NuXLFDR.h

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// 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 "NuXLReport.h"
#include <string>
#include <vector>
 
namespace OpenMS
{
 
class FalseDiscoveryRate;
 
class NuXLFDR
{
  public:
    enum class XLGroups
    {
      OFF,  
      ON,   
      AUTO  
    };
 
    static constexpr Size SHORT_XL_MAX_LENGTH = 9;      
    static constexpr Size SHORT_XL_MIN_NA_LENGTH = 2;   
    static constexpr Size AUTO_MIN_DECOYS = 10;         
    static constexpr double AUTO_FDR = 0.1;             
 
    explicit NuXLFDR(size_t report_top_hits, XLGroups xl_groups = XLGroups::OFF);
 
    static XLGroups xlGroupsFromString(const std::string& s);
 
    static bool isShortXL(const PeptideHit& hit);
 
    bool useShortXLGroup(const PeptideIdentificationList& xl_pi, Size& short_decoys) const;
 
    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:
    void setUpFDR_(FalseDiscoveryRate& fdr) const;
 
    size_t report_top_hits_; 
    XLGroups xl_groups_; 
};
 
}