts vectors [in] dist_method Distance measure [in] max_dist Maxium distance that will be represented with a graph edge [in] mark_links If true, existings links will be marked in binary matrix [in]
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Returns
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Disatances between k-mer counts vectors represented as a graph
Definition at line 648 of file kmercounts.hpp.
References CLinks::AddLink(), TKmerMethods< TKmerCounts >::eFractionCommonKmersLocal, i, int, and NCBI_THROW.
◆ ComputeDistMatrix() [1/4]
template<class TKmerCounts >
◆ ComputeDistMatrix() [2/4]
template<class TKmerCounts >
◆ ComputeDistMatrix() [3/4]
template<class TKmerCounts >
◆ ComputeDistMatrix() [4/4]
template<class TKmerCounts >
Compute matrix of distances between given list of counts vectors using distance function with additional normalizing values.
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Parameters
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counts List of k-mer counts vectors [in] dmat Distance matrix [out] fsim Function that computes distance betwee two vectors [in] normalizers List of normalizing arguments [in]
◆ SetParams() [1/2]
template<class TKmerCounts >
◆ SetParams() [2/2]
template<class TKmerCounts >
static void TKmerMethods< TKmerCounts >::SetParams ( unsigned kmer_len, unsigned alphabet_size ) inlinestatic
The documentation for this class was generated from the following file:
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