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PeptideProteinResolution.h
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34 
35 #ifndef OPENMS_ANALYSIS_ID_PROTEINPEPTIDERESOLUTION_H
36 #define OPENMS_ANALYSIS_ID_PROTEINPEPTIDERESOLUTION_H
37 
39 #include <OpenMS/CONCEPT/Types.h>
41 #include <vector>
42 #include <set>
43 
44 namespace OpenMS
45 {
46 
49  struct OPENMS_DLLAPI ConnectedComponent
50  {
51  std::set<Size> prot_grp_indices;
52  std::set<Size> pep_indices;
53 
54  // Default constructor
56 
58  friend std::ostream& operator << (std::ostream& os, const ConnectedComponent& conn_comp);
59  };
60 
61 
62 
79  class OPENMS_DLLAPI PeptideProteinResolution
80  {
81 
82  private:
83  // to build bipartite graph as two maps (adjacency "lists"):
84  // ProtGroups-Indices <-> PepID-Indices
85  // so we get bidirectional connectivity
86  // We always take first PepHit from PepID, because those were used for
87  // inference in Fido
88  typedef std::map<Size, std::set<Size> > IndexMap_;
89 
94 
98  std::map<String, Size> prot_acc_to_indist_prot_grp_;
99 
102 
103  public:
106  PeptideProteinResolution(bool statistics=false);
107 
108 
109 
113  void buildGraph(const ProteinIdentification& protein,
114  const std::vector<PeptideIdentification>& peptides);
115 
121  void resolveGraph(ProteinIdentification& protein,
122  std::vector<PeptideIdentification>& peptides);
123 
128  ConnectedComponent findConnectedComponent(Size& root_prot_grp);
129 
130 
144  void resolveConnectedComponent(ConnectedComponent& conn_comp,
145  ProteinIdentification& protein,
146  std::vector<PeptideIdentification>& peptides);
147 };
148 
149 } //namespace OpenMS
150 
151 #endif // OPENMS_ANALYSIS_ID_PEPTIDEPROTEINRESOLUTION_H
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
IndexMap_ pep_to_indist_prot_grp_
mapping indist. protein group indices <- peptide identification indices
Definition: PeptideProteinResolution.h:93
Resolves shared peptides based on protein scores.
Definition: PeptideProteinResolution.h:79
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::set< Size > prot_grp_indices
Definition: PeptideProteinResolution.h:51
IndexMap_ indist_prot_grp_to_pep_
mapping indist. protein group indices -> peptide identification indices
Definition: PeptideProteinResolution.h:91
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
bool statistics_
log debug information?
Definition: PeptideProteinResolution.h:101
Definition: PeptideProteinResolution.h:49
std::map< String, Size > prot_acc_to_indist_prot_grp_
Definition: PeptideProteinResolution.h:98
std::map< Size, std::set< Size > > IndexMap_
Definition: PeptideProteinResolution.h:88
std::set< Size > pep_indices
Definition: PeptideProteinResolution.h:52

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:53:51 using doxygen 1.8.9.1