ProteoWizard
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#include "IO.hpp"
#include "Diff.hpp"
#include "TextWriter.hpp"
#include "examples.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Std.hpp"
Go to the source code of this file.
Variables | |
ostream * | os_ = 0 |
void testObject | ( | const object_type & | a | ) |
Definition at line 41 of file IOTest.cpp.
References diff(), os_, pwiz::identdata::IO::read(), unit_assert, and pwiz::identdata::IO::write().
Referenced by testAmbiguousResidue(), testAnalysisCollection(), testAnalysisData(), testAnalysisProtocolCollection(), testAnalysisSampleCollection(), testAnalysisSoftware(), testBibliographicReference(), testComponent(), testComponentList(), testContactRole(), testCV(), testCVParam(), testDataCollection(), testDataProcessing(), testDBSequence(), testEnzyme(), testEnzymes(), testFileDescription(), testFilter(), testFragmentArray(), testIdentData(), testIdentifiable(), testIdentifiableParamContainer(), testInputs(), testInstrumentConfiguration(), testIonType(), testMassTable(), testMeasure(), testModification(), testNamedParamContainer(), testOrganization(), testParamGroup(), testPeptide(), testPeptideEvidence(), testPeptideHypothesis(), testPerson(), testPrecursor(), testProcessingMethod(), testProduct(), testProteinAmbiguityGroup(), testProteinDetection(), testProteinDetectionHypothesis(), testProteinDetectionList(), testProteinDetectionProtocol(), testProvider(), testResidue(), testSample(), testScanSettings(), testSearchDatabase(), testSearchModification(), testSequenceCollection(), testSoftware(), testSourceFile(), testSpectraData(), testSpectrumIdentification(), testSpectrumIdentificationItem(), testSpectrumIdentificationList(), testSpectrumIdentificationProtocol(), testSpectrumIdentificationResult(), testSubstitutionModification(), and testUserParam().
void testIdentifiable | ( | ) |
Definition at line 66 of file IOTest.cpp.
References pwiz::identdata::Identifiable::id, pwiz::identdata::Identifiable::name, os_, and testObject().
Referenced by test().
void testIdentifiableParamContainer | ( | ) |
Definition at line 78 of file IOTest.cpp.
References pwiz::identdata::IdentifiableParamContainer::id, MS_TIC, pwiz::identdata::IdentifiableParamContainer::name, os_, pwiz::data::ParamContainer::set(), testObject(), and pwiz::data::ParamContainer::userParams.
Referenced by test().
void testCV | ( | ) |
Definition at line 93 of file IOTest.cpp.
References pwiz::cv::CV::fullName, pwiz::cv::CV::id, os_, testObject(), pwiz::cv::CV::URI, and pwiz::cv::CV::version.
Referenced by test().
void testBibliographicReference | ( | ) |
Definition at line 107 of file IOTest.cpp.
References pwiz::identdata::BibliographicReference::authors, pwiz::identdata::BibliographicReference::editor, pwiz::identdata::Identifiable::id, pwiz::identdata::BibliographicReference::issue, os_, pwiz::identdata::BibliographicReference::pages, pwiz::identdata::BibliographicReference::publication, pwiz::identdata::BibliographicReference::publisher, testObject(), pwiz::identdata::BibliographicReference::title, pwiz::identdata::BibliographicReference::volume, and pwiz::identdata::BibliographicReference::year.
Referenced by test().
void testPerson | ( | ) |
Definition at line 128 of file IOTest.cpp.
References pwiz::identdata::Person::affiliations, pwiz::identdata::Person::firstName, pwiz::identdata::Person::lastName, pwiz::identdata::Person::midInitials, MS_contact_address, MS_contact_email, MS_contact_fax_number, MS_contact_phone_number, MS_contact_toll_free_phone_number, os_, pwiz::data::ParamContainer::set(), and testObject().
Referenced by test().
void testOrganization | ( | ) |
Definition at line 150 of file IOTest.cpp.
