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
31using namespace pwiz::util;
32using namespace pwiz::minimxml;
33using namespace pwiz::cv;
34using namespace pwiz::identdata;
35namespace proteome = pwiz::proteome;
36using boost::iostreams::stream_offset;
37
38ostream* os_ = 0;
39
40template <typename object_type>
41void 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;
63}
64
65
67{
68 if (os_) *os_ << "testIdentifiable\n" ;
69
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
93void 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");
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");
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.;
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);
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";
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}
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
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{
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}
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{
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
637 FragmentArrayPtr b(new FragmentArray());
638 a.fragmentArray.push_back(b);
639
640 testObject(a);
641}
642
643
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}
662
663
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}
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";
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"));
795
796 testObject(a);
797}
798
799
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}
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());
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();
850
851 // compare 'a' and 'b'
852
854 if (diff && os_) *os_ << "diff:\n" << diff << endl;
856 }
857}
858
859
908
909
910int 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
void diff(const string &filename1, const string &filename2)
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition XMLWriter.hpp:48
MS_programmer
programmer: Programmer role.
Definition cv.hpp:4224
MS_Trypsin
Trypsin: Enzyme trypsin.
Definition cv.hpp:4179
MS_FASTA_format
FASTA format: The sequence database was stored in the FASTA format.
Definition cv.hpp:4452
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
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
MS_DB_MW_filter
DB MW filter: Filtering applied specifically by protein molecular weight, specified as either a range...
Definition cv.hpp:3564
MS_parent_mass_type_mono
parent mass type mono: Mass type setting for parent mass was monoisotopic.
Definition cv.hpp:4062
MS_product_ion_m_z
product ion m/z: The m/z of the product ion.
Definition cv.hpp:4101
MS_ms_ms_search
ms-ms search: An MS2 search (with fragment ions).
Definition cv.hpp:3708
MS_mzML_format
mzML format: Proteomics Standards Inititative mzML file format.
Definition cv.hpp:2403
MS_contact_phone_number
contact phone number: Phone number of the contact person or organization.
Definition cv.hpp:5679
UNIMOD_Gln__pyro_Glu
Gln->pyro-Glu: Pyro-glu from Q.
Definition cv.hpp:9435
MS_Mascot_DAT_format
Mascot DAT format: Source file for this mzIdentML was in Mascot DAT file format.
Definition cv.hpp:4032
MS_DB_filter_on_accession_numbers
DB filter on accession numbers: Filtering applied specifically by accession number pattern.
Definition cv.hpp:3561
CVID_Unknown
Definition cv.hpp:114
MS_modification_specificity_peptide_N_term
modification specificity peptide N-term: As parameter for search engine: apply the modification only ...
Definition cv.hpp:4002
MS_septum
septum: A disc composed of a flexible material that seals the entrance to the reservoir....
Definition cv.hpp:483
MS_DB_filter_taxonomy
DB filter taxonomy: A taxonomy filter was to the database search.
Definition cv.hpp:3558
MS_Mascot
Mascot: The name of the Mascot search engine.
Definition cv.hpp:4050
MS_contact_email
contact email: Email address of the contact person or organization.
Definition cv.hpp:2418
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_software_vendor
software vendor: Software vendor role.
Definition cv.hpp:4221
MS_contact_fax_number
contact fax number: Fax number for the contact person or organization.
Definition cv.hpp:5682
MS_Mascot_score
Mascot:score: The Mascot result 'Score'.
Definition cv.hpp:3972
MS_frag__a_ion
frag: a ion: Fragmentation information, type of product: a ion.
Definition cv.hpp:4119
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
MS_peptide
peptide: A compound of low molecular weight that is composed of two or more amino acids.
Definition cv.hpp:3276
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
MS_protein_description
protein description: The protein description line from the sequence entry in the source database FAST...
Definition cv.hpp:3723
MS_role_type
role type: Role of a Person or Organization.
Definition cv.hpp:4218
void testSearchDatabase()
Definition IOTest.cpp:547
void testContactRole()
Definition IOTest.cpp:168
void testSpectraData()
Definition IOTest.cpp:533
int main(int argc, char *argv[])
Definition IOTest.cpp:910
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
PeptideHypothesis testPeptideHypothesis()
Definition IOTest.cpp:710
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 testObject(const object_type &a)
Definition IOTest.cpp:41
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
ostream * os_
Definition IOTest.cpp:38
void testModification()
Definition IOTest.cpp:256
void testSpectrumIdentificationItem()
Definition IOTest.cpp:664
void test()
Definition IOTest.cpp:860
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 testAnalysisSampleCollection()
Definition IOTest.cpp:228
void testAnalysisProtocolCollection()
Definition IOTest.cpp:517
void testSpectrumIdentificationList()
Definition IOTest.cpp:750
void testAnalysisSoftware()
Definition IOTest.cpp:210
void testMeasure()
Definition IOTest.cpp:601
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)
PWIZ_API_DECL void read(std::istream &is, CV &cv)
PWIZ_API_DECL void initializeTiny(IdentData &mzid)
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
Calculate diffs of objects in a ProteoWizard data model hierarchy.
Definition diff_std.hpp:143
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,...
Implementation of AmbiguousResidueType from the mzIdentML schema.
Implementation of AnalysisCollectionType from the mzIdentML schema.
std::vector< SpectrumIdentificationPtr > spectrumIdentification
Implementation of AnalysisDataType from the mzIdentML schema.
std::vector< SpectrumIdentificationListPtr > spectrumIdentificationList
ProteinDetectionListPtr proteinDetectionListPtr
Implementation of AnalysisProtocolCollectionType from the mzIdentML schema.
std::vector< ProteinDetectionProtocolPtr > proteinDetectionProtocol
std::vector< SpectrumIdentificationProtocolPtr > spectrumIdentificationProtocol
Implementation of AnalysisSampleCollectionType from mzIdentML schema.
