EdwardsLippertIterator.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
//
// 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,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Clemens Groepl,Andreas Bertsch$
// $Authors: $
// --------------------------------------------------------------------------

#ifndef OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H
#define OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H

#include <OpenMS/CHEMISTRY/PepIterator.h>

namespace OpenMS
{

  class OPENMS_DLLAPI EdwardsLippertIterator :
    public PepIterator
  {

public:

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

    virtual FASTAEntry operator*();

    virtual PepIterator & operator++();

    virtual PepIterator * operator++(int i);

    virtual void setFastaFile(const String & f);

    virtual String getFastaFile();

    virtual void setTolerance(DoubleReal t);

    virtual DoubleReal getTolerance();

    virtual void setSpectrum(const std::vector<DoubleReal> & s);

    virtual const std::vector<DoubleReal> & getSpectrum();

    virtual bool begin();

    virtual bool isAtEnd();

    virtual bool isDigestingEnd(char, char);

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

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

protected:
    virtual std::string next_();

    bool hasNext_();

    void goToNextAA_();

    virtual bool isInSpectrum_(DoubleReal & mass);

    String f_file_;         

    std::string actual_pep_;         

    std::vector<DoubleReal> spec_;         

    DoubleReal tol_;         

    DoubleReal masse_[255];         

    bool is_at_end_;         

    PepIterator * f_iterator_;         

    FASTAEntry f_entry_;         

    unsigned int b_, e_;        

    DoubleReal m_, massMax_;         


  };

}
#endif //OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H