XQuestScores.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Eugen Netz $
// $Authors: Eugen Netz $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CHEMISTRY/SimpleTSGXLMS.h>
#include <vector>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI XQuestScores
  {
 
  public:
    static float preScore(Size matched_alpha, Size ions_alpha, Size matched_beta, Size ions_beta);
 
    static float preScore(Size matched_alpha, Size ions_alpha);
 
    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);
 
    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);
 
 
    static double logOccupancyProb(const PeakSpectrum& theoretical_spec,  const Size matched_size, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm);
 
    static double weightedTICScoreXQuest(Size alpha_size, Size beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link);
 
    static double weightedTICScore(Size alpha_size, Size beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link);
 
    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);
 
    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);
 
    static std::vector< double > xCorrelation(const PeakSpectrum & spec1, const PeakSpectrum & spec2, Int maxshift, double tolerance);
 
    static double xCorrelationPrescore(const PeakSpectrum & spec1, const PeakSpectrum & spec2, double tolerance);
  };
 
}