FeatureGroupingAlgorithmUnlabeled.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 2002-2020.
//
// 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: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithm.h>
 
#include <OpenMS/KERNEL/ConversionHelper.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI FeatureGroupingAlgorithmUnlabeled :
    public FeatureGroupingAlgorithm
  {
public:
    FeatureGroupingAlgorithmUnlabeled();
 
    ~FeatureGroupingAlgorithmUnlabeled() override;
 
    template <typename MapType>
    void setReference(int map_id, const MapType & map)
    {
      MapConversion::convert(map_id, map, pairfinder_input_[0]);
    }
 
    ConsensusMap & getResultMap()
    {
      return pairfinder_input_[0];
    }
 
    void group(const std::vector<FeatureMap > & maps, ConsensusMap & out) override;
 
    void addToGroup(int map_id, const FeatureMap & feature_map);
 
    static FeatureGroupingAlgorithm * create()
    {
      return new FeatureGroupingAlgorithmUnlabeled();
    }
 
    static String getProductName()
    {
      return "unlabeled";
    }
 
private:
 
    // This vector should always have 2 elements
    // - the first element is the currently computed consensus map.
    //   After initialization of the algorithm, it will consist of the reference
    //   map alone, after adding all maps through addToGroup it will contain the
    //   final result (e.g. the consensus result of all maps).
    // - the second element is the map which was last added to the consensus map
    std::vector<ConsensusMap> pairfinder_input_;
 
    FeatureGroupingAlgorithmUnlabeled(const FeatureGroupingAlgorithmUnlabeled &);
    FeatureGroupingAlgorithmUnlabeled & operator=(const FeatureGroupingAlgorithmUnlabeled &);
 
  };
 
} // namespace OpenMS