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Public Member Functions | Private Member Functions | Private Attributes | List of all members
pwiz::identdata::TextWriter Class Reference

#include <TextWriter.hpp>

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

◆ TextWriter()

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

Definition at line 48 of file TextWriter.hpp.

49 : os_(os), depth_(depth), indent_(depth*2, ' ')
50 {
51 os_.precision(14);
52 }

References os_.

Member Function Documentation

◆ child()

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

Definition at line 55 of file TextWriter.hpp.

55{return TextWriter(os_, depth_+1);}
TextWriter(std::ostream &os, int depth=0)

References os_.

◆ operator()() [1/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const std::string &  text)
inline

Definition at line 58 of file TextWriter.hpp.

59 {
60 os_ << indent_ << text << std::endl;
61 return *this;
62 }

References os_.

◆ operator()() [2/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const float  value)
inline

Definition at line 65 of file TextWriter.hpp.

66 {
67 os_ << indent_ << value << std::endl;
68 return *this;
69 }
PWIZ_API_DECL std::string value(const std::string &id, const std::string &name)
convenience function to extract a named value from an id string

References os_.

◆ operator()() [3/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const CVParam cvParam)
inline

Definition at line 72 of file TextWriter.hpp.

73 {
74 os_ << indent_ << "cvParam: " << cvTermInfo(cvParam.cvid).name;
75 if (!cvParam.value.empty())
76 os_ << ", " << cvParam.value;
77 if (cvParam.units != CVID_Unknown)
78 os_ << ", " << cvParam.unitsName();
79 os_ << std::endl;
80 return *this;
81 }
CVID_Unknown
Definition cv.hpp:114
PWIZ_API_DECL const CVTermInfo & cvTermInfo(CVID cvid)
returns CV term info for the specified CVID
std::string name
Definition cv.hpp:14947

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.

◆ operator()() [4/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const std::string &  label,
const float &  v 
)
inline

Definition at line 84 of file TextWriter.hpp.

85 {
86 os_ << indent_ << label << v << std::endl;
87 return *this;
88 }

References os_.

◆ operator()() [5/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const std::string &  label,
const double &  v 
)
inline

Definition at line 91 of file TextWriter.hpp.

92 {
93 os_ << indent_ << label << v << std::endl;
94 return *this;
95 }

References os_.

◆ operator()() [6/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const std::string &  label,
const bool &  v 
)
inline

Definition at line 98 of file TextWriter.hpp.

99 {
100 os_ << indent_ << label << std::boolalpha << v << std::endl;
101 return *this;
102 }

References os_.

◆ operator()() [7/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const UserParam userParam)
inline

Definition at line 105 of file TextWriter.hpp.

106 {
107 os_ << indent_ << "userParam: " << userParam.name;
108 if (!userParam.value.empty()) os_ << ", " << userParam.value;
109 if (!userParam.type.empty()) os_ << ", " << userParam.type;
110 if (userParam.units != CVID_Unknown) os_ << ", " << cvTermInfo(userParam.units).name;
111 os_ << std::endl;
112 return *this;
113 }

References CVID_Unknown, pwiz::cv::cvTermInfo(), pwiz::cv::CVTermInfo::name, pwiz::data::UserParam::name, os_, pwiz::data::UserParam::type, pwiz::data::UserParam::units, and pwiz::data::UserParam::value.

◆ operator()() [8/64]

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.

118 {
119 (*this)(label);
120 for_each(v.begin(), v.end(), child());
121 return *this;
122 }

◆ operator()() [9/64]

template<typename object_type >
TextWriter & pwiz::identdata::TextWriter::operator() ( const std::vector< object_type > &  v)
inline

Definition at line 126 of file TextWriter.hpp.

127 {
128 for_each(v.begin(), v.end(), child());
129 return *this;
130 }

◆ operator()() [10/64]

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.

135 {
136 (*this)(label + boost::lexical_cast<std::string>(v));
137 return *this;
138 }

◆ operator()() [11/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const std::string &  label,
const ParamContainer paramContainer 
)
inline

Definition at line 141 of file TextWriter.hpp.

142 {
143 (*this)(label); // + ":"
144 for_each(paramContainer.cvParams.begin(), paramContainer.cvParams.end(), child());
145 for_each(paramContainer.userParams.begin(), paramContainer.userParams.end(), child());
146 return *this;
147 }

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

◆ operator()() [12/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const ParamContainer paramContainer)
inline

Definition at line 150 of file TextWriter.hpp.

151 {
152 for_each(paramContainer.cvParams.begin(), paramContainer.cvParams.end(), *this);
153 for_each(paramContainer.userParams.begin(), paramContainer.userParams.end(), *this);
154 return *this;
155 }

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

◆ operator()() [13/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const BibliographicReference br)
inline

Definition at line 158 of file TextWriter.hpp.