Implementation of AnalysisSoftwareType from the mzIdentML schema.
Implementation for the BibliographicReferenceType tag in the mzIdentML schema.
Definition IdentData.hpp:96
Implementation of ContactType from mzIdentML.
Implementation of ContactRoleType from the mzIdentML schema.
Implementation of DBSequenceType from the mzIdentML schema.
SearchDatabasePtr searchDatabasePtr
Implementation of DataCollectionType from the mzIdentML schema.
Implementation of EnzymeType from the mzIdentML schema.
proteome::Digestion::Specificity terminalSpecificity
ParamContainer enzymeName
Implementation of EnzymesType from the mzIdentML schema.
std::vector< EnzymePtr > enzymes
boost::logic::tribool independent
Implementation of FilterType from the mzIdentML schema.
ParamContainer exclude
ParamContainer filterType
ParamContainer include
Implementation of FragmentArrayType from the mzIdentML schema.
std::vector< double > values
Implementation of the MzIdentMLType from the mzIdentML schema.
SequenceCollection sequenceCollection
DataCollection dataCollection
AnalysisCollection analysisCollection
Parent class representing extensions of the IdentifiableType from the mzIdentML schema.
Definition IdentData.hpp:65
Parent class of all Identifiable objects that have ParamGroups.
Definition IdentData.hpp:80
Implementation of the InputsType from the mzIdentML schema.
std::vector< SourceFilePtr > sourceFile
std::vector< SearchDatabasePtr > searchDatabase
std::vector< SpectraDataPtr > spectraData
Implementation of IonTypeType from the mzIdentML schema.
std::vector< int > index
std::vector< FragmentArrayPtr > fragmentArray
Implementation of MassTableType from the mzIdentML schema.
std::vector< ResiduePtr > residues
std::vector< AmbiguousResiduePtr > ambiguousResidue
std::vector< int > msLevel
Implementation of MeasureType from the mzIdentML schema.
Implementation of ModificationType from the mzIdentML schema.
std::vector< char > residues
Implementation of AbstractOrganizationType from the mzIdentML schema.
boost::shared_ptr< Organization > parent
Implementation of PeptideEvidenceType from the mzIdentML schema.
TranslationTablePtr translationTablePtr
Implementation of PeptideType from the mzIdentML schema.
std::vector< ModificationPtr > modification
std::vector< SubstitutionModificationPtr > substitutionModification
Implementation of PeptideHypothesisType from the mzIdentML schema.
PeptideEvidencePtr peptideEvidencePtr
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItemPtr
Implementation of PersonType from the mzIdentML schema.
std::vector< OrganizationPtr > affiliations
Implementation of ProteinAmbiguityGroupType from the mzIdentML schema.
std::vector< ProteinDetectionHypothesisPtr > proteinDetectionHypothesis
Implementation of ProteinDetectionType from the mzIdentML schema.
ProteinDetectionProtocolPtr proteinDetectionProtocolPtr
ProteinDetectionListPtr proteinDetectionListPtr
Implementation of ProteinDetectionHypothesisType from the mzIdentML schema.
std::vector< PeptideHypothesis > peptideHypothesis
Implementation of ProteinDetectionListType from the mzIdentML schema.
std::vector< ProteinAmbiguityGroupPtr > proteinAmbiguityGroup
Implementation of ProteinDetectionProtocolType from the mzIdentML schema.
Implementation of ProviderType from the mzIdentML schema.
ContactRolePtr contactRolePtr
Implementation of ResidueType from the mzIdentML schema.
Implementation of the SampleType from the mzIdentML schema.
std::vector< boost::shared_ptr< Sample > > subSamples
std::vector< ContactRolePtr > contactRole
Implementation of SearchDatabaseType from the mzIdentML schema.
Implementation of SearchModificationType from the mzIdentML schema.
Implementation of SequenceCollectionType from the mzIdentML schema.
std::vector< DBSequencePtr > dbSequences
std::vector< PeptideEvidencePtr > peptideEvidence
std::vector< PeptidePtr > peptides
Implementation of SourceFileType from the mzIdentML schema.
std::vector< std::string > externalFormatDocumentation
Implementation of SpectraDataType from the mzIdentML schema.
std::vector< std::string > externalFormatDocumentation
Implementation of SpectrumIdentificationType from the mzIdentML schema.
std::vector< SpectraDataPtr > inputSpectra
SpectrumIdentificationListPtr spectrumIdentificationListPtr
std::vector< SearchDatabasePtr > searchDatabase
SpectrumIdentificationProtocolPtr spectrumIdentificationProtocolPtr
Implementation of SpectrumIdentificationItemType from the mzIdentML schema.
std::vector< PeptideEvidencePtr > peptideEvidencePtr
std::vector< IonTypePtr > fragmentation
Implementation of SpectrumIdentificationListType from the mzIdentML schema.
std::vector< SpectrumIdentificationResultPtr > spectrumIdentificationResult
std::vector< MeasurePtr > fragmentationTable
Implementation of SpectrumIdentificationProtocolType from the mzIdentML schema.
std::vector< SearchModificationPtr > modificationParams
Implementation of SpectrumIdentificationResultType from the mzIdentML schema.
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItem
Implementation of SubstitutionModificationType from the mzIdentML schema.
Implementation of TranslationTableType from the mzIdentML schema.
#define unit_assert(x)
Definition unit.hpp:85
#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