public class SmithWatermanGotoh extends Object implements StringMetric
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.
Constructor and Description |
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SmithWatermanGotoh()
Constructs a new Smith Waterman metric.
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SmithWatermanGotoh(float gapValue,
Substitution substitution)
Constructs a new Smith Waterman metric.
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Modifier and Type | Method and Description |
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float |
compare(String a,
String b)
Measures the similarity between strings a and b.
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String |
toString() |
public SmithWatermanGotoh()
public SmithWatermanGotoh(float gapValue, Substitution substitution)
gapValue
- a non-positive gap penaltysubstitution
- a substitution functionpublic float compare(String a, String b)
StringMetric
compare
in interface Metric<String>
compare
in interface StringMetric
a
- string a to compareb
- string b to compareCopyright © 2014–2018. All rights reserved.