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Public Member Functions | Private Member Functions | Private Attributes
pwiz::identdata::TextWriter Class Reference

#include <TextWriter.hpp>

List of all members.

Public Member Functions

 TextWriter (std::ostream &os, int depth=0)
TextWriter child ()
TextWriteroperator() (const std::string &text)
TextWriteroperator() (const float value)
TextWriteroperator() (const CVParam &cvParam)
TextWriteroperator() (const std::string &label, const float &v)
TextWriteroperator() (const std::string &label, const double &v)
TextWriteroperator() (const std::string &label, const bool &v)
TextWriteroperator() (const UserParam &userParam)
template<typename object_type >
TextWriteroperator() (const std::string &label, const std::vector< object_type > &v)
template<typename object_type >
TextWriteroperator() (const std::vector< object_type > &v)
template<typename object_type >
TextWriteroperator() (const std::string &label, const object_type &v)
TextWriteroperator() (const std::string &label, const ParamContainer &paramContainer)
TextWriteroperator() (const ParamContainer &paramContainer)
TextWriteroperator() (const BibliographicReference &br)
TextWriteroperator() (const TranslationTable &tt)
TextWriteroperator() (const DatabaseTranslation &dt)
TextWriteroperator() (const SpectrumIdentificationProtocol &si)
TextWriteroperator() (const DBSequence &ds)
TextWriteroperator() (const SubstitutionModification &ds)
TextWriteroperator() (const IonType &it)
TextWriteroperator() (const Measure &m)
TextWriteroperator() (const SearchDatabase &sd)
TextWriteroperator() (const SpectraData &sd)
TextWriteroperator() (const SpectrumIdentificationItem &sii)
TextWriteroperator() (const SpectrumIdentificationResult &sir)
TextWriteroperator() (const SpectrumIdentificationList &sil)
TextWriteroperator() (const ProteinDetectionList &pdl)
TextWriteroperator() (const AnalysisData &ad)
TextWriteroperator() (const FragmentArray &fa)
TextWriteroperator() (const SourceFile &sf)
TextWriteroperator() (const Inputs &inputs)
TextWriteroperator() (const DataCollection &dc)
TextWriteroperator() (const Filter &f)
TextWriteroperator() (const SearchModification &sm)
TextWriteroperator() (const Enzymes &ezs)
TextWriteroperator() (const MassTable &mt)
TextWriteroperator() (const AnalysisProtocolCollection &apc)
TextWriteroperator() (const PeptideHypothesis &ph)
TextWriteroperator() (const ProteinDetectionHypothesis &pdh)
TextWriteroperator() (const ProteinAmbiguityGroup &pag)
TextWriteroperator() (const ProteinDetection &pd)
TextWriteroperator() (const SpectrumIdentification &si)
TextWriteroperator() (const AnalysisCollection &ac)
TextWriteroperator() (const SequenceCollection &sc)
TextWriteroperator() (const Contact &cont)
TextWriteroperator() (const Person &per)
TextWriteroperator() (const Organization &org)
TextWriteroperator() (const ContactPtr cont)
TextWriteroperator() (const std::string &label, const ContactPtr cont)
TextWriteroperator() (const ContactRole &cr)
TextWriteroperator() (const Provider &provider)
TextWriteroperator() (const Sample &sample)
TextWriteroperator() (const AnalysisSampleCollection &asc)
TextWriteroperator() (const AnalysisSoftwarePtr &asp)
TextWriteroperator() (const Enzyme &enzyme)
TextWriteroperator() (const Identifiable &id)
TextWriteroperator() (const IdentifiableParamContainer &id)
TextWriteroperator() (const Residue &res)
TextWriteroperator() (const AmbiguousResidue &res)
TextWriteroperator() (const Modification &mod)
TextWriteroperator() (const Peptide &pep)
TextWriteroperator() (const PeptideEvidence &pe)
TextWriteroperator() (const IdentData &mzid)
TextWriteroperator() (const CV &cv)
template<typename object_type >
TextWriteroperator() (const boost::shared_ptr< object_type > &p)

Private Member Functions

template<typename object_type >
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=" ")

Private Attributes

std::ostream & os_
int depth_
std::string indent_

Detailed Description

Definition at line 44 of file TextWriter.hpp.


Constructor & Destructor Documentation

pwiz::identdata::TextWriter::TextWriter ( std::ostream &  os,
int  depth = 0 
)
inline

Definition at line 48 of file TextWriter.hpp.

References os_.