159 {
160 (*this)("BibliographicReference: ");
161 (*this)((Identifiable)br);
162 if (!br.authors.empty())
163 child()("authors: "+br.authors);
164 if (!br.publication.empty())
165 child()("publication: "+br.publication);
166 if (!br.publisher.empty())
167 child()(br.publisher);
168 if (!br.editor.empty())
169 child()("editor: "+br.editor);
170 if (br.year != 0)
171 child()("year: ", br.year);
172 if (!br.volume.empty())
173 child()("volume: "+br.volume);
174 if (!br.issue.empty())
175 child()("issue: "+br.issue);
176 if (!br.pages.empty())
177 child()("pages: "+br.pages);
178 if (!br.title.empty())
179 child()("title: "+br.title);
180
181 return *this;
182 }

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.

◆ operator()() [14/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const TranslationTable tt)
inline

Definition at line 185 of file TextWriter.hpp.

186 {
187 (*this)("TranslationTable:");
188 (*this)((const IdentifiableParamContainer&)tt);
189 return *this;
190 }

◆ operator()() [15/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const DatabaseTranslation dt)
inline

Definition at line 193 of file TextWriter.hpp.

194 {
195 (*this)("DatabaseTranslation:");
196 if (!dt.frames.empty())
197 child()("frames: ", dt.frames);
198 if (!dt.translationTable.empty())
199 child()("translationTable: ", dt.translationTable);
200 return *this;
201 }

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

◆ operator()() [16/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const SpectrumIdentificationProtocol si)
inline

Definition at line 204 of file TextWriter.hpp.

205 {
206 (*this)("SpectrumIdentificationProtocol:");
207 (*this)((Identifiable&)si);
208 if (si.analysisSoftwarePtr.get() &&
209 !si.analysisSoftwarePtr->empty())
210 child()("analysisSoftware_ref: "+si.analysisSoftwarePtr->id);
211 if (!si.searchType.empty())
212 child()("SearchType: ", si.searchType);
213 if (!si.additionalSearchParams.empty())
214 child()("AdditionalSearchParams", si.additionalSearchParams);
215 if (!si.modificationParams.empty())
216 child()("ModificationParams", si.modificationParams);
217 if (!si.enzymes.empty())
218 child()(si.enzymes);
219 if (!si.massTable.empty())
220 child()(si.massTable);
221 if (!si.fragmentTolerance.empty())
222 child()("FragmentTolerance", si.fragmentTolerance);
223 if (!si.parentTolerance.empty())
224 child()("ParentTolerance", si.parentTolerance);
225 if (!si.threshold.empty())
226 child()("Threshold", si.threshold);
227 if (!si.databaseFilters.empty())
228 child()("DatabaseFilters", si.databaseFilters);
229 if (si.databaseTranslation.get() && !si.databaseTranslation->empty())
230 child()("DatabaseTranslation", si.databaseTranslation);
231
232 return *this;
233 }

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.

◆ operator()() [17/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const DBSequence ds)
inline

Definition at line 236 of file TextWriter.hpp.

237 {
238 (*this)("DBSequence: ");
239 (*this)((const IdentifiableParamContainer&)ds);
240 if (ds.length!=0)
241 child()("length: ", ds.length);
242 if (!ds.accession.empty())
243 child()("accession: "+ds.accession);
244 if (ds.searchDatabasePtr.get() && !ds.searchDatabasePtr->empty())
245 child()("searchDatabase_ref: "+ds.searchDatabasePtr->id);
246 if (!ds.seq.empty())
247 child()("Seq: "+ds.seq);
248
249 return *this;
250 }

References pwiz::identdata::DBSequence::accession, pwiz::identdata::DBSequence::length, pwiz::identdata::DBSequence::searchDatabasePtr, and pwiz::identdata::DBSequence::seq.

◆ operator()() [18/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const SubstitutionModification ds)
inline

Definition at line 253 of file TextWriter.hpp.

254 {
255 (*this)("SubstitutionModification: ");
256 if (ds.originalResidue != 0)
257 child()("originalResidue: ", ds.originalResidue);
258 if (ds.replacementResidue != 0)
259 child()("replacementResidue: ", ds.replacementResidue);
260 if (ds.location != 0)
261 child()("location: ", ds.location);
262 child()("avgMassDelta: ", ds.avgMassDelta);
263 child()("monoisotopicMassDelta: ", ds.monoisotopicMassDelta);
264
265 return *this;
266 }

References pwiz::identdata::SubstitutionModification::avgMassDelta, pwiz::identdata::SubstitutionModification::location, pwiz::identdata::SubstitutionModification::monoisotopicMassDelta, pwiz::identdata::SubstitutionModification::originalResidue, and pwiz::identdata::SubstitutionModification::replacementResidue.

◆ operator()() [19/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const IonType it)
inline

Definition at line 269 of file TextWriter.hpp.

