Class SequenceAlignment

java.lang.Object

org.episteme.natural.biology.genetics.SequenceAlignment

public class SequenceAlignment
extends Object

Pairwise sequence alignment algorithms.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SequenceAlignment.AlignmentResult

Constructor Summary

Constructors

Constructor	Description
SequenceAlignment()

Method Summary

Modifier and Type	Method	Description
static SequenceAlignment.AlignmentResult	alignGlobal(String s1, String s2, int match, int mismatch, int gap)	Needleman-Wunsch algorithm for global alignment.
static SequenceAlignment.AlignmentResult	alignLocal(String s1, String s2, int match, int mismatch, int gap)	Smith-Waterman algorithm for local alignment.
static int	hammingDistance(String s1, String s2)	Hamming distance between two sequences of equal length.
static int	levenshteinDistance(String s1, String s2)	Levenshtein distance (edit distance).

Methods inherited from class Object

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

Constructor Details

SequenceAlignment

public SequenceAlignment()

Method Details

alignGlobal

public static SequenceAlignment.AlignmentResult alignGlobal(String s1,
 String s2,
 int match,
 int mismatch,
 int gap)

Needleman-Wunsch algorithm for global alignment.

Parameters:

s1 - First sequence

s2 - Second sequence

match - Score for a match

mismatch - Penalty for a mismatch

gap - Penalty for a gap

Returns:

Alignment metrics

alignLocal

public static SequenceAlignment.AlignmentResult alignLocal(String s1,
 String s2,
 int match,
 int mismatch,
 int gap)

Smith-Waterman algorithm for local alignment.

hammingDistance

public static int hammingDistance(String s1,
 String s2)

Hamming distance between two sequences of equal length. Number of mismatches.

levenshteinDistance

public static int levenshteinDistance(String s1,
 String s2)

Levenshtein distance (edit distance).