: os_(os), depth_(depth), indent_(depth*2, ' ')
{
os_.precision(14);
}

Member Function Documentation

TextWriter pwiz::identdata::TextWriter::child ( )
inline

Definition at line 55 of file TextWriter.hpp.

References os_.

{return TextWriter(os_, depth_+1);}
TextWriter& pwiz::identdata::TextWriter::operator() ( const std::string &  text)
inline

Definition at line 58 of file TextWriter.hpp.

References os_.

{
os_ << indent_ << text << std::endl;
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const float  value)
inline

Definition at line 65 of file TextWriter.hpp.

References os_.

{
os_ << indent_ << value << std::endl;
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const CVParam cvParam)
inline

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.

{
os_ << indent_ << "cvParam: " << cvTermInfo(cvParam.cvid).name;
if (!cvParam.value.empty())
os_ << ", " << cvParam.value;
if (cvParam.units != CVID_Unknown)
os_ << ", " << cvParam.unitsName();
os_ << std::endl;
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const std::string &  label,
const float &  v 
)
inline

Definition at line 84 of file TextWriter.hpp.

References os_.

{
os_ << indent_ << label << v << std::endl;
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const std::string &  label,
const double &  v 
)
inline

Definition at line 91 of file TextWriter.hpp.

References os_.

{
os_ << indent_ << label << v << std::endl;
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const std::string &  label,
const bool &  v 
)
inline

Definition at line 98 of file TextWriter.hpp.

References os_.

{
os_ << indent_ << label << std::boolalpha << v << std::endl;
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const UserParam userParam)
inline

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.

{
os_ << indent_ << "userParam: " << userParam.name;
if (!userParam.value.empty()) os_ << ", " << userParam.value;
if (!userParam.type.empty()) os_ << ", " << userParam.type;
if (userParam.units != CVID_Unknown) os_ << ", " << cvTermInfo(userParam.units).name;
os_ << std::endl;
return *this;
}
template<typename object_type >
TextWriter& pwiz::identdata::TextWriter::operator() ( const std::string &  label,
const std::vector< object_type > &  v 
)
inline

Definition at line 117 of file TextWriter.hpp.

{
(*this)(label);
for_each(v.begin(), v.end(), child());
return *this;
}
template<typename object_type >
TextWriter& pwiz::identdata::TextWriter::operator() ( const std::vector< object_type > &  v)
inline

Definition at line 126 of file TextWriter.hpp.

{
for_each(v.begin(), v.end(), child());
return *this;
}
template<typename object_type >
TextWriter& pwiz::identdata::TextWriter::operator() ( const std::string &  label,
const object_type &  v 
)
inline

Definition at line 134 of file TextWriter.hpp.

References boost::lexical_cast().

{
(*this)(label + boost::lexical_cast<std::string>(v));
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const std::string &  label,
const ParamContainer paramContainer 
)
inline

Definition at line 141 of file TextWriter.hpp.

References pwiz::data::ParamContainer::cvParams, and pwiz::data::ParamContainer::userParams.

{
(*this)(label); // + ":"
for_each(paramContainer.cvParams.begin(), paramContainer.cvParams.end(), child());
for_each(paramContainer.userParams.begin(), paramContainer.userParams.end(), child());
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const ParamContainer paramContainer)
inline

Definition at line 150 of file TextWriter.hpp.

References pwiz::data::ParamContainer::cvParams, and pwiz::data::ParamContainer::userParams.

{
for_each(paramContainer.cvParams.begin(), paramContainer.cvParams.end(), *this);
for_each(paramContainer.userParams.begin(), paramContainer.userParams.end(), *this);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const BibliographicReference br)
inline

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.

{
(*this)("BibliographicReference: ");
(*this)((Identifiable)br);
if (!br.authors.empty())
child()("authors: "+br.authors);
if (!br.publication.empty())
child()("publication: "+br.publication);
if (!br.publisher.empty())
child()(br.publisher);
if (!br.editor.empty())
child()("editor: "+br.editor);
if (br.year != 0)
child()("year: ", br.year);
if (!br.volume.empty())
child()("volume: "+br.volume);
if (!br.issue.empty())
child()("issue: "+br.issue);
if (!br.pages.empty())
child()("pages: "+br.pages);
if (!br.title.empty())
child()("title: "+br.title);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const TranslationTable tt)
inline

Definition at line 185 of file TextWriter.hpp.

