SimpleSearchEngineAlgorithm.h

Go to the documentation of this file.

// 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 $
// --------------------------------------------------------------------------
 
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 
#include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>
#include <OpenMS/CHEMISTRY/ModifiedPeptideGenerator.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <string_view>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
 
#include <vector>
 
namespace OpenMS
{
 
class OPENMS_DLLAPI SimpleSearchEngineAlgorithm :
  public DefaultParamHandler,
  public ProgressLogger
{
  public:
    SimpleSearchEngineAlgorithm();
 
    enum class ExitCodes
    {
      EXECUTION_OK,       
      INPUT_FILE_EMPTY,   
      UNEXPECTED_RESULT,  
      UNKNOWN_ERROR,      
      ILLEGAL_PARAMETERS  
    };
 
    ExitCodes search(const std::string& in_spectra,
      const std::string& in_db,
      std::vector<ProteinIdentification>& prot_ids,
      PeptideIdentificationList& pep_ids) const;
  protected:
    void updateMembers_() override;
 
    struct AnnotatedHit_
    {
      std::string_view sequence; 
      SignedSize peptide_mod_index; 
      // Layout: doubles first, then floats, then int, then uint16_t — minimizes padding
      double score = 0; 
      float prefix_fraction = 0; 
      float suffix_fraction = 0; 
      float mean_error = 0.0f; 
      int isotope_error = 0; 
      uint16_t matched_prefix_ions = 0; 
      uint16_t matched_suffix_ions = 0; 
 
      static bool hasBetterScore(const AnnotatedHit_& a, const AnnotatedHit_& b)
      {
        if (a.score != b.score) return a.score > b.score;
        if (b.peptide_mod_index != a.peptide_mod_index) return a.peptide_mod_index < b.peptide_mod_index;
        // Preserve the historical shortlex order (shorter sequence first, then lexicographic)
        // that OpenMS::StringView::operator< provided before its removal. PeptideIdentification::sort()
        // is a stable_sort by score only, so this tie-break order survives into the idXML output;
        // do NOT simplify to a plain 'a.sequence < b.sequence' (that would be lexicographic and reorder
        // equal-score hits of differing length). See StringView removal.
        if (a.sequence.size() != b.sequence.size()) return a.sequence.size() < b.sequence.size();
        return a.sequence < b.sequence;
      }
    };
 
    static void preprocessSpectra_(PeakMap& exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm);
 
    void postProcessHits_(const PeakMap& exp,
      std::vector<std::vector<SimpleSearchEngineAlgorithm::AnnotatedHit_> >& annotated_hits,
      std::vector<ProteinIdentification>& protein_ids,
      PeptideIdentificationList& peptide_ids,
      Size top_hits,
      const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications,
      const ModifiedPeptideGenerator::MapToResidueType& variable_modifications,
      Size max_variable_mods_per_peptide,
      const StringList& modifications_fixed,
      const StringList& modifications_variable,
      Int peptide_missed_cleavages,
      double precursor_mass_tolerance,
      double fragment_mass_tolerance,
      const std::string& precursor_mass_tolerance_unit_ppm,
      const std::string& fragment_mass_tolerance_unit_ppm,
      const Int precursor_min_charge,
      const Int precursor_max_charge,
      const std::string& enzyme,
      const std::string& database_name) const;
 
    double precursor_mass_tolerance_;       
    std::string precursor_mass_tolerance_unit_;  
 
    Size precursor_min_charge_;             
    Size precursor_max_charge_;             
 
    IntList precursor_isotopes_;            
 
    double fragment_mass_tolerance_;        
 
    std::string fragment_mass_tolerance_unit_;   
 
    StringList modifications_fixed_;        
 
    StringList modifications_variable_;     
 
    Size modifications_max_variable_mods_per_peptide_; 
 
    std::string enzyme_;                         
 
    bool decoys_;                           
 
    double fdr_psm_;                        
 
    StringList annotate_psm_;               
 
    Size peptide_min_size_;                 
    Size peptide_max_size_;                 
    Size peptide_missed_cleavages_;         
    EnzymaticDigestion::Specificity peptide_enzyme_specificity_{EnzymaticDigestion::SPEC_FULL}; 
 
    std::string peptide_motif_;                  
 
    Size report_top_hits_;                  
};
 
} // namespace