GenModel Class Reference

#include <GenModel.h>

Inheritance diagram for GenModel:

List of all members.

Public Member Functions
	GenModel ()
	GenModel (const string &exstarts, const string &exends, char strand, int cdsb, int cdse, const string &gi, int ii, const string &si) throw (InvalidModel)
	GenModel (const string &exstarts, const string &exends, char strand, int cdsb, int cdse, const string &gi, int ii, const string &si, const string &track, int trackid) throw (InvalidModel)
	~GenModel ()
ostream &	show (ostream &ous) const
Noschain	FivePrimeUTR () const
Noschain	ThreePrimeUTR () const
int	num5NoncodingExons () const
int	num3NoncodingExons () const
Noschain	CDS () const throw (PointOutChain)
Range	CDSRange () const
int	FivePrimeUTRLength () const
int	ThreePrimeUTRLength () const
int	UTRLength () const
int	CDSLength () const throw (PointOutChain)
double	CDSFraction () const
int	valid ()
bool	valid (const string &gs)
const string &	genomicId () const
const string &	modelName () const
const string &	getName () const
int	getId () const
string	CDSSeq (const string &gs) const throw (PointOutChain)
void	growEnd (int icr)
void	setEnd (int ne)
string	toString (char sep='\t') const
string	toSQLString (char sep=',') const
string	toJGIModel (char sep='\t') const
ostream &	printAllmod (ostream &ous, char sep='\t') const
bool	operator== (const GenModel &gm) const
bool	sameExons (const GenModel &gm) const
void	makeProtein (const string &gs)
const string &	pepstr () const
bool	hasBegin () const
bool	hasEnd () const
Private Attributes
string	gid
int	id
string	name
Range	cds
int	cdsphase
int	numstop
bool	hasstart
bool	hasstop
Protein *	pep
string	track
int	trackid
Static Private Attributes
static const int	minModelLen = 100
static const int	minCDSLen = 80

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Detailed Description

GenModel class This was originally named GModel. But this conflicts with earlier GModel that I have named in the bioseq directory. This class is for reading from JGI database and do subsequent processing. nrep program use this class. This class will be replaced with better one.

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Constructor & Destructor Documentation

GenModel::GenModel

(

)

[inline]

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

this is an input structure from JGI model track's two columns: sfStarts, sfEnds

Parameters:

	gi	genomic identifier.
	ii	unique integer id
	si	unique string id, usually name from feature table
	cdsb,cdse.	cds genomic bound.

Build a default phase 0 for CDS translation. Usually for input from a regular JGI track.

References Range::begin(), cds, Range::direction(), Range::end(), Noschain::insideExon(), Range::length(), Range::reverse(), and Noschain::setEnd().

GenModel::GenModel	(	const string &	exstarts,
		const string &	exends,
		char	strand,
		int	cdsb,
		int	cdse,
		const string &	gi,
		int	ii,
		const string &	si,
		const string &	track,
		int	trackid
	)			throw (InvalidModel)

add more identifier for tracking purposes

Parameters:

	track.	method of allmodel or featureTable in linkToAss.
	trackid.	id in allmodel or featureId in linkToAss.
	ii.	Has no equivalence in JGI schema, needs to use a counter.

References Range::begin(), cds, Range::direction(), Range::end(), Noschain::insideExon(), Range::length(), Range::reverse(), and Noschain::setEnd().

GenModel::~GenModel

(

)

References pep.

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Member Function Documentation

ostream & GenModel::show

(

ostream &

ous

)

const [virtual]

debug function

Reimplemented from Noschain.

References cds, gid, name, and Noschain::show().

Referenced by valid(), and writeResultToDatabase().

Noschain GenModel::FivePrimeUTR

(

)

const [inline]

References Range::begin(), cds, and Noschain::subchainBeforePoint().

Referenced by checkUTRChimera(), and num5NoncodingExons().

Noschain GenModel::ThreePrimeUTR

(

)

const [inline]

this may contain intron

References cds, Range::end(), and Noschain::subchainAfterPoint().

