ProteoWizard
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#include <TextWriter.hpp>
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std::string | makeDelimitedRefListString (const std::vector< boost::shared_ptr< object_type > > &objects, const char *delimiter=" ") |
template<typename object_type > | |
std::string | makeDelimitedListString (const std::vector< object_type > &objects, const char *delimiter=" ") |
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std::ostream & | os_ |
int | depth_ |
std::string | indent_ |
Definition at line 44 of file TextWriter.hpp.
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Definition at line 58 of file TextWriter.hpp.
References os_.
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Definition at line 72 of file TextWriter.hpp.
References pwiz::data::CVParam::cvid, CVID_Unknown, pwiz::cv::cvTermInfo(), pwiz::cv::CVTermInfo::name, os_, pwiz::data::CVParam::units, pwiz::data::CVParam::unitsName(), and pwiz::data::CVParam::value.
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Definition at line 84 of file TextWriter.hpp.
References os_.
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Definition at line 91 of file TextWriter.hpp.
References os_.
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Definition at line 98 of file TextWriter.hpp.
References os_.
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Definition at line 105 of file TextWriter.hpp.
References CVID_Unknown, pwiz::cv::cvTermInfo(), pwiz::data::UserParam::name, pwiz::cv::CVTermInfo::name, os_, pwiz::data::UserParam::type, pwiz::data::UserParam::units, and pwiz::data::UserParam::value.
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Definition at line 117 of file TextWriter.hpp.
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Definition at line 126 of file TextWriter.hpp.
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Definition at line 134 of file TextWriter.hpp.
References boost::lexical_cast().
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Definition at line 141 of file TextWriter.hpp.
References pwiz::data::ParamContainer::cvParams, and pwiz::data::ParamContainer::userParams.
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Definition at line 150 of file TextWriter.hpp.
References pwiz::data::ParamContainer::cvParams, and pwiz::data::ParamContainer::userParams.
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Definition at line 158 of file TextWriter.hpp.
References pwiz::identdata::BibliographicReference::authors, pwiz::identdata::BibliographicReference::editor, pwiz::identdata::BibliographicReference::issue, pwiz::identdata::BibliographicReference::pages, pwiz::identdata::BibliographicReference::publication, pwiz::identdata::BibliographicReference::publisher, pwiz::identdata::BibliographicReference::title, pwiz::identdata::BibliographicReference::volume, and pwiz::identdata::BibliographicReference::year.
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Definition at line 185 of file TextWriter.hpp.
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Definition at line 193 of file TextWriter.hpp.
References pwiz::identdata::DatabaseTranslation::frames, and pwiz::identdata::DatabaseTranslation::translationTable.
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Definition at line 204 of file TextWriter.hpp.
References pwiz::identdata::SpectrumIdentificationProtocol::additionalSearchParams, pwiz::identdata::SpectrumIdentificationProtocol::analysisSoftwarePtr, pwiz::identdata::SpectrumIdentificationProtocol::databaseFilters, pwiz::identdata::SpectrumIdentificationProtocol::databaseTranslation, pwiz::data::CVParam::empty(), pwiz::data::ParamContainer::empty(), pwiz::identdata::Enzymes::empty(), pwiz::identdata::SpectrumIdentificationProtocol::enzymes, pwiz::identdata::SpectrumIdentificationProtocol::fragmentTolerance, pwiz::identdata::SpectrumIdentificationProtocol::massTable, pwiz::identdata::SpectrumIdentificationProtocol::modificationParams, pwiz::identdata::SpectrumIdentificationProtocol::parentTolerance, pwiz::identdata::SpectrumIdentificationProtocol::searchType, and pwiz::identdata::SpectrumIdentificationProtocol::threshold.
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Definition at line 236 of file TextWriter.hpp.
References pwiz::identdata::DBSequence::accession, pwiz::identdata::DBSequence::length, pwiz::identdata::DBSequence::searchDatabasePtr, and pwiz::identdata::DBSequence::seq.
