JGIModel Class Reference

#include <RNAModel.h>

Inheritance diagram for JGIModel:

List of all members.

Public Member Functions
	JGIModel (const string &exstarts, const string &exends, char strand, int cdsb, int cdse, const string &gi, int ii, const string &si, const string &genomic) throw (InvalidModel)
bool	valid ()
string	toJGIString (char sep='\t') const
string	toSQLString (char sep=',') const
string	toString (char sep='\t') const
void	growEnd (int icr)
int	getId () const
const string &	getName () const
ostream &	show (ostream &ous) const
Private Attributes
int	id
string	name
int	cdsphase

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Detailed Description

special constructor for taking input from JGI database Special function to validate the model. Only in this model we introduced CDS phase (0,1,2) should we put it into mRNA model?

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Constructor & Destructor Documentation

JGIModel::JGIModel	(	const string &	exstarts,
		const string &	exends,
		char	strand,
		int	cdsb,
		int	cdse,
		const string &	gi,
		int	ii,
		const string &	si,
		const string &	genomic
	)			throw (InvalidModel)

References Range::direction(), Range::end(), mRNAModel::gcdsb, mRNAModel::gcdse, Noschain::insideExon(), itos(), Range::length(), Noschain::setEnd(), and mRNAModel::shortestmodel.

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Member Function Documentation

bool JGIModel::valid

(

)

return -1 for bad, 1 for good, 0 for not sure

References Range::begin(), mRNAModel::CDSDirection(), mRNAModel::CDSLength(), cdsphase, mRNAModel::CDSRange(), mRNAModel::CDSSeq(), Range::contain(), countInternalStops(), Range::direction(), Range::end(), Noschain::exonIndex(), mRNAModel::gcdsb, mRNAModel::gcdse, growEnd(), Range::length(), mRNAModel::numberOfInternalStops(), Noschain::numberOfRanges(), mRNAModel::pep, RNAModel::resetRNA(), RNAModel::RNALength(), Noschain::setBegin(), Noschain::setEnd(), mRNAModel::shortestmodel, mRNAModel::shortestpep, and translate().

string JGIModel::toJGIString

(

char

sep = '\t'

)

const

References Range::direction(), mRNAModel::gcdsb, mRNAModel::gcdse, RNAModel::genomicId(), getId(), getName(), Range::largerEnd(), max, min, Noschain::numberOfRanges(), Range::smallerEnd(), and Noschain::startEnd().

string JGIModel::toSQLString

(

char

sep = ','

)

const

References Range::begin(), cdsphase, Range::end(), mRNAModel::gcdsb, mRNAModel::gcdse, RNAModel::genomicId(), getId(), getName(), mRNAModel::hasStart(), mRNAModel::hasStop(), mRNAModel::pep, and Noschain::toString().

string JGIModel::toString

(

char

sep = '\t'

)

const

References mRNAModel::gcdsb, mRNAModel::gcdse, RNAModel::genomicId(), getId(), getName(), and Noschain::toString().

void JGIModel::growEnd

(

int

icr

)

extend the end of the model, both CDS end and the model end will be pushed out. Not well thought, should distinguish between + and - strand.

Reimplemented from Noschain.

References mRNAModel::gcdse, and Noschain::growEnd().

Referenced by valid().

int JGIModel::getId

(

)

const [inline]

References id.

Referenced by toJGIString(), toSQLString(), and toString().

const string& JGIModel::getName

(

)

const [inline]

References name.

Referenced by toJGIString(), toSQLString(), and toString().

ostream & JGIModel::show

(

ostream &

ous

)

const

debug function

Reimplemented from Noschain.

References mRNAModel::gcdsb, mRNAModel::gcdse, RNAModel::gid, name, and Noschain::show().

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Member Data Documentation

int JGIModel::id [private]

use the cached result

Referenced by getId().

string JGIModel::name [private]

Referenced by getName(), and show().

int JGIModel::cdsphase [private]

Referenced by toSQLString(), and valid().

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

• range/RNAModel.h
• range/RNAModel.cpp