ProteoWizard
SpectrumTable.hpp
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1//
2// $Id$
3//
4//
5// Original author: Darren Kessner <darren@proteowizard.org>
6//
7// Copyright 2008 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 _SPECTRUMTABLE_HPP_
25#define _SPECTRUMTABLE_HPP_
26
27
29#include "MSDataAnalyzer.hpp"
30#include "MSDataCache.hpp"
31#include "TabularConfig.hpp"
32
33namespace pwiz {
34namespace analysis {
35
36
37/// writes table of spectrum metadata to a file
39{
40 public:
41
43 {
44 Config(const std::string& args = "");
45 };
46
47
48 SpectrumTable(const MSDataCache& cache, const Config& config);
49
50 /// \name MSDataAnalyzer interface
51 //@{
52 virtual UpdateRequest updateRequested(const DataInfo& dataInfo,
53 const SpectrumIdentity& spectrumIdentity) const;
54
55 virtual void close(const DataInfo& dataInfo);
56 //@}
57
58 private:
61};
62
63
64template<>
66{
67 static const char* id() {return "spectrum_table";}
68 static const char* description() {return "write spectrum metadata as read from scan headers, in a table format";}
69 static const char* argsFormat() {return "[" TABULARCONFIG_DELIMITER_OPTIONS_STR "]";}
70 static std::vector<std::string> argsUsage()
71 {
72 return std::vector<std::string>(1, TABULARCONFIG_DELIMITER_USAGE_STR);
73 }
74};
75
76
77} // namespace analysis
78} // namespace pwiz
79
80
81#endif // _SPECTRUMTABLE_HPP_
82
#define PWIZ_API_DECL
Definition Export.hpp:32
#define TABULARCONFIG_DELIMITER_USAGE_STR
#define TABULARCONFIG_DELIMITER_OPTIONS_STR
Interface for MSData analyzers.
simple memory cache for common MSData info
writes table of spectrum metadata to a file
virtual void close(const DataInfo &dataInfo)
end analysis of the data
SpectrumTable(const MSDataCache &cache, const Config &config)
virtual UpdateRequest updateRequested(const DataInfo &dataInfo, const SpectrumIdentity &spectrumIdentity) const
ask analyzer if it wants an update
information about the data to be analyzed
Config(const std::string &args="")
static std::vector< std::string > argsUsage()
This auxilliary class should be specialized for MSDataAnalyzers whose instantiation is controlled by ...
Identifying information for a spectrum.
Definition MSData.hpp:471