ProteoWizard
SpectrumBinaryData.hpp
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1 //
2 // $Id: SpectrumBinaryData.hpp 7297 2015-03-12 05:30:33Z paragmallick $
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 _SPECTRUMBINARYDATA_HPP_
25 #define _SPECTRUMBINARYDATA_HPP_
26 
27 
29 #include "MSDataAnalyzer.hpp"
30 #include "MSDataCache.hpp"
31 
32 
33 namespace pwiz {
34 namespace analysis {
35 
36 
37 /// writes table of spectrum metadata to a file
39 {
40  public:
41 
43  {
44  size_t begin;
45  size_t end;
47  size_t precision;
48 
49  Config(const std::string& args = "");
50 
51  bool operator == (const Config &rhs) const
52  {
53  return begin==rhs.begin &&
54  end == rhs.end &&
55  interpretAsScanNumbers == rhs.interpretAsScanNumbers &&
56  precision == rhs.precision;
57  }
58  };
59 
60  SpectrumBinaryData(const MSDataCache& cache, const Config& config);
61 
62  /// \name MSDataAnalyzer interface
63  //@{
64  virtual UpdateRequest updateRequested(const DataInfo& dataInfo,
65  const SpectrumIdentity& spectrumIdentity) const;
66 
67  virtual void update(const DataInfo& dataInfo,
68  const Spectrum& spectrum);
69  //@}
70 
71  private:
73  const Config config_;
74 };
75 
76 
77 template<>
79 {
80  static const char* id() {return "binary";}
81 #define BINARY_INDEX_ARG "index"
82 #define BINARY_SCAN_ARG "sn"
83 #define BINARY_PRECISION_ARG "precision"
84  static const char* argsFormat() {return BINARY_INDEX_ARG "=<spectrumIndexLow>[,<spectrumIndexHigh>] | " BINARY_SCAN_ARG "=<scanNumberLow>[,<scanNumberHigh>] [" BINARY_PRECISION_ARG "=<precision>]";}
85 
86  static const char* description() {return "write binary data for selected spectra";}
87 
88  static std::vector<std::string> argsUsage()
89  {
90  std::vector<std::string> result;
91  result.push_back(BINARY_INDEX_ARG": write data for spectra in this index range");
92  result.push_back(BINARY_SCAN_ARG": write data for spectra in this scan number range");
93  result.push_back(BINARY_PRECISION_ARG": write d decimal places");
94  return result;
95  }
96 };
97 
98 
99 } // namespace analysis
100 } // namespace pwiz
101 
102 
103 #endif // _SPECTRUMBINARYDATA_HPP_
104 
simple memory cache for common MSData info
Definition: MSDataCache.hpp:74
#define BINARY_SCAN_ARG
writes table of spectrum metadata to a file
#define PWIZ_API_DECL
Definition: Export.hpp:32
This auxilliary class should be specialized for MSDataAnalyzers whose instantiation is controlled by ...
Identifying information for a spectrum.
Definition: MSData.hpp:469
#define BINARY_INDEX_ARG
#define BINARY_PRECISION_ARG
PWIZ_API_DECL bool operator==(const TruncatedLorentzianParameters &t, const TruncatedLorentzianParameters &u)
information about the data to be analyzed
The structure that captures the generation of a peak list (including the underlying acquisitions) ...
Definition: MSData.hpp:504
Interface for MSData analyzers.