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Definition at line 253 of file TextWriter.hpp.
References pwiz::identdata::SubstitutionModification::avgMassDelta, pwiz::identdata::SubstitutionModification::location, pwiz::identdata::SubstitutionModification::monoisotopicMassDelta, pwiz::identdata::SubstitutionModification::originalResidue, and pwiz::identdata::SubstitutionModification::replacementResidue.
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Definition at line 269 of file TextWriter.hpp.
References pwiz::identdata::IonType::charge, pwiz::identdata::IonType::fragmentArray, and pwiz::identdata::IonType::index.
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Definition at line 283 of file TextWriter.hpp.
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Definition at line 292 of file TextWriter.hpp.
References pwiz::identdata::SearchDatabase::databaseName, pwiz::data::CVParam::empty(), pwiz::data::ParamContainer::empty(), pwiz::identdata::SearchDatabase::fileFormat, pwiz::identdata::SearchDatabase::location, pwiz::identdata::SearchDatabase::numDatabaseSequences, pwiz::identdata::SearchDatabase::numResidues, pwiz::identdata::SearchDatabase::releaseDate, and pwiz::identdata::SearchDatabase::version.
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Definition at line 314 of file TextWriter.hpp.
References pwiz::data::CVParam::empty(), pwiz::identdata::SpectraData::externalFormatDocumentation, pwiz::identdata::SpectraData::fileFormat, pwiz::identdata::SpectraData::location, and pwiz::identdata::SpectraData::spectrumIDFormat.
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Definition at line 329 of file TextWriter.hpp.
References pwiz::identdata::SpectrumIdentificationItem::calculatedMassToCharge, pwiz::identdata::SpectrumIdentificationItem::calculatedPI, pwiz::identdata::SpectrumIdentificationItem::chargeState, pwiz::identdata::SpectrumIdentificationItem::empty(), pwiz::identdata::SpectrumIdentificationItem::experimentalMassToCharge, pwiz::identdata::SpectrumIdentificationItem::fragmentation, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::SpectrumIdentificationItem::massTablePtr, pwiz::identdata::IdentifiableParamContainer::name, pwiz::identdata::SpectrumIdentificationItem::passThreshold, pwiz::identdata::SpectrumIdentificationItem::peptideEvidencePtr, pwiz::identdata::SpectrumIdentificationItem::peptidePtr, pwiz::identdata::SpectrumIdentificationItem::rank, and pwiz::identdata::SpectrumIdentificationItem::samplePtr.
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Definition at line 365 of file TextWriter.hpp.
References pwiz::identdata::SpectrumIdentificationResult::spectraDataPtr, pwiz::identdata::SpectrumIdentificationResult::spectrumID, and pwiz::identdata::SpectrumIdentificationResult::spectrumIdentificationItem.
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Definition at line 380 of file TextWriter.hpp.
References pwiz::identdata::SpectrumIdentificationList::empty(), pwiz::identdata::SpectrumIdentificationList::fragmentationTable, pwiz::identdata::SpectrumIdentificationList::numSequencesSearched, and pwiz::identdata::SpectrumIdentificationList::spectrumIdentificationResult.
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Definition at line 394 of file TextWriter.hpp.
References pwiz::identdata::ProteinDetectionList::proteinAmbiguityGroup.
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Definition at line 404 of file TextWriter.hpp.
References pwiz::identdata::AnalysisData::proteinDetectionListPtr, and pwiz::identdata::AnalysisData::spectrumIdentificationList.
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Definition at line 418 of file TextWriter.hpp.
References pwiz::identdata::FragmentArray::measurePtr, and pwiz::identdata::FragmentArray::values.
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Definition at line 431 of file TextWriter.hpp.
References pwiz::data::CVParam::empty(), pwiz::identdata::SourceFile::externalFormatDocumentation, pwiz::identdata::SourceFile::fileFormat, and pwiz::identdata::SourceFile::location.
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Definition at line 448 of file TextWriter.hpp.
