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PeptideProteinResolution.h
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34 
35 #ifndef OPENMS_ANALYSIS_ID_PEPTIDEPROTEINRESOLUTION_H
36 #define OPENMS_ANALYSIS_ID_PEPTIDEPROTEINRESOLUTION_H
37 
39 #include <OpenMS/CONCEPT/Types.h>
43 #include <vector>
44 #include <set>
45 
46 namespace OpenMS
47 {
48 
51  struct OPENMS_DLLAPI ConnectedComponent
52  {
53  std::set<Size> prot_grp_indices;
54  std::set<Size> pep_indices;
55 
56  // Default constructor
58 
60  friend std::ostream& operator << (std::ostream& os, const ConnectedComponent& conn_comp);
61  };
62 
87  class OPENMS_DLLAPI PeptideProteinResolution
88  {
89 
90  private:
91  // to build bipartite graph as two maps (adjacency "lists"):
92  // ProtGroups-Indices <-> PepID-Indices
93  // so we get bidirectional connectivity
94  // We always take first PepHit from PepID, because those were used for
95  // inference in Fido
96  typedef std::map<Size, std::set<Size> > IndexMap_;
97 
102 
106  std::map<String, Size> prot_acc_to_indist_prot_grp_;
107 
110 
111  public:
114  PeptideProteinResolution(bool statistics=false);
115 
119  void buildGraph(const ProteinIdentification& protein,
120  const std::vector<PeptideIdentification>& peptides);
121 
127  void resolveGraph(ProteinIdentification& protein,
128  std::vector<PeptideIdentification>& peptides);
129 
134  ConnectedComponent findConnectedComponent(Size& root_prot_grp);
135 
136 
150  void resolveConnectedComponent(ConnectedComponent& conn_comp,
151  ProteinIdentification& protein,
152  std::vector<PeptideIdentification>& peptides);
153 };
154 
155 } //namespace OpenMS
156 
157 #endif // OPENMS_ANALYSIS_ID_PEPTIDEPROTEINRESOLUTION_H
Representation of a protein identification run.
Definition: ProteinIdentification.h:62
IndexMap_ pep_to_indist_prot_grp_
mapping indist. protein group indices <- peptide identification indices
Definition: PeptideProteinResolution.h:101
Resolves shared peptides based on protein scores.
Definition: PeptideProteinResolution.h:87
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::set< Size > prot_grp_indices
Definition: PeptideProteinResolution.h:53
IndexMap_ indist_prot_grp_to_pep_
mapping indist. protein group indices -> peptide identification indices
Definition: PeptideProteinResolution.h:99
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
bool statistics_
log debug information?
Definition: PeptideProteinResolution.h:109
Definition: PeptideProteinResolution.h:51
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
std::map< String, Size > prot_acc_to_indist_prot_grp_
Definition: PeptideProteinResolution.h:106
std::map< Size, std::set< Size > > IndexMap_
Definition: PeptideProteinResolution.h:96
std::set< Size > pep_indices
Definition: PeptideProteinResolution.h:54

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:03 using doxygen 1.8.13