RNAModel Class Reference

#include <RNAModel.h>

Inheritance diagram for RNAModel:

List of all members.

Public Member Functions
	RNAModel (const Noschain &seg, const string &chrom, const string &gs)
	RNAModel (const string &exstarts, const string &exends, char strand, const string &gi, const string &genomic)
void	setGenomic (const string &gs)
const string &	RNASequence () const
int	genomicIndex (int mrnaidx) const throw (OutsideGenomicSequence)
int	RNAIndex (int gidx) const throw (PointOutChain)
bool	sameExons (const RNAModel &gm) const
int	exonLength () const
bool	operator== (const RNAModel &rmd) const
const string &	genomicId () const
int	RNALength () const
void	resetRNA ()
string	seqGenomic () const
Protected Attributes
string	gid
const string *	gseq
string	rna

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Detailed Description

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

This class should be used to derive ESTModel. I all common operations between JGI model and ESTModel should be implemented in this class.

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Constructor & Destructor Documentation

RNAModel::RNAModel	(	const Noschain &	seg,
		const string &	chrom,
		const string &	gs
	)			[inline, explicit]

References gseq, rna, and Noschain::subsequence().

RNAModel::RNAModel	(	const string &	exstarts,
		const string &	exends,
		char	strand,
		const string &	gi,
		const string &	genomic
	)			[inline]

References gseq, rna, and Noschain::subsequence().

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Member Function Documentation

void RNAModel::setGenomic

(

const string &

gs

)

[inline]

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 gseq.

const string& RNAModel::RNASequence

(

)

const [inline]

write the object in several output streams

References rna.

Referenced by mRNAModel::JGITranscriptRow(), and ESTAssembly::write().

int RNAModel::genomicIndex

(

int

mrnaidx

)

const throw (OutsideGenomicSequence)

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

Referenced by mRNAModel::mRNAModel().

int RNAModel::RNAIndex

(

int

gidx

)

const throw (PointOutChain)

Referenced by mRNAModel::mRNAModel().

bool RNAModel::sameExons

(

const RNAModel &

gm

)

const [inline]

References Noschain::operator==().

int RNAModel::exonLength

(

)

const [inline]

in Noschain this is implemented as sum of exon length This derived class store the same information into the length of the RNA string. No computation is needed. Overwrite parent class method.

Reimplemented from Noschain.

References rna.

Referenced by mRNAModel::ThreePrimeUTRLength(), ESTAssembly::write(), and ESTAssembly::writetab().

bool RNAModel::operator==

(

const RNAModel &

rmd

)

const [inline]

more advanced than comparing the ranges. Now it is comparing the actual RNA sequence which is the spliced product. It could be very expensive comparing long sequences!

References rna.

const string& RNAModel::genomicId

(

)

const [inline]

References gid.

Referenced by JGIModel::toJGIString(), JGIModel::toSQLString(), JGIModel::toString(), ESTAssembly::write(), and ESTAssembly::writetab().

int RNAModel::RNALength

(

)

const [inline]

References rna.

Referenced by JGIModel::valid().

void RNAModel::resetRNA

(

)

[inline]

References gseq, rna, and Noschain::subsequence().

Referenced by JGIModel::valid().

string RNAModel::seqGenomic

(

)

const

References Range::begin(), Range::direction(), Range::end(), gseq, and reverseComplementInPlace().

Referenced by mRNAModel::JGITranscriptRow().

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Member Data Documentation

string RNAModel::gid [protected]

a unique identifier for genomic sequence usually scaffold1, or chromosome1

Referenced by genomicId(), mRNAModel::JGIModelRow(), and JGIModel::show().

const string* RNAModel::gseq [protected]

genomic sequence should be a pointer that are shared by many RNA objects

Referenced by resetRNA(), RNAModel(), seqGenomic(), and setGenomic().

string RNAModel::rna [protected]

for generic RNA model it stores the product of transcription and splicing

Referenced by mRNAModel::CDSSeq(), mRNAModel::CDSSequence(), exonLength(), mRNAModel::JGITranscriptRow(), mRNAModel::mRNAModel(), operator==(), resetRNA(), RNALength(), RNAModel(), RNASequence(), ESTAssembly::write(), and ESTAssembly::writetab().

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

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