SimplePairFinder.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: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
 
 
#ifndef OPENMS_ANALYSIS_MAPMATCHING_SIMPLEPAIRFINDER_H
#define OPENMS_ANALYSIS_MAPMATCHING_SIMPLEPAIRFINDER_H
 
#include <OpenMS/ANALYSIS/MAPMATCHING/BaseGroupFinder.h>
 
#define V_SimplePairFinder(bla) // std::cout << bla << std::endl;
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI SimplePairFinder :
    public BaseGroupFinder
  {
public:
    typedef BaseGroupFinder Base;
 
    SimplePairFinder();
    ~SimplePairFinder() override
    {
    }
 
    static BaseGroupFinder * create()
    {
      return new SimplePairFinder();
    }
 
    static const String getProductName()
    {
      return "simple";
    }
 
    void run(const std::vector<ConsensusMap> & input_maps, ConsensusMap & result_map) override;
 
protected:
 
    //docu in base class
    void updateMembers_() override;
 
    double diff_exponent_[2];
 
    double diff_intercept_[2];
 
    double pair_min_quality_;
 
    double similarity_(ConsensusFeature const & left, ConsensusFeature const & right) const;
 
  }; // SimplePairFinder
 
} // namespace OpenMS
 
#endif  // OPENMS_ANALYSIS_MAPMATCHING_SimplePairFinder_H
 
/*
 
gnuplot history - how the plot was created - please do not delete this receipt
 
f(x,intercept,exponent)=1/(1+(abs(x)*intercept)**exponent)
set terminal postscript enhanced color
set output "choosingsimplepairfinderparams.ps"
set size ratio .3
plot [-3:3] [0:1] f(x,1,1), f(x,2,1), f(x,1,2), f(x,2,2)
 
*/