270 {
271 (*this)("IonType: ");
272 if (!it.index.empty())
273 child()("index: " + makeDelimitedListString(it.index));
274 if (it.charge != 0)
275 child()("charge: ", it.charge);
276 if (!it.fragmentArray.empty())
277 (*this)(it.fragmentArray);
278 (*this)((const CVParam&)it);
279 return *this;
280 }
std::string makeDelimitedListString(const std::vector< object_type > &objects, const char *delimiter=" ")

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

◆ operator()() [20/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const Measure m)
inline

Definition at line 283 of file TextWriter.hpp.

284 {
285 (*this)("Measure: ");
286 (*this)((const ParamContainer&)m);
287
288 return *this;
289 }

◆ operator()() [21/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const SearchDatabase sd)
inline

Definition at line 292 of file TextWriter.hpp.

293 {
294 (*this)("SearchDatabase: ");
295 (*this)((const IdentifiableParamContainer&)sd);
296 if (!sd.location.empty())
297 child()("location: " + sd.location);
298 if (!sd.version.empty())
299 child()("version: " + sd.version);
300 if (!sd.releaseDate.empty())
301 child()("releaseDate: " + sd.releaseDate);
302 if (sd.numDatabaseSequences != 0)
303 child()("numDatabaseSequences: ", sd.numDatabaseSequences);
304 if (sd.numResidues != 0)
305 child()("numResidues: ", sd.numResidues);
306 if (!sd.fileFormat.empty())
307 child()("FileFormat: ", sd.fileFormat);
308 if (!sd.databaseName.empty())
309 child()("DatabaseName: ", sd.databaseName);
310 return *this;
311 }

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.

◆ operator()() [22/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const SpectraData sd)
inline

Definition at line 314 of file TextWriter.hpp.

315 {
316 (*this)("SpectraData: ");
317 if (!sd.location.empty())
318 child()("location: " + sd.location);
319 if (!sd.externalFormatDocumentation.empty())
320 child()("ExternalFormatDocumentation: ", sd.externalFormatDocumentation);
321 if (!sd.fileFormat.empty())
322 child()("FileFormat: ", sd.fileFormat);
323 if (!sd.spectrumIDFormat.empty())
324 child()("SpectrumIDFormat: ", sd.spectrumIDFormat);
325 return *this;
326 }

References pwiz::data::CVParam::empty(), pwiz::identdata::SpectraData::externalFormatDocumentation, pwiz::identdata::SpectraData::fileFormat, pwiz::identdata::SpectraData::location, and pwiz::identdata::SpectraData::spectrumIDFormat.

◆ operator()() [23/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const SpectrumIdentificationItem sii)
inline

Definition at line 329 of file TextWriter.hpp.

330 {
331 (*this)("SpectrumIdentificationItem:");
332 if (!sii.id.empty())
333 child()("id: ", sii.id);
334 if (!sii.name.empty())
335 child()("name: ", sii.name);
336 if (!sii.empty())
337 {
338 child()("rank: ", sii.rank);
339 child()("chargeState: ", sii.chargeState);
340 child()("experimentalMassToCharge: ", sii.experimentalMassToCharge);
341 child()("calculatedMassToCharge: ", sii.calculatedMassToCharge);
342 child()("calculatedPI: ", sii.calculatedPI);
343 child()("passThreshold: ", sii.passThreshold);
344 }
345 if (sii.peptidePtr.get() && !sii.peptidePtr->empty())
346 child()("peptide_ref: ", sii.peptidePtr->id);
347 if (sii.massTablePtr.get() && !sii.massTablePtr->empty())
348 child()("massTable_ref: ", sii.massTablePtr->id);
349 if (sii.samplePtr.get() && !sii.samplePtr->empty())
350 child()("sample_ref: ", sii.samplePtr->id);
351
352 BOOST_FOREACH(const PeptideEvidencePtr& pe, sii.peptideEvidencePtr)
353 if (pe.get() && !pe->empty())
354 child()("peptideEvidence_ref: ", pe->id);
355
356 if (!sii.fragmentation.empty())
357 child()("fragmentation", sii.fragmentation);
358
359 child()((const ParamContainer&)sii);
360
361 return *this;
362 }

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.

◆ operator()() [24/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const SpectrumIdentificationResult sir)
inline

Definition at line 365 of file TextWriter.hpp.

366 {
367 (*this)("SpectrumIdentificationResult: ");
368 (*this)((const IdentifiableParamContainer&)sir);
369 if (!sir.spectrumID.empty())
370 child()("spectrumID: "+sir.spectrumID);
371 if (sir.spectraDataPtr.get() && !sir.spectraDataPtr->empty())
372 child()("spectraData_ref: "+sir.spectraDataPtr->id);
373 if (!sir.spectrumIdentificationItem.empty())
374 (*this)(sir.spectrumIdentificationItem);
375
376 return *this;
377 }

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

◆ operator()() [25/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const SpectrumIdentificationList sil)
inline

Definition at line 380 of file TextWriter.hpp.

