OpenMS  3.0.0
XQuestScores.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 2002-2022.
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: Eugen Netz $
32 // $Authors: Eugen Netz $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
39 #include <OpenMS/CONCEPT/Types.h>
41 #include <vector>
42 
43 namespace OpenMS
44 {
45 
50  class OPENMS_DLLAPI XQuestScores
51  {
52 
53  public:
61  static float preScore(Size matched_alpha, Size ions_alpha, Size matched_beta, Size ions_beta);
62 
68  static float preScore(Size matched_alpha, Size ions_alpha);
69 
79  static double matchOddsScore(const PeakSpectrum& theoretical_spec, const Size matched_size, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool is_xlink_spectrum = false, Size n_charges = 1);
80 
81  static double matchOddsScoreSimpleSpec(const std::vector< SimpleTSGXLMS::SimplePeak >& theoretical_spec, const Size matched_size, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool is_xlink_spectrum = false, Size n_charges = 1);
82 
83 
91  static double logOccupancyProb(const PeakSpectrum& theoretical_spec, const Size matched_size, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm);
92 
103  static double weightedTICScoreXQuest(Size alpha_size, Size beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link);
104 
115  static double weightedTICScore(Size alpha_size, Size beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link);
116 
124  static double matchedCurrentChain(const std::vector< std::pair< Size, Size > >& matched_spec_linear, const std::vector< std::pair< Size, Size > >& matched_spec_xlinks, const PeakSpectrum& spectrum_linear_peaks, const PeakSpectrum& spectrum_xlink_peaks);
125 
135  static double totalMatchedCurrent(const std::vector< std::pair< Size, Size > >& matched_spec_linear_alpha, const std::vector< std::pair< Size, Size > >& matched_spec_linear_beta, const std::vector< std::pair< Size, Size > >& matched_spec_xlinks_alpha, const std::vector< std::pair< Size, Size > >& matched_spec_xlinks_beta, const PeakSpectrum& spectrum_linear_peaks, const PeakSpectrum& spectrum_xlink_peaks);
136 
144  static std::vector< double > xCorrelation(const PeakSpectrum & spec1, const PeakSpectrum & spec2, Int maxshift, double tolerance);
145 
152  static double xCorrelationPrescore(const PeakSpectrum & spec1, const PeakSpectrum & spec2, double tolerance);
153  };
154 
155 }
Types.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
SimpleTSGXLMS.h
OpenMS::XQuestScores
An implementation of the scores for cross-link identification from the xQuest algorithm (O....
Definition: XQuestScores.h:50
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
StandardTypes.h
MSSpectrum.h