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ProteoWizard
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#include "MinimumPepXML.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 |
| Specificity makeSpecificity | ( | ) |
Definition at line 32 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::Specificity::cut, pwiz::data::pepxml::Specificity::minSpace, pwiz::data::pepxml::Specificity::noCut, and pwiz::data::pepxml::Specificity::sense.
Referenced by makeSampleEnzyme(), and testSpecificity().
| SampleEnzyme makeSampleEnzyme | ( | ) |
Definition at line 44 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::SampleEnzyme::description, pwiz::data::pepxml::SampleEnzyme::fidelity, pwiz::data::pepxml::SampleEnzyme::independent, makeSpecificity(), pwiz::data::pepxml::SampleEnzyme::name, and pwiz::data::pepxml::SampleEnzyme::specificity.
Referenced by makeMSMSRunSummary(), and testSampleEnzyme().
| SearchDatabase makeSearchDatabase | ( | ) |
Definition at line 59 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::SearchDatabase::databaseName, pwiz::data::pepxml::SearchDatabase::databaseReleaseIdentifier, pwiz::data::pepxml::SearchDatabase::localPath, pwiz::data::pepxml::SearchDatabase::sizeInDbEntries, pwiz::data::pepxml::SearchDatabase::sizeOfResidues, and pwiz::data::pepxml::SearchDatabase::type.
Referenced by makeSearchSummary(), and testSearchDatabase().
| Q3RatioResult makeQ3RatioResult | ( | ) |
Definition at line 72 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::Q3RatioResult::decimalRatio, pwiz::data::pepxml::Q3RatioResult::heavyArea, pwiz::data::pepxml::Q3RatioResult::heavyFirstScan, pwiz::data::pepxml::Q3RatioResult::heavyLastScan, pwiz::data::pepxml::Q3RatioResult::heavyMass, pwiz::data::pepxml::Q3RatioResult::lightArea, pwiz::data::pepxml::Q3RatioResult::lightFirstScan, pwiz::data::pepxml::Q3RatioResult::lightLastScan, pwiz::data::pepxml::Q3RatioResult::lightMass, pwiz::data::pepxml::Q3RatioResult::q2HeavyArea, and pwiz::data::pepxml::Q3RatioResult::q2LightArea.
Referenced by testAnalysisResult(), and testQ3RatioResult().
| PeptideProphetResult makePeptideProphetResult | ( | ) |
Definition at line 91 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::PeptideProphetResult::allNttProb, and pwiz::data::pepxml::PeptideProphetResult::probability.
Referenced by makeAnalysisResult(), and testPeptideProphetResult().
| AnalysisResult makeAnalysisResult | ( | ) |
Definition at line 104 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::AnalysisResult::analysis, makePeptideProphetResult(), and pwiz::data::pepxml::AnalysisResult::peptideProphetResult.
Referenced by makeSearchHit(), and testAnalysisResult().
| AlternativeProtein makeAlternativeProtein | ( | ) |
Definition at line 116 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::AlternativeProtein::numTolTerm, pwiz::data::pepxml::AlternativeProtein::protein, and pwiz::data::pepxml::AlternativeProtein::proteinDescr.
Referenced by makeSearchHit(), and testAlternativeProtein().
| ModAminoAcidMass makeModAminoAcidMass | ( | ) |
Definition at line 127 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::ModAminoAcidMass::mass, and pwiz::data::pepxml::ModAminoAcidMass::position.
Referenced by makeModificationInfo(), and testModAminoAcidMass().
| ModificationInfo makeModificationInfo | ( | ) |
Definition at line 137 of file MinimumPepXMLTest.cpp.
References makeModAminoAcidMass(), pwiz::data::pepxml::ModificationInfo::modAminoAcidMass, and pwiz::data::pepxml::ModificationInfo::modifiedPeptide.
