ProteoWizard
References.hpp
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1 //
2 // $Id: References.hpp 1189 2009-08-14 17:36:06Z chambm $
3 //
4 //
5 // Original author: Darren Kessner <darren@proteowizard.org>
6 //
7 // Copyright 2007 Spielberg Family Center for Applied Proteomics
8 // Cedars-Sinai Medical Center, Los Angeles, California 90048
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 _REFERENCES_HPP_
25 #define _REFERENCES_HPP_
26 
27 
29 #include "MSData.hpp"
30 
31 
32 namespace pwiz {
33 namespace msdata {
34 
35 
36 /// functions for resolving references from objects into the internal MSData lists
37 namespace References {
38 
39 
40 PWIZ_API_DECL void resolve(ParamContainer& paramContainer, const MSData& msd);
41 PWIZ_API_DECL void resolve(FileDescription& fileDescription, const MSData& msd);
42 PWIZ_API_DECL void resolve(ComponentList& componentList, const MSData& msd);
43 PWIZ_API_DECL void resolve(InstrumentConfiguration& instrumentConfiguration, const MSData& msd);
44 PWIZ_API_DECL void resolve(ProcessingMethod& processingMethod, const MSData& msd);
45 PWIZ_API_DECL void resolve(DataProcessing& dataProcesssing, const MSData& msd);
46 PWIZ_API_DECL void resolve(ScanSettings& dataProcesssing, const MSData& msd);
47 PWIZ_API_DECL void resolve(Precursor& precursor, const MSData& msd);
48 PWIZ_API_DECL void resolve(Product& product, const MSData& msd);
49 PWIZ_API_DECL void resolve(Scan& scan, const MSData& msd);
50 PWIZ_API_DECL void resolve(ScanList& List, const MSData& msd);
51 PWIZ_API_DECL void resolve(BinaryDataArray& binaryDataArray, const MSData& msd);
52 PWIZ_API_DECL void resolve(Spectrum& spectrum, const MSData& msd);
53 PWIZ_API_DECL void resolve(Chromatogram& chromatogram, const MSData& msd);
54 PWIZ_API_DECL void resolve(Run& run, const MSData& msd);
55 
56 
57 ///
58 /// Resolve internal references in an MSData object.
59 ///
60 /// For an MSData object using a SpectrumListSimple to hold Spectrum objects in memory,
61 /// these references will be resolved as well.
62 ///
63 /// File-backed SpectrumList implementations using lazy evaluation of a Spectrum need
64 /// to call resolve(spectrum, msd) before returning it to the client.
65 ///
66 PWIZ_API_DECL void resolve(MSData& msd);
67 
68 
69 } // namespace References
70 
71 
72 } // namespace msdata
73 } // namespace pwiz
74 
75 
76 #endif // _REFERENCES_HPP_
77 
product ion information
Definition: MSData.hpp:346
Description of the way in which a particular software was used.
Definition: MSData.hpp:272
Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile...
Definition: MSData.hpp:368
The method of precursor ion selection and activation.
Definition: MSData.hpp:310
PWIZ_API_DECL void resolve(ParamContainer &paramContainer, const MSData &msd)
A single chromatogram.
Definition: MSData.hpp:573
Description of the default peak processing method. This element describes the base method used in the...
Definition: MSData.hpp:253
Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is sto...
Definition: MSData.hpp:83
A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument...
Definition: MSData.hpp:805
The base class for elements that may contain cvParams, userParams, or paramGroup references.
Definition: ParamTypes.hpp:244
#define PWIZ_API_DECL
Definition: Export.hpp:32
List with the different components used in the mass spectrometer. At least one source, one mass analyzer and one detector need to be specified.
Definition: MSData.hpp:155
Description of a particular hardware configuration of a mass spectrometer. Each configuration MUST ha...
Definition: MSData.hpp:228
The structure into which encoded binary data goes. Byte ordering is always little endian (Intel style...
Definition: MSData.hpp:403
Description of the acquisition settings of the instrument prior to the start of the run...
Definition: MSData.hpp:205
List and descriptions of scans.
Definition: MSData.hpp:394
The structure that captures the generation of a peak list (including the underlying acquisitions) ...
Definition: MSData.hpp:504
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
Definition: MSData.hpp:845