ProteoWizard
References.hpp
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1//
2// $Id$
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
32namespace pwiz {
33namespace msdata {
34
35
36/// functions for resolving references from objects into the internal MSData lists
37namespace References {
38
39
40PWIZ_API_DECL void resolve(ParamContainer& paramContainer, const MSData& msd);
41PWIZ_API_DECL void resolve(FileDescription& fileDescription, const MSData& msd);
42PWIZ_API_DECL void resolve(ComponentList& componentList, const MSData& msd);
43PWIZ_API_DECL void resolve(InstrumentConfiguration& instrumentConfiguration, const MSData& msd);
44PWIZ_API_DECL void resolve(ProcessingMethod& processingMethod, const MSData& msd);
45PWIZ_API_DECL void resolve(DataProcessing& dataProcesssing, const MSData& msd);
46PWIZ_API_DECL void resolve(ScanSettings& dataProcesssing, const MSData& msd);
47PWIZ_API_DECL void resolve(Precursor& precursor, const MSData& msd);
48PWIZ_API_DECL void resolve(Product& product, const MSData& msd);
49PWIZ_API_DECL void resolve(Scan& scan, const MSData& msd);
50PWIZ_API_DECL void resolve(ScanList& List, const MSData& msd);
51PWIZ_API_DECL void resolve(BinaryDataArray& binaryDataArray, const MSData& msd);
52PWIZ_API_DECL void resolve(Spectrum& spectrum, const MSData& msd);
53PWIZ_API_DECL void resolve(Chromatogram& chromatogram, const MSData& msd);
54PWIZ_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///
67
68
69} // namespace References
70
71
72} // namespace msdata
73} // namespace pwiz
74
75
76#endif // _REFERENCES_HPP_
77
#define PWIZ_API_DECL
Definition Export.hpp:32
PWIZ_API_DECL void resolve(ParamContainer &paramContainer, const MSData &msd)
The base class for elements that may contain cvParams, userParams, or paramGroup references.
The structure into which encoded binary data goes. Byte ordering is always little endian (Intel style...
Definition MSData.hpp:405
A single chromatogram.
Definition MSData.hpp:578
List with the different components used in the mass spectrometer. At least one source,...
Definition MSData.hpp:157
Description of the way in which a particular software was used.
Definition MSData.hpp:274
Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is sto...
Definition MSData.hpp:85
Description of a particular hardware configuration of a mass spectrometer. Each configuration MUST ha...
Definition MSData.hpp:230
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
Definition MSData.hpp:850
The method of precursor ion selection and activation.
Definition MSData.hpp:312
Description of the default peak processing method. This element describes the base method used in the...
Definition MSData.hpp:255
product ion information
Definition MSData.hpp:348
A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument.
Definition MSData.hpp:810
Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile.
Definition MSData.hpp:370
List and descriptions of scans.
Definition MSData.hpp:396
Description of the acquisition settings of the instrument prior to the start of the run.
Definition MSData.hpp:207
The structure that captures the generation of a peak list (including the underlying acquisitions)
Definition MSData.hpp:506