Referenced by makeSearchHit(), and testModificationInfo().
| SearchHit makeSearchHit | ( | ) |
Definition at line 146 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::SearchHit::alternativeProteins, pwiz::data::pepxml::SearchHit::analysisResult, pwiz::data::pepxml::SearchHit::calcNeutralPepMass, pwiz::data::pepxml::SearchHit::hitRank, pwiz::data::pepxml::SearchHit::isRejected, makeAlternativeProtein(), makeAnalysisResult(), makeModificationInfo(), pwiz::data::pepxml::SearchHit::massDiff, pwiz::data::pepxml::SearchHit::modificationInfo, pwiz::data::pepxml::SearchHit::numMatchedIons, pwiz::data::pepxml::SearchHit::numMissedCleavages, pwiz::data::pepxml::SearchHit::numTolTerm, pwiz::data::pepxml::SearchHit::numTotalProteins, pwiz::data::pepxml::SearchHit::peptide, pwiz::data::pepxml::SearchHit::peptideNextAA, pwiz::data::pepxml::SearchHit::peptidePrevAA, pwiz::data::pepxml::SearchHit::protein, and pwiz::data::pepxml::SearchHit::proteinDescr.
Referenced by makeSearchResult(), and testSearchHit().
| EnzymaticSearchConstraint makeEnzymaticSearchConstraint | ( | ) |
Definition at line 175 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::EnzymaticSearchConstraint::enzyme, pwiz::data::pepxml::EnzymaticSearchConstraint::maxNumInternalCleavages, and pwiz::data::pepxml::EnzymaticSearchConstraint::minNumTermini.
Referenced by makeSearchSummary(), and testEnzymaticSearchConstraint().
| AminoAcidModification makeAminoAcidModification | ( | ) |
Definition at line 187 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::AminoAcidModification::aminoAcid, pwiz::data::pepxml::AminoAcidModification::mass, pwiz::data::pepxml::AminoAcidModification::massDiff, pwiz::data::pepxml::AminoAcidModification::symbol, and pwiz::data::pepxml::AminoAcidModification::variable.
Referenced by makeSearchSummary(), and testAminoAcidModification().
| SearchSummary makeSearchSummary | ( | ) |
Definition at line 201 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::SearchSummary::aminoAcidModifications, pwiz::data::pepxml::SearchSummary::baseName, pwiz::data::pepxml::SearchSummary::enzymaticSearchConstraint, pwiz::data::pepxml::SearchSummary::fragmentMassType, makeAminoAcidModification(), makeEnzymaticSearchConstraint(), makeSearchDatabase(), pwiz::data::pepxml::SearchSummary::precursorMassType, pwiz::data::pepxml::SearchSummary::searchDatabase, pwiz::data::pepxml::SearchSummary::searchEngine, and pwiz::data::pepxml::SearchSummary::searchID.
Referenced by makeMSMSRunSummary(), and testSearchSummary().
| SearchResult makeSearchResult | ( | ) |
Definition at line 225 of file MinimumPepXMLTest.cpp.
References makeSearchHit(), and pwiz::data::pepxml::SearchResult::searchHit.
Referenced by makeSpectrumQuery(), and testSearchResult().
| SpectrumQuery makeSpectrumQuery | ( | ) |
Definition at line 235 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::SpectrumQuery::assumedCharge, pwiz::data::pepxml::SpectrumQuery::endScan, pwiz::data::pepxml::SpectrumQuery::index, makeSearchResult(), pwiz::data::pepxml::SpectrumQuery::precursorNeutralMass, pwiz::data::pepxml::SpectrumQuery::retentionTimeSec, pwiz::data::pepxml::SpectrumQuery::searchResult, pwiz::data::pepxml::SpectrumQuery::spectrum, and pwiz::data::pepxml::SpectrumQuery::startScan.
Referenced by makeMatch(), makeMSMSRunSummary(), and testSpectrumQuery().
| MSMSRunSummary makeMSMSRunSummary | ( | ) |
Definition at line 255 of file MinimumPepXMLTest.cpp.
References makeSampleEnzyme(), makeSearchSummary(), makeSpectrumQuery(), pwiz::data::pepxml::MSMSRunSummary::sampleEnzyme, pwiz::data::pepxml::MSMSRunSummary::searchSummary, and pwiz::data::pepxml::MSMSRunSummary::spectrumQueries.
Referenced by testMSMSPipelineAnalysis(), and testMSMSRunSummary().
| MatchPtr makeMatch | ( | ) |
Definition at line 273 of file MinimumPepXMLTest.cpp.
