ScoringP2S Class Reference

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

Inheritance diagram for ScoringP2S:

Collaboration diagram for ScoringP2S:

Public Member Functions
	ScoringP2S (SubMatrix *sub, AlignmentData *ad, Structure *str, Profile *pro, double cSeq)
	Default constructor. More...
	ScoringP2S (const ScoringP2S &orig)
	Copy constructor.
virtual	~ScoringP2S ()
	Destructor.
virtual bool	checkSequence (const string &s) const
	Check if s consists only of characters defined in sub.getResidues. More...
virtual void	copy (const ScoringP2S &orig)
	Copy orig object to this object ("deep copy").
virtual void	copy (const ScoringScheme &orig)
	Copy orig object to this object ("deep copy"). More...
virtual ScoringP2S *	newCopy ()
	Construct a new "deep copy" of this object.
ScoringP2S &	operator= (const ScoringP2S &orig)
	Assignment operator.
virtual void	reverse ()
	Reverse template sequence.
virtual double	scoring (int i, int j)
	Calculate scores to create matrix values.

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

Detailed Description

Calculate scores for profile to sequence alignment.

Constructor & Destructor Documentation

ScoringP2S	(	SubMatrix *	sub,
		AlignmentData *	ad,
		Structure *	str,
		Profile *	pro,
		double	cSeq
	)

Default constructor.

Parameters

sub
ad
str
pro
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 ScoringScheme &  orig )

virtualinherited

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

Parameters

orig

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

• Align2/Sources/ScoringP2S.h
• Align2/Sources/ScoringP2S.cc