ProteoWizard
Diff.hpp
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1 //
2 // $Id: Diff.hpp 2820 2011-06-27 22:51:16Z chambm $
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 
27 #include "pwiz/utility/misc/Export.hpp"
28 #include "IdentData.hpp"
29 
30 namespace pwiz { namespace identdata { struct DiffConfig; } }
31 
32 
33 namespace pwiz {
34 namespace data {
35 namespace diff_impl {
36 
37 using namespace identdata;
38 
39 PWIZ_API_DECL
40 void diff(const FragmentArray& a,
41  const FragmentArray& b,
42  FragmentArray& a_b,
43  FragmentArray& b_a,
44  const DiffConfig& config);
45 
46 PWIZ_API_DECL
47 void diff(const IonType& a,
48  const IonType& b,
49  IonType& a_b,
50  IonType& b_a,
51  const DiffConfig& config);
52 
53 PWIZ_API_DECL
54 void diff(const Measure& a,
55  const Measure& b,
56  Measure& a_b,
57  Measure& b_a,
58  const DiffConfig& config);
59 
60 PWIZ_API_DECL
61 void diff(const PeptideEvidence& a,
62  const PeptideEvidence& b,
63  PeptideEvidence& a_b,
64  PeptideEvidence& b_a,
65  const DiffConfig& config);
66 
67 PWIZ_API_DECL
68 void diff(const ProteinAmbiguityGroup& a,
69  const ProteinAmbiguityGroup& b,
70  ProteinAmbiguityGroup& a_b,
71  ProteinAmbiguityGroup& b_a,
72  const DiffConfig& config);
73 
74 PWIZ_API_DECL
75 void diff(const PeptideHypothesis& a,
76  const PeptideHypothesis& b,
77  PeptideHypothesis& a_b,
78  PeptideHypothesis& b_a,
79  const DiffConfig& config);
80 
81 PWIZ_API_DECL
82 void diff(const ProteinDetectionHypothesis& a,
83  const ProteinDetectionHypothesis& b,
84  ProteinDetectionHypothesis& a_b,
85  ProteinDetectionHypothesis& b_a,
86  const DiffConfig& config);
87 
88 PWIZ_API_DECL
89 void diff(const DataCollection& a,
90  const DataCollection& b,
91  DataCollection& a_b,
92  DataCollection& b_a,
93  const DiffConfig& config);
94 
95 PWIZ_API_DECL
96 void diff(const SpectrumIdentificationListPtr a,
97  const SpectrumIdentificationListPtr b,
98  SpectrumIdentificationListPtr a_b,
99  SpectrumIdentificationListPtr b_a,
100  const DiffConfig& config);
101 
102 PWIZ_API_DECL
103 void diff(const SpectrumIdentificationList& a,
104  const SpectrumIdentificationList& b,
105  SpectrumIdentificationList& a_b,
106  SpectrumIdentificationList& b_a,
107  const DiffConfig& config);
108 
109 PWIZ_API_DECL
110 void diff(const ProteinDetectionList& a,
111  const ProteinDetectionList& b,
112  ProteinDetectionList& a_b,
113  ProteinDetectionList& b_a,
114  const DiffConfig& config);
115 
116 PWIZ_API_DECL
117 void diff(const AnalysisData& a,
118  const AnalysisData& b,
119  AnalysisData& a_b,
120  AnalysisData& b_a,
121  const DiffConfig& config);
122 
123 PWIZ_API_DECL
124 void diff(const SearchDatabase& a,
125  const SearchDatabase& b,
126  SearchDatabase& a_b,
127  SearchDatabase& b_a,
128  const DiffConfig& config);
129 
130 PWIZ_API_DECL
131 void diff(const SpectraData& a,
132  const SpectraData& b,
133  SpectraData& a_b,
134  SpectraData& b_a,
135  const DiffConfig& config);
136 
137 PWIZ_API_DECL
138 void diff(const SourceFile& a,
139  const SourceFile& b,
140  SourceFile& a_b,
141  SourceFile& b_a,
142  const DiffConfig& config);
143 
144 PWIZ_API_DECL
145 void diff(const Inputs& a,
146  const Inputs& b,
147  Inputs& a_b,
