OPXLHelper.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Eugen Netz $
// $Authors: Eugen Netz $
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#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 <numeric>

namespace OpenMS
{
  class OPENMS_DLLAPI OPXLHelper
  {
    public:

      struct PeptideIDScoreComparator
      {
        bool operator() (const PeptideIdentification& a, const PeptideIdentification& b) const
        {
          if (a.getHits().size() > 0 && b.getHits().size() > 0)
          {
            return a.getHits()[0].getScore() < b.getHits()[0].getScore();
          }
          else
          {
            return false;
          }
        }
        bool operator() (const PeptideIdentification& a, const double& b) const
        {
          if (a.getHits().size() > 0)
          {
            return a.getHits()[0].getScore() < b;
          }
          else
          {
            return false;
          }
        }
        bool operator() (const double& a, const PeptideIdentification& b) const
        {
          if (b.getHits().size() > 0)
          {
            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<ResidueModification> getModificationsFromStringList(StringList modNames);

      static std::vector<OPXLDataStructs::AASeqWithMass> digestDatabase(std::vector<FASTAFile::FASTAEntry> fasta_db, EnzymaticDigestion digestor, Size min_peptide_length, StringList cross_link_residue1, StringList cross_link_residue2, std::vector<ResidueModification> fixed_modifications, std::vector<ResidueModification> 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,
                                                                                    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(std::vector<PeptideIdentification> & 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 std::vector< PeptideIdentification > combineTopRanksFromPairs(std::vector< PeptideIdentification > & peptide_ids, Size number_top_hits);

      static std::vector <OPXLDataStructs::ProteinProteinCrossLink> collectPrecursorCandidates(IntList precursor_correction_steps, double precursor_mass, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm, std::vector<OPXLDataStructs::AASeqWithMass> filtered_peptide_masses, double cross_link_mass, DoubleList cross_link_mass_mono_link, StringList cross_link_residue1, StringList cross_link_residue2, String cross_link_name);

      static double computePrecursorError(OPXLDataStructs::CrossLinkSpectrumMatch csm, double precursor_mz, int precursor_charge);

      static void isoPeakMeans(OPXLDataStructs::CrossLinkSpectrumMatch& csm, DataArrays::IntegerDataArray& num_iso_peaks_array, std::vector< std::pair< Size, Size > >& matched_spec_linear_alpha, std::vector< std::pair< Size, Size > >& matched_spec_linear_beta, std::vector< std::pair< Size, Size > >& matched_spec_xlinks_alpha, std::vector< std::pair< Size, Size > >& matched_spec_xlinks_beta);

    private:

      // helper function for enumerateCrossLinksAndMasses
      static bool filter_and_add_candidate(std::vector<OPXLDataStructs::XLPrecursor>& mass_to_candidates, const std::vector< double >& spectrum_precursors, std::vector< int >& precursor_correction_positions, bool precursor_mass_tolerance_unit_ppm, double precursor_mass_tolerance, OPXLDataStructs::XLPrecursor precursor);

  };
}