FastaIterator.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// $Maintainer: Clemens Groepl, Andreas Bertsch $
// $Authors: Chris Bauer $
// --------------------------------------------------------------------------


#ifndef OPENMS_FORMAT_FASTAITERATOR_H
#define OPENMS_FORMAT_FASTAITERATOR_H

#include <OpenMS/CHEMISTRY/PepIterator.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <fstream>
#include <vector>

namespace OpenMS
{

  class OPENMS_DLLAPI FastaIterator :
    public PepIterator
  {

public:

    typedef std::pair<String, String> FASTAEntry;
    FastaIterator();


    virtual ~FastaIterator();

    virtual FASTAEntry operator*();

    virtual PepIterator & operator++();

    virtual PepIterator * operator++(int i);

    virtual void setFastaFile(const String & f);

    virtual String getFastaFile();

    virtual void setSpectrum(const std::vector<DoubleReal> &)
    {
      throw Exception::NotImplemented(__FILE__, __LINE__, __PRETTY_FUNCTION__);
    }

    virtual const std::vector<DoubleReal> & getSpectrum()
    {
      throw Exception::NotImplemented(__FILE__, __LINE__, __PRETTY_FUNCTION__);
    }

    virtual void setTolerance(DoubleReal /* t */)
    {
      throw Exception::NotImplemented(__FILE__, __LINE__, __PRETTY_FUNCTION__);
    }

    virtual DoubleReal getTolerance()
    {
      throw Exception::NotImplemented(__FILE__, __LINE__, __PRETTY_FUNCTION__);
    }

    virtual bool begin();

    virtual bool isAtEnd();

    static const String getProductName()
    {
      return "FastaIterator";
    }

    static PepIterator * create()
    {
      return new FastaIterator;
    }

protected:
    virtual std::string next_();

    bool is_at_end_;     

    std::ifstream input_file_;     

    String fasta_file_;     

    std::string actual_seq_;     

    std::string header_;     

    std::string last_header_;     

private:
    FastaIterator(const FastaIterator &);

    FastaIterator & operator=(const FastaIterator &);


  };
}
#endif // OPENMS_FORMAT_FASTAITERATOR_H