BioProteinSequenceLocalAlignment Class Reference

#include <BioProteinSequenceLocalAlignment.h>

Inheritance diagram for BioProteinSequenceLocalAlignment:

Collaboration diagram for BioProteinSequenceLocalAlignment:

List of all members.

Public Member Functions
	BioProteinSequenceLocalAlignment ()
	~BioProteinSequenceLocalAlignment ()
	BioProteinSequenceLocalAlignment (BioProteinSequence, BioProteinSequence, string mat="BLOSUM62", int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioProteinSequence, BioProteinSequence, string, string, int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioProteinSequence, BioProteinSequence, int MS, int MMS, int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioProteinSequence, string, string mat="BLOSUM62", int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioProteinSequence, string, string, string, int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioProteinSequence, string, int MS, int MMS, int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioSwissProt, BioSwissProt, string mat="BLOSUM62", int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioSwissProt, BioSwissProt, string, string, int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioSwissProt, BioSwissProt, int MS, int MMS, int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioSwissProt, string, string mat="BLOSUM62", int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioSwissProt, string, string, string, int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioSwissProt, string, int MS, int MMS, int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (const BioFasta &, const BioFasta &, const string &mat="BLOSUM62", const int &GP=-50, const int &extn=-9999)
	BioProteinSequenceLocalAlignment (BioFasta, BioFasta, string, string, int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioFasta, string, string mat="BLOSUM62", int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioFasta, string, string, string, int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (BioFasta, string, int MS, int MMS, int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (const string &, const string &, const string &mat="BLOSUM62", int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (const string &, const string &, const string &, const string &, int GP=-50, int extn=-9999)
	BioProteinSequenceLocalAlignment (const string &, const 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 ()
long	getNumberOfSimilarities ()
float	getIdentity ()
float	getScore ()
string	getAlignedSequence1 ()
string	getAlignedSequence2 ()

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Constructor & Destructor Documentation

BioProteinSequenceLocalAlignment::BioProteinSequenceLocalAlignment

(

)

BioProteinSequenceLocalAlignment::~BioProteinSequenceLocalAlignment

(

)

BioProteinSequenceLocalAlignment::BioProteinSequenceLocalAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		string	mat = "BLOSUM62",
		int	GP = -50,
		int	extn = -9999
	)

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

BioProteinSequenceLocalAlignment::BioProteinSequenceLocalAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999
	)

BioProteinSequenceLocalAlignment::BioProteinSequenceLocalAlignment	(	BioProteinSequence	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -50,
		int	extn = -9999
	)

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

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

BioProteinSequenceLocalAlignment::BioProteinSequenceLocalAlignment	(	BioSwissProt	,
		BioSwissProt	,
		string	mat = "BLOSUM62",
		int	GP = -50,
		int	extn = -9999
	)

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

BioProteinSequenceLocalAlignment::BioProteinSequenceLocalAlignment	(	BioSwissProt	,
		BioSwissProt	,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999
	)

BioProteinSequenceLocalAlignment::BioProteinSequenceLocalAlignment	(	BioSwissProt	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -50,
		int	extn = -9999
	)

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

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

BioProteinSequenceLocalAlignment::BioProteinSequenceLocalAlignment	(	const BioFasta &	,
		const BioFasta &	,
		const string &	mat = "BLOSUM62",
		const int &	GP = -50,
		const int &	extn = -9999
	)

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

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

BioProteinSequenceLocalAlignment::BioProteinSequenceLocalAlignment	(	BioFasta	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -50,
		int	extn = -9999
	)

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

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

BioProteinSequenceLocalAlignment::BioProteinSequenceLocalAlignment	(	const string &	,
		const string &	,
		const string &	mat = "BLOSUM62",
		int	GP = -50,
		int	extn = -9999
	)

BioProteinSequenceLocalAlignment::BioProteinSequenceLocalAlignment	(	const string &	,
		const string &	,
		const string &	,
		const string &	,
		int	GP = -50,
		int	extn = -9999
	)

BioProteinSequenceLocalAlignment::BioProteinSequenceLocalAlignment	(	const string &	,
		const string &	,
		int	MS,
		int	MMS,
		int	GP = -50,
		int	extn = -9999
	)

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Member Function Documentation

string BioProteinSequenceLocalAlignment::getAlignedSequence1

(

)

string BioProteinSequenceLocalAlignment::getAlignedSequence2

(

)

float BioProteinSequenceLocalAlignment::getIdentity

(

)

long BioProteinSequenceLocalAlignment::getNumberOfIdentities

(

)

long BioProteinSequenceLocalAlignment::getNumberOfSimilarities

(

)

float BioProteinSequenceLocalAlignment::getScore

(

)

long BioProteinSequenceLocalAlignment::getSequence1AlignedPosition

(

)

long BioProteinSequenceLocalAlignment::getSequence2AlignedPosition

(

)

void BioProteinSequenceLocalAlignment::showAccumulationMatrix

(

ostream &

= cout

)

void BioProteinSequenceLocalAlignment::showAlignment

(

ostream &

= cout

)

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

• BioProteinSequenceLocalAlignment.h