OpenMS  3.0.0
FeatureGroupingAlgorithm.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm, Clemens Groepl, Chris Bielow $
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34 
35 #pragma once
36 
40 
41 namespace OpenMS
42 {
43 
49  class OPENMS_DLLAPI FeatureGroupingAlgorithm :
50  public DefaultParamHandler
51  {
52 public:
55 
57  ~FeatureGroupingAlgorithm() override;
58 
60  virtual void group(const std::vector<FeatureMap > & maps, ConsensusMap & out) = 0;
61 
65  virtual void group(const std::vector<ConsensusMap> & maps, ConsensusMap & out);
66 
68  void transferSubelements(const std::vector<ConsensusMap> & maps, ConsensusMap & out) const;
69 
71  static void registerChildren();
72 
73 protected:
74 
77  template<class MapType>
78  void postprocess_(const std::vector<MapType>& maps, ConsensusMap& out)
79  {
80  // add protein IDs and unassigned peptide IDs to the result map here,
81  // to keep the same order as the input maps (useful for output later):
82  auto& newIDs = out.getUnassignedPeptideIdentifications();
83  Size map_idx = 0;
84 
85  for (typename std::vector<MapType>::const_iterator map_it = maps.begin();
86  map_it != maps.end(); ++map_it)
87  {
88  // add protein identifications to result map:
89  out.getProteinIdentifications().insert(
90  out.getProteinIdentifications().end(),
91  map_it->getProteinIdentifications().begin(),
92  map_it->getProteinIdentifications().end());
93 
94  // assign the map_index to unassigned PepIDs as well.
95  // for the assigned ones, this has to be done in the subclass.
96  for (const PeptideIdentification& pepID : map_it->getUnassignedPeptideIdentifications())
97  {
98  auto newPepID = pepID;
99  // Note: during linking of _consensus_Maps we have the problem that old identifications
100  // should already have a map_index associated. Since we group the consensusFeatures only anyway
101  // (without keeping the subfeatures) the method for now is to "re"-index based on the input file/map index.
102  // Subfeatures have to be transferred in postprocessing if required
103  // (see FeatureGroupingAlgorithm::transferSubelements as used in the TOPP tools, i.e. FeatureLinkerBase),
104  // which also takes care of a re-re-indexing if the old map_index of the IDs was saved.
105  newPepID.setMetaValue("map_index", map_idx);
106  newIDs.push_back(newPepID);
107  }
108  map_idx++;
109  }
110 
111  // canonical ordering for checking the results:
112  out.sortByQuality();
113  out.sortByMaps();
114  out.sortBySize();
115  }
116 private:
121 
122 
123 
124  };
125 
126 } // namespace OpenMS
127 
DefaultParamHandler.h
OpenMS::ConsensusMap::sortByQuality
void sortByQuality(bool reverse=false)
Sorts the peaks according to ascending quality.
OpenMS::FeatureGroupingAlgorithm
Base class for all feature grouping algorithms.
Definition: FeatureGroupingAlgorithm.h:49
OpenMS::ConsensusMap::sortBySize
void sortBySize()
Sorts with respect to the size (number of elements)
ConsensusMap.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::ConsensusMap::sortByMaps
void sortByMaps()
Sorts with respect to the sets of maps covered by the consensus features (lexicographically).
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ConsensusMap::getProteinIdentifications
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
FeatureMap.h
OpenMS::ConsensusMap::getUnassignedPeptideIdentifications
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::FeatureGroupingAlgorithm::postprocess_
void postprocess_(const std::vector< MapType > &maps, ConsensusMap &out)
Definition: FeatureGroupingAlgorithm.h:78