OpenMS  3.0.0
MRMMapping.h
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31 // $Maintainer: Hannes Roest $
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34 
35 #pragma once
36 
38 
41 
42 namespace OpenMS
43 {
44 
49  class OPENMS_DLLAPI MRMMapping :
50  public DefaultParamHandler
51  {
52 public:
53 
57  MRMMapping();
59 
61  ~MRMMapping() override {}
63 
85  void mapExperiment(const OpenMS::PeakMap& input_chromatograms,
86  const OpenMS::TargetedExperiment& targeted_exp,
87  OpenMS::PeakMap& output) const;
88 
89 protected:
90 
92  MRMMapping(const MRMMapping & rhs);
93 
95  MRMMapping & operator=(const MRMMapping & rhs);
96 
98  void updateMembers_() override;
99 
101  double product_tol_;
104 
105  };
106 }
107 
DefaultParamHandler.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
TargetedExperiment.h
Size
OpenMS::Exception::InvalidValue
Invalid value exception.
Definition: Exception.h:327
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
MzMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
MRMMapping.h
OpenMS::TraMLFile::load
void load(const String &filename, TargetedExperiment &id)
Loads a map from a TraML file.
OpenMS::MRMMapping::mapExperiment
void mapExperiment(const OpenMS::PeakMap &input_chromatograms, const OpenMS::TargetedExperiment &targeted_exp, OpenMS::PeakMap &output) const
Maps input chromatograms to assays in a targeted experiment.
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::DataProcessingPtr
boost::shared_ptr< DataProcessing > DataProcessingPtr
Definition: DataProcessing.h:136
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::TraMLFile
File adapter for HUPO PSI TraML files.
Definition: TraMLFile.h:63
OpenMS::MRMMapping::~MRMMapping
~MRMMapping() override
destructor
Definition: MRMMapping.h:61
OpenMS::MRMMapping::error_on_unmapped_
bool error_on_unmapped_
Definition: MRMMapping.h:103
OpenMS::MSExperiment::getChromatograms
const std::vector< MSChromatogram > & getChromatograms() const
returns the chromatogram list
ProgressLogger.h
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
OpenMS::MSExperiment::setChromatograms
void setChromatograms(const std::vector< MSChromatogram > &chromatograms)
sets the chromatogram list
OpenMS::MRMMapping
A class to map targeted assays to chromatograms.
Definition: MRMMapping.h:49
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::DefaultParamHandler::getDefaults
const Param & getDefaults() const
Non-mutable access to the default parameters.
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
MSExperiment.h
OpenMS::Param::copy
Param copy(const std::string &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::DataProcessing
Description of the applied preprocessing steps.
Definition: DataProcessing.h:51
OpenMS::MRMMapping::map_multiple_assays_
bool map_multiple_assays_
Definition: MRMMapping.h:102
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::DataProcessing::FORMAT_CONVERSION
General file format conversion (if no other term applies)
Definition: DataProcessing.h:75
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
TraMLFile.h
OpenMS::MRMMapping::product_tol_
double product_tol_
Definition: MRMMapping.h:101
TOPPBase.h
OpenMS::MRMMapping::precursor_tol_
double precursor_tol_
Definition: MRMMapping.h:100