Sec Class Reference

Calculate structural scores with info derived from secondary structure. More...

Inheritance diagram for Sec:

Collaboration diagram for Sec:

Public Member Functions
	Sec (SubMatrix *subStr, AlignmentData *ad, double cSec)
	Default constructor. More...
	Sec (const Sec &orig)
	Copy constructor.
virtual	~Sec ()
	Destructor.
virtual void	copy (const Sec &orig)
	Copy orig object to this object ("deep copy"). More...
virtual void	copy (const Structure &orig)
	Copy orig object to this object ("deep copy").
virtual Sec *	newCopy ()
	Construct a new "deep copy" of this object. More...
Sec &	operator= (const Sec &orig)
	Assignment operator.
virtual void	reverse ()
	Reverse template secondary structure.
virtual double	scoringStr (int i, int j)
	Calculate structural scores to create matrix values. More...

Data Fields
SubMatrix *	subStr
	Structural substitution matrix.

Detailed Description

Calculate structural scores with info derived from secondary structure.

Constructor & Destructor Documentation

Sec	(	SubMatrix *	subStr,
		AlignmentData *	ad,
		double	cSec
	)

Default constructor.

Parameters

subStr
ad
cSec

Member Function Documentation

void copy ( const Sec &  orig )

virtual

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

Parameters

orig

Sec * newCopy ( )

virtual

Construct a new "deep copy" of this object.

Returns

Implements Structure.

double scoringStr ( int  i, int  j  )

virtual

Calculate structural scores to create matrix values.

Parameters

i
j

Returns

Implements Structure.

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

• Align2/Sources/Sec.h
• Align2/Sources/Sec.cc