#include "Exception.hpp"
#include "DateTime.hpp"
#include "Filesystem.hpp"
#include "pwiz/utility/math/round.hpp"
#include <string>
#include <sstream>
#include <cmath>

Namespaces
namespace	pwiz
	AMTContainer.hpp.
namespace	pwiz::util

Macros
#define	unit_assert(x) (!(x) ? throw std::runtime_error(unit_assert_message(__FILE__, __LINE__, #x)) : 0)
#define	unit_assert_operator_equal(expected, actual) (!(expected == actual) ? throw std::runtime_error(unit_assert_equal_message(__FILE__, __LINE__, lexical_cast<string>(expected), lexical_cast<string>(actual), #actual)) : 0)
#define	unit_assert_equal(x, y, epsilon) (!(fabs((x)-(y)) <= (epsilon)) ? throw std::runtime_error(unit_assert_numeric_equal_message(__FILE__, __LINE__, (x), (y), (epsilon))) : 0)
#define	unit_assert_throws(x, exception)
#define	unit_assert_throws_what(x, exception, whatStr)
#define	unit_assert_matrices_equal(A, B, epsilon) unit_assert(boost::numeric::ublas::norm_frobenius((A)-(B)) < (epsilon))
#define	unit_assert_vectors_equal(A, B, epsilon) unit_assert(boost::numeric::ublas::norm_2((A)-(B)) < (epsilon))
#define	TEST_PROLOG_EX(argc, argv, suffix)
#define	TEST_PROLOG(argc, argv) TEST_PROLOG_EX(argc, argv, "")
#define	TEST_FAILED(x)
#define	TEST_EPILOG

Functions
std::string	pwiz::util::unit_assert_message (const char filename, int line, const char expression)
std::string	pwiz::util::unit_assert_equal_message (const char filename, int line, const std::string &x, const std::string &y, const char expression)
std::string	pwiz::util::unit_assert_numeric_equal_message (const char *filename, int line, double x, double y, double epsilon)
std::string	pwiz::util::unit_assert_exception_message (const char filename, int line, const char expression, const std::string &exception)
std::string	pwiz::util::escape_teamcity_string (const std::string &str)

Macro Definition Documentation

#define unit_assert ( x ) (!(x) ? throw std::runtime_error(unit_assert_message(__FILE__, __LINE__, #x)) : 0)

Definition at line 82 of file unit.hpp.

