ProteoWizard
IO.hpp
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1//
2// $Id$
3//
4//
5// Original author: Matt Chambers <matt.chambers .@. vanderbilt.edu>
6//
7// Copyright 2009 Vanderbilt University - Nashville, TN 37232
8//
9// Licensed under the Apache License, Version 2.0 (the "License");
10// you may not use this file except in compliance with the License.
11// You may obtain a copy of the License at
12//
13// http://www.apache.org/licenses/LICENSE-2.0
14//
15// Unless required by applicable law or agreed to in writing, software
16// distributed under the License is distributed on an "AS IS" BASIS,
17// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
18// See the License for the specific language governing permissions and
19// limitations under the License.
20//
21
22
23#ifndef _TRADATA_IO_HPP_
24#define _TRADATA_IO_HPP_
25
26
28#include "TraData.hpp"
30
31
32namespace pwiz {
33namespace tradata {
34
35
36namespace IO {
37
38
39PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const CV& cv);
40PWIZ_API_DECL void read(std::istream& is, CV& cv);
41
42
43PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const UserParam& userParam);
44PWIZ_API_DECL void read(std::istream& is, UserParam& userParam);
45
46
48PWIZ_API_DECL void read(std::istream& is, CVParam& cv);
49
50
51PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Software& software);
52PWIZ_API_DECL void read(std::istream& is, Software& software);
53
54
56PWIZ_API_DECL void read(std::istream& is, RetentionTime& x);
57
58
59PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Instrument& instrument);
60PWIZ_API_DECL void read(std::istream& is, Instrument& instrument);
61
62
63PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const ProteinPtr& proteinPtr);
64PWIZ_API_DECL void read(std::istream& is, Protein& protein);
65
66
67PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Modification& modification);
68PWIZ_API_DECL void read(std::istream& is, Modification& modification);
69
70
71PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const PeptidePtr& peptidePtr);
72PWIZ_API_DECL void read(std::istream& is, Peptide& peptide);
73
74
75PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const CompoundPtr& compoundPtr);
76PWIZ_API_DECL void read(std::istream& is, Compound& compound);
77
78
79PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Precursor& precursor);
80PWIZ_API_DECL void read(std::istream& is, Precursor& precursor);
81
82
83PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Product& product);
84PWIZ_API_DECL void read(std::istream& is, Product& product);
85
86
87PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Transition& transition);
88PWIZ_API_DECL void read(std::istream& is, Transition& transition);
89
90
91PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Target& target);
92PWIZ_API_DECL void read(std::istream& is, Target& target);
93
94
96PWIZ_API_DECL void read(std::istream& is, TraData& td);
97
98
103
104
105} // namespace IO
106
107
108} // namespace tradata
109} // namespace pwiz
110
111
112#endif // _TRADATA_IO_HPP_
113
114
#define PWIZ_API_DECL
Definition Export.hpp:32
KernelTraitsBase< Kernel >::space_type::abscissa_type x
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition XMLWriter.hpp:48
represents a post-translational modification (PTM) modification formula or masses must be provided at...
represents a peptide or polypeptide (a sequence of amino acids)
Definition Peptide.hpp:62
boost::shared_ptr< Protein > ProteinPtr
PWIZ_API_DECL void read(std::istream &is, CV &cv)
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)
boost::shared_ptr< Compound > CompoundPtr
Definition TraData.hpp:254
boost::shared_ptr< Peptide > PeptidePtr
Definition TraData.hpp:236
Information about an ontology or CV source and a short 'lookup' tag to refer to.
Definition cv.hpp:14916
represents a tag-value pair, where the tag comes from the controlled vocabulary
Uncontrolled user parameters (essentially allowing free text). Before using these,...
Chemical compound other than a peptide for which one or more transitions.
Definition TraData.hpp:241
Instrument configuration used in the validation or optimization of the transitions.
Definition TraData.hpp:148
Instrument on which transitions are validated.
Definition TraData.hpp:133
A possible interpration of the product ion for a transition.
Definition TraData.hpp:164
Precursor (Q1) of the transition.
Definition TraData.hpp:259
Product (Q3) of the transition.
Definition TraData.hpp:267
A peptide or compound that is to be included or excluded from a target list of precursor m/z values.
Definition TraData.hpp:309