ProteoWizard
Functions | Variables
MinimumPepXMLTest.cpp File Reference
#include "MinimumPepXML.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Std.hpp"

Go to the source code of this file.

Functions

Specificity makeSpecificity ()
 
SampleEnzyme makeSampleEnzyme ()
 
SearchDatabase makeSearchDatabase ()
 
Q3RatioResult makeQ3RatioResult ()
 
PeptideProphetResult makePeptideProphetResult ()
 
AnalysisResult makeAnalysisResult ()
 
AlternativeProtein makeAlternativeProtein ()
 
ModAminoAcidMass makeModAminoAcidMass ()
 
ModificationInfo makeModificationInfo ()
 
SearchHit makeSearchHit ()
 
EnzymaticSearchConstraint makeEnzymaticSearchConstraint ()
 
AminoAcidModification makeAminoAcidModification ()
 
SearchSummary makeSearchSummary ()
 
SearchResult makeSearchResult ()
 
SpectrumQuery makeSpectrumQuery ()
 
MSMSRunSummary makeMSMSRunSummary ()
 
MatchPtr makeMatch ()
 
void testSpecificity ()
 
void testSampleEnzyme ()
 
void testSearchDatabase ()
 
void testQ3RatioResult ()
 
void testPeptideProphetResult ()
 
void testAnalysisResult ()
 
void testAlternativeProtein ()
 
void testModAminoAcidMass ()
 
void testModificationInfo ()
 
void testSearchHit ()
 
void testSearchResult ()
 
void testEnzymaticSearchConstraint ()
 
void testAminoAcidModification ()
 
void testSearchSummary ()
 
void testSpectrumQuery ()
 
void testMSMSRunSummary ()
 
void testMSMSPipelineAnalysis ()
 
void testMatch ()
 
void testMatchData ()
 
void testInvarianceUnderProteinProphet ()
 
int main (int argc, char *argv[])
 

Variables

ostream * os_ = 0
 

Function Documentation

◆ makeSpecificity()

Specificity makeSpecificity ( )

Definition at line 32 of file MinimumPepXMLTest.cpp.

33 {
34  Specificity specificity;
35  specificity.cut = "theCake";
36  specificity.noCut = "notTheCake";
37  specificity.sense = "non";
38  specificity.minSpace = 2;
39 
40  return specificity;
41 
42 }

References pwiz::data::pepxml::Specificity::cut, pwiz::data::pepxml::Specificity::minSpace, pwiz::data::pepxml::Specificity::noCut, and pwiz::data::pepxml::Specificity::sense.

Referenced by makeSampleEnzyme(), and testSpecificity().

◆ makeSampleEnzyme()

SampleEnzyme makeSampleEnzyme ( )

Definition at line 44 of file MinimumPepXMLTest.cpp.

45 {
46  SampleEnzyme sampleEnzyme;
47  sampleEnzyme.name = "oxiclean";
48  sampleEnzyme.description = "makes your whites whiter.";
49  sampleEnzyme.fidelity = "scoundrel";
50  sampleEnzyme.independent = true;
51 
52  Specificity specificity = makeSpecificity();
53  sampleEnzyme.specificity = specificity;
54 
55  return sampleEnzyme;
56 
57 }

References pwiz::data::pepxml::SampleEnzyme::description, pwiz::data::pepxml::SampleEnzyme::fidelity, pwiz::data::pepxml::SampleEnzyme::independent, makeSpecificity(), pwiz::data::pepxml::SampleEnzyme::name, and pwiz::data::pepxml::SampleEnzyme::specificity.

Referenced by makeMSMSRunSummary(), and testSampleEnzyme().

◆ makeSearchDatabase()

SearchDatabase makeSearchDatabase ( )

Definition at line 59 of file MinimumPepXMLTest.cpp.

60 {
61  SearchDatabase searchDatabase;
62  searchDatabase.localPath = "http://www.eharmony.com";
63  searchDatabase.databaseName = "yenta";
64  searchDatabase.databaseReleaseIdentifier = "village busy body";
65  searchDatabase.sizeInDbEntries = 2;
66  searchDatabase.sizeOfResidues = 3;
67  searchDatabase.type = "online dating service";
68 
69  return searchDatabase;
70 }

References pwiz::data::pepxml::SearchDatabase::databaseName, pwiz::data::pepxml::SearchDatabase::databaseReleaseIdentifier, pwiz::data::pepxml::SearchDatabase::localPath, pwiz::data::pepxml::SearchDatabase::sizeInDbEntries, pwiz::data::pepxml::SearchDatabase::sizeOfResidues, and pwiz::data::pepxml::SearchDatabase::type.

Referenced by makeSearchSummary(), and testSearchDatabase().

◆ makeQ3RatioResult()

Q3RatioResult makeQ3RatioResult ( )

◆ makePeptideProphetResult()

PeptideProphetResult makePeptideProphetResult ( )

Definition at line 91 of file MinimumPepXMLTest.cpp.

92 {
93  PeptideProphetResult peptideProphetResult;
94  peptideProphetResult.probability = 0.98;
95 
96  peptideProphetResult.allNttProb.push_back(0.0000);
97  peptideProphetResult.allNttProb.push_back(0.0000);
98  peptideProphetResult.allNttProb.push_back(0.780);
99 
100  return peptideProphetResult;
101 
102 }

References pwiz::data::pepxml::PeptideProphetResult::allNttProb, and pwiz::data::pepxml::PeptideProphetResult::probability.

Referenced by makeAnalysisResult(), and testPeptideProphetResult().

◆ makeAnalysisResult()

AnalysisResult makeAnalysisResult ( )

Definition at line 104 of file MinimumPepXMLTest.cpp.

105 {
106  AnalysisResult analysisResult;
107  analysisResult.analysis = "peptideprophet";
108 
110  analysisResult.peptideProphetResult = pp;
111 
112  return analysisResult;
113 
114 }

References pwiz::data::pepxml::AnalysisResult::analysis, makePeptideProphetResult(), and pwiz::data::pepxml::AnalysisResult::peptideProphetResult.

Referenced by makeSearchHit(), and testAnalysisResult().

◆ makeAlternativeProtein()

AlternativeProtein makeAlternativeProtein ( )

Definition at line 116 of file MinimumPepXMLTest.cpp.

117 {
118  AlternativeProtein alternativeProtein;
119  alternativeProtein.protein = "Dos Pinos";
120  alternativeProtein.proteinDescr = "leche";
121  alternativeProtein.numTolTerm = "5";
122 
123  return alternativeProtein;
124 
125 }

References pwiz::data::pepxml::AlternativeProtein::numTolTerm, pwiz::data::pepxml::AlternativeProtein::protein, and pwiz::data::pepxml::AlternativeProtein::proteinDescr.

Referenced by makeSearchHit(), and testAlternativeProtein().

◆ makeModAminoAcidMass()

ModAminoAcidMass makeModAminoAcidMass ( )

Definition at line 127 of file MinimumPepXMLTest.cpp.

128 {
129  ModAminoAcidMass modAminoAcidMass;
130  modAminoAcidMass.position = 2;
131  modAminoAcidMass.mass = 12.345;
132 
133  return modAminoAcidMass;
134 
135 }

References pwiz::data::pepxml::ModAminoAcidMass::mass, and pwiz::data::pepxml::ModAminoAcidMass::position.

Referenced by makeModificationInfo(), and testModAminoAcidMass().

◆ makeModificationInfo()

ModificationInfo makeModificationInfo ( )

Definition at line 137 of file MinimumPepXMLTest.cpp.