Referenced by checkSpectrumInfo(), checkTestPair(), compare(), compareRecords(), createTestPath(), diff(), doSomething(), main(), modificationTest(), operatorTest(), readData(), runSpecialTest(), SecondHandler::startElement(), test(), test1(), test2(), test256(), test5peptide(), test5peptideFT(), test_basic(), test_compute(), test_createFilter(), test_createFilters(), test_default_double(), test_default_float(), test_format_date_time(), test_integer(), test_multiplier(), test_mzML_1_0(), test_parse_date_time(), test_pdb(), test_pdb_vs_integer(), test_range(), test_SampledData(), test_SNR(), test_time_from_OADATE(), test_v3(), test_xml_datetime(), testAbbreviateByteSize(), testAccept(), testAddition(), testAdjustRT(), testAlternativeProtein(), testAmbiguousResidue(), testAminoAcidModification(), testAnalysisData(), testAnalysisResult(), testAnalysisSampleCollection(), testAnalysisSoftware(), testAnalyzer(), testAutomaticUpdate(), testBadFile(), testBandedComplex(), testBasic(), testBinaryDataArray(), testBinaryDataArrayExternalMetadata(), testBinaryDataOnly(), testBombesin(), testCancel(), testChromatogram(), testChromatogramList(), testChromatogramListWithPositions(), testChromatograms(), testCleavageAgents(), testComplex(), testComponent(), testComponentList(), testCompound(), testConfig(), testConfiguration(), testContact(), testContactRole(), testContacts(), testContainer(), testContains(), testCreation(), testCV(), testCVMap(), testCVMapIO(), testCVParam(), testData(), testData2_LocalMax(), testData2_Parabola(), testDatabaseTranslation(), testDataCollection(), testDataProcessing(), testDBSequence(), testDefault(), testDefaultTabHandler(), testDeisotoping(), testDetector(), testDigestedPeptides(), testDouble(), testEnzymaticSearchConstraint(), testEnzyme(), testEquality(), testEven(), testEvenMS2(), testEvidence(), testExpandPathmask(), testExtraction(), testFeature(), testFeatureAux(), testFeatureDetectorSimple(), testFeatureField(), testFile(), testFileContent(), testFileDescription(), testFilename(), testFileReads(), testFilter(), testFind(), testFloating(), testFormula(), testFormulaOperations(), testFragmentArray(), testGaussian_Bombesin2(), testGaussian_Bombesin3(), testGet(), testGetAnchors(), testHasBinaryData(), testIdentData(), testIdentifiable(), testIDParsing(), testIDTranslation(), testIndexSet(), testInfo(), testInputs(), testInstantiation(), testInstrument(), testInstrumentConfiguration(), testIntegralReally(), testIntensityThresholding(), testInterface(), testIntervalExtraction(), testIntervalExtraction2(), testIntExtraction(), testIO(), testIonisation(), testIonType(), testIs(), testIsA(), testIsChildOf(), testIStream(), testIsWithinTolerance(), testIteratorEquality(), testMassAbundance(), testMassAnalyzerFilter(), testMassTable(), testMatch(), testMatchData(), testMaxPrecisionDiff(), testMeasure(), testMemoryMRUCache(), testMerge(), testMetadata(), testMillion(), testModAminoAcidMass(), testModeBinaryDataOnly(), testModelAndManufacturer(), testModeMetaDataAndBinaryData(), testModeMetaDataAndSequence(), testModeMetaDataOnly(), testModeOff(), testModification(), testModificationInfo(), testMRU(), testMS2Activation(), testMS2Denoising(), testMSData(), testMSDataConstruction(), testMSDiffUpdate(), testMSInspectIStream(), testMSLevelSet(), testMSMSPipelineAnalysis(), testMSMSRunSummary(), testMulti(), testMultiplePeaks(), testNontrypticBSA(), testNormalization(), testObject(), testObject_ChromatogramList(), testObject_SpectrumList(), testObjectWithMSData(), testOtherRelations(), testParabola(), testParamContainer(), testParameterConversion(), testParamGroup(), testParse(), testParse2(), testPeak(), testPeakData(), testPeakel(), testPeakelAux(), testPeakelConstruction(), testPeakelField(), testPeakEquality(), testPeakFamily(), testPeptide(), testPeptideEvidence(), testPeptideHypothesis(), testPeptideID_dataFetcherConstructor(), testPeptideProphetResult(), testPepXMLSpecificity(), testPerson(), testPrecursor(), testPrecursorMassRemoval(), testPrecursorRefine(), testPredicate(), testPredicate_Feature(), testPrediction(), testProcessingMethod(), testProduct(), testProjected(), testProtein(), testProteinAmbiguityGroup(), testProteinDetectionHypothesis(), testProteinDetectionList(), testProteinDetectionProtocol(), testProteinList(), testProteinListSimple(), testProteomeData(), testQ3RatioResult(), testQR(), testRead(), testReader(), testRectangularQR(), testRegexCVMap(), testRegexCVMapIO(), testRemove(), testResidue(), testRetentionTime(), testReversedList(), testRun(), testSample(), testSampleEnzyme(), testScan(), testScanEventSet(), testScanList(), testScanNumberSet(), testScanSettings(), testScanTimeRange(), testSearchDatabase(), testSearchHit(), testSearchModification(), testSearchResult(), testSearchSummary(), testSelectedIndices(), testSemitrypticBSA(), testSemitrypticMethionineClippingBSA(), testSerialize(), testSerializeReally(), testSHA1(), testShuffledList(), testSieve(), testSnapModifications(), testSoftware(), testSource(), testSourceFile(), testSpecificity(), testSpectraData(), testSpectrum(), testSpectrumIdentificationList(), testSpectrumIdentificationProtocol(), testSpectrumList(), testSpectrumListSimple(), testSpectrumListWithPositions(), testSpectrumListWriteProgress(), testSpectrumQuery(), testStatic(), testStream(), testString(), testSynonyms(), testTarget(), testThreadSafety(), testThreadSafetyWorker(), testToy(), testToyExample(), testTraData(), testTransition(), testTranslation(), testTrypticBSA(), testUpdateRequest(), testUpperBound(), testUserParam(), testValidation(), testVectorIO(), testWrap(), testWrapActivation(), testWrapDefaultArrayLength(), testWrapMassAnalyzer(), testWrapMSLevel(), testWrapMZWindow(), testWrapPolarity(), testWrapScanTimeRange(), testWrapSortScanTime(), testWriteRead(), testWriteReadBMS1(), testWriteReadBMS2(), testWriteReadCMS1(), testWriteReadCMS2(), testWriteReadMS1(), testWriteReadMS2(), testZeroSamplesFilter(), validateRecalculation(), validateWriteRead(), verifyBombesinFeatures(), verifyBombesinPeakels(), verifyPrecursorInfo(), verifyPrecursorMZ(), MyWrapper::verifySize(), and verifySpectrumSize().