148  Inputs& b_a,
149  const DiffConfig& config);
150 
151 PWIZ_API_DECL
152 void diff(const Enzyme& a,
153  const Enzyme& b,
154  Enzyme& a_b,
155  Enzyme& b_a,
156  const DiffConfig& config);
157 
158 PWIZ_API_DECL
159 void diff(const Enzymes& a,
160  const Enzymes& b,
161  Enzymes& a_b,
162  Enzymes& b_a,
163  const DiffConfig& config);
164 
165 PWIZ_API_DECL
166 void diff(const MassTable& a,
167  const MassTable& b,
168  MassTable& a_b,
169  MassTable& b_a,
170  const DiffConfig& config);
171 
172 PWIZ_API_DECL
173 void diff(const Residue& a,
174  const Residue& b,
175  Residue& a_b,
176  Residue& b_a,
177  const DiffConfig& config);
178 
179 PWIZ_API_DECL
180 void diff(const AmbiguousResidue& a,
181  const AmbiguousResidue& b,
182  AmbiguousResidue& a_b,
183  AmbiguousResidue& b_a,
184  const DiffConfig& config);
185 
186 PWIZ_API_DECL
187 void diff(const Filter& a,
188  const Filter& b,
189  Filter& a_b,
190  Filter& b_a,
191  const DiffConfig& config);
192 
193 PWIZ_API_DECL
194 void diff(const DatabaseTranslation& a,
195  const DatabaseTranslation& b,
196  DatabaseTranslation& a_b,
197  DatabaseTranslation& b_a,
198  const DiffConfig& config);
199 
200 PWIZ_API_DECL
201 void diff(const SpectrumIdentificationProtocol& a,
202  const SpectrumIdentificationProtocol& b,
203  SpectrumIdentificationProtocol& a_b,
204  SpectrumIdentificationProtocol& b_a,
205  const DiffConfig& config);
206 
207 PWIZ_API_DECL
208 void diff(const ProteinDetectionProtocol& a,
209  const ProteinDetectionProtocol& b,
210  ProteinDetectionProtocol& a_b,
211  ProteinDetectionProtocol& b_a,
212  const DiffConfig& config);
213 
214 PWIZ_API_DECL
215 void diff(const AnalysisProtocolCollection& a,
216  const AnalysisProtocolCollection& b,
217  AnalysisProtocolCollection& a_b,
218  AnalysisProtocolCollection& b_a,
219  const DiffConfig& config);
220 
221 PWIZ_API_DECL
222 void diff(const Contact& a,
223  const Contact& b,
224  Contact& a_b,
225  Contact& b_a,
226  const DiffConfig& config);
227 
228 PWIZ_API_DECL
229 void diff(const Person& a,
230  const Person& b,
231  Person& a_b,
232  Person& b_a,
233  const DiffConfig& config);
234 
235 PWIZ_API_DECL
236 void diff(const Organization& a,
237  const Organization& b,
238  Organization& a_b,
239  Organization& b_a,
240  const DiffConfig& config);
241 
242 PWIZ_API_DECL
243 void diff(const BibliographicReference& a,
244  const BibliographicReference& b,
245  BibliographicReference& a_b,
246  BibliographicReference& b_a,
247  const DiffConfig& config);
248 
249 PWIZ_API_DECL
250 void diff(const ProteinDetection& a,
251  const ProteinDetection& b,
252  ProteinDetection& a_b,
253  ProteinDetection& b_a,
254  const DiffConfig& config);
255 
256 PWIZ_API_DECL
257 void diff(const SpectrumIdentification& a,
258  const SpectrumIdentification& b,
259  SpectrumIdentification& a_b,
260  SpectrumIdentification& b_a,
261  const DiffConfig& config);
262 
263 PWIZ_API_DECL
264 void diff(const AnalysisCollection& a,
265  const AnalysisCollection& b,
266  AnalysisCollection& a_b,
267  AnalysisCollection& b_a,
268  const DiffConfig& config);
269 
270 PWIZ_API_DECL
271 void diff(const DBSequence& a,
272  const DBSequence& b,
273  DBSequence& a_b,
274  DBSequence& b_a,