381 {
382 (*this)("SpectrumIdentificationList: ");
383 (*this)((const IdentifiableParamContainer&)sil);
384 if (!sil.empty())
385 child()("numSequencesSearched: ", sil.numSequencesSearched);
386 if (!sil.fragmentationTable.empty())
387 child()("FragmentationTable", sil.fragmentationTable);
388 if (!sil.spectrumIdentificationResult.empty())
389 (*this)(sil.spectrumIdentificationResult);
390 return *this;
391 }

References pwiz::identdata::SpectrumIdentificationList::empty(), pwiz::identdata::SpectrumIdentificationList::fragmentationTable, pwiz::identdata::SpectrumIdentificationList::numSequencesSearched, and pwiz::identdata::SpectrumIdentificationList::spectrumIdentificationResult.

◆ operator()() [26/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const ProteinDetectionList pdl)
inline

Definition at line 394 of file TextWriter.hpp.

395 {
396 (*this)("ProteinDetectionList: ");
397 if (!pdl.proteinAmbiguityGroup.empty())
398 (*this)(pdl.proteinAmbiguityGroup);
399 (*this)((const ParamContainer&)pdl);
400 return *this;
401 }

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

◆ operator()() [27/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const AnalysisData ad)
inline

Definition at line 404 of file TextWriter.hpp.

405 {
406 (*this)("AnalysisData: ");
407
408 if (!ad.spectrumIdentificationList.empty())
409 (*this)(ad.spectrumIdentificationList);
410 if (ad.proteinDetectionListPtr.get() &&
411 !ad.proteinDetectionListPtr->empty())
412 (*this)(*ad.proteinDetectionListPtr);
413
414 return *this;
415 }

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

◆ operator()() [28/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const FragmentArray fa)
inline

Definition at line 418 of file TextWriter.hpp.

419 {
420 (*this)("FragmentArray: ");
421
422 if (fa.measurePtr.get() && !fa.measurePtr->empty())
423 child()("measure_ref: " + fa.measurePtr->id);
424 if (!fa.values.empty())
425 child()("values: " + makeDelimitedListString(fa.values));
426
427 return *this;
428 }

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

◆ operator()() [29/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const SourceFile sf)
inline

Definition at line 431 of file TextWriter.hpp.

432 {
433 //(*this)("sourceFile: ");
434
435 (*this)((const IdentifiableParamContainer&)sf);
436 if (!sf.location.empty())
437 child()("location: " + sf.location);
438 if (!sf.fileFormat.empty())
439 child()(sf.fileFormat);
440 if (!sf.externalFormatDocumentation.empty())
441 child()("externalFormatDocumentation: ",
442 sf.externalFormatDocumentation);
443
444 return *this;
445 }

References pwiz::data::CVParam::empty(), pwiz::identdata::SourceFile::externalFormatDocumentation, pwiz::identdata::SourceFile::fileFormat, and pwiz::identdata::SourceFile::location.

◆ operator()() [30/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const Inputs inputs)
inline

Definition at line 448 of file TextWriter.hpp.

449 {
450 (*this)("Inputs: ");
451
452 if (!inputs.sourceFile.empty())
453 child()("sourceFile: ", inputs.sourceFile);
454 if (!inputs.searchDatabase.empty())
455 child()("searchDatabase: ", inputs.searchDatabase);
456 if (!inputs.spectraData.empty())
457 child()("spectraData: ", inputs.spectraData);
458
459 return *this;
460 }

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

◆ operator()() [31/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const DataCollection dc)
inline

Definition at line 463 of file TextWriter.hpp.

464 {
465 (*this)("DataCollection: ");
466
467 if (!dc.inputs.empty())
468 child()(dc.inputs);
469 if (!dc.analysisData.empty())
470 child()(dc.analysisData);
471
472 return *this;
473 }

References pwiz::identdata::DataCollection::analysisData, pwiz::identdata::Inputs::empty(), pwiz::identdata::AnalysisData::empty(), and pwiz::identdata::DataCollection::inputs.

◆ operator()() [32/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const Filter f)
inline

Definition at line 476 of file TextWriter.hpp.

477 {
478 (*this)("Filter: ");
479 if (!f.filterType.empty())
480 child()("filterType: ", f.filterType);
481 if (!f.include.empty())
482 child()("include: ", f.include);
483 if (!f.exclude.empty())
484 child()("exclude: ", f.exclude);
485 return *this;
486 }

References pwiz::data::ParamContainer::empty(), pwiz::identdata::Filter::exclude, pwiz::identdata::Filter::filterType, and pwiz::identdata::Filter::include.

◆ operator()() [33/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const SearchModification sm)
inline

Definition at line 489 of file TextWriter.hpp.