138 {
139  ModificationInfo modificationInfo;
140  modificationInfo.modifiedPeptide = "GATO";
141  modificationInfo.modAminoAcidMass = makeModAminoAcidMass();
142 
143  return modificationInfo;
144 }

References makeModAminoAcidMass(), pwiz::data::pepxml::ModificationInfo::modAminoAcidMass, and pwiz::data::pepxml::ModificationInfo::modifiedPeptide.

Referenced by makeSearchHit(), and testModificationInfo().

◆ makeSearchHit()

SearchHit makeSearchHit ( )

Definition at line 146 of file MinimumPepXMLTest.cpp.

147 {
148  SearchHit searchHit;
149  searchHit.hitRank = 1;
150  searchHit.peptide = "RAGMALLICK";
151  searchHit.peptidePrevAA = "R";
152  searchHit.peptideNextAA = "V";
153  searchHit.protein = "PA";
154  searchHit.proteinDescr = "Bioinfomagicist";
155  searchHit.numTotalProteins = 1;
156  searchHit.numMatchedIons = 9;
157  searchHit.calcNeutralPepMass = 4.21399;
158  searchHit.massDiff = .0004;
159  searchHit.numTolTerm = 2;
160  searchHit.numMissedCleavages = 3;
161  searchHit.isRejected = 0;
162 
163  AnalysisResult analysisResult = makeAnalysisResult();
164  searchHit.analysisResult = analysisResult;
165 
166  AlternativeProtein alternativeProtein = makeAlternativeProtein();
167  searchHit.alternativeProteins.push_back(alternativeProtein);
168 
170 
171  return searchHit;
172 
173 }

References pwiz::data::pepxml::SearchHit::alternativeProteins, pwiz::data::pepxml::SearchHit::analysisResult, pwiz::data::pepxml::SearchHit::calcNeutralPepMass, pwiz::data::pepxml::SearchHit::hitRank, pwiz::data::pepxml::SearchHit::isRejected, makeAlternativeProtein(), makeAnalysisResult(), makeModificationInfo(), pwiz::data::pepxml::SearchHit::massDiff, pwiz::data::pepxml::SearchHit::modificationInfo, pwiz::data::pepxml::SearchHit::numMatchedIons, pwiz::data::pepxml::SearchHit::numMissedCleavages, pwiz::data::pepxml::SearchHit::numTolTerm, pwiz::data::pepxml::SearchHit::numTotalProteins, pwiz::data::pepxml::SearchHit::peptide, pwiz::data::pepxml::SearchHit::peptideNextAA, pwiz::data::pepxml::SearchHit::peptidePrevAA, pwiz::data::pepxml::SearchHit::protein, and pwiz::data::pepxml::SearchHit::proteinDescr.

Referenced by makeSearchResult(), and testSearchHit().

◆ makeEnzymaticSearchConstraint()

EnzymaticSearchConstraint makeEnzymaticSearchConstraint ( )

Definition at line 175 of file MinimumPepXMLTest.cpp.

176 {
177  EnzymaticSearchConstraint enzymaticSearchConstraint;
178 
179  enzymaticSearchConstraint.enzyme = "emyzne";
180  enzymaticSearchConstraint.maxNumInternalCleavages = 1;
181  enzymaticSearchConstraint.minNumTermini = 1;
182 
183  return enzymaticSearchConstraint;
184 
185 }

References pwiz::data::pepxml::EnzymaticSearchConstraint::enzyme, pwiz::data::pepxml::EnzymaticSearchConstraint::maxNumInternalCleavages, and pwiz::data::pepxml::EnzymaticSearchConstraint::minNumTermini.

Referenced by makeSearchSummary(), and testEnzymaticSearchConstraint().

◆ makeAminoAcidModification()

AminoAcidModification makeAminoAcidModification ( )

Definition at line 187 of file MinimumPepXMLTest.cpp.

188 {
189  AminoAcidModification aminoAcidModification;
190 
191  aminoAcidModification.aminoAcid = "pm";
192  aminoAcidModification.massDiff = 9.63333;
193  aminoAcidModification.mass = 82.65;
194  aminoAcidModification.variable = "c";
195  aminoAcidModification.symbol = "r";
196 
197  return aminoAcidModification;
198 
199 }

References pwiz::data::pepxml::AminoAcidModification::aminoAcid, pwiz::data::pepxml::AminoAcidModification::mass, pwiz::data::pepxml::AminoAcidModification::massDiff, pwiz::data::pepxml::AminoAcidModification::symbol, and pwiz::data::pepxml::AminoAcidModification::variable.

Referenced by makeSearchSummary(), and testAminoAcidModification().

◆ makeSearchSummary()

SearchSummary makeSearchSummary ( )

Definition at line 201 of file MinimumPepXMLTest.cpp.

202 {
203  SearchSummary searchSummary;
204  searchSummary.baseName = "mseharmony";
205  searchSummary.searchEngine = "yahooooo";
206  searchSummary.precursorMassType = "A";
207  searchSummary.fragmentMassType = "B";
208  searchSummary.searchID = "ego";
209 
210  EnzymaticSearchConstraint enzymaticSearchConstraint = makeEnzymaticSearchConstraint();
211  searchSummary.enzymaticSearchConstraint = enzymaticSearchConstraint;
212 
213  AminoAcidModification aminoAcidModification = makeAminoAcidModification();
214  searchSummary.aminoAcidModifications.push_back(aminoAcidModification);
215  searchSummary.aminoAcidModifications.push_back(aminoAcidModification);
216 
217  SearchDatabase searchDatabase = makeSearchDatabase();
218  searchSummary.searchDatabase = searchDatabase;
219 
220  return searchSummary;
221 
222 }

References pwiz::data::pepxml::SearchSummary::aminoAcidModifications, pwiz::data::pepxml::SearchSummary::baseName, pwiz::data::pepxml::SearchSummary::enzymaticSearchConstraint, pwiz::data::pepxml::SearchSummary::fragmentMassType, makeAminoAcidModification(), makeEnzymaticSearchConstraint(), makeSearchDatabase(), pwiz::data::pepxml::SearchSummary::precursorMassType, pwiz::data::pepxml::SearchSummary::searchDatabase, pwiz::data::pepxml::SearchSummary::searchEngine, and pwiz::data::pepxml::SearchSummary::searchID.

Referenced by makeMSMSRunSummary(), and testSearchSummary().

◆ makeSearchResult()

SearchResult makeSearchResult ( )

Definition at line 225 of file MinimumPepXMLTest.cpp.

226 {
227  SearchResult searchResult;
228  SearchHit searchHit = makeSearchHit();
229  searchResult.searchHit.push_back(SearchHitPtr(new SearchHit(searchHit)));
230 
231  return searchResult;
232 
233 }

References makeSearchHit(), and pwiz::data::pepxml::SearchResult::searchHit.

Referenced by makeSpectrumQuery(), and testSearchResult().

◆ makeSpectrumQuery()

SpectrumQuery makeSpectrumQuery ( )

Definition at line 235 of file MinimumPepXMLTest.cpp.

236 {
237  SpectrumQuery spectrumQuery;
238  spectrumQuery.spectrum = "ultraviolet";
239  spectrumQuery.startScan = 19120414;
240  spectrumQuery.endScan = 19120415;
241  spectrumQuery.precursorNeutralMass = 46328;
242  spectrumQuery.assumedCharge = 1;
243  spectrumQuery.index = 3547;
244  spectrumQuery.retentionTimeSec = 432000;
245 
246  SearchResult searchResult = makeSearchResult();
247  SearchResultPtr srp(new SearchResult(searchResult));
248  spectrumQuery.searchResult.push_back(srp);
249 
250  return spectrumQuery;
251 
252 }

References pwiz::data::pepxml::SpectrumQuery::assumedCharge, pwiz::data::pepxml::SpectrumQuery::endScan, pwiz::data::pepxml::SpectrumQuery::index, makeSearchResult(), pwiz::data::pepxml::SpectrumQuery::precursorNeutralMass, pwiz::data::pepxml::SpectrumQuery::retentionTimeSec, pwiz::data::pepxml::SpectrumQuery::searchResult, pwiz::data::pepxml::SpectrumQuery::spectrum, and pwiz::data::pepxml::SpectrumQuery::startScan.

