M8MatchChain Class Reference

#include <Match.h>

List of all members.

Public Member Functions
	M8MatchChain ()
	M8MatchChain (M8Match *m)
void	add (M8Match *m)
void	nofirst ()
void	nolast ()
bool	hasFirst () const
bool	hasLast () const
int	getTargetBegin () const
int	getTargetEnd () const
int	getQueryBegin () const
int	getQueryEnd () const
char	direction () const
int	queryOverlap () const
int	queryLength () const
ostream &	output (ostream &ous, char delimiter[]="\t") const
float	avgIdentity () const
double	sumScore () const
int	size () const
Private Attributes
vector< M8Match * >	chain
bool	_first
bool	_last
RangeChain	qchain
double	sumiden
int	sumaln
double	sumscore
Friends
class	Tblastn
ostream &	operator<< (ostream &ous, const M8MatchChain &c)

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Detailed Description

this class is a collection of pointers to a few M8Matches No destructor is needed, other objects is responsible for memory allocation

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Constructor & Destructor Documentation

M8MatchChain::M8MatchChain

(

)

[inline]

M8MatchChain::M8MatchChain

(

M8Match *

m

)

[inline]

construct an object out of Boxchain This method needs to be debuged. This one is not correct to 100%, using a differnet class

References RangeChain::add(), chain, qchain, and Match::queryRange().

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Member Function Documentation

void M8MatchChain::add

(

M8Match *

m

)

insure that all matches are in the same direction by the target (genomic)

References RangeChain::add(), M8Match::alnlen(), chain, direction(), Range::direction(), M8Match::identity(), qchain, Match::queryRange(), M8Match::score(), sumaln, sumiden, sumscore, and Match::targetRange().

Referenced by Tblastn::findFootprint().

void M8MatchChain::nofirst

(

)

[inline]

References _first.

Referenced by Tblastn::findFootprint().

void M8MatchChain::nolast

(

)

[inline]

References _last.

Referenced by Tblastn::findFootprint().

bool M8MatchChain::hasFirst

(

)

const [inline]

References _first.

bool M8MatchChain::hasLast

(

)

const [inline]

References _last.

int M8MatchChain::getTargetBegin

(

)

const

References chain, and direction().

Referenced by Tblastn::outputModel().

int M8MatchChain::getTargetEnd

(

)

const

References chain, and direction().

Referenced by Tblastn::outputModel().

int M8MatchChain::getQueryBegin

(

)

const

References chain, and direction().

Referenced by Tblastn::outputModel().

int M8MatchChain::getQueryEnd

(

)

const

References chain, and direction().

Referenced by Tblastn::outputModel().

char M8MatchChain::direction

(

)

const

References chain.

Referenced by add(), getQueryBegin(), getQueryEnd(), getTargetBegin(), getTargetEnd(), operator<<(), and Tblastn::outputModel().

int M8MatchChain::queryOverlap

(

)

const [inline]

References RangeChain::getOverlap(), and qchain.

Referenced by output(), and Tblastn::outputModel().

int M8MatchChain::queryLength

(

)

const [inline]

References RangeChain::length(), and qchain.

Referenced by Tblastn::findFootprint(), output(), and Tblastn::outputModel().

ostream & M8MatchChain::output	(	ostream &	ous,
		char	delimiter[] = "\t"
	)			const

References avgIdentity(), chain, queryLength(), queryOverlap(), and sumscore.

float M8MatchChain::avgIdentity

(

)

const [inline]

weighted average sum(identity*alnlen)/sum(alnlen)

References sumaln, and sumiden.

Referenced by output(), and Tblastn::outputModel().

double M8MatchChain::sumScore

(

)

const [inline]

References sumscore.

Referenced by Tblastn::outputModel().

int M8MatchChain::size

(

)

const [inline]

References chain.

Referenced by Tblastn::outputModel().

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Friends And Related Function Documentation

friend class Tblastn [friend]

ostream& operator<<	(	ostream &	ous,
		const M8MatchChain &	c
	)			[friend]

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Member Data Documentation

vector<M8Match*> M8MatchChain::chain [private]

Referenced by add(), direction(), getQueryBegin(), getQueryEnd(), getTargetBegin(), getTargetEnd(), M8MatchChain(), operator<<(), output(), Tblastn::outputModel(), and size().

bool M8MatchChain::_first [private]

Referenced by hasFirst(), nofirst(), operator<<(), and Tblastn::outputModel().

bool M8MatchChain::_last [private]

Referenced by hasLast(), nolast(), operator<<(), and Tblastn::outputModel().

RangeChain M8MatchChain::qchain [private]

Referenced by add(), M8MatchChain(), queryLength(), and queryOverlap().

double M8MatchChain::sumiden [private]

Referenced by add(), and avgIdentity().

int M8MatchChain::sumaln [private]

Referenced by add(), and avgIdentity().

double M8MatchChain::sumscore [private]

Referenced by add(), output(), and sumScore().

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

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