AGPFunction Class Reference

Implement AGP (Affine Gap Penalty) function. More...

Inheritance diagram for AGPFunction:

Collaboration diagram for AGPFunction:

Public Member Functions
	AGPFunction ()
	Default constructor.
	AGPFunction (double o, double e)
	Constructor assigning o and e.
	AGPFunction (const AGPFunction &orig)
	Copy constructor.
virtual	~AGPFunction ()
	Destructor.
virtual void	copy (const AGPFunction &orig)
	Copy orig object to this object ("deep copy").
virtual void	copy (const GapFunction &orig)
	Copy orig object to this object ("deep copy").
virtual double	getExtensionPenalty (int p)
	Return extension gap penalty for template position p.
virtual double	getOpenPenalty (int p)
	Return open gap penalty for template position p.
virtual AGPFunction *	newCopy ()
	Construct a new "deep copy" of this object.
AGPFunction &	operator= (const AGPFunction &orig)
	Assignment operator.
virtual void	setExtensionPenalty (double pen)
	Set extension gap penalty.
virtual void	setOpenPenalty (double pen)
	Set open gap penalty.

Detailed Description

Implement AGP (Affine Gap Penalty) function.

---

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

• Align2/Sources/AGPFunction.h