Blmodel Class Reference

#include <Blmodel.h>

Inheritance diagram for Blmodel:

List of all members.

Public Member Functions
	Blmodel (const string &q, const string &t, int fp, int ql, int tl, int qb, int qe, int tb, int te, int ex, double sc, double ide, double qc, float ol)
	Blmodel (const mysqlpp::Row &r)
const string &	getQid () const
const string &	getTid () const
int	getFpnum () const
pair< int, int >	getExpectedTargetRange (int ease=500, double cr=4.1) const
int	getExonNum () const
double	getScore () const
double	getNormScore () const
int	queryLength () const
int	targetLength () const
bool	queryHasStart () const
bool	queryHasStop () const
Private Attributes
string	qid
string	tid
int	fpnum
int	qlen
int	tlen
int	numex
double	score
double	iden
double	qcov
float	olp
Friends
ostream &	operator<< (ostream &ous, const Blmodel &bm)

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Detailed Description

This is a simple representation of one row of the footprintSummary table. So the data member of this class is the same as the columns of the footprintSummary table. We are interested in the first and last exon to make decisions about how much border to take. If the last exon is short, the blast will miss it. If large then it will not be missed. We will implement this in the next version.

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Constructor & Destructor Documentation

Blmodel::Blmodel	(	const string &	q,
		const string &	t,
		int	fp,
		int	ql,
		int	tl,
		int	qb,
		int	qe,
		int	tb,
		int	te,
		int	ex,
		double	sc,
		double	ide,
		double	qc,
		float	ol
	)			[inline]

Blmodel::Blmodel

(

const mysqlpp::Row &

r

)

[inline]

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Member Function Documentation

const string& Blmodel::getQid

(

)

const [inline]

References qid.

const string& Blmodel::getTid

(

)

const [inline]

References tid.

Referenced by main().

int Blmodel::getFpnum

(

)

const [inline]

References fpnum.

Referenced by writeJobInstruction().

pair< int, int > Blmodel::getExpectedTargetRange	(	int	ease = 500,
		double	cr = 4.1
	)			const

References Range::direction(), Range::length(), qlen, Match::queryBegin(), Match::queryEnd(), queryHasStart(), queryHasStop(), Match::queryRange(), Match::targetBegin(), Match::targetEnd(), Match::targetRange(), and tlen.

Referenced by writeJobInstruction().

int Blmodel::getExonNum

(

)

const [inline]

References numex.

double Blmodel::getScore

(

)

const [inline]

References score.

double Blmodel::getNormScore

(

)

const [inline]

References olp, and score.

int Blmodel::queryLength

(

)

const [inline]

Reimplemented from Match.

References qlen.

int Blmodel::targetLength

(

)

const [inline]

Reimplemented from Match.

References tlen.

bool Blmodel::queryHasStart

(

)

const [inline]

References Match::queryBegin().

Referenced by getExpectedTargetRange().

bool Blmodel::queryHasStop

(

)

const [inline]

References qlen, and Match::queryEnd().

Referenced by getExpectedTargetRange().

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Friends And Related Function Documentation

ostream& operator<<	(	ostream &	ous,
		const Blmodel &	bm
	)			[friend]

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Member Data Documentation

string Blmodel::qid [private]

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

string Blmodel::tid [private]

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

int Blmodel::fpnum [private]

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

int Blmodel::qlen [private]

Referenced by getExpectedTargetRange(), operator<<(), queryHasStop(), and queryLength().

int Blmodel::tlen [private]

Referenced by getExpectedTargetRange(), operator<<(), and targetLength().

int Blmodel::numex [private]

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

double Blmodel::score [private]

Referenced by getNormScore(), getScore(), and operator<<().

double Blmodel::iden [private]

Referenced by operator<<().

double Blmodel::qcov [private]

Referenced by operator<<().

float Blmodel::olp [private]

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

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

• seqaln/Utility/Blmodel.h
• seqaln/Utility/Blmodel.cpp