StablePairFinder.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Timo Sachsenberg $
// $Authors: $
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#ifndef OPENMS_ANALYSIS_MAPMATCHING_STABLEPAIRFINDER_H
#define OPENMS_ANALYSIS_MAPMATCHING_STABLEPAIRFINDER_H
 
#include <OpenMS/ANALYSIS/MAPMATCHING/BaseGroupFinder.h>
 
namespace OpenMS
{
  class AASequence;
 
  class OPENMS_DLLAPI StablePairFinder :
    public BaseGroupFinder
  {
public:
 
    typedef BaseGroupFinder Base;
 
    StablePairFinder();
 
    ~StablePairFinder() override
    {
    }
 
    static BaseGroupFinder* create()
    {
      return new StablePairFinder();
    }
 
    static const String getProductName()
    {
      return "stable";
    }
 
    void run(const std::vector<ConsensusMap>& input_maps,
             ConsensusMap& result_map) override;
 
protected:
 
 
    enum
    {
      RT = Peak2D::RT,
      MZ = Peak2D::MZ
    };
 
    //docu in base class
    void updateMembers_() override;
 
    bool compatibleIDs_(const ConsensusFeature& feat1,
                        const ConsensusFeature& feat2) const;
 
    double second_nearest_gap_;
 
    bool use_IDs_;
 
    const AASequence& getBestHitSequence_(const PeptideIdentification& peptideIdentification) const;
  };
 
} // namespace OpenMS
 
#endif // OPENMS_ANALYSIS_MAPMATCHING_STABLEPAIRFINDER_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 "choosingstablepairfinderparams.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)
 
 */