OpenMS  2.4.0
PSProteinInference.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Alexandra Zerck $
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35 
36 #pragma once
37 
40 
41 namespace OpenMS
42 {
43 
52  class OPENMS_DLLAPI PSProteinInference
53  {
54 public:
55 
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 
74  {
75  solver_ = solver;
76  }
77 
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_;
88  };
89 
90 }
91 
92 
93 
A more convenient string class.
Definition: String.h:57
SOLVER
Definition: LPWrapper.h:130
std::vector< String > minimal_protein_list_accessions_
Definition: PSProteinInference.h:84
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::vector< double > probabilities_
Definition: PSProteinInference.h:86
This class implements protein inference for the precursor ion selection strategies.
Definition: PSProteinInference.h:52
std::vector< String > accessions_
Definition: PSProteinInference.h:85
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
LPWrapper::SOLVER solver_
Definition: PSProteinInference.h:87
void setSolver(LPWrapper::SOLVER solver)
Definition: PSProteinInference.h:73
LPWrapper::SOLVER getSolver()
Definition: PSProteinInference.h:78
int Int
Signed integer type.
Definition: Types.h:102