References MS_contact_address, MS_contact_email, MS_contact_fax_number, MS_contact_phone_number, MS_contact_toll_free_phone_number, os_, pwiz::identdata::Organization::parent, pwiz::data::ParamContainer::set(), and testObject().
Referenced by test().
void testContactRole | ( | ) |
Definition at line 168 of file IOTest.cpp.
References pwiz::identdata::ContactRole::contactPtr, pwiz::data::CVParam::cvid, MS_software_vendor, os_, and testObject().
Referenced by test().
void testProvider | ( | ) |
Definition at line 180 of file IOTest.cpp.
References pwiz::identdata::Provider::contactRolePtr, MS_role_type, os_, and testObject().
Referenced by test().
void testSample | ( | ) |
Definition at line 193 of file IOTest.cpp.
References pwiz::identdata::Sample::contactRole, MS_programmer, MS_septum, MS_software_vendor, os_, pwiz::data::ParamContainer::set(), pwiz::identdata::Sample::subSamples, and testObject().
Referenced by test().
void testAnalysisSoftware | ( | ) |
Definition at line 210 of file IOTest.cpp.
References pwiz::identdata::AnalysisSoftware::contactRolePtr, pwiz::identdata::AnalysisSoftware::customizations, MS_Mascot, MS_software_vendor, os_, pwiz::data::ParamContainer::set(), pwiz::identdata::AnalysisSoftware::softwareName, testObject(), pwiz::identdata::AnalysisSoftware::URI, and pwiz::identdata::AnalysisSoftware::version.
Referenced by test().
void testAnalysisSampleCollection | ( | ) |
Definition at line 228 of file IOTest.cpp.
References os_, and testObject().
void testDBSequence | ( | ) |
Definition at line 240 of file IOTest.cpp.
References pwiz::identdata::DBSequence::accession, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::DBSequence::length, MS_protein_description, pwiz::identdata::IdentifiableParamContainer::name, pwiz::identdata::DBSequence::searchDatabasePtr, pwiz::identdata::DBSequence::seq, pwiz::data::ParamContainer::set(), and testObject().
Referenced by test().
void testModification | ( | ) |
Definition at line 256 of file IOTest.cpp.
References pwiz::identdata::Modification::avgMassDelta, pwiz::identdata::Modification::location, pwiz::identdata::Modification::monoisotopicMassDelta, pwiz::identdata::Modification::residues, pwiz::data::ParamContainer::set(), testObject(), and UNIMOD_Gln__pyro_Glu.
Referenced by test().
void testSubstitutionModification | ( | ) |
Definition at line 272 of file IOTest.cpp.
References pwiz::identdata::SubstitutionModification::avgMassDelta, pwiz::identdata::SubstitutionModification::location, pwiz::identdata::SubstitutionModification::monoisotopicMassDelta, pwiz::identdata::SubstitutionModification::originalResidue, pwiz::identdata::SubstitutionModification::replacementResidue, and testObject().
Referenced by test().
void testPeptide | ( | ) |
Definition at line 286 of file IOTest.cpp.
References pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::Peptide::modification, MS_peptide, pwiz::identdata::IdentifiableParamContainer::name, pwiz::identdata::Peptide::peptideSequence, pwiz::data::ParamContainer::set(), pwiz::identdata::Peptide::substitutionModification, and testObject().
Referenced by test().
void testSequenceCollection | ( | ) |
Definition at line 308 of file IOTest.cpp.
References pwiz::identdata::SequenceCollection::dbSequences, pwiz::identdata::SequenceCollection::peptideEvidence, pwiz::identdata::SequenceCollection::peptides, and testObject().
Referenced by test().
void testSpectrumIdentification | ( | ) |
Definition at line 320 of file IOTest.cpp.
References pwiz::identdata::SpectrumIdentification::activityDate, pwiz::identdata::SpectrumIdentification::inputSpectra, os_, pwiz::identdata::SpectrumIdentification::searchDatabase, pwiz::identdata::SpectrumIdentification::spectrumIdentificationListPtr, pwiz::identdata::SpectrumIdentification::spectrumIdentificationProtocolPtr, and testObject().
