SpectrumAnnotator.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $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/SpectrumAlignment.h>
 
#include <OpenMS/KERNEL/Peak1D.h>
 
#include <OpenMS/METADATA/PeptideHit.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
 
#include <OpenMS/DATASTRUCTURES/RegularExpression.h>
 
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 addPeakAnnotationsToPeptideHit(PeptideHit& ph, const PeakSpectrum& spec, const TheoreticalSpectrumGenerator& tg, const SpectrumAlignment& sa, bool include_unmatched_peaks = false) 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 RegularExpression nt_regex_;
      static const RegularExpression ct_regex_;
      static const RegularExpression noloss_regex_;
      static const RegularExpression seriesposition_regex_;
  };
}