ProSEAlgorithm.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:  $
// $Authors: Raphael Förster $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 
#include <OpenMS/ANALYSIS/ID/FragmentIndex.h>
#include <OpenMS/ANALYSIS/ID/OpenSearchModificationAnalysis.h>
#include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>
#include <OpenMS/CHEMISTRY/ModifiedPeptideGenerator.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
 
#include <algorithm>   // std::min (used by inline computeModMatchTolerance_)
#include <vector>
 
namespace OpenMS
{
 
class TheoreticalSpectrumGenerator;
 
class OPENMS_DLLAPI ProSEAlgorithm :
  public DefaultParamHandler,
  public ProgressLogger
{
  public:
    ProSEAlgorithm(); 
 
    enum class ExitCodes
    {
      EXECUTION_OK,
      INPUT_FILE_EMPTY,
      UNEXPECTED_RESULT,
      UNKNOWN_ERROR,
      ILLEGAL_PARAMETERS
    };
 
    struct SearchResult
    {
      ExitCodes exit_code = ExitCodes::EXECUTION_OK;
      std::vector<ProteinIdentification> protein_ids;
      PeptideIdentificationList peptide_ids;
      OpenSearchModificationAnalysis::OpenSearchAnalysisResult modification_analysis;
      bool is_open_search = false;
    };
 
    struct MultiFileSearchResult
    {
      std::vector<SearchResult> per_file;
      SearchResult aggregate;
    };
 
    struct SearchContext
    {
      std::vector<FASTAFile::FASTAEntry> db;
      FragmentIndex fragment_index;
 
      bool release_fragment_index_after_scoring = false;
    };
 
    ExitCodes search(const std::string& in_spectra,
      const std::string& in_db,
      std::vector<ProteinIdentification>& prot_ids,
      PeptideIdentificationList& pep_ids) const;
 
    SearchResult searchWithModificationAnalysis(const std::string& in_spectra,
                                                const std::string& in_db,
                                                const std::string& output_base_name = "") const;
 
    ExitCodes search(PeakMap& spectra,
                     const std::vector<FASTAFile::FASTAEntry>& fasta_db,
                     std::vector<ProteinIdentification>& prot_ids,
                     PeptideIdentificationList& pep_ids) const;
 
    SearchContext prepareContext(const std::vector<FASTAFile::FASTAEntry>& fasta_db) const;
 
    ExitCodes search(PeakMap& spectra,
                     SearchContext& ctx,
                     std::vector<ProteinIdentification>& prot_ids,
                     PeptideIdentificationList& pep_ids) const;
 
    SearchResult searchWithModificationAnalysis(PeakMap& spectra,
                                                const std::vector<FASTAFile::FASTAEntry>& fasta_db,
                                                const std::string& output_base_name = "") const;
 
    MultiFileSearchResult searchWithModificationAnalysis(
        const std::vector<std::string>& in_spectra_files,
        const std::vector<FASTAFile::FASTAEntry>& fasta_db,
        const std::vector<std::string>& output_base_names = {},
        const std::string& aggregate_base_name = "") const;
 
    MultiFileSearchResult searchWithModificationAnalysis(
        const std::vector<std::string>& in_spectra_files,
        const std::string& in_db,
        const std::vector<std::string>& output_base_names = {},
        const std::string& aggregate_base_name = "") const;
 
  protected:
    void updateMembers_() override;
 
    struct AnnotatedHit_
    {
      AASequence sequence;
      /*
      std::string_view sequence;
      SignedSize peptide_mod_index; ///< enumeration index of the non-RNA peptide modification
      */
      // Layout: doubles first, then floats, then int, then uint16_t — minimizes padding (40 bytes excluding AASequence)
      double score = 0; 
      double delta_mass = 0.0; 
      float prefix_fraction = 0; 
      float suffix_fraction = 0; 
      float mean_error = 0.0f; 
      int isotope_error = 0; 
      uint16_t applied_charge = 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;
        return a.sequence < b.sequence;
      }
    };
 
    static void preprocessSpectra_(PeakMap& exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm);
 
    std::vector<FASTAFile::FASTAEntry> buildDecoyAugmentedDB_(
        const std::vector<FASTAFile::FASTAEntry>& fasta_db) const;
 
    std::vector<FASTAFile::FASTAEntry> buildCalibrationSample_(
        const std::vector<FASTAFile::FASTAEntry>& full_db) const;
 
