org.simmetrics.metrics

Class SmithWaterman

java.lang.Object

org.simmetrics.metrics.SmithWaterman

All Implemented Interfaces:

Metric<String>, StringMetric

public class SmithWaterman
extends Object
implements StringMetric

Smith-Waterman algorithm providing a similarity measure between two strings.

Implementation uses the implementation as described by Smith and Waterman. This implementation uses quadratic space and cubic time.

This class is immutable and thread-safe if its substitution and gap functions are.

See Also:

NeedlemanWunch, SmithWatermanGotoh, Wikipedia - Smith-Waterman algorithm

Constructor Summary

Constructors

Constructor and Description
SmithWaterman() Constructs a new Smith Waterman metric.
SmithWaterman(Gap gap, Substitution substitution, int windowSize) Constructs a new Smith Waterman 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

SmithWaterman

public SmithWaterman()

Constructs a new Smith Waterman metric. Uses an affine gap of -5.0 - gapLength a -3.0 substitution penalty for mismatches, 5.0 for matches.

SmithWaterman

public SmithWaterman(Gap gap,
                     Substitution substitution,
                     int windowSize)

Constructs a new Smith Waterman metric.

Parameters:

gap - a gap function to score gaps by

substitution - a substitution function to score substitutions by

windowSize - a non-negative window in which

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