org.simmetrics.metrics.functions

Class LinearGap

java.lang.Object

org.simmetrics.metrics.functions.LinearGap

All Implemented Interfaces:

Gap

public final class LinearGap
extends Object
implements Gap

A gap function that takes into account the length the gap. Assigns a penalty that is linear in the length of the gap.

This class is immutable and thread-safe.

See Also:

Wikipedia - Gap Penalty

Constructor Summary

Constructors

Constructor and Description
LinearGap(float gapValue) Constructs a linear gap function that scales the length of a gap with gapValue.

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

LinearGap

public LinearGap(float gapValue)

Constructs a linear gap function that scales the length of a gap with gapValue.

Parameters:

gapValue - a 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