BioDnaSequenceRepeatAlignment Class Reference

#include <BioDnaSequenceRepeatAlignment.h>

Inheritance diagram for BioDnaSequenceRepeatAlignment:

Collaboration diagram for BioDnaSequenceRepeatAlignment:

List of all members.

Public Member Functions
	BioDnaSequenceRepeatAlignment ()
	BioDnaSequenceRepeatAlignment (BioDnaSequence, BioDnaSequence, string, string MatName, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaSequenceRepeatAlignment (BioDnaSequence, string, string, string MatName, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaSequenceRepeatAlignment (BioDnaSequence, BioDnaSequence, string MatName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaSequenceRepeatAlignment (BioDnaSequence, string, string MatName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaSequenceRepeatAlignment (BioDnaSequence, BioDnaSequence, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10)
	BioDnaSequenceRepeatAlignment (BioDnaSequence, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10)
	BioDnaSequenceRepeatAlignment (BioFasta, BioFasta, string, string MatName, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaSequenceRepeatAlignment (BioFasta, string, string, string MatName, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaSequenceRepeatAlignment (BioFasta, BioFasta, string MatName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaSequenceRepeatAlignment (BioFasta, string, string MatName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaSequenceRepeatAlignment (BioFasta, BioFasta, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10)
	BioDnaSequenceRepeatAlignment (BioFasta, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10)
	BioDnaSequenceRepeatAlignment (string, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaSequenceRepeatAlignment (string, string, string matName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaSequenceRepeatAlignment (string, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10)
void	setThreshold (int)
void	setRepeatIdentity (int)
void	setGaps (int)
void	showAccumulationMatrix (ostream &=cout)
long	getNumberOfRepeats ()
long	getRepeatStartingPosition (long)
long	getRepeatEndingPosition (long)
BioSequence	getRepeat (long)
string	getAlignedRepeat (long)
long	getNumberOfIdentities ()
float	getIdentity (int)
int	getRepeatScore (int)
void	showAlignment (ostream &=cout)
void	showAlignment (BioPostScript &ps, float=100, float=650, float=450)
string	getAlignedSequence1 ()
string	getAlignedSequence2 ()
float	getScore ()
Friends
bool	operator> (const BioDnaSequenceRepeatAlignment &, const BioDnaSequenceRepeatAlignment &)
bool	operator< (const BioDnaSequenceRepeatAlignment &, const BioDnaSequenceRepeatAlignment &)
bool	operator== (const BioDnaSequenceRepeatAlignment &, const BioDnaSequenceRepeatAlignment &)

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Constructor & Destructor Documentation

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment

(

)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	BioDnaSequence	,
		BioDnaSequence	,
		string	,
		string	MatName,
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	BioDnaSequence	,
		string	,
		string	,
		string	MatName,
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	BioDnaSequence	,
		BioDnaSequence	,
		string	MatName = "IDENTITY",
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	BioDnaSequence	,
		string	,
		string	MatName = "IDENTITY",
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	BioDnaSequence	,
		BioDnaSequence	,
		int	ReapIden,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	BioDnaSequence	,
		string	,
		int	ReapIden,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	BioFasta	,
		BioFasta	,
		string	,
		string	MatName,
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	BioFasta	,
		string	,
		string	,
		string	MatName,
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	BioFasta	,
		BioFasta	,
		string	MatName = "IDENTITY",
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	BioFasta	,
		string	,
		string	MatName = "IDENTITY",
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	BioFasta	,
		BioFasta	,
		int	ReapIden,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	BioFasta	,
		string	,
		int	ReapIden,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	string	,
		string	,
		string	,
		string	,
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	string	,
		string	,
		string	matName = "IDENTITY",
		int	ReapIden = 100,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceRepeatAlignment::BioDnaSequenceRepeatAlignment	(	string	,
		string	,
		int	ReapIden,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999,
		int	TH = 10
	)

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Member Function Documentation

string BioDnaSequenceRepeatAlignment::getAlignedRepeat

(

long

)

string BioDnaSequenceRepeatAlignment::getAlignedSequence1

(

)

string BioDnaSequenceRepeatAlignment::getAlignedSequence2

(

)

float BioDnaSequenceRepeatAlignment::getIdentity

(

int

)

long BioDnaSequenceRepeatAlignment::getNumberOfIdentities

(

)

long BioDnaSequenceRepeatAlignment::getNumberOfRepeats

(

)

BioSequence BioDnaSequenceRepeatAlignment::getRepeat

(

long

)

long BioDnaSequenceRepeatAlignment::getRepeatEndingPosition

(

long

)

int BioDnaSequenceRepeatAlignment::getRepeatScore

(

int

)

long BioDnaSequenceRepeatAlignment::getRepeatStartingPosition

(

long

)

float BioDnaSequenceRepeatAlignment::getScore

(

)

void BioDnaSequenceRepeatAlignment::setGaps

(

int

)

void BioDnaSequenceRepeatAlignment::setRepeatIdentity

(

int

)

void BioDnaSequenceRepeatAlignment::setThreshold

(

int

)

void BioDnaSequenceRepeatAlignment::showAccumulationMatrix

(

ostream &

= cout

)

void BioDnaSequenceRepeatAlignment::showAlignment

(

ostream &

= cout

)

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

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Friends And Related Function Documentation

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

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

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

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

• BioDnaSequenceRepeatAlignment.h