Referenced by test().
void testProteinDetection | ( | ) |
Definition at line 337 of file IOTest.cpp.
References pwiz::identdata::ProteinDetection::activityDate, pwiz::identdata::Identifiable::id, pwiz::identdata::Identifiable::name, os_, pwiz::identdata::ProteinDetection::proteinDetectionListPtr, pwiz::identdata::ProteinDetection::proteinDetectionProtocolPtr, and testObject().
Referenced by test().
void testAnalysisCollection | ( | ) |
Definition at line 353 of file IOTest.cpp.
References pwiz::identdata::ProteinDetection::activityDate, os_, pwiz::identdata::AnalysisCollection::proteinDetection, pwiz::identdata::AnalysisCollection::spectrumIdentification, and testObject().
Referenced by test().
void testSearchModification | ( | ) |
Definition at line 368 of file IOTest.cpp.
References pwiz::data::CVParam::cvid, pwiz::identdata::SearchModification::fixedMod, pwiz::identdata::SearchModification::massDelta, MS_modification_specificity_peptide_N_term, os_, pwiz::identdata::SearchModification::residues, pwiz::data::ParamContainer::set(), pwiz::identdata::SearchModification::specificityRules, testObject(), and UNIMOD_Gln__pyro_Glu.
Referenced by test().
void testEnzyme | ( | ) |
Definition at line 385 of file IOTest.cpp.
References pwiz::identdata::Enzyme::cTermGain, pwiz::identdata::Enzyme::enzymeName, pwiz::identdata::Identifiable::id, pwiz::identdata::Enzyme::minDistance, pwiz::identdata::Enzyme::missedCleavages, MS_Trypsin, pwiz::identdata::Enzyme::nTermGain, os_, SemiSpecific, pwiz::data::ParamContainer::set(), pwiz::identdata::Enzyme::siteRegexp, pwiz::identdata::Enzyme::terminalSpecificity, and testObject().
Referenced by test().
void testEnzymes | ( | ) |
Definition at line 405 of file IOTest.cpp.
References pwiz::identdata::Enzymes::enzymes, pwiz::identdata::Enzymes::independent, os_, and testObject().
Referenced by test().
void testResidue | ( | ) |
Definition at line 419 of file IOTest.cpp.
References pwiz::identdata::Residue::code, pwiz::identdata::Residue::mass, os_, and testObject().
Referenced by test().
void testAmbiguousResidue | ( | ) |
Definition at line 432 of file IOTest.cpp.
References pwiz::identdata::AmbiguousResidue::code, MS_alternate_single_letter_codes, os_, pwiz::data::ParamContainer::set(), and testObject().
Referenced by test().
void testMassTable | ( | ) |
Definition at line 445 of file IOTest.cpp.
References pwiz::identdata::MassTable::ambiguousResidue, pwiz::identdata::MassTable::id, pwiz::identdata::MassTable::msLevel, pwiz::identdata::MassTable::residues, and testObject().
Referenced by test().
void testFilter | ( | ) |
Definition at line 464 of file IOTest.cpp.
References pwiz::identdata::Filter::exclude, pwiz::identdata::Filter::filterType, pwiz::identdata::Filter::include, MS_DB_filter_on_accession_numbers, MS_DB_filter_taxonomy, MS_DB_MW_filter, pwiz::data::ParamContainer::set(), and testObject().
Referenced by test().
void testSpectrumIdentificationProtocol | ( | ) |
Definition at line 476 of file IOTest.cpp.
