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.

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().

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 sense
Defines whether cleavage occurs on the C-terminal or N-terminal side of the residue(s) listed in cut ...
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.

§ makeSampleEnzyme()

SampleEnzyme makeSampleEnzyme ( )

Definition at line 44 of file MinimumPepXMLTest.cpp.

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().

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 }
std::string fidelity
Semispecific means that at least one end of a pepide must conform to the cleavage specificity...
Specificity makeSpecificity()
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.

§ makeSearchDatabase()

SearchDatabase makeSearchDatabase ( )

Definition at line 59 of file MinimumPepXMLTest.cpp.

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().

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 }

§ 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.

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

Referenced by makeAnalysisResult(), and testPeptideProphetResult().

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 }

§ makeAnalysisResult()

AnalysisResult makeAnalysisResult ( )

Definition at line 104 of file MinimumPepXMLTest.cpp.

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

Referenced by makeSearchHit(), and testAnalysisResult().

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

§ makeAlternativeProtein()

AlternativeProtein makeAlternativeProtein ( )

Definition at line 116 of file MinimumPepXMLTest.cpp.

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

Referenced by makeSearchHit(), and testAlternativeProtein().

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

§ makeModAminoAcidMass()

ModAminoAcidMass makeModAminoAcidMass ( )

Definition at line 127 of file MinimumPepXMLTest.cpp.

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

Referenced by makeModificationInfo(), and testModAminoAcidMass().

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

§ makeModificationInfo()

ModificationInfo makeModificationInfo ( )

Definition at line 137 of file MinimumPepXMLTest.cpp.

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

Referenced by makeSearchHit(), and testModificationInfo().

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

§ makeSearchHit()

SearchHit makeSearchHit ( )

Definition at line 146 of file MinimumPepXMLTest.cpp.

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().

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

§ makeEnzymaticSearchConstraint()

EnzymaticSearchConstraint makeEnzymaticSearchConstraint ( )

§ makeAminoAcidModification()

AminoAcidModification makeAminoAcidModification ( )

§ makeSearchSummary()

SearchSummary makeSearchSummary ( )

Definition at line 201 of file MinimumPepXMLTest.cpp.

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().

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

§ makeSearchResult()

SearchResult makeSearchResult ( )

Definition at line 225 of file MinimumPepXMLTest.cpp.

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

Referenced by makeSpectrumQuery(), and testSearchResult().

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

§ makeSpectrumQuery()

SpectrumQuery makeSpectrumQuery ( )

Definition at line 235 of file MinimumPepXMLTest.cpp.

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().

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

§ makeMSMSRunSummary()

MSMSRunSummary makeMSMSRunSummary ( )

Definition at line 255 of file MinimumPepXMLTest.cpp.

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().

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

§ makeMatch()

MatchPtr makeMatch ( )

Definition at line 273 of file MinimumPepXMLTest.cpp.

References makeSpectrumQuery().

Referenced by testMatch(), and testMatchData().

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
SpectrumQuery makeSpectrumQuery()

§ testSpecificity()

void testSpecificity ( )

Definition at line 284 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
ostream * os_
Specificity makeSpecificity()
void read(std::istream &is)
void write(XMLWriter &writer) const
#define unit_assert(x)
Definition: unit.hpp:85

§ testSampleEnzyme()

void testSampleEnzyme ( )

Definition at line 304 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
void write(XMLWriter &writer) const
ostream * os_
void read(std::istream &is)
SampleEnzyme makeSampleEnzyme()
#define unit_assert(x)
Definition: unit.hpp:85

§ testSearchDatabase()

void testSearchDatabase ( )

Definition at line 324 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
void write(XMLWriter &writer) const
ostream * os_
SearchDatabase makeSearchDatabase()
void read(std::istream &is)
#define unit_assert(x)
Definition: unit.hpp:85

§ testQ3RatioResult()

void testQ3RatioResult ( )

Definition at line 344 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
void read(std::istream &is)
ostream * os_
void write(XMLWriter &writer) const
Q3RatioResult makeQ3RatioResult()
#define unit_assert(x)
Definition: unit.hpp:85

§ testPeptideProphetResult()

void testPeptideProphetResult ( )

Definition at line 363 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
PeptideProphetResult makePeptideProphetResult()
ostream * os_
void write(XMLWriter &writer) const
#define unit_assert(x)
Definition: unit.hpp:85

§ testAnalysisResult()

void testAnalysisResult ( )

Definition at line 383 of file MinimumPepXMLTest.cpp.

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().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
void write(XMLWriter &writer) const
ostream * os_
AnalysisResult makeAnalysisResult()
void read(std::istream &is)
Q3RatioResult makeQ3RatioResult()
#define unit_assert(x)
Definition: unit.hpp:85

§ testAlternativeProtein()

void testAlternativeProtein ( )

Definition at line 419 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
ostream * os_
void write(XMLWriter &writer) const
AlternativeProtein makeAlternativeProtein()
#define unit_assert(x)
Definition: unit.hpp:85

§ testModAminoAcidMass()

void testModAminoAcidMass ( )

Definition at line 440 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
ostream * os_
void write(XMLWriter &writer) const
#define unit_assert(x)
Definition: unit.hpp:85
ModAminoAcidMass makeModAminoAcidMass()

§ testModificationInfo()

void testModificationInfo ( )

Definition at line 459 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
ostream * os_
ModificationInfo makeModificationInfo()
void write(XMLWriter &writer) const
#define unit_assert(x)
Definition: unit.hpp:85

§ testSearchHit()

void testSearchHit ( )

Definition at line 479 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
SearchHit makeSearchHit()
ostream * os_
void write(XMLWriter &writer) const
void read(std::istream &is)
#define unit_assert(x)
Definition: unit.hpp:85

§ testSearchResult()

void testSearchResult ( )

Definition at line 498 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
void read(std::istream &is)
ostream * os_
SearchResult makeSearchResult()
void write(XMLWriter &writer) const
#define unit_assert(x)
Definition: unit.hpp:85

§ testEnzymaticSearchConstraint()

void testEnzymaticSearchConstraint ( )

Definition at line 519 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
EnzymaticSearchConstraint makeEnzymaticSearchConstraint()
ostream * os_
void write(XMLWriter &writer) const
#define unit_assert(x)
Definition: unit.hpp:85

§ testAminoAcidModification()

void testAminoAcidModification ( )

Definition at line 539 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
ostream * os_
void write(XMLWriter &writer) const
AminoAcidModification makeAminoAcidModification()
#define unit_assert(x)
Definition: unit.hpp:85

§ testSearchSummary()

void testSearchSummary ( )

Definition at line 559 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
ostream * os_
void read(std::istream &is)
Database search settings.
void write(XMLWriter &writer) const
SearchSummary makeSearchSummary()
#define unit_assert(x)
Definition: unit.hpp:85

§ testSpectrumQuery()

void testSpectrumQuery ( )

Definition at line 579 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
ostream * os_
void write(XMLWriter &writer) const
void read(std::istream &is)
#define unit_assert(x)
Definition: unit.hpp:85
SpectrumQuery makeSpectrumQuery()

§ testMSMSRunSummary()

void testMSMSRunSummary ( )

Definition at line 603 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
ostream * os_
void write(XMLWriter &writer) const
void read(std::istream &is)
MSMSRunSummary makeMSMSRunSummary()
#define unit_assert(x)
Definition: unit.hpp:85

§ testMSMSPipelineAnalysis()

void testMSMSPipelineAnalysis ( )

Definition at line 623 of file MinimumPepXMLTest.cpp.

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().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
void write(XMLWriter &writer) const
ostream * os_
MSMSRunSummary makeMSMSRunSummary()
#define unit_assert(x)
Definition: unit.hpp:85

§ testMatch()

void testMatch ( )

Definition at line 651 of file MinimumPepXMLTest.cpp.

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

Referenced by main().

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 }
boost::shared_ptr< Match > MatchPtr
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
ostream * os_
void write(minimxml::XMLWriter &writer) const
void read(std::istream &is)
MatchPtr makeMatch()
#define unit_assert(x)
Definition: unit.hpp:85

§ testMatchData()

void testMatchData ( )

Definition at line 677 of file MinimumPepXMLTest.cpp.

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().

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
ostream * os_
void write(minimxml::XMLWriter &writer) const
void read(std::istream &is)
std::vector< MatchPtr > matches
MatchPtr makeMatch()
#define unit_assert(x)
Definition: unit.hpp:85

§ testInvarianceUnderProteinProphet()

void testInvarianceUnderProteinProphet ( )

Definition at line 712 of file MinimumPepXMLTest.cpp.

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

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 }
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
void write(XMLWriter &writer) const

§ main()

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

Definition at line 730 of file MinimumPepXMLTest.cpp.

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().

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 }
void testSampleEnzyme()
void testAlternativeProtein()
void testMatchData()
void testSearchDatabase()
void testModificationInfo()
void testSearchHit()
#define TEST_EPILOG
Definition: unit.hpp:182
void testQ3RatioResult()
void testSearchSummary()
ostream * os_
void testSpecificity()
void testEnzymaticSearchConstraint()
void testAnalysisResult()
void testSearchResult()
void testModAminoAcidMass()
void testMSMSPipelineAnalysis()
void testAminoAcidModification()
#define TEST_FAILED(x)
Definition: unit.hpp:176
void testPeptideProphetResult()
void testMSMSRunSummary()
#define TEST_PROLOG(argc, argv)
Definition: unit.hpp:174
void testSpectrumQuery()
void testMatch()

Variable Documentation

§ os_

ostream* os_ = 0