HalfAlignInterval Class Reference

#include <Interval.h>

Inheritance diagram for HalfAlignInterval:

List of all members.

Public Member Functions
	HalfAlignInterval (const int bb, const int ee, int iden, int alen, float cc)
	HalfAlignInterval (const HalfAlignInterval &i)
int	getIdentical () const
float	getIdentity () const
int	getAlnlen () const
float	getCov () const
Private Attributes
int	identical
int	alnlen
float	cov

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Detailed Description

Class HalfAlignInterval to represent half of the alignment. This class is used for chimera detection.

It extends Interval class.

It add identical, alnlen, and cov information for each alignment.

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Constructor & Destructor Documentation

HalfAlignInterval::HalfAlignInterval	(	const int	bb,
		const int	ee,
		int	iden,
		int	alen,
		float	cc
	)			[inline]

HalfAlignInterval::HalfAlignInterval

(

const HalfAlignInterval &

i

)

[inline]

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Member Function Documentation

int HalfAlignInterval::getIdentical

(

)

const [inline]

References identical.

Referenced by HalfAlignPile::computeIntermediateResult().

float HalfAlignInterval::getIdentity

(

)

const [inline]

References alnlen, and identical.

int HalfAlignInterval::getAlnlen

(

)

const [inline]

References alnlen.

Referenced by HalfAlignPile::computeIntermediateResult().

float HalfAlignInterval::getCov

(

)

const [inline]

References cov.

Referenced by HalfAlignPile::computeIntermediateResult().

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Member Data Documentation

int HalfAlignInterval::identical [private]

number of identical matches

Referenced by getIdentical(), and getIdentity().

int HalfAlignInterval::alnlen [private]

length of the alignment

Referenced by getAlnlen(), and getIdentity().

float HalfAlignInterval::cov [private]

How much this alignment covers the covers the sequence in question. A sequence with length >= alnlen is implied by this class.

This should be the target coverage

Referenced by getCov().

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

• range/Interval.h