NuXLPresets.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/CHEMISTRY/ResidueDB.h>
#include <OpenMS/CHEMISTRY/Residue.h>
#include <OpenMS/DATASTRUCTURES/StringListUtils.h>
#include <OpenMS/CONCEPT/LogStream.h>
 
namespace OpenMS
{
 
  // MS1 (modifications) and MS2 (fragments) for the different protocols
  namespace NuXLPresets
  {
    StringList getAllPresetsNames(const std::string& custom_presets_file = "");
 
   void getPresets(const std::string& p, 
    const std::string& custom_presets_file,
    StringList& nucleotides, 
    StringList& mapping, 
    StringList& modifications, 
    StringList& fragment_adducts, 
    std::string& can_cross_link,
    std::string& standalone); 
 
    void getPresets(const std::string& p, 
     StringList& nucleotides, 
     StringList& mapping, 
     StringList& modifications, 
     StringList& fragment_adducts, 
     std::string& can_cross_link,
     std::string& standalone);
  }
 
}