org.simmetrics.metrics

Class NeedlemanWunch

java.lang.Object

org.simmetrics.metrics.NeedlemanWunch

All Implemented Interfaces:

Metric<String>, StringMetric

public class NeedlemanWunch
extends Object
implements StringMetric

Needleman-Wunsch algorithm providing a similarity measure between two strings.

Implementation uses linear space.

This class is immutable and thread-safe if its substitution function is.

See Also:

SmithWatermanGotoh, SmithWaterman, Wikipedia - Needleman-Wunsch algorithm

Constructor Summary

Constructors

Constructor and Description
NeedlemanWunch() Constructs a new Needleman-Wunch metric.
NeedlemanWunch(float gapValue, Substitution substitution) Constructs a new Needleman-Wunch metric.

Method Summary

Modifier and Type	Method and Description
float	compare(String a, String b) Measures the similarity between strings a and b.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

NeedlemanWunch

public NeedlemanWunch()

Constructs a new Needleman-Wunch metric. Uses an gap of -2.0 a -1.0 substitution penalty for mismatches, 0 for matches.

NeedlemanWunch

public NeedlemanWunch(float gapValue,
                      Substitution substitution)

Constructs a new Needleman-Wunch metric.

Parameters:

gapValue - a non-positive penalty for gaps

substitution - a substitution function for mismatched characters

Method Detail

compare

public float compare(String a,
                     String b)

Description copied from interface: StringMetric

Measures the similarity between strings a and b. The measurement results in a value between 0 and 1 (inclusive). A value of zero indicates that the strings are dissimilar, a value of 1 indicates they are similar.

Specified by:

compare in interface Metric<String>

Specified by:

compare in interface StringMetric

Parameters:

a - string a to compare

b - string b to compare

Returns:

a value between 0 and 1 inclusive indicating similarity

toString

public String toString()

Overrides:

toString in class Object