EntrapmentEvaluation.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
 
#include <map>
#include <string>
#include <unordered_map>
#include <unordered_set>
#include <vector>
 
namespace OpenMS
{
  class PeptideHit;
 
  class OPENMS_DLLAPI EntrapmentEvaluation
  {
  public:
    enum class Kind
    {
      TARGET,     
      ENTRAPMENT, 
      DECOY       
    };
 
    enum class Level
    {
      PSM,     
      PEPTIDE  
    };
 
    struct OPENMS_DLLAPI Result
    {
      Size accepted = 0;                       
      Size entrapment = 0;                     
      Size entrapment_target_not_accepted = 0; 
      Size entrapment_above_target = 0;        
      bool paired = false;                     
      double te_ratio = 1.0;                   
 
      double lowerBoundFDP() const;
      double combinedFDP() const;
      double pairedFDP() const;
    };
 
    using PeptidePairs = std::unordered_map<std::string, std::string>;
 
    static Kind classify(const PeptideHit& hit, const std::string& entrapment_prefix,
                         const std::string& decoy_string = "", bool decoy_is_prefix = true);
 
    static double estimateTERatio(const std::vector<FASTAFile::FASTAEntry>& db,
                                  const std::string& entrapment_prefix,
                                  const std::string& decoy_string,
                                  bool decoy_is_prefix,
                                  const std::string& enzyme = "Trypsin",
                                  Size missed_cleavages = 2,
                                  Size min_length = 7,
                                  Size max_length = 40);
 
    static std::unordered_set<std::string> targetPeptides(const std::vector<FASTAFile::FASTAEntry>& db,
                                                          const std::string& entrapment_prefix,
                                                          const std::string& decoy_string,
                                                          bool decoy_is_prefix,
                                                          const std::string& enzyme = "Trypsin",
                                                          Size missed_cleavages = 2,
                                                          Size min_length = 7,
                                                          Size max_length = 40);
 
    static double qValue(const PeptideIdentification& pep_id, const PeptideHit& hit);
 
    static PeptidePairs pairPeptides(const std::vector<FASTAFile::FASTAEntry>& db,
                                     const std::string& entrapment_prefix,
                                     const std::string& decoy_string,
                                     bool decoy_is_prefix,
                                     const std::string& enzyme = "Trypsin",
                                     Size missed_cleavages = 2,
                                     Size min_length = 7,
                                     Size max_length = 40,
                                     Size* mismatched = nullptr);
 
    static std::map<std::string, Result> evaluate(const PeptideIdentificationList& pep_ids,
                                                  double q_threshold,
                                                  const std::string& entrapment_prefix,
                                                  double te_ratio,
                                                  Level level = Level::PSM,
                                                  const std::string& class_meta_value = "",
                                                  const std::unordered_set<std::string>* target_peptides = nullptr,
                                                  const PeptidePairs* pairs = nullptr,
                                                  const std::string& score_meta_value = "",
                                                  const std::string& decoy_string = "",
                                                  bool decoy_is_prefix = true);
  };
} // namespace OpenMS