Referenced by checkUTRChimera(), and num3NoncodingExons().

int GenModel::num5NoncodingExons

(

)

const [inline]

References FivePrimeUTR(), and Noschain::numberOfRanges().

int GenModel::num3NoncodingExons

(

)

const [inline]

References Noschain::numberOfRanges(), and ThreePrimeUTR().

Noschain GenModel::CDS

(

)

const throw (PointOutChain) [inline]

References cds, and Noschain::subchain().

Referenced by CDSLength(), and CDSSeq().

Range GenModel::CDSRange

(

)

const [inline]

References cds.

int GenModel::FivePrimeUTRLength

(

)

const [inline]

References Range::begin(), cds, Noschain::exonLength(), and Noschain::subchainBeforePoint().

Referenced by UTRLength().

int GenModel::ThreePrimeUTRLength

(

)

const [inline]

References cds, Range::end(), Noschain::exonLength(), and Noschain::subchainAfterPoint().

Referenced by UTRLength().

int GenModel::UTRLength

(

)

const [inline]

References FivePrimeUTRLength(), and ThreePrimeUTRLength().

int GenModel::CDSLength

(

)

const throw (PointOutChain) [inline]

References CDS(), and Noschain::exonLength().

Referenced by CDSFraction(), and valid().

double GenModel::CDSFraction

(

)

const [inline]

the CDS length divides the model length

References CDSLength(), and Range::length().

int GenModel::valid

(

)

calling this method will result in trying to fix bad models, if they are bad. If cannot be fixed then return false

Not sure to throw exception or return boolean?

This operation is sequence independent.

Check CDS too short, model too short CDS and model in the same direction CDS inside model if outside model and by less than 4 nt this function will fix the error. otherwise it will return an invalid model.

Should not use in the constructor. This version is for when you don't have sequence information.

Returns:

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

References Range::begin(), cds, Range::contain(), Range::direction(), Range::end(), Range::length(), minCDSLen, minModelLen, and setEnd().

Referenced by main(), ModelFactory::next(), and valid().

bool GenModel::valid

(

const string &

gs

)

when you supply genomic sequence, this function does further checking

CDS is multiple of 3

References cds, CDSLength(), cdsphase, CDSSeq(), Protein::countInternalStops(), Range::direction(), Range::end(), Noschain::exonIndex(), Noschain::exons, growEnd(), hasstart, hasstop, Protein::hasStop(), Range::length(), makeProtein(), minCDSLen, numstop, pep, show(), DNA::translate(), and valid().

const string& GenModel::genomicId

(

)

const [inline]

same as valid

References gid.

Referenced by toJGIModel(), toSQLString(), toString(), writeResultToDatabase(), and writeResultToFile().

const string& GenModel::modelName

(

)

const [inline]

should not modify this return name

References name.

Referenced by writeResultToDatabase(), and writeResultToFile().

const string& GenModel::getName

(

)

const [inline]

References name.

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

int GenModel::getId

(

)

const [inline]

References id.

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

string GenModel::CDSSeq

(

const string &

gs

)

const throw (PointOutChain)

extract the CDS sequence given a genomic sequence as input

References CDS(), Range::direction(), Noschain::getExons(), and reverseComplement().

Referenced by main(), makeProtein(), and valid().

void GenModel::growEnd

(

int

icr

)

this will grow both the CDS and the exon chain ends

Reimplemented from Noschain.

References cds, Range::growEnd(), and Noschain::growEnd().

Referenced by valid().

void GenModel::setEnd

(

int

ne

)

[inline]

not sure how to manage the CDS end

Reimplemented from Noschain.

References cds, Range::setEnd(), and Noschain::setEnd().

