ProteoWizard
IOTest.cpp
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1 //
2 // $Id$
3 //
4 //
5 // Original author: Robert Burke <robert.burke@proteowizard.org>
6 //
7 // Copyright 2009 Spielberg Family Center for Applied Proteomics
8 // University of Southern California, Los Angeles, California 90033
9 //
10 // Licensed under the Apache License, Version 2.0 (the "License");
11 // you may not use this file except in compliance with the License.
12 // You may obtain a copy of the License at
13 //
14 // http://www.apache.org/licenses/LICENSE-2.0
15 //
16 // Unless required by applicable law or agreed to in writing, software
17 // distributed under the License is distributed on an "AS IS" BASIS,
18 // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
19 // See the License for the specific language governing permissions and
20 // limitations under the License.
21 //
22 
23 
24 #include "IO.hpp"
25 #include "Diff.hpp"
26 #include "TextWriter.hpp"
27 #include "examples.hpp"
30 
31 using namespace pwiz::util;
32 using namespace pwiz::minimxml;
33 using namespace pwiz::cv;
34 using namespace pwiz::identdata;
35 namespace proteome = pwiz::proteome;
36 using boost::iostreams::stream_offset;
37 
38 ostream* os_ = 0;
39 
40 template <typename object_type>
41 void testObject(const object_type& a)
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 }
64 
65 
67 {
68  if (os_) *os_ << "testIdentifiable\n" ;
69 
70  Identifiable a;
71  a.id = "id";
72  a.name = "name";
73 
74  testObject(a);
75 }
76 
77 
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 }
91 
92 
93 void testCV()
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 }
105 
106 
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 }
126 
127 
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 }
148 
149 
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 }
166 
167 
169 {
170  if (os_) *os_ << "testContactRole\n" ;
171 
172  ContactRole a;
173  a.contactPtr = ContactPtr(new Contact("ref"));
175 
176  testObject(a);
177 }
178 
179 
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 }
191 
192 
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 }
208 
209 
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 }
226 
227 
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 }
238 
239 
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 }
254 
255 
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 }
270 
271 
273 {
275 
276  a.originalResidue = 'L';
277  a.replacementResidue = 'V';
278  a.location = 1;
279  a.avgMassDelta = 2.;
280  a.monoisotopicMassDelta = 3.;
281 
282  testObject(a);
283 }
284 
285 
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 }
306 
307 
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 }
318 
319 
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 }
335 
336 
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 }
351 
352 
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 }
366 
367 
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 }
383 
384 
386 {
387  if (os_) *os_ << "testEnzyme\n" ;
388 
389  Enzyme a;
390 
391  a.id = "id";
392  a.nTermGain = "n";
393  a.cTermGain = "c";
395  a.missedCleavages = 1;
396  a.minDistance = 2;
397 
398  a.siteRegexp = "tyrannosaurus regex";
400 
401  testObject(a);
402 }
403 
404 
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 }
417 
418 
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 }
430 
431 
433 {
434  if (os_) *os_ << "testAmbiguousResidue\n" ;
435 
437 
438  a.code = 'B';
440 
441  testObject(a);
442 }
443 
444 
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 }
462 
463 
465 {
466  Filter a;
467 
471 
472  testObject(a);
473 }
474 
475 
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 }
501 
502 
504 {
506 
507  a.id = "id";
508  a.id="PDP_MascotParser_1";
509  a.analysisSoftwarePtr = AnalysisSoftwarePtr(new AnalysisSoftware("ref"));
512 
513  testObject(a);
514 }
515 
516 
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 }
531 
532 
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 }
545 
546 
548 {
549  SearchDatabase a;
550 
551  a.id = "id";
552  a.location = "here";
553 
554  a.version = "1.01a";
555  a.releaseDate="now";
556  a.numDatabaseSequences = 1;
557  a.numResidues = 2;
558 
560  a.databaseName.userParams.push_back(UserParam("5peptideMix_20090515.fasta"));
561 
562  testObject(a);
563 }
564 
565 
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 }
579 
580 
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 }
599 
600 
602 {
603  Measure a;
604 
605  a.id = "id";
607 
608  testObject(a);
609 }
610 
611 
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 }
624 
625 
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 }
642 
643 
645 {
646  PeptideEvidence a;
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 }
662 
663 
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 }
689 
690 
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 }
708 
709 
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 }
720 
721 
723 {
725 
726  a.id = "id";
727  a.dbSequencePtr = DBSequencePtr(new DBSequence("dbs_ref"));
728  a.passThreshold = "pt";
730  a.set(MS_Mascot_score, "164.4");
731 
732  testObject(a);
733 }
734 
735 
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 }
748 
749 
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 }
768 
769 
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 }
782 
783 
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 }
798 
799 
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 }
814 
815 
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();
850 
851  // compare 'a' and 'b'
852 
854  if (diff && os_) *os_ << "diff:\n" << diff << endl;
855  unit_assert(!diff);
856  }
857 }
858 
859 
860 void test()
861 {
862  testCV();
866  testPerson();
868  testContactRole();
869  testProvider();
870  testSample();
872  testDBSequence();
875  testPeptide();
881  testEnzyme();
882  testEnzymes();
883  testResidue();
885  testMassTable();
886  testFilter();
890  testSpectraData();
892  testSourceFile();
893  testInputs();
894  testMeasure();
896  testIonType();
906  testIdentData();
907 }
908 
909 
910 int main(int argc, char* argv[])
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 }
931 
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
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
pwiz::cv
Definition: cv.hpp:108
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
TextWriter.hpp
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::proteome
Definition: AminoAcid.hpp:35
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
Definition: DefaultReaderList.hpp:33
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::util
Definition: almost_equal.hpp:33
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
examples.hpp
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
Std.hpp
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::minimxml
Definition: SAXParser.hpp:43
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
pwiz::identdata::IdentData::dataCollection
DataCollection dataCollection
Definition: IdentData.hpp:1020
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
main
int main(int argc, char *argv[])
Definition: IOTest.cpp:910
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
Diff.hpp
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
unit.hpp
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
IO.hpp
testIdentifiableParamContainer
void testIdentifiableParamContainer()
Definition: IOTest.cpp:78
pwiz::identdata::AnalysisSoftware::customizations
std::string customizations
Definition: IdentData.hpp:219
testAnalysisSampleCollection
void testAnalysisSampleCollection()
Definition: IOTest.cpp:228
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