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

#ifndef OPENMS_CHEMISTRY_PEPITERATOR_H
#define OPENMS_CHEMISTRY_PEPITERATOR_H

#include <OpenMS/DATASTRUCTURES/String.h>

namespace OpenMS
{

  /**
  @brief Abstract base class for different peptide iterators

  @note every derived class has to implement the static functions "PepIterator * create()" and "const String getProductName()" (see Factory for details)
  */
  class OPENMS_DLLAPI PepIterator
  {

public:

    typedef std::pair<String, String> FASTAEntry;

    /**
    @brief constructor
    */
    PepIterator();

    /**
    @brief destructor
    */
    virtual ~PepIterator();

    /**
    @brief copy constructor
    */
    PepIterator(const PepIterator & source);

    /**
    @brief * operator for accessing the value of the iterator
    @return FASTAEntry representing a peptide
    @throw InvalidIterator if iterator has not been initialized
    */
    virtual FASTAEntry operator*() = 0;

    /**
    @brief operator ++ for pre-increment
    @return Reference to PepIterator
    @throw InvalidIterator if iterator has not been initialized
    */
    virtual PepIterator & operator++() = 0;

    /**
    @brief operator ++ for post-increment
    @return pointer to PepIterator
    @throw Exception::InvalidIterator if iterator has not been initialized
    */
    virtual PepIterator * operator++(int) = 0;

    /**
    @brief setter for FASTA file
    @param f const String reference representing file location
    @throw Exception::FileNotFound
    @throw Exception::ParseError
    */
    virtual void setFastaFile(const String & f) = 0;

    /**
    @brief getter for FASTA file
    @return String with file location
    */
    virtual String getFastaFile() = 0;

    /**
    @brief setter for spectrum
    @param s ms spectrum given as vector of doubles
    @throw Exception::InvalidValue if spectrum is not sorted ascendingly
    */
    virtual void setSpectrum(const std::vector<double> & s) = 0;

    /**
    @brief getter for spectrum
    @return the used spectrum
    */
    virtual const std::vector<double> & getSpectrum() = 0;

    /**
    @brief setter for tolerance
    @param t tolerance value
    @throw Exception::InvalidValue if tolerance is negative
    */
    virtual void setTolerance(double t) = 0;

    /**
    @brief getter for tolerance
    @return tolerance
    */
    virtual double getTolerance() = 0;

    /**
    @brief initializing iterator
    */
    virtual bool begin() = 0;

    /**
    @brief indicator where iterator is at end
    */
    virtual bool isAtEnd() = 0;

    /**
        @brief all children has to be registered here
        @see Factory
    */
    static void registerChildren();

  };
}
#endif // OPENMS_CHEMISTRY_PEPITERATOR_H
