org.simmetrics.metrics

Class SmithWaterman

java.lang.Object

org.simmetrics.metrics.SmithWaterman

All Implemented Interfaces:

Metric<String>, StringMetric

public final class SmithWaterman
extends Object
implements StringMetric

Applies the Smith-Waterman algorithm to calculate the similarity 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