240 lines
10 KiB
Java
240 lines
10 KiB
Java
/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.utils;
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import org.apache.commons.io.FileUtils;
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import org.broadinstitute.sting.utils.io.IOUtils;
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import org.testng.Assert;
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import org.broadinstitute.sting.BaseTest;
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import org.testng.annotations.DataProvider;
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import org.testng.annotations.Test;
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import java.io.File;
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import java.util.*;
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/**
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* Testing framework for general purpose utilities class.
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*
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* @author hanna
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* @version 0.1
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*/
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public class UtilsUnitTest extends BaseTest {
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@Test
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public void testAppend() {
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for ( int leftSize : Arrays.asList(0, 1, 2, 3) ) {
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for ( final int rightSize : Arrays.asList(0, 1, 2) ) {
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final List<Integer> left = new LinkedList<Integer>();
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for ( int i = 0; i < leftSize; i++ ) left.add(i);
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final List<Integer> total = new LinkedList<Integer>();
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for ( int i = 0; i < leftSize + rightSize; i++ ) total.add(i);
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if ( rightSize == 0 )
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Assert.assertEquals(Utils.append(left), total);
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if ( rightSize == 1 )
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Assert.assertEquals(Utils.append(left, leftSize), total);
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if ( rightSize == 2 )
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Assert.assertEquals(Utils.append(left, leftSize, leftSize + 1), total);
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}
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}
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}
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@Test
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public void testDupStringNoChars() {
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String duped = Utils.dupString('a',0);
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Assert.assertEquals(duped.length(), 0, "dupString did not produce zero-length string");
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}
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@Test
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public void testDupStringOneChar() {
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String duped = Utils.dupString('b',1);
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Assert.assertEquals(duped.length(), 1, "dupString did not produce single character string");
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Assert.assertEquals(duped.charAt(0), 'b', "dupString character was incorrect");
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}
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@Test
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public void testXor() {
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Assert.assertEquals(Utils.xor(false, false), false, "xor F F failed");
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Assert.assertEquals(Utils.xor(false, true), true, "xor F T failed");
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Assert.assertEquals(Utils.xor(true, false), true, "xor T F failed");
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Assert.assertEquals(Utils.xor(true, true), false, "xor T T failed");
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}
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@Test
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public void testDupStringMultiChar() {
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String duped = Utils.dupString('c',5);
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Assert.assertEquals(duped.length(), 5, "dupString did not produce five character string");
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Assert.assertEquals(duped,"ccccc","dupString string was incorrect");
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}
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@Test
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public void testJoinMap() {
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Map<String,Integer> map = new LinkedHashMap<String,Integer>();
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map.put("one",1);
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map.put("two",2);
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String joined = Utils.joinMap("-",";",map);
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Assert.assertTrue("one-1;two-2".equals(joined));
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}
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@Test
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public void testJoinMapLargerSet() {
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Map<String,Integer> map = new LinkedHashMap<String,Integer>();
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map.put("one",1);
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map.put("two",2);
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map.put("three",1);
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map.put("four",2);
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map.put("five",1);
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map.put("six",2);
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String joined = Utils.joinMap("-",";",map);
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Assert.assertTrue("one-1;two-2;three-1;four-2;five-1;six-2".equals(joined));
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}
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@Test
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public void testConcat() {
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final String s1 = "A";
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final String s2 = "CC";
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final String s3 = "TTT";
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final String s4 = "GGGG";
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Assert.assertEquals(new String(Utils.concat()), "");
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Assert.assertEquals(new String(Utils.concat(s1.getBytes())), s1);
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Assert.assertEquals(new String(Utils.concat(s1.getBytes(), s2.getBytes())), s1 + s2);
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Assert.assertEquals(new String(Utils.concat(s1.getBytes(), s2.getBytes(), s3.getBytes())), s1 + s2 + s3);
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Assert.assertEquals(new String(Utils.concat(s1.getBytes(), s2.getBytes(), s3.getBytes(), s4.getBytes())), s1 + s2 + s3 + s4);