#define unit_assert_operator_equal	(	expected,
		actual
	)	(!(expected == actual) ? throw std::runtime_error(unit_assert_equal_message(__FILE__, __LINE__, lexical_cast<string>(expected), lexical_cast<string>(actual), #actual)) : 0)

Definition at line 86 of file unit.hpp.

Referenced by FirstHandler::characters(), FirstHandler::endElement(), FifthHandler::endElement(), main(), RootHandler::startElement(), AnotherRootHandler::startElement(), test(), testAllDataProcessing(), testBSADigestion(), testCleavageAgent(), testCleavageAgents(), testConversion(), testDatabaseTranslation(), testDecoding(), testDigestedPeptides(), testDigestionMetadata(), testDone(), testHasBinaryData(), testIdentifyFileFormat(), testIdSet(), testIndexSet(), testMeasure(), testMemoryMRUCache(), testModeBinaryDataOnly(), testModeMetaDataAndBinaryData(), testModeMetaDataAndSequence(), testModeMetaDataOnly(), testModeOff(), testNested(), testNoAutoUnescape(), testNontrypticBSA(), testNormalization(), testPepXMLSpecificity(), testPropertyValues(), testRootElement(), testSaxParserString(), testSelectedIndices(), testSemitrypticBSA(), testSemitrypticMethionineClippingBSA(), testStripChargeFromConventionalSpectrumId(), testWrap(), and testWrapTitleMaker().

#define unit_assert_equal	(	x,
		y,
		epsilon
	)	(!(fabs((x)-(y)) <= (epsilon)) ? throw std::runtime_error(unit_assert_numeric_equal_message(__FILE__, __LINE__, (x), (y), (epsilon))) : 0)

Definition at line 90 of file unit.hpp.

Referenced by checkSpectrumInfo(), compare(), fragmentTest(), modificationTest(), peptideTest(), test(), test2(), test_2Pass(), test_2Pass_NoSignal(), test_createFilters(), test_mzML_1_0(), test_pvalue(), test_real(), test_real_wrapper(), test_series(), test_v3(), testAnalysisData(), testBanded(), testBasic(), testColinearLinearWarp(), testConfig(), testConfiguration(), testData(), testData2_LocalMax(), testData2_Parabola(), testDouble(), testDoubleQR(), testExactFit(), testExactFitQR(), testFilename(), testFind(), testFit(), testFormula(), testFragmentArray(), testIDParsing(), testInputs(), testIonType(), testIStream(), testLeastSquares(), testLeastSquaresQR(), testMatrix(), testMaxPrecisionDiff(), testMetadata(), testMSInspectIStream(), testMultiplePeaks(), testMZ(), testNoiseFloorVarianceCalculation(), testNonColinearLinearWarp(), testNormalization(), testParabola(), testPeptideEvidence(), testPiecewiseLinearWarp(), testPPM(), testPrecursorMassRemoval(), testProbabilites(), testQR(), testRectangularQR(), testReflector(), testResidue(), testSearchDatabase(), testSearchModification(), testSimpleRectangleQR(), testSparse(), testSpectrumIdentificationList(), testSplineWarp(), testToy(), testToyExample(), testWarpRT(), testWeightedLeastSquares(), validateRecalculation(), verifyBombesinFeatures(), verifyPrecursorInfo(), and verifyPrecursorMZ().

