OpenMS
2.5.0
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A class to map targeted assays to chromatograms. More...
#include <OpenMS/ANALYSIS/TARGETED/MRMMapping.h>
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) |
Maps input chromatograms to assays in a targeted experiment. More... | |
MRMMapping (const MRMMapping &rhs) | |
copy constructor More... | |
MRMMapping & | operator= (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... | |
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
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 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< 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... | |
A class to map targeted assays to chromatograms.
MRMMapping | ( | ) |
default constructor
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destructor
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copy constructor
void mapExperiment | ( | const OpenMS::PeakMap & | input_chromatograms, |
const OpenMS::TargetedExperiment & | targeted_exp, | ||
OpenMS::PeakMap & | output | ||
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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.
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assignment operator
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overrideprotectedvirtual |
Synchronize members with param class.
Reimplemented from DefaultParamHandler.
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