Gmapalnseg Class Reference

#include <Gmapres.h>

List of all members.

Public Member Functions
	Gmapalnseg ()
	Gmapalnseg (const string &ln)
	Gmapalnseg (const Gmapalnseg &ga)
	Gmapalnseg (const vector< int > &row)
	~Gmapalnseg ()
const Range &	grange () const
int	length () const
int	identity () const
int	idenxlen () const
const Range &	cDNARange () const
const Range &	genomicRange () const
Private Attributes
Range	cr
Range	gr
int	iden
Friends
ostream &	operator<< (ostream &ous, const Gmapalnseg &as)

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Detailed Description

helper functions All helper moved to strformat.h extract all integer numbers in the string break a string into two parts according the the separator sep

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Constructor & Destructor Documentation

Gmapalnseg::Gmapalnseg

(

)

[inline]

Gmapalnseg::Gmapalnseg

(

const string &

ln

)

use one line of string as input -scaffold_4:1477477-1477366 (1-111) 99%

References cr, getAllInt(), gr, and iden.

Gmapalnseg::Gmapalnseg

(

const Gmapalnseg &

ga

)

[inline]

Gmapalnseg::Gmapalnseg

(

const vector< int > &

row

)

References cr, gr, and iden.

Gmapalnseg::~Gmapalnseg

(

)

[inline]

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Member Function Documentation

const Range& Gmapalnseg::grange

(

)

const [inline]

References gr.

int Gmapalnseg::length

(

)

const [inline]

return the shorter length of the cDNA Range or genomic length The genomic DNA range should have the same length for nearly all. I have not checked this.

References cr, gr, Range::length(), and min.

Referenced by idenxlen().

int Gmapalnseg::identity

(

)

const [inline]

References iden.

int Gmapalnseg::idenxlen

(

)

const [inline]

References iden, and length().

const Range& Gmapalnseg::cDNARange

(

)

const [inline]

References cr.

const Range& Gmapalnseg::genomicRange

(

)

const [inline]

References gr.

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Friends And Related Function Documentation

ostream& operator<<	(	ostream &	ous,
		const Gmapalnseg &	as
	)			[friend]

<cDNA range>=""> TAB <Genomic range>=""> TAB <Identity>

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Member Data Documentation

Range Gmapalnseg::cr [private]

Referenced by cDNARange(), Gmapalnseg(), length(), and operator<<().

Range Gmapalnseg::gr [private]

Referenced by genomicRange(), Gmapalnseg(), grange(), length(), and operator<<().

int Gmapalnseg::iden [private]

the percent identity of the alignment segment, use integer

Referenced by Gmapalnseg(), identity(), idenxlen(), and operator<<().

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

• range/Gmapres.h
• range/Gmapres.cpp