NuXLFDR.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/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/Param.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/ANALYSIS/NUXL/NuXLReport.h>
#include <vector>

namespace OpenMS
{

class OPENMS_DLLAPI NuXLFDR
{
  public:
    explicit NuXLFDR(size_t report_top_hits);

    // split by meta value "NuXL:isXL" == 0
    void splitIntoPeptidesAndXLs(const std::vector<PeptideIdentification>& peptide_ids, 
      std::vector<PeptideIdentification>& pep_pi, 
      std::vector<PeptideIdentification>& xl_pi) const;

    void mergePeptidesAndXLs(const std::vector<PeptideIdentification>& pep_pi, 
      const std::vector<PeptideIdentification>& xl_pi, 
      std::vector<PeptideIdentification>& peptide_ids) const;

    // calculate PSM-level q-values (irrespective of XL/non-XL class)
    void QValueAtPSMLevel(std::vector<PeptideIdentification>& peptide_ids) const;

    // calculate PSM-level q-values for XL and non-XL class separately.
    void calculatePeptideAndXLQValueAtPSMLevel(const std::vector<PeptideIdentification>& peptide_ids, 
      std::vector<PeptideIdentification>& pep_pi, 
      std::vector<PeptideIdentification>& xl_pi) const;

    // calculate separate FDRs, filter decoys, write PSM and protein reports
    void calculatePeptideAndXLQValueAndFilterAtPSMLevel(
      const std::vector<ProteinIdentification>& protein_ids,
      const std::vector<PeptideIdentification>& peptide_ids, 
      std::vector<PeptideIdentification>& pep,
      double peptide_PSM_qvalue_threshold,
      double peptide_peptide_qvalue_threshold,
      std::vector<PeptideIdentification>& xl_pi,
      std::vector<double> xl_PSM_qvalue_thresholds,
      std::vector<double> xl_peptidelevel_qvalue_thresholds,
      const String& out_idxml,
      int decoy_factor) const;

  private:
    size_t report_top_hits_;
};

}