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pwiz::msdata::TextWriter Class Reference

#include <TextWriter.hpp>

Public Member Functions

 TextWriter (std::ostream &os, int depth=0, int arrayExampleCount=3)
 constructs a TextWriter for MSData types
 
TextWriter child ()
 
TextWriteroperator() (const std::string &text)
 
TextWriteroperator() (const CVParam &cvParam)
 
TextWriteroperator() (const UserParam &userParam)
 
template<typename object_type >
TextWriteroperator() (const std::string &label, const std::vector< object_type > &v)
 
TextWriteroperator() (const MSData &msd, bool metadata_only=false)
 
TextWriteroperator() (const CV &cv)
 
TextWriteroperator() (const FileDescription &fd)
 
TextWriteroperator() (const ParamContainer &paramContainer)
 
TextWriteroperator() (const FileContent &fileContent)
 
TextWriteroperator() (const SourceFile &sf)
 
TextWriteroperator() (const Contact &contact)
 
TextWriteroperator() (const ParamGroup &paramGroup)
 
TextWriteroperator() (const Sample &sample)
 
TextWriteroperator() (const InstrumentConfiguration &instrumentConfiguration)
 
TextWriteroperator() (const ComponentList &componentList)
 
TextWriteroperator() (const Component &component)
 
TextWriteroperator() (const Software &software)
 
TextWriteroperator() (const ProcessingMethod &processingMethod)
 
TextWriteroperator() (const DataProcessing &dp)
 
TextWriteroperator() (const Target &target)
 
TextWriteroperator() (const ScanSettings &as)
 
TextWriteroperator() (const Run &run, bool metadata_only=false)
 
TextWriteroperator() (const SpectrumList &spectrumList, bool metadata_only=false)
 
TextWriteroperator() (const SpectrumListPtr &p, bool metadata_only=false)
 
TextWriteroperator() (const ChromatogramList &chromatogramList, bool metadata_only=false)
 
TextWriteroperator() (const ChromatogramListPtr &p, bool metadata_only=false)
 
TextWriteroperator() (const Spectrum &spectrum)
 
TextWriteroperator() (const Chromatogram &chromatogram)
 
TextWriteroperator() (const Scan &scan)
 
TextWriteroperator() (const ScanWindow &window)
 
TextWriteroperator() (const BinaryDataArrayPtr &p)
 
TextWriteroperator() (const SelectedIon &selectedIon)
 
TextWriteroperator() (const Precursor &precursor)
 
TextWriteroperator() (const Product &product)
 
TextWriteroperator() (const ScanList &scanList)
 
template<typename object_type >
TextWriteroperator() (const boost::shared_ptr< object_type > &p)
 

Private Attributes

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

Detailed Description

Definition at line 40 of file TextWriter.hpp.

Constructor & Destructor Documentation

◆ TextWriter()

pwiz::msdata::TextWriter::TextWriter ( std::ostream &  os,
int  depth = 0,
int  arrayExampleCount = 3 
)
inline

constructs a TextWriter for MSData types

Parameters
osThe ostream to write to.
depthThe number of indentations to prefix to each output line.
arrayExampleCountThe number of example values to print for arrays (i.e. m/z and intensity); -1 for unlimited

Definition at line 48 of file TextWriter.hpp.

49 : os_(os),
50 depth_(depth),
51 arrayExampleCount_(arrayExampleCount < 0 ? std::numeric_limits<size_t>::max()
52 : (size_t) arrayExampleCount),
53 indent_(depth*2, ' ')
54 {}

Member Function Documentation

◆ child()

TextWriter pwiz::msdata::TextWriter::child ( )
inline

Definition at line 56 of file TextWriter.hpp.

TextWriter(std::ostream &os, int depth=0, int arrayExampleCount=3)
constructs a TextWriter for MSData types

References os_.

Referenced by operator()(), and operator()().

◆ operator()() [1/36]

TextWriter & pwiz::msdata::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()() [2/36]

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

Definition at line 64 of file TextWriter.hpp.

65 {
66 os_ << indent_ << "cvParam: " << cvTermInfo(cvParam.cvid).name;
67 if (!cvParam.value.empty())
68 os_ << ", " << cvParam.value;
69 if (cvParam.units != CVID_Unknown)
70 os_ << ", " << cvParam.unitsName();
71 os_ << std::endl;
72 return *this;
73 }
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()() [3/36]

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

Definition at line 75 of file TextWriter.hpp.