275  const DiffConfig& config);
276 
277 PWIZ_API_DECL
278 void diff(const Modification& a,
279  const Modification& b,
280  Modification& a_b,
281  Modification& b_a,
282  const DiffConfig& config);
283 
284 PWIZ_API_DECL
285 void diff(const SubstitutionModification& a,
286  const SubstitutionModification& b,
287  SubstitutionModification& a_b,
288  SubstitutionModification& b_a,
289  const DiffConfig& config);
290 
291 PWIZ_API_DECL
292 void diff(const Peptide& a,
293  const Peptide& b,
294  Peptide& a_b,
295  Peptide& b_a,
296  const DiffConfig& config);
297 
298 PWIZ_API_DECL
299 void diff(const SequenceCollection& a,
300  const SequenceCollection& b,
301  SequenceCollection& a_b,
302  SequenceCollection& b_a,
303  const DiffConfig& config);
304 
305 PWIZ_API_DECL
306 void diff(const Sample& a,
307  const Sample& b,
308  Sample& a_b,
309  Sample& b_a,
310  const DiffConfig& config);
311 
312 PWIZ_API_DECL
313 void diff(const SearchModification& a,
314  const SearchModification& b,
315  SearchModification& a_b,
316  SearchModification& b_a,
317  const DiffConfig& config);
318 
319 PWIZ_API_DECL
320 void diff(const SpectrumIdentificationItem& a,
321  const SpectrumIdentificationItem& b,
322  SpectrumIdentificationItem& a_b,
323  SpectrumIdentificationItem& b_a,
324  const DiffConfig& config);
325 
326 PWIZ_API_DECL
327 void diff(const SpectrumIdentificationResult& a,
328  const SpectrumIdentificationResult& b,
329  SpectrumIdentificationResult& a_b,
330  SpectrumIdentificationResult& b_a,
331  const DiffConfig& config);
332 
333 PWIZ_API_DECL
334 void diff(const AnalysisSampleCollection& a,
335  const AnalysisSampleCollection& b,
336  AnalysisSampleCollection& a_b,
337  AnalysisSampleCollection& b_a,
338  const DiffConfig& config);
339 
340 PWIZ_API_DECL
341 void diff(const Provider& a,
342  const Provider& b,
343  Provider& a_b,
344  Provider& b_a,
345  const DiffConfig& config);
346 
347 PWIZ_API_DECL
348 void diff(const ContactRole& a,
349  const ContactRole& b,
350  ContactRole& a_b,
351  ContactRole& b_a,
352  const DiffConfig& config);
353 
354 PWIZ_API_DECL
355 void diff(const AnalysisSoftware& a,
356  const AnalysisSoftware& b,
357  AnalysisSoftware& a_b,
358  AnalysisSoftware& b_a,
359  const DiffConfig& config);
360 
361 PWIZ_API_DECL
362 void diff(const IdentData& a,
363  const IdentData& b,
364  IdentData& a_b,
365  IdentData& b_a,
366  const DiffConfig& config);
367 
368 PWIZ_API_DECL
369 void diff(const Identifiable& a,
370  const Identifiable& b,
371  Identifiable& a_b,
372  Identifiable& b_a,
373  const DiffConfig& config);
374 
375 PWIZ_API_DECL
376 void diff(const IdentifiableParamContainer& a,
377  const IdentifiableParamContainer& b,
378  IdentifiableParamContainer& a_b,
379  IdentifiableParamContainer& b_a,
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
389 #include "pwiz/data/common/diff_std.hpp"
390 
391 
392 namespace pwiz {
393 namespace identdata {
394 
395 struct PWIZ_API_DECL DiffConfig : public pwiz::data::BaseDiffConfig
396 {
397  DiffConfig()
398  : BaseDiffConfig(1.2e-6) // Hack to make the maxdiff work
399  {}
400 };
401 
402 
403 PWIZ_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_
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