ProteoWizard
Functions | Variables
IOTest.cpp File Reference
#include "IO.hpp"
#include "Diff.hpp"
#include "TextWriter.hpp"
#include "examples.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Std.hpp"

Go to the source code of this file.

Functions

template<typename object_type >
void testObject (const object_type &a)
 
void testIdentifiable ()
 
void testIdentifiableParamContainer ()
 
void testCV ()
 
void testBibliographicReference ()
 
void testPerson ()
 
void testOrganization ()
 
void testContactRole ()
 
void testProvider ()
 
void testSample ()
 
void testAnalysisSoftware ()
 
void testAnalysisSampleCollection ()
 
void testDBSequence ()
 
void testModification ()
 
void testSubstitutionModification ()
 
void testPeptide ()
 
void testSequenceCollection ()
 
void testSpectrumIdentification ()
 
void testProteinDetection ()
 
void testAnalysisCollection ()
 
void testSearchModification ()
 
void testEnzyme ()
 
void testEnzymes ()
 
void testResidue ()
 
void testAmbiguousResidue ()
 
void testMassTable ()
 
void testFilter ()
 
void testSpectrumIdentificationProtocol ()
 
void testProteinDetectionProtocol ()
 
void testAnalysisProtocolCollection ()
 
void testSpectraData ()
 
void testSearchDatabase ()
 
void testSourceFile ()
 
void testInputs ()
 
void testMeasure ()
 
void testFragmentArray ()
 
void testIonType ()
 
void testPeptideEvidence ()
 
void testSpectrumIdentificationItem ()
 
void testSpectrumIdentificationResult ()
 
PeptideHypothesis testPeptideHypothesis ()
 
void testProteinDetectionHypothesis ()
 
void testProteinAmbiguityGroup ()
 
void testSpectrumIdentificationList ()
 
void testProteinDetectionList ()
 
void testAnalysisData ()
 
void testDataCollection ()
 
void testIdentData ()
 
void test ()
 
int main (int argc, char *argv[])
 

Variables

ostream * os_ = 0
 

Function Documentation

◆ testObject()

template<typename object_type >
void testObject ( const object_type &  a)

Definition at line 41 of file IOTest.cpp.

42 {
43  if (os_) *os_ << "testObject(): " << typeid(a).name() << endl;
44 
45  // write 'a' out to a stream
46 
47  ostringstream oss;
48  XMLWriter writer(oss);
49  IO::write(writer, a);
50  if (os_) *os_ << oss.str() << endl;
51 
52  // read 'b' in from stream
53 
54  object_type b;
55  istringstream iss(oss.str());
56  IO::read(iss, b);
57 
58  // compare 'a' and 'b'
59 
61  if (diff && os_) *os_ << "diff:\n" << diff_string<TextWriter>(diff) << endl;
62  unit_assert(!diff);
63 }

References diff(), os_, pwiz::identdata::IO::read(), unit_assert, and pwiz::identdata::IO::write().

Referenced by testAmbiguousResidue(), testAnalysisCollection(), testAnalysisData(), testAnalysisProtocolCollection(), testAnalysisSampleCollection(), testAnalysisSoftware(), testBibliographicReference(), testComponent(), testComponentList(), testContactRole(), testCV(), testCVParam(), testDataCollection(), testDataProcessing(), testDBSequence(), testEnzyme(), testEnzymes(), testFileDescription(), testFilter(), testFragmentArray(), testIdentData(), testIdentifiable(), testIdentifiableParamContainer(), testInputs(), testInstrumentConfiguration(), testIonType(), testMassTable(), testMeasure(), testModification(), testNamedParamContainer(), testOrganization(), testParamGroup(), testPeptide(), testPeptideEvidence(), testPeptideHypothesis(), testPerson(), testPrecursor(), testProcessingMethod(), testProduct(), testProteinAmbiguityGroup(), testProteinDetection(), testProteinDetectionHypothesis(), testProteinDetectionList(), testProteinDetectionProtocol(), testProvider(), testResidue(), testSample(), testScanSettings(), testSearchDatabase(), testSearchModification(), testSequenceCollection(), testSoftware(), testSourceFile(), testSpectraData(), testSpectrumIdentification(), testSpectrumIdentificationItem(), testSpectrumIdentificationList(), testSpectrumIdentificationProtocol(), testSpectrumIdentificationResult(), testSubstitutionModification(), and testUserParam().

◆ testIdentifiable()

void testIdentifiable ( )

Definition at line 66 of file IOTest.cpp.

67 {
68  if (os_) *os_ << "testIdentifiable\n" ;
69 
70  Identifiable a;
71  a.id = "id";
72  a.name = "name";
73 
74  testObject(a);
75 }

References pwiz::identdata::Identifiable::id, pwiz::identdata::Identifiable::name, os_, and testObject().

Referenced by test().

◆ testIdentifiableParamContainer()

void testIdentifiableParamContainer ( )

Definition at line 78 of file IOTest.cpp.

79 {
80  if (os_) *os_ << "testIdentifiableParamContainer\n" ;
81 
83  a.id = "id";
84  a.name = "name";
85 
86  a.set(MS_TIC, 123);
87  a.userParams.push_back(UserParam("abc", "123", "!@#"));
88 
89  testObject(a);
90 }

References pwiz::identdata::IdentifiableParamContainer::id, MS_TIC, pwiz::identdata::IdentifiableParamContainer::name, os_, pwiz::data::ParamContainer::set(), testObject(), and pwiz::data::ParamContainer::userParams.

Referenced by test().

◆ testCV()

void testCV ( )

Definition at line 93 of file IOTest.cpp.

94 {
95  if (os_) *os_ << "testCV\n" ;
96 
97  CV a;
98  a.URI = "abcd";
99  a.id = "efgh";
100  a.fullName = "ijkl";
101  a.version = "mnop";
102 
103  testObject(a);
104 }

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

Referenced by test().

◆ testBibliographicReference()

void testBibliographicReference ( )

◆ testPerson()

void testPerson ( )

Definition at line 128 of file IOTest.cpp.

129 {
130  if (os_) *os_ << "testPerson\n" ;
131 
132  Person a;
133 
134  a.set(MS_contact_address, "123 abc");
135  a.set(MS_contact_phone_number, "456");
136  a.set(MS_contact_email, "efg@hijk.op");
137  a.set(MS_contact_fax_number, "789");
138  a.set(MS_contact_toll_free_phone_number, "012-345-678");
139 
140  a.lastName = "tuv";
141  a.firstName = "wx";
142  a.midInitials = "yz";
143 
144  a.affiliations.push_back(OrganizationPtr(new Organization("ref")));
145 
146  testObject(a);
147 }

References pwiz::identdata::Person::affiliations, pwiz::identdata::Person::firstName, pwiz::identdata::Person::lastName, pwiz::identdata::Person::midInitials, MS_contact_address, MS_contact_email, MS_contact_fax_number, MS_contact_phone_number, MS_contact_toll_free_phone_number, os_, pwiz::data::ParamContainer::set(), and testObject().

Referenced by test().

◆ testOrganization()

void testOrganization ( )

Definition at line 150 of file IOTest.cpp.

151 {
152  if (os_) *os_ << "testOrganization\n" ;
153 
154  Organization a;
155 
156  a.set(MS_contact_address, "123 abc");
157  a.set(MS_contact_phone_number, "456");
158  a.set(MS_contact_email, "efg@hijk.op");
159  a.set(MS_contact_fax_number, "789");
160  a.set(MS_contact_toll_free_phone_number, "012-345-678");
161 
162  a.parent = OrganizationPtr(new Organization("ref"));
163 
164  testObject(a);
165 }

References MS_contact_address, MS_contact_email, MS_contact_fax_number, MS_contact_phone_number, MS_contact_toll_free_phone_number, os_, pwiz::identdata::Organization::parent, pwiz::data::ParamContainer::set(), and testObject().

Referenced by test().

◆ testContactRole()

void testContactRole ( )

Definition at line 168 of file IOTest.cpp.

169 {
170  if (os_) *os_ << "testContactRole\n" ;
171 
172  ContactRole a;
173  a.contactPtr = ContactPtr(new Contact("ref"));
175 
176  testObject(a);
177 }

References pwiz::identdata::ContactRole::contactPtr, pwiz::data::CVParam::cvid, MS_software_vendor, os_, and testObject().

Referenced by test().

◆ testProvider()

void testProvider ( )

Definition at line 180 of file IOTest.cpp.

181 {
182  if (os_) *os_ << "testProvider\n" ;
183 
184  Provider a;
185 
186  // Reduced to a previously tested object.
187  a.contactRolePtr.reset(new ContactRole(MS_role_type, ContactPtr(new Contact("abc"))));
188 
189  testObject(a);
190 }

References pwiz::identdata::Provider::contactRolePtr, MS_role_type, os_, and testObject().

Referenced by test().

◆ testSample()

void testSample ( )

Definition at line 193 of file IOTest.cpp.

194 {
195  if (os_) *os_ << "testSample\n" ;
196 
197  Sample a;
198 
199  // Reduced to a previously tested object.
200  a.contactRole.push_back(ContactRolePtr(new ContactRole(MS_software_vendor, ContactPtr(new Contact("abc")))));
201  a.contactRole.push_back(ContactRolePtr(new ContactRole(MS_programmer, ContactPtr(new Contact("def")))));
202  a.set(MS_septum);
203 
204  a.subSamples.push_back(SamplePtr(new Sample("subSample_ref")));
205 
206  testObject(a);
207 }

References pwiz::identdata::Sample::contactRole, MS_programmer, MS_septum, MS_software_vendor, os_, pwiz::data::ParamContainer::set(), pwiz::identdata::Sample::subSamples, and testObject().

Referenced by test().

◆ testAnalysisSoftware()

void testAnalysisSoftware ( )

Definition at line 210 of file IOTest.cpp.

211 {
212  if (os_) *os_ << "testAnalysisSoftware\n" ;
213 
215  a.version = "abcd";
216  a.URI = "efg";
217  a.customizations = "hijk";
218  ContactRolePtr cont = ContactRolePtr(new ContactRole());
219  cont->contactPtr = ContactPtr(new Contact("ref"));
220  cont->cvid = MS_software_vendor;
221  a.contactRolePtr = cont;
223 
224  testObject(a);
225 }

References pwiz::identdata::AnalysisSoftware::contactRolePtr, pwiz::identdata::AnalysisSoftware::customizations, MS_Mascot, MS_software_vendor, os_, pwiz::data::ParamContainer::set(), pwiz::identdata::AnalysisSoftware::softwareName, testObject(), pwiz::identdata::AnalysisSoftware::URI, and pwiz::identdata::AnalysisSoftware::version.

Referenced by test().

◆ testAnalysisSampleCollection()

void testAnalysisSampleCollection ( )

Definition at line 228 of file IOTest.cpp.

229 {
230  if (os_) *os_ << "testAnalysisSampleCollection\n" ;
231 
233  SamplePtr b(new Sample());
234  b->subSamples.push_back(SamplePtr(new Sample("ref")));
235 
236  testObject(a);
237 }

References os_, and testObject().

◆ testDBSequence()

void testDBSequence ( )

Definition at line 240 of file IOTest.cpp.

241 {
242  DBSequence a;
243 
244  a.id = "id";
245  a.name = "name";
246  a.length = 3;
247  a.accession = "abc";
248  a.searchDatabasePtr = SearchDatabasePtr(new SearchDatabase("def"));
249  a.seq = "ghi";
250  a.set(MS_protein_description, "blahbitty blah blah");
251 
252  testObject(a);
253 }

References pwiz::identdata::DBSequence::accession, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::DBSequence::length, MS_protein_description, pwiz::identdata::IdentifiableParamContainer::name, pwiz::identdata::DBSequence::searchDatabasePtr, pwiz::identdata::DBSequence::seq, pwiz::data::ParamContainer::set(), and testObject().

Referenced by test().

◆ testModification()

void testModification ( )

Definition at line 256 of file IOTest.cpp.

257 {
258  Modification a;
259 
260  a.location = 1;
261  a.avgMassDelta = 1.001001;
262  a.residues.push_back('A');
263  a.residues.push_back('C');
264  a.monoisotopicMassDelta = 100.1001;
265 
267 
268  testObject(a);
269 }

References pwiz::identdata::Modification::avgMassDelta, pwiz::identdata::Modification::location, pwiz::identdata::Modification::monoisotopicMassDelta, pwiz::identdata::Modification::residues, pwiz::data::ParamContainer::set(), testObject(), and UNIMOD_Gln__pyro_Glu.

Referenced by test().

◆ testSubstitutionModification()

void testSubstitutionModification ( )

◆ testPeptide()

void testPeptide ( )

Definition at line 286 of file IOTest.cpp.

287 {
288  Peptide a;
289 
290  a.id = "id";
291  a.name = "name";
292  a.peptideSequence = "abc";
293 
294  ModificationPtr mod(new Modification);
295  mod->location = 1;
296  a.modification.push_back(mod);
297 
298  SubstitutionModificationPtr sub(new SubstitutionModification);
299  sub->location = 2;
300  a.substitutionModification.push_back(sub);
301 
302  a.set(MS_peptide);
303 
304  testObject(a);
305 }

References pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::Peptide::modification, MS_peptide, pwiz::identdata::IdentifiableParamContainer::name, pwiz::identdata::Peptide::peptideSequence, pwiz::data::ParamContainer::set(), pwiz::identdata::Peptide::substitutionModification, and testObject().

Referenced by test().

◆ testSequenceCollection()

void testSequenceCollection ( )

Definition at line 308 of file IOTest.cpp.

309 {
311 
312  a.dbSequences.push_back(DBSequencePtr(new DBSequence("db_id")));
313  a.peptides.push_back(PeptidePtr(new Peptide("pep_id")));
314  a.peptideEvidence.push_back(PeptideEvidencePtr(new PeptideEvidence("pe1")));
315 
316  testObject(a);
317 }

References pwiz::identdata::SequenceCollection::dbSequences, pwiz::identdata::SequenceCollection::peptideEvidence, pwiz::identdata::SequenceCollection::peptides, and testObject().

Referenced by test().

◆ testSpectrumIdentification()

void testSpectrumIdentification ( )

Definition at line 320 of file IOTest.cpp.

321 {
322  if (os_) *os_ << "testSpectrumIdentification\n" ;
323 
326  SpectrumIdentificationProtocolPtr( new SpectrumIdentificationProtocol("sip"));
328  SpectrumIdentificationListPtr(new SpectrumIdentificationList("sil"));
329  a.activityDate = "123";
330  a.inputSpectra.push_back(SpectraDataPtr(new SpectraData("is_sd")));
331  a.searchDatabase.push_back(SearchDatabasePtr(new SearchDatabase("sd_sd")));
332 
333  testObject(a);
334 }

References pwiz::identdata::SpectrumIdentification::activityDate, pwiz::identdata::SpectrumIdentification::inputSpectra, os_, pwiz::identdata::SpectrumIdentification::searchDatabase, pwiz::identdata::SpectrumIdentification::spectrumIdentificationListPtr, pwiz::identdata::SpectrumIdentification::spectrumIdentificationProtocolPtr, and testObject().

Referenced by test().

◆ testProteinDetection()

void testProteinDetection ( )

Definition at line 337 of file IOTest.cpp.

338 {
339  if (os_) *os_ << "testProteinDetection\n" ;
340 
342 
343  a.id = "id";
344  a.name = "name";
345  a.proteinDetectionProtocolPtr = ProteinDetectionProtocolPtr(new ProteinDetectionProtocol("abc"));
346  a.proteinDetectionListPtr = ProteinDetectionListPtr(new ProteinDetectionList("def"));
347  a.activityDate = "ghi";
348 
349  testObject(a);
350 }

References pwiz::identdata::ProteinDetection::activityDate, pwiz::identdata::Identifiable::id, pwiz::identdata::Identifiable::name, os_, pwiz::identdata::ProteinDetection::proteinDetectionListPtr, pwiz::identdata::ProteinDetection::proteinDetectionProtocolPtr, and testObject().

Referenced by test().

◆ testAnalysisCollection()

void testAnalysisCollection ( )

Definition at line 353 of file IOTest.cpp.

354 {
355  if (os_) *os_ << "testAnalysisCollection\n" ;
356 
358 
359  SpectrumIdentificationPtr b(new SpectrumIdentification());
360  b->activityDate = "abc";
361  a.spectrumIdentification.push_back(b);
362  a.proteinDetection.activityDate = "def";
363 
364  testObject(a);
365 }

References pwiz::identdata::ProteinDetection::activityDate, os_, pwiz::identdata::AnalysisCollection::proteinDetection, pwiz::identdata::AnalysisCollection::spectrumIdentification, and testObject().

Referenced by test().

◆ testSearchModification()

void testSearchModification ( )

◆ testEnzyme()

void testEnzyme ( )

◆ testEnzymes()

void testEnzymes ( )

Definition at line 405 of file IOTest.cpp.

406 {
407  if (os_) *os_ << "testEnzymes\n" ;
408 
409  Enzymes a;
410 
411  a.independent = "yes";
412  a.enzymes.push_back(EnzymePtr(new Enzyme()));
413  a.enzymes.back()->siteRegexp = "pxegeRetiS";
414 
415  testObject(a);
416 }

References pwiz::identdata::Enzymes::enzymes, pwiz::identdata::Enzymes::independent, os_, and testObject().

Referenced by test().

◆ testResidue()

void testResidue ( )

Definition at line 419 of file IOTest.cpp.

420 {
421  if (os_) *os_ << "testResidue\n" ;
422 
423  Residue a;
424 
425  a.code = 'A';
426  a.mass = 2;
427 
428  testObject(a);
429 }

References pwiz::identdata::Residue::code, pwiz::identdata::Residue::mass, os_, and testObject().

Referenced by test().

◆ testAmbiguousResidue()

void testAmbiguousResidue ( )

Definition at line 432 of file IOTest.cpp.

433 {
434  if (os_) *os_ << "testAmbiguousResidue\n" ;
435 
437 
438  a.code = 'B';
440 
441  testObject(a);
442 }

References pwiz::identdata::AmbiguousResidue::code, MS_alternate_single_letter_codes, os_, pwiz::data::ParamContainer::set(), and testObject().

Referenced by test().

◆ testMassTable()

void testMassTable ( )

Definition at line 445 of file IOTest.cpp.

446 {
447  MassTable a;
448 
449  a.id = "id";
450  a.msLevel.push_back(1);
451 
452  ResiduePtr b(new Residue());
453  b->code = 'B';
454  a.residues.push_back(b);
455 
456  AmbiguousResiduePtr c(new AmbiguousResidue());
457  c->code = 'C';
458  a.ambiguousResidue.push_back(c);
459 
460  testObject(a);
461 }

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

Referenced by test().

◆ testFilter()

void testFilter ( )

◆ testSpectrumIdentificationProtocol()

void testSpectrumIdentificationProtocol ( )

Definition at line 476 of file IOTest.cpp.

477 {
479 
480  a.id = "id";
481 
482  a.analysisSoftwarePtr = AnalysisSoftwarePtr(new AnalysisSoftware("ref"));
483 
486  a.modificationParams.push_back(SearchModificationPtr(new SearchModification()));
487  a.enzymes.independent = "no";
488  a.massTable.push_back(MassTablePtr(new MassTable("MT_1")));
489  a.massTable.back()->msLevel.push_back(1);
490  a.massTable.back()->msLevel.push_back(2);
494 
495  FilterPtr b(new Filter());
496  b->filterType.set(MS_DB_filter_taxonomy);
497  a.databaseFilters.push_back(b);
498 
499  testObject(a);
500 }

References pwiz::identdata::SpectrumIdentificationProtocol::additionalSearchParams, pwiz::identdata::SpectrumIdentificationProtocol::analysisSoftwarePtr, pwiz::data::CVParam::cvid, pwiz::identdata::SpectrumIdentificationProtocol::databaseFilters, pwiz::identdata::SpectrumIdentificationProtocol::enzymes, pwiz::identdata::SpectrumIdentificationProtocol::fragmentTolerance, pwiz::identdata::Identifiable::id, pwiz::identdata::Enzymes::independent, pwiz::identdata::SpectrumIdentificationProtocol::massTable, pwiz::identdata::SpectrumIdentificationProtocol::modificationParams, MS_DB_filter_taxonomy, MS_Mascot_SigThreshold, MS_ms_ms_search, MS_parent_mass_type_mono, MS_search_tolerance_plus_value, pwiz::identdata::SpectrumIdentificationProtocol::parentTolerance, pwiz::identdata::SpectrumIdentificationProtocol::searchType, pwiz::data::ParamContainer::set(), testObject(), pwiz::identdata::SpectrumIdentificationProtocol::threshold, and UO_dalton.

Referenced by test().

◆ testProteinDetectionProtocol()

void testProteinDetectionProtocol ( )

◆ testAnalysisProtocolCollection()

void testAnalysisProtocolCollection ( )

Definition at line 517 of file IOTest.cpp.

518 {
520 
521  SpectrumIdentificationProtocolPtr b(new SpectrumIdentificationProtocol());
522  b->analysisSoftwarePtr = AnalysisSoftwarePtr(new AnalysisSoftware("ref"));
523  a.spectrumIdentificationProtocol.push_back(b);
524 
525  ProteinDetectionProtocolPtr c(new ProteinDetectionProtocol());
526  c->analysisSoftwarePtr = AnalysisSoftwarePtr(new AnalysisSoftware("ref"));
527  a.proteinDetectionProtocol.push_back(c);
528 
529  testObject(a);
530 }

References pwiz::identdata::AnalysisProtocolCollection::proteinDetectionProtocol, pwiz::identdata::AnalysisProtocolCollection::spectrumIdentificationProtocol, and testObject().

Referenced by test().

◆ testSpectraData()

void testSpectraData ( )

◆ testSearchDatabase()

void testSearchDatabase ( )

◆ testSourceFile()

void testSourceFile ( )

◆ testInputs()

void testInputs ( )

Definition at line 581 of file IOTest.cpp.

582 {
583  Inputs a;
584 
585  SourceFilePtr b(new SourceFile());
586  b->location = "blah";
587  a.sourceFile.push_back(b);
588 
589  SearchDatabasePtr c(new SearchDatabase());
590  c->version = "1.0b";
591  a.searchDatabase.push_back(c);
592 
593  SpectraDataPtr d(new SpectraData());
594  d->location = "bleh";
595  a.spectraData.push_back(d);
596 
597  testObject(a);
598 }

References pwiz::identdata::Inputs::searchDatabase, pwiz::identdata::Inputs::sourceFile, pwiz::identdata::Inputs::spectraData, and testObject().

Referenced by test().

◆ testMeasure()

void testMeasure ( )

Definition at line 601 of file IOTest.cpp.

602 {
603  Measure a;
604 
605  a.id = "id";
607 
608  testObject(a);
609 }

References pwiz::identdata::IdentifiableParamContainer::id, MS_product_ion_m_z, pwiz::data::ParamContainer::set(), and testObject().

Referenced by test().

◆ testFragmentArray()

void testFragmentArray ( )

Definition at line 612 of file IOTest.cpp.

613 {
614  FragmentArray a;
615 
616  a.values.push_back(1.);
617  a.values.push_back(2.);
618  a.values.push_back(3.);
619  a.values.push_back(4.);
620  a.measurePtr = MeasurePtr(new Measure("ref"));
621 
622  testObject(a);
623 }

References pwiz::identdata::FragmentArray::measurePtr, testObject(), and pwiz::identdata::FragmentArray::values.

Referenced by test().

◆ testIonType()

void testIonType ( )

Definition at line 626 of file IOTest.cpp.

627 {
628  IonType a;
629 
630  a.index.push_back(0);
631  a.index.push_back(1);
632  a.index.push_back(2);
633  a.index.push_back(3);
634  a.charge = 2;
635 
636  a.cvid = MS_frag__a_ion;
637  FragmentArrayPtr b(new FragmentArray());
638  a.fragmentArray.push_back(b);
639 
640  testObject(a);
641 }

References pwiz::identdata::IonType::charge, pwiz::data::CVParam::cvid, pwiz::identdata::IonType::fragmentArray, pwiz::identdata::IonType::index, MS_frag__a_ion, and testObject().

Referenced by test().

◆ testPeptideEvidence()

void testPeptideEvidence ( )

◆ testSpectrumIdentificationItem()

void testSpectrumIdentificationItem ( )

Definition at line 664 of file IOTest.cpp.

665 {
667 
668  a.id = "id";
669 
670  a.chargeState = 1;
671  a.experimentalMassToCharge = 1.1;
672  a.calculatedMassToCharge = 2.2;
673  a.calculatedPI = 3.3;
674  a.peptidePtr = PeptidePtr(new Peptide("pep_ref"));
675  a.rank = 4;
676  a.passThreshold = true;
677  a.massTablePtr = MassTablePtr(new MassTable("mt_ref"));
678  a.samplePtr = SamplePtr(new Sample("s_ref"));
679  a.peptideEvidencePtr.push_back(PeptideEvidencePtr(new PeptideEvidence("pe_ref")));
680 
681  IonTypePtr c(new IonType());
682  c->charge = 5;
683  a.fragmentation.push_back(c);
684 
685  a.set(MS_Mascot_score, "15.71");
686 
687  testObject(a);
688 }

References pwiz::identdata::SpectrumIdentificationItem::calculatedMassToCharge, pwiz::identdata::SpectrumIdentificationItem::calculatedPI, pwiz::identdata::SpectrumIdentificationItem::chargeState, pwiz::identdata::SpectrumIdentificationItem::experimentalMassToCharge, pwiz::identdata::SpectrumIdentificationItem::fragmentation, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::SpectrumIdentificationItem::massTablePtr, MS_Mascot_score, pwiz::identdata::SpectrumIdentificationItem::passThreshold, pwiz::identdata::SpectrumIdentificationItem::peptideEvidencePtr, pwiz::identdata::SpectrumIdentificationItem::peptidePtr, pwiz::identdata::SpectrumIdentificationItem::rank, pwiz::identdata::SpectrumIdentificationItem::samplePtr, pwiz::data::ParamContainer::set(), and testObject().

Referenced by test().

◆ testSpectrumIdentificationResult()

void testSpectrumIdentificationResult ( )

Definition at line 691 of file IOTest.cpp.

692 {
694 
695  a.id = "id";
696 
697  a.spectrumID = "sid";
698  a.spectraDataPtr = SpectraDataPtr(new SpectraData("sd_ref"));
699 
700  SpectrumIdentificationItemPtr b(new SpectrumIdentificationItem());
701  b->chargeState = 1;
702  a.spectrumIdentificationItem.push_back(b);
703 
704  a.set(MS_Mascot_score, "15.71");
705 
706  testObject(a);
707 }

References pwiz::identdata::IdentifiableParamContainer::id, MS_Mascot_score, pwiz::data::ParamContainer::set(), pwiz::identdata::SpectrumIdentificationResult::spectraDataPtr, pwiz::identdata::SpectrumIdentificationResult::spectrumID, pwiz::identdata::SpectrumIdentificationResult::spectrumIdentificationItem, and testObject().

Referenced by test().

◆ testPeptideHypothesis()

PeptideHypothesis testPeptideHypothesis ( )

Definition at line 710 of file IOTest.cpp.

711 {
713 
714  a.peptideEvidencePtr.reset(new PeptideEvidence("pe1"));
715  a.spectrumIdentificationItemPtr.push_back(SpectrumIdentificationItemPtr(new SpectrumIdentificationItem("sii1")));
716 
717  testObject(a);
718  return a;
719 }

References pwiz::identdata::PeptideHypothesis::peptideEvidencePtr, pwiz::identdata::PeptideHypothesis::spectrumIdentificationItemPtr, and testObject().

Referenced by testProteinDetectionHypothesis().

◆ testProteinDetectionHypothesis()

void testProteinDetectionHypothesis ( )

◆ testProteinAmbiguityGroup()

void testProteinAmbiguityGroup ( )

Definition at line 736 of file IOTest.cpp.

737 {
739 
740  a.id = "id";
741  ProteinDetectionHypothesisPtr b(new ProteinDetectionHypothesis());
742  b->dbSequencePtr = DBSequencePtr(new DBSequence("dbs_ref"));
743  a.proteinDetectionHypothesis.push_back(b);
744  a.set(MS_Mascot_score, "164.4");
745 
746  testObject(a);
747 }

References pwiz::identdata::IdentifiableParamContainer::id, MS_Mascot_score, pwiz::identdata::ProteinAmbiguityGroup::proteinDetectionHypothesis, pwiz::data::ParamContainer::set(), and testObject().

Referenced by test().

◆ testSpectrumIdentificationList()

void testSpectrumIdentificationList ( )

Definition at line 750 of file IOTest.cpp.

751 {
753 
754  a.id = "id";
755  a.numSequencesSearched = 1;
756 
757  MeasurePtr b(new Measure());
758  b->set(MS_Mascot_score, "164.4");
759  a.fragmentationTable.push_back(b);
760 
761  SpectrumIdentificationResultPtr c(new SpectrumIdentificationResult());
762  c->id = "sid";
763  c->spectrumID = "sID";
764  a.spectrumIdentificationResult.push_back(c);
765 
766  testObject(a);
767 }

References pwiz::identdata::SpectrumIdentificationList::fragmentationTable, pwiz::identdata::IdentifiableParamContainer::id, MS_Mascot_score, pwiz::identdata::SpectrumIdentificationList::numSequencesSearched, pwiz::identdata::SpectrumIdentificationList::spectrumIdentificationResult, and testObject().

Referenced by test().

◆ testProteinDetectionList()

void testProteinDetectionList ( )

Definition at line 770 of file IOTest.cpp.

771 {
773 
774  a.id = "id";
775  ProteinAmbiguityGroupPtr b(new ProteinAmbiguityGroup());
776  a.proteinAmbiguityGroup.push_back(b);
777 
778  a.set(MS_Mascot_score, "164.4");
779 
780  testObject(a);
781 }

References pwiz::identdata::IdentifiableParamContainer::id, MS_Mascot_score, pwiz::identdata::ProteinDetectionList::proteinAmbiguityGroup, pwiz::data::ParamContainer::set(), and testObject().

Referenced by test().

◆ testAnalysisData()

void testAnalysisData ( )

Definition at line 784 of file IOTest.cpp.

785 {
786  AnalysisData a;
787 
788  SpectrumIdentificationListPtr b(new SpectrumIdentificationList());
789  b->id = "id";
790  b->numSequencesSearched = 5;
791  a.spectrumIdentificationList.push_back(b);
792 
793  a.proteinDetectionListPtr = ProteinDetectionListPtr(new ProteinDetectionList("id2"));
794  a.proteinDetectionListPtr->set(MS_Mascot_score, "164.4");
795 
796  testObject(a);
797 }

References MS_Mascot_score, pwiz::identdata::AnalysisData::proteinDetectionListPtr, pwiz::identdata::AnalysisData::spectrumIdentificationList, and testObject().

Referenced by test().

◆ testDataCollection()

void testDataCollection ( )

Definition at line 800 of file IOTest.cpp.

801 {
802  DataCollection a;
803 
804  SourceFilePtr b(new SourceFile());
805  a.inputs.sourceFile.push_back(b);
806 
807  SpectrumIdentificationListPtr c(new SpectrumIdentificationList());
808  c->id = "SIL_1";
809  c->numSequencesSearched = 5;
811 
812  testObject(a);
813 }

References pwiz::identdata::DataCollection::analysisData, pwiz::identdata::DataCollection::inputs, pwiz::identdata::Inputs::sourceFile, pwiz::identdata::AnalysisData::spectrumIdentificationList, and testObject().

Referenced by test().

◆ testIdentData()

void testIdentData ( )

Definition at line 816 of file IOTest.cpp.

817 {
818  IdentData a;
819 
821 
822  testObject(a);
823 
824  // test ignoring sequence collection and analysis data
825  {
826  // write 'a' out to a stream
827 
828  ostringstream oss;
829  XMLWriter writer(oss);
830  IO::write(writer, a);
831  if (os_) *os_ << oss.str() << endl;
832 
833  // read 'b' in from stream
834 
835  IdentData b;
836  istringstream iss(oss.str());
838 
839  // clear the original SequenceCollection
841  a.sequenceCollection.peptides.clear();
843 
844  // clear the original analysis data
845  BOOST_FOREACH(SpectrumIdentificationPtr& si, a.analysisCollection.spectrumIdentification)
846  si->spectrumIdentificationListPtr.reset();
847  a.analysisCollection.proteinDetection = b.analysisCollection.proteinDetection = ProteinDetection();
848  a.dataCollection.analysisData.spectrumIdentificationList.clear();
849  a.dataCollection.analysisData.proteinDetectionListPtr.reset();
850 
851  // compare 'a' and 'b'
852 
853  Diff<IdentData, DiffConfig> diff(a,b);
854  if (diff && os_) *os_ << "diff:\n" << diff << endl;
855  unit_assert(!diff);
856  }
857 }

References pwiz::identdata::IdentData::analysisCollection, pwiz::identdata::DataCollection::analysisData, pwiz::identdata::IdentData::dataCollection, pwiz::identdata::SequenceCollection::dbSequences, diff(), IgnoreAnalysisData, IgnoreSequenceCollection, pwiz::identdata::examples::initializeTiny(), os_, pwiz::identdata::SequenceCollection::peptideEvidence, pwiz::identdata::SequenceCollection::peptides, pwiz::identdata::AnalysisCollection::proteinDetection, pwiz::identdata::AnalysisData::proteinDetectionListPtr, pwiz::identdata::IO::read(), pwiz::identdata::IdentData::sequenceCollection, pwiz::identdata::AnalysisCollection::spectrumIdentification, pwiz::identdata::AnalysisData::spectrumIdentificationList, testObject(), unit_assert, and pwiz::identdata::IO::write().

Referenced by test().

◆ test()

void test ( )

Definition at line 860 of file IOTest.cpp.

References testAmbiguousResidue(), testAnalysisCollection(), testAnalysisData(), testAnalysisProtocolCollection(), testAnalysisSoftware(), testBibliographicReference(), testContactRole(), testCV(), testDataCollection(), testDBSequence(), testEnzyme(), testEnzymes(), testFilter(), testFragmentArray(), testIdentData(), testIdentifiable(), testIdentifiableParamContainer(), testInputs(), testIonType(), testMassTable(), testMeasure(), testModification(), testOrganization(), testPeptide(), testPeptideEvidence(), testPerson(), testProteinAmbiguityGroup(), testProteinDetection(), testProteinDetectionHypothesis(), testProteinDetectionList(), testProteinDetectionProtocol(), testProvider(), testResidue(), testSample(), testSearchDatabase(), testSearchModification(), testSequenceCollection(), testSourceFile(), testSpectraData(), testSpectrumIdentification(), testSpectrumIdentificationItem(), testSpectrumIdentificationList(), testSpectrumIdentificationProtocol(), testSpectrumIdentificationResult(), and testSubstitutionModification().

Referenced by main().

◆ main()

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

Definition at line 910 of file IOTest.cpp.

911 {
912  TEST_PROLOG_EX(argc, argv, "_IdentData")
913 
914  try
915  {
916  if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
917  test();
918  if (os_) *os_ << "ok\n";
919  }
920  catch (exception& e)
921  {
922  TEST_FAILED(e.what())
923  }
924  catch (...)
925  {
926  TEST_FAILED("Caught unknown exception.")
927  }
928 
930 }

References os_, test(), TEST_EPILOG, TEST_FAILED, and TEST_PROLOG_EX.

Variable Documentation

◆ os_

ostream* os_ = 0
pwiz::data::UserParam
Uncontrolled user parameters (essentially allowing free text). Before using these,...
Definition: ParamTypes.hpp:186
MS_product_ion_m_z
MS_product_ion_m_z
product ion m/z: The m/z of the product ion.
Definition: cv.hpp:4101
pwiz::identdata::SpectrumIdentificationProtocol::modificationParams
std::vector< SearchModificationPtr > modificationParams
Definition: IdentData.hpp:554
pwiz::cv::CV::fullName
std::string fullName
the usual name for the resource (e.g. The PSI-MS Controlled Vocabulary).
Definition: cv.hpp:14924
pwiz::identdata::Enzyme::nTermGain
std::string nTermGain
Definition: IdentData.hpp:413
pwiz::identdata::SpectrumIdentificationItem
Implementation of SpectrumIdentificationItemType from the mzIdentML schema.
Definition: IdentData.hpp:670
pwiz::identdata::Person
Implementation of PersonType from the mzIdentML schema.
Definition: IdentData.hpp:153
pwiz::minimxml::XMLWriter
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:48
pwiz::identdata::BibliographicReference::issue
std::string issue
Definition: IdentData.hpp:105
MS_peptide
MS_peptide
peptide: A compound of low molecular weight that is composed of two or more amino acids.
Definition: cv.hpp:3276
pwiz::identdata::SpectrumIdentificationResult::spectrumIdentificationItem
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItem
Definition: IdentData.hpp:730
pwiz::identdata::Person::lastName
std::string lastName
Definition: IdentData.hpp:157
IgnoreAnalysisData
IgnoreAnalysisData
Definition: IO.hpp:211
pwiz::identdata::FragmentArray::measurePtr
MeasurePtr measurePtr
Definition: IdentData.hpp:592
pwiz::identdata::PeptideEvidence
Implementation of PeptideEvidenceType from the mzIdentML schema.
Definition: IdentData.hpp:627
pwiz::identdata::AnalysisProtocolCollection::proteinDetectionProtocol
std::vector< ProteinDetectionProtocolPtr > proteinDetectionProtocol
Definition: IdentData.hpp:912
pwiz::identdata::MassTable::ambiguousResidue
std::vector< AmbiguousResiduePtr > ambiguousResidue
Definition: IdentData.hpp:488
pwiz::identdata::SpectraData::location
std::string location
Definition: IdentData.hpp:702
pwiz::identdata::PeptideEvidence::dbSequencePtr
DBSequencePtr dbSequencePtr
Definition: IdentData.hpp:632
pwiz::identdata::SubstitutionModification::avgMassDelta
double avgMassDelta
Definition: IdentData.hpp:356
MS_modification_specificity_peptide_N_term
MS_modification_specificity_peptide_N_term
modification specificity peptide N-term: As parameter for search engine: apply the modification only ...
Definition: cv.hpp:4002
testSequenceCollection
void testSequenceCollection()
Definition: IOTest.cpp:308
pwiz::identdata::SpectrumIdentificationItem::chargeState
int chargeState
Definition: IdentData.hpp:674
pwiz::identdata::DiffConfig
Definition: Diff.hpp:396
testDataCollection
void testDataCollection()
Definition: IOTest.cpp:800
pwiz::identdata::SpectrumIdentificationResult::spectraDataPtr
SpectraDataPtr spectraDataPtr
Definition: IdentData.hpp:728
pwiz::identdata::Residue
Implementation of ResidueType from the mzIdentML schema.
Definition: IdentData.hpp:446
pwiz::identdata::SpectrumIdentificationProtocol::additionalSearchParams
ParamContainer additionalSearchParams
Definition: IdentData.hpp:553
pwiz::identdata::MassTable::msLevel
std::vector< int > msLevel
Definition: IdentData.hpp:485
testSearchDatabase
void testSearchDatabase()
Definition: IOTest.cpp:547
pwiz::identdata::SearchDatabase::numDatabaseSequences
long numDatabaseSequences
Definition: IdentData.hpp:278
pwiz::identdata::Modification::monoisotopicMassDelta
double monoisotopicMassDelta
Definition: IdentData.hpp:336
pwiz::identdata::SpectrumIdentificationItem::samplePtr
SamplePtr samplePtr
Definition: IdentData.hpp:682
testPerson
void testPerson()
Definition: IOTest.cpp:128
pwiz::identdata::AmbiguousResidue
Implementation of AmbiguousResidueType from the mzIdentML schema.
Definition: IdentData.hpp:464
pwiz::cv::CV
Information about an ontology or CV source and a short 'lookup' tag to refer to.
Definition: cv.hpp:14916
testPeptideHypothesis
PeptideHypothesis testPeptideHypothesis()
Definition: IOTest.cpp:710
pwiz::cv::CV::URI
std::string URI
the URI for the resource.
Definition: cv.hpp:14921
pwiz::identdata::SpectrumIdentification::activityDate
std::string activityDate
Definition: IdentData.hpp:771
pwiz::identdata::Enzyme::missedCleavages
int missedCleavages
Definition: IdentData.hpp:416
pwiz::identdata::SpectrumIdentificationResult
Implementation of SpectrumIdentificationResultType from the mzIdentML schema.
Definition: IdentData.hpp:723
MS_contact_toll_free_phone_number
MS_contact_toll_free_phone_number
contact toll-free phone number: Toll-free phone number of the contact person or organization.
Definition: cv.hpp:5685
testSample
void testSample()
Definition: IOTest.cpp:193
pwiz::identdata::Enzyme::siteRegexp
std::string siteRegexp
Definition: IdentData.hpp:419
pwiz::identdata::ProteinDetectionHypothesis
Implementation of ProteinDetectionHypothesisType from the mzIdentML schema.
Definition: IdentData.hpp:820
MS_role_type
MS_role_type
role type: Role of a Person or Organization.
Definition: cv.hpp:4218
testInputs
void testInputs()
Definition: IOTest.cpp:581
pwiz::identdata::Filter::exclude
ParamContainer exclude
Definition: IdentData.hpp:505
pwiz::identdata::SpectraData
Implementation of SpectraDataType from the mzIdentML schema.
Definition: IdentData.hpp:698
testEnzyme
void testEnzyme()
Definition: IOTest.cpp:385
pwiz::identdata::Provider
Implementation of ProviderType from the mzIdentML schema.
Definition: IdentData.hpp:235
pwiz::identdata::SpectrumIdentificationResult::spectrumID
std::string spectrumID
Definition: IdentData.hpp:727
MS_parent_mass_type_mono
MS_parent_mass_type_mono
parent mass type mono: Mass type setting for parent mass was monoisotopic.
Definition: cv.hpp:4062
pwiz::identdata::DBSequence::searchDatabasePtr
SearchDatabasePtr searchDatabasePtr
Definition: IdentData.hpp:303
pwiz::identdata::IonType::fragmentArray
std::vector< FragmentArrayPtr > fragmentArray
Definition: IdentData.hpp:613
UNIMOD_Gln__pyro_Glu
UNIMOD_Gln__pyro_Glu
Gln->pyro-Glu: Pyro-glu from Q.
Definition: cv.hpp:9435
testContactRole
void testContactRole()
Definition: IOTest.cpp:168
pwiz::identdata::IdentData::analysisCollection
AnalysisCollection analysisCollection
Definition: IdentData.hpp:1016
pwiz::identdata::SpectrumIdentification::spectrumIdentificationProtocolPtr
SpectrumIdentificationProtocolPtr spectrumIdentificationProtocolPtr
Definition: IdentData.hpp:769
pwiz::identdata::SpectrumIdentificationProtocol::enzymes
Enzymes enzymes
Definition: IdentData.hpp:555
pwiz::identdata::SearchModification::specificityRules
CVParam specificityRules
Definition: IdentData.hpp:395
pwiz::identdata::SpectrumIdentificationList::numSequencesSearched
long numSequencesSearched
Definition: IdentData.hpp:748
pwiz::data::ParamContainer::userParams
std::vector< UserParam > userParams
a collection of uncontrolled user terms
Definition: ParamTypes.hpp:253
pwiz::identdata::ProteinDetectionProtocol::analysisParams
ParamContainer analysisParams
Definition: IdentData.hpp:793
MS_DB_MW_filter
MS_DB_MW_filter
DB MW filter: Filtering applied specifically by protein molecular weight, specified as either a range...
Definition: cv.hpp:3564
pwiz::identdata::SearchDatabase::location
std::string location
Definition: IdentData.hpp:275
pwiz::identdata::BibliographicReference::pages
std::string pages
Definition: IdentData.hpp:106
pwiz::identdata::SubstitutionModification
Implementation of SubstitutionModificationType from the mzIdentML schema.
Definition: IdentData.hpp:350
pwiz::cv::CV::id
std::string id
the short label to be used as a reference tag with which to refer to this particular Controlled Vocab...
Definition: cv.hpp:14918
pwiz::identdata::TranslationTable
Implementation of TranslationTableType from the mzIdentML schema.
Definition: IdentData.hpp:518
testSpectrumIdentificationList
void testSpectrumIdentificationList()
Definition: IOTest.cpp:750
MS_TIC
MS_TIC
TIC (total ion current): The sum of all the separate ion currents carried by the ions of different m/...
Definition: cv.hpp:1410
pwiz::identdata::ProteinDetectionHypothesis::peptideHypothesis
std::vector< PeptideHypothesis > peptideHypothesis
Definition: IdentData.hpp:826
testIonType
void testIonType()
Definition: IOTest.cpp:626
pwiz::identdata::SourceFile::externalFormatDocumentation
std::vector< std::string > externalFormatDocumentation
Definition: IdentData.hpp:928
pwiz::identdata::ProteinAmbiguityGroup::proteinDetectionHypothesis
std::vector< ProteinDetectionHypothesisPtr > proteinDetectionHypothesis
Definition: IdentData.hpp:844
pwiz::identdata::Contact
Implementation of ContactType from mzIdentML.
Definition: IdentData.hpp:118
pwiz::identdata::SearchModification::massDelta
double massDelta
Definition: IdentData.hpp:393
pwiz::identdata::SpectrumIdentificationProtocol::massTable
std::vector< MassTablePtr > massTable
Definition: IdentData.hpp:556
pwiz::identdata::ProteinDetection::proteinDetectionProtocolPtr
ProteinDetectionProtocolPtr proteinDetectionProtocolPtr
Definition: IdentData.hpp:877
pwiz::identdata::SourceFile
Implementation of SourceFileType from the mzIdentML schema.
Definition: IdentData.hpp:924
pwiz::identdata::PeptideEvidence::pre
char pre
Definition: IdentData.hpp:635
pwiz::identdata::AmbiguousResidue::code
char code
Definition: IdentData.hpp:467
pwiz::identdata::AnalysisCollection::spectrumIdentification
std::vector< SpectrumIdentificationPtr > spectrumIdentification
Definition: IdentData.hpp:897
pwiz::identdata::SpectrumIdentificationItem::calculatedMassToCharge
double calculatedMassToCharge
Definition: IdentData.hpp:676
pwiz::identdata::PeptideEvidence::translationTablePtr
TranslationTablePtr translationTablePtr
Definition: IdentData.hpp:637
pwiz::identdata::SpectrumIdentification::inputSpectra
std::vector< SpectraDataPtr > inputSpectra
Definition: IdentData.hpp:773
pwiz::identdata::PeptideEvidence::isDecoy
bool isDecoy
Definition: IdentData.hpp:639
testDBSequence
void testDBSequence()
Definition: IOTest.cpp:240
pwiz::identdata::Organization
Implementation of AbstractOrganizationType from the mzIdentML schema.
Definition: IdentData.hpp:136
pwiz::identdata::SpectraData::fileFormat
CVParam fileFormat
Definition: IdentData.hpp:705
pwiz::identdata::IonType
Implementation of IonTypeType from the mzIdentML schema.
Definition: IdentData.hpp:608
pwiz::identdata::ProteinDetection
Implementation of ProteinDetectionType from the mzIdentML schema.
Definition: IdentData.hpp:873
pwiz::identdata::Enzymes::enzymes
std::vector< EnzymePtr > enzymes
Definition: IdentData.hpp:435
pwiz::identdata::SpectrumIdentificationProtocol::databaseFilters
std::vector< FilterPtr > databaseFilters
Definition: IdentData.hpp:560
pwiz::cv::CV::version
std::string version
the version of the CV from which the referred-to terms are drawn.
Definition: cv.hpp:14927
pwiz::identdata::SearchDatabase::releaseDate
std::string releaseDate
Definition: IdentData.hpp:277
MS_alternate_single_letter_codes
MS_alternate_single_letter_codes
alternate single letter codes: List of standard residue one letter codes which are used to replace a ...
Definition: cv.hpp:4488
pwiz::identdata::Enzyme
Implementation of EnzymeType from the mzIdentML schema.
Definition: IdentData.hpp:409
MS_contact_address
MS_contact_address
contact address: Postal address of the contact person or organization.
Definition: cv.hpp:2412
pwiz::identdata::SpectrumIdentificationItem::calculatedPI
double calculatedPI
Definition: IdentData.hpp:677
testSpectrumIdentification
void testSpectrumIdentification()
Definition: IOTest.cpp:320
pwiz::identdata::SubstitutionModification::replacementResidue
char replacementResidue
Definition: IdentData.hpp:354
pwiz::identdata::IO::write
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)
pwiz::identdata::Peptide::modification
std::vector< ModificationPtr > modification
Definition: IdentData.hpp:374
pwiz::identdata::SpectrumIdentificationItem::rank
int rank
Definition: IdentData.hpp:679
pwiz::identdata::Peptide::peptideSequence
std::string peptideSequence
Definition: IdentData.hpp:373
pwiz::identdata::Residue::mass
double mass
Definition: IdentData.hpp:450
MS_contact_fax_number
MS_contact_fax_number
contact fax number: Fax number for the contact person or organization.
Definition: cv.hpp:5682
pwiz::identdata::SequenceCollection::peptideEvidence
std::vector< PeptideEvidencePtr > peptideEvidence
Definition: IdentData.hpp:656
pwiz::identdata::IonType::index
std::vector< int > index
Definition: IdentData.hpp:611
pwiz::identdata::Identifiable
Parent class representing extensions of the IdentifiableType from the mzIdentML schema.
Definition: IdentData.hpp:65
testProteinDetection
void testProteinDetection()
Definition: IOTest.cpp:337
MS_programmer
MS_programmer
programmer: Programmer role.
Definition: cv.hpp:4224
pwiz::identdata::DBSequence::length
int length
Definition: IdentData.hpp:301
pwiz::identdata::Residue::code
char code
Definition: IdentData.hpp:449
pwiz::identdata::BibliographicReference
Implementation for the BibliographicReferenceType tag in the mzIdentML schema.
Definition: IdentData.hpp:96
pwiz::data::Diff
Calculate diffs of objects in a ProteoWizard data model hierarchy.
Definition: diff_std.hpp:143
pwiz::identdata::AnalysisData::spectrumIdentificationList
std::vector< SpectrumIdentificationListPtr > spectrumIdentificationList
Definition: IdentData.hpp:962
testAnalysisCollection
void testAnalysisCollection()
Definition: IOTest.cpp:353
pwiz::identdata::PeptideHypothesis
Implementation of PeptideHypothesisType from the mzIdentML schema.
Definition: IdentData.hpp:807
testBibliographicReference
void testBibliographicReference()
Definition: IOTest.cpp:107
pwiz::identdata::Modification
Implementation of ModificationType from the mzIdentML schema.
Definition: IdentData.hpp:330
testAnalysisSoftware
void testAnalysisSoftware()
Definition: IOTest.cpp:210
pwiz::identdata::IdentifiableParamContainer::id
std::string id
Definition: IdentData.hpp:85
pwiz::identdata::Filter::filterType
ParamContainer filterType
Definition: IdentData.hpp:503
pwiz::identdata::ProteinDetectionList
Implementation of ProteinDetectionListType from the mzIdentML schema.
Definition: IdentData.hpp:856
pwiz::identdata::SpectrumIdentificationProtocol::searchType
CVParam searchType
Definition: IdentData.hpp:552
pwiz::identdata::Inputs
Implementation of the InputsType from the mzIdentML schema.
Definition: IdentData.hpp:944
pwiz::identdata::SpectraData::externalFormatDocumentation
std::vector< std::string > externalFormatDocumentation
Definition: IdentData.hpp:704
pwiz::identdata::FragmentArray
Implementation of FragmentArrayType from the mzIdentML schema.
Definition: IdentData.hpp:590
pwiz::identdata::Provider::contactRolePtr
ContactRolePtr contactRolePtr
Definition: IdentData.hpp:239
testSubstitutionModification
void testSubstitutionModification()
Definition: IOTest.cpp:272
pwiz::identdata::SearchDatabase::numResidues
long numResidues
Definition: IdentData.hpp:279
pwiz::identdata::ProteinDetectionHypothesis::passThreshold
bool passThreshold
Definition: IdentData.hpp:825
pwiz::identdata::SourceFile::fileFormat
CVParam fileFormat
Definition: IdentData.hpp:926
pwiz::identdata::AnalysisProtocolCollection
Implementation of AnalysisProtocolCollectionType from the mzIdentML schema.
Definition: IdentData.hpp:910
pwiz::identdata::SearchDatabase::version
std::string version
Definition: IdentData.hpp:276
pwiz::identdata::ProteinDetectionProtocol
Implementation of ProteinDetectionProtocolType from the mzIdentML schema.
Definition: IdentData.hpp:787
pwiz::identdata::ProteinDetection::proteinDetectionListPtr
ProteinDetectionListPtr proteinDetectionListPtr
Definition: IdentData.hpp:878
pwiz::identdata::SpectrumIdentificationItem::peptidePtr
PeptidePtr peptidePtr
Definition: IdentData.hpp:678
pwiz::identdata::AnalysisCollection
Implementation of AnalysisCollectionType from the mzIdentML schema.
Definition: IdentData.hpp:896
TEST_EPILOG
#define TEST_EPILOG
Definition: unit.hpp:183
pwiz::identdata::MassTable::residues
std::vector< ResiduePtr > residues
Definition: IdentData.hpp:487
testFilter
void testFilter()
Definition: IOTest.cpp:464
testSpectrumIdentificationResult
void testSpectrumIdentificationResult()
Definition: IOTest.cpp:691
pwiz::identdata::SpectrumIdentificationList::fragmentationTable
std::vector< MeasurePtr > fragmentationTable
Definition: IdentData.hpp:750
pwiz::identdata::Modification::avgMassDelta
double avgMassDelta
Definition: IdentData.hpp:335
pwiz::identdata::Peptide
Implementation of PeptideType from the mzIdentML schema.
Definition: IdentData.hpp:369
pwiz::identdata::SpectrumIdentificationProtocol
Implementation of SpectrumIdentificationProtocolType from the mzIdentML schema.
Definition: IdentData.hpp:546
pwiz::identdata::AnalysisSoftware::version
std::string version
Definition: IdentData.hpp:217
testOrganization
void testOrganization()
Definition: IOTest.cpp:150
pwiz::identdata::Sample::subSamples
std::vector< boost::shared_ptr< Sample > > subSamples
Definition: IdentData.hpp:201
pwiz::identdata::DataCollection::inputs
Inputs inputs
Definition: IdentData.hpp:976
pwiz::identdata::ContactRole::contactPtr
ContactPtr contactPtr
Definition: IdentData.hpp:180
CVID_Unknown
CVID_Unknown
Definition: cv.hpp:114
pwiz::identdata::BibliographicReference::year
int year
Definition: IdentData.hpp:103
pwiz::identdata::DBSequence::seq
std::string seq
Definition: IdentData.hpp:305
pwiz::identdata::Organization::parent
boost::shared_ptr< Organization > parent
Definition: IdentData.hpp:140
pwiz::identdata::IdentifiableParamContainer::name
std::string name
Definition: IdentData.hpp:86
pwiz::msdata::SamplePtr
boost::shared_ptr< Sample > SamplePtr
Definition: MSData.hpp:118
pwiz::identdata::ProteinDetectionProtocol::threshold
ParamContainer threshold
Definition: IdentData.hpp:794
pwiz::identdata::Filter::include
ParamContainer include
Definition: IdentData.hpp:504
pwiz::identdata::SearchModification
Implementation of SearchModificationType from the mzIdentML schema.
Definition: IdentData.hpp:389
pwiz::identdata::PeptideHypothesis::peptideEvidencePtr
PeptideEvidencePtr peptideEvidencePtr
Definition: IdentData.hpp:808
pwiz::identdata::PeptideEvidence::post
char post
Definition: IdentData.hpp:636
pwiz::identdata::SpectrumIdentificationProtocol::parentTolerance
ParamContainer parentTolerance
Definition: IdentData.hpp:558
pwiz::identdata::AnalysisData::proteinDetectionListPtr
ProteinDetectionListPtr proteinDetectionListPtr
Definition: IdentData.hpp:963
MS_software_vendor
MS_software_vendor
software vendor: Software vendor role.
Definition: cv.hpp:4221
pwiz::identdata::SequenceCollection
Implementation of SequenceCollectionType from the mzIdentML schema.
Definition: IdentData.hpp:653
pwiz::identdata::ProteinDetectionProtocol::analysisSoftwarePtr
AnalysisSoftwarePtr analysisSoftwarePtr
Definition: IdentData.hpp:791
os_
ostream * os_
Definition: IOTest.cpp:38
pwiz::identdata::ContactRole
Implementation of ContactRoleType from the mzIdentML schema.
Definition: IdentData.hpp:176
testProteinDetectionHypothesis
void testProteinDetectionHypothesis()
Definition: IOTest.cpp:722
pwiz::identdata::Person::firstName
std::string firstName
Definition: IdentData.hpp:158
pwiz::identdata::SpectrumIdentificationProtocol::analysisSoftwarePtr
AnalysisSoftwarePtr analysisSoftwarePtr
Definition: IdentData.hpp:550
testFragmentArray
void testFragmentArray()
Definition: IOTest.cpp:612
pwiz::identdata::MassTable
Implementation of MassTableType from the mzIdentML schema.
Definition: IdentData.hpp:481
MS_Trypsin
MS_Trypsin
Trypsin: Enzyme trypsin.
Definition: cv.hpp:4179
pwiz::identdata::MassTable::id
std::string id
Definition: IdentData.hpp:484
diff
void diff(const string &filename1, const string &filename2)
Definition: FrequencyDataTest.cpp:40
pwiz::identdata::SequenceCollection::dbSequences
std::vector< DBSequencePtr > dbSequences
Definition: IdentData.hpp:654
testProteinDetectionProtocol
void testProteinDetectionProtocol()
Definition: IOTest.cpp:503
testMassTable
void testMassTable()
Definition: IOTest.cpp:445
pwiz::identdata::DataCollection
Implementation of DataCollectionType from the mzIdentML schema.
Definition: IdentData.hpp:975
testCV
void testCV()
Definition: IOTest.cpp:93
pwiz::identdata::Modification::location
int location
Definition: IdentData.hpp:333
pwiz::identdata::examples::initializeTiny
PWIZ_API_DECL void initializeTiny(IdentData &mzid)
test
void test()
Definition: IOTest.cpp:860
pwiz::identdata::PeptideEvidence::frame
int frame
Definition: IdentData.hpp:638
pwiz::identdata::PeptideHypothesis::spectrumIdentificationItemPtr
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItemPtr
Definition: IdentData.hpp:809
pwiz::identdata::SearchDatabase
Implementation of SearchDatabaseType from the mzIdentML schema.
Definition: IdentData.hpp:271
pwiz::identdata::IdentData
Implementation of the MzIdentMLType from the mzIdentML schema.
Definition: IdentData.hpp:994
testAnalysisProtocolCollection
void testAnalysisProtocolCollection()
Definition: IOTest.cpp:517
pwiz::identdata::SourceFile::location
std::string location
Definition: IdentData.hpp:925
pwiz::identdata::ProteinDetectionList::proteinAmbiguityGroup
std::vector< ProteinAmbiguityGroupPtr > proteinAmbiguityGroup
Definition: IdentData.hpp:860
testProvider
void testProvider()
Definition: IOTest.cpp:180
pwiz::identdata::Sample
Implementation of the SampleType from the mzIdentML schema.
Definition: IdentData.hpp:196
pwiz::identdata::SpectrumIdentificationItem::experimentalMassToCharge
double experimentalMassToCharge
Definition: IdentData.hpp:675
pwiz::identdata::IdentData::sequenceCollection
SequenceCollection sequenceCollection
Definition: IdentData.hpp:1014
pwiz::identdata::SpectrumIdentification::searchDatabase
std::vector< SearchDatabasePtr > searchDatabase
Definition: IdentData.hpp:774
MS_protein_description
MS_protein_description
protein description: The protein description line from the sequence entry in the source database FAST...
Definition: cv.hpp:3723
pwiz::identdata::BibliographicReference::authors
std::string authors
Definition: IdentData.hpp:99
testSourceFile
void testSourceFile()
Definition: IOTest.cpp:566
testAnalysisData
void testAnalysisData()
Definition: IOTest.cpp:784
testObject
void testObject(const object_type &a)
Definition: IOTest.cpp:41
MS_contact_email
MS_contact_email
contact email: Email address of the contact person or organization.
Definition: cv.hpp:2418
MS_DB_filter_taxonomy
MS_DB_filter_taxonomy
DB filter taxonomy: A taxonomy filter was to the database search.
Definition: cv.hpp:3558
MS_septum
MS_septum
septum: A disc composed of a flexible material that seals the entrance to the reservoir....
Definition: cv.hpp:483
pwiz::identdata::SpectrumIdentificationItem::fragmentation
std::vector< IonTypePtr > fragmentation
Definition: IdentData.hpp:685
pwiz::identdata::Identifiable::id
std::string id
Definition: IdentData.hpp:70
pwiz::identdata::BibliographicReference::publisher
std::string publisher
Definition: IdentData.hpp:101
pwiz::identdata::Enzyme::terminalSpecificity
proteome::Digestion::Specificity terminalSpecificity
Definition: IdentData.hpp:415
pwiz::identdata::BibliographicReference::volume
std::string volume
Definition: IdentData.hpp:104
pwiz::identdata::Enzymes::independent
boost::logic::tribool independent
Definition: IdentData.hpp:433
MS_Mascot_SigThreshold
MS_Mascot_SigThreshold
Mascot:SigThreshold: Significance threshold below which the p-value of a peptide match must lie to be...
Definition: cv.hpp:4359
pwiz::identdata::Inputs::sourceFile
std::vector< SourceFilePtr > sourceFile
Definition: IdentData.hpp:946
testSpectraData
void testSpectraData()
Definition: IOTest.cpp:533
pwiz::identdata::SequenceCollection::peptides
std::vector< PeptidePtr > peptides
Definition: IdentData.hpp:655
pwiz::msdata::SourceFilePtr
boost::shared_ptr< SourceFile > SourceFilePtr
Description of the source file, including location and type.
Definition: MSData.hpp:76
pwiz::identdata::FragmentArray::values
std::vector< double > values
Definition: IdentData.hpp:591
MS_mzML_format
MS_mzML_format
mzML format: Proteomics Standards Inititative mzML file format.
Definition: cv.hpp:2403
MS_FASTA_format
MS_FASTA_format
FASTA format: The sequence database was stored in the FASTA format.
Definition: cv.hpp:4452
pwiz::identdata::IonType::charge
int charge
Definition: IdentData.hpp:612
TEST_FAILED
#define TEST_FAILED(x)
Definition: unit.hpp:177
UO_dalton
UO_dalton
dalton: An independently to the base SI units defined mass unit which is equal to one twelfth of the ...
Definition: cv.hpp:14460
pwiz::identdata::AnalysisData
Implementation of AnalysisDataType from the mzIdentML schema.
Definition: IdentData.hpp:961
pwiz::identdata::SubstitutionModification::originalResidue
char originalResidue
Definition: IdentData.hpp:353
testIdentData
void testIdentData()
Definition: IOTest.cpp:816
pwiz::identdata::BibliographicReference::title
std::string title
Definition: IdentData.hpp:107
pwiz::identdata::SpectrumIdentificationItem::passThreshold
bool passThreshold
Definition: IdentData.hpp:680
pwiz::identdata::Enzyme::minDistance
int minDistance
Definition: IdentData.hpp:417
pwiz::identdata::SearchDatabase::databaseName
ParamContainer databaseName
Definition: IdentData.hpp:282
MS_Mascot
MS_Mascot
Mascot: The name of the Mascot search engine.
Definition: cv.hpp:4050
pwiz::identdata::Measure
Implementation of MeasureType from the mzIdentML schema.
Definition: IdentData.hpp:574
testModification
void testModification()
Definition: IOTest.cpp:256
testProteinAmbiguityGroup
void testProteinAmbiguityGroup()
Definition: IOTest.cpp:736
testPeptide
void testPeptide()
Definition: IOTest.cpp:286
pwiz::identdata::Enzyme::enzymeName
ParamContainer enzymeName
Definition: IdentData.hpp:420
pwiz::identdata::DBSequence
Implementation of DBSequenceType from the mzIdentML schema.
Definition: IdentData.hpp:297
pwiz::data::ParamContainer::set
void set(CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
set/add a CVParam (not recursive)
testSpectrumIdentificationItem
void testSpectrumIdentificationItem()
Definition: IOTest.cpp:664
MS_ms_ms_search
MS_ms_ms_search
ms-ms search: An MS2 search (with fragment ions).
Definition: cv.hpp:3708
IgnoreSequenceCollection
IgnoreSequenceCollection
Definition: IO.hpp:255
pwiz::identdata::Person::midInitials
std::string midInitials
Definition: IdentData.hpp:159
testSearchModification
void testSearchModification()
Definition: IOTest.cpp:368
pwiz::identdata::PeptideEvidence::end
int end
Definition: IdentData.hpp:634
pwiz::identdata::BibliographicReference::publication
std::string publication
Definition: IdentData.hpp:100
pwiz::identdata::SearchModification::residues
std::vector< char > residues
Definition: IdentData.hpp:394
pwiz::identdata::SpectrumIdentificationList::spectrumIdentificationResult
std::vector< SpectrumIdentificationResultPtr > spectrumIdentificationResult
Definition: IdentData.hpp:751
pwiz::identdata::PeptideEvidence::start
int start
Definition: IdentData.hpp:633
pwiz::identdata::AnalysisSoftware
Implementation of AnalysisSoftwareType from the mzIdentML schema.
Definition: IdentData.hpp:212
MS_Mascot_DAT_format
MS_Mascot_DAT_format
Mascot DAT format: Source file for this mzIdentML was in Mascot DAT file format.
Definition: cv.hpp:4032
pwiz::identdata::SpectrumIdentificationProtocol::fragmentTolerance
ParamContainer fragmentTolerance
Definition: IdentData.hpp:557
pwiz::identdata::Filter
Implementation of FilterType from the mzIdentML schema.
Definition: IdentData.hpp:502
pwiz::identdata::SearchDatabase::fileFormat
CVParam fileFormat
Definition: IdentData.hpp:281
pwiz::identdata::ProteinDetectionHypothesis::dbSequencePtr
DBSequencePtr dbSequencePtr
Definition: IdentData.hpp:824
testMeasure
void testMeasure()
Definition: IOTest.cpp:601
pwiz::identdata::DBSequence::accession
std::string accession
Definition: IdentData.hpp:302
pwiz::identdata::Modification::residues
std::vector< char > residues
Definition: IdentData.hpp:334
TEST_PROLOG_EX
#define TEST_PROLOG_EX(argc, argv, suffix)
Definition: unit.hpp:157
pwiz::identdata::SubstitutionModification::location
int location
Definition: IdentData.hpp:355
MS_frag__a_ion
MS_frag__a_ion
frag: a ion: Fragmentation information, type of product: a ion.
Definition: cv.hpp:4119
MS_contact_phone_number
MS_contact_phone_number
contact phone number: Phone number of the contact person or organization.
Definition: cv.hpp:5679
MS_search_tolerance_plus_value
MS_search_tolerance_plus_value
search tolerance plus value:
Definition: cv.hpp:4635
testIdentifiable
void testIdentifiable()
Definition: IOTest.cpp:66
SemiSpecific
SemiSpecific
neither termini must match digestion motif(s)
Definition: Digestion.hpp:120
pwiz::identdata::AnalysisSampleCollection
Implementation of AnalysisSampleCollectionType from mzIdentML schema.
Definition: IdentData.hpp:259
testSpectrumIdentificationProtocol
void testSpectrumIdentificationProtocol()
Definition: IOTest.cpp:476
pwiz::identdata::Inputs::spectraData
std::vector< SpectraDataPtr > spectraData
Definition: IdentData.hpp:948
pwiz::identdata::AnalysisSoftware::URI
std::string URI
Definition: IdentData.hpp:218
pwiz::identdata::AnalysisProtocolCollection::spectrumIdentificationProtocol
std::vector< SpectrumIdentificationProtocolPtr > spectrumIdentificationProtocol
Definition: IdentData.hpp:911
testPeptideEvidence
void testPeptideEvidence()
Definition: IOTest.cpp:644
pwiz::data::CVParam::cvid
CVID cvid
Definition: ParamTypes.hpp:46
pwiz::identdata::ProteinDetection::activityDate
std::string activityDate
Definition: IdentData.hpp:879
pwiz::identdata::AnalysisCollection::proteinDetection
ProteinDetection proteinDetection
Definition: IdentData.hpp:898
pwiz::identdata::SpectrumIdentification::spectrumIdentificationListPtr
SpectrumIdentificationListPtr spectrumIdentificationListPtr
Definition: IdentData.hpp:770
testProteinDetectionList
void testProteinDetectionList()
Definition: IOTest.cpp:770
pwiz::identdata::SearchModification::fixedMod
bool fixedMod
Definition: IdentData.hpp:392
unit_assert
#define unit_assert(x)
Definition: unit.hpp:85
pwiz::identdata::DataCollection::analysisData
AnalysisData analysisData
Definition: IdentData.hpp:977
pwiz::identdata::SubstitutionModification::monoisotopicMassDelta
double monoisotopicMassDelta
Definition: IdentData.hpp:357
testResidue
void testResidue()
Definition: IOTest.cpp:419
pwiz::identdata::Enzymes
Implementation of EnzymesType from the mzIdentML schema.
Definition: IdentData.hpp:432
pwiz::tradata::ContactPtr
boost::shared_ptr< Contact > ContactPtr
Definition: TraData.hpp:57
pwiz::identdata::SpectrumIdentificationList
Implementation of SpectrumIdentificationListType from the mzIdentML schema.
Definition: IdentData.hpp:744
pwiz::identdata::SpectrumIdentificationProtocol::threshold
ParamContainer threshold
Definition: IdentData.hpp:559
MS_Mascot_score
MS_Mascot_score
Mascot:score: The Mascot result 'Score'.
Definition: cv.hpp:3972
testEnzymes
void testEnzymes()
Definition: IOTest.cpp:405
pwiz::identdata::IdentifiableParamContainer
Parent class of all Identifiable objects that have ParamGroups.
Definition: IdentData.hpp:80
pwiz::identdata::SpectrumIdentification
Implementation of SpectrumIdentificationType from the mzIdentML schema.
Definition: IdentData.hpp:765
pwiz::identdata::Identifiable::name
std::string name
Definition: IdentData.hpp:71
pwiz::identdata::Enzyme::cTermGain
std::string cTermGain
Definition: IdentData.hpp:414
MS_DB_filter_on_accession_numbers
MS_DB_filter_on_accession_numbers
DB filter on accession numbers: Filtering applied specifically by accession number pattern.
Definition: cv.hpp:3561
pwiz::identdata::Peptide::substitutionModification
std::vector< SubstitutionModificationPtr > substitutionModification
Definition: IdentData.hpp:375
pwiz::identdata::Sample::contactRole
std::vector< ContactRolePtr > contactRole
Definition: IdentData.hpp:200
pwiz::identdata::IO::read
PWIZ_API_DECL void read(std::istream &is, CV &cv)
pwiz::identdata::AnalysisSoftware::softwareName
ParamContainer softwareName
Definition: IdentData.hpp:223
pwiz::identdata::SpectrumIdentificationItem::peptideEvidencePtr
std::vector< PeptideEvidencePtr > peptideEvidencePtr
Definition: IdentData.hpp:684
pwiz::tradata::PeptidePtr
boost::shared_ptr< Peptide > PeptidePtr
Definition: TraData.hpp:236
pwiz::identdata::Inputs::searchDatabase
std::vector< SearchDatabasePtr > searchDatabase
Definition: IdentData.hpp:947
pwiz::identdata::BibliographicReference::editor
std::string editor
Definition: IdentData.hpp:102
pwiz::identdata::AnalysisSoftware::contactRolePtr
ContactRolePtr contactRolePtr
Definition: IdentData.hpp:222
testIdentifiableParamContainer
void testIdentifiableParamContainer()
Definition: IOTest.cpp:78
pwiz::identdata::AnalysisSoftware::customizations
std::string customizations
Definition: IdentData.hpp:219
pwiz::identdata::ProteinAmbiguityGroup
Implementation of ProteinAmbiguityGroupType from the mzIdentML schema.
Definition: IdentData.hpp:840
testAmbiguousResidue
void testAmbiguousResidue()
Definition: IOTest.cpp:432
pwiz::identdata::Person::affiliations
std::vector< OrganizationPtr > affiliations
Definition: IdentData.hpp:161
pwiz::identdata::SpectrumIdentificationItem::massTablePtr
MassTablePtr massTablePtr
Definition: IdentData.hpp:681