References pwiz::identdata::SpectrumIdentificationProtocol::additionalSearchParams, pwiz::identdata::SpectrumIdentificationProtocol::analysisSoftwarePtr, pwiz::data::CVParam::cvid, pwiz::identdata::SpectrumIdentificationProtocol::databaseFilters, pwiz::identdata::SpectrumIdentificationProtocol::enzymes, pwiz::identdata::SpectrumIdentificationProtocol::fragmentTolerance, pwiz::identdata::Identifiable::id, pwiz::identdata::Enzymes::independent, pwiz::identdata::SpectrumIdentificationProtocol::massTable, pwiz::identdata::SpectrumIdentificationProtocol::modificationParams, MS_DB_filter_taxonomy, MS_Mascot_SigThreshold, MS_ms_ms_search, MS_parent_mass_type_mono, MS_search_tolerance_plus_value, pwiz::identdata::SpectrumIdentificationProtocol::parentTolerance, pwiz::identdata::SpectrumIdentificationProtocol::searchType, pwiz::data::ParamContainer::set(), testObject(), pwiz::identdata::SpectrumIdentificationProtocol::threshold, and UO_dalton.
Referenced by test().
void testProteinDetectionProtocol | ( | ) |
Definition at line 503 of file IOTest.cpp.
References pwiz::identdata::ProteinDetectionProtocol::analysisParams, pwiz::identdata::ProteinDetectionProtocol::analysisSoftwarePtr, CVID_Unknown, pwiz::identdata::Identifiable::id, MS_Mascot_SigThreshold, pwiz::data::ParamContainer::set(), testObject(), and pwiz::identdata::ProteinDetectionProtocol::threshold.
Referenced by test().
void testAnalysisProtocolCollection | ( | ) |
Definition at line 517 of file IOTest.cpp.
References pwiz::identdata::AnalysisProtocolCollection::proteinDetectionProtocol, pwiz::identdata::AnalysisProtocolCollection::spectrumIdentificationProtocol, and testObject().
Referenced by test().
void testSpectraData | ( | ) |
Definition at line 533 of file IOTest.cpp.
References pwiz::data::CVParam::cvid, pwiz::identdata::SpectraData::externalFormatDocumentation, pwiz::identdata::SpectraData::fileFormat, pwiz::identdata::Identifiable::id, pwiz::identdata::SpectraData::location, MS_mzML_format, and testObject().
Referenced by test().
void testSearchDatabase | ( | ) |
Definition at line 547 of file IOTest.cpp.
References pwiz::data::CVParam::cvid, pwiz::identdata::SearchDatabase::databaseName, pwiz::identdata::SearchDatabase::fileFormat, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::SearchDatabase::location, MS_FASTA_format, pwiz::identdata::SearchDatabase::numDatabaseSequences, pwiz::identdata::SearchDatabase::numResidues, pwiz::identdata::SearchDatabase::releaseDate, testObject(), pwiz::data::ParamContainer::userParams, and pwiz::identdata::SearchDatabase::version.
Referenced by test().
void testSourceFile | ( | ) |
Definition at line 566 of file IOTest.cpp.
References pwiz::data::CVParam::cvid, pwiz::identdata::SourceFile::externalFormatDocumentation, pwiz::identdata::SourceFile::fileFormat, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::SourceFile::location, MS_Mascot_DAT_format, MS_mzML_format, pwiz::data::ParamContainer::set(), and testObject().
Referenced by test().
void testInputs | ( | ) |
Definition at line 581 of file IOTest.cpp.
References pwiz::identdata::Inputs::searchDatabase, pwiz::identdata::Inputs::sourceFile, pwiz::identdata::Inputs::spectraData, and testObject().
Referenced by test().
void testMeasure | ( | ) |
Definition at line 601 of file IOTest.cpp.
References pwiz::identdata::IdentifiableParamContainer::id, MS_product_ion_m_z, pwiz::data::ParamContainer::set(), and testObject().
Referenced by test().
void testFragmentArray | ( | ) |
Definition at line 612 of file IOTest.cpp.
References pwiz::identdata::FragmentArray::measurePtr, testObject(), and pwiz::identdata::FragmentArray::values.
Referenced by test().
void testIonType | ( | ) |
Definition at line 626 of file IOTest.cpp.
References pwiz::identdata::IonType::charge, pwiz::data::CVParam::cvid, pwiz::identdata::IonType::fragmentArray, pwiz::identdata::IonType::index, MS_frag__a_ion, and testObject().
Referenced by test().
void testPeptideEvidence | ( | ) |
Definition at line 644 of file IOTest.cpp.
