BioProteinSequenceAlignment Class Reference

#include <BioProteinSequenceAlignment.h>

Inheritance diagram for BioProteinSequenceAlignment:

Collaboration diagram for BioProteinSequenceAlignment:

List of all members.

Public Member Functions
void	setSequence1 (BioProteinSequence)
void	setSequence2 (BioProteinSequence)
void	setSequence1 (BioSwissProt)
void	setSequence2 (BioSwissProt)
void	setSequence1 (BioFasta)
void	setSequence2 (BioFasta)
void	setSequence1 (const string &)
void	setSequence2 (const string &)
void	setGapPenalty (int GP=-11, int extn=-9999)
void	setSubstitutionMatrix (const string &)
void	setSubstitutionMatrix (const string &, const string &)
void	setMatchMisMatchScore (int MS=1, int MMS=0)
void	showScoringMatrix (ostream &=cout)
void	setSequence1 (BioProteinSequence)
void	setSequence2 (BioProteinSequence)
void	setSequence1 (BioSwissProt)
void	setSequence2 (BioSwissProt)
void	setSequence1 (BioFasta)
void	setSequence2 (BioFasta)
void	setSequence1 (const string &)
void	setSequence2 (const string &)
void	setGapPenalty (int GP=-11, int extn=-9999)
void	setSubstitutionMatrix (const string &)
void	setSubstitutionMatrix (const string &, const string &)
void	setMatchMisMatchScore (int MS=1, int MMS=0)
void	showScoringMatrix (ostream &=cout)
void	setSequence1 (BioProteinSequence)
void	setSequence2 (BioProteinSequence)
void	setSequence1 (BioSwissProt)
void	setSequence2 (BioSwissProt)
void	setSequence1 (BioFasta)
void	setSequence2 (BioFasta)
void	setSequence1 (const string &)
void	setSequence2 (const string &)
void	setGapPenalty (int GP=-11, int extn=-9999)
void	setSubstitutionMatrix (const string &)
void	setSubstitutionMatrix (const string &, const string &)
void	setMatchMisMatchScore (int MS=1, int MMS=0)
void	showScoringMatrix (ostream &=cout)
void	setSequence1 (BioProteinSequence)
void	setSequence2 (BioProteinSequence)
void	setSequence1 (BioSwissProt)
void	setSequence2 (BioSwissProt)
void	setSequence1 (BioFasta)
void	setSequence2 (BioFasta)
void	setSequence1 (const string &)
void	setSequence2 (const string &)
void	setGapPenalty (int GP=-11, int extn=-9999)
void	setSubstitutionMatrix (const string &)
void	setSubstitutionMatrix (const string &, const string &)
void	setMatchMisMatchScore (int MS=1, int MMS=0)
void	showScoringMatrix (ostream &=cout)
void	setSequence1 (BioProteinSequence)
void	setSequence2 (BioProteinSequence)
void	setSequence1 (BioSwissProt)
void	setSequence2 (BioSwissProt)
void	setSequence1 (BioFasta)
void	setSequence2 (BioFasta)
void	setSequence1 (const string &)
void	setSequence2 (const string &)
void	setGapPenalty (int GP=-11, int extn=-9999)
void	setSubstitutionMatrix (const string &)
void	setSubstitutionMatrix (const string &, const string &)
void	setMatchMisMatchScore (int MS=1, int MMS=0)
void	showScoringMatrix (ostream &=cout)
Protected Member Functions
void	formScoringMatrix ()
int	getAccValMov (long, long, int)
void	init ()
	BioProteinSequenceAlignment ()
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const BioFasta &, const BioFasta &, const string &mat="BLOSUM62", const int &GP=-11, const int &extn=-9999)
	BioProteinSequenceAlignment (BioFasta, BioFasta, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, const string &mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, const string &, const string &, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, int MS, int MMS, int GP=-11, int extn=-9999)
void	formScoringMatrix ()
int	getAccValMov (long, long, int)
void	init ()
	BioProteinSequenceAlignment ()
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const BioFasta &, const BioFasta &, const string &mat="BLOSUM62", const int &GP=-11, const int &extn=-9999)
	BioProteinSequenceAlignment (BioFasta, BioFasta, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, const string &mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, const string &, const string &, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, int MS, int MMS, int GP=-11, int extn=-9999)
void	formScoringMatrix ()
int	getAccValMov (long, long, int)
void	init ()
	BioProteinSequenceAlignment ()
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const BioFasta &, const BioFasta &, const string &mat="BLOSUM62", const int &GP=-11, const int &extn=-9999)
	BioProteinSequenceAlignment (BioFasta, BioFasta, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, const string &mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, const string &, const string &, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, int MS, int MMS, int GP=-11, int extn=-9999)
void	formScoringMatrix ()
int	getAccValMov (long, long, int)
void	init ()
	BioProteinSequenceAlignment ()
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const BioFasta &, const BioFasta &, const string &mat="BLOSUM62", const int &GP=-11, const int &extn=-9999)
	BioProteinSequenceAlignment (BioFasta, BioFasta, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, const string &mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, const string &, const string &, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, int MS, int MMS, int GP=-11, int extn=-9999)
void	formScoringMatrix ()
int	getAccValMov (long, long, int)
void	init ()
	BioProteinSequenceAlignment ()
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, BioProteinSequence, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioProteinSequence, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, BioSwissProt, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioSwissProt, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const BioFasta &, const BioFasta &, const string &mat="BLOSUM62", const int &GP=-11, const int &extn=-9999)
	BioProteinSequenceAlignment (BioFasta, BioFasta, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, BioFasta, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, string mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, string, string, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (BioFasta, string, int MS, int MMS, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, const string &mat="BLOSUM62", int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, const string &, const string &, int GP=-11, int extn=-9999)
	BioProteinSequenceAlignment (const string &, const string &, int MS, int MMS, int GP=-11, int extn=-9999)
Protected Attributes
string	seq1_
string	seq2_
string	conseq_
string	outSeq1_
string	outSeq2_
string	seqName1_
string	seqName2_
int	gapPenalty
int	gapExtn
BioMatrix	substitutionMatrix
BioMatrix	scoringMatrix
int	status
Static Protected Attributes
static string	aminoAcidSeq_