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}
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@Test
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public void testEscapeExpressions() {
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String[] expected, actual;
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expected = new String[] {"one", "two", "three"};
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actual = Utils.escapeExpressions("one two three");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions(" one two three");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions("one two three ");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions(" one two three ");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions(" one two three ");
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Assert.assertEquals(actual, expected);
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expected = new String[] {"one", "two", "three four", "five", "six"};
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actual = Utils.escapeExpressions("one two 'three four' five six");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions(" one two 'three four' five six");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions("one two 'three four' five six ");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions(" one two 'three four' five six ");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions(" one two 'three four' five six ");
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Assert.assertEquals(actual, expected);
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expected = new String[] {"one two", "three", "four"};
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actual = Utils.escapeExpressions("'one two' three four");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions(" 'one two' three four");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions("'one two' three four ");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions(" 'one two' three four ");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions(" 'one two' three four ");
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Assert.assertEquals(actual, expected);
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expected = new String[] {"one", "two", "three four"};
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actual = Utils.escapeExpressions("one two 'three four'");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions(" one two 'three four'");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions("one two 'three four' ");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions(" one two 'three four' ");
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Assert.assertEquals(actual, expected);
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actual = Utils.escapeExpressions(" one two 'three four' ");
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Assert.assertEquals(actual, expected);
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}
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@Test
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public void testCalcMD5() throws Exception {
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final File source = new File(publicTestDir + "exampleFASTA.fasta");
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final String sourceMD5 = "36880691cf9e4178216f7b52e8d85fbe";
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final byte[] sourceBytes = IOUtils.readFileIntoByteArray(source);
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Assert.assertEquals(Utils.calcMD5(sourceBytes), sourceMD5);
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final String sourceString = FileUtils.readFileToString(source);
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Assert.assertEquals(Utils.calcMD5(sourceString), sourceMD5);
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}
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@Test
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public void testLongestCommonOps() {
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for ( int prefixLen = 0; prefixLen < 20; prefixLen++ ) {
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for ( int extraSeq1Len = 0; extraSeq1Len < 10; extraSeq1Len++ ) {
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for ( int extraSeq2Len = 0; extraSeq2Len < 10; extraSeq2Len++ ) {
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for ( int max = 0; max < 50; max++ ) {
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final String prefix = Utils.dupString("A", prefixLen);
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final int expected = Math.min(prefixLen, max);
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{
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final String seq1 = prefix + Utils.dupString("C", extraSeq1Len);
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final String seq2 = prefix + Utils.dupString("G", extraSeq1Len);
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Assert.assertEquals(Utils.longestCommonPrefix(seq1.getBytes(), seq2.getBytes(), max), expected, "LongestCommonPrefix failed: seq1 " + seq1 + " seq2 " + seq2 + " max " + max);
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}
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{
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final String seq1 = Utils.dupString("C", extraSeq1Len) + prefix;
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final String seq2 = Utils.dupString("G", extraSeq1Len) + prefix;
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Assert.assertEquals(Utils.longestCommonSuffix(seq1.getBytes(), seq2.getBytes(), max), expected, "longestCommonSuffix failed: seq1 " + seq1 + " seq2 " + seq2 + " max " + max);
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}
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}
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}
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}
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}
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}
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@DataProvider(name = "trim")
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public Object[][] createTrimTestData() {
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List<Object[]> tests = new ArrayList<Object[]>();
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final String s = "AAAA";
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for ( int front = 0; front < s.length(); front++ ) {
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for ( int back = 0; back < s.length(); back++ ) {
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if ( front + back <= s.length() )
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tests.add(new Object[]{s, front, back});
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}
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}
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return tests.toArray(new Object[][]{});
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}
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@Test(dataProvider = "trim", enabled = true)
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public void testTrim(final String s, final int frontTrim, final int backTrim) {
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Assert.assertEquals(s.length() - frontTrim - backTrim, Utils.trimArray(s.getBytes(), frontTrim, backTrim).length);
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}
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}
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