RNPxlReport.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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// This software is released under a three-clause BSD license:
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// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/ANALYSIS/RNPXL/RNPxlMarkerIonExtractor.h>
#include <OpenMS/DATASTRUCTURES/ListUtilsIO.h>
 
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/CONCEPT/Constants.h>
 
namespace OpenMS
{
 
struct OPENMS_DLLAPI RNPxlReportRow
{
  bool no_id;
  double rt;
  double original_mz;
  String accessions;
  String RNA;
  String peptide;
  double best_localization_score;
  String localization_scores;
  String best_localization;
  Int charge;
  double score;
  double peptide_weight;
  double RNA_weight;
  double xl_weight;
  double abs_prec_error;
  double rel_prec_error;
  RNPxlMarkerIonExtractor::MarkerIonsType marker_ions;
  double m_H;
  double m_2H;
  double m_3H;
  double m_4H;  
  int rank;
  String getString(const String& separator) const;
 
};
 
struct OPENMS_DLLAPI RNPxlReportRowHeader
{
  static String getString(const String& separator);
};
 
struct OPENMS_DLLAPI RNPxlReport
{
  static std::vector<RNPxlReportRow> annotate(const PeakMap& spectra, std::vector<PeptideIdentification>& peptide_ids, double marker_ions_tolerance);
};
 
}