rangePair Class Reference

#include <alnrange.h>

Inheritance diagram for rangePair:

List of all members.

Public Member Functions
	rangePair ()
	rangePair (const rangePair &r)
	rangePair (int b, int e, double s, double ng, double c, const string &tpi, double tc, int tmi, const string &tgi, char tst, int ts, int te)
double	getTcov () const
string	getTprtid () const
string	asTabedString () const
string	asDelimitedString (char sep[]=",") const
string	genomicInfo (char sep[]="\t") const
string	getGenomic () const
char	getStrand () const
string	essentialInfo () const
	~rangePair ()
bool	sameGene (const rangePair &r) const
Static Public Member Functions
static string	fields ()
static void	setIntronLimit (int length)
Private Attributes
string	tprtid
double	tcov
int	tmodelid
string	tgenomicid
char	tstrand
int	tstart
int	tend
Static Private Attributes
static float	ngdiff_cut = 0.25
static int	distance_cut = 2000

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Detailed Description

did not implement the copy constructor we will use the default bitwise supplied by the compiler

This simply a match two ranges. Could be implemented better.

---

Constructor & Destructor Documentation

rangePair::rangePair

(

)

[inline]

rangePair::rangePair

(

const rangePair &

r

)

References tcov, tend, tgenomicid, tmodelid, tprtid, tstart, and tstrand.

rangePair::rangePair	(	int	b,
		int	e,
		double	s,
		double	ng,
		double	c,
		const string &	tpi,
		double	tc,
		int	tmi,
		const string &	tgi,
		char	tst,
		int	ts,
		int	te
	)			[inline]

tpi: target proteinid tc: target coverage tmi: target model id tgi: target genomic id tst: target strand ts: target start, te: target end

rangePair::~rangePair

(

)

[inline]

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Member Function Documentation

double rangePair::getTcov

(

)

const [inline]

References tcov.

string rangePair::getTprtid

(

)

const [inline]

References tprtid.

string rangePair::asTabedString

(

)

const [virtual]

Out all fields in tab delimited format begin,end,ngidentity,cov, tprtid, tmodelid, tgenomicid, tstrand, tstart, tend, tcov

Reimplemented from alnrange.

References alnrange::asTabedString(), tcov, tend, tmodelid, tprtid, and tstart.

string rangePair::asDelimitedString

(

char

sep[] = ","

)

const [virtual]

Reimplemented from alnrange.

References alnrange::asDelimitedString(), tcov, tend, tmodelid, tprtid, and tstart.

string rangePair::genomicInfo

(

char

sep[] = "\t"

)

const [inline]

References sep, tgenomicid, and tstrand.

string rangePair::getGenomic

(

)

const [inline]

References tgenomicid.

char rangePair::getStrand

(

)

const [inline]

References tstrand.

string rangePair::fields

(

)

[static]

Reimplemented from alnrange.

References alnrange::fields().

Referenced by checksplit().

string rangePair::essentialInfo

(

)

const [virtual]

output string with field separator TAB '' begin, end, score, ngidentity, cov, tprtid, tmodelid, tstart, tend

Reimplemented from alnrange.

References alnrange::asTabedString(), tend, tmodelid, tprtid, and tstart.

bool rangePair::sameGene

(

const rangePair &

r

)

const

References distance_cut, ngdiff_cut, alnrange::ngidentity, tend, tgenomicid, tstart, and tstrand.

static void rangePair::setIntronLimit

(

int

length

)

[inline, static]

return a list of all fields. useful for generating database tables not very useful, itoa not implemented, too much trouble to implement this function

References distance_cut.

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Member Data Documentation

string rangePair::tprtid [private]

Referenced by asDelimitedString(), asTabedString(), essentialInfo(), getTprtid(), and rangePair().

double rangePair::tcov [private]

Referenced by asDelimitedString(), asTabedString(), getTcov(), and rangePair().

int rangePair::tmodelid [private]

Referenced by asDelimitedString(), asTabedString(), essentialInfo(), and rangePair().

string rangePair::tgenomicid [private]

Referenced by genomicInfo(), getGenomic(), rangePair(), and sameGene().

char rangePair::tstrand [private]

Referenced by genomicInfo(), getStrand(), rangePair(), and sameGene().

int rangePair::tstart [private]

Referenced by asDelimitedString(), asTabedString(), essentialInfo(), rangePair(), and sameGene().

int rangePair::tend [private]

Referenced by asDelimitedString(), asTabedString(), essentialInfo(), rangePair(), and sameGene().

float rangePair::ngdiff_cut = 0.25 [static, private]

Referenced by sameGene().

int rangePair::distance_cut = 2000 [static, private]

This parameter is related to the mean / stddev of the intron size from this particular organism

Referenced by sameGene(), and setIntronLimit().

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

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