Panchenko Class Reference

Calculate scores for profile to profile alignment using Panchenko method. More...

Inheritance diagram for Panchenko:

Collaboration diagram for Panchenko:

Public Member Functions
	Panchenko (Profile *pro1, Profile *pro2, PssmInput *pssm1, PssmInput *pssm2)
	Default constructor. More...
	Panchenko (const Panchenko &orig)
	Copy constructor.
virtual	~Panchenko ()
	Destructor.
virtual void	copy (const ScoringFunction &orig)
	Copy orig object to this object ("deep copy").
virtual void	copy (const Panchenko &orig)
	Copy orig object to this object ("deep copy"). More...
virtual Panchenko *	newCopy ()
	Construct a new "deep copy" of this object. More...
Panchenko &	operator= (const Panchenko &orig)
	Assignment operator. More...
int	returnAaColumnTarget (int i)
	Return the number of different aminoacids in column i. More...
int	returnAaColumnTemplate (int i)
	Return the number of different aminoacids in column i. More...
virtual double	scoringSeq (int i, int j)
	Calculate scores to create matrix values. More...

Detailed Description

Calculate scores for profile to profile alignment using Panchenko method.

Some explanations can be found in:

           Panchenko AR.
           Finding weak similarities between proteins by sequence
           profile comparison.
           Nucleic Acids Res. 2003 Jan 15;31(2):683-9.

Constructor & Destructor Documentation

Panchenko	(	Profile *	pro1,
		Profile *	pro2,
		PssmInput *	pssm1,
		PssmInput *	pssm2
	)

Default constructor.

Parameters

pro1
pro2
pssm1
pssm2

Member Function Documentation

void copy ( const Panchenko &  orig )

virtual

Copy orig object to this object ("deep copy").

Parameters

orig

Panchenko * newCopy ( )

virtual

Construct a new "deep copy" of this object.

Returns

Implements ScoringFunction.

Panchenko & operator=

(

const Panchenko &

orig

)

Assignment operator.

Parameters

orig

Returns

int returnAaColumnTarget

(

int

i

)

Return the number of different aminoacids in column i.

Parameters

i

Returns

int returnAaColumnTemplate

(

int

i

)

Return the number of different aminoacids in column i.

Parameters

i

Returns

double scoringSeq ( int  i, int  j  )

virtual

Calculate scores to create matrix values.

Parameters

i
j

Returns

Implements ScoringFunction.

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

• Align2/Sources/Panchenko.h
• Align2/Sources/Panchenko.cc