MapAlignmentAlgorithmKD.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 2002-2018.
//
// 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: Johannes Veit $
// $Authors: Johannes Veit $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/ANALYSIS/QUANTITATION/KDTreeFeatureMaps.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationModelLowess.h>

namespace OpenMS
{

class OPENMS_DLLAPI MapAlignmentAlgorithmKD
{
public:

  MapAlignmentAlgorithmKD(Size num_maps, const Param& param);

  virtual ~MapAlignmentAlgorithmKD();

  void addRTFitData(const KDTreeFeatureMaps& kd_data);

  void fitLOWESS();

  void transform(KDTreeFeatureMaps& kd_data) const;

protected:

  virtual void updateMembers_();

  Size computeCCs_(const KDTreeFeatureMaps& kd_data, std::vector<Size>& cc_index) const;

  void getCCs_(const KDTreeFeatureMaps& kd_data, std::map<Size, std::vector<Size> >& result) const;

  void filterCCs_(const KDTreeFeatureMaps& kd_data, const std::map<Size, std::vector<Size> >& ccs, std::map<Size, std::vector<Size> >& filtered_ccs) const;

private:

  MapAlignmentAlgorithmKD();

  std::vector<TransformationModel::DataPoints> fit_data_;

  std::vector<TransformationModelLowess*> transformations_;

  Param param_;

  double max_pairwise_log_fc_;

  double rt_tol_secs_;

  double mz_tol_;

  bool mz_ppm_;

};

} // namespace OpenMS