490 {
491 (*this)("SearchModification: ");
492 if (sm.fixedMod != 0)
493 child()("fixedMod: ", sm.fixedMod);
494 if (sm.massDelta != 0)
495 child()("massDelta: ", sm.massDelta);
496 if (!sm.residues.empty())
497 child()("residues: " + makeDelimitedListString(sm.residues));
498 if (!sm.specificityRules.empty())
499 child()("specificityRules: ", sm.specificityRules);
500 child()((const ParamContainer&)sm);
501 return *this;
502 }

References pwiz::data::CVParam::empty(), pwiz::identdata::SearchModification::fixedMod, pwiz::identdata::SearchModification::massDelta, pwiz::identdata::SearchModification::residues, and pwiz::identdata::SearchModification::specificityRules.

◆ operator()() [34/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const Enzymes ezs)
inline

Definition at line 505 of file TextWriter.hpp.

506 {
507 (*this)("Enzymes: ");
508 if (!indeterminate(ezs.independent))
509 child()("independent: ", (bool) ezs.independent);
510 if (!ezs.enzymes.empty())
511 child()("enzymes: ", ezs.enzymes);
512 return *this;
513 }

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

◆ operator()() [35/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const MassTable mt)
inline

Definition at line 516 of file TextWriter.hpp.

517 {
518 (*this)("MassTable: ");
519 if (!mt.id.empty())
520 child()("id: " + mt.id);
521 if (!mt.msLevel.empty())
522 child()("msLevel: ", mt.msLevel);
523 if (!mt.residues.empty())
524 child()("residues: ", mt.residues);
525 if (!mt.ambiguousResidue.empty())
526 child()("ambiguousResidue: ", mt.residues);
527 return *this;
528 }

References pwiz::identdata::MassTable::ambiguousResidue, pwiz::identdata::MassTable::id, pwiz::identdata::MassTable::msLevel, and pwiz::identdata::MassTable::residues.

◆ operator()() [36/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const AnalysisProtocolCollection apc)
inline

Definition at line 531 of file TextWriter.hpp.

532 {
533 (*this)("AnalysisProtocolCollection: ");
534 if (!apc.spectrumIdentificationProtocol.empty())
535 child()("spectrumIdentificationProtocol: ",
536 apc.spectrumIdentificationProtocol);
537 if (!apc.proteinDetectionProtocol.empty())
538 child()("proteinDetectionProtocol: ",
539 apc.proteinDetectionProtocol);
540 return *this;
541 }

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

◆ operator()() [37/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const PeptideHypothesis ph)
inline

Definition at line 544 of file TextWriter.hpp.

545 {
546 (*this)("PeptideHypothesis: ");
547
548 if (ph.peptideEvidencePtr.get())
549 child()("peptideEvidence: ", ph.peptideEvidencePtr->id);
550 child()("spectrumIdentificationItem: " + makeDelimitedRefListString(ph.spectrumIdentificationItemPtr));
551 return *this;
552 }
std::string makeDelimitedRefListString(const std::vector< boost::shared_ptr< object_type > > &objects, const char *delimiter=" ")

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

◆ operator()() [38/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const ProteinDetectionHypothesis pdh)
inline

Definition at line 555 of file TextWriter.hpp.

556 {
557 (*this)("ProteinDetectionHypothesis: ");
558 if (pdh.dbSequencePtr.get() && !pdh.dbSequencePtr->empty())
559 child()("DBSequence_ref: " + pdh.dbSequencePtr->id);
560 // TODO: Resolve if (!pdh.passThreshold.empty())
561 // child()("passThreshold: " + boost::lexical_cast<std::string>(pdh.passThreshold));
562 if (!pdh.peptideHypothesis.empty())
563 (*this)(pdh.peptideHypothesis);
564
565 child()((const ParamContainer&)pdh);
566 return *this;
567 }

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

◆ operator()() [39/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const ProteinAmbiguityGroup pag)
inline

Definition at line 570 of file TextWriter.hpp.

571 {
572 (*this)("ProteinAmbiguityGroup: ");
573 if (!pag.proteinDetectionHypothesis.empty())
574 (*this)(pag.proteinDetectionHypothesis);
575 (*this)((const ParamContainer&)pag);
576
577 return *this;
578 }

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

◆ operator()() [40/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const ProteinDetection pd)
inline

Definition at line 581 of file TextWriter.hpp.

582 {
583 (*this)("ProteinDetection: ");
584 if (pd.proteinDetectionProtocolPtr.get() &&
585 !pd.proteinDetectionProtocolPtr->empty())
586 child()("proteinDetectionProtocol_ref: "+pd.proteinDetectionProtocolPtr->id);
587 if (pd.proteinDetectionListPtr.get() &&
588 !pd.proteinDetectionListPtr->empty())
589 child()("proteinDetectionList_ref: "+pd.proteinDetectionListPtr->id);
590 if (!pd.activityDate.empty())
591 child()("activityDate: "+pd.activityDate);
592 child()("inputSpectrumIdentifications: " + makeDelimitedRefListString(pd.inputSpectrumIdentifications));
593 return *this;
594 }

References pwiz::identdata::ProteinDetection::activityDate, pwiz::identdata::ProteinDetection::inputSpectrumIdentifications, pwiz::identdata::ProteinDetection::proteinDetectionListPtr, and pwiz::identdata::ProteinDetection::proteinDetectionProtocolPtr.

