FASTAFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// $Maintainer: Timo Sachsenberg $
// $Authors: Nico Pfeifer, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/DATASTRUCTURES/String.h>
 
#include <functional>
#include <fstream>
#include <memory>
#include <utility>
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI FASTAFile
  {
public:
    struct FASTAEntry
  {
      String identifier;
      String description;
      String sequence;
 
      FASTAEntry() :
        identifier(),
        description(),
        sequence()
      {
      }
 
      FASTAEntry(String id, String desc, String seq) :
        identifier(id),
        description(desc),
        sequence(seq)
      {
      }
      
      FASTAEntry(const FASTAEntry& rhs)
        :
        identifier(rhs.identifier),
        description(rhs.description),
        sequence(rhs.sequence)
      {
      }
 
      FASTAEntry(FASTAEntry&& rhs) noexcept
       :
        identifier(::std::move(rhs.identifier)),
        description(::std::move(rhs.description)),
        sequence(::std::move(rhs.sequence)) 
      {
      }
 
      FASTAEntry& operator=(const FASTAEntry& rhs)
      {
        if (*this == rhs) return *this;
        identifier = rhs.identifier;
        description = rhs.description;
        sequence = rhs.sequence;
        return *this;
      }
 
      bool operator==(const FASTAEntry& rhs) const
      {
        return identifier == rhs.identifier
               && description == rhs.description
               && sequence == rhs.sequence;
      }
    
      bool headerMatches(const FASTAEntry& rhs) const
      {
        return identifier == rhs.identifier && 
         description == rhs.description;
      }
 
      bool sequenceMatches(const FASTAEntry& rhs) const
      {
        return sequence == rhs.sequence;
      }
    };
 
    FASTAFile();
 
    virtual ~FASTAFile();
 
    void readStart(const String& filename);
 
    bool readNext(FASTAEntry& protein);
 
    std::streampos position() const;
 
    bool atEnd() const;
 
    bool setPosition(const std::streampos& pos);
 
    void writeStart(const String& filename);
 
    void writeNext(const FASTAEntry& protein);
 
    void writeEnd();
    
 
    void static load(const String& filename, std::vector<FASTAEntry>& data);
 
    void static store(const String& filename, const std::vector<FASTAEntry>& data);
 
protected:
    std::fstream infile_;   
    std::ofstream outfile_; 
    std::unique_ptr<void, std::function<void(void*) > > reader_; 
    Size entries_read_; 
  };
 
} // namespace OpenMS