Tagger.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: Timo Sachsenberg, Eugen Netz $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <map>
 
namespace OpenMS
{
  class MSSpectrum;
 
  class OPENMS_DLLAPI Tagger
  {
    public:
      Tagger(size_t min_tag_length, double tolerance, size_t max_tag_length = 65535, size_t min_charge = 1, size_t max_charge = 1, const StringList& fixed_mods = StringList(), const StringList& var_mods = StringList(), bool tol_is_ppm = true);
 
      void getTag(const std::vector<double>& mzs, std::vector<std::string>& tags) const;
 
      void getTag(const MSSpectrum& spec, std::vector<std::string>& tags) const;
 
      void setMaxCharge(size_t max_charge);
 
 
    private:
      double min_gap_; 
      double max_gap_; 
      double tolerance_; 
      bool tol_is_ppm_; 
      size_t min_tag_length_; 
      size_t max_tag_length_; 
      size_t min_charge_; 
      size_t max_charge_; 
      std::map<double, char> mass2aa_; 
 
      char getAAByMass_(double m) const;
 
      void getTag_(std::string& tag, const std::vector<double>& mzs, const size_t i, std::vector<std::string>& tags, const size_t charge) const;
  };
}