feat: add needleman–wunsch sequence alignment algorithm (#6707)

Co-authored-by: a <alexanderklmn@gmail.com>
This commit is contained in:
Saahil Mahato
2025-10-09 00:12:30 +05:45
committed by GitHub
parent 061463a4df
commit 4fe37c3a10
2 changed files with 120 additions and 0 deletions

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package com.thealgorithms.dynamicprogramming;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertThrows;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.CsvSource;
/**
* Unit Tests for the {@code NeedlemanWunsch} class
*/
class NeedlemanWunschTest {
@Test
void testIdenticalStrings() {
int score = NeedlemanWunsch.align("GATTACA", "GATTACA", 1, -1, -2);
assertEquals(7, score); // All matches, 7*1
}
@Test
void testSimpleMismatch() {
int score = NeedlemanWunsch.align("GATTACA", "GACTATA", 1, -1, -2);
assertEquals(3, score);
}
@Test
void testInsertion() {
int score = NeedlemanWunsch.align("GATTACA", "GATACA", 1, -1, -2);
// One deletion (gap penalty)
assertEquals(4, score);
}
@Test
void testEmptyStrings() {
assertEquals(0, NeedlemanWunsch.align("", "", 1, -1, -2));
}
@Test
void testOneEmpty() {
assertEquals(-14, NeedlemanWunsch.align("GATTACA", "", 1, -1, -2)); // 7 gaps × -2
}
@Test
void testGapHeavyAlignment() {
int score = NeedlemanWunsch.align("AAAA", "AA", 1, -1, -2);
assertEquals(-2, score); // Two matches (2*1) + two gaps (2*-2)
}
@ParameterizedTest
@CsvSource({"null,ABC", "ABC,null", "null,null"})
void testNullInputs(String s1, String s2) {
// Interpret "null" literal as Java null
String first = "null".equals(s1) ? null : s1;
String second = "null".equals(s2) ? null : s2;
IllegalArgumentException ex = assertThrows(IllegalArgumentException.class, () -> NeedlemanWunsch.align(first, second, 1, -1, -2));
assertEquals("Input strings must not be null.", ex.getMessage());
}
}