76 {
77 os_ << indent_ << "userParam: " << userParam.name;
78 if (!userParam.value.empty()) os_ << ", " << userParam.value;
79 if (!userParam.type.empty()) os_ << ", " << userParam.type;
80 if (userParam.units != CVID_Unknown) os_ << ", " << cvTermInfo(userParam.units).name;
81 os_ << std::endl;
82 return *this;
83 }

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()() [4/36]

template<typename object_type >
TextWriter & pwiz::msdata::TextWriter::operator() ( const std::string &  label,
const std::vector< object_type > &  v 
)
inline

Definition at line 86 of file TextWriter.hpp.

87 {
88 (*this)(label);
89 for_each(v.begin(), v.end(), child());
90 return *this;
91 }

◆ operator()() [5/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const MSData msd,
bool  metadata_only = false 
)
inline

Definition at line 94 of file TextWriter.hpp.

95 {
96 (*this)("msdata:");
97 child()
98 ("id: " + msd.id);
99 if (!msd.accession.empty())
100 child()("accession: " + msd.accession);
101 if (!msd.version().empty())
102 child()("version: " + msd.version());
103 if (!msd.cvs.empty())
104 child()("cvList: ", msd.cvs);
105 if (!msd.fileDescription.empty())
106 child()(msd.fileDescription);
107 if (!msd.paramGroupPtrs.empty())
108 child()("paramGroupList: ", msd.paramGroupPtrs);
109 if (!msd.samplePtrs.empty())
110 child()("sampleList: " , msd.samplePtrs);
111 if (!msd.softwarePtrs.empty())
112 child()("softwareList: ", msd.softwarePtrs);
113 if (!msd.scanSettingsPtrs.empty())
114 child()("scanSettingsList: ", msd.scanSettingsPtrs);
115 if (!msd.instrumentConfigurationPtrs.empty())
116 child()("instrumentConfigurationList: ", msd.instrumentConfigurationPtrs);
117 if (!msd.dataProcessingPtrs.empty())
118 child()("dataProcessingList: ", msd.dataProcessingPtrs);
119
120 if (!msd.run.empty())
121 child()(msd.run, metadata_only);
122
123 return *this;
124 }

References pwiz::msdata::MSData::accession, pwiz::msdata::MSData::cvs, pwiz::msdata::MSData::dataProcessingPtrs, pwiz::msdata::FileDescription::empty(), pwiz::msdata::Run::empty(), pwiz::msdata::MSData::fileDescription, pwiz::msdata::MSData::id, pwiz::msdata::MSData::instrumentConfigurationPtrs, pwiz::msdata::MSData::paramGroupPtrs, pwiz::msdata::MSData::run, pwiz::msdata::MSData::samplePtrs, pwiz::msdata::MSData::scanSettingsPtrs, pwiz::msdata::MSData::softwarePtrs, and pwiz::msdata::MSData::version().

◆ operator()() [6/36]

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

Definition at line 126 of file TextWriter.hpp.

127 {
128 (*this)("cv:");
129 child()
130 ("id: " + cv.id)
131 ("fullName: " + cv.fullName)
132 ("version: " + cv.version)
133 ("URI: " + cv.URI);
134 return *this;
135 }
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()() [7/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const FileDescription fd)
inline

Definition at line 137 of file TextWriter.hpp.

138 {
139 (*this)("fileDescription:");
140 child()
141 (fd.fileContent)
142 ("sourceFileList: ", fd.sourceFilePtrs);
143 for_each(fd.contacts.begin(), fd.contacts.end(), child());
144 return *this;
145 }

References pwiz::msdata::FileDescription::contacts, pwiz::msdata::FileDescription::fileContent, and pwiz::msdata::FileDescription::sourceFilePtrs.

◆ operator()() [8/36]

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

Definition at line 147 of file TextWriter.hpp.

148 {
149 for (std::vector<ParamGroupPtr>::const_iterator it=paramContainer.paramGroupPtrs.begin();
150 it!=paramContainer.paramGroupPtrs.end(); ++it)
151 (*this)("referenceableParamGroupRef: " + (*it)->id);
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, pwiz::data::ParamContainer::paramGroupPtrs, and pwiz::data::ParamContainer::userParams.

◆ operator()() [9/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const FileContent fileContent)
inline

Definition at line 157 of file TextWriter.hpp.

