M8Match Class Reference

#include <Match.h>

Inheritance diagram for M8Match:

List of all members.

Public Member Functions
	M8Match ()
	M8Match (const M8Match &m)
	M8Match (float identity, int alnlen, int mismatches, int gaps, int qbegin, int qend, int tbegin, int tend, double expect, double score)
M8Match &	operator= (const M8Match &m)
float	identity () const
int	alnlen () const
double	expect () const
double	score () const
ostream &	output (ostream &ous, const char delimiter[]="\t") const
	M8Match Class ////////////////////////////.
string	asDelimitedString (const char delimiter[]=",") const
bool	contain (const M8Match &m, bool sameDirection=true, float factor=0.8) const
void	combine (const M8Match &m)
Protected Attributes
float	iden
int	len
int	mis
int	gap
double	e
double	_score
Friends
ostream &	operator<< (ostream &ous, M8Match &m)

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Detailed Description

specialized to tblastn m8 output format This format has identity, but does not have the counts for identical residues in the match. The <XML> format allows more information to be extracted, including the actual sequence. This represent one row of -m 8 output without the query and target because in the blast output, one queryxtarget pair can have multiple matches.

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Constructor & Destructor Documentation

M8Match::M8Match

(

)

[inline]

M8Match::M8Match

(

const M8Match &

m

)

[inline]

M8Match::M8Match	(	float	identity,
		int	alnlen,
		int	mismatches,
		int	gaps,
		int	qbegin,
		int	qend,
		int	tbegin,
		int	tend,
		double	expect,
		double	score
	)			[inline]

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Member Function Documentation

M8Match & M8Match::operator=

(

const M8Match &

m

)

Reimplemented in M8MatchEX.

References _score, e, gap, iden, len, mis, and Match::operator=().

Referenced by M8MatchEX::operator=().

float M8Match::identity

(

)

const [inline]

References iden.

Referenced by M8MatchChain::add(), and Boxchain::avgIdentity().

int M8Match::alnlen

(

)

const [inline]

References len.

Referenced by M8MatchChain::add(), and Boxchain::avgIdentity().

double M8Match::expect

(

)

const [inline]

References e.

double M8Match::score

(

)

const [inline]

References _score.

Referenced by M8MatchChain::add(), M8MatchEX::attachTo(), operator<<(), M8MatchEX::operator=(), and M8MatchEX::setDefault().

ostream & M8Match::output	(	ostream &	ous,
		const char	delimiter[] = "\t"
	)			const

M8Match Class ////////////////////////////.

Output one row. The format is the same as the m8 format, except the matching sequence id is missing, in tab-delimited format. For dumping into table file.

Reimplemented from Match.

References _score, e, gap, iden, len, mis, and Match::output().

Referenced by Boxchain::detailOutput(), and Tblastn::outputModel().

string M8Match::asDelimitedString

(

const char

delimiter[] = ","

)

const

this is mainly for inserting into database tables

Reimplemented from Match.

References _score, Match::asDelimitedString(), e, gap, iden, len, and mis.

bool M8Match::contain	(	const M8Match &	m,
		bool	sameDirection = true,
		float	factor = 0.8
	)			const

specialization of the parent class method, add ideneity and score checking if score of smaller range < factor*larger_range_score

References _score, Match::contain(), and iden.

void M8Match::combine

(

const M8Match &

m

)

References _score, Match::combine(), e, gap, iden, len, Range::length(), mis, Match::overlap(), Range::overlapFraction(), Match::q, and Match::t.

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Friends And Related Function Documentation

ostream& operator<<	(	ostream &	ous,
		M8Match &	m
	)			[friend]

output for human to read: using tabs iden, len, mis, gap, e, score

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Member Data Documentation

float M8Match::iden [protected]

percent identity

Referenced by asDelimitedString(), combine(), contain(), identity(), operator<<(), operator=(), and output().

int M8Match::len [protected]

alignment length

Referenced by alnlen(), asDelimitedString(), combine(), operator<<(), operator=(), and output().

int M8Match::mis [protected]

Referenced by asDelimitedString(), combine(), operator<<(), operator=(), and output().

int M8Match::gap [protected]

Referenced by asDelimitedString(), combine(), operator<<(), operator=(), and output().

double M8Match::e [protected]

Referenced by asDelimitedString(), combine(), expect(), operator<<(), operator=(), and output().

double M8Match::_score [protected]

Referenced by asDelimitedString(), combine(), contain(), operator<<(), operator=(), output(), and score().

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

• seqaln/Utility/Match.h
• seqaln/Utility/Match.cpp