---

Constructor & Destructor Documentation

BioProteinSequenceAlignment::BioProteinSequenceAlignment

(

)

[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const BioFasta &	,
		const BioFasta &	,
		const string &	mat = "BLOSUM62",
		const int &	GP = -11,
		const int &	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		BioFasta	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		BioFasta	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		const string &	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		const string &	,
		const string &	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment

(

)

[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const BioFasta &	,
		const BioFasta &	,
		const string &	mat = "BLOSUM62",
		const int &	GP = -11,
		const int &	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		BioFasta	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		BioFasta	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		const string &	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		const string &	,
		const string &	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment

(

)

[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const BioFasta &	,
		const BioFasta &	,
		const string &	mat = "BLOSUM62",
		const int &	GP = -11,
		const int &	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		BioFasta	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		BioFasta	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		const string &	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		const string &	,
		const string &	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment

(

)

[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const BioFasta &	,
		const BioFasta &	,
		const string &	mat = "BLOSUM62",
		const int &	GP = -11,
		const int &	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		BioFasta	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		BioFasta	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		const string &	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		const string &	,
		const string &	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment

(

)

[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		BioProteinSequence	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioProteinSequence	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		BioSwissProt	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioSwissProt	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const BioFasta &	,
		const BioFasta &	,
		const string &	mat = "BLOSUM62",
		const int &	GP = -11,
		const int &	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		BioFasta	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		BioFasta	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		string	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		string	,
		string	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	BioFasta	,
		string	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		const string &	mat = "BLOSUM62",
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		const string &	,
		const string &	,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

BioProteinSequenceAlignment::BioProteinSequenceAlignment	(	const string &	,
		const string &	,
		int	MS,
		int	MMS,
		int	GP = -11,
		int	extn = -9999
	)		[protected]

---

Member Function Documentation

void BioProteinSequenceAlignment::formScoringMatrix

(

)

[protected]

void BioProteinSequenceAlignment::formScoringMatrix

(

)