{
(*this)("TranslationTable:");
(*this)((const IdentifiableParamContainer&)tt);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const DatabaseTranslation dt)
inline

Definition at line 193 of file TextWriter.hpp.

References pwiz::identdata::DatabaseTranslation::frames, and pwiz::identdata::DatabaseTranslation::translationTable.

{
(*this)("DatabaseTranslation:");
if (!dt.frames.empty())
child()("frames: ", dt.frames);
if (!dt.translationTable.empty())
child()("translationTable: ", dt.translationTable);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const SpectrumIdentificationProtocol si)
inline

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.

{
(*this)("SpectrumIdentificationProtocol:");
(*this)((Identifiable&)si);
if (si.analysisSoftwarePtr.get() &&
!si.analysisSoftwarePtr->empty())
child()("analysisSoftware_ref: "+si.analysisSoftwarePtr->id);
if (!si.searchType.empty())
child()("SearchType: ", si.searchType);
if (!si.additionalSearchParams.empty())
child()("AdditionalSearchParams", si.additionalSearchParams);
if (!si.modificationParams.empty())
child()("ModificationParams", si.modificationParams);
if (!si.enzymes.empty())
child()(si.enzymes);
if (!si.massTable.empty())
child()(si.massTable);
if (!si.fragmentTolerance.empty())
child()("FragmentTolerance", si.fragmentTolerance);
if (!si.parentTolerance.empty())
child()("ParentTolerance", si.parentTolerance);
if (!si.threshold.empty())
child()("Threshold", si.threshold);
if (!si.databaseFilters.empty())
child()("DatabaseFilters", si.databaseFilters);
if (si.databaseTranslation.get() && !si.databaseTranslation->empty())
child()("DatabaseTranslation", si.databaseTranslation);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const DBSequence ds)
inline

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.

{
(*this)("DBSequence: ");
(*this)((const IdentifiableParamContainer&)ds);
if (ds.length!=0)
child()("length: ", ds.length);
if (!ds.accession.empty())
child()("accession: "+ds.accession);
if (ds.searchDatabasePtr.get() && !ds.searchDatabasePtr->empty())
child()("searchDatabase_ref: "+ds.searchDatabasePtr->id);
if (!ds.seq.empty())
child()("Seq: "+ds.seq);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const SubstitutionModification ds)
inline

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.

{
(*this)("SubstitutionModification: ");
if (ds.originalResidue != 0)
child()("originalResidue: ", ds.originalResidue);
if (ds.replacementResidue != 0)
child()("replacementResidue: ", ds.replacementResidue);
if (ds.location != 0)
child()("location: ", ds.location);
child()("avgMassDelta: ", ds.avgMassDelta);
child()("monoisotopicMassDelta: ", ds.monoisotopicMassDelta);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const IonType it)
inline

Definition at line 269 of file TextWriter.hpp.

References pwiz::identdata::IonType::charge, pwiz::identdata::IonType::fragmentArray, and pwiz::identdata::IonType::index.

{
(*this)("IonType: ");
if (!it.index.empty())
child()("index: " + makeDelimitedListString(it.index));
if (it.charge != 0)
child()("charge: ", it.charge);
if (!it.fragmentArray.empty())
(*this)(it.fragmentArray);
(*this)((const CVParam&)it);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const Measure m)
inline

Definition at line 283 of file TextWriter.hpp.

{
(*this)("Measure: ");
(*this)((const ParamContainer&)m);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const SearchDatabase sd)
inline

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.

{
(*this)("SearchDatabase: ");
(*this)((const IdentifiableParamContainer&)sd);
if (!sd.location.empty())
child()("location: " + sd.location);
if (!sd.version.empty())
child()("version: " + sd.version);
if (!sd.releaseDate.empty())
child()("releaseDate: " + sd.releaseDate);
if (sd.numDatabaseSequences != 0)
child()("numDatabaseSequences: ", sd.numDatabaseSequences);
if (sd.numResidues != 0)
child()("numResidues: ", sd.numResidues);
if (!sd.fileFormat.empty())
child()("FileFormat: ", sd.fileFormat);
if (!sd.databaseName.empty())
child()("DatabaseName: ", sd.databaseName);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const SpectraData sd)
inline

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.

{
(*this)("SpectraData: ");
if (!sd.location.empty())
child()("location: " + sd.location);
if (!sd.externalFormatDocumentation.empty())
child()("ExternalFormatDocumentation: ", sd.externalFormatDocumentation);
if (!sd.fileFormat.empty())
child()("FileFormat: ", sd.fileFormat);
if (!sd.spectrumIDFormat.empty())
child()("SpectrumIDFormat: ", sd.spectrumIDFormat);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const SpectrumIdentificationItem sii)
inline

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.

