OpenSwathScores.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#pragma once

#include <OpenMS/OpenMSConfig.h>
#include <OpenMS/CONCEPT/Types.h>

#include <string>

namespace OpenMS
{

  struct OPENMS_DLLAPI OpenSwath_Scores_Usage
  {
    bool use_coelution_score_ = true;
    bool use_shape_score_ = true;
    bool use_rt_score_ = true;
    bool use_library_score_ = true;
    bool use_elution_model_score_ = true;
    bool use_intensity_score_ = true;
    bool use_total_xic_score_ = true;
    bool use_total_mi_score_ = true;
    bool use_nr_peaks_score_ = true;
    bool use_sn_score_ = true;
    bool use_mi_score_ = true;
    bool use_dia_scores_ = true;
    bool use_sonar_scores = true;
    bool use_ms1_correlation = true;
    bool use_ms1_fullscan = true;
    bool use_ms1_mi = true;
    bool use_uis_scores = true;
  };

  struct OPENMS_DLLAPI OpenSwath_Scores
  {
    double elution_model_fit_score = 0;
    double library_corr = 0;
    double library_norm_manhattan = 0;
    double library_rootmeansquare = 0;
    double library_sangle = 0;
    double norm_rt_score = 0;

    double isotope_correlation = 0;
    double isotope_overlap = 0;
    double massdev_score = 0;
    double xcorr_coelution_score = 0;
    double xcorr_shape_score = 0;

    double yseries_score = 0;
    double bseries_score = 0;
    double log_sn_score = 0;

    double weighted_coelution_score = 0;
    double weighted_xcorr_shape = 0;
    double weighted_massdev_score = 0;
   
    double ms1_xcorr_coelution_score = -1;
    double ms1_xcorr_coelution_contrast_score = 0;
    double ms1_xcorr_coelution_combined_score = 0;
    double ms1_xcorr_shape_score = -1;
    double ms1_xcorr_shape_contrast_score = 0;
    double ms1_xcorr_shape_combined_score = 0;
    double ms1_ppm_score = 0;
    double ms1_isotope_correlation = 0;
    double ms1_isotope_overlap = 0;
    double ms1_mi_score = -1;
    double ms1_mi_contrast_score = 0;
    double ms1_mi_combined_score = 0;

    double sonar_sn = 0;
    double sonar_diff = 0;
    double sonar_trend = 0;
    double sonar_rsq = 0;
    double sonar_shape = 0;
    double sonar_lag = 0;

    double library_manhattan = 0;
    double library_dotprod = 0;
    double intensity = 0;
    double total_xic = 0;
    double nr_peaks = 0;
    double sn_ratio = 0;
    double mi_score = 0;
    double weighted_mi_score = 0;

    double rt_difference = 0;
    double normalized_experimental_rt = 0;
    double raw_rt_score = 0;

    double dotprod_score_dia = 0;
    double manhatt_score_dia = 0;

    OpenSwath_Scores() = default;

    double get_quick_lda_score(double library_corr_,
                               double library_norm_manhattan_,
                               double norm_rt_score_,
                               double xcorr_coelution_score_,
                               double xcorr_shape_score_,
                               double log_sn_score_) const;

    double calculate_lda_prescore(const OpenSwath_Scores& scores) const;

    double calculate_lda_single_transition(const OpenSwath_Scores& scores) const;

    double calculate_swath_lda_prescore(const OpenSwath_Scores& scores) const;

  };

  struct OPENMS_DLLAPI OpenSwath_Ind_Scores
  {
    int ind_num_transitions = 0;
    std::string ind_isotope_correlation = "";
    std::string ind_isotope_overlap = "";
    std::string ind_massdev_score = "";
    std::string ind_xcorr_coelution_score = "";
    std::string ind_xcorr_shape_score = "";
    std::string ind_log_sn_score = "";
    std::string ind_transition_names = "";
    std::string ind_area_intensity = "";
    std::string ind_total_area_intensity = "";
    std::string ind_intensity_score = "";
    std::string ind_apex_intensity = "";
    std::string ind_total_mi = "";
    std::string ind_log_intensity = "";
    std::string ind_intensity_ratio = "";
    std::string ind_mi_ratio = "";
    std::string ind_mi_score = "";

    OpenSwath_Ind_Scores() = default;

  };

}