IMSAlphabet.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
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//    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.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Anton Pervukhin <Anton.Pervukhin@CeBiTec.Uni-Bielefeld.DE> $
// --------------------------------------------------------------------------
//

#pragma once

#include <vector>
#include <string>
#include <ostream>

#include <OpenMS/CONCEPT/Exception.h>

#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSElement.h>
#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabetParser.h>

namespace OpenMS
{

  namespace ims
  {

    class OPENMS_DLLAPI IMSAlphabet
    {

public:
      typedef IMSElement element_type;
      typedef element_type::mass_type mass_type;
      typedef element_type::name_type name_type;
      typedef std::vector<element_type> container;
      typedef container::size_type size_type;
      typedef container::iterator iterator;
      typedef container::const_iterator const_iterator;
      typedef std::vector<name_type> name_container;
      typedef name_container::iterator name_iterator;
      typedef name_container::const_iterator const_name_iterator;
      typedef std::vector<mass_type> mass_container;
      typedef mass_container::iterator mass_iterator;
      typedef mass_container::const_iterator const_mass_iterator;
      typedef std::vector<mass_type> masses_type;

      IMSAlphabet() {}


      explicit IMSAlphabet(const container & elements) :
        elements_(elements)
      {}


      IMSAlphabet(const IMSAlphabet & alphabet) :
        elements_(alphabet.elements_)
      {}

      size_type size() const
      {
        return elements_.size();
      }

      const element_type & getElement(size_type index) const
      {
        return elements_[index];
      }

      void setElement(const name_type & name, mass_type mass, bool forced = false);

      bool erase(const name_type & name);

      const element_type & getElement(const name_type & name) const;

      const name_type & getName(size_type index) const;

      mass_type getMass(const name_type & name) const;

      mass_type getMass(size_type index) const;

      masses_type getMasses(size_type isotope_index = 0) const;

      masses_type getAverageMasses() const;

      bool hasName(const name_type & name) const;

      void push_back(const name_type & name, mass_type value)
      {
        push_back(element_type(name, value));
      }

      void push_back(const element_type & element)
      {
        elements_.push_back(element);
      }

      void clear()
      {
        elements_.clear();
      }

      virtual void sortByNames();


      virtual void sortByValues();


      virtual void load(const std::string & fname);


      virtual void load(const std::string & fname, IMSAlphabetParser<> * parser);


      virtual ~IMSAlphabet() {}

private:
      container elements_;

      class OPENMS_DLLAPI MassSortingCriteria_
      {
public:
        bool operator()(const element_type & el1,
                        const element_type & el2) const
        {
          return el1.getMass() < el2.getMass();
        }

      };

    };

    OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const IMSAlphabet & alphabet);

  } // namespace ims

} // namespace OpenMS