| OpenMS 2.5.0

Public Member Functions | Private Attributes | List of all members
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:

## 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)
| Score a spectrum given a transition group. More...
void | operator() (OpenSwath::SpectrumAccessPtr swath_ptr, OpenSwath::LightTargetedExperiment &transition_exp_used, OpenSwath::IDataFrameWriter *ivw)
| 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...
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...

## Private Attributes

double | dia_extract_window_
int | nr_isotopes_
int | nr_charges_

## Additional Inherited Members

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...

## 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 | ( |  | ) |

## ◆ 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() | ( | OpenSwath::SpectrumAccessPtr | swath_ptr,
|  | OpenSwath::LightTargetedExperiment & | transition_exp_used,
|  | OpenSwath::IDataFrameWriter * | ivw
| ) |  |

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
| ) |  |

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_ | ( |  | ) |

override virtual

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