[protected]

void BioProteinSequenceAlignment::formScoringMatrix

(

)

[protected]

void BioProteinSequenceAlignment::formScoringMatrix

(

)

[protected]

void BioProteinSequenceAlignment::formScoringMatrix

(

)

[protected]

int BioProteinSequenceAlignment::getAccValMov	(	long	,
		long	,
		int
	)		[protected]

int BioProteinSequenceAlignment::getAccValMov	(	long	,
		long	,
		int
	)		[protected]

int BioProteinSequenceAlignment::getAccValMov	(	long	,
		long	,
		int
	)		[protected]

int BioProteinSequenceAlignment::getAccValMov	(	long	,
		long	,
		int
	)		[protected]

int BioProteinSequenceAlignment::getAccValMov	(	long	,
		long	,
		int
	)		[protected]

void BioProteinSequenceAlignment::init

(

)

[protected]

void BioProteinSequenceAlignment::init

(

)

[protected]

void BioProteinSequenceAlignment::init

(

)

[protected]

void BioProteinSequenceAlignment::init

(

)

[protected]

void BioProteinSequenceAlignment::init

(

)

[protected]

void BioProteinSequenceAlignment::setGapPenalty	(	int	GP = -11,
		int	extn = -9999
	)

void BioProteinSequenceAlignment::setGapPenalty	(	int	GP = -11,
		int	extn = -9999
	)

void BioProteinSequenceAlignment::setGapPenalty	(	int	GP = -11,
		int	extn = -9999
	)

void BioProteinSequenceAlignment::setGapPenalty	(	int	GP = -11,
		int	extn = -9999
	)

void BioProteinSequenceAlignment::setGapPenalty	(	int	GP = -11,
		int	extn = -9999
	)

void BioProteinSequenceAlignment::setMatchMisMatchScore	(	int	MS = 1,
		int	MMS = 0
	)

void BioProteinSequenceAlignment::setMatchMisMatchScore	(	int	MS = 1,
		int	MMS = 0
	)

void BioProteinSequenceAlignment::setMatchMisMatchScore	(	int	MS = 1,
		int	MMS = 0
	)

void BioProteinSequenceAlignment::setMatchMisMatchScore	(	int	MS = 1,
		int	MMS = 0
	)

void BioProteinSequenceAlignment::setMatchMisMatchScore	(	int	MS = 1,
		int	MMS = 0
	)

void BioProteinSequenceAlignment::setSequence1

(

BioProteinSequence

)

void BioProteinSequenceAlignment::setSequence1

(

BioProteinSequence

)

void BioProteinSequenceAlignment::setSequence1

(

BioProteinSequence

)

void BioProteinSequenceAlignment::setSequence1

(

BioProteinSequence

)

void BioProteinSequenceAlignment::setSequence1

(

BioProteinSequence

)

void BioProteinSequenceAlignment::setSequence1

(

BioSwissProt

)

void BioProteinSequenceAlignment::setSequence1

(

BioSwissProt

)

void BioProteinSequenceAlignment::setSequence1

(

BioSwissProt

)

void BioProteinSequenceAlignment::setSequence1

(

BioSwissProt

)

void BioProteinSequenceAlignment::setSequence1

(

BioSwissProt

)

void BioProteinSequenceAlignment::setSequence1

(

BioFasta

)

void BioProteinSequenceAlignment::setSequence1

(

BioFasta

)

void BioProteinSequenceAlignment::setSequence1

(

BioFasta

)

void BioProteinSequenceAlignment::setSequence1

(

BioFasta

)

void BioProteinSequenceAlignment::setSequence1

(

BioFasta

)

void BioProteinSequenceAlignment::setSequence1

(

const string &

)

void BioProteinSequenceAlignment::setSequence1

(

const string &

)

void BioProteinSequenceAlignment::setSequence1

(

const string &

)

void BioProteinSequenceAlignment::setSequence1

(

const string &

)

void BioProteinSequenceAlignment::setSequence1

(

const string &

)

void BioProteinSequenceAlignment::setSequence2

(

BioProteinSequence

)

void BioProteinSequenceAlignment::setSequence2

(

BioProteinSequence

)