{
(*this)("SpectrumIdentificationItem:");
if (!sii.id.empty())
child()("id: ", sii.id);
if (!sii.name.empty())
child()("name: ", sii.name);
if (!sii.empty())
{
child()("rank: ", sii.rank);
child()("chargeState: ", sii.chargeState);
child()("experimentalMassToCharge: ", sii.experimentalMassToCharge);
child()("calculatedMassToCharge: ", sii.calculatedMassToCharge);
child()("calculatedPI: ", sii.calculatedPI);
child()("passThreshold: ", sii.passThreshold);
}
if (sii.peptidePtr.get() && !sii.peptidePtr->empty())
child()("peptide_ref: ", sii.peptidePtr->id);
if (sii.massTablePtr.get() && !sii.massTablePtr->empty())
child()("massTable_ref: ", sii.massTablePtr->id);
if (sii.samplePtr.get() && !sii.samplePtr->empty())
child()("sample_ref: ", sii.samplePtr->id);
BOOST_FOREACH(const PeptideEvidencePtr& pe, sii.peptideEvidencePtr)
if (pe.get() && !pe->empty())
child()("peptideEvidence_ref: ", pe->id);
if (!sii.fragmentation.empty())
child()("fragmentation", sii.fragmentation);
child()((const ParamContainer&)sii);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const SpectrumIdentificationResult sir)
inline

Definition at line 365 of file TextWriter.hpp.

References pwiz::identdata::SpectrumIdentificationResult::spectraDataPtr, pwiz::identdata::SpectrumIdentificationResult::spectrumID, and pwiz::identdata::SpectrumIdentificationResult::spectrumIdentificationItem.

{
(*this)("SpectrumIdentificationResult: ");
(*this)((const IdentifiableParamContainer&)sir);
if (!sir.spectrumID.empty())
child()("spectrumID: "+sir.spectrumID);
if (sir.spectraDataPtr.get() && !sir.spectraDataPtr->empty())
child()("spectraData_ref: "+sir.spectraDataPtr->id);
if (!sir.spectrumIdentificationItem.empty())
(*this)(sir.spectrumIdentificationItem);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const SpectrumIdentificationList sil)
inline

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.

{
(*this)("SpectrumIdentificationList: ");
(*this)((Identifiable)sil);
if (!sil.empty())
child()("numSequencesSearched: ", sil.numSequencesSearched);
if (!sil.fragmentationTable.empty())
child()("FragmentationTable", sil.fragmentationTable);
if (!sil.spectrumIdentificationResult.empty())
(*this)(sil.spectrumIdentificationResult);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const ProteinDetectionList pdl)
inline

Definition at line 394 of file TextWriter.hpp.

References pwiz::identdata::ProteinDetectionList::proteinAmbiguityGroup.

{
(*this)("ProteinDetectionList: ");
if (!pdl.proteinAmbiguityGroup.empty())
(*this)(pdl.proteinAmbiguityGroup);
(*this)((const ParamContainer&)pdl);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const AnalysisData ad)
inline

Definition at line 404 of file TextWriter.hpp.

References pwiz::identdata::AnalysisData::proteinDetectionListPtr, and pwiz::identdata::AnalysisData::spectrumIdentificationList.

{
(*this)("AnalysisData: ");
if (!ad.spectrumIdentificationList.empty())
(*this)(ad.spectrumIdentificationList);
if (ad.proteinDetectionListPtr.get() &&
!ad.proteinDetectionListPtr->empty())
(*this)(*ad.proteinDetectionListPtr);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const FragmentArray fa)
inline

Definition at line 418 of file TextWriter.hpp.

References pwiz::identdata::FragmentArray::measurePtr, and pwiz::identdata::FragmentArray::values.

{
(*this)("FragmentArray: ");
if (fa.measurePtr.get() && !fa.measurePtr->empty())
child()("measure_ref: " + fa.measurePtr->id);
if (!fa.values.empty())
child()("values: " + makeDelimitedListString(fa.values));
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const SourceFile sf)
inline

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.

{
//(*this)("sourceFile: ");
(*this)((const IdentifiableParamContainer&)sf);
if (!sf.location.empty())
child()("location: " + sf.location);
if (!sf.fileFormat.empty())
child()(sf.fileFormat);
if (!sf.externalFormatDocumentation.empty())
child()("externalFormatDocumentation: ",
sf.externalFormatDocumentation);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const Inputs inputs)
inline

Definition at line 448 of file TextWriter.hpp.