References pwiz::identdata::Inputs::searchDatabase, pwiz::identdata::Inputs::sourceFile, and pwiz::identdata::Inputs::spectraData.
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Definition at line 463 of file TextWriter.hpp.
References pwiz::identdata::DataCollection::analysisData, pwiz::identdata::Inputs::empty(), pwiz::identdata::AnalysisData::empty(), and pwiz::identdata::DataCollection::inputs.
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Definition at line 476 of file TextWriter.hpp.
References pwiz::data::ParamContainer::empty(), pwiz::identdata::Filter::exclude, pwiz::identdata::Filter::filterType, and pwiz::identdata::Filter::include.
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Definition at line 489 of file TextWriter.hpp.
References pwiz::data::CVParam::empty(), pwiz::identdata::SearchModification::fixedMod, pwiz::identdata::SearchModification::massDelta, pwiz::identdata::SearchModification::residues, and pwiz::identdata::SearchModification::specificityRules.
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Definition at line 505 of file TextWriter.hpp.
References pwiz::identdata::Enzymes::enzymes, and pwiz::identdata::Enzymes::independent.
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Definition at line 516 of file TextWriter.hpp.
References pwiz::identdata::MassTable::ambiguousResidue, pwiz::identdata::MassTable::id, pwiz::identdata::MassTable::msLevel, and pwiz::identdata::MassTable::residues.
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Definition at line 531 of file TextWriter.hpp.
References pwiz::identdata::AnalysisProtocolCollection::proteinDetectionProtocol, and pwiz::identdata::AnalysisProtocolCollection::spectrumIdentificationProtocol.
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Definition at line 544 of file TextWriter.hpp.
References pwiz::identdata::PeptideHypothesis::peptideEvidencePtr, and pwiz::identdata::PeptideHypothesis::spectrumIdentificationItemPtr.
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Definition at line 555 of file TextWriter.hpp.
References pwiz::identdata::ProteinDetectionHypothesis::dbSequencePtr, and pwiz::identdata::ProteinDetectionHypothesis::peptideHypothesis.
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Definition at line 570 of file TextWriter.hpp.
References pwiz::identdata::ProteinAmbiguityGroup::proteinDetectionHypothesis.
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Definition at line 581 of file TextWriter.hpp.
References pwiz::identdata::ProteinDetection::activityDate, pwiz::identdata::ProteinDetection::inputSpectrumIdentifications, pwiz::identdata::ProteinDetection::proteinDetectionListPtr, and pwiz::identdata::ProteinDetection::proteinDetectionProtocolPtr.
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Definition at line 597 of file TextWriter.hpp.
References pwiz::identdata::SpectrumIdentification::activityDate, pwiz::identdata::SpectrumIdentification::inputSpectra, pwiz::identdata::SpectrumIdentification::searchDatabase, pwiz::identdata::SpectrumIdentification::spectrumIdentificationListPtr, and pwiz::identdata::SpectrumIdentification::spectrumIdentificationProtocolPtr.
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Definition at line 617 of file TextWriter.hpp.
References pwiz::identdata::ProteinDetection::empty(), pwiz::identdata::AnalysisCollection::proteinDetection, and pwiz::identdata::AnalysisCollection::spectrumIdentification.
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Definition at line 626 of file TextWriter.hpp.
References pwiz::identdata::SequenceCollection::dbSequences, pwiz::identdata::SequenceCollection::peptideEvidence, and pwiz::identdata::SequenceCollection::peptides.
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Definition at line 639 of file TextWriter.hpp.
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Definition at line 647 of file TextWriter.hpp.
References pwiz::identdata::Person::affiliations, pwiz::identdata::Person::firstName, pwiz::identdata::Person::lastName, and pwiz::identdata::Person::midInitials.
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Definition at line 664 of file TextWriter.hpp.
References pwiz::identdata::Organization::parent.
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Definition at line 675 of file TextWriter.hpp.
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Definition at line 688 of file TextWriter.hpp.
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Definition at line 697 of file TextWriter.hpp.
