ChromatogramExtractorAlgorithm.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 2002-2017.
//
// 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,
// 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: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_OPENSWATH_CHROMATOGRAMEXTRACTORALGORITHM_H
#define OPENMS_ANALYSIS_OPENSWATH_CHROMATOGRAMEXTRACTORALGORITHM_H

#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>

namespace OpenMS
{

  class OPENMS_DLLAPI ChromatogramExtractorAlgorithm :
    public ProgressLogger
  {

public:

    struct ExtractionCoordinates
    {
      double mz; 
      double mz_precursor; 
      double rt_start; 
      double rt_end; 
      std::string id; 

      static bool SortExtractionCoordinatesByMZ(
          const ChromatogramExtractorAlgorithm::ExtractionCoordinates& left,
          const ChromatogramExtractorAlgorithm::ExtractionCoordinates& right)
      {
        return left.mz < right.mz;
      }
      static bool SortExtractionCoordinatesReverseByMZ(
          const ChromatogramExtractorAlgorithm::ExtractionCoordinates& left,
          const ChromatogramExtractorAlgorithm::ExtractionCoordinates& right)
      {
        return left.mz > right.mz;
      }
    };

    void extractChromatograms(const OpenSwath::SpectrumAccessPtr input, 
        std::vector< OpenSwath::ChromatogramPtr >& output, 
        std::vector<ExtractionCoordinates> extraction_coordinates, double mz_extraction_window,
        bool ppm, String filter);

    void extract_value_tophat(const std::vector<double>::const_iterator& mz_start, std::vector<double>::const_iterator& mz_it,
                              const std::vector<double>::const_iterator& mz_end, std::vector<double>::const_iterator& int_it,
                              const double& mz, double& integrated_intensity, const double& mz_extraction_window, bool ppm);

private:

    int getFilterNr_(String filter);

  };

}

#endif // OPENMS_ANALYSIS_OPENSWATH_CHROMATOGRAMEXTRACTORALGORITHM_H