References pwiz::identdata::PeptideEvidence::dbSequencePtr, pwiz::identdata::PeptideEvidence::end, pwiz::identdata::PeptideEvidence::frame, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::PeptideEvidence::isDecoy, MS_Mascot_score, pwiz::identdata::PeptideEvidence::post, pwiz::identdata::PeptideEvidence::pre, pwiz::data::ParamContainer::set(), pwiz::identdata::PeptideEvidence::start, testObject(), and pwiz::identdata::PeptideEvidence::translationTablePtr.
Referenced by test().
void testSpectrumIdentificationItem | ( | ) |
Definition at line 664 of file IOTest.cpp.
References pwiz::identdata::SpectrumIdentificationItem::calculatedMassToCharge, pwiz::identdata::SpectrumIdentificationItem::calculatedPI, pwiz::identdata::SpectrumIdentificationItem::chargeState, pwiz::identdata::SpectrumIdentificationItem::experimentalMassToCharge, pwiz::identdata::SpectrumIdentificationItem::fragmentation, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::SpectrumIdentificationItem::massTablePtr, MS_Mascot_score, pwiz::identdata::SpectrumIdentificationItem::passThreshold, pwiz::identdata::SpectrumIdentificationItem::peptideEvidencePtr, pwiz::identdata::SpectrumIdentificationItem::peptidePtr, pwiz::identdata::SpectrumIdentificationItem::rank, pwiz::identdata::SpectrumIdentificationItem::samplePtr, pwiz::data::ParamContainer::set(), and testObject().
Referenced by test().
void testSpectrumIdentificationResult | ( | ) |
Definition at line 691 of file IOTest.cpp.
References pwiz::identdata::IdentifiableParamContainer::id, MS_Mascot_score, pwiz::data::ParamContainer::set(), pwiz::identdata::SpectrumIdentificationResult::spectraDataPtr, pwiz::identdata::SpectrumIdentificationResult::spectrumID, pwiz::identdata::SpectrumIdentificationResult::spectrumIdentificationItem, and testObject().
Referenced by test().
PeptideHypothesis testPeptideHypothesis | ( | ) |
Definition at line 710 of file IOTest.cpp.
References pwiz::identdata::PeptideHypothesis::peptideEvidencePtr, pwiz::identdata::PeptideHypothesis::spectrumIdentificationItemPtr, and testObject().
Referenced by testProteinDetectionHypothesis().
void testProteinDetectionHypothesis | ( | ) |
Definition at line 722 of file IOTest.cpp.
References pwiz::identdata::ProteinDetectionHypothesis::dbSequencePtr, pwiz::identdata::IdentifiableParamContainer::id, MS_Mascot_score, pwiz::identdata::ProteinDetectionHypothesis::passThreshold, pwiz::identdata::ProteinDetectionHypothesis::peptideHypothesis, pwiz::data::ParamContainer::set(), testObject(), and testPeptideHypothesis().
Referenced by test().
void testProteinAmbiguityGroup | ( | ) |
Definition at line 736 of file IOTest.cpp.
References pwiz::identdata::IdentifiableParamContainer::id, MS_Mascot_score, pwiz::identdata::ProteinAmbiguityGroup::proteinDetectionHypothesis, pwiz::data::ParamContainer::set(), and testObject().
Referenced by test().
void testSpectrumIdentificationList | ( | ) |
Definition at line 750 of file IOTest.cpp.
References pwiz::identdata::SpectrumIdentificationList::fragmentationTable, pwiz::identdata::IdentifiableParamContainer::id, MS_Mascot_score, pwiz::identdata::SpectrumIdentificationList::numSequencesSearched, pwiz::identdata::SpectrumIdentificationList::spectrumIdentificationResult, and testObject().
Referenced by test().
void testProteinDetectionList | ( | ) |
Definition at line 770 of file IOTest.cpp.
References pwiz::identdata::IdentifiableParamContainer::id, MS_Mascot_score, pwiz::identdata::ProteinDetectionList::proteinAmbiguityGroup, pwiz::data::ParamContainer::set(), and testObject().
