FLASHTnTAlgorithm.h

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// Copyright (c) 2002-2024, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Kyowon Jeong $
// $Authors: Kyowon Jeong $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvAlgorithm.h>
#include <OpenMS/CHEMISTRY/Residue.h>
#include <OpenMS/CHEMISTRY/ResidueDB.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/METADATA/ProteinHit.h>
#include <boost/dynamic_bitset.hpp>
#include <iomanip>
#include <iostream>
 
namespace OpenMS
{
class OPENMS_DLLAPI FLASHTnTAlgorithm : public DefaultParamHandler, public ProgressLogger
{
public:
  FLASHTnTAlgorithm();
 
  ~FLASHTnTAlgorithm() override = default;
 
  FLASHTnTAlgorithm(const FLASHTnTAlgorithm&);
 
  FLASHTnTAlgorithm(FLASHTnTAlgorithm&& other) = default;
 
  FLASHTnTAlgorithm& operator=(const FLASHTnTAlgorithm& other);
 
 
  void run(const MSExperiment& map, const std::vector<FASTAFile::FASTAEntry>& fasta_entry);
  void getProteoformHitsMatchedBy(const FLASHHelperClasses::Tag& tag, std::vector<ProteinHit>& hits) const;
  void getTags(std::vector<FLASHHelperClasses::Tag>& tags) const;
  void getProteoforms(std::vector<ProteinHit>& hits) const
  {
    for (const auto& hit : proteoform_hits_)
    {
      hits.push_back(hit);
    }
  }
 
protected:
  void updateMembers_() override;
  void setDefaultParams_();
 
private:
  Param tagger_param_, extender_param_;
  double decoy_factor_ = 0, prsm_fdr_ = 1, pro_fdr_ = 1;
  bool keep_decoy_ = false;
  bool keep_underdetermined_ = true;
  bool multiple_hits_per_spec_ = false;
  std::vector<ProteinHit> proteoform_hits_;
  std::vector<FLASHHelperClasses::Tag> tags_;
  std::map<int, std::vector<int>> matching_hits_indices_;
  bool areConsistent_(const ProteinHit& a, const ProteinHit& b, double tol) const;
  void markRepresentativeProteoformHits_(double tol);
};
} // namespace OpenMS