| OpenMS 2.5.0

PSProteinInference.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: Alexandra Zerck $
33 // --------------------------------------------------------------------------
34 //
35
36 #pragma once
37
38 #include <OpenMS/METADATA/PeptideIdentification.h>
39 #include <OpenMS/DATASTRUCTURES/LPWrapper.h>
40
41 namespace OpenMS
42 {
43
52 class OPENMS_DLLAPI PSProteinInference
53 {
54 public:
55
56 PSProteinInference();
57
58 virtual ~PSProteinInference();
59
60
61 Size findMinimalProteinList(const std::vector<PeptideIdentification> & peptide_ids);
62
63 void calculateProteinProbabilities(const std::vector<PeptideIdentification> & ids);
64
65 // double getProteinProbability(const String& acc,const std::vector<String>& accessions, const std::vector<double>& probabilities);
66
67 double getProteinProbability(const String & acc);
68
69 bool isProteinInMinimalList(const String & acc);
70 Int getNumberOfProtIds(double protein_id_threshold);
71 Int getNumberOfProtIdsPeptideRule(Int min_peptides, std::map<String, std::set<String> > & prot_id_counter);
72
73 void setSolver(LPWrapper::SOLVER solver)
74 {
75 solver_ = solver;
76 }
77
78 LPWrapper::SOLVER getSolver()
79 {
80 return solver_;
81 }
82
83 private:
84 std::vector<String> minimal_protein_list_accessions_;
85 std::vector<String> accessions_;
86 std::vector<double> probabilities_;
87 LPWrapper::SOLVER solver_;
88 };
89
90 }
91
92
93
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::PSProteinInference
This class implements protein inference for the precursor ion selection strategies.
Definition: PSProteinInference.h:52
OpenMS::PSProteinInference::getSolver
LPWrapper::SOLVER getSolver()
Definition: PSProteinInference.h:78
OpenMS::PSProteinInference::setSolver
void setSolver(LPWrapper::SOLVER solver)
Definition: PSProteinInference.h:73
OpenMS::PSProteinInference::minimal_protein_list_accessions_
std::vector< String > minimal_protein_list_accessions_
Definition: PSProteinInference.h:84
OpenMS::PSProteinInference::solver_
LPWrapper::SOLVER solver_
Definition: PSProteinInference.h:87
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
LPWrapper.h
OpenMS::PSProteinInference::accessions_
std::vector< String > accessions_
Definition: PSProteinInference.h:85
OpenMS::PSProteinInference::probabilities_
std::vector< double > probabilities_
Definition: PSProteinInference.h:86
int
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::LPWrapper::SOLVER
SOLVER
Definition: LPWrapper.h:130