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NCBI C++ ToolKit: CSparseKmerCounts Class Reference

Search Toolkit Book for CSparseKmerCounts

Kmer counts for alignment free sequence similarity computation implemented as a sparse vector. More...

#include <algo/cobalt/kmercounts.hpp>

Kmer counts for alignment free sequence similarity computation implemented as a sparse vector.

Definition at line 61 of file kmercounts.hpp.

◆ TCount ◆ TNonZeroCounts_CI ◆ CSparseKmerCounts() [1/2] CSparseKmerCounts::CSparseKmerCounts ( void ) inline ◆ CSparseKmerCounts() [2/2] CSparseKmerCounts::CSparseKmerCounts ( const objects::CSeq_loc & seq, objects::CScope & scope )

Create k-mer counts vector from SSeqLoc with defalut k-mer length and alphabet size.

Parameters: seq The sequence to be represented as k-mer counts [in] scope Scope

Definition at line 69 of file kmercounts.cpp.

References Reset().

◆ BeginNonZero()

Get non-zero counts iterator.

Returns: Non-zero counts iterator pointing to the begining

Definition at line 127 of file kmercounts.hpp.

Referenced by Print().

◆ CountCommonKmers() ◆ EndNonZero()

Get non-zero counts iterator.

Returns: Non-zero counts iterator pointing to the end

Definition at line 132 of file kmercounts.hpp.

Referenced by Print().

◆ FractionCommonKmersDist()

k + 1), where t - k-mer, n_x(t) - number of k-mer t in x, L_x - length of x excluding Xaa, k - k-mer length F(x, y) is described in RC Edgar, BMC Bioinformatics 5:113, 2004

Definition at line 369 of file kmercounts.cpp.

References _ASSERT, CountCommonKmers(), GetKmerLength(), GetNumCounts(), and v2.

◆ FractionCommonKmersGlobalDist()

k + 1), where t - k-mer, n_x(t) - number of k-mer t in x, L_x - length of x excluding Xaa, k - k-mer length F(x, y) is modified version of measure presented RC Edgar, BMC Bioinformatics 5:113, 2004

Definition at line 389 of file kmercounts.cpp.

References _ASSERT, CountCommonKmers(), GetKmerLength(), GetNumCounts(), and v2.

◆ GetAALetter() ◆ GetAlphabetSize() static unsigned int CSparseKmerCounts::GetAlphabetSize ( void ) inlinestatic

Get default alphabet size.

Returns: Default alphabet size

Definition at line 122 of file kmercounts.hpp.

◆ GetKmerLength() static unsigned int CSparseKmerCounts::GetKmerLength ( void ) inlinestatic ◆ GetNumCounts() unsigned int CSparseKmerCounts::GetNumCounts ( void ) const inline ◆ GetSeqLength() unsigned int CSparseKmerCounts::GetSeqLength ( void ) const inline ◆ InitPosBits() bool CSparseKmerCounts::InitPosBits ( const objects::CSeqVector & sv, Uint4 & pos, unsigned int & index, Uint4 num_bits, Uint4 kmer_len ) staticprivate

Initializes element index as bit vector for first k letters, skipping Xaa.

Parameters: sv Sequence [in] pos Element index in sparse vector [out] index Index of letter in the sequence where k-mer counting starts. At exit index points to the next letter after first k-mer [in|out] num_bits Number of bits in pos per letter [in] kmer_len K-mer length [in]

Returns: True if pos was initialized, false otherwise (if no k-mer without X was found)

Definition at line 82 of file kmercounts.cpp.

References GetAALetter(), i, and kXaa.

Referenced by Reset().

◆ PostCount() void CSparseKmerCounts::PostCount ( void ) static ◆ PreCount() void CSparseKmerCounts::PreCount ( void ) static ◆ Print() ◆ ReserveCountsMem() ◆ Reset() void CSparseKmerCounts::Reset ( const objects::CSeq_loc & seq, objects::CScope & scope )

Reset the counts vector.

Parameters

Definition at line 157 of file kmercounts.cpp.

References _ASSERT, AutoArray< X, Del >::get(), GetAALetter(), i, InitPosBits(), kLengthBitsThreshold, kXaa, m_Counts, m_NumCounts, m_SeqLength, MarkUsed(), mask, max(), NCBI_THROW, NULL, ReserveCountsMem(), AutoArray< X, Del >::reset(), sm_AlphabetSize, sm_Buffer, sm_ForceSmallerMem, sm_KmerLength, sm_TransTable, and sm_UseCompressed.

Referenced by CSparseKmerCounts().

◆ SetAlphabetSize() static void CSparseKmerCounts::SetAlphabetSize ( unsigned size ) inlinestatic ◆ SetKmerLength() static void CSparseKmerCounts::SetKmerLength ( unsigned len ) inlinestatic ◆ SetTransTable() static vector<Uint1>& CSparseKmerCounts::SetTransTable ( void ) inlinestatic ◆ SetUseCompressed() static void CSparseKmerCounts::SetUseCompressed ( bool use_comp ) inlinestatic ◆ kLengthBitsThreshold const unsigned int CSparseKmerCounts::kLengthBitsThreshold = 32 staticprotected ◆ m_Counts ◆ m_NumCounts unsigned int CSparseKmerCounts::m_NumCounts protected ◆ m_SeqLength unsigned int CSparseKmerCounts::m_SeqLength protected ◆ sm_AlphabetSize ◆ sm_Buffer ◆ sm_ForceSmallerMem bool CSparseKmerCounts::sm_ForceSmallerMem = false staticprotected ◆ sm_KmerLength unsigned int CSparseKmerCounts::sm_KmerLength = 4 staticprotected ◆ sm_TransTable ◆ sm_UseCompressed bool CSparseKmerCounts::sm_UseCompressed = false staticprotected

The documentation for this class was generated from the following files:

include/algo/cobalt/kmercounts.hpp
src/algo/cobalt/kmercounts.cpp

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