Referenced by valid().

string GenModel::toString

(

char

sep = '\t'

)

const

overwrite parent method to produce the same columns as toSQLString method. Produce tab-delimited row for bulk upload id, genomicid,name, exons, mb, me, gcdsb, gcdse, cdsphase, hasstart, hasstop, pep, track, trackid

References Range::begin(), cds, cdsphase, Range::end(), genomicId(), getId(), getName(), bioseq::getSequence(), hasstart, hasstop, pep, Noschain::toString(), track, and trackid.

string GenModel::toSQLString

(

char

sep = ','

)

const

References Range::begin(), cds, cdsphase, Range::end(), genomicId(), getId(), getName(), bioseq::getSequence(), hasstart, hasstop, pep, Noschain::toString(), track, and trackid.

string GenModel::toJGIModel

(

char

sep = '\t'

)

const

return a text row of string separated by sep default TAB to be written to a file that can be uploaded

References cds, Range::direction(), genomicId(), getId(), getName(), Range::largerEnd(), Noschain::numberOfRanges(), Range::smallerEnd(), and Noschain::startEnd().

ostream & GenModel::printAllmod	(	ostream &	ous,
		char	sep = '\t'
	)			const

produce the allmodels schema format | method | varchar(90) | NO | PRI | id | int(11) | NO | PRI | name | varchar(250) | NO | MUL | chrom | varchar(50) | YES | MUL | strand | char(1) | YES | | fstart | int(11) | YES | | fend | int(11) | YES | | cdsstart | int(11) | YES | | cdsend | int(11) | YES | | sfcount | int(11) | YES | | sfstarts | text | YES | | sfends | text | YES | Not this proteinid | int(11) | YES | MUL The object does not store this entry!

References cds, Range::direction(), gid, Range::largerEnd(), name, Noschain::numberOfRanges(), Range::smallerEnd(), Noschain::startEnd(), track, and trackid.

bool GenModel::operator==

(

const GenModel &

gm

)

const [inline]

References cds, and Noschain::operator==().

bool GenModel::sameExons

(

const GenModel &

gm

)

const [inline]

References Noschain::operator==().

void GenModel::makeProtein

(

const string &

gs

)

References cdsphase, CDSSeq(), pep, and DNA::translate().

Referenced by main(), and valid().

const string& GenModel::pepstr

(

)

const [inline]

References bioseq::getSequence(), and pep.

Referenced by main().

bool GenModel::hasBegin

(

)

const [inline]

References hasstart.

bool GenModel::hasEnd

(

)

const [inline]

References hasstop.

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Member Data Documentation

string GenModel::gid [private]

genomic identifier, usually string for convinence, template would be better. Which genomic DNA owns this model. For complete genome, this is usually chromosome number such as Chrom1, chrom_2, some variations.

Referenced by genomicId(), printAllmod(), and show().

int GenModel::id [private]

a unique idetifier for this object in some database table, usualy a primary key We use an integer type. This is the id column of allmodels table.

Referenced by getId().

string GenModel::name [private]

usually a human readable name that is also unique in some database table but not uniqe in the JGI database!

Referenced by getName(), modelName(), printAllmod(), and show().

Range GenModel::cds [private]

where the CDS starts and ends This should be in the same direction as the Model This information is redundant. It is for convinence. This is the genomic postion, not the RNA position.

Referenced by CDS(), CDSRange(), FivePrimeUTR(), FivePrimeUTRLength(), GenModel(), growEnd(), operator==(), printAllmod(), setEnd(), show(), ThreePrimeUTR(), ThreePrimeUTRLength(), toJGIModel(), toSQLString(), toString(), and valid().

int GenModel::cdsphase [private]

0, 1, or 2 for start of translation within the range of CDS

Referenced by makeProtein(), toSQLString(), toString(), and valid().

int GenModel::numstop [private]

record the number of internal stop codons

Referenced by valid().

bool GenModel::hasstart [private]

Referenced by hasBegin(), toSQLString(), toString(), and valid().

bool GenModel::hasstop [private]

Referenced by hasEnd(), toSQLString(), toString(), and valid().

Protein* GenModel::pep [private]

Referenced by makeProtein(), pepstr(), toSQLString(), toString(), valid(), and ~GenModel().

string GenModel::track [private]

for trackin the source from JGI database it is featureTable

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

int GenModel::trackid [private]

same as featureId

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

const int GenModel::minModelLen = 100 [static, private]

with and without intron should be treated differently. CDS length should be enough.

Referenced by valid().

const int GenModel::minCDSLen = 80 [static, private]

shortest CDS to be considered to be valid model

Referenced by valid().

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

• range/GenModel.h
• range/GenModel.cpp