QTClusterFinder.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// $Maintainer: Hendrik Weisser $
// $Authors: Steffen Sass, Hendrik Weisser $
// --------------------------------------------------------------------------


#ifndef OPENMS_ANALYSIS_MAPMATCHING_QTCLUSTERFINDER_H
#define OPENMS_ANALYSIS_MAPMATCHING_QTCLUSTERFINDER_H

#include <OpenMS/ANALYSIS/MAPMATCHING/BaseGroupFinder.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/COMPARISON/CLUSTERING/HashGrid.h>
#include <OpenMS/DATASTRUCTURES/GridFeature.h>
#include <OpenMS/DATASTRUCTURES/QTCluster.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureDistance.h>

namespace OpenMS
{

  class OPENMS_DLLAPI QTClusterFinder :
    public BaseGroupFinder
  {
private:
    typedef std::map<std::pair<GridFeature *, GridFeature *>, DoubleReal>
    PairDistances;

    typedef HashGrid<GridFeature *> Grid;

    Size num_maps_;

    bool use_IDs_;

    DoubleReal max_diff_rt_;

    DoubleReal max_diff_mz_;

    FeatureDistance feature_distance_;

    PairDistances distances_;

    DoubleReal getDistance_(GridFeature * left, GridFeature * right);

    bool compatibleIDs_(QTCluster & cluster, const GridFeature * neighbor);

    void setParameters_(DoubleReal max_intensity, DoubleReal max_mz);

    void makeConsensusFeature_(std::list<QTCluster> & clustering,
                               ConsensusFeature & feature);

    void computeClustering_(Grid & grid, std::list<QTCluster> & clustering);

    template <typename MapType>
    void run_(const std::vector<MapType> &
              input_maps, ConsensusMap & result_map);

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

public:
    QTClusterFinder();

    virtual ~QTClusterFinder();

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

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

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

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

  };

}

#endif /* OPENMS_ANALYSIS_MAPMATCHING_QTCLUSTERFINDER_H */