◆ operator()() [41/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const SpectrumIdentification si)
inline

Definition at line 597 of file TextWriter.hpp.

598 {
599 (*this)("SpectrumIdentification: ");
600 if (si.spectrumIdentificationProtocolPtr.get() &&
601 !si.spectrumIdentificationProtocolPtr->empty())
602 child()("spectrumIdentificationProtocol_ref: "+si.spectrumIdentificationProtocolPtr->id);
603 if (si.spectrumIdentificationListPtr.get() &&
604 !si.spectrumIdentificationListPtr->empty())
605 child()("spectrumIdentificationList_ref: "+si.spectrumIdentificationListPtr->id);
606 if (!si.activityDate.empty())
607 child()("activityDate: "+si.activityDate);
608 if (!si.inputSpectra.empty())
609 child()("inputSpectra: " + makeDelimitedRefListString(si.inputSpectra));
610 if (!si.searchDatabase.empty())
611 child()("searchDatabase: " + makeDelimitedRefListString(si.searchDatabase));
612
613 return *this;
614 }

References pwiz::identdata::SpectrumIdentification::activityDate, pwiz::identdata::SpectrumIdentification::inputSpectra, pwiz::identdata::SpectrumIdentification::searchDatabase, pwiz::identdata::SpectrumIdentification::spectrumIdentificationListPtr, and pwiz::identdata::SpectrumIdentification::spectrumIdentificationProtocolPtr.

◆ operator()() [42/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const AnalysisCollection ac)
inline

Definition at line 617 of file TextWriter.hpp.

618 {
619 (*this)("AnalysisCollection: ", ac.spectrumIdentification);
620 if (!ac.proteinDetection.empty())
621 child()(ac.proteinDetection);
622 return *this;
623 }

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

◆ operator()() [43/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const SequenceCollection sc)
inline

Definition at line 626 of file TextWriter.hpp.

627 {
628 (*this)("SequenceCollection: ");
629 if (!sc.dbSequences.empty())
630 child()("dbSequences: ", sc.dbSequences);
631 if (!sc.peptides.empty())
632 child()("peptides: ", sc.peptides);
633 if (!sc.peptideEvidence.empty())
634 child()("peptideEvidence: ", sc.peptideEvidence);
635 return *this;
636 }

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

◆ operator()() [44/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const Contact cont)
inline

Definition at line 639 of file TextWriter.hpp.

640 {
641 (*this)((const IdentifiableParamContainer&)cont);
642
643 return *this;
644 }

◆ operator()() [45/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const Person per)
inline

Definition at line 647 of file TextWriter.hpp.

648 {
649 (*this)("Person: ");
650 (*this)((const Contact&)per);
651 if (!per.lastName.empty())
652 child()("lastName: "+per.lastName);
653 if (!per.firstName.empty())
654 child()("firstName: "+per.firstName);
655 if (!per.midInitials.empty())
656 child()("midInitials: "+per.midInitials);
657 if (!per.affiliations.empty())
658 child()("affiliations: ", per.affiliations);
659
660 return *this;
661 }

References pwiz::identdata::Person::affiliations, pwiz::identdata::Person::firstName, pwiz::identdata::Person::lastName, and pwiz::identdata::Person::midInitials.

◆ operator()() [46/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const Organization org)
inline

Definition at line 664 of file TextWriter.hpp.

665 {
666 (*this)("Organization: ");
667 (*this)((const Contact&)org);
668 if (org.parent.get())
669 child()("Parent: ", org.parent->id);
670
671 return *this;
672 }

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

◆ operator()() [47/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const ContactPtr  cont)
inline

Definition at line 675 of file TextWriter.hpp.

676 {
677 if (dynamic_cast<Person*>(cont.get()))
678 (*this)((const Person&)(*cont));
679 else if (dynamic_cast<Organization*>(cont.get()))
680 (*this)((const Organization&)(*cont));
681 else
682 (*this)(*cont);
683
684 return *this;
685 }

◆ operator()() [48/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const std::string &  label,
const ContactPtr  cont 
)
inline

Definition at line 688 of file TextWriter.hpp.

689 {
690 (*this)(label);
691 (*this)(cont);
692
693 return *this;
694 }

◆ operator()() [49/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const ContactRole cr)
inline

Definition at line 697 of file TextWriter.hpp.

698 {
699 (*this)("ContactRole: ");
700 if (cr.contactPtr.get() && !cr.contactPtr->empty())
701 child()("contact_ref: ", cr.contactPtr->id);
702 if (!cr.CVParam::empty())
703 child()("Role: ", (const CVParam&)cr);
704 return (*this);
705 }

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

◆ operator()() [50/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const Provider provider)
inline

Definition at line 708 of file TextWriter.hpp.

