| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
MRMMapping Class Reference

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

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

Inheritance diagram for MRMMapping:

## Public Member Functions

void | mapExperiment (const OpenMS::PeakMap &input_chromatograms, const OpenMS::TargetedExperiment &targeted_exp, OpenMS::PeakMap &output)
| Maps input chromatograms to assays in a targeted experiment. More...
Constructors and destructors
| MRMMapping ()
| default constructor More...
| ~MRMMapping () override
| destructor More...
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...
virtual DefaultParamHandler & | operator= (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 Param & | getParameters () const
| Non-mutable access to the parameters. More...
const Param & | getDefaults () const
| Non-mutable access to the default parameters. More...
const String & | getName () 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...

## Protected Member Functions

| MRMMapping (const MRMMapping &rhs)
| copy constructor More...
MRMMapping & | operator= (const MRMMapping &rhs)
| assignment operator More...
void | updateMembers_ () override
| Synchronize members with param class. More...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Protected Attributes

double | precursor_tol_
double | product_tol_
bool | map_multiple_assays_
bool | error_on_unmapped_
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< String > | subsections_
| 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]

MRMMapping | ( |  | ) |

default constructor

## ◆ ~MRMMapping()

~MRMMapping | ( |  | ) |

inline override

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
| ) |  |

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).

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_ | ( |  | ) |

override protected virtual

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