ProteoWizard
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#include "Serializer_pepXML.hpp"
#include "Diff.hpp"
#include "References.hpp"
#include "examples.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include "pwiz/utility/misc/Filesystem.hpp"
#include "pwiz/data/proteome/Digestion.hpp"
#include "TextWriter.hpp"
#include "boost/range/adaptor/transformed.hpp"
#include "boost/range/algorithm/max_element.hpp"
#include "boost/range/algorithm/min_element.hpp"
#include <cstring>
Go to the source code of this file.
Classes | |
struct | EnzymePtr_specificity |
struct | EnzymePtr_missedCleavages |
Functions | |
void | stripUnmappedMetadata (IdentData &mzid) |
void | testTranslation (const string &str) |
void | testSerializeReally (IdentData &mzid, const Serializer_pepXML::Config &config) |
void | testSerialize () |
void | testPepXMLSpecificity () |
void | testStripChargeFromConventionalSpectrumId () |
int | main (int argc, char **argv) |
Variables | |
ostream * | os_ = 0 |
void stripUnmappedMetadata | ( | IdentData & | mzid | ) |
Definition at line 57 of file Serializer_pepXML_Test.cpp.
References pwiz::identdata::IdentData::analysisCollection, pwiz::identdata::DataCollection::analysisData, pwiz::identdata::IdentData::analysisProtocolCollection, pwiz::identdata::IdentData::analysisSampleCollection, pwiz::identdata::IdentData::analysisSoftwareList, pwiz::identdata::IdentData::auditCollection, BFS_STRING, pwiz::identdata::IdentData::bibliographicReference, pwiz::data::ParamContainer::clear(), pwiz::identdata::SpectrumIdentificationProtocol::databaseFilters, pwiz::identdata::SpectrumIdentificationProtocol::databaseTranslation, pwiz::identdata::IdentData::dataCollection, pwiz::identdata::SequenceCollection::dbSequences, pwiz::identdata::PeptideEvidence::end, pwiz::identdata::Enzymes::enzymes, pwiz::identdata::SpectrumIdentificationProtocol::enzymes, pwiz::identdata::DataCollection::inputs, pwiz::identdata::SpectrumIdentificationProtocol::massTable, max(), pwiz::identdata::peptide(), pwiz::identdata::SequenceCollection::peptides, pwiz::identdata::PeptideEvidence::post, pwiz::identdata::PeptideEvidence::pre, pwiz::identdata::AnalysisCollection::proteinDetection, pwiz::identdata::AnalysisData::proteinDetectionListPtr, pwiz::identdata::IdentData::provider, pwiz::identdata::AnalysisSampleCollection::samples, pwiz::identdata::IdentData::sequenceCollection, pwiz::identdata::Inputs::sourceFile, pwiz::identdata::AnalysisCollection::spectrumIdentification, pwiz::identdata::AnalysisData::spectrumIdentificationList, pwiz::identdata::AnalysisProtocolCollection::spectrumIdentificationProtocol, pwiz::identdata::PeptideEvidence::start, and pwiz::identdata::SpectrumIdentificationProtocol::threshold.
Referenced by testSerialize().
void testTranslation | ( | const string & | str | ) |
Definition at line 144 of file Serializer_pepXML_Test.cpp.
References unit_assert.
Referenced by testSerializeReally().
void testSerializeReally | ( | IdentData & | mzid, |
const Serializer_pepXML::Config & | config | ||
) |
Definition at line 160 of file Serializer_pepXML_Test.cpp.
References diff(), os_, pwiz::identdata::Serializer_pepXML::read(), pwiz::identdata::Serializer_pepXML::Config::readSpectrumQueries, pwiz::identdata::References::resolve(), testTranslation(), unit_assert, and pwiz::identdata::Serializer_pepXML::write().
Referenced by testSerialize().
void testSerialize | ( | ) |
Definition at line 183 of file Serializer_pepXML_Test.cpp.
References pwiz::identdata::IdentData::analysisCollection, pwiz::identdata::DataCollection::analysisData, pwiz::identdata::IdentData::analysisProtocolCollection, pwiz::identdata::IdentData::dataCollection, pwiz::identdata::SequenceCollection::dbSequences, pwiz::identdata::examples::initializeBasicSpectrumIdentification(), MS_Asp_N, MS_Trypsin_P, NonSpecific, pwiz::identdata::SequenceCollection::peptideEvidence, pwiz::identdata::SequenceCollection::peptides, pwiz::identdata::AnalysisData::proteinDetectionListPtr, SemiSpecific, pwiz::identdata::IdentData::sequenceCollection, pwiz::identdata::AnalysisCollection::spectrumIdentification, pwiz::identdata::AnalysisData::spectrumIdentificationList, pwiz::identdata::AnalysisProtocolCollection::spectrumIdentificationProtocol, stripUnmappedMetadata(), and testSerializeReally().
void testPepXMLSpecificity | ( | ) |
Definition at line 245 of file Serializer_pepXML_Test.cpp.
References pwiz::data::ParamContainer::clear(), pwiz::identdata::cleavageAgent(), pwiz::identdata::PepXMLSpecificity::cut, e(), pwiz::identdata::Enzyme::enzymeName, pwiz::proteome::Digestion::getCleavageAgentRegex(), pwiz::proteome::Digestion::getCleavageAgents(), MS_Asp_N, MS_Trypsin, MS_Trypsin_P, pwiz::identdata::Identifiable::name, pwiz::identdata::PepXMLSpecificity::no_cut, pwiz::identdata::pepXMLSpecificity(), pwiz::identdata::PepXMLSpecificity::sense, pwiz::data::ParamContainer::set(), pwiz::identdata::Enzyme::siteRegexp, unit_assert, unit_assert_operator_equal, and pwiz::data::ParamContainer::userParams.
Referenced by main().
void testStripChargeFromConventionalSpectrumId | ( | ) |
Definition at line 360 of file Serializer_pepXML_Test.cpp.
References pwiz::identdata::stripChargeFromConventionalSpectrumId(), and unit_assert_operator_equal.
Referenced by main().
int main | ( | int | argc, |
char ** | argv | ||
) |
Definition at line 374 of file Serializer_pepXML_Test.cpp.
References e(), os_, TEST_EPILOG, TEST_FAILED, TEST_PROLOG, testPepXMLSpecificity(), testSerialize(), and testStripChargeFromConventionalSpectrumId().
ostream* os_ = 0 |
Definition at line 43 of file Serializer_pepXML_Test.cpp.