CSeqSummary Struct Reference

Search Toolkit Book for CSeqSummary

#include "discrepancy_core.hpp"
(Private to src/misc/discrepancy.)

Collaboration diagram for CSeqSummary:

Public Member Functions
	CSeqSummary ()
void	clear ()
string	GetStats () const

Public Attributes
size_t	Len
size_t	A
size_t	C
size_t	G
size_t	T
size_t	N
size_t	Other
size_t	Gaps
size_t	MaxN
size_t	MinQ
bool	First
bool	StartsWithGap
bool	EndsWithGap
bool	HasRef
string	Label
vector< pair< size_t, size_t > >	NRuns
size_t	_QS
size_t	_CBscore [WINDOW_SIZE]
size_t	_CBposition [WINDOW_SIZE]
size_t	_CBread
size_t	_CBwrite
size_t	_Pos
size_t	_Ns
string	Stats

Static Public Attributes
static const size_t	WINDOW_SIZE = 30

Detailed Description

Definition at line 256 of file discrepancy_core.hpp.

Constructor & Destructor Documentation

CSeqSummary()

CSeqSummary::CSeqSummary ( )

inline

Definition at line 259 of file discrepancy_core.hpp.

References clear().

Member Function Documentation

clear()

void CSeqSummary::clear ( void  )

inline

Definition at line 260 of file discrepancy_core.hpp.

References _CBposition, _CBread, _CBscore, _CBwrite, _Ns, _Pos, _QS, A, C, EndsWithGap, First, G, Gaps, HasRef, Label, Len, MaxN, MinQ, N, NRuns, Other, StartsWithGap, Stats, and T.

Referenced by CDiscrepancyContext::BuildSeqSummary(), and CSeqSummary().

GetStats()

string CSeqSummary::GetStats

(

void

)

const

Definition at line 165 of file discrepancy_context.cpp.

References Gaps, Len, N, NStr::NumericToString(), Other, and Stats.

Member Data Documentation

_CBposition

size_t CSeqSummary::_CBposition[WINDOW_SIZE]

Definition at line 287 of file discrepancy_core.hpp.

Referenced by _QualityScore(), and clear().

_CBread

size_t CSeqSummary::_CBread

Definition at line 288 of file discrepancy_core.hpp.

Referenced by _QualityScore(), and clear().

_CBscore

size_t CSeqSummary::_CBscore[WINDOW_SIZE]

Definition at line 286 of file discrepancy_core.hpp.

Referenced by _QualityScore(), and clear().

_CBwrite

size_t CSeqSummary::_CBwrite

Definition at line 289 of file discrepancy_core.hpp.

Referenced by _QualityScore(), and clear().

_Ns

size_t CSeqSummary::_Ns

Definition at line 291 of file discrepancy_core.hpp.

Referenced by _notN(), clear(), and sN().

_Pos

size_t CSeqSummary::_Pos

Definition at line 290 of file discrepancy_core.hpp.

Referenced by _notN(), _QualityScore(), clear(), and CountNucleotides().

_QS

size_t CSeqSummary::_QS

Definition at line 285 of file discrepancy_core.hpp.

Referenced by _QualityScore(), and clear().

A

size_t CSeqSummary::A

Definition at line 269 of file discrepancy_core.hpp.

Referenced by clear(), and sA().

C

size_t CSeqSummary::C

Definition at line 270 of file discrepancy_core.hpp.

Referenced by clear(), and sC().

EndsWithGap

bool CSeqSummary::EndsWithGap

Definition at line 280 of file discrepancy_core.hpp.

Referenced by CDiscrepancyContext::BuildSeqSummary(), clear(), CountNucleotides(), and sN().

First

bool CSeqSummary::First

Definition at line 278 of file discrepancy_core.hpp.

Referenced by CDiscrepancyContext::BuildSeqSummary(), clear(), CountNucleotides(), and sN().

G

size_t CSeqSummary::G

Definition at line 271 of file discrepancy_core.hpp.

Referenced by clear(), and sG().

Gaps

size_t CSeqSummary::Gaps

Definition at line 275 of file discrepancy_core.hpp.

Referenced by CDiscrepancyContext::BuildSeqSummary(), clear(), and GetStats().

HasRef

bool CSeqSummary::HasRef

Definition at line 281 of file discrepancy_core.hpp.

Referenced by CDiscrepancyContext::BuildSeqSummary(), and clear().

Label

string CSeqSummary::Label

Definition at line 282 of file discrepancy_core.hpp.

Referenced by CDiscrepancyContext::BuildSeqSummary(), and clear().

Len

size_t CSeqSummary::Len

Definition at line 268 of file discrepancy_core.hpp.

Referenced by CDiscrepancyContext::BuildSeqSummary(), clear(), and GetStats().

MaxN

size_t CSeqSummary::MaxN

Definition at line 276 of file discrepancy_core.hpp.

Referenced by clear(), and sN().

MinQ

size_t CSeqSummary::MinQ

Definition at line 277 of file discrepancy_core.hpp.

Referenced by _QualityScore(), and clear().

N

size_t CSeqSummary::N

Definition at line 273 of file discrepancy_core.hpp.

Referenced by clear(), GetStats(), and sN().

NRuns

vector<pair<size_t, size_t> > CSeqSummary::NRuns

Definition at line 284 of file discrepancy_core.hpp.

Referenced by _notN(), and clear().

Other

size_t CSeqSummary::Other

Definition at line 274 of file discrepancy_core.hpp.

Referenced by clear(), GetStats(), and sZ().

StartsWithGap

bool CSeqSummary::StartsWithGap

Definition at line 279 of file discrepancy_core.hpp.

Referenced by clear(), and sN().

Stats

string CSeqSummary::Stats

mutable

Definition at line 293 of file discrepancy_core.hpp.

Referenced by clear(), and GetStats().

T

size_t CSeqSummary::T

Definition at line 272 of file discrepancy_core.hpp.

Referenced by clear(), and sT().

WINDOW_SIZE

const size_t CSeqSummary::WINDOW_SIZE = 30

static

Definition at line 258 of file discrepancy_core.hpp.

Referenced by _QualityScore().

---

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

• src/misc/discrepancy/discrepancy_core.hpp
• src/misc/discrepancy/discrepancy_context.cpp