/*
* 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
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* 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,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* 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,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.utils;
import htsjdk.tribble.Tribble;
import htsjdk.tribble.readers.LineIterator;
import htsjdk.tribble.readers.PositionalBufferedStream;
import htsjdk.tribble.util.TabixUtils;
import htsjdk.variant.bcf2.BCF2Codec;
import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.vcf.VCFCodec;
import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLine;
import org.apache.log4j.AppenderSkeleton;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.PatternLayout;
import org.apache.log4j.spi.LoggingEvent;
import org.broadinstitute.gatk.utils.collections.Pair;
import org.broadinstitute.gatk.utils.commandline.CommandLineUtils;
import org.broadinstitute.gatk.utils.crypt.CryptUtils;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import org.broadinstitute.gatk.utils.io.IOUtils;
import org.broadinstitute.gatk.utils.variant.GATKVCFUtils;
import org.testng.Assert;
import org.testng.Reporter;
import org.testng.SkipException;
import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.*;
/**
*
* User: aaron
* Date: Apr 14, 2009
* Time: 10:24:30 AM
*
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2009 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
*
*/
/**
* @author aaron
* @version 1.0
* @date Apr 14, 2009
* <p/>
* Class BaseTest
* <p/>
* This is the base test class for all of our test cases. All test cases should extend from this
* class; it sets up the logger, and resolves the location of directories that we rely on.
*/
@SuppressWarnings("unchecked")
public abstract class BaseTest {
/** our log, which we want to capture anything from org.broadinstitute.sting */
public static final Logger logger = CommandLineUtils.getStingLogger();
private static final String CURRENT_DIRECTORY = System.getProperty("user.dir");
public static final String gatkDirectory = System.getProperty("gatkdir", CURRENT_DIRECTORY) + "/";
public static final String baseDirectory = System.getProperty("basedir", CURRENT_DIRECTORY) + "/";
public static final String testType = System.getProperty("testType"); // May be null
public static final String testTypeSubDirectory = testType == null ? "" : ("/" + testType); // May be empty
public static final String hg18Reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
public static final String hg19Reference = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta";
public static final String b36KGReference = "/humgen/1kg/reference/human_b36_both.fasta";
//public static final String b37KGReference = "/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta";
public static final String b37KGReference = "/humgen/1kg/reference/human_g1k_v37.fasta";
public static final String b37KGReferenceWithDecoy = "/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37_decoy.fasta";
public static final String hg19RefereneWithChrPrefixInChromosomeNames = "/humgen/gsa-hpprojects/GATK/bundle/current/hg19/ucsc.hg19.fasta";
public static final String GATKDataLocation = "/humgen/gsa-hpprojects/GATK/data/";
public static final String validationDataLocation = GATKDataLocation + "Validation_Data/";
public static final String evaluationDataLocation = GATKDataLocation + "Evaluation_Data/";
public static final String comparisonDataLocation = GATKDataLocation + "Comparisons/";
public static final String annotationDataLocation = GATKDataLocation + "Annotations/";
public static final String b37GoodBAM = validationDataLocation + "/CEUTrio.HiSeq.b37.chr20.10_11mb.bam";
public static final String b37GoodNA12878BAM = validationDataLocation + "/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam";
public static final String b37_NA12878_OMNI = validationDataLocation + "/NA12878.omni.vcf";
public static final String dbsnpDataLocation = GATKDataLocation;
public static final String b36dbSNP129 = dbsnpDataLocation + "dbsnp_129_b36.vcf";
public static final String b37dbSNP129 = dbsnpDataLocation + "dbsnp_129_b37.vcf";
public static final String b37dbSNP132 = dbsnpDataLocation + "dbsnp_132_b37.vcf";
public static final String b37dbSNP138 = "/humgen/gsa-hpprojects/GATK/bundle/current/b37/dbsnp_138.b37.vcf";
public static final String hg18dbSNP132 = dbsnpDataLocation + "dbsnp_132.hg18.vcf";
public static final String hapmapDataLocation = comparisonDataLocation + "Validated/HapMap/3.3/";
public static final String b37hapmapGenotypes = hapmapDataLocation + "genotypes_r27_nr.b37_fwd.vcf";
public static final String intervalsLocation = "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/";
