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 (Badinput, InvalidJGIModel, InvalidModel, PointOutChain, exception)
	JGIModel (const string &exstarts, const string &exends, char strand, int cdsb, int cdse, const string &gi, const string &si, const string &genomic) throw (Badinput, InvalidJGIModel, InvalidModel, PointOutChain, exception)
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
ostream &	print (ostream &ous) const
modeltype	objtype () const
Private Attributes
string	name

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Detailed Description

special constructor for taking input from JGI database Special function to validate the model. should we put it into mRNA model? Frame was introduced in 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 (Badinput, InvalidJGIModel, InvalidModel, PointOutChain, exception)

This is the constructor for input operations from tack table.

Parameters:

	ii.	integer id. Identifier from external.
	si,string	id which is the name column of JGI
	cdsb.	Genomic cdsbegin position. 1-based index
	cdse.	Genomic cdsEnd position, 1-based index.
	genomic.	The genomic sequence.
	gi.	genomic id.

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

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

use internal id counter

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 true for good false for bad. checking A: Noschain::directionAgree(); B: rna.length = sumexonlen

References Range::begin(), mRNAModel::CDSDirection(), mRNAModel::CDSLength(), mRNAModel::CDSRange(), mRNAModel::CDSSeq(), Range::contain(), countInternalStops(), Range::direction(), Range::end(), Noschain::exonIndex(), mRNAModel::frame, 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().

Referenced by readJGIModel().

string JGIModel::toJGIString

(

char

sep = '\t'

)

const

Written out as id <sep> genomicid <sep> name <sep> chain_str <sep> gcdsb <sep> gcdse

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(), Range::end(), mRNAModel::frame, 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. Whether CDS is being pushed or just the transcript.

Reimplemented from Noschain.

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

Referenced by valid().

int JGIModel::getId

(

)

const [inline]

alias for RNAModel::getOid()

References RNAModel::getOid().

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

const string& JGIModel::getName

(

)

const [inline]

References name.

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

ostream & JGIModel::show

(

ostream &

ous

)

const [virtual]

debug function

Reimplemented from mRNAModel.

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

ostream & JGIModel::print

(

ostream &

ous

)

const [virtual]

add name to the ouput of mRNA::print()

Reimplemented from mRNAModel.

References name, and mRNAModel::print().

modeltype JGIModel::objtype

(

)

const [inline, virtual]

use the cached result

Reimplemented from mRNAModel.

References JGI.

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Member Data Documentation

string JGIModel::name [private]

string name from JGI name column of model track table.

Referenced by getName(), print(), and show().

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

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