TrypticIterator.h

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//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Chris Bauer $
// --------------------------------------------------------------------------

#ifndef OPENMS_CHEMISTRY_TRYPTICITERATOR_H
#define OPENMS_CHEMISTRY_TRYPTICITERATOR_H

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

namespace OpenMS
{
  class OPENMS_DLLAPI TrypticIterator :
    public PepIterator
  {

public:

    typedef std::pair<String, String> FASTAEntry;
    TrypticIterator();
    TrypticIterator(const TrypticIterator &);
    virtual ~TrypticIterator();

    virtual FASTAEntry operator*();

    virtual PepIterator & operator++();

    virtual PepIterator * operator++(int i);

    virtual void setFastaFile(const String & f);

    virtual String getFastaFile();

    virtual void setTolerance(double)
    {
      throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }

    virtual double getTolerance()
    {
      throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
    }

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

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

    virtual bool begin();

    virtual bool isAtEnd();

    virtual bool isDigestingEnd(char aa1, char aa2);

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

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

protected:
    virtual std::string next_();

    bool hasNext_();

    void goToNextAA_();

    String f_file_;     

    std::string actual_pep_;     

    bool is_at_end_;     

    PepIterator * f_iterator_;    

    FASTAEntry f_entry_;     

    unsigned int b_, e_;    



  };

}
#endif //OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H