OpenMS
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 
47  class OPENMS_DLLAPI PSProteinInference
48  {
49 public:
50 
52 
54 
55 
56  Size findMinimalProteinList(const std::vector<PeptideIdentification> & peptide_ids);
57 
58  void calculateProteinProbabilities(const std::vector<PeptideIdentification> & ids);
59 
60 // double getProteinProbability(const String& acc,const std::vector<String>& accessions, const std::vector<double>& probabilities);
61 
62  double getProteinProbability(const String & acc);
63 
64  bool isProteinInMinimalList(const String & acc);
65  Int getNumberOfProtIds(double protein_id_threshold);
66  Int getNumberOfProtIdsPeptideRule(Int min_peptides, std::map<String, std::set<String> > & prot_id_counter);
67 
69  {
70  return solver_;
71  }
72 
73 private:
74  std::vector<String> minimal_protein_list_accessions_;
75  std::vector<String> accessions_;
76  std::vector<double> probabilities_;
78  };
79 
80 }
81 
82 
83 
SOLVER
Definition: LPWrapper.h:134
This class implements protein inference for the precursor ion selection strategies.
Definition: PSProteinInference.h:48
std::vector< String > minimal_protein_list_accessions_
Definition: PSProteinInference.h:74
bool isProteinInMinimalList(const String &acc)
Int getNumberOfProtIds(double protein_id_threshold)
void calculateProteinProbabilities(const std::vector< PeptideIdentification > &ids)
std::vector< double > probabilities_
Definition: PSProteinInference.h:76
std::vector< String > accessions_
Definition: PSProteinInference.h:75
double getProteinProbability(const String &acc)
LPWrapper::SOLVER getSolver()
Definition: PSProteinInference.h:68
Size findMinimalProteinList(const std::vector< PeptideIdentification > &peptide_ids)
Int getNumberOfProtIdsPeptideRule(Int min_peptides, std::map< String, std::set< String > > &prot_id_counter)
LPWrapper::SOLVER solver_
Definition: PSProteinInference.h:77
A more convenient string class.
Definition: String.h:60
int Int
Signed integer type.
Definition: Types.h:102
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48