public static final String hg19Intervals = intervalsLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list";
public static final String hg19Chr20Intervals = GATKDataLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.chr20.interval_list";
public static final boolean REQUIRE_NETWORK_CONNECTION = false;
private static final String networkTempDirRoot = "/broad/hptmp/";
private static final boolean networkTempDirRootExists = new File(networkTempDirRoot).exists();
private static final File networkTempDirFile;
private static final String privateTestDirRelative = "private/gatk-tools-private/src/test/resources/";
public static final String privateTestDir = new File(gatkDirectory, privateTestDirRelative).getAbsolutePath() + "/";
protected static final String privateTestDirRoot = privateTestDir.replace(privateTestDirRelative, "");
private static final String publicTestDirRelative = "public/gatk-engine/src/test/resources/";
public static final String publicTestDir = new File(gatkDirectory, publicTestDirRelative).getAbsolutePath() + "/";
protected static final String publicTestDirRoot = publicTestDir.replace(publicTestDirRelative, "");
public static final String keysDataLocation = validationDataLocation + "keys/";
public static final String gatkKeyFile = CryptUtils.GATK_USER_KEY_DIRECTORY + "gsamembers_broadinstitute.org.key";
public static final String exampleFASTA = publicTestDir + "exampleFASTA.fasta";
public final static String NA12878_PCRFREE = privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam";
public final static String NA12878_WEx = privateTestDir + "CEUTrio.HiSeq.WEx.b37_decoy.NA12878.20_10_11mb.bam";
public static final boolean queueTestRunModeIsSet = System.getProperty("queuetest.run", "").equals("true");
/** before the class starts up */
static {
// setup a basic log configuration
CommandLineUtils.configureConsoleLogging();
// setup our log layout
PatternLayout layout = new PatternLayout();
layout.setConversionPattern("TEST %C{1}.%M - %d{HH:mm:ss,SSS} - %m%n");
// now set the layout of all the loggers to our layout
CommandLineUtils.setLayout(logger, layout);
// Set the Root logger to only output warnings.
logger.setLevel(Level.WARN);
if (networkTempDirRootExists) {
networkTempDirFile = IOUtils.tempDir("temp.", ".dir", new File(networkTempDirRoot + System.getProperty("user.name")));
networkTempDirFile.deleteOnExit();
} else {
networkTempDirFile = null;
}
if ( REQUIRE_NETWORK_CONNECTION ) {
// find our file sources
if (!fileExist(hg18Reference) || !fileExist(hg19Reference) || !fileExist(b36KGReference)) {
logger.fatal("We can't locate the reference directories. Aborting!");
throw new RuntimeException("BaseTest setup failed: unable to locate the reference directories");
}
}
}
/**
* Simple generic utility class to creating TestNG data providers:
*
* 1: inherit this class, as in
*
* private class SummarizeDifferenceTest extends TestDataProvider {
* public SummarizeDifferenceTest() {
* super(SummarizeDifferenceTest.class);
* }
* ...
* }
*
* Provide a reference to your class to the TestDataProvider constructor.
*
* 2: Create instances of your subclass. Return from it the call to getTests, providing
* the class type of your test
*
* <code>
* {@literal @}DataProvider(name = "summaries")
* public Object[][] createSummaries() {
* new SummarizeDifferenceTest().addDiff("A", "A").addSummary("A:2");
* new SummarizeDifferenceTest().addDiff("A", "B").addSummary("A:1", "B:1");
* return SummarizeDifferenceTest.getTests(SummarizeDifferenceTest.class);
* }
* </code>
*
* This class magically tracks created objects of this
*/
public static class TestDataProvider {
private static final Map<Class, List<Object>> tests = new HashMap<>();
protected String name;
/**
* Create a new TestDataProvider instance bound to the class variable C
*/
public TestDataProvider(Class c, String name) {
if ( ! tests.containsKey(c) )
tests.put(c, new ArrayList<>());
tests.get(c).add(this);
this.name = name;
}
public TestDataProvider(Class c) {
this(c, "");
}
public void setName(final String name) {
this.name = name;
}
/**
* Return all of the data providers in the form expected by TestNG of type class C
* @param c
* @return
*/
public static Object[][] getTests(Class c) {
List<Object[]> params2 = new ArrayList<Object[]>();
for ( Object x : tests.get(c) ) params2.add(new Object[]{x});
return params2.toArray(new Object[][]{});
}
@Override
public String toString() {
return "TestDataProvider("+name+")";
}
}
/**
* test if the file exists
*
* @param file name as a string
* @return true if it exists
*/
public static boolean fileExist(String file) {
File temp = new File(file);
return temp.exists();
}
/**
* this appender looks for a specific message in the log4j stream.
* It can be used to verify that a specific message was generated to the logging system.
