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 2002-2017.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_RNPXL_RNPXLREPORT_H
#define OPENMS_ANALYSIS_RNPXL_RNPXLREPORT_H

#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 to hold a single report line
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;
  String fragment_annotation_string;  
  String getString(const String& separator) const;

};

// create header line
struct OPENMS_DLLAPI RNPxlReportRowHeader
{
  static String getString(const String& separator);
};

// create report
struct OPENMS_DLLAPI RNPxlReport
{
  static std::vector<RNPxlReportRow> annotate(const PeakMap& spectra, std::vector<PeptideIdentification>& peptide_ids, double marker_ions_tolerance);
};

}

#endif