gdiagnosis Class Reference

#include <group.h>

Inheritance diagram for gdiagnosis:

List of all members.

Public Member Functions
	gdiagnosis ()
	gdiagnosis (double cut)
	gdiagnosis (const gdiagnosis &gd)
ostream &	dumpWithZval (ostream &ou) const
bool	next (int &q, istream &in)
void	setzcut (double c)
double	getzcut () const
gdiagnosis &	operator= (const gdiagnosis &g)
bool	qcovpass ()
bool	scorepass ()
bool	qualitypass ()
bool	passed (const double zcut) const
bool	goodQuality (double zcut) const
bool	passedAvg (const double zcut) const
bool	passedQcov (const double zcut) const
bool	passedIdentity (const double zcut) const
bool	passedLength (const double zcut) const
bool	passedall (const double zcut) const
bool	coverageDefect (double zcut) const
bool	lastTest () const
void	calzval ()
vector< int >	rmlow (double lowercut=-3, double avgzc=3)
double	getAvgZval () const
double	avgzval () const
bool	targetPartial (int i) const
bool	anchorPartial () const
bool	trimAndTest (ostream &ou, double zcut)
void	trimByIden ()
bool	fixScoreAndTest (double szcut, gdiagnosis &d) const
Static Public Member Functions
static void	readGuid (istream &in)
Private Member Functions
void	getspace ()
Private Attributes
vector< vector< double > >	zval
vector< vector< double > >	norm
int	hgrm [4][FEAT]
double	zcut
Static Private Attributes
static vector< vector< vector < double > > >	guid
Friends
ostream &	operator<< (ostream &ou, const gdiagnosis &g)

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Detailed Description

for group diagnosis of quality control this class will work on individual groups of divisions and figure out whether they are the same orthologue cluster or not

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Constructor & Destructor Documentation

gdiagnosis::gdiagnosis

(

)

References getspace().

gdiagnosis::gdiagnosis

(

double

cut

)

References getspace().

gdiagnosis::gdiagnosis

(

const gdiagnosis &

gd

)

References gconst::divisions, FEAT, getspace(), hgrm, norm, and zval.

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Member Function Documentation

ostream & gdiagnosis::dumpWithZval

(

ostream &

ou

)

const

References gconst::divisions, group::divm, FEAT, divstat::idxidentity(), divstat::idxmatchlen(), divstat::idxscore(), gconst::pivotdividx, group::query, group::stat, and zval.

bool gdiagnosis::next	(	int &	q,
		istream &	in
	)

Reimplemented from group.

References calzval(), and group::next().

Referenced by main().

void gdiagnosis::setzcut

(

double

c

)

[inline]

References zcut.

double gdiagnosis::getzcut

(

)

const [inline]

References zcut.

gdiagnosis & gdiagnosis::operator=

(

const gdiagnosis &

g

)

References gconst::divisions, FEAT, hgrm, norm, group::operator=(), and zval.

bool gdiagnosis::qcovpass

(

)

[inline]

References hgrm, and divstat::idxqcov().

Referenced by main().

bool gdiagnosis::scorepass

(

)

[inline]

References hgrm, and divstat::idxscore().

Referenced by main().

bool gdiagnosis::qualitypass

(

)

References hgrm, divstat::idxidentity(), divstat::idxngidentity(), and divstat::idxsimilarity().

Referenced by main().

bool gdiagnosis::passed

(

const double

zcut

)

const

References gconst::divisions, FEAT, and zval.

Referenced by passedall().

bool gdiagnosis::goodQuality

(

double

zcut

)

const

References group::divCnt, group::isConserved(), and passedAvg().

Referenced by passedall(), and trimAndTest().

bool gdiagnosis::passedAvg

(

const double

zcut

)

const

References getAvgZval().

Referenced by goodQuality(), goodQuality(), and passedall().

bool gdiagnosis::passedQcov

(

const double

zcut

)

const

References gconst::divisions, divstat::idxqcov(), and zval.

Referenced by passedall().

bool gdiagnosis::passedIdentity

(

const double

zcut

)

const

References gconst::divisions, divstat::idxidentity(), divstat::idxngidentity(), divstat::idxsimilarity(), and zval.

Referenced by passedall().

bool gdiagnosis::passedLength

(

const double

zcut

)

const

References gconst::divisions, divstat::idxmatchlen(), divstat::idxnogaplen(), and zval.

