| OpenMS 2.5.0

FeatureGroupingAlgorithm.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm, Clemens Groepl, Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
38 #include <OpenMS/KERNEL/FeatureMap.h>
39 #include <OpenMS/KERNEL/ConsensusMap.h>
40
41 namespace OpenMS
42 {
43
49 class OPENMS_DLLAPI FeatureGroupingAlgorithm :
50 public DefaultParamHandler
51 {
52 public:
54 FeatureGroupingAlgorithm();
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:
118 FeatureGroupingAlgorithm(const FeatureGroupingAlgorithm &);
120 FeatureGroupingAlgorithm & operator=(const FeatureGroupingAlgorithm &);
121
122
123
124 };
125
126 } // namespace OpenMS
127
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::ConsensusMap::sortByQuality
void sortByQuality(bool reverse=false)
Sorts the peaks according to ascending quality.
OpenMS::ConsensusMap::sortBySize
void sortBySize()
Sorts with respect to the size (number of elements)
OpenMS::ConsensusMap::getUnassignedPeptideIdentifications
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
OpenMS::ConsensusMap::getProteinIdentifications
const std::vector< ProteinIdentification > & getProteinIdentifications() const
non-mutable access to the protein identifications
OpenMS::FeatureGroupingAlgorithm::postprocess_
void postprocess_(const std::vector< MapType > &maps, ConsensusMap &out)
Definition: FeatureGroupingAlgorithm.h:78
OpenMS::FeatureGroupingAlgorithm
Base class for all feature grouping algorithms.
Definition: FeatureGroupingAlgorithm.h:49
ConsensusMap.h
OpenMS::ConsensusMap::sortByMaps
void sortByMaps()
Sorts with respect to the sets of maps covered by the consensus features (lexicographically).
FeatureMap.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
DefaultParamHandler.h
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127