OpenMS
MassFeatureTrace Class Reference

Feature trace in mass dimension for FLASHDeconv This class performs mass tracing on the deconvolved masses by FLASHDeconvAlgorithm In other words, per spectrum deconvolved masses are converted into deconvolved features Currently only works for MS1 spectra. (Top-down DIA is not yet used much). Every time an MS1 spectrum is deconvolved, the relevant information is stored in this class. Tracing is performed at the end of FLASHDeconv run. This class also comes with tsv, TopFD, ProMex format output functions. More...

#include <OpenMS/ANALYSIS/TOPDOWN/MassFeatureTrace.h>

Inheritance diagram for MassFeatureTrace:
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Collaboration diagram for MassFeatureTrace:
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Public Types

typedef FLASHDeconvHelperStructs::PrecalculatedAveragine PrecalculatedAveragine
 
typedef FLASHDeconvHelperStructs::LogMzPeak LogMzPeak
 

Public Member Functions

 MassFeatureTrace ()
 constructor More...
 
 ~MassFeatureTrace () override=default
 destructor More...
 
 MassFeatureTrace (const MassFeatureTrace &)=default
 copy constructor More...
 
 MassFeatureTrace (MassFeatureTrace &&other)=default
 move constructor More...
 
MassFeatureTraceoperator= (const MassFeatureTrace &fd)=default
 assignment operator More...
 
MassFeatureTraceoperator= (MassFeatureTrace &&fd)=default
 
void storeInformationFromDeconvolvedSpectrum (DeconvolvedSpectrum &deconvolved_spectrum)
 Obtain and store information from deconvolved_spectrum (necessary information for mass tracing afterwards) More...
 
std::vector< FLASHDeconvHelperStructs::MassFeaturefindFeatures (const PrecalculatedAveragine &averagine)
 Find mass features. 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...
 
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...
 

Protected Member Functions

void updateMembers_ () override
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Private Attributes

double min_isotope_cosine_
 cosine thresholds for scoring and filtering More...
 
std::map< double, std::map< double, PeakGroup > > peak_group_map_
 peak group information is stored in here for tracing More...
 

Additional Inherited Members

- 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 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

Feature trace in mass dimension for FLASHDeconv This class performs mass tracing on the deconvolved masses by FLASHDeconvAlgorithm In other words, per spectrum deconvolved masses are converted into deconvolved features Currently only works for MS1 spectra. (Top-down DIA is not yet used much). Every time an MS1 spectrum is deconvolved, the relevant information is stored in this class. Tracing is performed at the end of FLASHDeconv run. This class also comes with tsv, TopFD, ProMex format output functions.

Member Typedef Documentation

◆ LogMzPeak

◆ PrecalculatedAveragine

Constructor & Destructor Documentation

◆ MassFeatureTrace() [1/3]

constructor

◆ ~MassFeatureTrace()

~MassFeatureTrace ( )
overridedefault

destructor

◆ MassFeatureTrace() [2/3]

MassFeatureTrace ( const MassFeatureTrace )
default

copy constructor

◆ MassFeatureTrace() [3/3]

MassFeatureTrace ( MassFeatureTrace &&  other)
default

move constructor

Member Function Documentation

◆ findFeatures()

std::vector<FLASHDeconvHelperStructs::MassFeature> findFeatures ( const PrecalculatedAveragine averagine)

Find mass features.

Parameters
averagineprecalculated averagine for cosine calculation

◆ operator=() [1/2]

MassFeatureTrace& operator= ( const MassFeatureTrace fd)
default

assignment operator

◆ operator=() [2/2]

MassFeatureTrace& operator= ( MassFeatureTrace &&  fd)
default

◆ storeInformationFromDeconvolvedSpectrum()

void storeInformationFromDeconvolvedSpectrum ( DeconvolvedSpectrum deconvolved_spectrum)

Obtain and store information from deconvolved_spectrum (necessary information for mass tracing afterwards)

◆ updateMembers_()

void updateMembers_ ( )
overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ min_isotope_cosine_

double min_isotope_cosine_
private

cosine thresholds for scoring and filtering

◆ peak_group_map_

std::map<double, std::map<double, PeakGroup> > peak_group_map_
private

peak group information is stored in here for tracing