ESTModel Class Reference

#include <ESTCombined.h>

Inheritance diagram for ESTModel:

List of all members.

Public Member Functions
	ESTModel (const Noschain &seg, int nume, const string &chrom)
	ESTModel (const Noschain &seg, int nume, const string &chrom, const string &gs, int cngid)
void	setGenomic (const string &gs)
void	write (ostream &mod, ostream &exon, ostream &track, ostream &ousest, ostream &ouspep, char sep='\t') const
const DNA &	getseq () const
const Protein &	getpep () const
Static Public Attributes
static const char	modelheader [] = "modelid\tcongid\tgenomicid\tbegin\tend\tnumest\tnumexon\texonLength\texons\tCDSstart\tCDSend"
static const char	exonheader [] = "exonid\tmodelid\texstart\texfinish"
static const char	trackheader [] = "id\tname\tchrom\tstrand\tstart\tend\tsfCount\tsfStarts\tsfEnds"
Private Attributes
string	gid
int	congid
int	numest
const string *	gseq
DNA	estseq
int	orfb
int	orfe
Protein	pep
Static Private Attributes
static int	id = 1
static int	exonid = 1
static int	shortestorf = 95

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Detailed Description

now build a more permanent class for storage and model compare and update

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Constructor & Destructor Documentation

ESTModel::ESTModel	(	const Noschain &	seg,
		int	nume,
		const string &	chrom
	)			[inline, explicit]

ESTModel::ESTModel	(	const Noschain &	seg,
		int	nume,
		const string &	chrom,
		const string &	gs,
		int	cngid
	)			[explicit]

will try to guess at the best ORF, may reverse the chain

Parameters:

cngid

congregation id, user increment this value outside this object. This value is used for output only, not for computation. It is class member of Graph

References anyToString(), estseq, bioseq::getSequence(), gseq, DNA::longestORFForward(), name, Noschain::numberOfRanges(), numest, orfb, orfe, pep, DNA::revcomp(), Noschain::reverse(), bioseq::setName(), bioseq::setTitle(), shortestorf, Noschain::subsequence(), bioseq::substr(), and Noschain::toString().

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Member Function Documentation

void ESTModel::setGenomic

(

const string &

gs

)

[inline]

References gseq.

void ESTModel::write	(	ostream &	mod,
		ostream &	exon,
		ostream &	track,
		ostream &	ousest,
		ostream &	ouspep,
		char	sep = '\t'
	)			const

write the object in several output streams

References Range::begin(), congid, Range::end(), estseq, exonid, Noschain::exonLength(), Noschain::exons, gid, id, Noschain::jgiformat(), Noschain::numberOfRanges(), numest, orfb, orfe, pep, and Noschain::toString().

const DNA& ESTModel::getseq

(

)

const [inline]

References estseq.

const Protein& ESTModel::getpep

(

)

const [inline]

References pep.

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Member Data Documentation

const char ESTModel::modelheader = "modelid\tcongid\tgenomicid\tbegin\tend\tnumest\tnumexon\texonLength\texons\tCDSstart\tCDSend" [static]

given a index in spliced mRNA, translated into index in genomic position, this should avoid introns

const char ESTModel::exonheader = "exonid\tmodelid\texstart\texfinish" [static]

const char ESTModel::trackheader = "id\tname\tchrom\tstrand\tstart\tend\tsfCount\tsfStarts\tsfEnds" [static]

string ESTModel::gid [private]

Referenced by write().

int ESTModel::congid [private]

Referenced by write().

int ESTModel::numest [private]

Referenced by ESTModel(), and write().

const string* ESTModel::gseq [private]

Referenced by ESTModel(), and setGenomic().

DNA ESTModel::estseq [private]

Referenced by ESTModel(), getseq(), and write().

int ESTModel::orfb [private]

ORF begin index and end index for estseq.

Referenced by ESTModel(), and write().

int ESTModel::orfe [private]

Referenced by ESTModel(), and write().

Protein ESTModel::pep [private]

Referenced by ESTModel(), getpep(), and write().

int ESTModel::id = 1 [static, private]

Referenced by write().

int ESTModel::exonid = 1 [static, private]

Referenced by write().

int ESTModel::shortestorf = 95 [static, private]

Referenced by ESTModel().

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

• range/ESTCombined.h
• range/ESTCombined.cpp