709 {
710 (*this)("Provider: ");
711 (*this)((Identifiable&)provider);
712 if (provider.contactRolePtr.get() && !provider.contactRolePtr->empty())
713 child()(provider.contactRolePtr);
714 return *this;
715 }

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

◆ operator()() [51/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const Sample sample)
inline

Definition at line 718 of file TextWriter.hpp.

719 {
720 (*this)("Sample: ");
721 (*this)((const IdentifiableParamContainer&)sample);
722 (*this)(sample.contactRole);
723 child()(sample.cvParams);
724 child()("SubSamples:", sample.subSamples);
725
726 return *this;
727 }

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

◆ operator()() [52/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const AnalysisSampleCollection asc)
inline

Definition at line 730 of file TextWriter.hpp.

731 {
732 (*this)("AnalysisSampleCollection: ", asc.samples);
733
734 return *this;
735 }

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

◆ operator()() [53/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const AnalysisSoftwarePtr &  asp)
inline

Definition at line 738 of file TextWriter.hpp.

739 {
740 (*this)("analysisSoftware:");
741 (*this)((Identifiable)*asp);
742 if (!asp->version.empty())
743 child()("version: "+asp->version);
744 if (asp->contactRolePtr.get() && asp->contactRolePtr->empty())
745 child()(*asp->contactRolePtr);
746 if (!asp->softwareName.empty())
747 child()("softwareName: ", asp->softwareName);
748 if (!asp->URI.empty())
749 child()("uri: "+asp->URI);
750 if (!asp->customizations.empty())
751 child()("customizations: "+asp->customizations);
752 return *this;
753 }

◆ operator()() [54/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const Enzyme enzyme)
inline

Definition at line 756 of file TextWriter.hpp.

757 {
758 (*this)("Enzyme: ");
759 if (!enzyme.id.empty())
760 child()("id: "+enzyme.id);
761 if (!enzyme.nTermGain.empty())
762 child()("nTermGain: "+enzyme.nTermGain);
763 if (!enzyme.cTermGain.empty())
764 child()("cTermGain: "+enzyme.cTermGain);
765 child()("semiSpecific: ", (enzyme.terminalSpecificity != proteome::Digestion::FullySpecific ? "true": "false"));
766 if (enzyme.missedCleavages != 0)
767 child()("missedCleavages: ", enzyme.missedCleavages);
768 if (enzyme.minDistance != 0)
769 child()("minDistance: ", enzyme.minDistance);
770 if (!enzyme.siteRegexp.empty())
771 child()("SiteRegexp: "+enzyme.siteRegexp);
772 if (!enzyme.enzymeName.empty())
773 child()("EnzymeName: ", enzyme.enzymeName);
774
775 return *this;
776 }

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.

◆ operator()() [55/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const Identifiable id)
inline

Definition at line 779 of file TextWriter.hpp.

780 {
781 if (!id.id.empty())
782 child()("id: "+id.id);
783 if (!id.name.empty())
784 child()("name: "+id.name);
785
786 return *this;
787 }

◆ operator()() [56/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const IdentifiableParamContainer id)
inline

Definition at line 790 of file TextWriter.hpp.

791 {
792 if (!id.id.empty())
793 child()("id: "+id.id);
794 if (!id.name.empty())
795 child()("name: "+id.name);
796
797 child()((const ParamContainer&)id);
798
799 return *this;
800 }

◆ operator()() [57/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const Residue res)
inline

Definition at line 803 of file TextWriter.hpp.

804 {
805 (*this)("Residue: ");
806 if (res.code != 0)
807 child()("code: ", res.code);
808 if (res.mass != 0)
809 child()("mass: ", res.mass);
810 return *this;
811 }

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

◆ operator()() [58/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const AmbiguousResidue res)
inline

Definition at line 814 of file TextWriter.hpp.

815 {
816 (*this)("AmbiguousResidue: ");
817 if (res.code != 0)
818 child()("code: ", res.code);
819 (*this)((const ParamContainer&)res);
820
821 return *this;
822 }

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

◆ operator()() [59/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const Modification mod)
inline

Definition at line 825 of file TextWriter.hpp.

826 {
827 (*this)("Modification: ");
828 if (mod.location != 0)
829 child()("location: ", mod.location);
830 if (!mod.residues.empty())
831 child()("residues: " + makeDelimitedListString(mod.residues));
832 if (mod.avgMassDelta != 0)
833 child()("avgMassDelta: ", mod.avgMassDelta);
834 if (mod.monoisotopicMassDelta != 0)
835 child()("monoisotopicMassDelta: ", mod.monoisotopicMassDelta);
836 child()((const ParamContainer&)mod);
837
838 return *this;
839 }

References pwiz::identdata::Modification::avgMassDelta, pwiz::identdata::Modification::location, pwiz::identdata::Modification::monoisotopicMassDelta, and pwiz::identdata::Modification::residues.

◆ operator()() [60/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const Peptide pep)
inline

Definition at line 842 of file TextWriter.hpp.

