NAdapterSearch::CUnpairedAdapterDetector Class Reference

Search Toolkit Book for NAdapterSearch::CUnpairedAdapterDetector

This class assembles adapter sequence based on distribution of word counts. More...

#include <algo/sequence/adapter_search.hpp>

Inheritance diagram for NAdapterSearch::CUnpairedAdapterDetector:

Collaboration diagram for NAdapterSearch::CUnpairedAdapterDetector:

Public Member Functions
	CUnpairedAdapterDetector ()
virtual void	AddExemplar (const char *seq, size_t len)
	Add sequence of a spot from an SRA run (single or paired-end read) More...
virtual string	InferAdapterSeq () const
	returns IUPAC seq of the inferred adapter seq; empty if not found. More...
Public Member Functions inherited from NAdapterSearch::IAdapterDetector
SParams &	SetParams ()
const SParams &	GetParams () const
virtual	~IAdapterDetector ()

Private Member Functions
TWord	x_FindAdapterSeed () const
	Find a word that is likely adapter-specific, if any. More...
TWord	x_GetAdjacent (TWord w, bool right) const
	if right, return most frequent word whose 11-prefix = 11-suffix of w; otherwise, return most frequent word whose 11-suffix = 11-prefix of w More...
void	x_ExtendSeed (TWords &words, size_t top_count, bool right) const
	Extend the seed one way, as long as it satisfies extension thresholds. More...

Private Attributes
TCounts	m_counts

Additional Inherited Members
Protected Attributes inherited from NAdapterSearch::IAdapterDetector
SParams	m_params

Detailed Description

This class assembles adapter sequence based on distribution of word counts.

Definition at line 170 of file adapter_search.hpp.

Constructor & Destructor Documentation

CUnpairedAdapterDetector()

NAdapterSearch::CUnpairedAdapterDetector::CUnpairedAdapterDetector ( )

inline

Definition at line 173 of file adapter_search.hpp.

Member Function Documentation

AddExemplar()

void NAdapterSearch::CUnpairedAdapterDetector::AddExemplar ( const char *  seq, size_t  len  )

virtual

Add sequence of a spot from an SRA run (single or paired-end read)

Implements NAdapterSearch::IAdapterDetector.

Definition at line 314 of file adapter_search.cpp.

References ITERATE, len, m_counts, and NAdapterSearch::s_Translate().

InferAdapterSeq()

string NAdapterSearch::CUnpairedAdapterDetector::InferAdapterSeq ( ) const

virtual

returns IUPAC seq of the inferred adapter seq; empty if not found.

Implements NAdapterSearch::IAdapterDetector.

Definition at line 326 of file adapter_search.cpp.

References NAdapterSearch::s_AsIUPAC(), NAdapterSearch::s_IsHomopolymer(), and seed.

x_ExtendSeed()

void NAdapterSearch::CUnpairedAdapterDetector::x_ExtendSeed ( TWords &  words, size_t  top_count, bool  right  ) const

private

Extend the seed one way, as long as it satisfies extension thresholds.

Definition at line 428 of file adapter_search.cpp.

x_FindAdapterSeed()

NAdapterSearch::TWord NAdapterSearch::CUnpairedAdapterDetector::x_FindAdapterSeed ( ) const

private

Find a word that is likely adapter-specific, if any.

Definition at line 360 of file adapter_search.cpp.

References count, ERR_POST, Info(), log, n, NAdapterSearch::s_AsIUPAC(), and NAdapterSearch::s_IsLowComplexity().

x_GetAdjacent()

NAdapterSearch::TWord NAdapterSearch::CUnpairedAdapterDetector::x_GetAdjacent ( TWord  w, bool  right  ) const

private

if right, return most frequent word whose 11-prefix = 11-suffix of w; otherwise, return most frequent word whose 11-suffix = 11-prefix of w

Definition at line 407 of file adapter_search.cpp.

References count, and letter().

Member Data Documentation

m_counts

TCounts NAdapterSearch::CUnpairedAdapterDetector::m_counts

private

Definition at line 194 of file adapter_search.hpp.

Referenced by AddExemplar().

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

• include/algo/sequence/adapter_search.hpp
• src/algo/sequence/adapter_search.cpp