158 {
159 (*this)("fileContent:");
160 child()(static_cast<const ParamContainer&>(fileContent));
161 return *this;
162 }

◆ operator()() [10/36]

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

Definition at line 164 of file TextWriter.hpp.

165 {
166 (*this)("sourceFile:");
167 child()
168 ("id: " + sf.id)
169 ("name: " + sf.name)
170 ("location: " + sf.location)
171 (static_cast<const ParamContainer&>(sf));
172 return *this;
173 }

References pwiz::msdata::SourceFile::id, pwiz::msdata::SourceFile::location, and pwiz::msdata::SourceFile::name.

◆ operator()() [11/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const Contact contact)
inline

Definition at line 175 of file TextWriter.hpp.

176 {
177 (*this)("contact:");
178 child()(static_cast<const ParamContainer&>(contact));
179 return *this;
180 }

◆ operator()() [12/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const ParamGroup paramGroup)
inline

Definition at line 182 of file TextWriter.hpp.

183 {
184 (*this)("paramGroup:");
185 child()
186 ("id: " + paramGroup.id)
187 (static_cast<const ParamContainer&>(paramGroup));
188 return *this;
189 }

References pwiz::data::ParamGroup::id.

◆ operator()() [13/36]

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

Definition at line 191 of file TextWriter.hpp.

192 {
193 (*this)("sample:");
194 child()
195 ("id: " + sample.id)
196 ("name: " + sample.name)
197 (static_cast<const ParamContainer&>(sample));
198 return *this;
199 }

References pwiz::msdata::Sample::id, and pwiz::msdata::Sample::name.

◆ operator()() [14/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const InstrumentConfiguration instrumentConfiguration)
inline

Definition at line 201 of file TextWriter.hpp.

202 {
203 (*this)("instrumentConfiguration:");
204 child()
205 ("id: " + instrumentConfiguration.id)
206 (static_cast<const ParamContainer&>(instrumentConfiguration));
207 if (!instrumentConfiguration.componentList.empty())
208 child()(instrumentConfiguration.componentList);
209 if (instrumentConfiguration.softwarePtr.get() && !instrumentConfiguration.softwarePtr->empty())
210 child()("softwareRef: " + instrumentConfiguration.softwarePtr->id);
211 return *this;
212 }

References pwiz::msdata::InstrumentConfiguration::componentList, pwiz::msdata::InstrumentConfiguration::id, and pwiz::msdata::InstrumentConfiguration::softwarePtr.

◆ operator()() [15/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const ComponentList componentList)
inline

Definition at line 214 of file TextWriter.hpp.

215 {
216 (*this)("componentList:");
217 for (size_t i=0; i < componentList.size(); ++i)
218 child()(componentList[i]);
219 return *this;
220 }

◆ operator()() [16/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const Component component)
inline

Definition at line 222 of file TextWriter.hpp.

223 {
224 switch(component.type)
225 {
227 (*this)("source: ");
228 break;
230 (*this)("analyzer: ");
231 break;
233 (*this)("detector: ");
234 break;
235 default:
236 break;
237 }
238 child()
239 ("order: " + boost::lexical_cast<std::string>(component.order))
240 (static_cast<const ParamContainer&>(component));
241 return *this;
242 }
@ ComponentType_Analyzer
Definition MSData.hpp:125
@ ComponentType_Detector
Definition MSData.hpp:126
@ ComponentType_Source
Definition MSData.hpp:124

References pwiz::msdata::ComponentType_Analyzer, pwiz::msdata::ComponentType_Detector, pwiz::msdata::ComponentType_Source, pwiz::msdata::Component::order, and pwiz::msdata::Component::type.

◆ operator()() [17/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const Software software)
inline

Definition at line 244 of file TextWriter.hpp.

245 {
246 (*this)("software:");
247 child()
248 ("id: " + software.id)
249 ("version: " + software.version)
250 (static_cast<const ParamContainer&>(software));
251 return *this;
252 }

References pwiz::msdata::Software::id, and pwiz::msdata::Software::version.

◆ operator()() [18/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const ProcessingMethod processingMethod)
inline

Definition at line 254 of file TextWriter.hpp.

255 {
256 (*this)("processingMethod:");
257 child()
258 ("order: " + boost::lexical_cast<std::string>(processingMethod.order));
259 if (processingMethod.softwarePtr.get() && !processingMethod.softwarePtr->empty())
260 child()("softwareRef: " + processingMethod.softwarePtr->id);
261 child()
262 (static_cast<const ParamContainer&>(processingMethod));
263 return *this;
264 }

References pwiz::msdata::ProcessingMethod::order, and pwiz::msdata::ProcessingMethod::softwarePtr.

