alnrange Class Reference

#include <alnrange.h>

Inheritance diagram for alnrange:

List of all members.

Public Member Functions
	alnrange ()
	alnrange (const alnrange &r)
	alnrange (int b, int e, double s, double ng, double c)
virtual	~alnrange ()
alnrange &	operator= (const alnrange &r)
bool	overlap (const alnrange &r, const int margin)
bool	overlap (const alnrange &r)
int	length () const
int	getBegin () const
int	getEnd () const
double	getScore () const
double	getNg () const
double	getCov () const
virtual string	asTabedString () const
virtual string	asDelimitedString (char sep[]=",") const
virtual string	essentialInfo () const
Static Public Member Functions
static string	fields ()
static void	setmargin (int olpcut, float olpfrac)
Protected Attributes
int	begin
int	end
double	score
double	ngidentity
double	cov
Static Protected Attributes
static int	ovlpcut = 5
static float	ovlpfraction = 0.1
Friends
ostream &	operator<< (ostream &ous, const alnrange &r)

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Detailed Description

alnrange class the range is an individual, not a collection or average need another object to keep this information

Using another data type such as PgDatabase may not be good.

Input and output should use standard lib containners instead of database connection object. This will make the class more portable.

There is a much better and more generic implementation of ragne in range directory. I should rename the range in this directory.

Should be alnrange

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Constructor & Destructor Documentation

alnrange::alnrange

(

)

[inline]

alnrange::alnrange

(

const alnrange &

r

)

References begin, cov, end, ngidentity, and score.

alnrange::alnrange	(	int	b,
		int	e,
		double	s,
		double	ng,
		double	c
	)			[inline]

b: begin of the match; e: end of the match s: score; ng: ngidentity, c: coverage

virtual alnrange::~alnrange

(

)

[inline, virtual]

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Member Function Documentation

alnrange & alnrange::operator=

(

const alnrange &

r

)

References begin, cov, end, ngidentity, and score.

bool alnrange::overlap	(	const alnrange &	r,
		const int	margin
	)

References begin, getBegin(), and getEnd().

Referenced by overlap().

bool alnrange::overlap

(

const alnrange &

r

)

References begin, end, getBegin(), getEnd(), overlap(), ovlpcut, and ovlpfraction.

int alnrange::length

(

)

const [inline]

References begin, and end.

int alnrange::getBegin

(

)

const [inline]

References begin.

Referenced by avgrange::avgrange(), avgrange::merge(), avgrange::overlap(), and overlap().

int alnrange::getEnd

(

)

const [inline]

References end.

Referenced by avgrange::avgrange(), avgrange::merge(), avgrange::overlap(), and overlap().

double alnrange::getScore

(

)

const [inline]

References score.

Referenced by avgrange::avgrange(), and avgrange::merge().

double alnrange::getNg

(

)

const [inline]

References ngidentity.

Referenced by avgrange::avgrange(), and avgrange::merge().

double alnrange::getCov

(

)

const [inline]

References cov.

Referenced by avgrange::avgrange(), and avgrange::merge().

string alnrange::asTabedString

(

)

const [virtual]

Reimplemented in rangePair.

References begin.

Referenced by rangePair::asTabedString(), rangePair::essentialInfo(), and operator<<().

string alnrange::asDelimitedString

(

char

sep[] = ","

)

const [virtual]

Reimplemented in rangePair.

References begin.

Referenced by rangePair::asDelimitedString().

string alnrange::fields

(

)

[static]

Reimplemented in rangePair.

Referenced by rangePair::fields().

string alnrange::essentialInfo

(

)

const [virtual]

Reimplemented in rangePair.

References begin.

static void alnrange::setmargin	(	int	olpcut,
		float	olpfrac
	)			[inline, static]

References ovlpcut, and ovlpfraction.

Referenced by checkchimera(), and checksplit().

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Friends And Related Function Documentation

ostream& operator<<	(	ostream &	ous,
		const alnrange &	r
	)			[friend]

this function is not very useful, further more itoa is not implemented in this stdlib.h list<string> rangePair::fieldsAsList() const { list<string> tmp; char buff[12]; tmp.push_back(itoa(begin,buff)); tmp.push_back(itoa(end,buff)); tmp.push_back(gcvt(score,10,buff)); tmp.push_back(gcvt(cov,3,buff)); tmp.push_back(tprtid); tmp.push_back(itoa(tmodelid,10,buff)); tmp.push_back(tgenomicid); tmp.push_back(tstrand); tmp.push_back(itoa(tstart,10,buff)); tmp.push_back(itoa(tend,10,buff)); tmp.push_back(gcvt(tcov,3,buff)); return tmp; }

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Member Data Documentation

int alnrange::begin [protected]

Referenced by alnrange(), asDelimitedString(), asTabedString(), essentialInfo(), getBegin(), length(), operator=(), and overlap().

int alnrange::end [protected]

Referenced by alnrange(), getEnd(), length(), operator=(), and overlap().

double alnrange::score [protected]

addable score from blast or alignment programs

Referenced by alnrange(), getScore(), and operator=().

double alnrange::ngidentity [protected]

non-gapped identity, identity should also be fine

Referenced by alnrange(), getNg(), operator=(), and rangePair::sameGene().

double alnrange::cov [protected]

coverage on query

Referenced by alnrange(), getCov(), and operator=().

int alnrange::ovlpcut = 5 [static, protected]

Referenced by overlap(), and setmargin().

float alnrange::ovlpfraction = 0.1 [static, protected]

Referenced by overlap(), and setmargin().

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

• cluster/alnrange.h
• cluster/alnrange.cpp