Referenced by passedall().

bool gdiagnosis::passedall

(

const double

zcut

)

const [inline]

References goodQuality(), passed(), passedAvg(), passedIdentity(), passedLength(), and passedQcov().

bool gdiagnosis::coverageDefect

(

double

zcut

)

const

References gconst::divisions, group::getIdenSMratio(), group::getMlenSMratio(), group::getQcovSMratio(), group::getTcovSMratio(), divstat::idxidentity(), divstat::idxqcov(), divstat::idxtcov(), group::stat, and zval.

Referenced by trimAndTest().

bool gdiagnosis::lastTest

(

)

const

References gconst::divisions, divstat::idxidentity(), divstat::idxscore(), and zval.

void gdiagnosis::calzval

(

)

References group::anchor, group::divCnt, gconst::divisions, group::divm, FEAT, guid, hgrm, norm, zcut, and zval.

Referenced by fixScoreAndTest(), next(), rmlow(), trimAndTest(), and trimByIden().

vector< int > gdiagnosis::rmlow	(	double	lowercut = -3,
		double	avgzc = 3
	)

References group::anchor, anchorPartial(), avgzval(), calzval(), group::divCnt, gconst::divisions, group::divm, divstat::idxidentity(), divstat::idxngidentity(), divstat::idxqcov(), divstat::idxscore(), divstat::idxsimilarity(), group::nextAnchor(), group::query, group::rmbranch(), zcut, and zval.

Referenced by main().

double gdiagnosis::getAvgZval

(

)

const [inline]

References group::divCnt, gconst::divisions, FEAT, and zval.

Referenced by passedAvg().

double gdiagnosis::avgzval

(

)

const [inline]

References group::divCnt, gconst::divisions, FEAT, and zval.

Referenced by rmlow().

bool gdiagnosis::targetPartial

(

int

i

)

const

References group::anchor, group::divm, divstat::idxidentity(), divstat::idxngidentity(), divstat::idxsimilarity(), and zval.

bool gdiagnosis::anchorPartial

(

)

const

References group::anchor, group::divm, group::maxidentity(), group::maxmatchlen(), group::maxngidentity(), group::maxnogaplen(), group::maxqcov(), group::maxscore(), and group::maxsimilarity().

Referenced by rmlow().

bool gdiagnosis::trimAndTest	(	ostream &	ou,
		double	zcut
	)

References group::anchor, calzval(), coverageDefect(), group::divCnt, gconst::divisions, group::divm, FEAT, goodQuality(), group::rmbranch(), and zval.

void gdiagnosis::trimByIden

(

)

References calzval(), group::divm, and group::rmbranch().

bool gdiagnosis::fixScoreAndTest	(	double	szcut,
		gdiagnosis &	d
	)			const

References calzval(), gconst::divisions, group::divm, divstat::idxqcov(), divstat::idxscore(), and zval.

void gdiagnosis::readGuid

(

istream &

in

)

[static]

References gconst::divisions, FEAT, and guid.

Referenced by main().

void gdiagnosis::getspace

(

)

[private]

References gconst::divisions, FEAT, norm, and zval.

Referenced by gdiagnosis().

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Friends And Related Function Documentation

ostream& operator<<	(	ostream &	ou,
		const gdiagnosis &	g
	)			[friend]

Referenced by operator<<().

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Member Data Documentation

vector< vector< vector< double > > > gdiagnosis::guid [static, private]

Initial value:

                vector< vector< vector<double> > >(divisions.size())

Referenced by calzval(), and readGuid().

vector< vector<double> > gdiagnosis::zval [private]

Referenced by avgzval(), calzval(), coverageDefect(), dumpWithZval(), fixScoreAndTest(), gdiagnosis(), getAvgZval(), getspace(), lastTest(), operator=(), passed(), passedIdentity(), passedLength(), passedQcov(), rmlow(), targetPartial(), and trimAndTest().

vector< vector<double> > gdiagnosis::norm [private]

Referenced by calzval(), gdiagnosis(), getspace(), and operator=().

int gdiagnosis::hgrm[4][FEAT] [private]

Referenced by calzval(), gdiagnosis(), operator=(), qcovpass(), qualitypass(), and scorepass().

double gdiagnosis::zcut [private]

Referenced by calzval(), getzcut(), rmlow(), and setzcut().

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

• cluster/group.h
• cluster/group.cpp