References pwiz::identdata::Inputs::searchDatabase, pwiz::identdata::Inputs::sourceFile, and pwiz::identdata::Inputs::spectraData.

{
(*this)("Inputs: ");
if (!inputs.sourceFile.empty())
child()("sourceFile: ", inputs.sourceFile);
if (!inputs.searchDatabase.empty())
child()("searchDatabase: ", inputs.searchDatabase);
if (!inputs.spectraData.empty())
child()("spectraData: ", inputs.spectraData);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const DataCollection dc)
inline

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.

{
(*this)("DataCollection: ");
if (!dc.inputs.empty())
child()(dc.inputs);
if (!dc.analysisData.empty())
child()(dc.analysisData);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const Filter f)
inline

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.

{
(*this)("Filter: ");
if (!f.filterType.empty())
child()("filterType: ", f.filterType);
if (!f.include.empty())
child()("include: ", f.include);
if (!f.exclude.empty())
child()("exclude: ", f.exclude);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const SearchModification sm)
inline

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.

{
(*this)("SearchModification: ");
if (sm.fixedMod != 0)
child()("fixedMod: ", sm.fixedMod);
if (sm.massDelta != 0)
child()("massDelta: ", sm.massDelta);
if (!sm.residues.empty())
child()("residues: " + makeDelimitedListString(sm.residues));
if (!sm.specificityRules.empty())
child()("specificityRules: ", sm.specificityRules);
child()((const ParamContainer&)sm);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const Enzymes ezs)
inline

Definition at line 505 of file TextWriter.hpp.

References pwiz::identdata::Enzymes::enzymes, and pwiz::identdata::Enzymes::independent.

{
(*this)("Enzymes: ");
if (!indeterminate(ezs.independent))
child()("independent: ", ezs.independent);
if (!ezs.enzymes.empty())
child()("enzymes: ", ezs.enzymes);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const MassTable mt)
inline

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.

{
(*this)("MassTable: ");
if (!mt.id.empty())
child()("id: " + mt.id);
if (!mt.msLevel.empty())
child()("msLevel: ", mt.msLevel);
if (!mt.residues.empty())
child()("residues: ", mt.residues);
if (!mt.ambiguousResidue.empty())
child()("ambiguousResidue: ", mt.residues);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const AnalysisProtocolCollection apc)
inline

Definition at line 531 of file TextWriter.hpp.

References pwiz::identdata::AnalysisProtocolCollection::proteinDetectionProtocol, and pwiz::identdata::AnalysisProtocolCollection::spectrumIdentificationProtocol.

{
(*this)("AnalysisProtocolCollection: ");
if (!apc.spectrumIdentificationProtocol.empty())
child()("spectrumIdentificationProtocol: ",
apc.spectrumIdentificationProtocol);
if (!apc.proteinDetectionProtocol.empty())
child()("proteinDetectionProtocol: ",
apc.proteinDetectionProtocol);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const PeptideHypothesis ph)
inline

Definition at line 544 of file TextWriter.hpp.

References pwiz::identdata::PeptideHypothesis::peptideEvidencePtr, and pwiz::identdata::PeptideHypothesis::spectrumIdentificationItemPtr.

{
(*this)("PeptideHypothesis: ");
if (ph.peptideEvidencePtr.get())
child()("peptideEvidence: ", ph.peptideEvidencePtr->id);
child()("spectrumIdentificationItem: " + makeDelimitedRefListString(ph.spectrumIdentificationItemPtr));
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const ProteinDetectionHypothesis pdh)
inline

Definition at line 555 of file TextWriter.hpp.

References pwiz::identdata::ProteinDetectionHypothesis::dbSequencePtr, and pwiz::identdata::ProteinDetectionHypothesis::peptideHypothesis.

{
(*this)("ProteinDetectionHypothesis: ");
if (pdh.dbSequencePtr.get() && !pdh.dbSequencePtr->empty())
child()("DBSequence_ref: " + pdh.dbSequencePtr->id);
// TODO: Resolve if (!pdh.passThreshold.empty())
// child()("passThreshold: " + boost::lexical_cast<std::string>(pdh.passThreshold));
if (!pdh.peptideHypothesis.empty())
(*this)(pdh.peptideHypothesis);
child()((const ParamContainer&)pdh);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const ProteinAmbiguityGroup pag)
inline

Definition at line 570 of file TextWriter.hpp.

