2.5.0/html/OpenSwathScores_8h_source.html

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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 2002-2020.

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// This software is released under a three-clause BSD license:

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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"

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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 <OpenMS/DATASTRUCTURES/String.h>

#include <vector>


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_im_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 im_xcorr_coelution_score = 0;

    double im_xcorr_shape_score = 0;

    double im_delta_score = 0;

    double im_ms1_delta_score = 0;

    double im_drift = 0;

    double im_drift_weighted = 0;

    double im_ms1_contrast_coelution = 0;

    double im_ms1_contrast_shape = 0;

    double im_ms1_sum_contrast_coelution = 0;

    double im_ms1_sum_contrast_shape = 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::vector<OpenMS::String> ind_transition_names;

    std::vector<double> ind_isotope_correlation;

    std::vector<double> ind_isotope_overlap;

    std::vector<double> ind_massdev_score;

    std::vector<double> ind_xcorr_coelution_score;

    std::vector<double> ind_xcorr_shape_score;

    std::vector<double> ind_log_sn_score;

    std::vector<double> ind_area_intensity;

    std::vector<double> ind_total_area_intensity;

    std::vector<double> ind_intensity_score;

    std::vector<double> ind_apex_intensity;

    std::vector<double> ind_total_mi;

    std::vector<double> ind_log_intensity;

    std::vector<double> ind_intensity_ratio;

    std::vector<double> ind_mi_ratio;

    std::vector<double> ind_mi_score;


    OpenSwath_Ind_Scores() = default;


  };


}