OpenMS  2.8.0
PeptideProteinResolution.h
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31 // $Maintainer: Julianus Pfeuffer $
32 // $Authors: Julianus Pfeuffer $
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34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.h>
41 #include <vector>
42 #include <set>
43 
44 namespace OpenMS
45 {
48  struct OPENMS_DLLAPI ConnectedComponent
49  {
50  std::set<Size> prot_grp_indices;
51  std::set<Size> pep_indices;
53  friend std::ostream& operator<<(std::ostream& os, const ConnectedComponent& conn_comp);
54  };
55 
79  class OPENMS_DLLAPI PeptideProteinResolution
80  {
81 
82  private:
88  typedef std::map<Size, std::set<Size> > IndexMap_;
89 
91  // TODO WIP for better tie resolution
92  // std::vector<std::pair<bool,bool>> indist_prot_grp_td_;
97 
101  std::map<String, Size> prot_acc_to_indist_prot_grp_;
102 
105 
106  public:
109  PeptideProteinResolution(bool statistics = false);
110 
111 
119  static void resolve(ProteinIdentification& protein,
120  std::vector<PeptideIdentification>& peptides,
121  bool resolve_ties,
122  bool targets_first);
123 
128  static void run(std::vector<ProteinIdentification>& inferred_protein_id,
129  std::vector<PeptideIdentification>& inferred_peptide_ids);
130 
138  const std::vector<PeptideIdentification>& peptides,
139  bool skip_sort = false);
140 
148  std::vector<PeptideIdentification>& peptides);
149 
155 
156 
171  ProteinIdentification& protein,
172  std::vector<PeptideIdentification>& peptides);
173 };
174 
175 } //namespace OpenMS
176 
Resolves shared peptides based on protein scores.
Definition: PeptideProteinResolution.h:80
std::map< String, Size > prot_acc_to_indist_prot_grp_
Definition: PeptideProteinResolution.h:101
void buildGraph(ProteinIdentification &protein, const std::vector< PeptideIdentification > &peptides, bool skip_sort=false)
void resolveGraph(ProteinIdentification &protein, std::vector< PeptideIdentification > &peptides)
IndexMap_ pep_to_indist_prot_grp_
mapping indist. protein group indices <- peptide identification indices
Definition: PeptideProteinResolution.h:96
static void run(std::vector< ProteinIdentification > &inferred_protein_id, std::vector< PeptideIdentification > &inferred_peptide_ids)
ConnectedComponent findConnectedComponent(Size &root_prot_grp)
IndexMap_ indist_prot_grp_to_pep_
if the protein group at index i contains a target (first) and/or decoy (second)
Definition: PeptideProteinResolution.h:94
static void resolve(ProteinIdentification &protein, std::vector< PeptideIdentification > &peptides, bool resolve_ties, bool targets_first)
std::map< Size, std::set< Size > > IndexMap_
Definition: PeptideProteinResolution.h:88
bool statistics_
log debug information?
Definition: PeptideProteinResolution.h:104
PeptideProteinResolution(bool statistics=false)
void resolveConnectedComponent(ConnectedComponent &conn_comp, ProteinIdentification &protein, std::vector< PeptideIdentification > &peptides)
Representation of a protein identification run.
Definition: ProteinIdentification.h:72
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:47
Definition: PeptideProteinResolution.h:49
friend std::ostream & operator<<(std::ostream &os, const ConnectedComponent &conn_comp)
Overloaded operator '<<' for ConnectedComponents.
std::set< Size > pep_indices
Definition: PeptideProteinResolution.h:51
std::set< Size > prot_grp_indices
Definition: PeptideProteinResolution.h:50