#include "PeptideDatabase.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include <boost/filesystem/operations.hpp>
#include <iostream>

Functions
void	compareRecords (const PeptideDatabase pdb1, const PeptideDatabaseRecord record1, const PeptideDatabase pdb2, const PeptideDatabaseRecord record2)
void	test_basic ()
void	test_range ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0

Function Documentation

void compareRecords	(	const PeptideDatabase *	pdb1,
		const PeptideDatabaseRecord *	record1,
		const PeptideDatabase *	pdb2,
		const PeptideDatabaseRecord *	record2
	)

Definition at line 38 of file PeptideDatabaseTest.cpp.

References pwiz::proteome::PeptideDatabaseRecord::abundance, pwiz::proteome::PeptideDatabaseRecord::formula, pwiz::proteome::PeptideDatabaseRecord::id_ipi, pwiz::proteome::PeptideDatabaseRecord::mass, pwiz::proteome::PeptideDatabase::sequence(), and unit_assert.

Referenced by test_basic().

{
    unit_assert(record1->id_ipi == record2->id_ipi);
    unit_assert(record1->abundance == record2->abundance);
    unit_assert(record1->mass == record2->mass);
    unit_assert(record1->formula == record2->formula);
    unit_assert(pdb1->sequence(*record1) == pdb2->sequence(*record2));
}

void test_basic ( )

Definition at line 49 of file PeptideDatabaseTest.cpp.

References pwiz::proteome::PeptideDatabaseRecord::abundance, pwiz::proteome::PeptideDatabase::append(), pwiz::proteome::PeptideDatabase::begin(), compareRecords(), pwiz::proteome::PeptideDatabase::end(), pwiz::proteome::PeptideDatabaseRecord::formula, pwiz::proteome::PeptideDatabaseRecord::mass, os_, pwiz::proteome::AminoAcid::Info::record(), pwiz::proteome::PeptideDatabase::records(), pwiz::proteome::PeptideDatabase::sequence(), pwiz::proteome::PeptideDatabase::size(), unit_assert, and pwiz::proteome::PeptideDatabase::write().

Referenced by main().

{
    auto_ptr<PeptideDatabase> pdb = PeptideDatabase::create();
    PeptideDatabaseRecord record;
    record.abundance = 10;
    record.mass = 27;
    record.formula = PeptideDatabaseFormula(1, 2, 3, 4, 5);
    pdb->append(record, "darren");
    record.abundance = 20;
    record.mass = 666;
    record.formula = PeptideDatabaseFormula(6, 7, 8, 9, 10);
    pdb->append(record, "goo");
    unit_assert(pdb->size()==2);
   
    const PeptideDatabaseRecord* p = pdb->records();
    unit_assert(p->abundance == 10);
    unit_assert(p->mass == 27);
    unit_assert(p->formula.C == 1); 
    unit_assert(pdb->sequence(*p) == "darren");
    
    p++;
    unit_assert(p->abundance == 20);
    unit_assert(p->mass == 666);
    unit_assert(p->formula.C == 6);
    unit_assert(p->formula.S == 10);
    unit_assert(pdb->sequence(*p) == "goo");
     
    // iterator interface 
    if (os_)
        for (PeptideDatabase::iterator it=pdb->begin(); it!=pdb->end(); ++it) 
            *os_ << *it << " " << pdb->sequence(*it) << endl;
    // test i/o
    string filename = "PeptideDatabaseTest.output.pdb";
    {
        pdb->write(filename);
        auto_ptr<const PeptideDatabase> pdb2 = PeptideDatabase::create(filename);
        unit_assert(pdb2->size() == pdb->size());
      
        for (int i=0; i<pdb->size(); ++i)
        {
            const PeptideDatabaseRecord* record1 = pdb->records()+i;
            const PeptideDatabaseRecord* record2 = pdb2->records()+i;
            compareRecords(pdb.get(), record1, pdb2.get(), record2);
        }
    }
    boost::filesystem::remove(filename);
}

void test_range ( )

Definition at line 104 of file PeptideDatabaseTest.cpp.

References pwiz::proteome::PeptideDatabase::append(), pwiz::proteome::PeptideDatabase::begin(), pwiz::proteome::PeptideDatabaseRecord::mass, pwiz::proteome::PeptideDatabase::mass_lower_bound(), pwiz::proteome::PeptideDatabase::mass_upper_bound(), pwiz::proteome::AminoAcid::Info::record(), and unit_assert.