References pwiz::identdata::ProteinAmbiguityGroup::proteinDetectionHypothesis.

{
(*this)("ProteinAmbiguityGroup: ");
if (!pag.proteinDetectionHypothesis.empty())
(*this)(pag.proteinDetectionHypothesis);
(*this)((const ParamContainer&)pag);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const ProteinDetection pd)
inline

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.

{
(*this)("ProteinDetection: ");
if (pd.proteinDetectionProtocolPtr.get() &&
!pd.proteinDetectionProtocolPtr->empty())
child()("proteinDetectionProtocol_ref: "+pd.proteinDetectionProtocolPtr->id);
if (pd.proteinDetectionListPtr.get() &&
!pd.proteinDetectionListPtr->empty())
child()("proteinDetectionList_ref: "+pd.proteinDetectionListPtr->id);
if (!pd.activityDate.empty())
child()("activityDate: "+pd.activityDate);
child()("inputSpectrumIdentifications: " + makeDelimitedRefListString(pd.inputSpectrumIdentifications));
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const SpectrumIdentification si)
inline

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.

{
(*this)("SpectrumIdentification: ");
if (si.spectrumIdentificationProtocolPtr.get() &&
!si.spectrumIdentificationProtocolPtr->empty())
child()("spectrumIdentificationProtocol_ref: "+si.spectrumIdentificationProtocolPtr->id);
if (si.spectrumIdentificationListPtr.get() &&
!si.spectrumIdentificationListPtr->empty())
child()("spectrumIdentificationList_ref: "+si.spectrumIdentificationListPtr->id);
if (!si.activityDate.empty())
child()("activityDate: "+si.activityDate);
if (!si.inputSpectra.empty())
child()("inputSpectra: " + makeDelimitedRefListString(si.inputSpectra));
if (!si.searchDatabase.empty())
child()("searchDatabase: " + makeDelimitedRefListString(si.searchDatabase));
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const AnalysisCollection ac)
inline

Definition at line 617 of file TextWriter.hpp.

References pwiz::identdata::ProteinDetection::empty(), pwiz::identdata::AnalysisCollection::proteinDetection, and pwiz::identdata::AnalysisCollection::spectrumIdentification.

{
(*this)("AnalysisCollection: ", ac.spectrumIdentification);
if (!ac.proteinDetection.empty())
child()(ac.proteinDetection);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const SequenceCollection sc)
inline

Definition at line 626 of file TextWriter.hpp.

References pwiz::identdata::SequenceCollection::dbSequences, pwiz::identdata::SequenceCollection::peptideEvidence, and pwiz::identdata::SequenceCollection::peptides.

{
(*this)("SequenceCollection: ");
if (!sc.dbSequences.empty())
child()("dbSequences: ", sc.dbSequences);
if (!sc.peptides.empty())
child()("peptides: ", sc.peptides);
if (!sc.peptideEvidence.empty())
child()("peptideEvidence: ", sc.peptideEvidence);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const Contact cont)
inline

Definition at line 639 of file TextWriter.hpp.

{
(*this)((const IdentifiableParamContainer&)cont);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const Person per)
inline

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.

{
(*this)("Person: ");
(*this)((const Contact&)per);
if (!per.lastName.empty())
child()("lastName: "+per.lastName);
if (!per.firstName.empty())
child()("firstName: "+per.firstName);
if (!per.midInitials.empty())
child()("midInitials: "+per.midInitials);
if (!per.affiliations.empty())
child()("affiliations: ", per.affiliations);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const Organization org)
inline

Definition at line 664 of file TextWriter.hpp.

References pwiz::identdata::Organization::parent.

{
(*this)("Organization: ");
(*this)((const Contact&)org);
if (org.parent.get())
child()("Parent: ", org.parent->id);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const ContactPtr  cont)
inline

Definition at line 675 of file TextWriter.hpp.

{
if (dynamic_cast<Person*>(cont.get()))
(*this)((const Person&)(*cont));
else if (dynamic_cast<Organization*>(cont.get()))
(*this)((const Organization&)(*cont));
else
(*this)(*cont);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const std::string &  label,
const ContactPtr  cont 
)
inline

Definition at line 688 of file TextWriter.hpp.

{
(*this)(label);
(*this)(cont);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const ContactRole cr)
inline

Definition at line 697 of file TextWriter.hpp.

