org.simmetrics.metrics.functions

Class MatchMismatch

java.lang.Object

org.simmetrics.metrics.functions.MatchMismatch

All Implemented Interfaces:

Substitution

public class MatchMismatch
extends Object
implements Substitution

A substitution function that assigns one value to equal characters, another value to unequal characters.

This class is immutable and thread-safe.

Constructor Summary

Constructors

Constructor and Description
MatchMismatch(float matchValue, float mismatchValue) Constructs a new match-mismatch substitution function.

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
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

MatchMismatch

public MatchMismatch(float matchValue,
                     float mismatchValue)

Constructs a new match-mismatch substitution function. When two characters are equal a score of matchValue is assigned. In case of a mismatch a score of mismatchValue. The matchValue must be strictly greater then mismatchValue

Parameters:

matchValue - value when characters are equal

mismatchValue - value when characters are not equal

Method Detail

compare

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

Description copied from interface: Substitution

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

Specified by:

compare in interface Substitution

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

public float max()

Description copied from interface: Substitution

Returns the maximum value a gap can have

Specified by:

max in interface Substitution

Returns:

the maximum value a gap can have

min

public float min()

Description copied from interface: Substitution

Returns the minimum value a gap can have

Specified by:

min in interface Substitution

Returns:

the minimum value a gap can have

toString

public String toString()

Overrides:

toString in class Object