avgrange Class Reference

#include <alnrange.h>

List of all members.

Public Member Functions
	avgrange ()
	avgrange (const alnrange &r)
	avgrange (const alnrange *rp)
	~avgrange ()
bool	overlap (const alnrange &r, const int margin=10)
void	merge (const alnrange *r)
void	merge (const avgrange *ar)
double	length () const
double	getBegin () const
double	getEnd () const
double	getScore () const
double	getNg () const
double	getCov () const
int	maxlength () const
int	minbegin () const
int	maxend () const
int	getCount () const
const vector< const alnrange * > &	getMembers () const
ostream &	writeTable (ostream &ous) const
string	asDelimitedString (const char sep[]=",") const
ostream &	sqlinfo (ostream &ous)
double	getMedianCov () const
string	checkSplit_debug (const avgrange &r) const
list< string >	checkSplit (const avgrange &r, char sep[]=",") const
SplitResult	testSplit (const avgrange &r, char sep[]=",") const
Static Public Member Functions
static string	colheaders ()
Private Attributes
int	begin
int	end
int	sumbegin
int	sumend
double	sumscore
double	sumng
double	sumcov
int	n
vector< double >	covs
bool	sorted
vector< const alnrange * >	members
Friends
ostream &	operator<< (ostream &ous, const avgrange &ar)

---

Detailed Description

class avgrange This class have design problem. I have put the parameters into the range. There should be a hierchy of classes to derive from the base class

---

Constructor & Destructor Documentation

avgrange::avgrange

(

)

[inline]

avgrange::avgrange

(

const alnrange &

r

)

References begin, covs, alnrange::getBegin(), alnrange::getCov(), alnrange::getEnd(), alnrange::getNg(), alnrange::getScore(), members, sumbegin, sumcov, sumend, sumng, and sumscore.

avgrange::avgrange

(

const alnrange *

rp

)

References begin, covs, alnrange::getBegin(), alnrange::getCov(), alnrange::getEnd(), alnrange::getNg(), alnrange::getScore(), members, sumbegin, sumcov, sumend, sumng, and sumscore.

avgrange::~avgrange

(

)

References members.

---

Member Function Documentation

bool avgrange::overlap	(	const alnrange &	r,
		const int	margin = 10
	)

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

void avgrange::merge

(

const alnrange *

r

)

References begin, covs, alnrange::getBegin(), alnrange::getCov(), alnrange::getEnd(), alnrange::getNg(), alnrange::getScore(), members, n, sumbegin, sumcov, sumend, sumng, and sumscore.

Referenced by merge().

void avgrange::merge

(

const avgrange *

ar

)

References getCount(), members, and merge().

double avgrange::length

(

)

const [inline]

References n, sumbegin, and sumend.

double avgrange::getBegin

(

)

const [inline]

References n, and sumbegin.

Referenced by asDelimitedString(), operator<<(), sqlinfo(), and writeTable().

double avgrange::getEnd

(

)

const [inline]

References n, and sumend.

Referenced by asDelimitedString(), operator<<(), sqlinfo(), and writeTable().

double avgrange::getScore

(

)

const [inline]

References sumcov, and sumscore.

Referenced by asDelimitedString(), operator<<(), sqlinfo(), and writeTable().

double avgrange::getNg

(

)

const [inline]

References sumcov, and sumng.

Referenced by asDelimitedString(), operator<<(), sqlinfo(), and writeTable().

double avgrange::getCov

(

)

const [inline]

References n, and sumcov.

Referenced by asDelimitedString(), operator<<(), sqlinfo(), and writeTable().

int avgrange::maxlength

(

)

const [inline]

References begin, and end.

int avgrange::minbegin

(

)

const [inline]

References begin.

int avgrange::maxend

(

)

const [inline]

References end.

int avgrange::getCount

(

)

const [inline]

References members.

Referenced by merge().

const vector<const alnrange* >& avgrange::getMembers

(

)

const [inline]

References members.

ostream & avgrange::writeTable

(

ostream &

ous

)

const

References begin, getBegin(), getCov(), getEnd(), getMedianCov(), getNg(), getScore(), and n.

string avgrange::asDelimitedString

(

const char

sep[] = ","

)

const

This method is an analogue of the above method. It returns a tab-delimited string

References begin, getBegin(), getCov(), getEnd(), getMedianCov(), getNg(), getScore(), and n.

ostream & avgrange::sqlinfo

(

ostream &

ous

)

References begin, getBegin(), getCov(), getEnd(), getMedianCov(), getNg(), getScore(), and n.

double avgrange::getMedianCov

(

)

const

References covs, n, and sorted.

Referenced by asDelimitedString(), operator<<(), sqlinfo(), and writeTable().

string avgrange::checkSplit_debug

(

const avgrange &

r

)

const

1. ngidentity should be similar comparison is directional, left to right

References members.

list< string > avgrange::checkSplit	(	const avgrange &	r,
		char	sep[] = ","
	)			const

References members.

SplitResult avgrange::testSplit	(	const avgrange &	r,
		char	sep[] = ","
	)			const

References SplitResult::add(), and members.

static string avgrange::colheaders

(

)

[inline, static]

Referenced by checkchimera().

---

Friends And Related Function Documentation

ostream& operator<<	(	ostream &	ous,
		const avgrange &	ar
	)			[friend]

---

Member Data Documentation

int avgrange::begin [private]

Referenced by asDelimitedString(), avgrange(), maxlength(), merge(), minbegin(), operator<<(), overlap(), sqlinfo(), and writeTable().

int avgrange::end [private]

Referenced by maxend(), maxlength(), and operator<<().

int avgrange::sumbegin [private]

Referenced by avgrange(), getBegin(), length(), and merge().

int avgrange::sumend [private]

Referenced by avgrange(), getEnd(), length(), and merge().

double avgrange::sumscore [private]

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

double avgrange::sumng [private]

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

double avgrange::sumcov [private]

Referenced by avgrange(), getCov(), getNg(), getScore(), and merge().

int avgrange::n [private]

Referenced by asDelimitedString(), getBegin(), getCov(), getEnd(), getMedianCov(), length(), merge(), operator<<(), sqlinfo(), and writeTable().

vector<double> avgrange::covs [mutable, private]

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

bool avgrange::sorted [mutable, private]

Referenced by getMedianCov().

vector<const alnrange*> avgrange::members [private]

all the ranges in this collection. No particular ordering.

Referenced by avgrange(), checkSplit(), checkSplit_debug(), getCount(), getMembers(), merge(), testSplit(), and ~avgrange().

---

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

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