*/
public static class ValidationAppender extends AppenderSkeleton {
private boolean foundString = false;
private String targetString = "";
public ValidationAppender(String target) {
targetString = target;
}
@Override
protected void append(LoggingEvent loggingEvent) {
if (loggingEvent.getMessage().equals(targetString))
foundString = true;
}
public void close() {
// do nothing
}
public boolean requiresLayout() {
return false;
}
public boolean foundString() {
return foundString;
}
}
/**
* Creates a temp file that will be deleted on exit after tests are complete.
* @param name Prefix of the file.
* @param extension Extension to concat to the end of the file.
* @return A file in the temporary directory starting with name, ending with extension, which will be deleted after the program exits.
*/
public static File createTempFile(final String name, final String extension) {
try {
final File file = File.createTempFile(name, extension);
file.deleteOnExit();
// Mark corresponding indices for deletion on exit as well just in case an index is created for the temp file:
new File(file.getAbsolutePath() + Tribble.STANDARD_INDEX_EXTENSION).deleteOnExit();
new File(file.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION).deleteOnExit();
new File(file.getAbsolutePath() + ".bai").deleteOnExit();
new File(file.getAbsolutePath().replaceAll(extension + "$", ".bai")).deleteOnExit();
return file;
} catch (IOException ex) {
throw new ReviewedGATKException("Cannot create temp file: " + ex.getMessage(), ex);
}
}
/**
* Creates a temp list file that will be deleted on exit after tests are complete.
* @param tempFilePrefix Prefix of the file.
* @param lines lines to write to the file.
* @return A list file in the temporary directory starting with tempFilePrefix, which will be deleted after the program exits.
*/
public static File createTempListFile(final String tempFilePrefix, final String... lines) {
try {
final File tempListFile = createTempFile(tempFilePrefix, ".list");
final PrintWriter out = new PrintWriter(tempListFile);
for (final String line : lines) {
out.println(line);
}
out.close();
return tempListFile;
} catch (IOException ex) {
throw new ReviewedGATKException("Cannot create temp file: " + ex.getMessage(), ex);
}
}
/**
* Creates a temp file that will be deleted on exit after tests are complete.
* @param name Name of the file.
* @return A file in the network temporary directory with name, which will be deleted after the program exits.
* @throws SkipException when the network is not available.
*/
public static File tryCreateNetworkTempFile(String name) {
if (!networkTempDirRootExists)
throw new SkipException("Network temporary directory does not exist: " + networkTempDirRoot);
File file = new File(networkTempDirFile, name);
file.deleteOnExit();
return file;
}
/**
* Log this message so that it shows up inline during output as well as in html reports
*
* @param message
*/
public static void log(final String message) {
Reporter.log(message, true);
}
private static final double DEFAULT_FLOAT_TOLERANCE = 1e-1;
public static final void assertEqualsDoubleSmart(final Object actual, final Double expected) {
Assert.assertTrue(actual instanceof Double, "Not a double");
assertEqualsDoubleSmart((double)(Double)actual, (double)expected);
}
public static final void assertEqualsDoubleSmart(final Object actual, final Double expected, final double tolerance) {
Assert.assertTrue(actual instanceof Double, "Not a double");
assertEqualsDoubleSmart((double)(Double)actual, (double)expected, tolerance);
}
public static final void assertEqualsDoubleSmart(final double actual, final double expected) {
assertEqualsDoubleSmart(actual, expected, DEFAULT_FLOAT_TOLERANCE);
}
public static final <T> void assertEqualsSet(final Set<T> actual, final Set<T> expected, final String info) {
final Set<T> actualSet = new HashSet<T>(actual);
final Set<T> expectedSet = new HashSet<T>(expected);
Assert.assertTrue(actualSet.equals(expectedSet), info); // note this is necessary due to testng bug for set comps
}
public static void assertEqualsDoubleSmart(final double actual, final double expected, final double tolerance) {
assertEqualsDoubleSmart(actual, expected, tolerance, null);
}
public static void assertEqualsDoubleSmart(final double actual, final double expected, final double tolerance, final String message) {
if ( Double.isNaN(expected) ) // NaN == NaN => false unfortunately
Assert.assertTrue(Double.isNaN(actual), "expected is nan, actual is not");
else if ( Double.isInfinite(expected) ) // NaN == NaN => false unfortunately
Assert.assertTrue(Double.isInfinite(actual), "expected is infinite, actual is not");
else {
final double delta = Math.abs(actual - expected);