References makeSpectrumQuery().
Referenced by testMatch(), and testMatchData().
| void testSpecificity | ( | ) |
Definition at line 284 of file MinimumPepXMLTest.cpp.
References makeSpecificity(), os_, pwiz::data::pepxml::Specificity::read(), unit_assert, and pwiz::data::pepxml::Specificity::write().
Referenced by main().
| void testSampleEnzyme | ( | ) |
Definition at line 304 of file MinimumPepXMLTest.cpp.
References makeSampleEnzyme(), os_, pwiz::data::pepxml::SampleEnzyme::read(), unit_assert, and pwiz::data::pepxml::SampleEnzyme::write().
Referenced by main().
| void testSearchDatabase | ( | ) |
Definition at line 324 of file MinimumPepXMLTest.cpp.
References makeSearchDatabase(), os_, pwiz::data::pepxml::SearchDatabase::read(), unit_assert, and pwiz::data::pepxml::SearchDatabase::write().
Referenced by main().
| void testQ3RatioResult | ( | ) |
Definition at line 344 of file MinimumPepXMLTest.cpp.
References makeQ3RatioResult(), os_, pwiz::data::pepxml::Q3RatioResult::read(), unit_assert, and pwiz::data::pepxml::Q3RatioResult::write().
Referenced by main().
| void testPeptideProphetResult | ( | ) |
Definition at line 363 of file MinimumPepXMLTest.cpp.
References makePeptideProphetResult(), os_, pwiz::data::pepxml::PeptideProphetResult::read(), unit_assert, and pwiz::data::pepxml::PeptideProphetResult::write().
Referenced by main().
| void testAnalysisResult | ( | ) |
Definition at line 383 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::AnalysisResult::analysis, makeAnalysisResult(), makeQ3RatioResult(), os_, pwiz::data::pepxml::AnalysisResult::q3RatioResult, pwiz::data::pepxml::AnalysisResult::read(), unit_assert, and pwiz::data::pepxml::AnalysisResult::write().
Referenced by main().
| void testAlternativeProtein | ( | ) |
Definition at line 419 of file MinimumPepXMLTest.cpp.
References makeAlternativeProtein(), os_, pwiz::data::pepxml::AlternativeProtein::read(), unit_assert, and pwiz::data::pepxml::AlternativeProtein::write().
Referenced by main().
| void testModAminoAcidMass | ( | ) |
Definition at line 440 of file MinimumPepXMLTest.cpp.
References makeModAminoAcidMass(), os_, pwiz::data::pepxml::ModAminoAcidMass::read(), unit_assert, and pwiz::data::pepxml::ModAminoAcidMass::write().
Referenced by main().
| void testModificationInfo | ( | ) |
Definition at line 459 of file MinimumPepXMLTest.cpp.
References makeModificationInfo(), os_, pwiz::data::pepxml::ModificationInfo::read(), unit_assert, and pwiz::data::pepxml::ModificationInfo::write().
Referenced by main().
| void testSearchHit | ( | ) |
Definition at line 479 of file MinimumPepXMLTest.cpp.
References makeSearchHit(), os_, pwiz::data::pepxml::SearchHit::read(), unit_assert, and pwiz::data::pepxml::SearchHit::write().
Referenced by main().
| void testSearchResult | ( | ) |
Definition at line 498 of file MinimumPepXMLTest.cpp.
References makeSearchResult(), os_, pwiz::data::pepxml::SearchResult::read(), unit_assert, and pwiz::data::pepxml::SearchResult::write().
Referenced by main().
| void testEnzymaticSearchConstraint | ( | ) |
Definition at line 519 of file MinimumPepXMLTest.cpp.
References makeEnzymaticSearchConstraint(), os_, pwiz::data::pepxml::EnzymaticSearchConstraint::read(), unit_assert, and pwiz::data::pepxml::EnzymaticSearchConstraint::write().
Referenced by main().
| void testAminoAcidModification | ( | ) |
Definition at line 539 of file MinimumPepXMLTest.cpp.
