| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | Private Member Functions | List of all members
PeakAlignment Class Reference
Spectrum Comparison

make a PeakAlignment of two PeakSpectra More...

`#include <OpenMS/COMPARISON/SPECTRA/PeakAlignment.h>`

Inheritance diagram for PeakAlignment:

## Public Member Functions

| PeakAlignment ()
| default constructor More...
| PeakAlignment (const PeakAlignment &source)
| copy constructor More...
| ~PeakAlignment () override
| destructor More...
PeakAlignment & | operator= (const PeakAlignment &source)
| assignment operator More...
double | operator() (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const override
double | operator() (const PeakSpectrum &spec) const override
| function call operator, calculates self similarity More...
std::vector< std::pair< Size, Size > > | getAlignmentTraceback (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const
| make alignment and get the traceback More...
Public Member Functions inherited from PeakSpectrumCompareFunctor
| PeakSpectrumCompareFunctor ()
| default constructor More...
| PeakSpectrumCompareFunctor (const PeakSpectrumCompareFunctor &source)
| copy constructor More...
| ~PeakSpectrumCompareFunctor () override
| destructor More...
PeakSpectrumCompareFunctor & | operator= (const PeakSpectrumCompareFunctor &source)
| assignment operator 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...

## Static Public Member Functions

static PeakSpectrumCompareFunctor * | create ()
static const String | getProductName ()
| get the identifier for this DefaultParamHandler More...
Static Public Member Functions inherited from PeakSpectrumCompareFunctor
static void | registerChildren ()
| registers all derived products More...
static const String | getProductName ()

## Private Member Functions

double | peakPairScore_ (double &pos1, double &intens1, double &pos2, double &intens2, const double &sigma) const
| calculates the score for aligning two peaks More...

## Additional Inherited Members

Protected Member Functions inherited from DefaultParamHandler
virtual void | updateMembers_ ()
| This method is used to update extra member variables at the end of the setParameters() method. More...
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

make a PeakAlignment of two PeakSpectra

The alignment is done according to the Needleman-Wunsch Algorithm (local alignment considering gaps).

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
epsilon | float | 0.2 |  | defines the absolute error of the mass spectrometer
normalized | int | 1 |  | is set 1 if the similarity-measurement is normalized to the range [0,1]
heuristic_level | int | 0 |  | set 0 means no heuristic is applied otherwise the given value is interpreted as unsigned integer, the number of strongest peaks considered for heurisitcs - in those sets of peaks has to be at least one match to conduct comparison
precursor_mass_tolerance | float | 3.0 |  | Mass tolerance of the precursor peak, defines the distance of two PrecursorPeaks for which they are supposed to be from different peptides

Note:

- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.

## Constructor & Destructor Documentation

## ◆ PeakAlignment() [1/2]

PeakAlignment | ( |  | ) |

default constructor

## ◆ PeakAlignment() [2/2]

PeakAlignment | ( | const PeakAlignment & | source | ) |

copy constructor

## ◆ ~PeakAlignment()

~PeakAlignment | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ create()

static PeakSpectrumCompareFunctor* create | ( |  | ) |

inline static

## ◆ getAlignmentTraceback()

std::vector<std::pair<Size, Size> > getAlignmentTraceback | ( | const PeakSpectrum & | spec1,
|  | const PeakSpectrum & | spec2
| ) |  | const

make alignment and get the traceback

## ◆ getProductName()

static const String getProductName | ( |  | ) |

inline static

get the identifier for this DefaultParamHandler

## ◆ operator()() [1/2]

double operator() | ( | const PeakSpectrum & | spec1,
|  | const PeakSpectrum & | spec2
| ) |  | const

override virtual

function call operator, calculates the similarity of the given arguments

Parameters

  spec1 | First spectrum given in a binned representation
  spec2 | Second spectrum given in a binned representation

Implements PeakSpectrumCompareFunctor.

## ◆ operator()() [2/2]

double operator() | ( | const PeakSpectrum & | spec | ) | const

override virtual

function call operator, calculates self similarity

Implements PeakSpectrumCompareFunctor.

## ◆ operator=()

PeakAlignment& operator= | ( | const PeakAlignment & | source | ) |

assignment operator

## ◆ peakPairScore_()

double peakPairScore_ | ( | double & | pos1,
|  | double & | intens1,
|  | double & | pos2,
|  | double & | intens2,
|  | const double & | sigma
| ) |  | const

private

calculates the score for aligning two peaks