ProteoWizard
Diff.hpp
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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#ifndef _MSIDDATA_DIFF_HPP_
25#define _MSIDDATA_DIFF_HPP_
26
28#include "IdentData.hpp"
29
30namespace pwiz { namespace identdata { struct DiffConfig; } }
31
32
33namespace pwiz {
34namespace data {
35namespace diff_impl {
36
37using namespace identdata;
38
40void diff(const FragmentArray& a,
41 const FragmentArray& b,
42 FragmentArray& a_b,
43 FragmentArray& b_a,
44 const DiffConfig& config);
45
47void diff(const IonType& a,
48 const IonType& b,
49 IonType& a_b,
50 IonType& b_a,
51 const DiffConfig& config);
52
54void diff(const Measure& a,
55 const Measure& b,
56 Measure& a_b,
57 Measure& b_a,
58 const DiffConfig& config);
59
61void diff(const PeptideEvidence& a,
62 const PeptideEvidence& b,
63 PeptideEvidence& a_b,
64 PeptideEvidence& b_a,
65 const DiffConfig& config);
66
69 const ProteinAmbiguityGroup& b,
72 const DiffConfig& config);
73
75void diff(const PeptideHypothesis& a,
76 const PeptideHypothesis& b,
79 const DiffConfig& config);
80
86 const DiffConfig& config);
87
89void diff(const DataCollection& a,
90 const DataCollection& b,
91 DataCollection& a_b,
92 DataCollection& b_a,
93 const DiffConfig& config);
94
96void diff(const SpectrumIdentificationListPtr a,
97 const SpectrumIdentificationListPtr b,
98 SpectrumIdentificationListPtr a_b,
99 SpectrumIdentificationListPtr b_a,
100 const DiffConfig& config);
101
107 const DiffConfig& config);
108
111 const ProteinDetectionList& b,
114 const DiffConfig& config);
115
117void diff(const AnalysisData& a,
118 const AnalysisData& b,
119 AnalysisData& a_b,
120 AnalysisData& b_a,
121 const DiffConfig& config);
122
124void diff(const SearchDatabase& a,
125 const SearchDatabase& b,
126 SearchDatabase& a_b,
127 SearchDatabase& b_a,
128 const DiffConfig& config);
129
131void diff(const SpectraData& a,
132 const SpectraData& b,
133 SpectraData& a_b,
134 SpectraData& b_a,
135 const DiffConfig& config);
136
138void diff(const SourceFile& a,
139 const SourceFile& b,
140 SourceFile& a_b,
141 SourceFile& b_a,
142 const DiffConfig& config);
143
145void diff(const Inputs& a,
146 const Inputs& b,
147 Inputs& a_b,
148 Inputs& b_a,
149 const DiffConfig& config);
150
152void diff(const Enzyme& a,
153 const Enzyme& b,
154 Enzyme& a_b,
155 Enzyme& b_a,
156 const DiffConfig& config);
157
159void diff(const Enzymes& a,
160 const Enzymes& b,
161 Enzymes& a_b,
162 Enzymes& b_a,
163 const DiffConfig& config);
164
166void diff(const MassTable& a,
167 const MassTable& b,
168 MassTable& a_b,
169 MassTable& b_a,
170 const DiffConfig& config);
171
173void diff(const Residue& a,
174 const Residue& b,
175 Residue& a_b,
176 Residue& b_a,
177 const DiffConfig& config);
178
180void diff(const AmbiguousResidue& a,
181 const AmbiguousResidue& b,
182 AmbiguousResidue& a_b,
183 AmbiguousResidue& b_a,
184 const DiffConfig& config);
185
187void diff(const Filter& a,
188 const Filter& b,
189 Filter& a_b,
190 Filter& b_a,
191 const DiffConfig& config);
192
195 const DatabaseTranslation& b,
198 const DiffConfig& config);
199
205 const DiffConfig& config);
206
212 const DiffConfig& config);
213
219 const DiffConfig& config);
220
222void diff(const Contact& a,
223 const Contact& b,
224 Contact& a_b,
225 Contact& b_a,
226 const DiffConfig& config);
227
229void diff(const Person& a,
230 const Person& b,
231 Person& a_b,
232 Person& b_a,
233 const DiffConfig& config);
234
236void diff(const Organization& a,
237 const Organization& b,
238 Organization& a_b,
239 Organization& b_a,
240 const DiffConfig& config);
241
244 const BibliographicReference& b,
247 const DiffConfig& config);
248
250void diff(const ProteinDetection& a,
251 const ProteinDetection& b,
252 ProteinDetection& a_b,
253 ProteinDetection& b_a,
254 const DiffConfig& config);
255
258 const SpectrumIdentification& b,
261 const DiffConfig& config);
262
265 const AnalysisCollection& b,
268 const DiffConfig& config);
269
271void diff(const DBSequence& a,
272 const DBSequence& b,
273 DBSequence& a_b,
274 DBSequence& b_a,
275 const DiffConfig& config);
276
278void diff(const Modification& a,
279 const Modification& b,
280 Modification& a_b,
281 Modification& b_a,
282 const DiffConfig& config);
283
289 const DiffConfig& config);
290
292void diff(const Peptide& a,
293 const Peptide& b,
294 Peptide& a_b,
295 Peptide& b_a,
296 const DiffConfig& config);
297
300 const SequenceCollection& b,
303 const DiffConfig& config);
304
306void diff(const Sample& a,
307 const Sample& b,
308 Sample& a_b,
309 Sample& b_a,
310 const DiffConfig& config);
