| OpenMS 2.5.0

ConsensusIDAlgorithm.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: Hendrik Weisser $
32 // $Authors: Andreas Bertsch, Marc Sturm, Sven Nahnsen, Hendrik Weisser $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
38 #include <OpenMS/METADATA/PeptideIdentification.h>
39
40 #include <map>
41 #include <vector>
42
43 namespace OpenMS
44 {
59 class OPENMS_DLLAPI ConsensusIDAlgorithm :
60 public DefaultParamHandler
61 {
62 public:
71 void apply(std::vector<PeptideIdentification>& ids,
72 Size number_of_runs = 0);
73
75 ~ConsensusIDAlgorithm() override;
76
77 protected:
79 typedef std::map<AASequence, std::pair<Int, std::vector<double> > >
80 SequenceGrouping;
81
83 Size considered_hits_;
84
86 Size number_of_runs_;
87
89 double min_support_;
90
92 bool count_empty_;
93
95 ConsensusIDAlgorithm();
96
103 virtual void apply_(std::vector<PeptideIdentification>& ids,
104 SequenceGrouping& results) = 0;
105
107 void updateMembers_() override;
108
110 void compareChargeStates_(Int& recorded_charge, Int new_charge,
111 const AASequence& peptide);
112
113 private:
115 ConsensusIDAlgorithm(const ConsensusIDAlgorithm&);
116
118 ConsensusIDAlgorithm& operator=(const ConsensusIDAlgorithm&);
119
120 };
121
122 } // namespace OpenMS
123
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::ConsensusIDAlgorithm::SequenceGrouping
std::map< AASequence, std::pair< Int, std::vector< double > > > SequenceGrouping
Mapping: peptide sequence -> (charge, scores)
Definition: ConsensusIDAlgorithm.h:80
OpenMS::ConsensusIDAlgorithm::number_of_runs_
Size number_of_runs_
Number of ID runs.
Definition: ConsensusIDAlgorithm.h:86
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
DefaultParamHandler.h
OpenMS::ConsensusIDAlgorithm::min_support_
double min_support_
Fraction of required support by other ID runs (input parameter)
Definition: ConsensusIDAlgorithm.h:89
OpenMS::ConsensusIDAlgorithm
Abstract base class for all ConsensusID algorithms (that calculate a consensus from multiple ID runs)...
Definition: ConsensusIDAlgorithm.h:59
OpenMS::ConsensusIDAlgorithm::considered_hits_
Size considered_hits_
Number of peptide hits considered per ID run (input parameter)
Definition: ConsensusIDAlgorithm.h:83
int
OpenMS::ConsensusIDAlgorithm::count_empty_
bool count_empty_
Count empty runs in "min_support" calculation? (input parameter)
Definition: ConsensusIDAlgorithm.h:92
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127