OPXLHelper.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: Eugen Netz $
// $Authors: Eugen Netz $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/ANALYSIS/XLMS/OPXLDataStructs.h>
#include <OpenMS/CHEMISTRY/ResidueModification.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>
#include <OpenMS/CHEMISTRY/ModifiedPeptideGenerator.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <numeric>
 
namespace OpenMS
{
  class OPENMS_DLLAPI OPXLHelper
  {
    public:
 
      struct PeptideIDScoreComparator
      {
        bool operator() (const PeptideIdentification& a, const PeptideIdentification& b) const
        {
          if (!a.getHits().empty() && !b.getHits().empty())
          {
            return a.getHits()[0].getScore() < b.getHits()[0].getScore();
          }
          else
          {
            return false;
          }
        }
        bool operator() (const PeptideIdentification& a, const double& b) const
        {
          if (!a.getHits().empty())
          {
            return a.getHits()[0].getScore() < b;
          }
          else
          {
            return false;
          }
        }
        bool operator() (const double& a, const PeptideIdentification& b) const
        {
          if (!b.getHits().empty())
          {
            return a < b.getHits()[0].getScore();
          }
          else
          {
            return false;
          }
        }
      };
 
      static std::vector<OPXLDataStructs::XLPrecursor> enumerateCrossLinksAndMasses(const std::vector<OPXLDataStructs::AASeqWithMass>&  peptides, double cross_link_mass_light, const DoubleList& cross_link_mass_mono_link, const StringList& cross_link_residue1, const StringList& cross_link_residue2, const std::vector< double >& spectrum_precursors, std::vector< int >& precursor_correction_positions, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm);
 
      static std::vector<OPXLDataStructs::AASeqWithMass> digestDatabase(std::vector<FASTAFile::FASTAEntry> fasta_db,
        const EnzymaticDigestion& digestor, Size min_peptide_length, const StringList& cross_link_residue1, const StringList& cross_link_residue2,
        const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications,
        const ModifiedPeptideGenerator::MapToResidueType& variable_modifications,
        Size max_variable_mods_per_peptide);
 
      static std::vector <OPXLDataStructs::ProteinProteinCrossLink> buildCandidates(const std::vector< OPXLDataStructs::XLPrecursor > & candidates,
                                                                                    const std::vector< int > & precursor_corrections,
                                                                                    const std::vector< int > & precursor_correction_positions,
                                                                                    const std::vector<OPXLDataStructs::AASeqWithMass> & peptide_masses,
                                                                                    const StringList & cross_link_residue1,
                                                                                    const StringList & cross_link_residue2,
                                                                                    double cross_link_mass,
                                                                                    const DoubleList & cross_link_mass_mono_link,
                                                                                    const std::vector< double >& spectrum_precursor_vector,
                                                                                    const std::vector< double >& allowed_error_vector,
                                                                                    const String& cross_link_name);
 
      static void buildFragmentAnnotations(std::vector<PeptideHit::PeakAnnotation> & frag_annotations, const std::vector< std::pair< Size, Size > > & matching, const PeakSpectrum & theoretical_spectrum, const PeakSpectrum & experiment_spectrum);
 
      static void buildPeptideIDs(PeptideIdentificationList & peptide_ids, const std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > & top_csms_spectrum, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > & all_top_csms, Size all_top_csms_current_index, const PeakMap & spectra, Size scan_index, Size scan_index_heavy);
 
      static void addProteinPositionMetaValues(std::vector< PeptideIdentification > & peptide_ids);
 
      static void addProteinPositionMetaValues(PeptideIdentificationList & peptide_ids);
 
      static void addXLTargetDecoyMV(std::vector< PeptideIdentification > & peptide_ids);
 
      static void addXLTargetDecoyMV(PeptideIdentificationList & peptide_ids);
 
      static void addBetaAccessions(std::vector< PeptideIdentification > & peptide_ids);
 
      static void addBetaAccessions(PeptideIdentificationList & peptide_ids);
 
      static void removeBetaPeptideHits(std::vector< PeptideIdentification > & peptide_ids);
 
      static void removeBetaPeptideHits(PeptideIdentificationList & peptide_ids);
 
      static void addPercolatorFeatureList(ProteinIdentification& prot_id);
 
      static void computeDeltaScores(std::vector< PeptideIdentification >& peptide_ids);
 
      static void computeDeltaScores(PeptideIdentificationList & peptide_ids);
 
      static std::vector< PeptideIdentification > combineTopRanksFromPairs(std::vector< PeptideIdentification > & peptide_ids, Size number_top_hits);
 
      static std::vector< PeptideIdentification > combineTopRanksFromPairs(PeptideIdentificationList & peptide_ids, Size number_top_hits);
 
      static std::vector <OPXLDataStructs::ProteinProteinCrossLink> collectPrecursorCandidates(const IntList& precursor_correction_steps,
                                                                                                double precursor_mass,
                                                                                                double precursor_mass_tolerance,
                                                                                                bool precursor_mass_tolerance_unit_ppm,
                                                                                                const std::vector<OPXLDataStructs::AASeqWithMass>& filtered_peptide_masses,
                                                                                                double cross_link_mass,
                                                                                                const DoubleList& cross_link_mass_mono_link,
                                                                                                const StringList& cross_link_residue1,
                                                                                                const StringList& cross_link_residue2,
                                                                                                String cross_link_name,
                                                                                                bool use_sequence_tags = false,
                                                                                                const std::vector<std::string>& tags = std::vector<std::string>());
 
      static double computePrecursorError(const OPXLDataStructs::CrossLinkSpectrumMatch& csm, double precursor_mz, int precursor_charge);
 
      static void isoPeakMeans(OPXLDataStructs::CrossLinkSpectrumMatch& csm,
                               const DataArrays::IntegerDataArray& num_iso_peaks_array,
                               const std::vector< std::pair< Size, Size > >& matched_spec_linear_alpha,
                               const std::vector< std::pair< Size, Size > >& matched_spec_linear_beta,
                               const std::vector< std::pair< Size, Size > >& matched_spec_xlinks_alpha,
                               const std::vector< std::pair< Size, Size > >& matched_spec_xlinks_beta);
 
      static void filterPrecursorsByTags(std::vector <OPXLDataStructs::XLPrecursor>& candidates, std::vector< int >& precursor_correction_positions, const std::vector<std::string>& tags);
  };
}