org.simmetrics.metrics.functions

Interface Gap

All Known Implementing Classes:

AffineGap, ConstantGap, LinearGap

public interface Gap

A gap function assigns penalty to the creation of a gap in a string when matching against another string.

The penalty returned must be non-positive value to be consistent with the results of the substitution function.

This class is immutable and thread-safe.

See Also:

Substitution, Wikipedia - Gap Penalty

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.
float	value(int fromIndex, int toIndex) Returns the penalty for creating a gap from fromIndex to toIndex -1.

Method Detail

value

float value(int fromIndex,
            int toIndex)

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

Parameters:

fromIndex - index at which the gap starts

toIndex - index after the last gap entry

Returns:

a gap penalty

max

float max()

Returns the minimum value a gap can have.

Returns:

the minimum value a gap can have

min

float min()

Returns the maximum value a gap can have.

Returns:

the maximum value a gap can have