References pwiz::identdata::ContactRole::contactPtr.

{
(*this)("ContactRole: ");
if (cr.contactPtr.get() && !cr.contactPtr->empty())
child()("contact_ref: ", cr.contactPtr->id);
if (!cr.CVParam::empty())
child()("Role: ", (const CVParam&)cr);
return (*this);
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const Provider provider)
inline

Definition at line 708 of file TextWriter.hpp.

References pwiz::identdata::Provider::contactRolePtr.

{
(*this)("Provider: ");
(*this)((Identifiable&)provider);
if (provider.contactRolePtr.get() && !provider.contactRolePtr->empty())
child()(provider.contactRolePtr);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const Sample sample)
inline

Definition at line 718 of file TextWriter.hpp.

References pwiz::identdata::Sample::contactRole, pwiz::data::ParamContainer::cvParams, and pwiz::identdata::Sample::subSamples.

{
(*this)("Sample: ");
(*this)((const IdentifiableParamContainer&)sample);
(*this)(sample.contactRole);
child()(sample.cvParams);
child()("SubSamples:", sample.subSamples);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const AnalysisSampleCollection asc)
inline

Definition at line 730 of file TextWriter.hpp.

References pwiz::identdata::AnalysisSampleCollection::samples.

{
(*this)("AnalysisSampleCollection: ", asc.samples);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const AnalysisSoftwarePtr &  asp)
inline

Definition at line 738 of file TextWriter.hpp.

{
(*this)("analysisSoftware:");
(*this)((Identifiable)*asp);
if (!asp->version.empty())
child()("version: "+asp->version);
if (asp->contactRolePtr.get() && asp->contactRolePtr->empty())
child()(*asp->contactRolePtr);
if (!asp->softwareName.empty())
child()("softwareName: ", asp->softwareName);
if (!asp->URI.empty())
child()("uri: "+asp->URI);
if (!asp->customizations.empty())
child()("customizations: "+asp->customizations);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const Enzyme enzyme)
inline

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.

{
(*this)("Enzyme: ");
if (!enzyme.id.empty())
child()("id: "+enzyme.id);
if (!enzyme.nTermGain.empty())
child()("nTermGain: "+enzyme.nTermGain);
if (!enzyme.cTermGain.empty())
child()("cTermGain: "+enzyme.cTermGain);
child()("semiSpecific: ", (enzyme.terminalSpecificity != proteome::Digestion::FullySpecific ? "true": "false"));
if (enzyme.missedCleavages != 0)
child()("missedCleavages: ", enzyme.missedCleavages);
if (enzyme.minDistance != 0)
child()("minDistance: ", enzyme.minDistance);
if (!enzyme.siteRegexp.empty())
child()("SiteRegexp: "+enzyme.siteRegexp);
if (!enzyme.enzymeName.empty())
child()("EnzymeName: ", enzyme.enzymeName);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const Identifiable id)
inline

Definition at line 779 of file TextWriter.hpp.

{
if (!id.id.empty())
child()("id: "+id.id);
if (!id.name.empty())
child()("name: "+id.name);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const IdentifiableParamContainer id)
inline

Definition at line 790 of file TextWriter.hpp.

{
if (!id.id.empty())
child()("id: "+id.id);
if (!id.name.empty())
child()("name: "+id.name);
child()((const ParamContainer&)id);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const Residue res)
inline

Definition at line 803 of file TextWriter.hpp.

References pwiz::identdata::Residue::code, and pwiz::identdata::Residue::mass.

{
(*this)("Residue: ");
if (res.code != 0)
child()("code: ", res.code);
if (res.mass != 0)
child()("mass: ", res.mass);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const AmbiguousResidue res)
inline

Definition at line 814 of file TextWriter.hpp.

References pwiz::identdata::AmbiguousResidue::code.

{
(*this)("AmbiguousResidue: ");
if (res.code != 0)
child()("code: ", res.code);
(*this)((const ParamContainer&)res);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const Modification mod)
inline

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.

{
(*this)("Modification: ");
if (mod.location != 0)
child()("location: ", mod.location);
if (!mod.residues.empty())
child()("residues: " + makeDelimitedListString(mod.residues));
if (mod.avgMassDelta != 0)
child()("avgMassDelta: ", mod.avgMassDelta);
if (mod.monoisotopicMassDelta != 0)
child()("monoisotopicMassDelta: ", mod.monoisotopicMassDelta);
child()((const ParamContainer&)mod);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const Peptide pep)
inline

Definition at line 842 of file TextWriter.hpp.

