ProteaseDB.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: Xiao Liang $
// $Authors: Xiao Liang, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/DigestionEnzymeDB.h>
#include <OpenMS/CHEMISTRY/DigestionEnzymeProtein.h>
#include <OpenMS/DATASTRUCTURES/StringUtils.h>
 
#include <memory>
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI ProteaseDB: public DigestionEnzymeDB<DigestionEnzymeProtein, ProteaseDB>
  {
    // allow access to constructor in DigestionEnzymeDB::getInstance():
    friend class DigestionEnzymeDB<DigestionEnzymeProtein, ProteaseDB>;
 
  protected:
    ProteaseDB();
 
  public:
    explicit ProteaseDB(std::vector<std::unique_ptr<DigestionEnzymeDataProvider<DigestionEnzymeProtein>>> providers);
 
    void getAllXTandemNames(std::vector<std::string>& all_names) const;
 
    void getAllCometNames(std::vector<std::string>& all_names) const;
 
    void getAllOMSSANames(std::vector<std::string>& all_names) const;
 
    void getAllMSGFNames(std::vector<std::string>& all_names) const;
 
    void writeTSV(const std::string& filename) const;
  };
}