BioProteinSequenceRepeatAlignment Class Reference

#include <BioProteinSequenceRepeatAlignment.h>

Inheritance diagram for BioProteinSequenceRepeatAlignment:

Collaboration diagram for BioProteinSequenceRepeatAlignment:

List of all members.

Public Member Functions
	BioProteinSequenceRepeatAlignment ()
	BioProteinSequenceRepeatAlignment (BioProteinSequence, BioProteinSequence, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioProteinSequence, BioProteinSequence, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioProteinSequence, BioProteinSequence, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioProteinSequence, string, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioProteinSequence, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioProteinSequence, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioSwissProt, BioSwissProt, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioSwissProt, BioSwissProt, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioSwissProt, BioSwissProt, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioSwissProt, string, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioSwissProt, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioSwissProt, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioFasta, BioFasta, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioFasta, BioFasta, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioFasta, BioFasta, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioFasta, string, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioFasta, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (BioFasta, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (string, string, string="BLOSUM62", int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (string, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=20)
	BioProteinSequenceRepeatAlignment (string, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=20)
void	setThreshold (int)
void	setRepeatIdentity (int)
void	setGaps (int)
void	showAccumulationMatrix (ostream &=cout)
void	showAlignment (ostream &=cout)
long	getNumberOfRepeats ()
long	getRepeatStartingPosition (long)
long	getRepeatEndingPosition (long)
BioSequence	getRepeat (long)
string	getAlignedRepeat (long)
void	showAlignment (BioPostScript &ps, float=100, float=650, float=450)
long	getNumberOfIdentities ()
long	getNumberOfSimilarities ()
float	getIdentity (int)
int	getRepeatScore (int)
float	getScore ()
string	getAlignedSequence1 ()
string	getAlignedSequence2 ()
Friends
bool	operator> (const BioProteinSequenceRepeatAlignment &, const BioProteinSequenceRepeatAlignment &)
bool	operator< (const BioProteinSequenceRepeatAlignment &, const BioProteinSequenceRepeatAlignment &)
bool	operator== (const BioProteinSequenceRepeatAlignment &, const BioProteinSequenceRepeatAlignment &)

---

Constructor & Destructor Documentation

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment

(

)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		string	= "BLOSUM62",
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		string	,
		string	,
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		int	ReapIden,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioProteinSequence	,
		string	,
		string	= "BLOSUM62",
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioProteinSequence	,
		string	,
		string	,
		string	,
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioProteinSequence	,
		string	,
		int	ReapIden,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioSwissProt	,
		BioSwissProt	,
		string	= "BLOSUM62",
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioSwissProt	,
		BioSwissProt	,
		string	,
		string	,
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioSwissProt	,
		BioSwissProt	,
		int	ReapIden,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioSwissProt	,
		string	,
		string	= "BLOSUM62",
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioSwissProt	,
		string	,
		string	,
		string	,
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioSwissProt	,
		string	,
		int	ReapIden,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioFasta	,
		BioFasta	,
		string	= "BLOSUM62",
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioFasta	,
		BioFasta	,
		string	,
		string	,
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioFasta	,
		BioFasta	,
		int	ReapIden,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioFasta	,
		string	,
		string	= "BLOSUM62",
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioFasta	,
		string	,
		string	,
		string	,
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	BioFasta	,
		string	,
		int	ReapIden,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	string	,
		string	,
		string	= "BLOSUM62",
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	string	,
		string	,
		string	,
		string	,
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

BioProteinSequenceRepeatAlignment::BioProteinSequenceRepeatAlignment	(	string	,
		string	,
		int	ReapIden,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 20
	)

---

Member Function Documentation

string BioProteinSequenceRepeatAlignment::getAlignedRepeat

(

long

)

string BioProteinSequenceRepeatAlignment::getAlignedSequence1

(

)

string BioProteinSequenceRepeatAlignment::getAlignedSequence2

(

)

float BioProteinSequenceRepeatAlignment::getIdentity

(

int

)

long BioProteinSequenceRepeatAlignment::getNumberOfIdentities

(

)

long BioProteinSequenceRepeatAlignment::getNumberOfRepeats

(

)

long BioProteinSequenceRepeatAlignment::getNumberOfSimilarities

(

)

BioSequence BioProteinSequenceRepeatAlignment::getRepeat

(

long

)

long BioProteinSequenceRepeatAlignment::getRepeatEndingPosition

(

long

)

int BioProteinSequenceRepeatAlignment::getRepeatScore

(

int

)

long BioProteinSequenceRepeatAlignment::getRepeatStartingPosition

(

long

)

float BioProteinSequenceRepeatAlignment::getScore

(

)

void BioProteinSequenceRepeatAlignment::setGaps

(

int

)

void BioProteinSequenceRepeatAlignment::setRepeatIdentity

(

int

)

void BioProteinSequenceRepeatAlignment::setThreshold

(

int

)

void BioProteinSequenceRepeatAlignment::showAccumulationMatrix

(

ostream &

= cout

)

void BioProteinSequenceRepeatAlignment::showAlignment

(

ostream &

= cout

)

void BioProteinSequenceRepeatAlignment::showAlignment	(	BioPostScript &	ps,
		float	= 100,
		float	= 650,
		float	= 450
	)

---

Friends And Related Function Documentation

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

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

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

---

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

• BioProteinSequenceRepeatAlignment.h