#define unit_assert_throws	(	x,
		exception
	)

Value:

{ \
        bool threw = false; \
        try { (x); } \
        catch (exception&) \
        { \
            threw = true; \
        } \
        if (!threw) \
            throw std::runtime_error(unit_assert_exception_message(__FILE__, __LINE__, #x, #exception)); \
    }

Definition at line 94 of file unit.hpp.

Referenced by test(), testCleavageAgents(), testFind(), testInterface(), testRootElement(), testWrapActivation(), testWrapMassAnalyzer(), and testWrapPolarity().

#define unit_assert_throws_what	(	x,
		exception,
		whatStr
	)

Value:

{ \
        bool threw = false; \
        try { (x); } \
        catch (exception& e) \
        { \
            if (e.what() == std::string(whatStr)) \
                threw = true; \
            else \
                throw std::runtime_error(unit_assert_exception_message(__FILE__, __LINE__, #x, std::string(#exception)+" "+(whatStr)+"\nBut a different exception was thrown: ")+(e.what())); \
        } \
        if (!threw) \
            throw std::runtime_error(unit_assert_exception_message(__FILE__, __LINE__, #x, std::string(#exception)+" "+(whatStr))); \
    }

Definition at line 107 of file unit.hpp.

Referenced by modificationTest(), test(), testDuplicateId(), and testInfo().

#define unit_assert_matrices_equal	(	A,
		B,
		epsilon
	)	unit_assert(boost::numeric::ublas::norm_frobenius((A)-(B)) < (epsilon))

Definition at line 123 of file unit.hpp.

Referenced by test(), pwiz::frequency::DerivativeTest::testDerivatives(), and testDifferenceQuotient().

#define unit_assert_vectors_equal	(	A,
		B,
		epsilon
	)	unit_assert(boost::numeric::ublas::norm_2((A)-(B)) < (epsilon))

Definition at line 127 of file unit.hpp.

Referenced by test().

#define TEST_PROLOG_EX	(	argc,
		argv,
		suffix
	)

Value:

bfs::path testName = bfs::change_extension(bfs::basename(argv[0]), (suffix)); \
    string teamcityTestName = pwiz::util::escape_teamcity_string(testName.string()); \
    bpt::ptime testStartTime; \
    vector<string> testArgs(argv, argv+argc); \
    bool teamcityTestDecoration = find(testArgs.begin(), testArgs.end(), "--teamcity-test-decoration") != testArgs.end(); \
    if (teamcityTestDecoration) \
    { \
        testStartTime = bpt::microsec_clock::local_time(); \
        cout << "##teamcity[testStarted name='" << teamcityTestName << "']" << endl; \
    } \
    int testExitStatus = 0;

Definition at line 145 of file unit.hpp.

Referenced by main().

#define TEST_PROLOG	(	argc,
		argv
	)	TEST_PROLOG_EX(argc, argv, "")

Definition at line 158 of file unit.hpp.

Referenced by main().

#define TEST_FAILED ( x )

Value:

if (teamcityTestDecoration) \
        cout << "##teamcity[testFailed name='" << teamcityTestName << "' message='" << pwiz::util::escape_teamcity_string((x)) << "']\n"; \
    cerr << (x) << endl; \
    testExitStatus = 1;

Definition at line 160 of file unit.hpp.

Referenced by main().

#define TEST_EPILOG

Value:

if (teamcityTestDecoration) \
        cout << "##teamcity[testFinished name='" << teamcityTestName << \
                "' duration='" << round((bpt::microsec_clock::local_time() - testStartTime).total_microseconds() / 1000.0) << "']" << endl; \
    return testExitStatus;

Definition at line 166 of file unit.hpp.

Referenced by main().

Namespaces

Macros

Functions

Macro Definition Documentation