StablePairFinder.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Clemens Groepl $
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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 OPENMS_DLLAPI StablePairFinder :
    public BaseGroupFinder
  {
public:

    typedef BaseGroupFinder Base;

    StablePairFinder();

    virtual ~StablePairFinder()
    {
    }

    static BaseGroupFinder* create()
    {
      return new StablePairFinder();
    }

    static const String getProductName()
    {
      return "stable";
    }

    void run(const std::vector<ConsensusMap>& input_maps,
             ConsensusMap& result_map);

protected:


    enum
    {
      RT = Peak2D::RT,
      MZ = Peak2D::MZ
    };

    //docu in base class
    virtual void updateMembers_();

    bool compatibleIDs_(const ConsensusFeature& feat1,
                        const ConsensusFeature& feat2) const;

    DoubleReal 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)

 */