final double ratio = Math.abs(actual / expected - 1.0);
Assert.assertTrue(delta < tolerance || ratio < tolerance, "expected = " + expected + " actual = " + actual
+ " not within tolerance " + tolerance
+ (message == null ? "" : "message: " + message));
}
}
public static void assertVariantContextsAreEqual( final VariantContext actual, final VariantContext expected ) {
Assert.assertNotNull(actual, "VariantContext expected not null");
Assert.assertEquals(actual.getChr(), expected.getChr(), "chr");
Assert.assertEquals(actual.getStart(), expected.getStart(), "start");
Assert.assertEquals(actual.getEnd(), expected.getEnd(), "end");
Assert.assertEquals(actual.getID(), expected.getID(), "id");
Assert.assertEquals(actual.getAlleles(), expected.getAlleles(), "alleles for " + expected + " vs " + actual);
assertAttributesEquals(actual.getAttributes(), expected.getAttributes());
Assert.assertEquals(actual.filtersWereApplied(), expected.filtersWereApplied(), "filtersWereApplied");
Assert.assertEquals(actual.isFiltered(), expected.isFiltered(), "isFiltered");
assertEqualsSet(actual.getFilters(), expected.getFilters(), "filters");
assertEqualsDoubleSmart(actual.getPhredScaledQual(), expected.getPhredScaledQual());
Assert.assertEquals(actual.hasGenotypes(), expected.hasGenotypes(), "hasGenotypes");
if ( expected.hasGenotypes() ) {
assertEqualsSet(actual.getSampleNames(), expected.getSampleNames(), "sample names set");
Assert.assertEquals(actual.getSampleNamesOrderedByName(), expected.getSampleNamesOrderedByName(), "sample names");
final Set<String> samples = expected.getSampleNames();
for ( final String sample : samples ) {
assertGenotypesAreEqual(actual.getGenotype(sample), expected.getGenotype(sample));
}
}
}
public static void assertVariantContextStreamsAreEqual(final Iterable<VariantContext> actual, final Iterable<VariantContext> expected) {
final Iterator<VariantContext> actualIT = actual.iterator();
final Iterator<VariantContext> expectedIT = expected.iterator();
while ( expectedIT.hasNext() ) {
final VariantContext expectedVC = expectedIT.next();
if ( expectedVC == null )
continue;
VariantContext actualVC;
do {
Assert.assertTrue(actualIT.hasNext(), "Too few records found in actual");
actualVC = actualIT.next();
} while ( actualIT.hasNext() && actualVC == null );
if ( actualVC == null )
Assert.fail("Too few records in actual");
assertVariantContextsAreEqual(actualVC, expectedVC);
}
Assert.assertTrue(! actualIT.hasNext(), "Too many records found in actual");
}
public static void assertGenotypesAreEqual(final Genotype actual, final Genotype expected) {
Assert.assertEquals(actual.getSampleName(), expected.getSampleName(), "Genotype names");
Assert.assertEquals(actual.getAlleles(), expected.getAlleles(), "Genotype alleles");
Assert.assertEquals(actual.getGenotypeString(), expected.getGenotypeString(), "Genotype string");
Assert.assertEquals(actual.getType(), expected.getType(), "Genotype type");
// filters are the same
Assert.assertEquals(actual.getFilters(), expected.getFilters(), "Genotype fields");
Assert.assertEquals(actual.isFiltered(), expected.isFiltered(), "Genotype isFiltered");
// inline attributes
Assert.assertEquals(actual.getDP(), expected.getDP(), "Genotype dp");
Assert.assertTrue(Arrays.equals(actual.getAD(), expected.getAD()));
Assert.assertEquals(actual.getGQ(), expected.getGQ(), "Genotype gq");
Assert.assertEquals(actual.hasPL(), expected.hasPL(), "Genotype hasPL");
Assert.assertEquals(actual.hasAD(), expected.hasAD(), "Genotype hasAD");
Assert.assertEquals(actual.hasGQ(), expected.hasGQ(), "Genotype hasGQ");
Assert.assertEquals(actual.hasDP(), expected.hasDP(), "Genotype hasDP");
Assert.assertEquals(actual.hasLikelihoods(), expected.hasLikelihoods(), "Genotype haslikelihoods");
Assert.assertEquals(actual.getLikelihoodsString(), expected.getLikelihoodsString(), "Genotype getlikelihoodsString");
Assert.assertEquals(actual.getLikelihoods(), expected.getLikelihoods(), "Genotype getLikelihoods");
Assert.assertTrue(Arrays.equals(actual.getPL(), expected.getPL()));
Assert.assertEquals(actual.getPhredScaledQual(), expected.getPhredScaledQual(), "Genotype phredScaledQual");
assertAttributesEquals(actual.getExtendedAttributes(), expected.getExtendedAttributes());
Assert.assertEquals(actual.isPhased(), expected.isPhased(), "Genotype isPhased");
Assert.assertEquals(actual.getPloidy(), expected.getPloidy(), "Genotype getPloidy");
}
public static void assertVCFHeadersAreEqual(final VCFHeader actual, final VCFHeader expected) {
Assert.assertEquals(actual.getMetaDataInSortedOrder().size(), expected.getMetaDataInSortedOrder().size(), "No VCF header lines");
// for some reason set.equals() is returning false but all paired elements are .equals(). Perhaps compare to is busted?
