Class SequenceAligner

java.lang.Object

org.episteme.natural.biology.genetics.SequenceAligner

public class SequenceAligner
extends Object

Pairwise Sequence Alignment using Needleman-Wunsch algorithm with high-precision scores.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final record	SequenceAligner.AlignmentResult

Constructor Summary

Constructors

Constructor	Description
SequenceAligner(Real matchScore, Real mismatchScore, Real gapScore)

Method Summary

Modifier and Type	Method	Description
SequenceAligner.AlignmentResult	align(String seq1, String seq2)
static SequenceAligner	defaultDNA()
static SequenceAligner	defaultProtein()
SequenceAligner.AlignmentResult	localAlign(String seq1, String seq2)	Smith-Waterman local alignment algorithm.

Methods inherited from class Object

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

Constructor Details

SequenceAligner

public SequenceAligner(Real matchScore,
 Real mismatchScore,
 Real gapScore)

Method Details

defaultDNA

public static SequenceAligner defaultDNA()

defaultProtein

public static SequenceAligner defaultProtein()

align

public SequenceAligner.AlignmentResult align(String seq1,
 String seq2)

localAlign

public SequenceAligner.AlignmentResult localAlign(String seq1,
 String seq2)

Smith-Waterman local alignment algorithm. Finds the best local alignment (highest-scoring substring match).