org.simmetrics.metrics.functions

Interface Substitution

All Known Implementing Classes:

MatchMismatch

public interface Substitution

A substitution function assigns value to the substitution of one character for another matching against another string.

A positive value indicates the characters are similar, a negative value indicates they are dissimilar.

This class is immutable and thread-safe.

See Also:

Gap, Wikipedia - Smith–Waterman algorithm

Method Summary

Modifier and Type	Method and Description
float	compare(String a, int aIndex, String b, int bIndex) Rates the substitution of character a.getChar(aIndex) against b.getChar(bIndex).
float	max() Returns the maximum value a gap can have
float	min() Returns the minimum value a gap can have

Method Detail

compare

float compare(String a,
              int aIndex,
              String b,
              int bIndex)

Rates the substitution of character a.getChar(aIndex) against b.getChar(bIndex).

Parameters:

a - a string to check in

aIndex - index of character at string a to compare

b - another string to check in

bIndex - index of character at string b to compare

Returns:

a score indicating the characters (dis) similarity

max

float max()

Returns the maximum value a gap can have

Returns:

the maximum value a gap can have

min

float min()

Returns the minimum value a gap can have

Returns:

the minimum value a gap can have