    ExitCodes searchChunked_(
        PeakMap& spectra,
        std::vector<FASTAFile::FASTAEntry>& full_db,
        std::vector<ProteinIdentification>& protein_ids,
        PeptideIdentificationList& peptide_ids) const;
 
    void scoreSpectraAgainstIndex_(
        const PeakMap& spectra,
        FragmentIndex& fi,
        const std::vector<FASTAFile::FASTAEntry>& db,
        const TheoreticalSpectrumGenerator& spectrum_generator,
        double effective_fragment_tol,
        bool fragment_mass_tolerance_unit_ppm,
        bool open_search_mode,
        std::vector<std::vector<AnnotatedHit_>>& annotated_hits,
        const std::string& progress_label) const;
 
    void postProcessHits_(const PeakMap& exp,
      std::vector<std::vector<ProSEAlgorithm::AnnotatedHit_> >& annotated_hits,
      std::vector<ProteinIdentification>& protein_ids,
      PeptideIdentificationList& peptide_ids,
      Size top_hits,
      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;
 
    mutable double precursor_mass_tolerance_lower_{20.0};   
    mutable double precursor_mass_tolerance_upper_{20.0};   
    std::string precursor_mass_tolerance_unit_{"ppm"};
 
    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_;
    std::string decoy_prefix_;
 
    double fdr_psm_{0.0};
    double fdr_protein_{0.0};
 
    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_;
 
    bool add_a_ions_{false};
    bool add_b_ions_{true};
    bool add_c_ions_{false};
    bool add_x_ions_{false};
    bool add_y_ions_{true};
    bool add_z_ions_{false};
 
    Size database_chunk_size_{0};  
 
    bool calibration_enabled_{false};
    double calibration_subset_ratio_{0.1};
    Size calibration_min_psms_{50};
 
    struct CalibrationResult_
    {
      double precursor_shift{0};     
      double precursor_spread{0};    
      double cal_lower{0};           
      double cal_upper{0};           
      double fragment_tolerance{0};  
      double fragment_shift{0};      
      bool extreme_bias{false};      
      bool success{false};           
    };
 
    mutable CalibrationResult_ last_calibration_result_;
 
    mutable double last_mod_match_tolerance_used_{-1.0};
 
    double computeModMatchTolerance_() const
    {
      if (precursor_mass_tolerance_lower_ <= 0.0) return precursor_mass_tolerance_upper_;
      if (precursor_mass_tolerance_upper_ <= 0.0) return precursor_mass_tolerance_lower_;
      return std::min(precursor_mass_tolerance_lower_, precursor_mass_tolerance_upper_);
    }
 
    CalibrationResult_ runCalibrationPass_(PeakMap& spectra,
                                           FragmentIndex& fragment_index,
                                           const std::vector<FASTAFile::FASTAEntry>& db) const;
 
    void logModificationAnalysisSummary_(const SearchResult& result,
                                         const std::string& output_base_name) const;
 
    void logSearchDiagnostics_(const PeakMap& spectra,
                               const std::vector<ProteinIdentification>& protein_ids,
                               const PeptideIdentificationList& peptide_ids) const;
 
    bool isOpenSearchMode_() const
    {
      return FragmentIndex::isOpenSearchMode(precursor_mass_tolerance_lower_,
                                             precursor_mass_tolerance_upper_,
                                             precursor_mass_tolerance_unit_ == "ppm");
    }
};
 
} // namespace