311
314 const SearchModification& b,
317 const DiffConfig& config);
318
324 const DiffConfig& config);
325
331 const DiffConfig& config);
332
338 const DiffConfig& config);
339
341void diff(const Provider& a,
342 const Provider& b,
343 Provider& a_b,
344 Provider& b_a,
345 const DiffConfig& config);
346
348void diff(const ContactRole& a,
349 const ContactRole& b,
350 ContactRole& a_b,
351 ContactRole& b_a,
352 const DiffConfig& config);
353
355void diff(const AnalysisSoftware& a,
356 const AnalysisSoftware& b,
357 AnalysisSoftware& a_b,
358 AnalysisSoftware& b_a,
359 const DiffConfig& config);
360
362void diff(const IdentData& a,
363 const IdentData& b,
364 IdentData& a_b,
365 IdentData& b_a,
366 const DiffConfig& config);
367
369void diff(const Identifiable& a,
370 const Identifiable& b,
371 Identifiable& a_b,
372 Identifiable& b_a,
373 const DiffConfig& config);
374
380 const DiffConfig& config);
381
382} // namespace diff_impl
383} // namespace data
384} // namespace pwiz
385
386
387
388// this include must come after the above declarations or GCC won't see them
390
391
392namespace pwiz {
393namespace identdata {
394
396{
398 : BaseDiffConfig(1.2e-6) // Hack to make the maxdiff work
399 {}
400};
401
402
403PWIZ_API_DECL std::ostream& operator<<(std::ostream& os, const data::Diff<IdentData, DiffConfig>& diff);
404
405} // namespace identdata
406} // namespace pwiz
407
408#endif // _MSIDDATA_DIFF_HPP_
#define PWIZ_API_DECL
Definition Export.hpp:32
void diff(const string &filename1, const string &filename2)
PWIZ_API_DECL void diff(const std::string &a, const std::string &b, std::string &a_b, std::string &b_a, const BaseDiffConfig &config)
std::ostream & operator<<(std::ostream &os, const Diff< object_type, config_type > &diff)
stream insertion of Diff results
Definition diff_std.hpp:200
Calculate diffs of objects in a ProteoWizard data model hierarchy.
Definition diff_std.hpp:143
Implementation of AmbiguousResidueType from the mzIdentML schema.
Implementation of AnalysisCollectionType from the mzIdentML schema.
Implementation of AnalysisDataType from the mzIdentML schema.
Implementation of AnalysisProtocolCollectionType from the mzIdentML schema.
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.
Implementation of DataCollectionType from the mzIdentML schema.
Implementation of DatabaseTranslationType from the mzIdentML schema.
Implementation of EnzymeType from the mzIdentML schema.
Implementation of EnzymesType from the mzIdentML schema.
Implementation of FilterType from the mzIdentML schema.
Implementation of FragmentArrayType from the mzIdentML schema.
Implementation of the MzIdentMLType from the mzIdentML schema.
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.
Implementation of IonTypeType from the mzIdentML schema.
Implementation of MassTableType from the mzIdentML schema.
Implementation of MeasureType from the mzIdentML schema.
Implementation of ModificationType from the mzIdentML schema.
Implementation of AbstractOrganizationType from the mzIdentML schema.
Implementation of PeptideEvidenceType from the mzIdentML schema.
Implementation of PeptideType from the mzIdentML schema.
Implementation of PeptideHypothesisType from the mzIdentML schema.
Implementation of PersonType from the mzIdentML schema.
Implementation of ProteinAmbiguityGroupType from the mzIdentML schema.
Implementation of ProteinDetectionType from the mzIdentML schema.
Implementation of ProteinDetectionHypothesisType from the mzIdentML schema.
Implementation of ProteinDetectionListType from the mzIdentML schema.
Implementation of ProteinDetectionProtocolType from the mzIdentML schema.
Implementation of ProviderType from the mzIdentML schema.
Implementation of ResidueType from the mzIdentML schema.
Implementation of the SampleType from the mzIdentML schema.
Implementation of SearchDatabaseType from the mzIdentML schema.
Implementation of SearchModificationType from the mzIdentML schema.
Implementation of SequenceCollectionType from the mzIdentML schema.
Implementation of SourceFileType from the mzIdentML schema.
Implementation of SpectraDataType from the mzIdentML schema.
Implementation of SpectrumIdentificationType from the mzIdentML schema.
Implementation of SpectrumIdentificationItemType from the mzIdentML schema.
Implementation of SpectrumIdentificationListType from the mzIdentML schema.
Implementation of SpectrumIdentificationProtocolType from the mzIdentML schema.
Implementation of SpectrumIdentificationResultType from the mzIdentML schema.
Implementation of SubstitutionModificationType from the mzIdentML schema.