MapAlignmentAlgorithmIdentification.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Hendrik Weisser $
// $Authors: Eva Lange, Clemens Groepl, Hendrik Weisser $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMIDENTIFICATION_H
#define OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMIDENTIFICATION_H

#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithm.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
#include <OpenMS/KERNEL/ConsensusMap.h>

#include <map>

namespace OpenMS
{
  class OPENMS_DLLAPI MapAlignmentAlgorithmIdentification :
    public MapAlignmentAlgorithm
  {
public:
    MapAlignmentAlgorithmIdentification();

    virtual ~MapAlignmentAlgorithmIdentification();

    // Docu in base class
    virtual void alignPeakMaps(std::vector<MSExperiment<> > &,
                               std::vector<TransformationDescription> &);

    // Docu in base class
    virtual void alignFeatureMaps(std::vector<FeatureMap<> > &,
                                  std::vector<TransformationDescription> &);

    // Docu in base class
    virtual void alignConsensusMaps(std::vector<ConsensusMap> &,
                                    std::vector<TransformationDescription> &);

    // Docu in base class
    virtual void alignPeptideIdentifications(
      std::vector<std::vector<PeptideIdentification> > &,
      std::vector<TransformationDescription> &);

    // Docu in base class
    virtual void setReference(Size reference_index = 0,
                              const String & reference_file = "");

    template <typename MapType>
    void alignMaps(std::vector<MapType> & maps,
                   std::vector<TransformationDescription> & transformations)
    {
      checkParameters_(maps.size());
      startProgress(0, 3, "aligning maps");

      if (reference_index_)     // reference is one of the input files
      {
        SeqToList rt_data;
        getRetentionTimes_(maps[reference_index_ - 1], rt_data);
        computeMedians_(rt_data, reference_, true);
      }

      // one set of RT data for each input map, except reference:
      std::vector<SeqToList> rt_data(maps.size() - bool(reference_index_));
      for (Size i = 0, j = 0; i < maps.size(); ++i)
      {
        if (i == reference_index_ - 1) continue;  // skip reference map, if any

        getRetentionTimes_(maps[i], rt_data[j++]);
      }
      setProgress(1);

      computeTransformations_(rt_data, transformations, true);

      setProgress(3);
      endProgress();
    }

    static MapAlignmentAlgorithm * create()
    {
      return new MapAlignmentAlgorithmIdentification();
    }

    static String getProductName()
    {
      return "identification";
    }

protected:

    typedef std::map<String, DoubleList> SeqToList;

    typedef std::map<String, DoubleReal> SeqToValue;

    Size reference_index_;

    SeqToValue reference_;

    DoubleReal score_threshold_;

    Size min_run_occur_;

    void computeMedians_(SeqToList & rt_data, SeqToValue & medians,
                         bool sorted = false);

    bool hasGoodHit_(PeptideIdentification & peptide);

    void getRetentionTimes_(std::vector<PeptideIdentification> & peptides,
                            SeqToList & rt_data);

    void getRetentionTimes_(MSExperiment<> & experiment, SeqToList & rt_data);

    template <typename MapType>
    void getRetentionTimes_(MapType & features, SeqToList & rt_data);

    void computeTransformations_(std::vector<SeqToList> & rt_data,
                                 std::vector<TransformationDescription> &
                                 transforms, bool sorted = false);

    void checkParameters_(const Size runs);

    void getReference_();

private:

    MapAlignmentAlgorithmIdentification(const MapAlignmentAlgorithmIdentification &);

    MapAlignmentAlgorithmIdentification & operator=(const MapAlignmentAlgorithmIdentification &);

  };

} // namespace OpenMS

#endif // OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMIDENTIFICATION_H