OpenMS
MRMMapping Class Reference

A class to map targeted assays to chromatograms. More...

#include <OpenMS/ANALYSIS/TARGETED/MRMMapping.h>

Inheritance diagram for MRMMapping:
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Collaboration diagram for MRMMapping:
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Constructors and destructors

double precursor_tol_
 
double product_tol_
 
bool map_multiple_assays_
 
bool error_on_unmapped_
 
 MRMMapping ()
 default constructor More...
 
 ~MRMMapping () override
 destructor More...
 
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. More...
 
 MRMMapping (const MRMMapping &rhs)
 copy constructor More...
 
MRMMappingoperator= (const MRMMapping &rhs)
 assignment operator More...
 
void updateMembers_ () override
 Synchronize members with param class. More...
 

Additional Inherited Members

- Public Member Functions inherited from DefaultParamHandler
 DefaultParamHandler (const String &name)
 Constructor with name that is displayed in error messages. More...
 
 DefaultParamHandler (const DefaultParamHandler &rhs)
 Copy constructor. More...
 
virtual ~DefaultParamHandler ()
 Destructor. More...
 
DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () const
 Non-mutable access to the name. More...
 
void setName (const String &name)
 Mutable access to the name. More...
 
const std::vector< String > & getSubsections () const
 Non-mutable access to the registered subsections. More...
 
- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 
- Protected Attributes inherited from DefaultParamHandler
Param param_
 Container for current parameters. More...
 
Param defaults_
 Container for default parameters. This member should be filled in the constructor of derived classes! More...
 
std::vector< Stringsubsections_
 Container for registered subsections. This member should be filled in the constructor of derived classes! More...
 
String error_name_
 Name that is displayed in error messages during the parameter checking. More...
 
bool check_defaults_
 If this member is set to false no checking if parameters in done;. More...
 
bool warn_empty_defaults_
 If this member is set to false no warning is emitted when defaults are empty;. More...
 

Detailed Description

A class to map targeted assays to chromatograms.

Constructor & Destructor Documentation

◆ MRMMapping() [1/2]

default constructor

◆ ~MRMMapping()

~MRMMapping ( )
inlineoverride

destructor

◆ MRMMapping() [2/2]

MRMMapping ( const MRMMapping rhs)
protected

copy constructor

Member Function Documentation

◆ 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.

The output chromatograms are an annotated copy of the input chromatograms with native id, precursor information and peptide sequence (if available) annotated in the chromatogram files.

The algorithm tries to match a given set of chromatograms and targeted assays. It iterates through all the chromatograms retrieves one or more matching targeted assay for the chromatogram. By default, the algorithm assumes that a 1:1 mapping exists. If a chromatogram cannot be mapped (does not have a corresponding assay) the algorithm issues a warning, the user can specify that the program should abort in such a case (see error_on_unmapped).

Note
If multiple mapping is enabled (see map_multiple_assays parameter) then each mapped assay will get its own chromatogram that contains the same raw data but different meta-annotation. This can be useful if the same transition is used to monitor multiple analytes but may also indicate a problem with too wide mapping tolerances.

◆ operator=()

MRMMapping& operator= ( const MRMMapping rhs)
protected

assignment operator

◆ updateMembers_()

void updateMembers_ ( )
overrideprotectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ error_on_unmapped_

bool error_on_unmapped_
protected

◆ map_multiple_assays_

bool map_multiple_assays_
protected

◆ precursor_tol_

double precursor_tol_
protected

◆ product_tol_

double product_tol_
protected