BioDnaMultiPatternAlignment Class Reference

#include <BioDnaMultiPatternAlignment.h>

List of all members.

Public Member Functions
	~BioDnaMultiPatternAlignment ()
	BioDnaMultiPatternAlignment ()
	BioDnaMultiPatternAlignment (BioDnaSequence, string, string, string MatName, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaMultiPatternAlignment (BioDnaSequence, string, string MatName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaMultiPatternAlignment (BioDnaSequence, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10)
	BioDnaMultiPatternAlignment (BioFasta, string, string, string MatName, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaMultiPatternAlignment (BioFasta, string, string MatName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaMultiPatternAlignment (BioFasta, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10)
	BioDnaMultiPatternAlignment (string, string, string, string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaMultiPatternAlignment (string, string, string matName="IDENTITY", int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
	BioDnaMultiPatternAlignment (string, string, int ReapIden, int MS, int MMS, int GP=-50, int extn=-9999, int TH=10)
void	setSequence (BioDnaSequence)
void	setSequence (BioFasta)
void	setSequence (string)
void	addPattern (string, int ReapIden=100, int GP=-50, int extn=-9999, int TH=10)
void	setSubstitutionMatrix (string)
void	setSubstitutionMatrix (string, string)
void	setMatchMisMatchScore (int MS=1, int MMS=0)
void	setGapPenalty (int GP=-11, int extn=-9999, int index=-1)
void	setRepeatIdentity (int identity, int index=-1)
void	setThreshold (int, int index=-1)
void	setOffsetRange (int st, int ed, int index=-1)
void	setOrder (string)
void	setGaps (int cou, int index=-1)
void	showAlignment (ostream &=cout)
void	showAlignment (BioPostScript &ps, float=100, float=650, float=450)
int	getRepeatStartingPosition (int)
int	getRepeatEndingPosition (int)
int	getNumberOfRepeats ()
int	getScore (int)
string	getRepeat (int)
string	getAlignedRepeat (int)
Friends
bool	operator> (const BioDnaMultiPatternAlignment &, const BioDnaMultiPatternAlignment &)
bool	operator< (const BioDnaMultiPatternAlignment &, const BioDnaMultiPatternAlignment &)
bool	operator== (const BioDnaMultiPatternAlignment &, const BioDnaMultiPatternAlignment &)

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Constructor & Destructor Documentation

BioDnaMultiPatternAlignment::~BioDnaMultiPatternAlignment

(

)

BioDnaMultiPatternAlignment::BioDnaMultiPatternAlignment

(

)

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

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

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

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

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

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

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

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

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

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Member Function Documentation

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

string BioDnaMultiPatternAlignment::getAlignedRepeat

(

int

)

int BioDnaMultiPatternAlignment::getNumberOfRepeats

(

)

string BioDnaMultiPatternAlignment::getRepeat

(

int

)

int BioDnaMultiPatternAlignment::getRepeatEndingPosition

(

int

)

int BioDnaMultiPatternAlignment::getRepeatStartingPosition

(

int

)

int BioDnaMultiPatternAlignment::getScore

(

int

)

void BioDnaMultiPatternAlignment::setGapPenalty	(	int	GP = -11,
		int	extn = -9999,
		int	index = -1
	)

void BioDnaMultiPatternAlignment::setGaps	(	int	cou,
		int	index = -1
	)

void BioDnaMultiPatternAlignment::setMatchMisMatchScore	(	int	MS = 1,
		int	MMS = 0
	)

void BioDnaMultiPatternAlignment::setOffsetRange	(	int	st,
		int	ed,
		int	index = -1
	)

void BioDnaMultiPatternAlignment::setOrder

(

string

)

void BioDnaMultiPatternAlignment::setRepeatIdentity	(	int	identity,
		int	index = -1
	)

void BioDnaMultiPatternAlignment::setSequence

(

BioDnaSequence

)

void BioDnaMultiPatternAlignment::setSequence

(

BioFasta

)

void BioDnaMultiPatternAlignment::setSequence

(

string

)

void BioDnaMultiPatternAlignment::setSubstitutionMatrix

(

string

)

void BioDnaMultiPatternAlignment::setSubstitutionMatrix	(	string	,
		string
	)

void BioDnaMultiPatternAlignment::setThreshold	(	int	,
		int	index = -1
	)

void BioDnaMultiPatternAlignment::showAlignment

(

ostream &

= cout

)

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

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Friends And Related Function Documentation

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

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

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

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

• BioDnaMultiPatternAlignment.h