org.simmetrics.metrics.functions

Class AffineGap

java.lang.Object

org.simmetrics.metrics.functions.AffineGap

All Implemented Interfaces:

Gap

public final class AffineGap
extends Object
implements Gap

A gap function that calculates the gap penalty as A+(B * GapLegth).

This class is immutable and thread-safe.

See Also:

Substitution, Wikipedia - Gap Penalty

Constructor Summary

Constructors

Constructor and Description
AffineGap(float startValue, float gapValue) Constructs a constant gap function that assigns a penalty of startValue + gapValue * gapLenght to a gap.

Method Summary

Modifier and Type	Method and Description
float	max() Returns the minimum value a gap can have.
float	min() Returns the maximum value a gap can have.
String	toString()
float	value(int fromIndex, int toIndex) Returns the penalty for creating a gap from fromIndex to toIndex -1.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

AffineGap

public AffineGap(float startValue,
                 float gapValue)

Constructs a constant gap function that assigns a penalty of startValue + gapValue * gapLenght to a gap. .

Parameters:

startValue - a non-positive initial penalty for creating a gap

gapValue - a non-positive constant gap value

Method Detail

value

public final float value(int fromIndex,
                         int toIndex)

Description copied from interface: Gap

Returns the penalty for creating a gap from fromIndex to toIndex -1. The value must be non-positive.

Specified by:

value in interface Gap

Parameters:

fromIndex - index at which the gap starts

toIndex - index after the last gap entry

Returns:

a gap penalty

max

public final float max()

Description copied from interface: Gap

Returns the minimum value a gap can have.

Specified by:

max in interface Gap

Returns:

the minimum value a gap can have

min

public final float min()

Description copied from interface: Gap

Returns the maximum value a gap can have.

Specified by:

min in interface Gap

Returns:

the maximum value a gap can have

toString

public String toString()

Overrides:

toString in class Object