◆ operator()() [19/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const DataProcessing dp)
inline

Definition at line 266 of file TextWriter.hpp.

267 {
268 (*this)("dataProcessing:");
269 child()
270 ("id: " + dp.id);
271 for_each(dp.processingMethods.begin(), dp.processingMethods.end(), child());
272 return *this;
273 }

References pwiz::msdata::DataProcessing::id, and pwiz::msdata::DataProcessing::processingMethods.

◆ operator()() [20/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const Target target)
inline

Definition at line 275 of file TextWriter.hpp.

276 {
277 (*this)("target:");
278 child()(static_cast<const ParamContainer&>(target));
279 return *this;
280 }

◆ operator()() [21/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const ScanSettings as)
inline

Definition at line 282 of file TextWriter.hpp.

283 {
284 (*this)("scanSettings:");
285 child()
286 ("id: " + as.id);
287 for_each(as.targets.begin(), as.targets.end(), child());
288 child()("sourceFileList: ", as.sourceFilePtrs);
289 return *this;
290 }

References pwiz::msdata::ScanSettings::id, pwiz::msdata::ScanSettings::sourceFilePtrs, and pwiz::msdata::ScanSettings::targets.

◆ operator()() [22/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const Run run,
bool  metadata_only = false 
)
inline

Definition at line 292 of file TextWriter.hpp.

293 {
294 (*this)("run:");
295 child()("id: " + run.id);
296 if (run.defaultInstrumentConfigurationPtr.get())
297 child()("defaultInstrumentConfigurationRef: " + run.defaultInstrumentConfigurationPtr->id);
298 if (run.samplePtr.get())
299 child()("sampleRef: " + run.samplePtr->id);
300 if (!run.startTimeStamp.empty())
301 child()("startTimeStamp: " + run.startTimeStamp);
302 child()(static_cast<const ParamContainer&>(run));
303 if (run.defaultSourceFilePtr.get())
304 child()("defaultSourceFileRef: " + run.defaultSourceFilePtr->id);
305 if (run.spectrumListPtr.get())
306 child()(run.spectrumListPtr, metadata_only);
307 if (run.chromatogramListPtr.get())
308 child()(run.chromatogramListPtr, metadata_only);
309 return *this;
310 }

References pwiz::msdata::Run::chromatogramListPtr, pwiz::msdata::Run::defaultInstrumentConfigurationPtr, pwiz::msdata::Run::defaultSourceFilePtr, pwiz::msdata::Run::id, pwiz::msdata::Run::samplePtr, pwiz::msdata::Run::spectrumListPtr, and pwiz::msdata::Run::startTimeStamp.

◆ operator()() [23/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const SpectrumList spectrumList,
bool  metadata_only = false 
)
inline

Definition at line 312 of file TextWriter.hpp.

313 {
314 std::string text("spectrumList (" + boost::lexical_cast<std::string>(spectrumList.size()) + " spectra)");
315 if (!metadata_only)
316 text += ":";
317
318 (*this)(text);
319
320 if (spectrumList.dataProcessingPtr().get())
321 child()(*spectrumList.dataProcessingPtr());
322
323 if (!metadata_only)
324 for (size_t index=0; index<spectrumList.size(); ++index)
325 child()
326 (*spectrumList.spectrum(index, true));
327 return *this;
328 }

References pwiz::msdata::SpectrumList::dataProcessingPtr(), pwiz::msdata::SpectrumList::size(), and pwiz::msdata::SpectrumList::spectrum().

◆ operator()() [24/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const SpectrumListPtr p,
bool  metadata_only = false 
)
inline

Definition at line 330 of file TextWriter.hpp.

331 {
332 return p.get() ? (*this)(*p, metadata_only) : *this;
333 }

◆ operator()() [25/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const ChromatogramList chromatogramList,
bool  metadata_only = false 
)
inline

Definition at line 335 of file TextWriter.hpp.