References pwiz::identdata::Peptide::modification, pwiz::identdata::Peptide::peptideSequence, and pwiz::identdata::Peptide::substitutionModification.

{
(*this)("Peptide: ");
(*this)((const IdentifiableParamContainer&)pep);
if (!pep.peptideSequence.empty())
child()("peptideSequence: "+pep.peptideSequence);
if (!pep.modification.empty())
child()("modification", pep.modification);
if (!pep.substitutionModification.empty())
child()(pep.substitutionModification);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const PeptideEvidence pe)
inline

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.

{
(*this)("PeptideEvidence: ");
(*this)((const IdentifiableParamContainer&)pe);
if (pe.peptidePtr.get() && !pe.peptidePtr->empty())
child()("peptide_ref: "+pe.peptidePtr->id);
if (pe.dbSequencePtr.get() && !pe.dbSequencePtr->empty())
child()("dBSequence_ref: "+pe.dbSequencePtr->id);
if (pe.start != 0)
child()("start: ", pe.start);
if (pe.end != 0)
child()("end: ", pe.end);
if (pe.pre != 0)
child()("pre: ", pe.pre);
if (pe.post != 0)
child()("post: ", pe.post);
if (pe.translationTablePtr.get() && !pe.translationTablePtr->empty())
child()("translationTable_ref: "+pe.translationTablePtr->id);
if (pe.frame != 0)
child()("frame: ", pe.frame);
child()("isDecoy: ", pe.isDecoy);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const IdentData mzid)
inline

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().

{
(*this)("mzid:");
child()((Identifiable)mzid);
("version: " + mzid.version());
if (!mzid.cvs.empty())
child()("cvList: ", mzid.cvs);
if (!mzid.analysisSoftwareList.empty())
child()("analysisSoftwareList: ", mzid.analysisSoftwareList);
if (!mzid.provider.empty())
child()(mzid.provider);
if (!mzid.auditCollection.empty())
child()("auditCollection: ", mzid.auditCollection);
if (!mzid.analysisSampleCollection.empty())
child()(mzid.analysisSampleCollection);
if (!mzid.sequenceCollection.empty())
child()(mzid.sequenceCollection);
if (!mzid.analysisCollection.empty())
child()(mzid.analysisCollection);
if (!mzid.analysisProtocolCollection.empty())
child()(mzid.analysisProtocolCollection);
if (!mzid.dataCollection.empty())
child()(mzid.dataCollection);
if (!mzid.bibliographicReference.empty())
child()(mzid.bibliographicReference);
return *this;
}
TextWriter& pwiz::identdata::TextWriter::operator() ( const CV cv)
inline

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.

{
(*this)("cv:");
("id: " + cv.id)
("fullName: " + cv.fullName)
("version: " + cv.version)
("URI: " + cv.URI);
return *this;
}
template<typename object_type >
TextWriter& pwiz::identdata::TextWriter::operator() ( const boost::shared_ptr< object_type > &  p)
inline

Definition at line 926 of file TextWriter.hpp.

{
return p.get() ? (*this)(*p) : *this;
}
template<typename object_type >
std::string pwiz::identdata::TextWriter::makeDelimitedRefListString ( const std::vector< boost::shared_ptr< object_type > > &  objects,
const char *  delimiter = " " 
)
inlineprivate

Definition at line 937 of file TextWriter.hpp.

{
std::ostringstream oss;
for (size_t i=0; i < objects.size(); ++i)
{
if (i > 0) oss << delimiter;
oss << objects[i]->id;
}
return oss.str();
}
template<typename object_type >
std::string pwiz::identdata::TextWriter::makeDelimitedListString ( const std::vector< object_type > &  objects,
const char *  delimiter = " " 
)
inlineprivate

Definition at line 949 of file TextWriter.hpp.

{
std::ostringstream oss;
oss.precision(9);
for (size_t i=0; i < objects.size(); ++i)
{
if (i > 0) oss << delimiter;
oss << objects[i];
}
return oss.str();
}

Member Data Documentation

std::ostream& pwiz::identdata::TextWriter::os_
private

Definition at line 932 of file TextWriter.hpp.

int pwiz::identdata::TextWriter::depth_
private

Definition at line 933 of file TextWriter.hpp.

std::string pwiz::identdata::TextWriter::indent_
private

Definition at line 934 of file TextWriter.hpp.


The documentation for this class was generated from the following file: