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;
63}
void diff(const string &filename1, const string &filename2)
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition XMLWriter.hpp:48
ostream * os_
Definition IOTest.cpp:38
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)
PWIZ_API_DECL void read(std::istream &is, CV &cv)
Calculate diffs of objects in a ProteoWizard data model hierarchy.
Definition diff_std.hpp:143
#define unit_assert(x)
Definition unit.hpp:85

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

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

◆ testIdentifiable()

void testIdentifiable ( )

Definition at line 66 of file IOTest.cpp.

67{
68 if (os_) *os_ << "testIdentifiable\n" ;
69
71 a.id = "id";
72 a.name = "name";
73
74 testObject(a);
75}
void testObject(const object_type &a)
Definition IOTest.cpp:41
Parent class representing extensions of the IdentifiableType from the mzIdentML schema.
Definition IdentData.hpp:65

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}
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
void set(CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
set/add a CVParam (not recursive)
std::vector< UserParam > userParams
a collection of uncontrolled user terms
Uncontrolled user parameters (essentially allowing free text). Before using these,...
Parent class of all Identifiable objects that have ParamGroups.
Definition IdentData.hpp:80

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}
Information about an ontology or CV source and a short 'lookup' tag to refer to.
Definition cv.hpp:14916
std::string id
the short label to be used as a reference tag with which to refer to this particular Controlled Vocab...
Definition cv.hpp:14918
std::string fullName
the usual name for the resource (e.g. The PSI-MS Controlled Vocabulary).
Definition cv.hpp:14924
std::string URI
the URI for the resource.
Definition cv.hpp:14921
std::string version
the version of the CV from which the referred-to terms are drawn.
Definition cv.hpp:14927

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

Referenced by test().

◆ testBibliographicReference()

void testBibliographicReference ( )

Definition at line 107 of file IOTest.cpp.

108{
109 if (os_) *os_ << "testBibliographicReference\n" ;
110
112
113 br.id = "id";
114 br.authors = "abcd";
115 br.publication = "efg";
116 br.publisher = "hijk";
117 br.editor = "lmnop";
118 br.year = 1984;
119 br.volume = "qrs";
120 br.issue = "tuv";
121 br.pages = "wx";
122 br.title = "yz";
123
124 testObject(br);
125}
Implementation for the BibliographicReferenceType tag in the mzIdentML schema.
Definition IdentData.hpp:96

References pwiz::identdata::BibliographicReference::authors, pwiz::identdata::BibliographicReference::editor, pwiz::identdata::Identifiable::id, pwiz::identdata::BibliographicReference::issue, os_, pwiz::identdata::BibliographicReference::pages, pwiz::identdata::BibliographicReference::publication, pwiz::identdata::BibliographicReference::publisher, testObject(), pwiz::identdata::BibliographicReference::title, pwiz::identdata::BibliographicReference::volume, and pwiz::identdata::BibliographicReference::year.

Referenced by test().

◆ 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");
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}
MS_contact_phone_number
contact phone number: Phone number of the contact person or organization.
Definition cv.hpp:5679
MS_contact_email
contact email: Email address of the contact person or organization.
Definition cv.hpp:2418
MS_contact_fax_number
contact fax number: Fax number for the contact person or organization.
Definition cv.hpp:5682
MS_contact_address
contact address: Postal address of the contact person or organization.
Definition cv.hpp:2412
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
Implementation of AbstractOrganizationType from the mzIdentML schema.
Implementation of PersonType from the mzIdentML schema.
std::vector< OrganizationPtr > affiliations

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");
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}
boost::shared_ptr< Organization > parent

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}
MS_software_vendor
software vendor: Software vendor role.
Definition cv.hpp:4221
boost::shared_ptr< Contact > ContactPtr
Definition TraData.hpp:57
Implementation of ContactType from mzIdentML.
Implementation of ContactRoleType from the mzIdentML schema.

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}
MS_role_type
role type: Role of a Person or Organization.
Definition cv.hpp:4218
Implementation of ProviderType from the mzIdentML schema.
ContactRolePtr contactRolePtr

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}
MS_programmer
programmer: Programmer role.
Definition cv.hpp:4224
MS_septum
septum: A disc composed of a flexible material that seals the entrance to the reservoir....
Definition cv.hpp:483
boost::shared_ptr< Sample > SamplePtr
Definition MSData.hpp:118
Implementation of the SampleType from the mzIdentML schema.
std::vector< boost::shared_ptr< Sample > > subSamples
std::vector< ContactRolePtr > contactRole

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}
MS_Mascot
Mascot: The name of the Mascot search engine.
Definition cv.hpp:4050
Implementation of AnalysisSoftwareType from the mzIdentML schema.

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}
Implementation of AnalysisSampleCollectionType from mzIdentML schema.

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}
MS_protein_description
protein description: The protein description line from the sequence entry in the source database FAST...
Definition cv.hpp:3723
Implementation of DBSequenceType from the mzIdentML schema.
SearchDatabasePtr searchDatabasePtr
Implementation of SearchDatabaseType from the mzIdentML schema.

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}
UNIMOD_Gln__pyro_Glu
Gln->pyro-Glu: Pyro-glu from Q.
Definition cv.hpp:9435
Implementation of ModificationType from the mzIdentML schema.
std::vector< char > residues

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}
MS_peptide
peptide: A compound of low molecular weight that is composed of two or more amino acids.
Definition cv.hpp:3276
Implementation of PeptideType from the mzIdentML schema.
std::vector< ModificationPtr > modification
std::vector< SubstitutionModificationPtr > substitutionModification

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}
boost::shared_ptr< Peptide > PeptidePtr
Definition TraData.hpp:236
Implementation of PeptideEvidenceType from the mzIdentML schema.
Implementation of SequenceCollectionType from the mzIdentML schema.
std::vector< DBSequencePtr > dbSequences
std::vector< PeptideEvidencePtr > peptideEvidence
std::vector< PeptidePtr > peptides

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}
Implementation of SpectraDataType from the mzIdentML schema.
Implementation of SpectrumIdentificationType from the mzIdentML schema.
std::vector< SpectraDataPtr > inputSpectra
SpectrumIdentificationListPtr spectrumIdentificationListPtr
std::vector< SearchDatabasePtr > searchDatabase
SpectrumIdentificationProtocolPtr spectrumIdentificationProtocolPtr
Implementation of SpectrumIdentificationListType from the mzIdentML schema.
Implementation of SpectrumIdentificationProtocolType from the mzIdentML schema.

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}
Implementation of ProteinDetectionType from the mzIdentML schema.
ProteinDetectionProtocolPtr proteinDetectionProtocolPtr
ProteinDetectionListPtr proteinDetectionListPtr
Implementation of ProteinDetectionListType from the mzIdentML schema.
Implementation of ProteinDetectionProtocolType from the mzIdentML schema.

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);
363
364 testObject(a);
365}
Implementation of AnalysisCollectionType from the mzIdentML schema.
std::vector< SpectrumIdentificationPtr > spectrumIdentification

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

Referenced by test().

◆ testSearchModification()

void testSearchModification ( )

Definition at line 368 of file IOTest.cpp.

369{
370 if (os_) *os_ << "testSearchModification\n" ;
371
373
374 a.fixedMod = true;
375 a.massDelta = 3.14;
376 a.residues.push_back('Q');
377 a.residues.push_back('E');
380
381 testObject(a);
382}
MS_modification_specificity_peptide_N_term
modification specificity peptide N-term: As parameter for search engine: apply the modification only ...
Definition cv.hpp:4002
Implementation of SearchModificationType from the mzIdentML schema.

References pwiz::data::CVParam::cvid, pwiz::identdata::SearchModification::fixedMod, pwiz::identdata::SearchModification::massDelta, MS_modification_specificity_peptide_N_term, os_, pwiz::identdata::SearchModification::residues, pwiz::data::ParamContainer::set(), pwiz::identdata::SearchModification::specificityRules, testObject(), and UNIMOD_Gln__pyro_Glu.

Referenced by test().

◆ testEnzyme()

void testEnzyme ( )

Definition at line 385 of file IOTest.cpp.

386{
387 if (os_) *os_ << "testEnzyme\n" ;
388
389 Enzyme a;
390
391 a.id = "id";
392 a.nTermGain = "n";
393 a.cTermGain = "c";
394 a.terminalSpecificity = proteome::Digestion::SemiSpecific;
395 a.missedCleavages = 1;
396 a.minDistance = 2;
397
398 a.siteRegexp = "tyrannosaurus regex";
400
401 testObject(a);
402}
MS_Trypsin
Trypsin: Enzyme trypsin.
Definition cv.hpp:4179
Implementation of EnzymeType from the mzIdentML schema.
proteome::Digestion::Specificity terminalSpecificity
ParamContainer enzymeName

References pwiz::identdata::Enzyme::cTermGain, pwiz::identdata::Enzyme::enzymeName, pwiz::identdata::Identifiable::id, pwiz::identdata::Enzyme::minDistance, pwiz::identdata::Enzyme::missedCleavages, MS_Trypsin, pwiz::identdata::Enzyme::nTermGain, os_, pwiz::data::ParamContainer::set(), pwiz::identdata::Enzyme::siteRegexp, pwiz::identdata::Enzyme::terminalSpecificity, and testObject().

Referenced by test().

◆ 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}
Implementation of EnzymesType from the mzIdentML schema.
std::vector< EnzymePtr > enzymes
boost::logic::tribool independent

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}
Implementation of ResidueType from the mzIdentML schema.

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}
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
Implementation of AmbiguousResidueType from the mzIdentML schema.

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}
Implementation of MassTableType from the mzIdentML schema.
std::vector< ResiduePtr > residues
std::vector< AmbiguousResiduePtr > ambiguousResidue
std::vector< int > msLevel

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 ( )

Definition at line 464 of file IOTest.cpp.

465{
466 Filter a;
467
471
472 testObject(a);
473}
MS_DB_MW_filter
DB MW filter: Filtering applied specifically by protein molecular weight, specified as either a range...
Definition cv.hpp:3564
MS_DB_filter_on_accession_numbers
DB filter on accession numbers: Filtering applied specifically by accession number pattern.
Definition cv.hpp:3561
MS_DB_filter_taxonomy
DB filter taxonomy: A taxonomy filter was to the database search.
Definition cv.hpp:3558
Implementation of FilterType from the mzIdentML schema.
ParamContainer exclude
ParamContainer filterType
ParamContainer include

References pwiz::identdata::Filter::exclude, pwiz::identdata::Filter::filterType, pwiz::identdata::Filter::include, MS_DB_filter_on_accession_numbers, MS_DB_filter_taxonomy, MS_DB_MW_filter, pwiz::data::ParamContainer::set(), and testObject().

Referenced by test().

◆ 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}
MS_parent_mass_type_mono
parent mass type mono: Mass type setting for parent mass was monoisotopic.
Definition cv.hpp:4062
MS_ms_ms_search
ms-ms search: An MS2 search (with fragment ions).
Definition cv.hpp:3708
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
MS_Mascot_SigThreshold
Mascot:SigThreshold: Significance threshold below which the p-value of a peptide match must lie to be...
Definition cv.hpp:4359
MS_search_tolerance_plus_value
search tolerance plus value:
Definition cv.hpp:4635
std::vector< SearchModificationPtr > modificationParams

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}
Implementation of AnalysisProtocolCollectionType from the mzIdentML schema.
std::vector< ProteinDetectionProtocolPtr > proteinDetectionProtocol
std::vector< SpectrumIdentificationProtocolPtr > spectrumIdentificationProtocol

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

Referenced by test().

◆ testSpectraData()

void testSpectraData ( )

Definition at line 533 of file IOTest.cpp.

534{
535 SpectraData a;
536
537 a.id = "id";
538
539 a.location = "here";
540 a.externalFormatDocumentation.push_back("there");
542
543 testObject(a);
544}
MS_mzML_format
mzML format: Proteomics Standards Inititative mzML file format.
Definition cv.hpp:2403
std::vector< std::string > externalFormatDocumentation

References pwiz::data::CVParam::cvid, pwiz::identdata::SpectraData::externalFormatDocumentation, pwiz::identdata::SpectraData::fileFormat, pwiz::identdata::Identifiable::id, pwiz::identdata::SpectraData::location, MS_mzML_format, and testObject().

Referenced by test().

◆ testSearchDatabase()

void testSearchDatabase ( )

Definition at line 547 of file IOTest.cpp.

548{
550
551 a.id = "id";
552 a.location = "here";
553
554 a.version = "1.01a";
555 a.releaseDate="now";
557 a.numResidues = 2;
558
560 a.databaseName.userParams.push_back(UserParam("5peptideMix_20090515.fasta"));
561
562 testObject(a);
563}
MS_FASTA_format
FASTA format: The sequence database was stored in the FASTA format.
Definition cv.hpp:4452

References pwiz::data::CVParam::cvid, pwiz::identdata::SearchDatabase::databaseName, pwiz::identdata::SearchDatabase::fileFormat, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::SearchDatabase::location, MS_FASTA_format, pwiz::identdata::SearchDatabase::numDatabaseSequences, pwiz::identdata::SearchDatabase::numResidues, pwiz::identdata::SearchDatabase::releaseDate, testObject(), pwiz::data::ParamContainer::userParams, and pwiz::identdata::SearchDatabase::version.

