BioProteinSequenceGlobalAlignment Class Reference

#include <BioProteinSequenceGlobalAlignment.h>

Inheritance diagram for BioProteinSequenceGlobalAlignment:

Collaboration diagram for BioProteinSequenceGlobalAlignment:

List of all members.

Public Member Functions
	BioProteinSequenceGlobalAlignment ()
	BioProteinSequenceGlobalAlignment (BioProteinSequence, BioProteinSequence, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioProteinSequence, BioProteinSequence, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioProteinSequence, BioProteinSequence, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioProteinSequence, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioProteinSequence, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioProteinSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioSwissProt, BioSwissProt, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioSwissProt, BioSwissProt, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioSwissProt, BioSwissProt, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioSwissProt, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioSwissProt, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioSwissProt, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioFasta, BioFasta, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioFasta, BioFasta, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioFasta, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioFasta, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (string, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (string, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceGlobalAlignment (string, string, int MS, int MMS, int GP=-11, int extn=-9999)
void	showAccumulationMatrix (ostream &=cout)
void	showAlignment (ostream &=cout)
long	getNumberOfIdentities ()
long	getNumberOfSimilarities ()
float	getIdentity ()
float	getScore ()
string	getAlignedSequence1 ()
string	getAlignedSequence2 ()
string	getConsensusSequence ()

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Constructor & Destructor Documentation

BioProteinSequenceGlobalAlignment::BioProteinSequenceGlobalAlignment

(

)

BioProteinSequenceGlobalAlignment::BioProteinSequenceGlobalAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)

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

BioProteinSequenceGlobalAlignment::BioProteinSequenceGlobalAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)

BioProteinSequenceGlobalAlignment::BioProteinSequenceGlobalAlignment	(	BioProteinSequence	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)

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

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

BioProteinSequenceGlobalAlignment::BioProteinSequenceGlobalAlignment	(	BioSwissProt	,
		BioSwissProt	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)

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

BioProteinSequenceGlobalAlignment::BioProteinSequenceGlobalAlignment	(	BioSwissProt	,
		BioSwissProt	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)

BioProteinSequenceGlobalAlignment::BioProteinSequenceGlobalAlignment	(	BioSwissProt	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)

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

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

BioProteinSequenceGlobalAlignment::BioProteinSequenceGlobalAlignment	(	BioFasta	,
		BioFasta	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)

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

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

BioProteinSequenceGlobalAlignment::BioProteinSequenceGlobalAlignment	(	BioFasta	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)

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

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

BioProteinSequenceGlobalAlignment::BioProteinSequenceGlobalAlignment	(	string	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)

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

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

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Member Function Documentation

string BioProteinSequenceGlobalAlignment::getAlignedSequence1

(

)

string BioProteinSequenceGlobalAlignment::getAlignedSequence2

(

)

string BioProteinSequenceGlobalAlignment::getConsensusSequence

(

)

float BioProteinSequenceGlobalAlignment::getIdentity

(

)

long BioProteinSequenceGlobalAlignment::getNumberOfIdentities

(

)

long BioProteinSequenceGlobalAlignment::getNumberOfSimilarities

(

)

float BioProteinSequenceGlobalAlignment::getScore

(

)

void BioProteinSequenceGlobalAlignment::showAccumulationMatrix

(

ostream &

= cout

)

void BioProteinSequenceGlobalAlignment::showAlignment

(

ostream &

= cout

)

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

• BioProteinSequenceGlobalAlignment.h