LogAverage Class Reference

Calculate scores for profile to profile alignment using sum of pairs method. More...

Inheritance diagram for LogAverage:

Collaboration diagram for LogAverage:

Public Member Functions
	LogAverage (SubMatrix *sub, Profile *pro1, Profile *pro2)
	Default constructor. More...
	LogAverage (const LogAverage &orig)
	Copy constructor.
virtual	~LogAverage ()
	Destructor.
virtual void	copy (const ScoringFunction &orig)
	Copy orig object to this object ("deep copy").
virtual void	copy (const LogAverage &orig)
	Copy orig object to this object ("deep copy"). More...
virtual LogAverage *	newCopy ()
	Construct a new "deep copy" of this object. More...
LogAverage &	operator= (const LogAverage &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 sum of pairs method.

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

LogAverage	(	SubMatrix *	sub,
		Profile *	pro1,
		Profile *	pro2
	)

Default constructor.

Parameters

sub
pro1
pro2

Member Function Documentation

void copy ( const LogAverage &  orig )

virtual

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

Parameters

orig

LogAverage * newCopy ( )

virtual

Construct a new "deep copy" of this object.

Returns

Implements ScoringFunction.

LogAverage & operator=

(

const LogAverage &

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/LogAverage.h
• Align2/Sources/LogAverage.cc