BioDnaSequenceLocalAlignment Class Reference

#include <BioDnaSequenceLocalAlignment.h>

Inheritance diagram for BioDnaSequenceLocalAlignment:

Collaboration diagram for BioDnaSequenceLocalAlignment:

List of all members.

Public Member Functions
	BioDnaSequenceLocalAlignment ()
	BioDnaSequenceLocalAlignment (BioDnaSequence, BioDnaSequence, string, string MatName, int GP=-50, int extn=-9999)
	BioDnaSequenceLocalAlignment (BioDnaSequence, string, string, string MatName, int GP=-50, int extn=-9999)
	BioDnaSequenceLocalAlignment (BioDnaSequence, BioDnaSequence, string mat="IDENTITY", int GP=-50, int extn=-9999)
	BioDnaSequenceLocalAlignment (BioDnaSequence, string, string mat="IDENTITY", int GP=-50, int extn=-9999)
	BioDnaSequenceLocalAlignment (BioDnaSequence, BioDnaSequence, int MS, int MMS, int GP=-50, int extn=-9999)
	BioDnaSequenceLocalAlignment (BioDnaSequence, string, int MS, int MMS, int GP=-50, int extn=-9999)
	BioDnaSequenceLocalAlignment (BioFasta, BioFasta, string, string MatName, int GP=-50, int extn=-9999)
	BioDnaSequenceLocalAlignment (BioFasta, string, string, string MatName, int GP=-50, int extn=-9999)
	BioDnaSequenceLocalAlignment (BioFasta, BioFasta, string mat="IDENTITY", int GP=-50, int extn=-9999)
	BioDnaSequenceLocalAlignment (BioFasta, string, string mat="IDENTITY", int GP=-50, int extn=-9999)
	BioDnaSequenceLocalAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-50, int extn=-9999)
	BioDnaSequenceLocalAlignment (BioFasta, string, int MS, int MMS, int GP=-50, int extn=-9999)
	BioDnaSequenceLocalAlignment (string, string, string, string, int GP=-50, int extn=-9999)
	BioDnaSequenceLocalAlignment (string, string, string mat="IDENTITY", int GP=-50, int extn=-9999)
	BioDnaSequenceLocalAlignment (string, string, int MS, int MMS, int GP=-50, int extn=-9999)
void	showAccumulationMatrix (ostream &=cout)
void	showAlignment (ostream &=cout)
long	getSequence1AlignedPosition ()
long	getSequence2AlignedPosition ()
long	getNumberOfIdentities ()
float	getIdentity ()
float	getScore ()
string	getAlignedSequence1 ()
string	getAlignedSequence2 ()

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Constructor & Destructor Documentation

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment

(

)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	BioDnaSequence	,
		BioDnaSequence	,
		string	,
		string	MatName,
		int	GP = -50,
		int	extn = -9999
	)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	BioDnaSequence	,
		string	,
		string	,
		string	MatName,
		int	GP = -50,
		int	extn = -9999
	)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	BioDnaSequence	,
		BioDnaSequence	,
		string	mat = "IDENTITY",
		int	GP = -50,
		int	extn = -9999
	)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	BioDnaSequence	,
		string	,
		string	mat = "IDENTITY",
		int	GP = -50,
		int	extn = -9999
	)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	BioDnaSequence	,
		BioDnaSequence	,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999
	)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	BioDnaSequence	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999
	)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	BioFasta	,
		BioFasta	,
		string	,
		string	MatName,
		int	GP = -50,
		int	extn = -9999
	)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	BioFasta	,
		string	,
		string	,
		string	MatName,
		int	GP = -50,
		int	extn = -9999
	)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	BioFasta	,
		BioFasta	,
		string	mat = "IDENTITY",
		int	GP = -50,
		int	extn = -9999
	)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	BioFasta	,
		string	,
		string	mat = "IDENTITY",
		int	GP = -50,
		int	extn = -9999
	)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	BioFasta	,
		BioFasta	,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999
	)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	BioFasta	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999
	)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	string	,
		string	,
		string	,
		string	,
		int	GP = -50,
		int	extn = -9999
	)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	string	,
		string	,
		string	mat = "IDENTITY",
		int	GP = -50,
		int	extn = -9999
	)

BioDnaSequenceLocalAlignment::BioDnaSequenceLocalAlignment	(	string	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999
	)

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Member Function Documentation

string BioDnaSequenceLocalAlignment::getAlignedSequence1

(

)

string BioDnaSequenceLocalAlignment::getAlignedSequence2

(

)

float BioDnaSequenceLocalAlignment::getIdentity

(

)

long BioDnaSequenceLocalAlignment::getNumberOfIdentities

(

)

float BioDnaSequenceLocalAlignment::getScore

(

)

long BioDnaSequenceLocalAlignment::getSequence1AlignedPosition

(

)

long BioDnaSequenceLocalAlignment::getSequence2AlignedPosition

(

)

void BioDnaSequenceLocalAlignment::showAccumulationMatrix

(

ostream &

= cout

)

void BioDnaSequenceLocalAlignment::showAlignment

(

ostream &

= cout

)

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

• BioDnaSequenceLocalAlignment.h