fixes #1008

otter606 · heuermh · commit 9e44b2425dc4 · 2022-01-03T12:59:21.000-06:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SequenceTools.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/SequenceTools.java
@@ -35,28 +35,16 @@ public class SequenceTools {
 	 * @param n The number of characters to permute by; can be positive or negative; values greater than the length of the array are acceptable
 	 */
 	public static String permuteCyclic(String string, int n) {
-		// single letters are char[]; full names are Character[]
-		Character[] permuted = new Character[string.length()];
-		char[] c = string.toCharArray();
-		Character[] charArray = new Character[c.length];
-		for (int i = 0; i < c.length; i++) {
-			charArray[i] = c[i];
-		}
-		permuteCyclic(charArray, permuted, n);
-		char[] p = new char[permuted.length];
-		for (int i = 0; i < p.length; i++) {
-			p[i] = permuted[i];
-		}
-		return String.valueOf(p);
+		return permuteCyclic2(string, n);
 	}
 
-	/**
+	/*
 	 * Improved implementation that is generally 10-100x faster, and fixes some edge-case bugs.
 	 * @param string The string to permute
 	 * @param n The number of characters to permute by; can be positive or negative; values greater than the length of the array are acceptable
 	 * @return
 	 */
-	public static String permuteCyclic2(String string, int n) {
+	private static String permuteCyclic2(String string, int n) {
 		String toMutate = string + string;
 		n = n % string.length();
 		if (n < 0) {
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/util/SequenceToolsTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/util/SequenceToolsTest.java
@@ -57,25 +57,11 @@ void permuteCycleIntMaxMin(String original, String expected) {
 		@DisplayName("Edge case fixed")
 		void permuteCycleIntMaxMin2(String original, String expected) {
 			assertAll(
-					()->assertEquals(expected, SequenceTools.permuteCyclic2(original, Integer.MAX_VALUE)),
-					()->assertEquals(expected, SequenceTools.permuteCyclic2(original, Integer.MIN_VALUE))
+					()->assertEquals(expected, SequenceTools.permuteCyclic(original, Integer.MAX_VALUE)),
+					()->assertEquals(expected, SequenceTools.permuteCyclic(original, Integer.MIN_VALUE))
 				);
 		}
-		
-		@Test
-		void permuteCyclicPerformance() {
-			String dna = randomDNA(10_000_000);
-			long start = System.currentTimeMillis();
-			String rotated = SequenceTools.permuteCyclic(dna, 5_000_000);
-			long end = System.currentTimeMillis();
-			System.err.println(end-start);
-			
-			long start2 = System.currentTimeMillis();
-			String rotated2 = SequenceTools.permuteCyclic2(dna, 5_000_000);
-			long end2 = System.currentTimeMillis();
-			System.err.println(end2-start2);
-			assertTrue((end-start)/(end2-start2) > 5);
-		}
+
 	}
 
 	@Nested
