BioSequence Class Reference

#include <BioSequence.h>

Inheritance diagram for BioSequence:

List of all members.

Public Member Functions
	BioSequence ()
	BioSequence (const string &filename)
	BioSequence (const string &seqnam, const string &seq)
void	setSequence (const string &seqnam, const string &seq)
void	setSequence (const string &seq)
void	setSequenceName (const string &seqnam)
bool	checkSequence ()
int	readFasta (ifstream &)
string	getSequenceName () const
string	getSequence () const
long	getSequenceLength () const
long	getNumberOfOccurrences (const char &ch)
long	getNumberOfOccurrences (const string &pattern)
bool	findPattern (const string &pat)
bool	find (const string &words)
string	getSequenceSegment (const long &a, const long &b)
void	showPositionsOfPattern (const string &pat, ostream &os=cout)
void	showPositionsOfPattern (const string &pat, BioPostScript &ps, const int &xpos=100, const int &ypos=650, const int &w=450, const int &h=20)
vector< long >	getPositionsOfPattern (const string &pat)
string	getMutatedSequence (const long &, const char &)
string	getMutatedSequence (const long &, const string &)
string	getMutatedSequence (const char &, const char &)
string	getMutatedSequence (const string &, const string &)
string	getMutatedSequence (const long &, const long &, const string &)
string	getInsertedSequence (const long &, const string &)
string	getDeletedSequence (const long &, const long &)
void	showInFasta (ostream &=cout)
string	getMutatedSequence (string &s1)
long	getNumberOfSSRs (const string &pat, const int &repeats)
vector< long >	getPositionsOfSSRs (const string &pat, const int &repeats)
void	showSSRs (const string &pat, const int &repeats, ostream &os=cout)
void	showSSRs (const string &pat, const int &repeats, BioPostScript &ps, const int &xpos=100, const int &ypos=650, const int &w=450, const int &h=20)
string	getShuffledSequence ()
void	showShuffledSequence (ostream &os=cout)
Protected Attributes
string	seqname_
string	sequence_
Friends
bool	operator> (const BioSequence &, const BioSequence &)
bool	operator< (const BioSequence &, const BioSequence &)
bool	operator== (const BioSequence &, const BioSequence &)

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Constructor & Destructor Documentation

BioSequence::BioSequence

(

)

BioSequence::BioSequence

(

const string &

filename

)

BioSequence::BioSequence	(	const string &	seqnam,
		const string &	seq
	)

---

Member Function Documentation

bool BioSequence::checkSequence

(

)

bool BioSequence::find

(

const string &

words

)

bool BioSequence::findPattern

(

const string &

pat

)

string BioSequence::getDeletedSequence	(	const long &	,
		const long &
	)

string BioSequence::getInsertedSequence	(	const long &	,
		const string &
	)

string BioSequence::getMutatedSequence	(	const long &	,
		const char &
	)

string BioSequence::getMutatedSequence	(	const long &	,
		const string &
	)

string BioSequence::getMutatedSequence	(	const char &	,
		const char &
	)

string BioSequence::getMutatedSequence	(	const string &	,
		const string &
	)

string BioSequence::getMutatedSequence	(	const long &	,
		const long &	,
		const string &
	)

string BioSequence::getMutatedSequence

(

string &

s1

)

long BioSequence::getNumberOfOccurrences

(

const char &

ch

)

long BioSequence::getNumberOfOccurrences

(

const string &

pattern

)

long BioSequence::getNumberOfSSRs	(	const string &	pat,
		const int &	repeats
	)

vector<long> BioSequence::getPositionsOfPattern

(

const string &

pat

)

vector< long > BioSequence::getPositionsOfSSRs	(	const string &	pat,
		const int &	repeats
	)

string BioSequence::getSequence

(

)

const

long BioSequence::getSequenceLength

(

)

const

string BioSequence::getSequenceName

(

)

const

string BioSequence::getSequenceSegment	(	const long &	a,
		const long &	b
	)

string BioSequence::getShuffledSequence

(

)

int BioSequence::readFasta

(

ifstream &

)

void BioSequence::setSequence	(	const string &	seqnam,
		const string &	seq
	)

Reimplemented in BioDnaSequence, and BioProteinSequence.

void BioSequence::setSequence

(

const string &

seq

)

Reimplemented in BioDnaSequence.

void BioSequence::setSequenceName

(

const string &

seqnam

)

Reimplemented in BioDnaSequence.

void BioSequence::showInFasta

(

ostream &

= cout

)

Reimplemented in BioFasta.

void BioSequence::showPositionsOfPattern	(	const string &	pat,
		ostream &	os = cout
	)

void BioSequence::showPositionsOfPattern	(	const string &	pat,
		BioPostScript &	ps,
		const int &	xpos = 100,
		const int &	ypos = 650,
		const int &	w = 450,
		const int &	h = 20
	)

void BioSequence::showShuffledSequence

(

ostream &

os = cout

)

void BioSequence::showSSRs	(	const string &	pat,
		const int &	repeats,
		ostream &	os = cout
	)

void BioSequence::showSSRs	(	const string &	pat,
		const int &	repeats,
		BioPostScript &	ps,
		const int &	xpos = 100,
		const int &	ypos = 650,
		const int &	w = 450,
		const int &	h = 20
	)

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Friends And Related Function Documentation

bool operator<	(	const BioSequence &	,
		const BioSequence &
	)		[friend]

bool operator==	(	const BioSequence &	,
		const BioSequence &
	)		[friend]

bool operator>	(	const BioSequence &	,
		const BioSequence &
	)		[friend]

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Member Data Documentation

string BioSequence::seqname_ [protected]

string BioSequence::sequence_ [protected]

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

• BioSequence.h