Pearson Class Reference

Calculate scores for profile to profile alignment using Pearson's correlation coefficient. More...

Inheritance diagram for Pearson:

Collaboration diagram for Pearson:

Public Member Functions
	Pearson (Profile *pro1, Profile *pro2)
	Default constructor. More...
	Pearson (const Pearson &orig)
	Copy constructor. More...
virtual	~Pearson ()
	Destructor.
virtual void	copy (const ScoringFunction &orig)
	Copy orig object to this object ("deep copy").
virtual void	copy (const Pearson &orig)
	Copy orig object to this object ("deep copy"). More...
virtual Pearson *	newCopy ()
	Construct a new "deep copy" of this object. More...
Pearson &	operator= (const Pearson &orig)
	Assignment operator. 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 Pearson's correlation coefficient.

Some explanations can be found in:

Guoli Wang, Roland L. Dunbrack jr. Scoring profile-to-profile sequence alignments. Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA. March 16, 2004.

Constructor & Destructor Documentation

Pearson	(	Profile *	pro1,
		Profile *	pro2
	)

Default constructor.

Parameters

pro1
pro2

Pearson

(

const Pearson &

orig

)

Copy constructor.

Parameters

orig

Member Function Documentation

void copy ( const Pearson &  orig )

virtual

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

Parameters

orig

Pearson * newCopy ( )

virtual

Construct a new "deep copy" of this object.

Returns

Implements ScoringFunction.

Pearson & operator=

(

const Pearson &

orig

)

Assignment operator.

Parameters

orig

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/Pearson.h
• Align2/Sources/Pearson.cc