JensenShannon Class Reference

Calculate scores for profile to profile alignment using Jensen-Shannon method. More...

Inheritance diagram for JensenShannon:

Collaboration diagram for JensenShannon:

Public Member Functions
	JensenShannon (Profile *pro1, Profile *pro2)
	Default constructor. More...
	JensenShannon (const JensenShannon &orig)
	Copy constructor.
virtual	~JensenShannon ()
	Destructor.
virtual void	copy (const JensenShannon &orig)
	Copy orig object to this object ("deep copy"). More...
virtual void	copy (const ScoringFunction &orig)
	Copy orig object to this object ("deep copy").
virtual JensenShannon *	newCopy ()
	Construct a new "deep copy" of this object. More...
JensenShannon &	operator= (const JensenShannon &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 Jensen-Shannon 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

JensenShannon	(	Profile *	pro1,
		Profile *	pro2
	)

Default constructor.

Parameters

pro1
pro2

Member Function Documentation

void copy ( const JensenShannon &  orig )

virtual

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

Parameters

orig

JensenShannon * newCopy ( )

virtual

Construct a new "deep copy" of this object.

Returns

Implements ScoringFunction.

JensenShannon & operator=

(

const JensenShannon &

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/JensenShannon.h
• Align2/Sources/JensenShannon.cc