Referenced by makeMatch(), makeMSMSRunSummary(), and testSpectrumQuery().

◆ makeMSMSRunSummary()

MSMSRunSummary makeMSMSRunSummary ( )

Definition at line 255 of file MinimumPepXMLTest.cpp.

256 {
257  MSMSRunSummary msmsRunSummary;
258 
259  SampleEnzyme sampleEnzyme = makeSampleEnzyme();
260  msmsRunSummary.sampleEnzyme = makeSampleEnzyme();
261 
262  SearchSummary searchSummary = makeSearchSummary();
263  msmsRunSummary.searchSummary.push_back(SearchSummaryPtr(new SearchSummary(searchSummary)));
264 
265  SpectrumQuery spectrumQuery = makeSpectrumQuery();
266  msmsRunSummary.spectrumQueries.push_back(SpectrumQueryPtr(new SpectrumQuery(spectrumQuery)));
267  msmsRunSummary.spectrumQueries.push_back(SpectrumQueryPtr(new SpectrumQuery(spectrumQuery)));
268 
269  return msmsRunSummary;
270 
271 }

References makeSampleEnzyme(), makeSearchSummary(), makeSpectrumQuery(), pwiz::data::pepxml::MSMSRunSummary::sampleEnzyme, pwiz::data::pepxml::MSMSRunSummary::searchSummary, and pwiz::data::pepxml::MSMSRunSummary::spectrumQueries.

Referenced by testMSMSPipelineAnalysis(), and testMSMSRunSummary().

◆ makeMatch()

MatchPtr makeMatch ( )

Definition at line 273 of file MinimumPepXMLTest.cpp.

274 {
275  MatchPtr match(new Match());
276  match->spectrumQuery = makeSpectrumQuery();
277  match->feature->mz = 1.234;
278  match->feature->retentionTime = 5.678;
279 
280  return match;
281 
282 }

References makeSpectrumQuery().

Referenced by testMatch(), and testMatchData().

◆ testSpecificity()

void testSpecificity ( )

Definition at line 284 of file MinimumPepXMLTest.cpp.

285 {
286  if (os_) *os_ << "\ntestSpecificity() ... \n";
287 
288  Specificity specificity = makeSpecificity();
289 
290  ostringstream oss;
291  XMLWriter writer(oss);
292  specificity.write(writer);
293 
294  Specificity readSpecificity;
295  istringstream iss(oss.str());
296  readSpecificity.read(iss);
297 
298  unit_assert(specificity == readSpecificity);
299 
300  if (os_) *os_ << oss.str() << endl;
301 
302 }

References makeSpecificity(), os_, pwiz::data::pepxml::Specificity::read(), unit_assert, and pwiz::data::pepxml::Specificity::write().

Referenced by main().

◆ testSampleEnzyme()

void testSampleEnzyme ( )

Definition at line 304 of file MinimumPepXMLTest.cpp.

305 {
306  if (os_) *os_ << "\ntestSampleEnzyme() ... \n";
307 
308  SampleEnzyme sampleEnzyme = makeSampleEnzyme();
309 
310  ostringstream oss;
311  XMLWriter writer(oss);
312  sampleEnzyme.write(writer);
313 
314  SampleEnzyme readSampleEnzyme;
315  istringstream iss(oss.str());
316  readSampleEnzyme.read(iss);
317 
318  unit_assert(sampleEnzyme == readSampleEnzyme);
319 
320  if (os_) *os_ << oss.str() << endl;
321 
322 }

References makeSampleEnzyme(), os_, pwiz::data::pepxml::SampleEnzyme::read(), unit_assert, and pwiz::data::pepxml::SampleEnzyme::write().

Referenced by main().

◆ testSearchDatabase()

void testSearchDatabase ( )

Definition at line 324 of file MinimumPepXMLTest.cpp.

325 {
326  if (os_) *os_ << "\ntestSearchDatabase() ... \n";
327 
328  SearchDatabase searchDatabase = makeSearchDatabase();
329 
330  ostringstream oss;
331  XMLWriter writer(oss);
332  searchDatabase.write(writer);
333 
334  SearchDatabase readSearchDatabase;
335  istringstream iss(oss.str());
336  readSearchDatabase.read(iss);
337 
338  unit_assert(searchDatabase == readSearchDatabase);
339 
340  if (os_) *os_ << oss.str() << endl;
341 
342 }

References makeSearchDatabase(), os_, pwiz::data::pepxml::SearchDatabase::read(), unit_assert, and pwiz::data::pepxml::SearchDatabase::write().

Referenced by main().

◆ testQ3RatioResult()

void testQ3RatioResult ( )

Definition at line 344 of file MinimumPepXMLTest.cpp.

345 {
346  if (os_) *os_ << "\ntestQ3RatioResult() ... \n";
347 
349 
350  ostringstream oss;
351  XMLWriter writer(oss);
352  q.write(writer);
353 
354  Q3RatioResult readQ;
355  istringstream iss(oss.str());
356  readQ.read(iss);
357 
358  unit_assert(q == readQ);
359  if (os_) *os_ << oss.str() << endl;
360 
361 }

References makeQ3RatioResult(), os_, pwiz::data::pepxml::Q3RatioResult::read(), unit_assert, and pwiz::data::pepxml::Q3RatioResult::write().

Referenced by main().

◆ testPeptideProphetResult()

void testPeptideProphetResult ( )

Definition at line 363 of file MinimumPepXMLTest.cpp.

364 {
365  if (os_) *os_ << "\ntestPeptideProphetResult() ... \n";
366 
368 
369  ostringstream oss;
370  XMLWriter writer(oss);
371  pp.write(writer);
372 
373  PeptideProphetResult readPeptideProphetResult;
374  istringstream iss(oss.str());
375  readPeptideProphetResult.read(iss);
376 
377  unit_assert(pp == readPeptideProphetResult);
378 
379  if (os_) *os_ << oss.str() << endl;
380 
381 }

References makePeptideProphetResult(), os_, pwiz::data::pepxml::PeptideProphetResult::read(), unit_assert, and pwiz::data::pepxml::PeptideProphetResult::write().

Referenced by main().

◆ testAnalysisResult()

void testAnalysisResult ( )

Definition at line 383 of file MinimumPepXMLTest.cpp.

384 {
385  if (os_) *os_ << "\ntestAnalysisResult() ...\n";
386 
387  AnalysisResult analysisResult = makeAnalysisResult();
388 
389  ostringstream oss;
390  XMLWriter writer(oss);
391  analysisResult.write(writer);
392 
393  AnalysisResult readAnalysisResult;
394  istringstream iss(oss.str());
395  readAnalysisResult.read(iss);
396 
397  unit_assert(analysisResult == readAnalysisResult);
398 
399  if(os_) *os_ << oss.str() << endl;
400 
401  AnalysisResult analysisResult2;
402  analysisResult2.analysis = "q3";
403  analysisResult2.q3RatioResult = makeQ3RatioResult();
404 
405  ostringstream oss2;
406  XMLWriter writer2(oss2);
407  analysisResult2.write(writer2);
408 
409  AnalysisResult readAnalysisResult2;
410  istringstream iss2(oss2.str());
411  readAnalysisResult2.read(iss2);
412 
413  unit_assert(analysisResult2 == readAnalysisResult2);
414 
415  if(os_) *os_ << oss2.str() << endl;
416 
417 }

References pwiz::data::pepxml::AnalysisResult::analysis, makeAnalysisResult(), makeQ3RatioResult(), os_, pwiz::data::pepxml::AnalysisResult::q3RatioResult, pwiz::data::pepxml::AnalysisResult::read(), unit_assert, and pwiz::data::pepxml::AnalysisResult::write().

Referenced by main().

◆ testAlternativeProtein()

void testAlternativeProtein ( )

Definition at line 419 of file MinimumPepXMLTest.cpp.

420 {
421 
422  if (os_) *os_ << "\ntestAlternativeProtein() ...\n";
423 
424  AlternativeProtein alternativeProtein = makeAlternativeProtein();
425 
426  ostringstream oss;
427  XMLWriter writer(oss);
428  alternativeProtein.write(writer);
429 
430  AlternativeProtein readAlternativeProtein;
431  istringstream iss(oss.str());
432  readAlternativeProtein.read(iss);
433 
434  unit_assert(alternativeProtein == readAlternativeProtein);
435 
436  if(os_) *os_ << oss.str() << endl;
437 
438 }

References makeAlternativeProtein(), os_, pwiz::data::pepxml::AlternativeProtein::read(), unit_assert, and pwiz::data::pepxml::AlternativeProtein::write().

Referenced by main().

◆ testModAminoAcidMass()

void testModAminoAcidMass ( )

Definition at line 440 of file MinimumPepXMLTest.cpp.

441 {
442  if (os_) *os_ << "\ntestModAminoAcidMass() ...\n";
443 
444  ModAminoAcidMass modAminoAcidMass = makeModAminoAcidMass();
445 
446  ostringstream oss;
447  XMLWriter writer(oss);
448  modAminoAcidMass.write(writer);
449 
450  ModAminoAcidMass readModAminoAcidMass;
451  istringstream iss(oss.str());
452  readModAminoAcidMass.read(iss);
453 
454  unit_assert(modAminoAcidMass == readModAminoAcidMass);
455 
456  if(os_) *os_ << oss.str() << endl;
457 }

References makeModAminoAcidMass(), os_, pwiz::data::pepxml::ModAminoAcidMass::read(), unit_assert, and pwiz::data::pepxml::ModAminoAcidMass::write().

Referenced by main().

◆ testModificationInfo()

void testModificationInfo ( )

Definition at line 459 of file MinimumPepXMLTest.cpp.

460 {
461  if (os_) *os_ << "\ntestModificationInfo() ...\n";
462 
463  ModificationInfo modificationInfo = makeModificationInfo();
464 
465  ostringstream oss;
466  XMLWriter writer(oss);
467  modificationInfo.write(writer);
468 
469  ModificationInfo readModificationInfo;
470  istringstream iss(oss.str());
471  readModificationInfo.read(iss);
472 
473  unit_assert(modificationInfo == readModificationInfo);
474 
475  if(os_) *os_ << oss.str() << endl;
476 
477 }

References makeModificationInfo(), os_, pwiz::data::pepxml::ModificationInfo::read(), unit_assert, and pwiz::data::pepxml::ModificationInfo::write().

Referenced by main().

◆ testSearchHit()

void testSearchHit ( )

Definition at line 479 of file MinimumPepXMLTest.cpp.

480 {
481  if (os_) *os_ << "\ntestSearchHit() ...\n";
482 
483  SearchHit searchHit = makeSearchHit();
484 
485  ostringstream oss;
486  XMLWriter writer(oss);
487  searchHit.write(writer);
488 
489  SearchHit readSearchHit;
490  istringstream iss(oss.str());
491  readSearchHit.read(iss);
492 
493  unit_assert(searchHit == readSearchHit);
494 
495  if(os_) *os_ << oss.str() << endl;
496 }

References makeSearchHit(), os_, pwiz::data::pepxml::SearchHit::read(), unit_assert, and pwiz::data::pepxml::SearchHit::write().

Referenced by main().

◆ testSearchResult()

void testSearchResult ( )

Definition at line 498 of file MinimumPepXMLTest.cpp.

499 {
500  if(os_) *os_ << "\ntestSearchResult() ... \n";
501 
502  SearchResult searchResult = makeSearchResult();
503 
504  ostringstream oss;
505  XMLWriter writer(oss);
506  searchResult.write(writer);
507 
508  SearchResult readSearchResult;
509  istringstream iss(oss.str());
510  readSearchResult.read(iss);
511 
512  unit_assert(searchResult == readSearchResult);
513 
514  if(os_) *os_ << oss.str() << endl;
515 
516 
517 }

References makeSearchResult(), os_, pwiz::data::pepxml::SearchResult::read(), unit_assert, and pwiz::data::pepxml::SearchResult::write().

Referenced by main().

◆ testEnzymaticSearchConstraint()

void testEnzymaticSearchConstraint ( )

Definition at line 519 of file MinimumPepXMLTest.cpp.

520 {
521  if (os_) *os_ << "\ntestEnzymaticSearchConstraint() ... \n";
522 
523  EnzymaticSearchConstraint enzymaticSearchConstraint = makeEnzymaticSearchConstraint();
524 
525  ostringstream oss;
526  XMLWriter writer(oss);
527  enzymaticSearchConstraint.write(writer);
528 
529  EnzymaticSearchConstraint readEnzymaticSearchConstraint;
530  istringstream iss(oss.str());
531  readEnzymaticSearchConstraint.read(iss);
532 
533  unit_assert(enzymaticSearchConstraint == readEnzymaticSearchConstraint);
534 
535  if(os_) *os_ << oss.str() << endl;
536 
537 }

References makeEnzymaticSearchConstraint(), os_, pwiz::data::pepxml::EnzymaticSearchConstraint::read(), unit_assert, and pwiz::data::pepxml::EnzymaticSearchConstraint::write().

Referenced by main().

◆ testAminoAcidModification()

void testAminoAcidModification ( )

Definition at line 539 of file MinimumPepXMLTest.cpp.

540 {
541  if (os_) *os_ << "\ntestAminoAcidModification() ... \n";
542 
543  AminoAcidModification aminoAcidModification = makeAminoAcidModification();
544 
545  ostringstream oss;
546  XMLWriter writer(oss);
547  aminoAcidModification.write(writer);
548 
549  AminoAcidModification readAminoAcidModification;
550  istringstream iss(oss.str());
551  readAminoAcidModification.read(iss);
552 
553  unit_assert(aminoAcidModification == readAminoAcidModification);
554 
555  if(os_) *os_ << oss.str() << endl;
556 
557 }

References makeAminoAcidModification(), os_, pwiz::data::pepxml::AminoAcidModification::read(), unit_assert, and pwiz::data::pepxml::AminoAcidModification::write().

Referenced by main().

◆ testSearchSummary()

void testSearchSummary ( )

Definition at line 559 of file MinimumPepXMLTest.cpp.

560 {
561  if(os_) *os_ << "\ntestSearchSummary() ... \n";
562 
563  SearchSummary searchSummary = makeSearchSummary();
564 
565  ostringstream oss;
566  XMLWriter writer(oss);
567  searchSummary.write(writer);
568 
569  SearchSummary readSearchSummary;
570  istringstream iss(oss.str());
571  readSearchSummary.read(iss);
572 
573  unit_assert(searchSummary == readSearchSummary);
574 
575  if(os_) *os_ << oss.str() << endl;
576 
577 }

References makeSearchSummary(), os_, pwiz::data::pepxml::SearchSummary::read(), unit_assert, and pwiz::data::pepxml::SearchSummary::write().

Referenced by main().

◆ testSpectrumQuery()

void testSpectrumQuery ( )

Definition at line 579 of file MinimumPepXMLTest.cpp.

580 {
581  if(os_) *os_ << "\ntestSpectrumQuery() ... \n";
582 
583  SpectrumQuery spectrumQuery = makeSpectrumQuery();
584 
585  ostringstream oss;
586  XMLWriter writer(oss);
587  spectrumQuery.write(writer);
588 
589  if(os_) *os_ << oss.str() << endl;
590 
591  SpectrumQuery readSpectrumQuery;
592  istringstream iss(oss.str());
593  readSpectrumQuery.read(iss);
594 
595  readSpectrumQuery.write(writer);
596  if(os_) *os_ << oss.str() << endl;
597  unit_assert(spectrumQuery == readSpectrumQuery);
598 
599  if(os_) *os_ << oss.str() << endl;
600 
601 }

References makeSpectrumQuery(), os_, pwiz::data::pepxml::SpectrumQuery::read(), unit_assert, and pwiz::data::pepxml::SpectrumQuery::write().

Referenced by main().

◆ testMSMSRunSummary()

void testMSMSRunSummary ( )

Definition at line 603 of file MinimumPepXMLTest.cpp.

604 {
605  if(os_) *os_ << "\ntestMSMSRunSummary() ... \n";
606 
607  MSMSRunSummary msmsRunSummary = makeMSMSRunSummary();
608 
609  ostringstream oss;
610  XMLWriter writer(oss);
611  msmsRunSummary.write(writer);
612 
613  MSMSRunSummary readMSMSRunSummary;
614  istringstream iss(oss.str());
615  readMSMSRunSummary.read(iss);
616 
617  unit_assert(msmsRunSummary == readMSMSRunSummary);
618 
619  if(os_) *os_ << oss.str() << endl;
620 
621 }

References makeMSMSRunSummary(), os_, pwiz::data::pepxml::MSMSRunSummary::read(), unit_assert, and pwiz::data::pepxml::MSMSRunSummary::write().

Referenced by main().

◆ testMSMSPipelineAnalysis()

void testMSMSPipelineAnalysis ( )

Definition at line 623 of file MinimumPepXMLTest.cpp.

624 {
625  if(os_) *os_ << "\ntestMSMSPipelineAnalysis() ... \n";
626 
627  MSMSPipelineAnalysis msmsPipelineAnalysis;
628  msmsPipelineAnalysis.date = "20000101";
629  msmsPipelineAnalysis.summaryXML = "/2000/01/20000101/20000101.xml";
630  msmsPipelineAnalysis.xmlns = "http://regis-web.systemsbiology.net/pepXML";
631  msmsPipelineAnalysis.xmlnsXSI = "aruba";
632  msmsPipelineAnalysis.XSISchemaLocation = "jamaica";
633 
635  msmsPipelineAnalysis.msmsRunSummary = msrs;
636 
637  ostringstream oss;
638  XMLWriter writer(oss);
639  msmsPipelineAnalysis.write(writer);
640 
641  MSMSPipelineAnalysis readMSMSPipelineAnalysis;
642  istringstream iss(oss.str());
643  readMSMSPipelineAnalysis.read(iss);
644 
645  unit_assert(msmsPipelineAnalysis == readMSMSPipelineAnalysis);
646 
647  if(os_) *os_ << oss.str() << endl;
648 
649 }

References pwiz::data::pepxml::MSMSPipelineAnalysis::date, makeMSMSRunSummary(), pwiz::data::pepxml::MSMSPipelineAnalysis::msmsRunSummary, os_, pwiz::data::pepxml::MSMSPipelineAnalysis::read(), pwiz::data::pepxml::MSMSPipelineAnalysis::summaryXML, unit_assert, pwiz::data::pepxml::MSMSPipelineAnalysis::write(), pwiz::data::pepxml::MSMSPipelineAnalysis::xmlns, pwiz::data::pepxml::MSMSPipelineAnalysis::xmlnsXSI, and pwiz::data::pepxml::MSMSPipelineAnalysis::XSISchemaLocation.

Referenced by main().

◆ testMatch()

void testMatch ( )

Definition at line 651 of file MinimumPepXMLTest.cpp.

652 {
653  if(os_) *os_ << "\ntestMatch() ... \n";
654 
655  MatchPtr match = makeMatch();
656 
657  ostringstream oss;
658  XMLWriter writer(oss);
659  match->write(writer);
660 
661  Match readMatch;
662  istringstream iss(oss.str());
663  readMatch.read(iss);
664 
665  ostringstream checkstream;
666  XMLWriter check(checkstream);
667  readMatch.write(check);
668  // unit_assert(*match == readMatch);
669 
670  if(os_) *os_ << oss.str() << endl;
671  if(os_) *os_ << checkstream.str() << endl;
672 
673  unit_assert(*match == readMatch);
674 
675 }

References makeMatch(), os_, pwiz::data::pepxml::Match::read(), unit_assert, and pwiz::data::pepxml::Match::write().

Referenced by main().

◆ testMatchData()

void testMatchData ( )

Definition at line 677 of file MinimumPepXMLTest.cpp.

678 {
679  if(os_) *os_ << "\ntestMatchData() ... \n";
680 
681  MatchData matchData;
682  matchData.warpFunctionCalculator = "Spock";
683  matchData.searchNbhdCalculator = "Mr. Rogers";
684  matchData.matches.push_back(makeMatch());
685  matchData.matches.push_back(makeMatch());
686 
687  ostringstream oss;
688  XMLWriter writer(oss);
689  matchData.write(writer);
690 
691  MatchData readMatchData;
692  istringstream iss(oss.str());
693  readMatchData.read(iss);
694 
695 
696  ostringstream checkstream;
697  XMLWriter check(checkstream);
698  readMatchData.write(check);
699  // unit_assert(*match == readMatch);
700 
701  if(os_) *os_ << oss.str() << endl;
702  if(os_) *os_ << checkstream.str() << endl;
703 
704 
705 
706  unit_assert(matchData == readMatchData);
707 
708  if(os_) *os_ << oss.str() << endl;
709 
710 }

References makeMatch(), pwiz::data::pepxml::MatchData::matches, os_, pwiz::data::pepxml::MatchData::read(), pwiz::data::pepxml::MatchData::searchNbhdCalculator, unit_assert, pwiz::data::pepxml::MatchData::warpFunctionCalculator, and pwiz::data::pepxml::MatchData::write().

Referenced by main().

◆ testInvarianceUnderProteinProphet()

void testInvarianceUnderProteinProphet ( )

Definition at line 712 of file MinimumPepXMLTest.cpp.

713 {
714  ifstream ifs("20080619-A-6mixtestRG_Data10_msprefix.pep.xml");
715  if (!(ifs.good()) )
716  {
717  throw runtime_error("bad ifs");
718  return;
719  }
720 
721  MSMSPipelineAnalysis msmsPipelineAnalysis;
722  msmsPipelineAnalysis.read(ifs);
723 
724  ofstream ofs("test.pep.xml", ios::app);
725  XMLWriter writer(ofs);
726  msmsPipelineAnalysis.write(writer);
727 
728 }

References pwiz::data::pepxml::MSMSPipelineAnalysis::read(), and pwiz::data::pepxml::MSMSPipelineAnalysis::write().

◆ main()

int main ( int  argc,
char *  argv[] 
)

Definition at line 730 of file MinimumPepXMLTest.cpp.

731 {
732  TEST_PROLOG(argc, argv)
733 
734 
735  try
736  {
737  if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
738  if (os_) *os_ << "MinimumPepXMLTest ... \n";
739 
740  testSpecificity();
749  testSearchHit();
757  testMatch();
758  testMatchData();
759  //testInvarianceUnderProteinProphet();
760 
761  }
762  catch (exception& e)
763  {
764  TEST_FAILED(e.what())
765  }
766  catch (...)
767  {
768  TEST_FAILED("Caught unknown exception.")
769  }
770 
772 }

References os_, TEST_EPILOG, TEST_FAILED, TEST_PROLOG, testAlternativeProtein(), testAminoAcidModification(), testAnalysisResult(), testEnzymaticSearchConstraint(), testMatch(), testMatchData(), testModAminoAcidMass(), testModificationInfo(), testMSMSPipelineAnalysis(), testMSMSRunSummary(), testPeptideProphetResult(), testQ3RatioResult(), testSampleEnzyme(), testSearchDatabase(), testSearchHit(), testSearchResult(), testSearchSummary(), testSpecificity(), and testSpectrumQuery().

Variable Documentation

◆ os_

ostream* os_ = 0
pwiz::data::pepxml::EnzymaticSearchConstraint::enzyme
std::string enzyme
Definition: MinimumPepXML.hpp:390
pwiz::data::pepxml::SpectrumQuery::index
int index
Search constraint applied specifically to this query.
Definition: MinimumPepXML.hpp:505
pwiz::data::pepxml::MSMSPipelineAnalysis::summaryXML
std::string summaryXML
Definition: MinimumPepXML.hpp:603
pwiz::data::pepxml::SampleEnzyme::fidelity
std::string fidelity
Semispecific means that at least one end of a pepide must conform to the cleavage specificity,...
Definition: MinimumPepXML.hpp:93
pwiz::minimxml::XMLWriter
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
pwiz::data::pepxml::SearchHit::analysisResult
AnalysisResult analysisResult
Definition: MinimumPepXML.hpp:345
pwiz::data::pepxml::MSMSPipelineAnalysis::xmlnsXSI
std::string xmlnsXSI
Definition: MinimumPepXML.hpp:605
pwiz::data::pepxml::SearchSummary::fragmentMassType
std::string fragmentMassType
average or monoisotopic
Definition: MinimumPepXML.hpp:439
testAminoAcidModification
void testAminoAcidModification()
Definition: MinimumPepXMLTest.cpp:539
pwiz::data::pepxml::SpectrumQuery::write
void write(XMLWriter &writer) const
makeSearchResult
SearchResult makeSearchResult()
Definition: MinimumPepXMLTest.cpp:225
makeModificationInfo
ModificationInfo makeModificationInfo()
Definition: MinimumPepXMLTest.cpp:137
pwiz::data::pepxml::SearchHit::numTolTerm
int numTolTerm
Definition: MinimumPepXML.hpp:342
pwiz::data::pepxml::SearchSummary::precursorMassType
std::string precursorMassType
average or monoisotopic
Definition: MinimumPepXML.hpp:436
pwiz::data::pepxml::MatchData::read
void read(std::istream &is)
makeAminoAcidModification
AminoAcidModification makeAminoAcidModification()
Definition: MinimumPepXMLTest.cpp:187
pwiz::data::pepxml::AlternativeProtein::read
void read(std::istream &is)
makeQ3RatioResult
Q3RatioResult makeQ3RatioResult()
Definition: MinimumPepXMLTest.cpp:72
pwiz::data::pepxml::SearchHit::peptidePrevAA
std::string peptidePrevAA
Definition: MinimumPepXML.hpp:333
testMSMSRunSummary
void testMSMSRunSummary()
Definition: MinimumPepXMLTest.cpp:603
makeAnalysisResult
AnalysisResult makeAnalysisResult()
Definition: MinimumPepXMLTest.cpp:104
makeSearchSummary
SearchSummary makeSearchSummary()
Definition: MinimumPepXMLTest.cpp:201
pwiz::data::pepxml::SearchSummary::searchEngine
std::string searchEngine
SEQUEST, Mascot, COMET, etc.
Definition: MinimumPepXML.hpp:433
pwiz::data::pepxml::AminoAcidModification::read
void read(std::istream &is)
pwiz::data::pepxml::SampleEnzyme::read
void read(std::istream &is)
testMatch
void testMatch()
Definition: MinimumPepXMLTest.cpp:651
pwiz::data::pepxml::SearchHit
Definition: MinimumPepXML.hpp:327
pwiz::data::pepxml::SearchHit::isRejected
int isRejected
Definition: MinimumPepXML.hpp:344
pwiz::data::pepxml::MSMSPipelineAnalysis
Definition: MinimumPepXML.hpp:598
pwiz::data::pepxml::MSMSRunSummary::searchSummary
std::vector< SearchSummaryPtr > searchSummary
Definition: MinimumPepXML.hpp:538
pwiz::data::pepxml::SearchHit::peptideNextAA
std::string peptideNextAA
Definition: MinimumPepXML.hpp:334
pwiz::data::pepxml::Q3RatioResult::lightFirstScan
int lightFirstScan
Definition: MinimumPepXML.hpp:135
pwiz::data::pepxml::Match
Definition: MinimumPepXML.hpp:644
pwiz::data::pepxml::ModificationInfo::modifiedPeptide
std::string modifiedPeptide
Definition: MinimumPepXML.hpp:283
makeAlternativeProtein
AlternativeProtein makeAlternativeProtein()
Definition: MinimumPepXMLTest.cpp:116
pwiz::data::pepxml::SpectrumQuery::endScan
int endScan
last scan number integrated into MS/MS spectrum
Definition: MinimumPepXML.hpp:497
pwiz::data::pepxml::Match::write
void write(minimxml::XMLWriter &writer) const
pwiz::data::pepxml::AminoAcidModification::variable
std::string variable
Definition: MinimumPepXML.hpp:409
testPeptideProphetResult
void testPeptideProphetResult()
Definition: MinimumPepXMLTest.cpp:363
pwiz::data::pepxml::SearchResult::read
void read(std::istream &is)
testMSMSPipelineAnalysis
void testMSMSPipelineAnalysis()
Definition: MinimumPepXMLTest.cpp:623
pwiz::data::pepxml::SearchHit::peptide
std::string peptide
Definition: MinimumPepXML.hpp:332
pwiz::data::pepxml::MSMSRunSummary
Definition: MinimumPepXML.hpp:524
makeMatch
MatchPtr makeMatch()
Definition: MinimumPepXMLTest.cpp:273
pwiz::data::pepxml::MSMSPipelineAnalysis::XSISchemaLocation
std::string XSISchemaLocation
Definition: MinimumPepXML.hpp:606
pwiz::data::pepxml::SearchHit::read
void read(std::istream &is)
testSampleEnzyme
void testSampleEnzyme()
Definition: MinimumPepXMLTest.cpp:304
pwiz::data::pepxml::Specificity
Definition: MinimumPepXML.hpp:44
pwiz::data::pepxml::AlternativeProtein::protein
std::string protein
Definition: MinimumPepXML.hpp:252
pwiz::data::pepxml::Q3RatioResult::heavyArea
double heavyArea
Definition: MinimumPepXML.hpp:142
pwiz::data::pepxml::SpectrumQuery::assumedCharge
int assumedCharge
Precursor ion charge used for search.
Definition: MinimumPepXML.hpp:502
pwiz::data::pepxml::Q3RatioResult::read
void read(std::istream &is)
pwiz::data::pepxml::SearchSummary::baseName
std::string baseName
Full path location of mzXML file for this search run (without the .mzXML extension)
Definition: MinimumPepXML.hpp:430
pwiz::data::pepxml::SearchHit::alternativeProteins
std::vector< AlternativeProtein > alternativeProteins
Definition: MinimumPepXML.hpp:346
pwiz::data::pepxml::EnzymaticSearchConstraint
Definition: MinimumPepXML.hpp:386
makeModAminoAcidMass
ModAminoAcidMass makeModAminoAcidMass()
Definition: MinimumPepXMLTest.cpp:127
pwiz::data::pepxml::SearchSummary::write
void write(XMLWriter &writer) const
pwiz::data::pepxml::SearchDatabase
Definition: MinimumPepXML.hpp:112
pwiz::data::pepxml::PeptideProphetResult::read
