CrossProduct Class Reference

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

Inheritance diagram for CrossProduct:

Collaboration diagram for CrossProduct:

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

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

Default constructor.

Parameters

sub
pro1
pro2

CrossProduct

(

const CrossProduct &

orig

)

Copy constructor.

Parameters

orig

Member Function Documentation

void copy ( const CrossProduct &  orig )

virtual

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

Parameters

orig

CrossProduct * newCopy ( )

virtual

Construct a new "deep copy" of this object.

Returns

Implements ScoringFunction.

CrossProduct & operator=

(

const CrossProduct &

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/CrossProduct.h
• Align2/Sources/CrossProduct.cc