| OpenMS 2.5.0

DataProcessing.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 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/METADATA/MetaInfoInterface.h>
38 #include <OpenMS/METADATA/Software.h>
39 #include <OpenMS/DATASTRUCTURES/DateTime.h>
40
41 #include <set>
42 #include <boost/shared_ptr.hpp>
43
44 namespace OpenMS
45 {
51 class OPENMS_DLLAPI DataProcessing :
52 public MetaInfoInterface
53 {
54
55 public:
56
57 //The different processing types
58 enum ProcessingAction
59 {
60 DATA_PROCESSING,
61 CHARGE_DECONVOLUTION,
62 DEISOTOPING,
63 SMOOTHING,
64 CHARGE_CALCULATION,
65 PRECURSOR_RECALCULATION,
66 BASELINE_REDUCTION,
67 PEAK_PICKING,
68 ALIGNMENT,
69 CALIBRATION,
70 NORMALIZATION,
71 FILTERING,
72 QUANTITATION,
73 FEATURE_GROUPING,
74 IDENTIFICATION_MAPPING,
75 FORMAT_CONVERSION,
76 CONVERSION_MZDATA,
77 CONVERSION_MZML,
78 CONVERSION_MZXML,
79 CONVERSION_DTA,
80 SIZE_OF_PROCESSINGACTION
81 };
83 static const std::string NamesOfProcessingAction[SIZE_OF_PROCESSINGACTION];
84
86 DataProcessing() = default;
88 DataProcessing(const DataProcessing &) = default;
89
90 // note: we implement the move constructor ourselves due to a bug in MSVS
91 // 2015/2017 which cannot produce a default move constructor for classes
92 // that contain STL containers (other than vector).
93
95 DataProcessing(DataProcessing&&) noexcept;
97 ~DataProcessing();
98
100 DataProcessing & operator=(const DataProcessing &) = default;
102 DataProcessing& operator=(DataProcessing&&) & = default;
103
105 bool operator==(const DataProcessing & rhs) const;
107 bool operator!=(const DataProcessing & rhs) const;
108
110 const Software & getSoftware() const;
112 Software & getSoftware();
114 void setSoftware(const Software & software);
115
117 const std::set<ProcessingAction> & getProcessingActions() const;
119 std::set<ProcessingAction> & getProcessingActions();
121 void setProcessingActions(const std::set<ProcessingAction> & actions);
122
124 const DateTime & getCompletionTime() const;
126 void setCompletionTime(const DateTime & completion_time);
127
128 protected:
129
130 Software software_;
131 std::set<ProcessingAction> processing_actions_;
132 DateTime completion_time_;
133 };
134
135 typedef boost::shared_ptr<DataProcessing> DataProcessingPtr;
136 typedef boost::shared_ptr<const DataProcessing> ConstDataProcessingPtr;
137
138 } // namespace OpenMS
139
OpenMS::DataProcessing::CONVERSION_MZML
Conversion to mzML format.
Definition: DataProcessing.h:77
OpenMS::DataProcessing::FILTERING
Data filtering or extraction.
Definition: DataProcessing.h:71
OpenMS::DataProcessing::DEISOTOPING
Deisotoping.
Definition: DataProcessing.h:62
OpenMS::DataProcessing::CONVERSION_MZDATA
Conversion to mzData format.
Definition: DataProcessing.h:76
OpenMS::DataProcessing
Description of the applied preprocessing steps.
Definition: DataProcessing.h:51
OpenMS::DataProcessing::CONVERSION_MZXML
Conversion to mzXML format.
Definition: DataProcessing.h:78
OpenMS::DataProcessing::BASELINE_REDUCTION
Baseline reduction.
Definition: DataProcessing.h:66
OpenMS::DataProcessing::PEAK_PICKING
Peak picking (conversion from raw to peak data)
Definition: DataProcessing.h:67
OpenMS::DataProcessing::FORMAT_CONVERSION
General file format conversion (if no other term applies)
Definition: DataProcessing.h:75
OpenMS::DataProcessing::FEATURE_GROUPING
Feature grouping
Definition: DataProcessing.h:73
OpenMS::DataProcessing::PRECURSOR_RECALCULATION
Recalculation of precursor m/z.
Definition: DataProcessing.h:65
OpenMS::DataProcessing::DATA_PROCESSING
General data processing (if no other term applies)
Definition: DataProcessing.h:60
std
STL namespace.
OpenMS::Software
Description of the software used for processing.
Definition: Software.h:48
OpenMS::DataProcessing::SMOOTHING
Smoothing of the signal to reduce noise.
Definition: DataProcessing.h:63
OpenMS::DataProcessing::CHARGE_DECONVOLUTION
Charge deconvolution.
Definition: DataProcessing.h:61
boost
OpenMS::DataProcessing::ALIGNMENT
Retention time alignment of different maps.
Definition: DataProcessing.h:68
OpenMS::DataProcessing::NORMALIZATION
Normalization of intensity values.
Definition: DataProcessing.h:70
OpenMS::DataProcessing::CALIBRATION
Calibration of m/z positions.
Definition: DataProcessing.h:69
DateTime.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::DataProcessing::CHARGE_CALCULATION
Determination of the peak charge.
Definition: DataProcessing.h:64
OpenMS::DataProcessingPtr
boost::shared_ptr< DataProcessing > DataProcessingPtr
Definition: DataProcessing.h:135
Software.h
OpenMS::DateTime
DateTime Class.
Definition: DateTime.h:54
OpenMS::DataProcessing::CONVERSION_DTA
Conversion to DTA format.
Definition: DataProcessing.h:79
OpenMS::DataProcessing::IDENTIFICATION_MAPPING
Identification mapping
Definition: DataProcessing.h:74
OpenMS::DataProcessing::ProcessingAction
ProcessingAction
Definition: DataProcessing.h:58
OpenMS::ConstDataProcessingPtr
boost::shared_ptr< const DataProcessing > ConstDataProcessingPtr
Definition: DataProcessing.h:136
MetaInfoInterface.h
OpenMS::DataProcessing::QUANTITATION
Quantitation.
Definition: DataProcessing.h:72
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60