336 {
337 std::string text("chromatogramList (" + boost::lexical_cast<std::string>(chromatogramList.size()) + " chromatograms)");
338 if (!metadata_only)
339 text += ":";
340
341 (*this)(text);
342
343 if (chromatogramList.dataProcessingPtr().get())
344 child()(*chromatogramList.dataProcessingPtr());
345
346 if (!metadata_only)
347 for (size_t index=0; index<chromatogramList.size(); ++index)
348 child()
349 (*chromatogramList.chromatogram(index, true));
350 return *this;
351 }

References pwiz::msdata::ChromatogramList::chromatogram(), pwiz::msdata::ChromatogramList::dataProcessingPtr(), and pwiz::msdata::ChromatogramList::size().

◆ operator()() [26/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const ChromatogramListPtr p,
bool  metadata_only = false 
)
inline

Definition at line 353 of file TextWriter.hpp.

354 {
355 return p.get() ? (*this)(*p, metadata_only) : *this;
356 }

◆ operator()() [27/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const Spectrum spectrum)
inline

Definition at line 358 of file TextWriter.hpp.

359 {
360 (*this)("spectrum:");
361 child()
362 ("index: " + boost::lexical_cast<std::string>(spectrum.index))
363 ("id: " + spectrum.id);
364 if (!spectrum.spotID.empty())
365 child()("spotID: " + spectrum.spotID);
366 if (spectrum.sourceFilePtr.get())
367 child()(spectrum.sourceFilePtr);
368 child()
369 ("defaultArrayLength: " + boost::lexical_cast<std::string>(spectrum.defaultArrayLength))
370 (spectrum.dataProcessingPtr)
371 (static_cast<const ParamContainer&>(spectrum));
372 if (!spectrum.scanList.empty())
373 child()(spectrum.scanList);
374 if (!spectrum.precursors.empty())
375 child()("precursorList: ", spectrum.precursors);
376 for_each(spectrum.binaryDataArrayPtrs.begin(), spectrum.binaryDataArrayPtrs.end(), child());
377 return *this;
378 }

References pwiz::msdata::Spectrum::binaryDataArrayPtrs, pwiz::msdata::Spectrum::dataProcessingPtr, pwiz::msdata::Spectrum::defaultArrayLength, pwiz::msdata::ScanList::empty(), pwiz::msdata::SpectrumIdentity::id, pwiz::msdata::SpectrumIdentity::index, pwiz::msdata::Spectrum::precursors, pwiz::msdata::Spectrum::scanList, pwiz::msdata::Spectrum::sourceFilePtr, and pwiz::msdata::SpectrumIdentity::spotID.

◆ operator()() [28/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const Chromatogram chromatogram)
inline

Definition at line 380 of file TextWriter.hpp.

381 {
382 (*this)("chromatogram:");
383 child()
384 ("index: " + boost::lexical_cast<std::string>(chromatogram.index))
385 ("id: " + chromatogram.id)
386 ("defaultArrayLength: " + boost::lexical_cast<std::string>(chromatogram.defaultArrayLength))
387 (chromatogram.dataProcessingPtr)
388 (static_cast<const ParamContainer&>(chromatogram));
389 if (!chromatogram.precursor.empty())
390 child()(chromatogram.precursor);
391 if (!chromatogram.product.empty())
392 child()(chromatogram.product);
393 for_each(chromatogram.binaryDataArrayPtrs.begin(), chromatogram.binaryDataArrayPtrs.end(), child());
394 return *this;
395 }

References pwiz::msdata::Chromatogram::binaryDataArrayPtrs, pwiz::msdata::Chromatogram::dataProcessingPtr, pwiz::msdata::Chromatogram::defaultArrayLength, pwiz::msdata::Precursor::empty(), pwiz::msdata::Product::empty(), pwiz::msdata::ChromatogramIdentity::id, pwiz::msdata::ChromatogramIdentity::index, pwiz::msdata::Chromatogram::precursor, and pwiz::msdata::Chromatogram::product.

◆ operator()() [29/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const Scan scan)
inline

Definition at line 397 of file TextWriter.hpp.

398 {
399 (*this)("scan:");
400 if (!scan.spectrumID.empty()) child()("spectrumID: " + scan.spectrumID);
401 if (!scan.externalSpectrumID.empty()) child()("externalSpectrumID: " + scan.externalSpectrumID);
402 if (scan.sourceFilePtr) child()(*scan.sourceFilePtr);
403 if (scan.instrumentConfigurationPtr.get()) child()(*scan.instrumentConfigurationPtr);
404 child()(static_cast<const ParamContainer&>(scan));
405 if (!scan.scanWindows.empty())
406 child()("scanWindowList: ", scan.scanWindows);
407 return *this;
408 }

References pwiz::msdata::Scan::externalSpectrumID, pwiz::msdata::Scan::instrumentConfigurationPtr, pwiz::msdata::Scan::scanWindows, pwiz::msdata::Scan::sourceFilePtr, and pwiz::msdata::Scan::spectrumID.

