gatk-3.8/public/java/test/org/broadinstitute/sting/utils/UtilsUnitTest.java

/*
* Copyright (c) 2012 The Broad Institute
* 
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
* 
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* 
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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package org.broadinstitute.sting.utils;

import org.apache.commons.io.FileUtils;
import org.broadinstitute.sting.utils.io.IOUtils;
import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import java.io.File;
import java.util.*;

/**
 * Testing framework for general purpose utilities class.
 *
 * @author hanna
 * @version 0.1
 */

public class UtilsUnitTest extends BaseTest {
    @Test
    public void testAppend() {
        for ( int leftSize : Arrays.asList(0, 1, 2, 3) ) {
            for ( final int rightSize : Arrays.asList(0, 1, 2) ) {
                final List<Integer> left = new LinkedList<Integer>();
                for ( int i = 0; i < leftSize; i++ ) left.add(i);
                final List<Integer> total = new LinkedList<Integer>();
                for ( int i = 0; i < leftSize + rightSize; i++ ) total.add(i);

                if ( rightSize == 0 )
                    Assert.assertEquals(Utils.append(left), total);
                if ( rightSize == 1 )
                    Assert.assertEquals(Utils.append(left, leftSize), total);
                if ( rightSize == 2 )
                    Assert.assertEquals(Utils.append(left, leftSize, leftSize + 1), total);
            }
        }

    }

    @Test
    public void testDupStringNoChars() {
        String duped = Utils.dupString('a',0);
        Assert.assertEquals(duped.length(), 0, "dupString did not produce zero-length string");
    }

    @Test
    public void testDupStringOneChar() {
        String duped = Utils.dupString('b',1);
        Assert.assertEquals(duped.length(), 1, "dupString did not produce single character string");
        Assert.assertEquals(duped.charAt(0), 'b', "dupString character was incorrect");
    }

    @Test
    public void testXor() {
        Assert.assertEquals(Utils.xor(false, false), false, "xor F F failed");
        Assert.assertEquals(Utils.xor(false, true), true, "xor F T failed");
        Assert.assertEquals(Utils.xor(true, false), true, "xor T F failed");
        Assert.assertEquals(Utils.xor(true, true), false, "xor T T failed");
    }

    @Test
    public void testDupStringMultiChar() {
        String duped = Utils.dupString('c',5);
        Assert.assertEquals(duped.length(), 5, "dupString did not produce five character string");
        Assert.assertEquals(duped,"ccccc","dupString string was incorrect");
    }

    @Test
    public void testJoinMap() {
        Map<String,Integer> map = new LinkedHashMap<String,Integer>();
        map.put("one",1);
        map.put("two",2);
        String joined = Utils.joinMap("-",";",map);
        Assert.assertTrue("one-1;two-2".equals(joined));
    }

    @Test
    public void testJoinMapLargerSet() {
        Map<String,Integer> map = new LinkedHashMap<String,Integer>();
        map.put("one",1);
        map.put("two",2);
        map.put("three",1);
        map.put("four",2);
        map.put("five",1);
        map.put("six",2);
        String joined = Utils.joinMap("-",";",map);
        Assert.assertTrue("one-1;two-2;three-1;four-2;five-1;six-2".equals(joined));
    }

    @Test
    public void testConcat() {
        final String s1 = "A";
        final String s2 = "CC";
        final String s3 = "TTT";
        final String s4 = "GGGG";
        Assert.assertEquals(new String(Utils.concat()), "");
        Assert.assertEquals(new String(Utils.concat(s1.getBytes())), s1);
        Assert.assertEquals(new String(Utils.concat(s1.getBytes(), s2.getBytes())), s1 + s2);
        Assert.assertEquals(new String(Utils.concat(s1.getBytes(), s2.getBytes(), s3.getBytes())), s1 + s2 + s3);
        Assert.assertEquals(new String(Utils.concat(s1.getBytes(), s2.getBytes(), s3.getBytes(), s4.getBytes())), s1 + s2 + s3 + s4);
    }

    @Test
    public void testEscapeExpressions() {
        String[] expected, actual;

        expected = new String[] {"one", "two", "three"};
        actual = Utils.escapeExpressions("one two three");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions(" one two three");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions("one two three ");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions(" one two three ");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions("  one  two  three  ");
        Assert.assertEquals(actual, expected);

        expected = new String[] {"one", "two", "three four", "five", "six"};
        actual = Utils.escapeExpressions("one two 'three four' five six");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions(" one two 'three four' five six");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions("one two 'three four' five six ");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions(" one two 'three four' five six ");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions("  one  two  'three four'  five  six  ");
        Assert.assertEquals(actual, expected);

        expected = new String[] {"one two", "three", "four"};
        actual = Utils.escapeExpressions("'one two' three four");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions(" 'one two' three four");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions("'one two' three four ");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions(" 'one two' three four ");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions("  'one two'  three  four  ");
        Assert.assertEquals(actual, expected);

        expected = new String[] {"one", "two", "three four"};
        actual = Utils.escapeExpressions("one two 'three four'");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions(" one two 'three four'");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions("one two 'three four' ");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions(" one two 'three four' ");
        Assert.assertEquals(actual, expected);
        actual = Utils.escapeExpressions("  one  two  'three four'  ");
        Assert.assertEquals(actual, expected);
    }

    @Test
    public void testCalcMD5() throws Exception {
        final File source = new File(publicTestDir + "exampleFASTA.fasta");
        final String sourceMD5 = "36880691cf9e4178216f7b52e8d85fbe";

        final byte[] sourceBytes = IOUtils.readFileIntoByteArray(source);
        Assert.assertEquals(Utils.calcMD5(sourceBytes), sourceMD5);

        final String sourceString = FileUtils.readFileToString(source);
        Assert.assertEquals(Utils.calcMD5(sourceString), sourceMD5);
    }

    @Test
    public void testLongestCommonOps() {
        for ( int prefixLen = 0; prefixLen < 20; prefixLen++ ) {
            for ( int extraSeq1Len = 0; extraSeq1Len < 10; extraSeq1Len++ ) {
                for ( int extraSeq2Len = 0; extraSeq2Len < 10; extraSeq2Len++ ) {
                    for ( int max = 0; max < 50; max++ ) {
                        final String prefix = Utils.dupString("A", prefixLen);
                        final int expected = Math.min(prefixLen, max);

                        {
                            final String seq1 = prefix + Utils.dupString("C", extraSeq1Len);
                            final String seq2 = prefix + Utils.dupString("G", extraSeq1Len);
                            Assert.assertEquals(Utils.longestCommonPrefix(seq1.getBytes(), seq2.getBytes(), max), expected, "LongestCommonPrefix failed: seq1 " + seq1 + " seq2 " + seq2 + " max " + max);
                        }

                        {
                            final String seq1 = Utils.dupString("C", extraSeq1Len) + prefix;
                            final String seq2 = Utils.dupString("G", extraSeq1Len) + prefix;
                            Assert.assertEquals(Utils.longestCommonSuffix(seq1.getBytes(), seq2.getBytes(), max), expected, "longestCommonSuffix failed: seq1 " + seq1 + " seq2 " + seq2 + " max " + max);
                        }
                    }
                }
            }
        }
    }
}