| OpenMS 2.5.0

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

Similarity score of SpectraST. More...

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

Inheritance diagram for SpectraSTSimilarityScore:

## Public Member Functions

SpectraSTSimilarityScore & | operator= (const SpectraSTSimilarityScore &source)
| assignment operator More...
double | operator() (const PeakSpectrum &spec1, const PeakSpectrum &spec2) const override
| : calculates the dot product of the two spectra More...
double | operator() (const BinnedSpectrum &bin1, const BinnedSpectrum &bin2) const
| : calculates the dot product of the two spectra More...
double | operator() (const PeakSpectrum &spec) const override
| : calculates the dot product of itself More...
bool | preprocess (PeakSpectrum &spec, float remove_peak_intensity_threshold=2.01, UInt cut_peaks_below=1000, Size min_peak_number=5, Size max_peak_number=150)
| Preprocesses the spectrum. More...
BinnedSpectrum | transform (const PeakSpectrum &spec)
| spectrum is transformed into a binned spectrum with bin size 1 and spread 1 and the intensities are normalized. More...
double | dot_bias (const BinnedSpectrum &bin1, const BinnedSpectrum &bin2, double dot_product=-1) const
| Calculates how much of the dot product is dominated by a few peaks. More...
double | delta_D (double top_hit, double runner_up)
| calculates the normalized distance between top_hit and runner_up. More...
double | compute_F (double dot_product, double delta_D, double dot_bias)
| : computes the overall all score More...
| SpectraSTSimilarityScore ()
| default constructor More...
| SpectraSTSimilarityScore (const SpectraSTSimilarityScore &source)
| copy constructor More...
| ~SpectraSTSimilarityScore () override
| destructor 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 ()
| Reimplemented from PeakSpectrumCompareFunctor. More...
Static Public Member Functions inherited from PeakSpectrumCompareFunctor
static void | registerChildren ()
| registers all derived products More...
static const String | getProductName ()

## 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

Similarity score of SpectraST.

Unlike the other similarity scores this score is used for matching a spectrum against a whole library, although the dot product seems to be an effective method for scoring on its own. For calculating the SpectraST score, first preprocess the spectra if not already done. Transform them and calculate the dot product and the dot bias. Afterwards get the best two hits and calculate delta_D. Now for every spectrum from the library you can calculate the final score.

The details of the score can be found in: H. Lam et al., Development and validation of a spectral library searching method for peptide identification from MS/MS, Proteomics, 7 , 655-667, 2007

## Constructor & Destructor Documentation

## ◆ SpectraSTSimilarityScore() [1/2]

SpectraSTSimilarityScore | ( |  | ) |

default constructor

## ◆ SpectraSTSimilarityScore() [2/2]

SpectraSTSimilarityScore | ( | const SpectraSTSimilarityScore & | source | ) |

copy constructor

## ◆ ~SpectraSTSimilarityScore()

~SpectraSTSimilarityScore | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ compute_F()

double compute_F | ( | double | dot_product,
|  | double | delta_D,
|  | double | dot_bias
| ) |  |

: computes the overall all score

Parameters

  dot_product | of a match
  delta_D | should be calculated after all dot products for a unidentified spectrum are computed
  dot_bias |

Returns
  the SpectraST similarity score

## ◆ create()

static PeakSpectrumCompareFunctor* create | ( |  | ) |

inline static

## ◆ delta_D()

double delta_D | ( | double | top_hit,
|  | double | runner_up
| ) |  |

calculates the normalized distance between top_hit and runner_up.

Parameters

  top_hit | is the best score for a given match.
  runner_up | a match with a worse score than top_hit, e.g. the second best score.

Returns
  normalized distance

Exceptions

  DividedByZero | exception if top_hit is 0.

Note
  Range of the dot products is between 0 and 1.

## ◆ dot_bias()

double dot_bias | ( | const BinnedSpectrum & | bin1,
|  | const BinnedSpectrum & | bin2,
|  | double | dot_product = `-1`
| ) |  | const

Calculates how much of the dot product is dominated by a few peaks.

Parameters

  dot_product | if -1 this value will be calculated as well.
  bin1 | first spectrum in binned representation
  bin2 | second spectrum in binned representation

## ◆ getProductName()

static const String getProductName | ( |  | ) |

inline static

Reimplemented from PeakSpectrumCompareFunctor.

## ◆ operator()() [1/3]

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

override virtual

: calculates the dot product of the two spectra

Implements PeakSpectrumCompareFunctor.

## ◆ operator()() [2/3]

double operator() | ( | const BinnedSpectrum & | bin1,
|  | const BinnedSpectrum & | bin2
| ) |  | const

: calculates the dot product of the two spectra

## ◆ operator()() [3/3]

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

override virtual

: calculates the dot product of itself

Implements PeakSpectrumCompareFunctor.

## ◆ operator=()

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

assignment operator

## ◆ preprocess()

bool preprocess | ( | PeakSpectrum & | spec,
|  | float | remove_peak_intensity_threshold = `2.01`,
|  | UInt | cut_peaks_below = `1000`,
|  | Size | min_peak_number = `5`,
|  | Size | max_peak_number = `150`
| ) |  |

Preprocesses the spectrum.

The preprocessing removes peak below a intensity threshold, reject spectra that does not have enough peaks, and cuts peaks exceeding the max_peak_number most intense peaks.

Returns
  true if spectrum passes filtering

## ◆ transform()

BinnedSpectrum transform | ( | const PeakSpectrum & | spec | ) |

spectrum is transformed into a binned spectrum with bin size 1 and spread 1 and the intensities are normalized.