void BioProteinSequenceAlignment::setSequence2

(

BioProteinSequence

)

void BioProteinSequenceAlignment::setSequence2

(

BioProteinSequence

)

void BioProteinSequenceAlignment::setSequence2

(

BioProteinSequence

)

void BioProteinSequenceAlignment::setSequence2

(

BioSwissProt

)

void BioProteinSequenceAlignment::setSequence2

(

BioSwissProt

)

void BioProteinSequenceAlignment::setSequence2

(

BioSwissProt

)

void BioProteinSequenceAlignment::setSequence2

(

BioSwissProt

)

void BioProteinSequenceAlignment::setSequence2

(

BioSwissProt

)

void BioProteinSequenceAlignment::setSequence2

(

BioFasta

)

void BioProteinSequenceAlignment::setSequence2

(

BioFasta

)

void BioProteinSequenceAlignment::setSequence2

(

BioFasta

)

void BioProteinSequenceAlignment::setSequence2

(

BioFasta

)

void BioProteinSequenceAlignment::setSequence2

(

BioFasta

)

void BioProteinSequenceAlignment::setSequence2

(

const string &

)

void BioProteinSequenceAlignment::setSequence2

(

const string &

)

void BioProteinSequenceAlignment::setSequence2

(

const string &

)

void BioProteinSequenceAlignment::setSequence2

(

const string &

)

void BioProteinSequenceAlignment::setSequence2

(

const string &

)

void BioProteinSequenceAlignment::setSubstitutionMatrix

(

const string &

)

void BioProteinSequenceAlignment::setSubstitutionMatrix

(

const string &

)

void BioProteinSequenceAlignment::setSubstitutionMatrix

(

const string &

)

void BioProteinSequenceAlignment::setSubstitutionMatrix

(

const string &

)

void BioProteinSequenceAlignment::setSubstitutionMatrix	(	const string &	,
		const string &
	)

void BioProteinSequenceAlignment::setSubstitutionMatrix

(

const string &

)

void BioProteinSequenceAlignment::setSubstitutionMatrix	(	const string &	,
		const string &
	)

void BioProteinSequenceAlignment::setSubstitutionMatrix	(	const string &	,
		const string &
	)

void BioProteinSequenceAlignment::setSubstitutionMatrix	(	const string &	,
		const string &
	)

void BioProteinSequenceAlignment::setSubstitutionMatrix	(	const string &	,
		const string &
	)

void BioProteinSequenceAlignment::showScoringMatrix

(

ostream &

= cout

)

void BioProteinSequenceAlignment::showScoringMatrix

(

ostream &

= cout

)

void BioProteinSequenceAlignment::showScoringMatrix

(

ostream &

= cout

)

void BioProteinSequenceAlignment::showScoringMatrix

(

ostream &

= cout

)

void BioProteinSequenceAlignment::showScoringMatrix

(

ostream &

= cout

)

---

Member Data Documentation

static string BioProteinSequenceAlignment::aminoAcidSeq_ [static, protected]

string BioProteinSequenceAlignment::conseq_ [protected]

int BioProteinSequenceAlignment::gapExtn [protected]

int BioProteinSequenceAlignment::gapPenalty [protected]

string BioProteinSequenceAlignment::outSeq1_ [protected]

string BioProteinSequenceAlignment::outSeq2_ [protected]

BioMatrix BioProteinSequenceAlignment::scoringMatrix [protected]

string BioProteinSequenceAlignment::seq1_ [protected]

string BioProteinSequenceAlignment::seq2_ [protected]

string BioProteinSequenceAlignment::seqName1_ [protected]

string BioProteinSequenceAlignment::seqName2_ [protected]

int BioProteinSequenceAlignment::status [protected]

BioMatrix BioProteinSequenceAlignment::substitutionMatrix [protected]

---

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

• GlobalAlignment/BioProteinSequenceAlignment.h
• LocalAlignment/BioProteinSequenceAlignment.h
• MultiPattern/BioProteinSequenceAlignment.h
• Overlap/BioProteinSequenceAlignment.h
• Repeats/BioProteinSequenceAlignment.h