843 {
844 (*this)("Peptide: ");
845 (*this)((const IdentifiableParamContainer&)pep);
846 if (!pep.peptideSequence.empty())
847 child()("peptideSequence: "+pep.peptideSequence);
848 if (!pep.modification.empty())
849 child()("modification", pep.modification);
850 if (!pep.substitutionModification.empty())
851 child()(pep.substitutionModification);
852
853 return *this;
854 }

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

◆ operator()() [61/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const PeptideEvidence pe)
inline

Definition at line 857 of file TextWriter.hpp.

858 {
859 (*this)("PeptideEvidence: ");
860 (*this)((const IdentifiableParamContainer&)pe);
861 if (pe.peptidePtr.get() && !pe.peptidePtr->empty())
862 child()("peptide_ref: "+pe.peptidePtr->id);
863 if (pe.dbSequencePtr.get() && !pe.dbSequencePtr->empty())
864 child()("dBSequence_ref: "+pe.dbSequencePtr->id);
865 if (pe.start != 0)
866 child()("start: ", pe.start);
867 if (pe.end != 0)
868 child()("end: ", pe.end);
869 if (pe.pre != 0)
870 child()("pre: ", pe.pre);
871 if (pe.post != 0)
872 child()("post: ", pe.post);
873 if (pe.translationTablePtr.get() && !pe.translationTablePtr->empty())
874 child()("translationTable_ref: "+pe.translationTablePtr->id);
875 if (pe.frame != 0)
876 child()("frame: ", pe.frame);
877 child()("isDecoy: ", pe.isDecoy);
878
879 return *this;
880 }

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.

◆ operator()() [62/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const IdentData mzid)
inline

Definition at line 883 of file TextWriter.hpp.

884 {
885 (*this)("mzid:");
886 child()((Identifiable)mzid);
887 ("version: " + mzid.version());
888 if (!mzid.cvs.empty())
889 child()("cvList: ", mzid.cvs);
890 if (!mzid.analysisSoftwareList.empty())
891 child()("analysisSoftwareList: ", mzid.analysisSoftwareList);
892 if (!mzid.provider.empty())
893 child()(mzid.provider);
894 if (!mzid.auditCollection.empty())
895 child()("auditCollection: ", mzid.auditCollection);
896 if (!mzid.analysisSampleCollection.empty())
897 child()(mzid.analysisSampleCollection);
898 if (!mzid.sequenceCollection.empty())
899 child()(mzid.sequenceCollection);
900 if (!mzid.analysisCollection.empty())
901 child()(mzid.analysisCollection);
902 if (!mzid.analysisProtocolCollection.empty())
903 child()(mzid.analysisProtocolCollection);
904 if (!mzid.dataCollection.empty())
905 child()(mzid.dataCollection);
906 if (!mzid.bibliographicReference.empty())
907 child()(mzid.bibliographicReference);
908 return *this;
909 }

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().

◆ operator()() [63/64]

TextWriter & pwiz::identdata::TextWriter::operator() ( const CV cv)
inline

Definition at line 912 of file TextWriter.hpp.

913 {
914 (*this)("cv:");
915 child()
916 ("id: " + cv.id)
917 ("fullName: " + cv.fullName)
918 ("version: " + cv.version)
919 ("URI: " + cv.URI);
920 return *this;
921 }
PWIZ_API_DECL const CV & cv(const std::string &prefix)
returns a CV object for the specified namespace (prefix); currently supported namespaces are: MS UO
std::string id
the short label to be used as a reference tag with which to refer to this particular Controlled Vocab...
Definition cv.hpp:14918
std::string fullName
the usual name for the resource (e.g. The PSI-MS Controlled Vocabulary).
Definition cv.hpp:14924
std::string URI
the URI for the resource.
Definition cv.hpp:14921
std::string version
the version of the CV from which the referred-to terms are drawn.
Definition cv.hpp:14927

References pwiz::cv::cv(), pwiz::cv::CV::fullName, pwiz::cv::CV::id, pwiz::cv::CV::URI, and pwiz::cv::CV::version.

◆ operator()() [64/64]

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.

927 {
928 return p.get() ? (*this)(*p) : *this;
929 }

◆ makeDelimitedRefListString()

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.

938 {
939 std::ostringstream oss;
940 for (size_t i=0; i < objects.size(); ++i)
941 {
942 if (i > 0) oss << delimiter;
943 oss << objects[i]->id;
944 }
945 return oss.str();
946 }

◆ makeDelimitedListString()

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.

950 {
951 std::ostringstream oss;
952 oss.precision(9);
953 for (size_t i=0; i < objects.size(); ++i)
954 {
955 if (i > 0) oss << delimiter;
956 oss << objects[i];
957 }
958 return oss.str();
959 }

Member Data Documentation

◆ os_

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

Definition at line 932 of file TextWriter.hpp.

◆ depth_

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

Definition at line 933 of file TextWriter.hpp.

◆ indent_

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: