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}
std::string noCut
Zero or more 1-letter residue codes.
size_t minSpace
minimum separation between adjacent cleavages. default 1.
std::string cut
One or more 1-letter residue codes.
std::string sense
Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut ...

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}
Specificity makeSpecificity()
std::string fidelity
Semispecific means that at least one end of a pepide must conform to the cleavage specificity,...
std::string name
Controlled code name for the enzyme that can be referred to by applications.
boost::tribool independent
If there are multiple specificities and independent is true, then a single peptide cannot exhibit one...
std::string description
Free text to describe alternative names, special conditions, etc.

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 ( )

Definition at line 72 of file MinimumPepXMLTest.cpp.

References pwiz::data::pepxml::Q3RatioResult::decimalRatio, pwiz::data::pepxml::Q3RatioResult::heavyArea, pwiz::data::pepxml::Q3RatioResult::heavyFirstScan, pwiz::data::pepxml::Q3RatioResult::heavyLastScan, pwiz::data::pepxml::Q3RatioResult::heavyMass, pwiz::data::pepxml::Q3RatioResult::lightArea, pwiz::data::pepxml::Q3RatioResult::lightFirstScan, pwiz::data::pepxml::Q3RatioResult::lightLastScan, pwiz::data::pepxml::Q3RatioResult::lightMass, pwiz::data::pepxml::Q3RatioResult::q2HeavyArea, and pwiz::data::pepxml::Q3RatioResult::q2LightArea.

Referenced by testAnalysisResult(), and testQ3RatioResult().

◆ 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}
PeptideProphetResult makePeptideProphetResult()
PeptideProphetResult peptideProphetResult

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}
ModAminoAcidMass makeModAminoAcidMass()

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}
AlternativeProtein makeAlternativeProtein()
ModificationInfo makeModificationInfo()
AnalysisResult makeAnalysisResult()
std::vector< AlternativeProtein > alternativeProteins

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 ( )

◆ makeAminoAcidModification()

AminoAcidModification makeAminoAcidModification ( )

◆ 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}
AminoAcidModification makeAminoAcidModification()
SearchDatabase makeSearchDatabase()
EnzymaticSearchConstraint makeEnzymaticSearchConstraint()
Database search settings.
SearchDatabase searchDatabase
runner up search hit data type extension (e.g. .tgz)
std::vector< AminoAcidModification > aminoAcidModifications
std::string fragmentMassType
average or monoisotopic
std::string searchEngine
SEQUEST, Mascot, COMET, etc.
std::string searchID
Format of file storing the runner up peptides (if not present in pepXML)
std::string baseName
Full path location of mzXML file for this search run (without the .mzXML extension)
std::string precursorMassType
average or monoisotopic
EnzymaticSearchConstraint enzymaticSearchConstraint

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}
SearchHit makeSearchHit()
boost::shared_ptr< SearchHit > SearchHitPtr
std::vector< SearchHitPtr > searchHit

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}
SearchResult makeSearchResult()
boost::shared_ptr< SearchResult > SearchResultPtr
std::vector< SearchResultPtr > searchResult
double retentionTimeSec
Unique identifier.
int index
Search constraint applied specifically to this query.
int startScan
first scan number integrated into MS/MS spectrum
int endScan
last scan number integrated into MS/MS spectrum
int assumedCharge
Precursor ion charge used for search.

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}
SpectrumQuery makeSpectrumQuery()
SampleEnzyme makeSampleEnzyme()
SearchSummary makeSearchSummary()
boost::shared_ptr< SearchSummary > SearchSummaryPtr
boost::shared_ptr< SpectrumQuery > SpectrumQueryPtr
std::vector< SpectrumQueryPtr > spectrumQueries
std::vector< SearchSummaryPtr > searchSummary

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}
boost::shared_ptr< Match > MatchPtr

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}
ostream * os_
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition XMLWriter.hpp:48
void read(std::istream &is)
void write(XMLWriter &writer) const
#define unit_assert(x)
Definition unit.hpp:85

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}
void read(std::istream &is)
void write(XMLWriter &writer) const

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}
void read(std::istream &is)
void write(XMLWriter &writer) const

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}
Q3RatioResult makeQ3RatioResult()
void write(XMLWriter &writer) const
void read(std::istream &is)

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}
void write(XMLWriter &writer) const

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}
void write(XMLWriter &writer) const
void read(std::istream &is)

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}
void write(XMLWriter &writer) const

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}
void write(XMLWriter &writer) const

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}
void write(XMLWriter &writer) const

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}
void read(std::istream &is)
void write(XMLWriter &writer) const

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}
void read(std::istream &is)
void write(XMLWriter &writer) const

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}
void write(XMLWriter &writer) const

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}
void write(XMLWriter &writer) const

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}
void write(XMLWriter &writer) const
void read(std::istream &is)

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}
void read(std::istream &is)
void write(XMLWriter &writer) const

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}
MSMSRunSummary makeMSMSRunSummary()
void read(std::istream &is)
void write(XMLWriter &writer) const

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}
void write(XMLWriter &writer) const

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}
MatchPtr makeMatch()
void write(minimxml::XMLWriter &writer) const
void read(std::istream &is)

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}
std::vector< MatchPtr > matches
void write(minimxml::XMLWriter &writer) const
void read(std::istream &is)

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
757 testMatch();
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}
void testSearchDatabase()
void testMatchData()
void testPeptideProphetResult()
void testAnalysisResult()
void testEnzymaticSearchConstraint()
void testModificationInfo()
void testSearchSummary()
void testMSMSRunSummary()
void testModAminoAcidMass()
void testSpecificity()
void testMatch()
void testAminoAcidModification()
void testMSMSPipelineAnalysis()
void testSampleEnzyme()
void testSpectrumQuery()
void testSearchResult()
void testAlternativeProtein()
void testQ3RatioResult()
void testSearchHit()
#define TEST_EPILOG
Definition unit.hpp:183
#define TEST_FAILED(x)
Definition unit.hpp:177
#define TEST_PROLOG(argc, argv)
Definition unit.hpp:175

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