| OpenMS 2.5.0

FIAMSScheduler.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Svetlana Kutuzova, Douglas McCloskey $
32 // $Authors: Svetlana Kutuzova, Douglas McCloskey $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/FORMAT/CsvFile.h>
38 #include <map>
39
40 namespace OpenMS
41 {
42 class MzMLFile;
43 /*
44 @brief Scheduler for FIA-MS data batches. Works with FIAMSDataProcessor.
45
46 The class is initialised with the path to the csv file that must contain the following columns:
47 - *filename* - the mzML filename for the sample. Must not contains the extension and path. The results filenames follow the pattern @filename_@n_seconds.
48 - *dir_input* - the location of the directory with the mzML file
49 - *dir_output* - the location of the directory where the results will be stored
50 - *resolution* - the resolution of the instrument
51 - *polarity* - the charge of the instrument, accepts "positive" or "negative"
52 - *db:mapping* - database input file containing three tab-separated columns of mass, formula, identifier for the accurate mass search
53 - *db:struct* - database input file containing four tab-separated columns of identifier, name, SMILES, INCHI for the accurate mass search
54 - *positive_adducts* - file containing the list of potential positive adducts for the accurate mass search
55 - *negative_adducts* - file containing the list of potential negative adducts for the accurate mass search
56 - *time* - ";"-separated numbers of seconds to process, f.e. "30;60;90;180"
57 */
58 class OPENMS_DLLAPI FIAMSScheduler
59 {
60 public:
61 FIAMSScheduler() = default;
62
64 FIAMSScheduler(
65 String filename,
66 String base_dir = "/",
67 bool load_cached_ = true
68 );
69
71 ~FIAMSScheduler() = default;
72
74 FIAMSScheduler(const FIAMSScheduler& cp) = default;
75
77 FIAMSScheduler& operator=(const FIAMSScheduler& fdp) = default;
78
82 void run();
83
87 const std::vector<std::map<String, String>>& getSamples();
88
92 const String& getBaseDir();
93
94 private:
98 void loadSamples_();
99
100 String filename_;
101 String base_dir_;
102 bool load_cached_;
103 std::vector<std::map<String, String>> samples_;
104 };
105 } // namespace OpenMS
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::FIAMSScheduler::load_cached_
bool load_cached_
Definition: FIAMSScheduler.h:102
OpenMS::FIAMSScheduler::base_dir_
String base_dir_
Definition: FIAMSScheduler.h:101
CsvFile.h
OpenMS::FIAMSScheduler
Definition: FIAMSScheduler.h:58
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::FIAMSScheduler::filename_
String filename_
Definition: FIAMSScheduler.h:100
OpenMS::FIAMSScheduler::samples_
std::vector< std::map< String, String > > samples_
Definition: FIAMSScheduler.h:103