NuXLAnnotateAndLocate.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: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/CHEMISTRY/ModifiedPeptideGenerator.h>
#include "NuXLParameterParsing.h"
#include "NuXLAnnotatedHit.h"
#include "NuXLSiteLocalization.h"
 
#include <set>
#include <map>
#include <vector>
#include <algorithm>
 
namespace OpenMS
{
class NuXLAnnotateAndLocate
{
  public:
 
  static void annotateAndLocate_(
    const PeakMap& exp,
    std::vector<std::vector<NuXLAnnotatedHit>>& annotated_hits,
    const NuXLModificationMassesResult& mm,
    const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications,
    const ModifiedPeptideGenerator::MapToResidueType& variable_modifications,
    Size max_variable_mods_per_peptide,
    double fragment_mass_tolerance,
    bool fragment_mass_tolerance_unit_ppm,
    const NuXLParameterParsing::PrecursorsToMS2Adducts & all_feasible_adducts,
    bool nhs_localization = false,
    const NuXLSiteLocalization::ProteinTermini* protein_termini = nullptr,
    bool enzyme_cleaves_after_lysine = false);
 
};
} // namespace OpenMS