◆ operator()() [30/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const ScanWindow window)
inline

Definition at line 410 of file TextWriter.hpp.

411 {
412 (*this)("scanWindow:");
413 for_each(window.cvParams.begin(), window.cvParams.end(), child());
414 return *this;
415 }

References pwiz::data::ParamContainer::cvParams.

◆ operator()() [31/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const BinaryDataArrayPtr p)
inline

Definition at line 417 of file TextWriter.hpp.

418 {
419 if (!p.get() || p->empty()) return *this;
420
421 std::stringstream oss;
422 oss << "[" << boost::lexical_cast<std::string>(p->data.size()) << "] ";
423 oss.precision(12);
424 for (size_t i=0; i < arrayExampleCount_ && i < p->data.size(); i++)
425 oss << p->data[i] << " ";
426 if (p->data.size() > arrayExampleCount_)
427 oss << "...";
428
429 (*this)("binaryDataArray:");
430 child() (static_cast<const ParamContainer&>(*p));
431 if (p->dataProcessingPtr.get() && !p->dataProcessingPtr->empty())
432 child()(p->dataProcessingPtr);
433 if (!p->data.empty())
434 child()("binary: " + oss.str());
435 return *this;
436 }

◆ operator()() [32/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const SelectedIon selectedIon)
inline

Definition at line 438 of file TextWriter.hpp.

439 {
440 (*this)("selectedIon:");
441 child()(static_cast<const ParamContainer&>(selectedIon));
442 return *this;
443 }

◆ operator()() [33/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const Precursor precursor)
inline

Definition at line 445 of file TextWriter.hpp.

446 {
447 (*this)("precursor:");
448 child()
449 ("spectrumRef: " + precursor.spectrumID)
450 (static_cast<const ParamContainer&>(precursor));
451
452 if (!precursor.isolationWindow.empty())
453 {
454 child()("isolationWindow:");
455 child().child()(precursor.isolationWindow);
456 }
457
458 if (!precursor.selectedIons.empty())
459 {
460 child()("selectedIons:", precursor.selectedIons);
461 }
462
463 if (!precursor.activation.empty())
464 {
465 child()("activation:");
466 child().child()(precursor.activation);
467 }
468
469 return *this;
470 }

References pwiz::msdata::Precursor::activation, child(), pwiz::data::ParamContainer::empty(), pwiz::msdata::Precursor::isolationWindow, pwiz::msdata::Precursor::selectedIons, and pwiz::msdata::Precursor::spectrumID.

◆ operator()() [34/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const Product product)
inline

Definition at line 472 of file TextWriter.hpp.

473 {
474 (*this)("product:");
475
476 if (!product.isolationWindow.empty())
477 {
478 child()("isolationWindow:");
479 child().child()(product.isolationWindow);
480 }
481
482 return *this;
483 }

References child(), pwiz::data::ParamContainer::empty(), and pwiz::msdata::Product::isolationWindow.

◆ operator()() [35/36]

TextWriter & pwiz::msdata::TextWriter::operator() ( const ScanList scanList)
inline

Definition at line 485 of file TextWriter.hpp.

486 {
487 (*this)
488 (static_cast<const ParamContainer&>(scanList))
489 ("scanList:", scanList.scans);
490 return *this;
491 }

References pwiz::msdata::ScanList::scans.

◆ operator()() [36/36]

template<typename object_type >
TextWriter & pwiz::msdata::TextWriter::operator() ( const boost::shared_ptr< object_type > &  p)
inline

Definition at line 495 of file TextWriter.hpp.

496 {
497 return p.get() ? (*this)(*p) : *this;
498 }

Member Data Documentation

◆ os_

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

Definition at line 502 of file TextWriter.hpp.

◆ depth_

int pwiz::msdata::TextWriter::depth_
private

Definition at line 503 of file TextWriter.hpp.

◆ arrayExampleCount_

size_t pwiz::msdata::TextWriter::arrayExampleCount_
private

Definition at line 504 of file TextWriter.hpp.

◆ indent_

std::string pwiz::msdata::TextWriter::indent_
private

Definition at line 505 of file TextWriter.hpp.


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