ProteoWizard
IO.hpp
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1 //
2 // $Id: IO.hpp 1605 2009-12-09 23:50:27Z chambm $
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 
32 namespace pwiz {
33 namespace tradata {
34 
35 
36 namespace IO {
37 
38 
39 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const CV& cv);
40 PWIZ_API_DECL void read(std::istream& is, CV& cv);
41 
42 
43 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const UserParam& userParam);
44 PWIZ_API_DECL void read(std::istream& is, UserParam& userParam);
45 
46 
47 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const CVParam& cv);
48 PWIZ_API_DECL void read(std::istream& is, CVParam& cv);
49 
50 
51 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Software& software);
52 PWIZ_API_DECL void read(std::istream& is, Software& software);
53 
54 
56 PWIZ_API_DECL void read(std::istream& is, RetentionTime& x);
57 
58 
59 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Instrument& instrument);
60 PWIZ_API_DECL void read(std::istream& is, Instrument& instrument);
61 
62 
63 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const ProteinPtr& proteinPtr);
64 PWIZ_API_DECL void read(std::istream& is, Protein& protein);
65 
66 
68 PWIZ_API_DECL void read(std::istream& is, Modification& modification);
69 
70 
71 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const PeptidePtr& peptidePtr);
72 PWIZ_API_DECL void read(std::istream& is, Peptide& peptide);
73 
74 
75 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const CompoundPtr& compoundPtr);
76 PWIZ_API_DECL void read(std::istream& is, Compound& compound);
77 
78 
79 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Precursor& precursor);
80 PWIZ_API_DECL void read(std::istream& is, Precursor& precursor);
81 
82 
83 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Product& product);
84 PWIZ_API_DECL void read(std::istream& is, Product& product);
85 
86 
87 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Transition& transition);
88 PWIZ_API_DECL void read(std::istream& is, Transition& transition);
89 
90 
91 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Target& target);
92 PWIZ_API_DECL void read(std::istream& is, Target& target);
93 
94 
95 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const TraData& td);
96 PWIZ_API_DECL void read(std::istream& is, TraData& td);
97 
98 
99 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Contact& c);
100 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Publication& p);
101 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Interpretation& x);
102 PWIZ_API_DECL void write(minimxml::XMLWriter& writer, const Configuration& x);
103 
104 
105 } // namespace IO
106 
107 
108 } // namespace tradata
109 } // namespace pwiz
110 
111 
112 #endif // _TRADATA_IO_HPP_
113 
114 
PWIZ_API_DECL const Modification & modification(CVID cvid)
find a modification by CVID
PWIZ_API_DECL const CV & cv(const std::string &prefix)
returns a CV object for the specified namespace (prefix); currently supported namespaces are: MS UO ...
The XMLWriter class provides simple, tag-level XML syntax writing.
Definition: XMLWriter.hpp:47
Precursor (Q1) of the transition.
Definition: TraData.hpp:258
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)
boost::shared_ptr< Protein > ProteinPtr
Definition: TraData.hpp:184
PWIZ_API_DECL proteome::Peptide peptide(const Peptide &peptide)
creates a proteome::Peptide from an identdata::Peptide
Information about an ontology or CV source and a short &#39;lookup&#39; tag to refer to.
Definition: cv.hpp:13353
Instrument on which transitions are validated.
Definition: TraData.hpp:132
A peptide or compound that is to be included or excluded from a target list of precursor m/z values...
Definition: TraData.hpp:308
Instrument configuration used in the validation or optimization of the transitions.
Definition: TraData.hpp:147
represents a post-translational modification (PTM) modification formula or masses must be provided at...
A possible interpration of the product ion for a transition.
Definition: TraData.hpp:163
boost::shared_ptr< Compound > CompoundPtr
Definition: TraData.hpp:254
Chemical compound other than a peptide for which one or more transitions.
Definition: TraData.hpp:240
represents a peptide or polypeptide (a sequence of amino acids)
Definition: Peptide.hpp:61
Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead.
Definition: ParamTypes.hpp:185
PWIZ_API_DECL void read(std::istream &is, CV &cv)
Product (Q3) of the transition.
Definition: TraData.hpp:266
#define PWIZ_API_DECL
Definition: Export.hpp:32
boost::shared_ptr< Peptide > PeptidePtr
Definition: TraData.hpp:236
KernelTraitsBase< Kernel >::space_type::abscissa_type x
represents a tag-value pair, where the tag comes from the controlled vocabulary
Definition: ParamTypes.hpp:44