ScoringP2P Class Reference

Calculate scores for profile to profile alignment. More...

Inheritance diagram for ScoringP2P:

Collaboration diagram for ScoringP2P:

Public Member Functions
	ScoringP2P (SubMatrix *sub, AlignmentData *ad, Structure *str, Profile *pro1, Profile *pro2, ScoringFunction *fun, double cSeq)
	Default constructor. More...
	ScoringP2P (const ScoringP2P &orig)
	Copy constructor.
virtual	~ScoringP2P ()
	Destructor.
virtual bool	checkSequence (const string &s) const
	Check if s consists only of characters defined in sub.getResidues. More...
virtual void	copy (const ScoringP2P &orig)
	Copy orig object to this object ("deep copy"). More...
virtual void	copy (const ScoringScheme &orig)
	Copy orig object to this object ("deep copy"). More...
virtual ScoringP2P *	newCopy ()
	Construct a new "deep copy" of this object. More...
ScoringP2P &	operator= (const ScoringP2P &orig)
	Assignment operator. More...
virtual void	reverse ()
	Reverse template sequence and profile.
virtual double	scoring (int i, int j)
	Calculate scores to create matrix values. More...

Data Fields
AlignmentData *	ad
	Pointer to AlignmentData.
Structure *	str
	Pointer to Structure.
SubMatrix *	sub
	Substitution matrix.

Detailed Description

Calculate scores for profile to profile alignment.

Constructor & Destructor Documentation

ScoringP2P	(	SubMatrix *	sub,
		AlignmentData *	ad,
		Structure *	str,
		Profile *	pro1,
		Profile *	pro2,
		ScoringFunction *	fun,
		double	cSeq
	)

Default constructor.

Parameters

sub
ad
str
pro1
pro2
fun
cSeq

Member Function Documentation

bool checkSequence ( const string &  s ) const

virtualinherited

Check if s consists only of characters defined in sub.getResidues.

Parameters

s

Returns

void copy ( const ScoringP2P &  orig )

virtual

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

Parameters

orig

void copy ( const ScoringScheme &  orig )

virtualinherited

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

Parameters

orig

ScoringP2P * newCopy ( )

virtual

Construct a new "deep copy" of this object.

Returns

Implements ScoringScheme.

ScoringP2P & operator=

(

const ScoringP2P &

orig

)

Assignment operator.

Parameters

orig

Returns

double scoring ( int  i, int  j  )

virtual

Calculate scores to create matrix values.

Parameters

i
j

Returns

Implements ScoringScheme.

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

• Align2/Sources/ScoringP2P.h
• Align2/Sources/ScoringP2P.cc