NuXLAnnotatedHit.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 2002-2020.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/METADATA/PeptideHit.h> // for PeakAnnotation
#include <OpenMS/DATASTRUCTURES/StringView.h>

namespace OpenMS
{
class NuXLAnnotatedHit
{
  public:
  /*
     Slim indices/views to lookup the actual sequence
   */
  StringView sequence;
  SignedSize peptide_mod_index = 0; // enumeration index of the non-NA peptide modification
  Size NA_mod_index = 0; // index of the NA modification
  Size NA_adduct_amb_index = 0; // store index the entry in the set of ambiguous precursor adducts (e.g, C-NH3 vs. U-H2O)

  int isotope_error = 0; // wheter the hit has been matched with isotopic misassignment

  static constexpr const char UNKNOWN_NUCLEOTIDE = '?';
  char cross_linked_nucleotide = UNKNOWN_NUCLEOTIDE;

  float score = 0;

  float mass_error_p = 0;

  //
  // Scores exclusively calculated from peaks without nucleotide shifts:
  //
  
  float total_loss_score = 0;

  float immonium_score = 0;
  float precursor_score = 0;

  float MIC = 0;
  float err = 0;
  float Morph = 0;

  float modds = 0;

  //
  // Scores exclusively calculated from nucleotide shifted peaks:
  //
 
  float partial_loss_score = 0;

  float pl_MIC = 0;
  float pl_err = 0.0;
  float pl_Morph = 0;

  /*
     The match odds (-log10) of observing this number of b-,a-, and y-ions with nucleotide shifts assuming a uniform distribution of noise peaks.      
  */
  float pl_modds = 0;

  /*
     The MIC of precursor with all nucleotide shifts.
     Three variants: No additional loss, loss of water, and loss ammonia.
     Charge states considered: 1..N (precursor charge)
  */
  float pl_pc_MIC = 0;

  float pl_im_MIC = 0;

  //
  // Scores calculated from peaks with AND without nucleotide shifts:
  //
  
  float total_MIC = 0;

  float marker_ions_score = 0;

  float ladder_score = 0;
  float sequence_score = 0;

  float best_localization_score = 0;
  String localization_scores = 0;
  String best_localization;
  int best_localization_position = -1; // UNKNOWN
  std::vector<PeptideHit::PeakAnnotation> fragment_annotations;

  size_t tag_unshifted = 0;
  size_t tag_shifted = 0;
  size_t tag_XLed = 0;  // tag that contains the transition from unshifted to shifted

  double explained_peak_fraction = 0;
  double matched_theo_fraction = 0;
  double wTop50 = 0;

  size_t n_theoretical_peaks = 0;

  static bool hasBetterScore(const NuXLAnnotatedHit& a, const NuXLAnnotatedHit& b)
  {
    return a.score > b.score;
  }
};
}