divstat Class Reference

#include <group.h>

List of all members.

Public Member Functions
	divstat ()
	divstat (istream &in)
void	read (istream &in)
	divstat (result &qres, int row)
	divstat (const divstat &d)
string	getid ()
bool	operator== (const char s[])
divstat &	operator= (const divstat &d)
bool	operator> (const divstat &ds) const
bool	operator< (const divstat &ds) const
bool	smallerThan (const divstat &d, double k) const
bool	smallerThan (const divstat *const d, const double k) const
void	scale (double f)
double	getQcov () const
double	getTcov () const
double	getScore () const
double	getIdentity () const
double	getNgidentity () const
double	getSimilarity () const
double	getMatchlen () const
double	getNogaplen () const
ostream &	dump (ostream &ou)
Static Public Member Functions
static int	idxqcov ()
static int	idxtcov ()
static int	idxscore ()
static int	idxidentity ()
static int	idxngidentity ()
static int	idxsimilarity ()
static int	idxmatchlen ()
static int	idxnogaplen ()
Public Attributes
char	id [5]
double	feat [FEAT]
Static Public Attributes
static const char *	features [FEAT]
Friends
ostream &	operator<< (ostream &o, const divstat &ds)

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Detailed Description

A simple statistical representation of the max(...) features from each division. In the first test run I used 5 features. Now I have a much richer features: max of 0 qcov float4, 1 tcov float4, 2 score float, 3 identity float4, 4 ngidentity float4, 5 matchlen integer, 6 nogaplen integer, 7 similarity float4, ====== all the features except the simple feature that should be count count(distinct(simple)) if == 2 means mixed and lower quality of some of the hits.

This class simply holds the values.

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Constructor & Destructor Documentation

divstat::divstat

(

)

References feat, and FEAT.

divstat::divstat

(

istream &

in

)

References feat, and id.

divstat::divstat	(	result &	qres,
		int	row
	)

constructor from database input now the result type of the pqxx

References feat, FEAT, and features.

divstat::divstat

(

const divstat &

d

)

References feat, FEAT, and id.

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Member Function Documentation

void divstat::read

(

istream &

in

)

References feat, and id.

string divstat::getid

(

)

[inline]

References string().

Referenced by group::group(), and group::next().

bool divstat::operator==

(

const char

s[]

)

[inline]

divstat & divstat::operator=

(

const divstat &

d

)

References feat, FEAT, and id.

bool divstat::operator>

(

const divstat &

ds

)

const

References getScore().

bool divstat::operator<

(

const divstat &

ds

)

const

References getScore().

bool divstat::smallerThan	(	const divstat &	d,
		double	k
	)			const

References scale().

bool divstat::smallerThan	(	const divstat *const	d,
		const double	k
	)			const

References scale().

void divstat::scale

(

double

f

)

References feat, and FEAT.

Referenced by smallerThan().

double divstat::getQcov

(

)

const [inline]

References feat.

double divstat::getTcov

(

)

const [inline]

References feat.

double divstat::getScore

(

)

const [inline]

References feat.

Referenced by operator<(), and operator>().

double divstat::getIdentity

(

)

const [inline]

References feat.

double divstat::getNgidentity

(

)

const [inline]

References feat.

double divstat::getSimilarity

(

)

const [inline]

References feat.

double divstat::getMatchlen

(

)

const [inline]

References feat.

double divstat::getNogaplen

(

)

const [inline]

References feat.

ostream & divstat::dump

(

ostream &

ou

)

References feat, FEAT, and id.

static int divstat::idxqcov

(

)

[inline, static]

Referenced by gdiagnosis::coverageDefect(), gdiagnosis::fixScoreAndTest(), group::getQcovSMratio(), group::maxqcov(), gdiagnosis::passedQcov(), gdiagnosis::qcovpass(), and gdiagnosis::rmlow().

static int divstat::idxtcov

(

)

[inline, static]

Referenced by gdiagnosis::coverageDefect(), group::getTcovSMratio(), and group::maxtcov().

static int divstat::idxscore

(

)

[inline, static]

Referenced by gdiagnosis::dumpWithZval(), gdiagnosis::fixScoreAndTest(), group::getScoreSMratio(), gdiagnosis::lastTest(), group::maxscore(), gdiagnosis::rmlow(), and gdiagnosis::scorepass().

static int divstat::idxidentity

(

)

[inline, static]

Referenced by gdiagnosis::coverageDefect(), gdiagnosis::dumpWithZval(), group::getIdenSMratio(), group::isConserved(), gdiagnosis::lastTest(), group::maxidentity(), gdiagnosis::passedIdentity(), gdiagnosis::qualitypass(), gdiagnosis::rmlow(), and gdiagnosis::targetPartial().

static int divstat::idxngidentity

(

)

[inline, static]

Referenced by group::isConserved(), group::maxngidentity(), gdiagnosis::passedIdentity(), gdiagnosis::qualitypass(), gdiagnosis::rmlow(), and gdiagnosis::targetPartial().

static int divstat::idxsimilarity

(

)

[inline, static]

Referenced by group::maxsimilarity(), gdiagnosis::passedIdentity(), gdiagnosis::qualitypass(), gdiagnosis::rmlow(), and gdiagnosis::targetPartial().

static int divstat::idxmatchlen

(

)

[inline, static]

Referenced by gdiagnosis::dumpWithZval(), group::getMlenSMratio(), group::maxmatchlen(), and gdiagnosis::passedLength().

static int divstat::idxnogaplen

(

)

[inline, static]

Referenced by group::maxnogaplen(), and gdiagnosis::passedLength().

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Friends And Related Function Documentation

ostream& operator<<	(	ostream &	o,
		const divstat &	ds
	)			[friend]

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Member Data Documentation

char divstat::id[5]

Referenced by divstat(), dump(), operator<<(), operator=(), and read().

double divstat::feat[FEAT]

Referenced by divstat(), dump(), getIdentity(), getMatchlen(), getNgidentity(), getNogaplen(), getQcov(), getScore(), getSimilarity(), getTcov(), operator<<(), operator=(), read(), and scale().

const char * divstat::features [static]

Initial value:

 { 
   "qcov", "tcov", "score", "identity",
                "ngidentity", "similarity", "matchlen", "nogaplen" }

Referenced by divstat(), and operator<<().

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

• cluster/group.h
• cluster/group.cpp