References pwiz::identdata::ContactRole::contactPtr.
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Definition at line 708 of file TextWriter.hpp.
References pwiz::identdata::Provider::contactRolePtr.
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Definition at line 718 of file TextWriter.hpp.
References pwiz::identdata::Sample::contactRole, pwiz::data::ParamContainer::cvParams, and pwiz::identdata::Sample::subSamples.
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Definition at line 730 of file TextWriter.hpp.
References pwiz::identdata::AnalysisSampleCollection::samples.
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Definition at line 738 of file TextWriter.hpp.
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Definition at line 756 of file TextWriter.hpp.
References pwiz::identdata::Enzyme::cTermGain, pwiz::data::ParamContainer::empty(), pwiz::identdata::Enzyme::enzymeName, pwiz::identdata::Identifiable::id, pwiz::identdata::Enzyme::minDistance, pwiz::identdata::Enzyme::missedCleavages, pwiz::identdata::Enzyme::nTermGain, pwiz::identdata::Enzyme::siteRegexp, and pwiz::identdata::Enzyme::terminalSpecificity.
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Definition at line 779 of file TextWriter.hpp.
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Definition at line 790 of file TextWriter.hpp.
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Definition at line 803 of file TextWriter.hpp.
References pwiz::identdata::Residue::code, and pwiz::identdata::Residue::mass.
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Definition at line 814 of file TextWriter.hpp.
References pwiz::identdata::AmbiguousResidue::code.
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Definition at line 825 of file TextWriter.hpp.
References pwiz::identdata::Modification::avgMassDelta, pwiz::identdata::Modification::location, pwiz::identdata::Modification::monoisotopicMassDelta, and pwiz::identdata::Modification::residues.
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Definition at line 842 of file TextWriter.hpp.
References pwiz::identdata::Peptide::modification, pwiz::identdata::Peptide::peptideSequence, and pwiz::identdata::Peptide::substitutionModification.
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Definition at line 857 of file TextWriter.hpp.
References pwiz::identdata::PeptideEvidence::dbSequencePtr, pwiz::identdata::PeptideEvidence::end, pwiz::identdata::PeptideEvidence::frame, pwiz::identdata::PeptideEvidence::isDecoy, pwiz::identdata::PeptideEvidence::peptidePtr, pwiz::identdata::PeptideEvidence::post, pwiz::identdata::PeptideEvidence::pre, pwiz::identdata::PeptideEvidence::start, and pwiz::identdata::PeptideEvidence::translationTablePtr.
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Definition at line 883 of file TextWriter.hpp.
References pwiz::identdata::IdentData::analysisCollection, pwiz::identdata::IdentData::analysisProtocolCollection, pwiz::identdata::IdentData::analysisSampleCollection, pwiz::identdata::IdentData::analysisSoftwareList, pwiz::identdata::IdentData::auditCollection, pwiz::identdata::IdentData::bibliographicReference, pwiz::identdata::IdentData::cvs, pwiz::identdata::IdentData::dataCollection, pwiz::identdata::Provider::empty(), pwiz::identdata::AnalysisSampleCollection::empty(), pwiz::identdata::SequenceCollection::empty(), pwiz::identdata::AnalysisCollection::empty(), pwiz::identdata::AnalysisProtocolCollection::empty(), pwiz::identdata::DataCollection::empty(), pwiz::identdata::IdentData::provider, pwiz::identdata::IdentData::sequenceCollection, and pwiz::identdata::IdentData::version().
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Definition at line 912 of file TextWriter.hpp.
References pwiz::cv::CV::fullName, pwiz::cv::CV::id, pwiz::cv::CV::URI, and pwiz::cv::CV::version.
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Definition at line 926 of file TextWriter.hpp.
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Definition at line 937 of file TextWriter.hpp.
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Definition at line 949 of file TextWriter.hpp.
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Definition at line 932 of file TextWriter.hpp.
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Definition at line 933 of file TextWriter.hpp.
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Definition at line 934 of file TextWriter.hpp.