GapFunction Class Reference

Base class for gap functions. More...

Inheritance diagram for GapFunction:

Public Member Functions
	GapFunction ()
	Default constructor.
	GapFunction (const GapFunction &orig)
	Copy constructor.
virtual	~GapFunction ()
	Destructor.
virtual void	copy (const GapFunction &orig)
	Copy orig object to this object ("deep copy").
virtual double	getExtensionPenalty (int p)=0
	Return extension gap penalty for template position p.
virtual double	getOpenPenalty (int p)=0
	Return open gap penalty for template position p.
virtual GapFunction *	newCopy ()=0
	Construct a new "deep copy" of this object.
GapFunction &	operator= (const GapFunction &orig)
	Assignment operator.
virtual void	setExtensionPenalty (double pen)=0
	Set extension gap penalty.
virtual void	setOpenPenalty (double pen)=0
	Set open gap penalty.

Detailed Description

Base class for gap functions.

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

• Align2/Sources/GapFunction.h