void read(std::istream &is)
pwiz::data::pepxml::Q3RatioResult::heavyFirstScan
int heavyFirstScan
Definition: MinimumPepXML.hpp:138
pwiz::data::pepxml::AnalysisResult::peptideProphetResult
PeptideProphetResult peptideProphetResult
Definition: MinimumPepXML.hpp:237
pwiz::data::pepxml::Specificity::write
void write(XMLWriter &writer) const
makeSearchHit
SearchHit makeSearchHit()
Definition: MinimumPepXMLTest.cpp:146
pwiz::data::pepxml::SpectrumQuery::spectrum
std::string spectrum
Definition: MinimumPepXML.hpp:491
pwiz::data::pepxml::MatchData::warpFunctionCalculator
std::string warpFunctionCalculator
Definition: MinimumPepXML.hpp:679
pwiz::data::pepxml::SampleEnzyme
Definition: MinimumPepXML.hpp:76
pwiz::data::pepxml::Q3RatioResult::lightMass
double lightMass
Definition: MinimumPepXML.hpp:137
pwiz::data::pepxml::Q3RatioResult::q2HeavyArea
double q2HeavyArea
Definition: MinimumPepXML.hpp:144
pwiz::data::pepxml::SearchHit::hitRank
int hitRank
Definition: MinimumPepXML.hpp:331
pwiz::data::pepxml::SampleEnzyme::write
void write(XMLWriter &writer) const
pwiz::data::pepxml::SearchHit::protein
std::string protein
Definition: MinimumPepXML.hpp:335
pwiz::data::pepxml::SearchResult::searchHit
std::vector< SearchHitPtr > searchHit
Definition: MinimumPepXML.hpp:371
testSearchSummary
void testSearchSummary()
Definition: MinimumPepXMLTest.cpp:559
pwiz::data::pepxml::AnalysisResult::write
void write(XMLWriter &writer) const
pwiz::data::pepxml::AlternativeProtein::proteinDescr
std::string proteinDescr
Definition: MinimumPepXML.hpp:253
TEST_EPILOG
#define TEST_EPILOG
Definition: unit.hpp:183
pwiz::data::pepxml::SearchHit::massDiff
double massDiff
Definition: MinimumPepXML.hpp:341
pwiz::data::pepxml::AlternativeProtein::numTolTerm
std::string numTolTerm
Definition: MinimumPepXML.hpp:254
pwiz::data::pepxml::Specificity::minSpace
size_t minSpace
minimum separation between adjacent cleavages. default 1.
Definition: MinimumPepXML.hpp:66
pwiz::data::pepxml::SpectrumQuery
Definition: MinimumPepXML.hpp:487
pwiz::data::pepxml::SearchSummary
Database search settings.
Definition: MinimumPepXML.hpp:424
pwiz::data::pepxml::SpectrumQuery::startScan
int startScan
first scan number integrated into MS/MS spectrum
Definition: MinimumPepXML.hpp:494
pwiz::data::pepxml::AminoAcidModification::symbol
std::string symbol
Definition: MinimumPepXML.hpp:413
pwiz::data::pepxml::SearchSummary::searchDatabase
SearchDatabase searchDatabase
runner up search hit data type extension (e.g. .tgz)
Definition: MinimumPepXML.hpp:446
pwiz::data::pepxml::Q3RatioResult::decimalRatio
double decimalRatio
Definition: MinimumPepXML.hpp:145
makeSampleEnzyme
SampleEnzyme makeSampleEnzyme()
Definition: MinimumPepXMLTest.cpp:44
makeSpecificity
Specificity makeSpecificity()
Definition: MinimumPepXMLTest.cpp:32
pwiz::data::pepxml::MSMSRunSummary::write
void write(XMLWriter &writer) const
pwiz::data::pepxml::SearchHitPtr
boost::shared_ptr< SearchHit > SearchHitPtr
Definition: MinimumPepXML.hpp:359
makeSpectrumQuery
SpectrumQuery makeSpectrumQuery()
Definition: MinimumPepXMLTest.cpp:235
pwiz::data::pepxml::SearchDatabase::write
void write(XMLWriter &writer) const
pwiz::data::pepxml::SearchSummaryPtr
boost::shared_ptr< SearchSummary > SearchSummaryPtr
Definition: MinimumPepXML.hpp:464
pwiz::data::pepxml::SearchDatabase::localPath
std::string localPath
Definition: MinimumPepXML.hpp:116
pwiz::data::pepxml::Specificity::noCut
std::string noCut
Zero or more 1-letter residue codes.
Definition: MinimumPepXML.hpp:58
pwiz::data::pepxml::SearchHit::numTotalProteins
int numTotalProteins
Definition: MinimumPepXML.hpp:337
testSearchHit
void testSearchHit()
Definition: MinimumPepXMLTest.cpp:479
pwiz::data::pepxml::SearchSummary::read
void read(std::istream &is)
pwiz::data::pepxml::SampleEnzyme::specificity
Specificity specificity
Definition: MinimumPepXML.hpp:102
pwiz::data::pepxml::Q3RatioResult::heavyLastScan
int heavyLastScan
Definition: MinimumPepXML.hpp:139
pwiz::data::pepxml::SampleEnzyme::independent
boost::tribool independent
If there are multiple specificities and independent is true, then a single peptide cannot exhibit one...
Definition: MinimumPepXML.hpp:100
pwiz::data::pepxml::MatchData
Definition: MinimumPepXML.hpp:673
makeMSMSRunSummary
MSMSRunSummary makeMSMSRunSummary()
Definition: MinimumPepXMLTest.cpp:255
pwiz::data::pepxml::MSMSPipelineAnalysis::read
void read(std::istream &is)
pwiz::data::pepxml::PeptideProphetResult::allNttProb
std::vector< double > allNttProb
Definition: MinimumPepXML.hpp:219
makePeptideProphetResult
PeptideProphetResult makePeptideProphetResult()
Definition: MinimumPepXMLTest.cpp:91
pwiz::data::pepxml::SpectrumQuery::retentionTimeSec
double retentionTimeSec
Unique identifier.
Definition: MinimumPepXML.hpp:508
pwiz::data::pepxml::SearchDatabase::databaseName
std::string databaseName
Definition: MinimumPepXML.hpp:117
pwiz::data::pepxml::SpectrumQuery::read
void read(std::istream &is)
pwiz::data::pepxml::MSMSRunSummary::read
void read(std::istream &is)
pwiz::data::pepxml::ModAminoAcidMass::read
void read(std::istream &is)
os_
ostream * os_
Definition: MinimumPepXMLTest.cpp:30
pwiz::data::pepxml::Q3RatioResult::write
void write(XMLWriter &writer) const
pwiz::data::pepxml::AnalysisResult::read
void read(std::istream &is)
pwiz::data::pepxml::EnzymaticSearchConstraint::maxNumInternalCleavages
int maxNumInternalCleavages
Definition: MinimumPepXML.hpp:391
pwiz::data::pepxml::MSMSPipelineAnalysis::date
std::string date
Definition: MinimumPepXML.hpp:602
testSpecificity
void testSpecificity()
Definition: MinimumPepXMLTest.cpp:284
pwiz::data::pepxml::Q3RatioResult::lightLastScan
int lightLastScan
Definition: MinimumPepXML.hpp:136
pwiz::data::pepxml::AminoAcidModification::massDiff
double massDiff
Definition: MinimumPepXML.hpp:407
pwiz::data::pepxml::AnalysisResult::analysis
std::string analysis
Definition: MinimumPepXML.hpp:236
pwiz::data::pepxml::Q3RatioResult::q2LightArea
double q2LightArea
Definition: MinimumPepXML.hpp:143
pwiz::data::pepxml::SearchSummary::enzymaticSearchConstraint
EnzymaticSearchConstraint enzymaticSearchConstraint
Definition: MinimumPepXML.hpp:451
pwiz::data::pepxml::AminoAcidModification::write
void write(XMLWriter &writer) const
TEST_FAILED
#define TEST_FAILED(x)
Definition: unit.hpp:177
pwiz::data::pepxml::Specificity::cut
std::string cut
One or more 1-letter residue codes.
Definition: MinimumPepXML.hpp:52
TEST_PROLOG
#define TEST_PROLOG(argc, argv)
Definition: unit.hpp:175
pwiz::data::pepxml::MatchData::write
void write(minimxml::XMLWriter &writer) const
pwiz::data::pepxml::SpectrumQueryPtr
boost::shared_ptr< SpectrumQuery > SpectrumQueryPtr
Definition: MinimumPepXML.hpp:520
pwiz::data::pepxml::SearchDatabase::sizeOfResidues
size_t sizeOfResidues
