NuXLFDR.h

Go to the documentation of this file.

// Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $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/PeptideIdentificationList.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);
 
    void splitIntoPeptidesAndXLs(const PeptideIdentificationList& peptide_ids,
      PeptideIdentificationList& pep_pi,
      PeptideIdentificationList& xl_pi) const;
 
    void mergePeptidesAndXLs(const PeptideIdentificationList& pep_pi,
      const PeptideIdentificationList& xl_pi,
      PeptideIdentificationList& peptide_ids) const;
 
    void QValueAtPSMLevel(PeptideIdentificationList& peptide_ids) const;
 
    void calculatePeptideAndXLQValueAtPSMLevel(const PeptideIdentificationList& peptide_ids,
      PeptideIdentificationList& pep_pi,
      PeptideIdentificationList& xl_pi) const;
 
    void calculatePeptideAndXLQValueAndFilterAtPSMLevel(
      const std::vector<ProteinIdentification>& protein_ids,
      const PeptideIdentificationList& peptide_ids,
      PeptideIdentificationList& pep,
      double peptide_PSM_qvalue_threshold,
      double peptide_peptide_qvalue_threshold,
      PeptideIdentificationList& xl_pi,
      std::vector<double> xl_PSM_qvalue_thresholds,
      std::vector<double> xl_peptidelevel_qvalue_thresholds,
      const std::string& out_idxml,
      int decoy_factor) const;
 
  private:
    size_t report_top_hits_; 
};
 
}