ProteoWizard
RunSummary.hpp
Go to the documentation of this file.
1//
2// $Id$
3//
4//
5// Original author: Matt Chambers <matt.chambers <a.t> vanderbilt.edu>
6//
7// Copyright 2010 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 _RUNSUMMARY_HPP_
24#define _RUNSUMMARY_HPP_
25
26
28#include "MSDataAnalyzer.hpp"
29#include "MSDataCache.hpp"
30#include "TabularConfig.hpp"
32
33
34namespace pwiz {
35namespace analysis {
36
37
38/// writes table of spectrum metadata to a file
40{
41 public:
42
50
51
52 RunSummary(const MSDataCache& cache, const Config& config);
53
54 /// \name MSDataAnalyzer interface
55 //@{
56 virtual UpdateRequest updateRequested(const DataInfo& dataInfo,
57 const SpectrumIdentity& spectrumIdentity) const;
58
59 virtual void close(const DataInfo& dataInfo);
60 //@}
61
62 private:
65};
66
67
68template<>
70{
71 static const char* id() {return "run_summary";}
72 static const char* description() {return "print summary statistics about a run";}
73 static const char* argsFormat() {return "[msLevels=<int_set>] [charges=<int_set>] [" TABULARCONFIG_DELIMITER_OPTIONS_STR "]";}
74 static std::vector<std::string> argsUsage()
75 {
76 std::vector<std::string> result;
77 result.push_back("msLevels: if specified, summary only operates on these MS levels; default is all MS levels");
78 result.push_back("charges: if specified, summary only operates on these charge states; default is all charges");
79 result.push_back(TABULARCONFIG_DELIMITER_USAGE_STR);
80 return result;
81 }
82};
83
84
85} // namespace analysis
86} // namespace pwiz
87
88
89#endif // _RUNSUMMARY_HPP_
90
#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
RunSummary(const MSDataCache &cache, const Config &config)
const MSDataCache & cache_
virtual UpdateRequest updateRequested(const DataInfo &dataInfo, const SpectrumIdentity &spectrumIdentity) const
ask analyzer if it wants an update
virtual void close(const DataInfo &dataInfo)
end analysis of the data
a virtual container of integers, accessible via an iterator interface, stored as union of intervals
information about the data to be analyzed
Config(const std::string &args="")
pwiz::util::IntegerSet charges
pwiz::util::IntegerSet msLevels
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