BioDnaSequenceGlobalAlignment Class Reference

#include <BioDnaSequenceGlobalAlignment.h>

Inheritance diagram for BioDnaSequenceGlobalAlignment:

Collaboration diagram for BioDnaSequenceGlobalAlignment:

List of all members.

Public Member Functions
	BioDnaSequenceGlobalAlignment ()
	BioDnaSequenceGlobalAlignment (BioDnaSequence, BioDnaSequence, string, string MatName, int GP=-11, int extn=-9999)
	BioDnaSequenceGlobalAlignment (BioDnaSequence, string, string, string MatName, int GP=-11, int extn=-9999)
	BioDnaSequenceGlobalAlignment (BioDnaSequence, BioDnaSequence, string mat="IDENTITY", int GP=-11, int extn=-9999)
	BioDnaSequenceGlobalAlignment (BioDnaSequence, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
	BioDnaSequenceGlobalAlignment (BioDnaSequence, BioDnaSequence, int MS, int MMS, int GP=-11, int extn=-9999)
	BioDnaSequenceGlobalAlignment (BioDnaSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioDnaSequenceGlobalAlignment (BioFasta, BioFasta, string, string MatName, int GP=-11, int extn=-9999)
	BioDnaSequenceGlobalAlignment (BioFasta, string, string, string MatName, int GP=-11, int extn=-9999)
	BioDnaSequenceGlobalAlignment (BioFasta, BioFasta, string mat="IDENTITY", int GP=-11, int extn=-9999)
	BioDnaSequenceGlobalAlignment (BioFasta, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
	BioDnaSequenceGlobalAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)
	BioDnaSequenceGlobalAlignment (BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioDnaSequenceGlobalAlignment (string, string, string, string, int GP=-11, int extn=-9999)
	BioDnaSequenceGlobalAlignment (string, string, string mat="IDENTITY", int GP=-11, int extn=-9999)
	BioDnaSequenceGlobalAlignment (string, string, int MS, int MMS, int GP=-11, int extn=-9999)
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

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment

(

)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	BioDnaSequence	,
		BioDnaSequence	,
		string	,
		string	MatName,
		int	GP = -11,
		int	extn = -9999
	)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	BioDnaSequence	,
		string	,
		string	,
		string	MatName,
		int	GP = -11,
		int	extn = -9999
	)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	BioDnaSequence	,
		BioDnaSequence	,
		string	mat = "IDENTITY",
		int	GP = -11,
		int	extn = -9999
	)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	BioDnaSequence	,
		string	,
		string	mat = "IDENTITY",
		int	GP = -11,
		int	extn = -9999
	)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	BioDnaSequence	,
		BioDnaSequence	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	BioDnaSequence	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	BioFasta	,
		BioFasta	,
		string	,
		string	MatName,
		int	GP = -11,
		int	extn = -9999
	)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	BioFasta	,
		string	,
		string	,
		string	MatName,
		int	GP = -11,
		int	extn = -9999
	)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	BioFasta	,
		BioFasta	,
		string	mat = "IDENTITY",
		int	GP = -11,
		int	extn = -9999
	)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	BioFasta	,
		string	,
		string	mat = "IDENTITY",
		int	GP = -11,
		int	extn = -9999
	)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	BioFasta	,
		BioFasta	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	BioFasta	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	string	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	string	,
		string	,
		string	mat = "IDENTITY",
		int	GP = -11,
		int	extn = -9999
	)

BioDnaSequenceGlobalAlignment::BioDnaSequenceGlobalAlignment	(	string	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)

---

Member Function Documentation

string BioDnaSequenceGlobalAlignment::getAlignedSequence1

(

)

string BioDnaSequenceGlobalAlignment::getAlignedSequence2

(

)

float BioDnaSequenceGlobalAlignment::getIdentity

(

)

long BioDnaSequenceGlobalAlignment::getNumberOfIdentities

(

)

float BioDnaSequenceGlobalAlignment::getScore

(

)

void BioDnaSequenceGlobalAlignment::showAccumulationMatrix

(

ostream &

= cout

)

void BioDnaSequenceGlobalAlignment::showAlignment

(

ostream &

= cout

)

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

• BioDnaSequenceGlobalAlignment.h