Gfeature Class Reference

#include <gfeature.h>

Inheritance diagram for Gfeature:

List of all members.

Public Member Functions
	Gfeature ()
	Gfeature (vector< string > &loc, const string &ftype, map< string, string > *qls) throw (InvalidQualifier)
	~Gfeature ()
void	writeGBTab () const
const string &	getQualifier (const string &key) const
const string &	getType () const
const string &	featureType () const
void	writeGBTab (ostream &ous) const
Static Protected Member Functions
static bool	validq (const string &ql)
Protected Attributes
map< string, string > *	qual
string	type
vector< Range >	exons
bool	has_start
bool	has_end
Private Member Functions
ostream &	writeGBLocation (ostream &ous) const
Static Private Attributes
static ValidQualifier *	vq = ValidQualifier::getValidQualifier()

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Constructor & Destructor Documentation

Gfeature::Gfeature

(

)

[inline]

Gfeature::Gfeature	(	vector< string > &	loc,
		const string &	ftype,
		map< string, string > *	qls
	)			throw (InvalidQualifier)

Parameters:

	loc	is location in string format (<123, 345, 444, >789) must be even number of numbers.
	type	is the feature identifier string This constructor will validate the qualifiers. The external methods do not have to do it. However the external methods could set the qualifer with different list of valid qualifers this will be reflected in this method since I am using a singleton design pattern for the validator.

References qual().

Gfeature::~Gfeature

(

)

[inline]

References qual.

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Member Function Documentation

void Gfeature::writeGBTab

(

)

const

this is a lower level method

const string & Gfeature::getQualifier

(

const string &

key

)

const

References qual.

const string& Gfeature::getType

(

)

const [inline]

References type.

const string& Gfeature::featureType

(

)

const [inline]

References type.

Referenced by GReaderStateC::processInput(), GReaderStateM::processInput(), and GReaderStateS::processInput().

void Gfeature::writeGBTab

(

ostream &

ous

)

const

in gbsubmit format

static bool Gfeature::validq

(

const string &

ql

)

[inline, static, protected]

References ValidQualifier::valid(), and vq.

ostream & Gfeature::writeGBLocation

(

ostream &

ous

)

const [private]

References exons, has_end, and has_start.

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Member Data Documentation

map<string,string>* Gfeature::qual [protected]

qualifier key => value pair, for boolean key, value _TAG_

Referenced by getQualifier(), and ~Gfeature().

string Gfeature::type [protected]

type of feature mRNA, CDS, gene, ... for convinience. This is much better than derived classes, that will be difficult to deal with the changing world. We can have infinite object types!

Referenced by featureType(), and getType().

vector<Range> Gfeature::exons [protected]

Referenced by writeGBLocation().

bool Gfeature::has_start [protected]

Referenced by writeGBLocation().

bool Gfeature::has_end [protected]

Referenced by writeGBLocation().

ValidQualifier * Gfeature::vq = ValidQualifier::getValidQualifier() [static, private]

Referenced by validq().

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

• annotation/gfeature.h
• annotation/gfeature.cpp