OpenMS
SpectraSTSimilarityScore.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2023.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: David Wojnar $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
39 
40 namespace OpenMS
41 {
42 
62  class OPENMS_DLLAPI SpectraSTSimilarityScore :
64  {
65 public:
66 
67  // @name Constructors and Destructors
68  // @{
71 
74 
77  // @}
78 
81 
85  double operator()(const PeakSpectrum & spec1, const PeakSpectrum & spec2) const override;
89  double operator()(const BinnedSpectrum & bin1, const BinnedSpectrum & bin2) const;
93  double operator()(const PeakSpectrum & spec) const override;
94 
103  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);
104 
105 
108 
116  double dot_bias(const BinnedSpectrum & bin1, const BinnedSpectrum & bin2, double dot_product = -1) const;
117 
128  double delta_D(double top_hit, double runner_up);
129 
138  double compute_F(double dot_product, double delta_D, double dot_bias);
139 
140 
141 
144 
146  static const String getProductName()
147  {
148  return "SpectraSTSimilarityScore";
149  }
150 
151 protected:
152 
153 
154  };
155 
156 }
This is a binned representation of a PeakSpectrum.
Definition: BinnedSpectrum.h:81
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
Base class for compare functors of spectra, that return a similarity value for two spectra.
Definition: PeakSpectrumCompareFunctor.h:54
Similarity score of SpectraST.
Definition: SpectraSTSimilarityScore.h:64
SpectraSTSimilarityScore & operator=(const SpectraSTSimilarityScore &source)
assignment operator
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.
double delta_D(double top_hit, double runner_up)
calculates the normalized distance between top_hit and runner_up.
~SpectraSTSimilarityScore() override
destructor
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.
double operator()(const BinnedSpectrum &bin1, const BinnedSpectrum &bin2) const
: calculates the dot product of the two spectra
SpectraSTSimilarityScore()
default constructor
double operator()(const PeakSpectrum &spec1, const PeakSpectrum &spec2) const override
: calculates the dot product of the two spectra
double operator()(const PeakSpectrum &spec) const override
: calculates the dot product of itself
SpectraSTSimilarityScore(const SpectraSTSimilarityScore &source)
copy constructor
BinnedSpectrum transform(const PeakSpectrum &spec)
spectrum is transformed into a binned spectrum with bin size 1 and spread 1 and the intensities are n...
static PeakSpectrumCompareFunctor * create()
Definition: SpectraSTSimilarityScore.h:143
double compute_F(double dot_product, double delta_D, double dot_bias)
computes the overall all score
static const String getProductName()
Reimplemented from PeakSpectrumCompareFunctor.
Definition: SpectraSTSimilarityScore.h:146
A more convenient string class.
Definition: String.h:60
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48