IsobaricChannelExtractor.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 2002-2021.
//
// 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: Chris Bielow $
// $Authors: Stephan Aiche, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/Peak2D.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/StandardTypes.h>
 
namespace OpenMS
{
  class IsobaricQuantitationMethod;
  class ConsensusMap;
  class ConsensusFeature;
 
  class OPENMS_DLLAPI IsobaricChannelExtractor :
    public DefaultParamHandler
  {
public:
    explicit IsobaricChannelExtractor(const IsobaricQuantitationMethod* const quant_method);
 
    IsobaricChannelExtractor(const IsobaricChannelExtractor& other);
 
    IsobaricChannelExtractor& operator=(const IsobaricChannelExtractor& rhs);
 
    void extractChannels(const PeakMap& ms_exp_data, ConsensusMap& consensus_map);
 
private:
    struct PuritySate_
    {
      PeakMap::ConstIterator precursorScan;
      PeakMap::ConstIterator followUpScan;
 
      bool hasFollowUpScan;
      const PeakMap& baseExperiment;
 
      PuritySate_(const PeakMap& targetExp);
 
      void advanceFollowUp(const double rt);
 
      bool followUpValid(const double rt) const;
    };
 
    const IsobaricQuantitationMethod* quant_method_;
 
    String selected_activation_;
 
    Peak2D::CoordinateType reporter_mass_shift_;
 
    Peak2D::IntensityType min_precursor_intensity_;
 
    bool keep_unannotated_precursor_;
 
    Peak2D::IntensityType min_reporter_intensity_;
 
    bool remove_low_intensity_quantifications_;
 
    double min_precursor_purity_;
 
    double max_precursor_isotope_deviation_;
 
    bool interpolate_precursor_purity_;
 
    void registerChannelsInOutputMap_(ConsensusMap& consensus_map);
 
    bool isValidPrecursor_(const Precursor& precursor) const;
 
    bool hasLowIntensityReporter_(const ConsensusFeature& cf) const;
 
    double computePrecursorPurity_(const PeakMap::ConstIterator& ms2_spec, const PuritySate_& pState) const;
 
    double computeSingleScanPrecursorPurity_(const PeakMap::ConstIterator& ms2_spec, const PeakMap::SpectrumType& precursor_spec) const;
 
    String getActivationMethod_(const PeakMap::SpectrumType& s) const
    {
      for (std::vector<Precursor>::const_iterator it = s.getPrecursors().begin(); it != s.getPrecursors().end(); ++it)
      {
        if (!it->getActivationMethods().empty()) return Precursor::NamesOfActivationMethod[*(it->getActivationMethods().begin())];
      }
      return "";
    }
 
 
protected:
    void setDefaultParams_();
 
    void updateMembers_() override;
  };
} // namespace