M8MatchEX Class Reference

#include <Match.h>

Inheritance diagram for M8MatchEX:

List of all members.

Public Member Functions
	M8MatchEX ()
	M8MatchEX (const M8MatchEX &m)
	M8MatchEX (const M8Match &m)
M8MatchEX &	operator= (const M8MatchEX &m)
M8MatchEX &	operator= (const M8Match &m)
double	getMaxScore () const
void	setMaxScore (double sc)
void	attachTo (M8MatchEX &m)
M8MatchEX *	previous () const
M8MatchEX *	next () const
void	setPrevious (M8MatchEX *p)
void	setNext (M8MatchEX *p)
void	setDefault ()
Private Attributes
double	maxScore
M8MatchEX *	before
M8MatchEX *	after
Friends
class	Boxchain
ostream &	operator<< (ostream &ous, const M8MatchEX &m)

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Detailed Description

this class is created to do chaining We have to make copies of the objects, less efficient but cleanner code.

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Constructor & Destructor Documentation

M8MatchEX::M8MatchEX

(

)

[inline]

M8MatchEX::M8MatchEX

(

const M8MatchEX &

m

)

[inline]

M8MatchEX::M8MatchEX

(

const M8Match &

m

)

[inline]

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Member Function Documentation

M8MatchEX & M8MatchEX::operator=

(

const M8MatchEX &

m

)

References after, before, maxScore, and M8Match::operator=().

M8MatchEX & M8MatchEX::operator=

(

const M8Match &

m

)

Reimplemented from M8Match.

References after, before, maxScore, M8Match::operator=(), and M8Match::score().

double M8MatchEX::getMaxScore

(

)

const [inline]

References maxScore.

Referenced by Linkmatch::bestModel(), Boxchain::maxScore(), Boxchain::summaryOutput(), and Boxchain::sumScore().

void M8MatchEX::setMaxScore

(

double

sc

)

[inline]

References maxScore.

void M8MatchEX::attachTo

(

M8MatchEX &

m

)

[inline]

References before, maxScore, and M8Match::score().

M8MatchEX* M8MatchEX::previous

(

)

const [inline]

References before.

Referenced by Boxchain::Boxchain(), Linkmatch::removeChain(), and Linkmatch::showBest().

M8MatchEX* M8MatchEX::next

(

)

const [inline]

References after.

Referenced by Boxchain::avgIdentity(), Boxchain::Boxchain(), Boxchain::detailOutput(), Boxchain::operator=(), Tblastn::outputModel(), Boxchain::queryOverlap(), Boxchain::querySeqCovered(), and Boxchain::show().

void M8MatchEX::setPrevious

(

M8MatchEX *

p

)

[inline]

References before.

Referenced by Boxchain::Boxchain(), and Boxchain::operator=().

void M8MatchEX::setNext

(

M8MatchEX *

p

)

[inline]

References after.

Referenced by Boxchain::Boxchain(), and Boxchain::operator=().

void M8MatchEX::setDefault

(

)

[inline]

References before, maxScore, and M8Match::score().

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Friends And Related Function Documentation

friend class Boxchain [friend]

ostream& operator<<	(	ostream &	ous,
		const M8MatchEX &	m
	)			[friend]

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Member Data Documentation

double M8MatchEX::maxScore [private]

for dynamimc chaining algorithm

Referenced by attachTo(), getMaxScore(), operator<<(), operator=(), setDefault(), and setMaxScore().

M8MatchEX* M8MatchEX::before [private]

for the chaining algorithm, point to the previous M8MatchEX

Referenced by attachTo(), operator<<(), operator=(), previous(), setDefault(), and setPrevious().

M8MatchEX* M8MatchEX::after [private]

Referenced by next(), operator<<(), operator=(), and setNext().

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

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