hit Class Reference

#include <match.h>

List of all members.

Public Member Functions
	hit ()
	hit (string &q, string &t, istream &in) throw (end, inputException)
void	getNext (istream &in)
bool	sameQuery (const string &nq) const
bool	sameTarget (const string &nt) const
bool	sameHit (const string &q, const string &t) const
bool	overlap (const match &m) const
bool	scoreAsBigAs (const hit &h, float r) const
int	getLength () const
int	getMatchCount () const
int	getTotalMatch () const
void	dumpRaw (ostream &o) const
float	getIdentity () const
float	getScore () const
	hit ()
	hit (string &q, string &t, istream &in) throw (end, inputException)
void	getNext (istream &in)
bool	sameQuery (const string &nq) const
bool	sameTarget (const string &nt) const
bool	sameHit (const string &q, const string &t) const
bool	overlap (const match &m) const
bool	scoreAsBigAs (const hit &h, float r) const
int	getLength () const
int	getMatchCount () const
int	getTotalMatch () const
void	dumpRaw (ostream &o) const
float	getIdentity () const
float	getScore () const
Static Public Attributes
static char	fields [] = "query, target, average_identity, sum_match_length, sum_score, selratio, minE, prodE(products of all non-overlapping E)"
Private Attributes
string	query
string	target
vector< match >	matches
float	score
int	matchCnt
int	length
float	identity
double	minE
double	prodE
Friends
ostream &	operator<< (ostream &o, const hit &h)
ostream &	operator<< (ostream &o, const hit &h)
Classes
class	end

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Constructor & Destructor Documentation

hit::hit

(

)

[inline]

hit::hit	(	string &	q,
		string &	t,
		istream &	in
	)			throw (end, inputException)

References length.

hit::hit

(

)

[inline]

hit::hit	(	string &	q,
		string &	t,
		istream &	in
	)			throw (end, inputException)

---

Member Function Documentation

void hit::getNext

(

istream &

in

)

References identity, length, matches, minE, overlap(), and prodE.

bool hit::sameQuery

(

const string &

nq

)

const [inline]

References query.

Referenced by main().

bool hit::sameTarget

(

const string &

nt

)

const [inline]

References target.

bool hit::sameHit	(	const string &	q,
		const string &	t
	)			const

bool hit::overlap

(

const match &

m

)

const

References matches.

Referenced by getNext().

bool hit::scoreAsBigAs	(	const hit &	h,
		float	r
	)			const [inline]

References score.

Referenced by main().

int hit::getLength

(

)

const [inline]

References length.

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

int hit::getMatchCount

(

)

const [inline]

References matches.

Referenced by operator<<().

int hit::getTotalMatch

(

)

const [inline]

References matchCnt.

Referenced by operator<<().

void hit::dumpRaw

(

ostream &

o

)

const

References matches, query, and target.

Referenced by main().

float hit::getIdentity

(

)

const [inline]

References identity.

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

float hit::getScore

(

)

const [inline]

References score.

void hit::getNext

(

istream &

in

)

bool hit::sameQuery

(

const string &

nq

)

const [inline]

References query.

bool hit::sameTarget

(

const string &

nt

)

const [inline]

References target.

bool hit::sameHit	(	const string &	q,
		const string &	t
	)			const

bool hit::overlap

(

const match &

m

)

const

bool hit::scoreAsBigAs	(	const hit &	h,
		float	r
	)			const [inline]

References score.

int hit::getLength

(

)

const [inline]

References length.

int hit::getMatchCount

(

)

const [inline]

References matches.

int hit::getTotalMatch

(

)

const [inline]

References matchCnt.

void hit::dumpRaw

(

ostream &

o

)

const

float hit::getIdentity

(

)

const [inline]

References identity.

float hit::getScore

(

)

const [inline]

References score.

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Friends And Related Function Documentation

ostream& operator<<	(	ostream &	o,
		const hit &	h
	)			[friend]

ostream& operator<<	(	ostream &	o,
		const hit &	h
	)			[friend]

---

Member Data Documentation

static char hit::fields = "query, target, average_identity, sum_match_length, sum_score, selratio, minE, prodE(products of all non-overlapping E)" [static]

Referenced by main().

string hit::query [private]

Referenced by dumpRaw(), operator<<(), and sameQuery().

string hit::target [private]

Referenced by dumpRaw(), operator<<(), and sameTarget().

vector< match > hit::matches [private]

Referenced by dumpRaw(), getMatchCount(), getNext(), and overlap().

float hit::score [private]

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

int hit::matchCnt [private]

Referenced by getTotalMatch().

int hit::length [private]

Referenced by getLength(), and getNext().

float hit::identity [private]

Referenced by getIdentity(), and getNext().

double hit::minE [private]

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

double hit::prodE [private]

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

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

• seqana/blastio/match.h
• seqana/match.h
• seqana/blastio/match.cpp
• seqana/match.cpp