OpenMS
DiaPrescore Class Reference

Scoring of an spectrum given library intensities of a transition group. More...

#include <OpenMS/ANALYSIS/OPENSWATH/DIAPrescoring.h>

Inheritance diagram for DiaPrescore:
[legend]
Collaboration diagram for DiaPrescore:
[legend]

Public Member Functions

 DiaPrescore ()
 
 DiaPrescore (double dia_extract_window, int nr_isotopes=4, int nr_charges=4)
 
void defineDefaults ()
 
void updateMembers_ () override
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
void score (OpenSwath::SpectrumPtr spec, const std::vector< OpenSwath::LightTransition > &lt, double &dotprod, double &manhattan) const
 Score a spectrum given a transition group. More...
 
void operator() (const OpenSwath::SpectrumAccessPtr &swath_ptr, OpenSwath::LightTargetedExperiment &transition_exp_used, OpenSwath::IDataFrameWriter *ivw) const
 Compute manhattan and dotprod score for all spectra which can be accessed by the SpectrumAccessPtr for all transitions groups in the LightTargetedExperiment. 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...
 

Private Attributes

double dia_extract_window_
 
int nr_isotopes_
 
int nr_charges_
 

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 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

Scoring of an spectrum given library intensities of a transition group.

In DIA (data independent acquisition) / SWATH analysis, at each chromatographic point a full MS2 spectrum is recorded. This class allows to compute a number of scores based on the full MS2 spectrum available. The scores are the following:

See also class DIAScoring.

Simulate theoretical spectrum from library intensities of transition group and compute manhattan distance and dotprod score between spectrum intensities and simulated spectrum.

Constructor & Destructor Documentation

◆ DiaPrescore() [1/2]

◆ DiaPrescore() [2/2]

DiaPrescore ( double  dia_extract_window,
int  nr_isotopes = 4,
int  nr_charges = 4 
)

Member Function Documentation

◆ defineDefaults()

void defineDefaults ( )

◆ operator()()

void operator() ( const OpenSwath::SpectrumAccessPtr swath_ptr,
OpenSwath::LightTargetedExperiment transition_exp_used,
OpenSwath::IDataFrameWriter ivw 
) const

Compute manhattan and dotprod score for all spectra which can be accessed by the SpectrumAccessPtr for all transitions groups in the LightTargetedExperiment.

◆ score()

void score ( OpenSwath::SpectrumPtr  spec,
const std::vector< OpenSwath::LightTransition > &  lt,
double &  dotprod,
double &  manhattan 
) const

Score a spectrum given a transition group.

Simulate theoretical spectrum from library intensities of transition group and compute manhattan distance and dotprod score between spectrum intensities and simulated spectrum.

◆ updateMembers_()

void updateMembers_ ( )
overridevirtual

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

◆ dia_extract_window_

double dia_extract_window_
private

◆ nr_charges_

int nr_charges_
private

◆ nr_isotopes_

int nr_isotopes_
private