Referenced by test().

◆ testSourceFile()

void testSourceFile ( )

Definition at line 566 of file IOTest.cpp.

567{
568 SourceFile a;
569
570 a.id = "id";
571
572 a.location = "there";
574 a.externalFormatDocumentation.push_back("somewhere else");
576
577 testObject(a);
578}
MS_Mascot_DAT_format
Mascot DAT format: Source file for this mzIdentML was in Mascot DAT file format.
Definition cv.hpp:4032
Implementation of SourceFileType from the mzIdentML schema.
std::vector< std::string > externalFormatDocumentation

References pwiz::data::CVParam::cvid, pwiz::identdata::SourceFile::externalFormatDocumentation, pwiz::identdata::SourceFile::fileFormat, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::SourceFile::location, MS_Mascot_DAT_format, MS_mzML_format, pwiz::data::ParamContainer::set(), and testObject().

Referenced by test().

◆ 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}
boost::shared_ptr< SourceFile > SourceFilePtr
Description of the source file, including location and type.
Definition MSData.hpp:76
Implementation of the InputsType from the mzIdentML schema.
std::vector< SourceFilePtr > sourceFile
std::vector< SearchDatabasePtr > searchDatabase
std::vector< SpectraDataPtr > spectraData

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}
MS_product_ion_m_z
product ion m/z: The m/z of the product ion.
Definition cv.hpp:4101
Implementation of MeasureType from the mzIdentML schema.

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{
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}
Implementation of FragmentArrayType from the mzIdentML schema.
std::vector< double > values

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
637 FragmentArrayPtr b(new FragmentArray());
638 a.fragmentArray.push_back(b);
639
640 testObject(a);
641}
MS_frag__a_ion
frag: a ion: Fragmentation information, type of product: a ion.
Definition cv.hpp:4119
Implementation of IonTypeType from the mzIdentML schema.
std::vector< int > index
std::vector< FragmentArrayPtr > fragmentArray

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 ( )

Definition at line 644 of file IOTest.cpp.

645{
647
648 a.id = "id";
649 a.dbSequencePtr = DBSequencePtr(new DBSequence("dbs_ref"));
650 a.start = 1;
651 a.end = 2;
652 a.pre = 'A';
653 a.post = 'C';
654 a.translationTablePtr = TranslationTablePtr(new TranslationTable("tranny_ref"));
655 a.frame = 3;
656 a.isDecoy = true;
657
658 a.set(MS_Mascot_score, "15.71");
659
660 testObject(a);
661}
MS_Mascot_score
Mascot:score: The Mascot result 'Score'.
Definition cv.hpp:3972
TranslationTablePtr translationTablePtr
Implementation of TranslationTableType from the mzIdentML schema.

References pwiz::identdata::PeptideEvidence::dbSequencePtr, pwiz::identdata::PeptideEvidence::end, pwiz::identdata::PeptideEvidence::frame, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::PeptideEvidence::isDecoy, MS_Mascot_score, pwiz::identdata::PeptideEvidence::post, pwiz::identdata::PeptideEvidence::pre, pwiz::data::ParamContainer::set(), pwiz::identdata::PeptideEvidence::start, testObject(), and pwiz::identdata::PeptideEvidence::translationTablePtr.

Referenced by test().

◆ testSpectrumIdentificationItem()

void testSpectrumIdentificationItem ( )

Definition at line 664 of file IOTest.cpp.

665{
667
668 a.id = "id";
669
670 a.chargeState = 1;
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}
Implementation of SpectrumIdentificationItemType from the mzIdentML schema.
std::vector< PeptideEvidencePtr > peptideEvidencePtr
std::vector< IonTypePtr > fragmentation

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}
Implementation of SpectrumIdentificationResultType from the mzIdentML schema.
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItem

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}
Implementation of PeptideHypothesisType from the mzIdentML schema.
PeptideEvidencePtr peptideEvidencePtr
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItemPtr

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}
Implementation of ProteinAmbiguityGroupType from the mzIdentML schema.
std::vector< ProteinDetectionHypothesisPtr > proteinDetectionHypothesis

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";
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}
std::vector< SpectrumIdentificationResultPtr > spectrumIdentificationResult
std::vector< MeasurePtr > fragmentationTable

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}
std::vector< ProteinAmbiguityGroupPtr > proteinAmbiguityGroup

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"));
795
796 testObject(a);
797}
Implementation of AnalysisDataType from the mzIdentML schema.
std::vector< SpectrumIdentificationListPtr > spectrumIdentificationList
ProteinDetectionListPtr proteinDetectionListPtr

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{
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}
Implementation of DataCollectionType from the mzIdentML schema.

