RibonucleotideDB.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/Ribonucleotide.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <unordered_map>
 
namespace OpenMS
{
  class OPENMS_DLLAPI RibonucleotideDB
  {
  public:
    using ConstRibonucleotidePtr = const Ribonucleotide *;
 
    typedef std::vector<ConstRibonucleotidePtr>::const_iterator ConstIterator;
 
    static RibonucleotideDB* getInstance();
 
    virtual ~RibonucleotideDB();
 
    RibonucleotideDB(const RibonucleotideDB& other) = delete;
 
    RibonucleotideDB& operator=(const RibonucleotideDB& other) = delete;
 
    inline ConstIterator begin() const
    {
      return ribonucleotides_.begin();
    }
 
    inline ConstIterator end() const
    {
      return ribonucleotides_.end();
    }
 
    ConstRibonucleotidePtr getRibonucleotide(const std::string& code);
 
    ConstRibonucleotidePtr getRibonucleotidePrefix(const std::string& seq);
 
    std::pair<ConstRibonucleotidePtr, ConstRibonucleotidePtr> getRibonucleotideAlternatives(const std::string& code);
 
 
  protected:
    RibonucleotideDB();
 
    void readFromFile_(const std::string& path);
 
    ConstRibonucleotidePtr parseRow_(const std::string& row, Size line_count);
 
    std::vector<ConstRibonucleotidePtr> ribonucleotides_;
 
    std::unordered_map<std::string, Size> code_map_;
 
    std::map<std::string, std::pair<ConstRibonucleotidePtr, ConstRibonucleotidePtr>> ambiguity_map_;
 
    Size max_code_length_;
  };
}