References makeAminoAcidModification(), os_, pwiz::data::pepxml::AminoAcidModification::read(), unit_assert, and pwiz::data::pepxml::AminoAcidModification::write().
Referenced by main().
| void testSearchSummary | ( | ) |
Definition at line 559 of file MinimumPepXMLTest.cpp.
References makeSearchSummary(), os_, pwiz::data::pepxml::SearchSummary::read(), unit_assert, and pwiz::data::pepxml::SearchSummary::write().
Referenced by main().
| void testSpectrumQuery | ( | ) |
Definition at line 579 of file MinimumPepXMLTest.cpp.
References makeSpectrumQuery(), os_, pwiz::data::pepxml::SpectrumQuery::read(), unit_assert, and pwiz::data::pepxml::SpectrumQuery::write().
Referenced by main().
| void testMSMSRunSummary | ( | ) |
Definition at line 603 of file MinimumPepXMLTest.cpp.
References makeMSMSRunSummary(), os_, pwiz::data::pepxml::MSMSRunSummary::read(), unit_assert, and pwiz::data::pepxml::MSMSRunSummary::write().
Referenced by main().
| void testMSMSPipelineAnalysis | ( | ) |
Definition at line 623 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::MSMSPipelineAnalysis::date, makeMSMSRunSummary(), pwiz::data::pepxml::MSMSPipelineAnalysis::msmsRunSummary, os_, pwiz::data::pepxml::MSMSPipelineAnalysis::read(), pwiz::data::pepxml::MSMSPipelineAnalysis::summaryXML, unit_assert, pwiz::data::pepxml::MSMSPipelineAnalysis::write(), pwiz::data::pepxml::MSMSPipelineAnalysis::xmlns, pwiz::data::pepxml::MSMSPipelineAnalysis::xmlnsXSI, and pwiz::data::pepxml::MSMSPipelineAnalysis::XSISchemaLocation.
Referenced by main().
| void testMatch | ( | ) |
Definition at line 651 of file MinimumPepXMLTest.cpp.
References makeMatch(), os_, pwiz::data::pepxml::Match::read(), unit_assert, and pwiz::data::pepxml::Match::write().
Referenced by main().
| void testMatchData | ( | ) |
Definition at line 677 of file MinimumPepXMLTest.cpp.
References makeMatch(), pwiz::data::pepxml::MatchData::matches, os_, pwiz::data::pepxml::MatchData::read(), pwiz::data::pepxml::MatchData::searchNbhdCalculator, unit_assert, pwiz::data::pepxml::MatchData::warpFunctionCalculator, and pwiz::data::pepxml::MatchData::write().
Referenced by main().
| void testInvarianceUnderProteinProphet | ( | ) |
Definition at line 712 of file MinimumPepXMLTest.cpp.
References pwiz::data::pepxml::MSMSPipelineAnalysis::read(), and pwiz::data::pepxml::MSMSPipelineAnalysis::write().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
Definition at line 730 of file MinimumPepXMLTest.cpp.
References os_, TEST_EPILOG, TEST_FAILED, TEST_PROLOG, testAlternativeProtein(), testAminoAcidModification(), testAnalysisResult(), testEnzymaticSearchConstraint(), testMatch(), testMatchData(), testModAminoAcidMass(), testModificationInfo(), testMSMSPipelineAnalysis(), testMSMSRunSummary(), testPeptideProphetResult(), testQ3RatioResult(), testSampleEnzyme(), testSearchDatabase(), testSearchHit(), testSearchResult(), testSearchSummary(), testSpecificity(), and testSpectrumQuery().
| ostream* os_ = 0 |
Definition at line 30 of file MinimumPepXMLTest.cpp.
Referenced by main(), testAlternativeProtein(), testAminoAcidModification(), testAnalysisResult(), testEnzymaticSearchConstraint(), testMatch(), testMatchData(), testModAminoAcidMass(), testModificationInfo(), testMSMSPipelineAnalysis(), testMSMSRunSummary(), testPeptideProphetResult(), testQ3RatioResult(), testSampleEnzyme(), testSearchDatabase(), testSearchHit(), testSearchResult(), testSearchSummary(), testSpecificity(), and testSpectrumQuery().
1.8.13