Definition: MinimumPepXML.hpp:120
pwiz::data::pepxml::ModificationInfo::write
void write(XMLWriter &writer) const
pwiz::data::pepxml::SearchHit::modificationInfo
ModificationInfo modificationInfo
Definition: MinimumPepXML.hpp:347
testModificationInfo
void testModificationInfo()
Definition: MinimumPepXMLTest.cpp:459
pwiz::data::pepxml::ModAminoAcidMass::mass
double mass
Definition: MinimumPepXML.hpp:269
pwiz::data::pepxml::AnalysisResult::q3RatioResult
Q3RatioResult q3RatioResult
Definition: MinimumPepXML.hpp:238
pwiz::data::pepxml::ModificationInfo
Definition: MinimumPepXML.hpp:279
pwiz::data::pepxml::SearchHit::numMatchedIons
int numMatchedIons
Definition: MinimumPepXML.hpp:338
pwiz::data::pepxml::Q3RatioResult::heavyMass
double heavyMass
Definition: MinimumPepXML.hpp:140
pwiz::data::pepxml::AnalysisResult
Definition: MinimumPepXML.hpp:232
pwiz::data::pepxml::MSMSRunSummary::spectrumQueries
std::vector< SpectrumQueryPtr > spectrumQueries
Definition: MinimumPepXML.hpp:539
pwiz::data::pepxml::SpectrumQuery::searchResult
std::vector< SearchResultPtr > searchResult
Definition: MinimumPepXML.hpp:510
pwiz::data::pepxml::SearchResult::write
void write(XMLWriter &writer) const
pwiz::data::pepxml::SearchDatabase::sizeInDbEntries
size_t sizeInDbEntries
Definition: MinimumPepXML.hpp:119
pwiz::data::pepxml::SampleEnzyme::name
std::string name
Controlled code name for the enzyme that can be referred to by applications.
Definition: MinimumPepXML.hpp:82
testAlternativeProtein
void testAlternativeProtein()
Definition: MinimumPepXMLTest.cpp:419
pwiz::data::pepxml::ModAminoAcidMass::write
void write(XMLWriter &writer) const
pwiz::data::pepxml::SpectrumQuery::precursorNeutralMass
double precursorNeutralMass
Definition: MinimumPepXML.hpp:499
testSpectrumQuery
void testSpectrumQuery()
Definition: MinimumPepXMLTest.cpp:579
testEnzymaticSearchConstraint
void testEnzymaticSearchConstraint()
Definition: MinimumPepXMLTest.cpp:519
pwiz::data::pepxml::SearchResultPtr
boost::shared_ptr< SearchResult > SearchResultPtr
Definition: MinimumPepXML.hpp:381
pwiz::data::pepxml::MatchData::searchNbhdCalculator
std::string searchNbhdCalculator
Definition: MinimumPepXML.hpp:680
pwiz::data::pepxml::AlternativeProtein
Definition: MinimumPepXML.hpp:248
pwiz::data::pepxml::EnzymaticSearchConstraint::write
void write(XMLWriter &writer) const
pwiz::data::pepxml::SearchHit::write
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pwiz::data::pepxml::Match::read
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pwiz::data::pepxml::MatchData::matches
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Definition: MinimumPepXML.hpp:681
pwiz::data::pepxml::Specificity::sense
std::string sense
Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut ...
Definition: MinimumPepXML.hpp:63
pwiz::data::pepxml::ModificationInfo::read
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pwiz::data::pepxml::ModAminoAcidMass::position
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Definition: MinimumPepXML.hpp:268
pwiz::data::pepxml::Specificity::read
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pwiz::data::pepxml::SearchResult
Definition: MinimumPepXML.hpp:364
pwiz::data::pepxml::MatchPtr
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Definition: MinimumPepXML.hpp:668
pwiz::data::pepxml::EnzymaticSearchConstraint::minNumTermini
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Definition: MinimumPepXML.hpp:392
pwiz::data::pepxml::AminoAcidModification
Definition: MinimumPepXML.hpp:402
pwiz::data::pepxml::Q3RatioResult
Definition: MinimumPepXML.hpp:131
pwiz::data::pepxml::PeptideProphetResult
Definition: MinimumPepXML.hpp:214
makeSearchDatabase
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Definition: MinimumPepXMLTest.cpp:59
pwiz::data::pepxml::SearchHit::calcNeutralPepMass
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Definition: MinimumPepXML.hpp:340
testAnalysisResult
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Definition: MinimumPepXMLTest.cpp:383
testQ3RatioResult
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Definition: MinimumPepXMLTest.cpp:344
testSearchDatabase
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Definition: MinimumPepXMLTest.cpp:324
pwiz::data::pepxml::MSMSPipelineAnalysis::write
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testModAminoAcidMass
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Definition: MinimumPepXMLTest.cpp:440
pwiz::data::pepxml::SearchHit::numMissedCleavages
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Definition: MinimumPepXML.hpp:343
pwiz::data::pepxml::MSMSPipelineAnalysis::msmsRunSummary
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Definition: MinimumPepXML.hpp:634
unit_assert
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Definition: unit.hpp:85
makeEnzymaticSearchConstraint
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Definition: MinimumPepXMLTest.cpp:175
pwiz::data::pepxml::ModAminoAcidMass
Definition: MinimumPepXML.hpp:264
pwiz::data::pepxml::SearchSummary::aminoAcidModifications
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Definition: MinimumPepXML.hpp:452
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Definition: MinimumPepXMLTest.cpp:677
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Definition: MinimumPepXML.hpp:141
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Definition: MinimumPepXML.hpp:408
pwiz::data::pepxml::SearchDatabase::type
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Definition: MinimumPepXML.hpp:121
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Free text to describe alternative names, special conditions, etc.
Definition: MinimumPepXML.hpp:86
pwiz::data::pepxml::AminoAcidModification::aminoAcid
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Definition: MinimumPepXML.hpp:406
pwiz::data::pepxml::SearchSummary::searchID
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Format of file storing the runner up peptides (if not present in pepXML)
Definition: MinimumPepXML.hpp:443
pwiz::data::pepxml::MSMSRunSummary::sampleEnzyme
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Definition: MinimumPepXML.hpp:537
pwiz::data::pepxml::MSMSPipelineAnalysis::xmlns
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Definition: MinimumPepXML.hpp:604
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Definition: MinimumPepXMLTest.cpp:498
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Definition: MinimumPepXML.hpp:336
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Definition: MinimumPepXML.hpp:284
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Definition: MinimumPepXML.hpp:118
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Definition: MinimumPepXML.hpp:218