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());
837 IO::read(iss, b, 0, IO::IgnoreSequenceCollection, IO::IgnoreAnalysisData);
838
839 // clear the original SequenceCollection
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
854 if (diff && os_) *os_ << "diff:\n" << diff << endl;
856 }
857}
PWIZ_API_DECL void initializeTiny(IdentData &mzid)
Implementation of the MzIdentMLType from the mzIdentML schema.
SequenceCollection sequenceCollection
AnalysisCollection analysisCollection

References pwiz::identdata::IdentData::analysisCollection, pwiz::identdata::DataCollection::analysisData, pwiz::identdata::IdentData::dataCollection, pwiz::identdata::SequenceCollection::dbSequences, diff(), 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.

861{
862 testCV();
866 testPerson();
869 testProvider();
870 testSample();
875 testPeptide();
881 testEnzyme();
882 testEnzymes();
883 testResidue();
886 testFilter();
893 testInputs();
894 testMeasure();
896 testIonType();
907}
void testSearchDatabase()
Definition IOTest.cpp:547
void testContactRole()
Definition IOTest.cpp:168
void testSpectraData()
Definition IOTest.cpp:533
void testSearchModification()
Definition IOTest.cpp:368
void testEnzyme()
Definition IOTest.cpp:385
void testIdentifiable()
Definition IOTest.cpp:66
void testInputs()
Definition IOTest.cpp:581
void testSample()
Definition IOTest.cpp:193
void testSourceFile()
Definition IOTest.cpp:566
void testOrganization()
Definition IOTest.cpp:150
void testSubstitutionModification()
Definition IOTest.cpp:272
void testAnalysisData()
Definition IOTest.cpp:784
void testAmbiguousResidue()
Definition IOTest.cpp:432
void testProteinDetectionHypothesis()
Definition IOTest.cpp:722
void testDBSequence()
Definition IOTest.cpp:240
void testSpectrumIdentificationResult()
Definition IOTest.cpp:691
void testProteinDetectionList()
Definition IOTest.cpp:770
void testPerson()
Definition IOTest.cpp:128
void testDataCollection()
Definition IOTest.cpp:800
void testPeptide()
Definition IOTest.cpp:286
void testProteinDetectionProtocol()
Definition IOTest.cpp:503
void testFilter()
Definition IOTest.cpp:464
void testBibliographicReference()
Definition IOTest.cpp:107
void testCV()
Definition IOTest.cpp:93
void testSpectrumIdentificationProtocol()
Definition IOTest.cpp:476
void testIonType()
Definition IOTest.cpp:626
void testIdentifiableParamContainer()
Definition IOTest.cpp:78
void testFragmentArray()
Definition IOTest.cpp:612
void testEnzymes()
Definition IOTest.cpp:405
void testIdentData()
Definition IOTest.cpp:816
void testProvider()
Definition IOTest.cpp:180
void testModification()
Definition IOTest.cpp:256
void testSpectrumIdentificationItem()
Definition IOTest.cpp:664
void testAnalysisCollection()
Definition IOTest.cpp:353
void testSpectrumIdentification()
Definition IOTest.cpp:320
void testProteinAmbiguityGroup()
Definition IOTest.cpp:736
void testSequenceCollection()
Definition IOTest.cpp:308
void testResidue()
Definition IOTest.cpp:419
void testPeptideEvidence()
Definition IOTest.cpp:644
void testMassTable()
Definition IOTest.cpp:445
void testProteinDetection()
Definition IOTest.cpp:337
void testAnalysisProtocolCollection()
Definition IOTest.cpp:517
void testSpectrumIdentificationList()
Definition IOTest.cpp:750
void testAnalysisSoftware()
Definition IOTest.cpp:210
void testMeasure()
Definition IOTest.cpp:601

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}
void test()
Definition IOTest.cpp:860
#define TEST_PROLOG_EX(argc, argv, suffix)
Definition unit.hpp:157
#define TEST_EPILOG
Definition unit.hpp:183
#define TEST_FAILED(x)
Definition unit.hpp:177

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

Variable Documentation

◆ os_

ostream* os_ = 0