org.simmetrics.metrics

Class SmithWatermanGotoh

java.lang.Object

org.simmetrics.metrics.SmithWatermanGotoh

All Implemented Interfaces:

Metric<String>, StringMetric

public class SmithWatermanGotoh
extends Object
implements StringMetric

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

Implementation uses optimizations described in Osamu Gotoh (1982). "An improved algorithm for matching biological sequences". Journal of molecular biology 162: 705". This implementation uses constant space and quadratic time.

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

See Also:

NeedlemanWunch, SmithWaterman, Wikipedia - Smith-Waterman algorithm

Constructor Summary

Constructors

Constructor and Description
SmithWatermanGotoh() Constructs a new Smith Waterman metric.
SmithWatermanGotoh(float gapValue, Substitution substitution) 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

SmithWatermanGotoh

public SmithWatermanGotoh()

Constructs a new Smith Waterman metric. Gap penalty is -0.5, mismatch penalty -2.0 and a matching score 1.0.

SmithWatermanGotoh

public SmithWatermanGotoh(float gapValue,
                          Substitution substitution)

Constructs a new Smith Waterman metric.

Parameters:

gapValue - a non-positive gap penalty

substitution - a substitution function

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