Referenced by main().

{
    auto_ptr<PeptideDatabase> pdb = PeptideDatabase::create();
    for (int i=0; i<10; i++)
    {
        PeptideDatabaseRecord record;
        record.mass = i;
        pdb->append(record);
    }
    PeptideDatabase::iterator begin = pdb->begin();
    PeptideDatabase::iterator six = pdb->mass_lower_bound(5.5);
    PeptideDatabase::iterator eight = pdb->mass_upper_bound(7.5);
    unit_assert(six == begin+6);
    unit_assert(eight == begin+8);
}

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 123 of file PeptideDatabaseTest.cpp.

References e(), os_, test_basic(), and test_range().

{
    try
    {
        if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
        if (os_) *os_ << "PeptideDatabaseTest\n";
        test_basic();
        test_range();
        return 0;
    }
    catch (exception& e)
    {
        cerr << e.what() << endl;
        return 1;
    }
}

Variable Documentation

ostream* os_ = 0

Definition at line 35 of file PeptideDatabaseTest.cpp.

Referenced by PrintEventHandler::characters(), checkSpectrumInfo(), checkTestPair(), pwiz::proteome::TextWriter::child(), pwiz::tradata::TextWriter::child(), pwiz::identdata::TextWriter::child(), pwiz::msdata::TextWriter::child(), cleanTests(), createProteinList(), createSpectrumList(), demo(), diff(), doSomething(), PrintEventHandler::endElement(), extractPeaks(), fragmentTest(), Reader1::identify(), Reader2::identify(), infoExample(), main(), modificationTest(), WriteCVParam::operator()(), pwiz::proteome::TextWriter::operator()(), pwiz::tradata::TextWriter::operator()(), pwiz::msdata::TextWriter::operator()(), pwiz::identdata::TextWriter::operator()(), PrintAttribute::operator()(), peptideTest(), printSpectrumList(), PrintEventHandler::processingInstruction(), SimpleProgressCallback::progress(), CancelProgressCallback::progress(), Reader1::read(), Reader2::read(), runSpecialTest(), PrintEventHandler::startElement(), test(), test2(), test256(), test5peptide(), test5peptideFT(), test_2Pass(), test_2Pass_NoSignal(), test_basic(), test_compute(), test_createFilter(), test_createFilters(), test_format_date_time(), test_kernel(), test_parse_date_time(), test_real(), test_real_wrapper(), test_SampledData(), test_series(), test_SNR(), test_time_from_OADATE(), test_v3(), test_xml_datetime(), testAccept(), testAdjustRT(), testAlternativeProtein(), testAmbiguousResidue(), testAminoAcidModification(), testAnalysisCollection(), testAnalysisData(), testAnalysisProtocolCollection(), testAnalysisResult(), testAnalysisSampleCollection(), testAnalysisSoftware(), testAnalyzer(), testArray(), testAutomaticUpdate(), testBadFile(), testBadXML(), testBanded(), testBandedComplex(), testBasic(), testBibliographicReference(), testBinaryDataArray(), testBinaryDataOnly(), testBombesin(), testBSADigestion(), testCancel(), testChromatogram(), testChromatogramList(), testChromatogramListWithPositions(), testCleavageAgents(), testColinearLinearWarp(), testComplex(), testComponent(), testComponentList(), testCompound(), testConfig(), testConfiguration(), testContact(), testContactRole(), testContainer(), testCreation(), testCV(), testCVMap(), testCVMapIO(), testCVParam(), testData(), testData2_LocalMax(), testData2_Parabola(), testDatabaseTranslation(), testDataCollection(), testDataProcessing(), testDBSequence(), testDerivatives(), testDetector(), testDifferenceQuotient(), testDone(), testDouble(), testDoubleQR(), testDuplicateId(), testEnzymaticSearchConstraint(), testEnzyme(), testEnzymes(), testEquality(), testErrorFunction(), testErrorLorentzian(), testEven(), testEvenMS2(), testEvidence(), testExactFit(), testExactFitQR(), testFeature(), testFeatureDetectorSimple(), testFeatureField(), testFile(), testFileContent(), testFileDescription(), testFilter(), testFind(), testFit(), testForEach(), testFormula(), testFormulaOperations(), testFragmentArray(), testGaussian_Bombesin2(), testGaussian_Bombesin3(), testGet(), testHasBinaryData(), testIdentData(), testIdentifiable(), testIdentifiableParamContainer(), testIdSet(), testIndexSet(), testInfo(), testInputs(), testInstantiationWithNull(), testInstrument(), testInstrumentConfiguration(), testIntegerSet(), testIntegralReally(), testIO(), testIonisation(), testIonType(), testIsChildOf(), testIteratorEquality(), testLeastSquares(), testLeastSquaresQR(), testMassAnalyzerFilter(), testMassTable(), testMatch(), testMatchData(), testMaxPrecisionDiff(), testMeasure(), testMerge(), testMetadata(), testMillion(), testModAminoAcidMass(), testModeBinaryDataOnly(), testModelAndManufacturer(), testModeMetaDataAndBinaryData(), testModeMetaDataAndSequence(), testModeMetaDataOnly(), testModeOff(), testModification(), testModificationInfo(), testMRU(), testMS2Activation(), testMSData(), testMSDataConstruction(), testMSDiffUpdate(), testMSLevelSet(), testMSMSPipelineAnalysis(), testMSMSRunSummary(), testMulti(), testMultiplePeaks(), testNested(), testNoAutoUnescape(), testNoiseFloor(), testNoiseFloorVarianceCalculation(), testNonColinearLinearWarp(), testNontrypticBSA(), testNormalization(), testObject(), testObject_ChromatogramList(), testObject_SpectrumList(), testObjectWithMSData(), testOrganization(), testParabola(), testParamContainer(), testParamGroup(), testPeak(), testPeakData(), testPeakel(), testPeakelField(), testPeakEquality(), testPeakFamily(), testPeptide(), testPeptideEvidence(), testPeptideHypothesis(), testPeptideID_dataFetcherConstructor(), testPeptideProphetResult(), testPerson(), testPiecewiseLinearWarp(), testPolysiloxane(), testPrecursor(), testPrecursorRefine(), testPredicate(), testPrediction(), testProbabilites(), testProcessingMethod(), testProduct(), testProjected(), testProtein(), testProteinAmbiguityGroup(), testProteinDetection(), testProteinDetectionHypothesis(), testProteinDetectionList(), testProteinDetectionProtocol(), testProteinList(), testProteomeData(), testProvider(), testQ3RatioResult(), testQR(), testRead(), testReader(), testRectangularQR(), testReflector(), testRegexCVMap(), testRegexCVMapIO(), testRemove(), testResidue(), testRetentionTime(), testReversedList(), testRootElement(), testRun(), testSample(), testSampleComponent(), testSampleEnzyme(), testScan(), testScanEventSet(), testScanList(), testScanNumberSet(), testScanSettings(), testScanTimeRange(), testSearchDatabase(), testSearchHit(), testSearchModification(), testSearchResult(), testSearchSummary(), testSelectedIndices(), testSemitrypticBSA(), testSemitrypticMethionineClippingBSA(), testSequenceCollection(), testSerialize(), testSerializeRead(), testSerializeReally(), testSerializeWrite(), testSHA1(), testShuffledList(), testSieve(), testSimpleRectangleQR(), testSnapModifications(), testSoftware(), testSource(), testSourceFile(), testSparse(), testSpecificity(), testSpectraData(), testSpectrum(), testSpectrumIdentification(), testSpectrumIdentificationItem(), testSpectrumIdentificationList(), testSpectrumIdentificationProtocol(), testSpectrumIdentificationResult(), testSpectrumList(), testSpectrumListWithPositions(), testSpectrumListWriteProgress(), testSpectrumQuery(), testStatic(), testStream(), testString(), testSubstitutionModification(), testTarget(), testThreadSafety(), testTime(), testToy(), testTraData(), testTransition(), testTrypticBSA(), testUpdateRequest(), testUsage(), testUserParam(), testValidation(), testVectorCustomPair(), testVectorDouble(), testVectorIO(), testVectorOrderedPair(), testWeightedLeastSquares(), testWriteRead(), testWriteReadBMS1(), testWriteReadBMS2(), testWriteReadCMS1(), testWriteReadCMS2(), testWriteReadMS1(), testWriteReadMS2(), pwiz::identdata::TextWriter::TextWriter(), TestListener::update(), SimpleAnalyzer::update(), CancelListener::update(), validateRecalculation(), validateWriteRead(), verifyBombesinPeakels(), verifyPrecursorInfo(), verifyPrecursorMZ(), and pwiz::identdata::DelimWriter::write().

Functions

Variables

Function Documentation

Variable Documentation