BioDnaSequenceOverlapAlignment Class Reference

#include <BioDnaSequenceOverlapAlignment.h>

Inheritance diagram for BioDnaSequenceOverlapAlignment:

Collaboration diagram for BioDnaSequenceOverlapAlignment:

List of all members.

Public Member Functions
	BioDnaSequenceOverlapAlignment ()
	BioDnaSequenceOverlapAlignment (BioDnaSequence, BioDnaSequence, string, string MatName, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioDnaSequence, string, string, string MatName, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioDnaSequence, BioDnaSequence, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioDnaSequence, string, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioDnaSequence, BioDnaSequence, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioDnaSequence, string, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioGenBank, BioGenBank, string, string MatName, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioGenBank, string, string, string MatName, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioGenBank, BioGenBank, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioGenBank, string, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioGenBank, BioGenBank, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioGenBank, string, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioFasta, BioFasta, string, string MatName, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioFasta, string, string, string MatName, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioFasta, BioFasta, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioFasta, string, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioEmbl, BioEmbl, string, string MatName, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioEmbl, string, string, string MatName, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioEmbl, BioEmbl, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioEmbl, string, string MatName="IDENTITY", int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioEmbl, BioEmbl, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (BioEmbl, string, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (string, string, string, string, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (string, string, string, int GP=-11, int extn=-9999, int TH=10)
	BioDnaSequenceOverlapAlignment (string, string, int MS, int MMS, int GP=-11, int extn=-9999, int TH=10)
void	setThreshold (int)
void	showAccumulationMatrix (ostream &=cout)
void	showAlignment (ostream &=cout)
long	getNumberOfIdentities ()
float	getIdentity ()
float	getScore ()
string	getAlignedSequence1 ()
string	getAlignedSequence2 ()

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Constructor & Destructor Documentation

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment

(

)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioDnaSequence	,
		BioDnaSequence	,
		string	,
		string	MatName,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioDnaSequence	,
		string	,
		string	,
		string	MatName,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioDnaSequence	,
		BioDnaSequence	,
		string	MatName = "IDENTITY",
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioDnaSequence	,
		string	,
		string	MatName = "IDENTITY",
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioDnaSequence	,
		BioDnaSequence	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioDnaSequence	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioGenBank	,
		BioGenBank	,
		string	,
		string	MatName,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioGenBank	,
		string	,
		string	,
		string	MatName,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioGenBank	,
		BioGenBank	,
		string	MatName = "IDENTITY",
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioGenBank	,
		string	,
		string	MatName = "IDENTITY",
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioGenBank	,
		BioGenBank	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioGenBank	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioFasta	,
		BioFasta	,
		string	,
		string	MatName,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioFasta	,
		string	,
		string	,
		string	MatName,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioFasta	,
		BioFasta	,
		string	MatName = "IDENTITY",
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioFasta	,
		string	,
		string	MatName = "IDENTITY",
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioFasta	,
		BioFasta	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioFasta	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioEmbl	,
		BioEmbl	,
		string	,
		string	MatName,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioEmbl	,
		string	,
		string	,
		string	MatName,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioEmbl	,
		BioEmbl	,
		string	MatName = "IDENTITY",
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioEmbl	,
		string	,
		string	MatName = "IDENTITY",
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioEmbl	,
		BioEmbl	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	BioEmbl	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	string	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

BioDnaSequenceOverlapAlignment::BioDnaSequenceOverlapAlignment	(	string	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999,
		int	TH = 10
	)

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Member Function Documentation

string BioDnaSequenceOverlapAlignment::getAlignedSequence1

(

)

string BioDnaSequenceOverlapAlignment::getAlignedSequence2

(

)

float BioDnaSequenceOverlapAlignment::getIdentity

(

)

long BioDnaSequenceOverlapAlignment::getNumberOfIdentities

(

)

float BioDnaSequenceOverlapAlignment::getScore

(

)

void BioDnaSequenceOverlapAlignment::setThreshold

(

int

)

void BioDnaSequenceOverlapAlignment::showAccumulationMatrix

(

ostream &

= cout

)

void BioDnaSequenceOverlapAlignment::showAlignment

(

ostream &

= cout

)

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

• BioDnaSequenceOverlapAlignment.h