SpectrumAnnotator.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
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//  * 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
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// $Maintainer: Mathias Walzer $
// $Authors: Mathias Walzer $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
#include <OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h>

#include <OpenMS/KERNEL/Peak1D.h>

#include <OpenMS/METADATA/PeptideHit.h>
#include <OpenMS/METADATA/PeptideIdentification.h>

#include <boost/regex.hpp>

namespace OpenMS
{
  class OPENMS_DLLAPI SpectrumAnnotator :
    public DefaultParamHandler
  {
    public:

    SpectrumAnnotator();

    SpectrumAnnotator(const SpectrumAnnotator & source);

    ~SpectrumAnnotator() override;

    SpectrumAnnotator & operator=(const SpectrumAnnotator & tsg);


    void annotateMatches(PeakSpectrum &spec, const PeptideHit& ph, const TheoreticalSpectrumGenerator& tg, const SpectrumAlignment& sa) const;

    void addIonMatchStatistics(PeptideIdentification& pi, MSSpectrum &spec, const TheoreticalSpectrumGenerator& tg, const SpectrumAlignment& sa) const;

    void updateMembers_() override;


    protected:
      bool basic_statistics_;
      bool list_of_ions_matched_;
      bool max_series_;
      bool SN_statistics_;
      bool precursor_statistics_;
      unsigned topNmatch_fragmenterrors_;
      bool fragmenterror_statistics_;
      bool terminal_series_match_ratio_;

      static const boost::regex nt_regex_;
      static const boost::regex ct_regex_;
      static const boost::regex noloss_regex_;
      static const boost::regex seriesposition_regex_;

  };
}