diff --git a/src/main/java/com/thealgorithms/dynamicprogramming/SmithWaterman.java b/src/main/java/com/thealgorithms/dynamicprogramming/SmithWaterman.java new file mode 100644 index 000000000000..c0d66f68b502 --- /dev/null +++ b/src/main/java/com/thealgorithms/dynamicprogramming/SmithWaterman.java @@ -0,0 +1,56 @@ +package com.thealgorithms.dynamicprogramming; + +/** + * Smith–Waterman algorithm for local sequence alignment. + * Finds the highest scoring local alignment between substrings of two sequences. + * + * Time Complexity: O(n * m) + * Space Complexity: O(n * m) + */ +public final class SmithWaterman { + + private SmithWaterman() { + // Utility Class + } + + /** + * Computes the Smith–Waterman local alignment score between two strings. + * + * @param s1 first string + * @param s2 second string + * @param matchScore score for a match + * @param mismatchPenalty penalty for mismatch (negative) + * @param gapPenalty penalty for insertion/deletion (negative) + * @return the maximum local alignment score + */ + public static int align(String s1, String s2, int matchScore, int mismatchPenalty, int gapPenalty) { + if (s1 == null || s2 == null) { + throw new IllegalArgumentException("Input strings must not be null."); + } + + int n = s1.length(); + int m = s2.length(); + int maxScore = 0; + + int[][] dp = new int[n + 1][m + 1]; + + for (int i = 1; i <= n; i++) { + for (int j = 1; j <= m; j++) { + int matchOrMismatch = (s1.charAt(i - 1) == s2.charAt(j - 1)) ? matchScore : mismatchPenalty; + + dp[i][j] = Math.max(0, + Math.max(Math.max(dp[i - 1][j - 1] + matchOrMismatch, // match/mismatch + dp[i - 1][j] + gapPenalty // deletion + ), + dp[i][j - 1] + gapPenalty // insertion + )); + + if (dp[i][j] > maxScore) { + maxScore = dp[i][j]; + } + } + } + + return maxScore; + } +} diff --git a/src/test/java/com/thealgorithms/dynamicprogramming/SmithWatermanTest.java b/src/test/java/com/thealgorithms/dynamicprogramming/SmithWatermanTest.java new file mode 100644 index 000000000000..46c47e376989 --- /dev/null +++ b/src/test/java/com/thealgorithms/dynamicprogramming/SmithWatermanTest.java @@ -0,0 +1,53 @@ +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 SmithWaterman} class. + */ +class SmithWatermanTest { + + @Test + void testIdenticalStrings() { + int score = SmithWaterman.align("GATTACA", "GATTACA", 2, -1, -2); + assertEquals(14, score); // full match, 7*2 + } + + @Test + void testPartialMatch() { + int score = SmithWaterman.align("GATTACA", "TTAC", 2, -1, -2); + assertEquals(8, score); // best local alignment "TTAC" + } + + @Test + void testNoMatch() { + int score = SmithWaterman.align("AAAA", "TTTT", 1, -1, -2); + assertEquals(0, score); // no alignment worth keeping + } + + @Test + void testInsertionDeletion() { + int score = SmithWaterman.align("ACGT", "ACGGT", 1, -1, -2); + assertEquals(3, score); // local alignment "ACG" + } + + @Test + void testEmptyStrings() { + assertEquals(0, SmithWaterman.align("", "", 1, -1, -2)); + } + + @ParameterizedTest + @CsvSource({"null,ABC", "ABC,null", "null,null"}) + void testNullInputs(String s1, String s2) { + String first = "null".equals(s1) ? null : s1; + String second = "null".equals(s2) ? null : s2; + + IllegalArgumentException ex = assertThrows(IllegalArgumentException.class, () -> SmithWaterman.align(first, second, 1, -1, -2)); + assertEquals("Input strings must not be null.", ex.getMessage()); + } +}