Referenced by test().
void testAnalysisData | ( | ) |
Definition at line 784 of file IOTest.cpp.
References MS_Mascot_score, pwiz::identdata::AnalysisData::proteinDetectionListPtr, pwiz::identdata::AnalysisData::spectrumIdentificationList, and testObject().
Referenced by test().
void testDataCollection | ( | ) |
Definition at line 800 of file IOTest.cpp.
References pwiz::identdata::DataCollection::analysisData, pwiz::identdata::DataCollection::inputs, pwiz::identdata::Inputs::sourceFile, pwiz::identdata::AnalysisData::spectrumIdentificationList, and testObject().
Referenced by test().
void testIdentData | ( | ) |
Definition at line 816 of file IOTest.cpp.
References pwiz::identdata::IdentData::analysisCollection, pwiz::identdata::DataCollection::analysisData, pwiz::identdata::IdentData::dataCollection, pwiz::identdata::SequenceCollection::dbSequences, diff(), IgnoreAnalysisData, IgnoreSequenceCollection, pwiz::identdata::examples::initializeTiny(), os_, pwiz::identdata::SequenceCollection::peptideEvidence, pwiz::identdata::SequenceCollection::peptides, pwiz::identdata::AnalysisCollection::proteinDetection, pwiz::identdata::AnalysisData::proteinDetectionListPtr, pwiz::identdata::IO::read(), pwiz::identdata::IdentData::sequenceCollection, pwiz::identdata::AnalysisCollection::spectrumIdentification, pwiz::identdata::AnalysisData::spectrumIdentificationList, testObject(), unit_assert, and pwiz::identdata::IO::write().
Referenced by test().
void test | ( | ) |
Definition at line 860 of file IOTest.cpp.
References testAmbiguousResidue(), testAnalysisCollection(), testAnalysisData(), testAnalysisProtocolCollection(), testAnalysisSoftware(), testBibliographicReference(), testContactRole(), testCV(), testDataCollection(), testDBSequence(), testEnzyme(), testEnzymes(), testFilter(), testFragmentArray(), testIdentData(), testIdentifiable(), testIdentifiableParamContainer(), testInputs(), testIonType(), testMassTable(), testMeasure(), testModification(), testOrganization(), testPeptide(), testPeptideEvidence(), testPerson(), testProteinAmbiguityGroup(), testProteinDetection(), testProteinDetectionHypothesis(), testProteinDetectionList(), testProteinDetectionProtocol(), testProvider(), testResidue(), testSample(), testSearchDatabase(), testSearchModification(), testSequenceCollection(), testSourceFile(), testSpectraData(), testSpectrumIdentification(), testSpectrumIdentificationItem(), testSpectrumIdentificationList(), testSpectrumIdentificationProtocol(), testSpectrumIdentificationResult(), and testSubstitutionModification().
Referenced by main().
int main | ( | int | argc, |
char * | argv[] | ||
) |
Definition at line 910 of file IOTest.cpp.
References os_, test(), TEST_EPILOG, TEST_FAILED, and TEST_PROLOG_EX.
ostream* os_ = 0 |
Definition at line 38 of file IOTest.cpp.
Referenced by main(), testAmbiguousResidue(), testAnalysisCollection(), testAnalysisSampleCollection(), testAnalysisSoftware(), testBibliographicReference(), testBinaryDataArray(), testChromatogram(), testChromatogramListWithPositions(), testContactRole(), testCV(), testEnzyme(), testEnzymes(), testIdentData(), testIdentifiable(), testIdentifiableParamContainer(), testMSData(), testObject(), testObject_ChromatogramList(), testObject_SpectrumList(), testObjectWithMSData(), testOrganization(), testPerson(), testProteinDetection(), testProvider(), testResidue(), testRun(), testSample(), testSearchModification(), testSpectrum(), testSpectrumIdentification(), testSpectrumListWithPositions(), testSpectrumListWriteProgress(), and testTraData().