//Assert.assertEquals(actual.getMetaDataInInputOrder(), expected.getMetaDataInInputOrder());
final List<VCFHeaderLine> actualLines = new ArrayList<VCFHeaderLine>(actual.getMetaDataInSortedOrder());
final List<VCFHeaderLine> expectedLines = new ArrayList<VCFHeaderLine>(expected.getMetaDataInSortedOrder());
for ( int i = 0; i < actualLines.size(); i++ ) {
Assert.assertEquals(actualLines.get(i), expectedLines.get(i), "VCF header lines");
}
}
public static void assertVCFandBCFFilesAreTheSame(final File vcfFile, final File bcfFile) throws IOException {
final Pair<VCFHeader, GATKVCFUtils.VCIterable<LineIterator>> vcfData = GATKVCFUtils.readAllVCs(vcfFile, new VCFCodec());
final Pair<VCFHeader, GATKVCFUtils.VCIterable<PositionalBufferedStream>> bcfData = GATKVCFUtils.readAllVCs(bcfFile, new BCF2Codec());
assertVCFHeadersAreEqual(bcfData.getFirst(), vcfData.getFirst());
assertVariantContextStreamsAreEqual(bcfData.getSecond(), vcfData.getSecond());
}
private static void assertAttributeEquals(final String key, final Object actual, final Object expected) {
if ( expected instanceof Double ) {
// must be very tolerant because doubles are being rounded to 2 sig figs
assertEqualsDoubleSmart(actual, (Double) expected, 1e-2);
} else
Assert.assertEquals(actual, expected, "Attribute " + key);
}
private static void assertAttributesEquals(final Map<String, Object> actual, Map<String, Object> expected) {
final Set<String> expectedKeys = new HashSet<String>(expected.keySet());
for ( final Map.Entry<String, Object> act : actual.entrySet() ) {
final Object actualValue = act.getValue();
if ( expected.containsKey(act.getKey()) && expected.get(act.getKey()) != null ) {
final Object expectedValue = expected.get(act.getKey());
if ( expectedValue instanceof List ) {
final List<Object> expectedList = (List<Object>)expectedValue;
Assert.assertTrue(actualValue instanceof List, act.getKey() + " should be a list but isn't");
final List<Object> actualList = (List<Object>)actualValue;
Assert.assertEquals(actualList.size(), expectedList.size(), act.getKey() + " size");
for ( int i = 0; i < expectedList.size(); i++ )
assertAttributeEquals(act.getKey(), actualList.get(i), expectedList.get(i));
} else
assertAttributeEquals(act.getKey(), actualValue, expectedValue);
} else {
// it's ok to have a binding in x -> null that's absent in y
Assert.assertNull(actualValue, act.getKey() + " present in one but not in the other");
}
expectedKeys.remove(act.getKey());
}
// now expectedKeys contains only the keys found in expected but not in actual,
// and they must all be null
for ( final String missingExpected : expectedKeys ) {
final Object value = expected.get(missingExpected);
Assert.assertTrue(isMissing(value), "Attribute " + missingExpected + " missing in one but not in other" );
}
}
private static final boolean isMissing(final Object value) {
if ( value == null ) return true;
else if ( value.equals(VCFConstants.MISSING_VALUE_v4) ) return true;
else if ( value instanceof List ) {
// handles the case where all elements are null or the list is empty
for ( final Object elt : (List)value)
if ( elt != null )
return false;
return true;
} else
return false;
}
/**
* Checks whether two double array contain the same values or not.
* @param actual actual produced array.
* @param expected expected array.
* @param tolerance maximum difference between double value to be consider equivalent.
*/
protected static void assertEqualsDoubleArray(final double[] actual, final double[] expected, final double tolerance) {
if (expected == null)
Assert.assertNull(actual);
else {
Assert.assertNotNull(actual);
Assert.assertEquals(actual.length,expected.length,"array length");
}
for (int i = 0; i < actual.length; i++)
Assert.assertEquals(actual[i],expected[i],tolerance,"array position " + i);
}
}