FeatureGroupingAlgorithm.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm, Clemens Groepl, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
 
#include <algorithm>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI FeatureGroupingAlgorithm :
    public DefaultParamHandler
  {
public:
    FeatureGroupingAlgorithm();
 
    ~FeatureGroupingAlgorithm() override;
 
    virtual void group(const std::vector<FeatureMap > & maps, ConsensusMap & out) = 0;
 
    virtual void group(const std::vector<ConsensusMap> & maps, ConsensusMap & out);
 
    void transferSubelements(const std::vector<ConsensusMap> & maps, ConsensusMap & out) const;
 
 
protected:
 
    template<class MapType>
    void postprocess_(const std::vector<MapType>& maps, ConsensusMap& out)
    {
      // add protein IDs and unassigned peptide IDs to the result map here,
      // to keep the same order as the input maps (useful for output later):
      auto& newIDs = out.getUnassignedPeptideIdentifications();
      Size map_idx = 0;
 
      for (typename std::vector<MapType>::const_iterator map_it = maps.begin();
           map_it != maps.end(); ++map_it)
      {
        // add protein identifications to result map:
        out.getProteinIdentifications().insert(
            out.getProteinIdentifications().end(),
            map_it->getProteinIdentifications().begin(),
            map_it->getProteinIdentifications().end());
 
        // assign the map_index to unassigned PepIDs as well.
        // for the assigned ones, this has to be done in the subclass.
        for (const PeptideIdentification& pepID : map_it->getUnassignedPeptideIdentifications())
        {
          auto newPepID = pepID;
          // Note: during linking of _consensus_Maps we have the problem that old identifications
          // should already have a map_index associated. Since we group the consensusFeatures only anyway
          // (without keeping the subfeatures) the method for now is to "re"-index based on the input file/map index.
          // Subfeatures have to be transferred in postprocessing if required
          // (see FeatureGroupingAlgorithm::transferSubelements as used in the TOPP tools, i.e. FeatureLinkerBase),
          // which also takes care of a re-re-indexing if the old map_index of the IDs was saved.
          newPepID.setMetaValue("map_index", map_idx);
          newIDs.push_back(newPepID);
        }
        map_idx++;
      }
 
      // Position first, so the order is independent of the features' (random) unique ids;
      // size/maps/quality only break exact-position ties.
      std::stable_sort(out.begin(), out.end(),
        [](const ConsensusFeature& a, const ConsensusFeature& b)
        {
          if (ConsensusFeature::PositionLess()(a, b)) { return true; }   // asc
          if (ConsensusFeature::PositionLess()(b, a)) { return false; }
          if (ConsensusFeature::SizeLess()(b, a)) { return true; }       // desc
          if (ConsensusFeature::SizeLess()(a, b)) { return false; }
          if (ConsensusFeature::MapsLess()(a, b)) { return true; }       // asc
          if (ConsensusFeature::MapsLess()(b, a)) { return false; }
          if (ConsensusFeature::QualityLess()(a, b)) { return true; }    // asc
          if (ConsensusFeature::QualityLess()(b, a)) { return false; }
          return false;
        });
    }
private:
    FeatureGroupingAlgorithm(const FeatureGroupingAlgorithm &);
    FeatureGroupingAlgorithm & operator=(const FeatureGroupingAlgorithm &);
 
 
 
  };
 
} // namespace OpenMS